Microbially mediated fossil concretions and their characterization by the latest methodologies: a review

Abstract

The study of well-preserved organic matter (OM) within mineral concretions has provided key insights into depositional and environmental conditions in deep time. Concretions of varied compositions, including carbonate, phosphate, and iron-based minerals, have been found to host exceptionally preserved fossils. Organic geochemical characterization of concretion-encapsulated OM promises valuable new information of fossil preservation, paleoenvironments, and even direct taxonomic information to further illuminate the evolutionary dynamics of our planet and its biota. Full exploitation of this largely untapped geochemical archive, however, requires a sophisticated understanding of the prevalence, formation controls and OM sequestration properties of mineral concretions. Past research has led to the proposal of different models of concretion formation and OM preservation. Nevertheless, the formation mechanisms and controls on OM preservation in concretions remain poorly understood. Here we provide a detailed review of the main types of concretions and formation pathways with a focus on the role of microbes and their metabolic activities. In addition, we provide a comprehensive account of organic geochemical, and complimentary inorganic geochemical, morphological, microbial and paleontological, analytical methods, including recent advancements, relevant to the characterization of concretions and sequestered OM. The application and outcome of several early organic geochemical studies of concretion-impregnated OM are included to demonstrate how this underexploited geo-biological record can provide new insights into the Earth’s evolutionary record. This paper also attempts to shed light on the current status of this research and major challenges that lie ahead in the further application of geo-paleo-microbial and organic geochemical research of concretions and their host fossils. Recent efforts to bridge the knowledge and communication gaps in this multidisciplinary research area are also discussed, with particular emphasis on research with significance for interpreting the molecular record in extraordinarily preserved fossils.

Introduction

The fossil record is fundamental to our understanding of major events in the evolution of life and our planet. However, the fossil record suffers from numerous biases, and not all fossils are created equally (Allison and Bottjer, 2011). The process of fossilization is a complex interplay of biological, microbial and geochemical processes including decay and preservation through mineralization (Briggs, 2003b).

Three broad modes of fossilization have been proposed previously (Grice et al., 2019), as summarized in Figure 1. In ‘normal’ fossil preservation, the remains of dead organisms are subject to a range of complex biogeochemical processes encompassing degradation via eogenesis and diagenesis (within the water column and surface sediments), burial, microbial activity, authigenic mineralization and metagenesis (in sediments), weathering and exhumation. These processes destroy nearly all OM. In ‘selective’ fossil preservation, certain extremely resistant or recalcitrant biopolymers are fossilized. These include, for example, leaf cuticles of higher plants (Nip et al., 1986; Goth et al., 1988; Gelin et al., 1994; Grice et al., 2001, 2003) and the cell walls of marine and freshwater algae, which are relatively persistent in geological sediments. High molecular-weight (MW), aliphatic biomolecules are some of the more recalcitrant organic compounds (Tissot and Welte, 1984). Finally, a small fraction of organisms die in environments conducive to soft tissue preservation, which is termed ‘exceptional’ fossil preservation. Exceptionally preserved fossils have the potential to preserve biomarkers, and in special cases intact biolipids (e.g., sterols), which retain important information about extinct organisms and are vital for establishing paleodiets and reconstructing paleoenvironments at the microbial level (Grice et al., 2019; Tripp et al., 2022).

Figure 1

One fossilization pathway that appears to have high potential for exceptional fossilization, and therefore for soft tissue preservation, is concretion formation (Irwin et al., 1977; Martill, 1990; Briggs and Kear, 1993a,c; Bojanowski and Clarkson, 2012; McCoy, 2014; Cotroneo et al., 2016). When this process is sufficiently rapid, it decreases permeability and consequently protects OM from significant degradation, allowing ‘closed chemical system’ preservation of soft tissues (Allison and Pye, 1994; Farmer and Des Marais, 1999; McCoy et al., 2015b). This is a relatively uncommon pathway, but has led to the soft parts of various organisms being fossilized and entombed in concretions across a vast spatiotemporal range (Martill, 1990, 1993; Trinajstic et al., 2007, 2022a,b; Marshall and Pirrie, 2013; McCoy, 2014). Concretionary lagerstätten are known to represent a variety of different palaeoenvironments, from hypersaline to marine, estuarine to lacustrine, and freshwater to terrestrial (Marshall and Pirrie, 2013; McCoy, 2014), but the majority appear to pertain to transitional environments, i.e., those at the interface between the marine and terrestrial realms (McCoy et al., 2015a). Whole or parts of organisms can be preserved via several processes, including entombment or primary cementation in concretions of calcite, silica, phosphate, siderite, pyrite or dolomite, with carbonate concretions being the most common (Baird et al., 1986; Allison and Pye, 1994; McCoy, 2014). Concretions are often hosted in fine-grained sedimentary rocks like shales and mudstones (McCoy, 2014). Their relatively low permeability can effectively implement a closed chemical system, isolating the remains of the organism from other organic matter and redox influences thereby inhibiting diagenetic reactions and supporting the preservation of fossilized soft tissue (s) and biosignatures (McCoy et al., 2015a,b). Although the size of the nucleating fossil within the concretion is often the controlling factor on concretion size, this is not always the case: for example, sub-centimeter ostracods form the nuclei of multi-meter concretions in the Devonian-aged Huron Member of the Ohio Shale (Clifton, 1957).

Recently, it has been hypothesized from fossil evidence that microbial metabolic processes are responsible for the preservation and mineralization of the organic tissues in the fossil record (Briggs, 1995b, 2003a,b; Sagemann et al., 1999; O'Brien et al., 2002; Briggs et al., 2005; Raff et al., 2008). Microorganisms live both on the surface of, and within, living organisms, and they can remain active on or in a carcass well after the time of death of an organism (Allison, 1988a; Briggs, 1995b; Sagemann et al., 1999; Janssen et al., 2022). Certain microbially-induced carbonate concretions have recently been recognized for their excellent potential to sequester OM, including organic compounds preserving a direct link to their biological origins (i.e., molecular fossils or biomarkers) and often also providing valuable information about past depositional environments (Melendez et al., 2013a,b; Plet et al., 2016). Initial heterotrophic decay by microorganisms leads to the release of high concentrations of ions ranging from H⁺, OH⁻, Na⁺, K⁺, Ca²⁺, Mg²⁺, Fe³⁺, NH⁴⁺, S²⁻ into their immediate environment. This can facilitate the stabilization of the remaining tissues of a carcass and can influence mineralization; thus, microbial activity can lead to excellent preservation, provided that the rate of mineralization or stabilization exceeds that of tissue decomposition (Gehling, 1999; Sagemann et al., 1999; Petrovich, 2001; Carpenter, 2005; Janssen et al., 2022). Theoretical models and experimental observations that have highlighted the role of microbes in the fossilization process have also identified the physico-chemical conditions that can inhibit microbial mineral precipitation (Gehling, 1999; Briggs, 2003a; Martin et al., 2003; Bolhuis et al., 2013; Gäb et al., 2020). The influence of microbial activities on fossilization processes occurs in the early stages of eogenesis and diagenesis (Dupraz and Visscher, 2005; Raff et al., 2013; Dang and Lovell, 2016; Janssen et al., 2022). Detailed investigations into the role of intrinsic and extrinsic microbial metabolic activities, prevalence of sites/types of fossils, role of substrate, formation controls, bio-physico-chemical environments, type of organic matrix, governing reaction kinetics and comprehensive characterization of biomolecules from nano- to micro-scales are pivotal in understanding the fossilization story over geologic timeframes.

This review discusses the study of well-preserved OM in mineral concretions and how it can provide information on depositional and environmental conditions and the evolutionary history of life on Earth. Various concretion types and their formation modes are described, as well as the variety of methodologies employed in their characterization. The review also includes examples of organic geochemical (biomarker) and isotopic studies and the enormous potential for the molecular record to reveal insights about extinct organisms. Challenges and knowledge gaps in the field are presented, along with recent efforts to bridge them.

Exceptionally preserved fossils in concretions through space and time

Fossiliferous concretions have been identified in strata ranging in age from Mesoproterozoic to Holocene (Mozley and Burns, 1993; Marshall and Pirrie, 2013; McCoy, 2014; Wang et al., 2017; Mojarro et al., 2022) as seen in Figures 2, 3 and Table 1. The Mesoproterozoic Xiamaling Formation (~1.37 giga annum [Ga]), which preserves silicified bitumen concretions in black shale and green chert, antedates the evolution of multicellular organisms. Consequently, the nuclei for these concretions are bacterial and include microbial mats (Wang et al., 2017; Liu et al., 2019; Liu A. et al., 2020). Concretion-bearing deposits are far more common in Phanerozoic deposits than in Proterozoic or older strata. In lower Paleozoic deposits, the fossils dominantly preserved in concretions are invertebrates; examples of deposits where this is the case are the upper Cambrian Alum Shale Formation of Sweden (Dworatzek, 1987; Maeda et al., 2011) and the lower Ordovician Fezouata Formation of Morocco (Gaines et al., 2012; Van Roy et al., 2015; Saleh et al., 2021). The rocks hosting the concretions in each of these cases are shales, but the concretions in the former are calcareous, whereas those in the latter are siliceous. The middle Silurian Coalbrookdale Formation of the UK (Herefordshire Lagerstätte) also preserves invertebrates with soft tissue in calcareous concretions, but the host rock in this instance is bentonite (Siveter et al., 2020).

Figure 2

Figure 3

One of the most famous concretion-bearing and soft-tissue preserving fossil deposits in the world is the Middle–Upper Devonian Gogo Formation of Western Australia (Long and Trinajstic, 2010; Melendez et al., 2013b; Lengger et al., 2017; Trinajstic et al., 2022a). Fossils from this unit have provided unprecedented insights into the soft tissue anatomy and ecology of early fishes (e.g., Trinajstic et al., 2007, 2013, 2022b; Long et al., 2008, 2009; Ahlberg et al., 2009). In addition, molecular and isotopic studies of a fossil crustacean from this unit revealed the oldest intact biolipids (i.e., cholesterol) in the fossil record, as well as the entire diagenetic continuum of steroids representing transformations that occurred in the water column and in the surface sediments (Melendez et al., 2013a,b). Biomarkers such as isorenieratane indicative of green-brown sulfur bacteria (GSB) indicated the pivotal role that anaerobic photosynthesis played in the exceptional soft tissue preservation of this ancient crustacean. δ¹³C of cholestane (−30.5 ‰), short-chain C₁₇/C₁₉n-alkanes (−34.8 ‰) and phytane (−34.0 ‰) support a source from phytoplankton consumed by the crustacean; the different values for these compounds reflect differences in biosynthetic pathways for different compound classes within phytoplankton cells (Schouten et al., 1998). Strongly ¹³C-depleted values of long chain n-alkanes (average-40 ‰) indicate a source from autolithified sulfate reducing bacteria (SRB) involved in concretion formation (Melendez et al., 2013b).

Another world-renowned concretion-bearing fossil site is the upper Carboniferous Mazon Creek site of Illinois, USA, hosted in the Francis Creek Shale Member of the Carbondale Formation (Johnson and Richardson, 1966; Woodland and Stenstrom, 1979; Baird et al., 1985a,b, 1986; Archer et al., 1995; Clements et al., 2018). The fossils preserved at this site include exquisitely and rarely preserved jellyfish, anemones, and shark-egg sacs, among a diverse deltaic and marine flora and fauna (Baird et al., 1985a, 1986; Clements et al., 2018; Plotnick et al., 2023). Recent geochemical studies on fossils from this site have informed the debate over the phylogenetic position of the enigmatic “Tully Monster” (McCoy et al., 2016, 2020). It has also been demonstrated that the encapsulation of coprolite fossils at this site was sufficiently rapid that intact dietary sterols were preserved (Tripp et al., 2022). An abundance of cholestane (86–99% of total steranes) alongside other cholesterol-derived compounds, including unaltered 5α-cholestan-3β-ol and coprostanol, were detected within the coprolite, whereas these compounds were comparatively low in abundance in the surrounding concretionary matrix (Tripp et al., 2022). This supports the interpretation that these compounds were derived from the original fecal material, and therefore could be treated as informative of the producer’s dietary habits. Whereas these compounds were determined to be derived from animals, supporting a primarily carnivorous diet for the coprolite producer, the n-alkanes were identified as of palaeoenvironmental origin. The cholestane was slightly ¹³C-depleted compared to n-alkanes, of palaeoenvironmental sources, and bulk OM (Tripp et al., 2022).

Moving into the Mesozoic, the Lower Jurassic Sachrang Formation of Holzmaden, Germany (often dubbed the Posidonia Shale) has produced countless exceptionally preserved fossils in concretions, including an ichthyosaur bone that preserves intact cholesterol (Plet et al., 2016, 2017). In addition, the well-preserved internal tissue of the bone included structures that resemble white- and red-blood cells (RBCs) (Plet et al., 2017). The cell-like structures interpreted as RBCs are ~20% the size of modern mammal RBCs, and their small size was explained as an evolutionary adaptation to low atmospheric oxygen levels during the Jurassic period. However, several arguments against the interpretation of these structures as ichthyosaur RBCs have been put forth: some have noted that extant reptile RBCs are considerably larger than those of mammals, and therefore much bigger than the supposed ichthyosaur RBCs (Eriksson et al., 2022; Senter, 2022); others have observed that reptilian RBCs are nucleated, unlike non-nucleated mammalian RBCs (Eriksson et al., 2022); and still others have posited that small RBCs could be inconsistent with the pelagic, deep-diving lifestyle inferred for ichthyosaurs, a lifestyle normally accompanied by an increase in RBC size (Sander, 2021; Sander and Wintrich, 2021). The cell-like structures described by Plet et al. (2017) have alternatively been linked to degraded, collagen-rich connective tissue (Senter, 2022), although their true identity remains an open question and therefore requires further research.

Several Mesozoic deposits in the Americas are known to host fossiliferous carbonate concretions in shales [e.g., the Upper Jurassic Cordillera de Domeyko Fromation in Chile (Schultze, 1989; Arratia and Schultze, 1999); the Lower Cretaceous black shales of Magdalena Valley, Colombia (Weeks, 1953, 1957)], although perhaps the most renowned is the famous Lower Cretaceous Santana Group of northeast Brazil (Mabesoone and Tinoco, 1973; Martill, 1988, 1989, 1990, 1993, 2007; Maisey, 1991; Fara et al., 2005; Varejão et al., 2021). The preservation quality of this site is sufficiently exceptional that even the hearts of fish are fossilized (Maldanis et al., 2016).

Among Cenozoic deposits with fossiliferous concretions, the Eocene London Clay Formation of the UK is perhaps one of the best known and studied (Allison, 1988b; Huggett, 1994; Huggett et al., 2000). Concretions with organismal nuclei are also known from deposits as young as Holocene in some regions, attesting to rapid encapsulation in certain modern environments. Examples of Holocene sites yielding fossiliferous concretions include North Norfolk, UK (Pye, 1984; Pye et al., 1990; Allison and Pye, 1994), Onondaga Lake, New York (Dence, 1956; Sondheimer et al., 1966; Wilcox and Effler, 1981), and Kangerlussuaq, Greenland and Ottawa, Canada (Mojarro et al., 2022). In the case of the carbonate concretions from Greenland and Canada, the capelin fish fossils conserved within were determined to have been preserved in different depositional settings from each other, providing a unique opportunity to analyze recently formed concretions for their biomarker and fatty acid compositions (Mojarro et al., 2022). Mojarro et al. (2022) demonstrated that concretions from both sites had similar organic carbon sources and environments of deposition, but that the degree and quality of organic preservation were highly divergent: one concretion exhibited exceptional soft tissue preservation, whereas the other only showed skeletal preservation. The free and bound organic fractions of the two concretions were similarly disparate: the fossil concretion with exceptionally preserved soft tissues also contained a diversity of lipids, whereas the skeletal fossil was largely overprinted by environmental lipid signals. The δ¹³C of n-alkanes and fatty acids (C_19-30) varied between −28 ‰ to −32 ‰, which was attributed to input from C3 plants. Short-chain fatty acids, probably of a bacterial origin (C_14-18) showed lower δ values (−24 ‰ to −30 ‰).

Concretion formation mechanisms

The formation of concretions has traditionally been explained by diffusion, carbonate inter-conversion reactions, and slow three-dimensional advection of water (Berner, 1968b; Wilkinson and Dampier, 1990). Microbial processes are becoming recognized as crucial in concretion formation as well (e.g., Curtis et al., 1972; Irwin et al., 1977; Hudson, 1978; Gautier, 1982; Coleman and Raiswell, 1995; Raiswell and Fisher, 2000; Yoshida et al., 2018), and factors such as the input and decay rate of OM, carbonate saturation, porewater velocity and rate of authigenic precipitation all contribute to the exceptional preservation seen in fossil concretions (Butts and Briggs, 2011; Gaines et al., 2012; Melendez et al., 2013b; Farrell, 2014; Wilmeth et al., 2018; Grice et al., 2019; Janssen et al., 2022). Recent research has shown that microbes and their associated metabolic activities play a crucial role in the destruction, preservation and mineralization of organic tissue (s) (Allison, 1988b; Briggs, 1995a, 2003a,b; Gehling, 1999; Sagemann et al., 1999; Krause and Jachau, 2002; O'Brien et al., 2002; Briggs et al., 2005; Raff et al., 2008; McNamara et al., 2009; Janssen et al., 2022). Raff et al. (2013) and Butler et al. (2015) demonstrated that the interactions of microbes play an important role in preservation by generation of pseudomorphs which can stabilize the carcass and protect it from destruction. In another study of Eagan et al. (2017)Bacillus strains isolated from decaying shrimp (Artemia sinica) larvae and sea urchin (Heliocidaris erythrogramma) embryos were recorded to destroy the soft tissue. Melendez et al. (2013b) also showed evidence for the anaerobic recycling of crustacean organic matter through microbial sulfate reduction and photosynthesis (e.g., performed by the green sulfur bacteria Chlorobi) via biomarker analysis. In some instances, initial, rapid heterotrophic decay leads to the release of high concentrations of cations (often calcium) to the immediate environment; this may result in the stabilization and preservation of the remaining tissues, provided that the rates of the mineralization or stabilization processes remain higher than tissue decomposition (Riley, 1997; Sagemann et al., 1999; Gupta et al., 2007; Janssen et al., 2022). So, the rate of OM decay governs the rate of destruction, preservation and mineralization of organic tissues in concretion formation. The occurrence of soft tissue fossils in carbonate concretions is therefore enigmatic, as concretions are proposed to form as a result of the balanced interactions between decaying OM, microbes and the local chemical environment (Weiner and Dove, 2003; Dupraz et al., 2009; Melendez et al., 2013b).

Role of microbes in concretion formation

Biologically induced mineralization (BIM) with organic matter (OM) is the most relevant process for fossilization and has been extensively studied by researchers over the last century (Weiner and Dove, 2003; Dupraz et al., 2009; Wilmeth et al., 2018; Dong et al., 2022). BIM is the process by which microbial metabolic activities promote mineral precipitation as a result of biochemical changes around the cell surface (Dhami et al., 2013b; Zhu and Dittrich, 2016; Murugan et al., 2021). For example, hydrolysis of urea by bacterial urease leads to an increase in pH, which supports the precipitation of calcium carbonate (Dhami et al., 2013b; Zhu and Dittrich, 2016). BIM can play a role in fossilization by interacting with decaying OM, including extracellular biopolymers or by-products of the microbial metabolic processes (Weiner and Dove, 2003; Dupraz et al., 2009; Zhu and Dittrich, 2016; Wilmeth et al., 2018). The surrounding environment of this decaying OM can act as a source of ions, influencing the chemical composition of precipitated minerals by development of appropriate conditions for free cation attachment to the nucleation sites, which are often degrading OM (Reitner, 2004; Li et al., 2015; Janssen et al., 2022).

The process of concretion formation is in essence a two-step process: (1) microbial communities adhere to the substrate, leading to the formation of a biofilm; and (2) the biofilms act as a nucleation site which, in the presence of soluble calcium ions under a high pH environment, results in biomineralization of calcium carbonate (Weiner and Dove, 2003; Dupraz et al., 2009; Melendez et al., 2013b).

During BIM, biofilm formation occurs with the adhesion of microbial communities on surfaces, which combine to form clusters or microcolonies. Microcolonies progress to a threshold density and form a biofilm, which then induces the expression of biosynthesis genes that control the synthesis of extracellular polymeric substances (EPS); these EPSs then become encapsulated within the biofilm (Costerton et al., 1995; Percival et al., 2011; Janssen et al., 2022). Biomineralization usually occurs on biofilms with heterogeneous structures because of cell aggregation (Li et al., 2015). With these differential structures, the microenvironment both within and external to the biofilm is modified to facilitate mineralization (Iniesto et al., 2015, 2016, 2018). For example, the biofilm formation of Pseudomonas aeruginosa accumulates minerals on the inside and outside of the biofilm by trapping fine abiotic calcite particles as well as granules of calcite through biomineralization (Bai et al., 2017). Biofilms are also known to exhibit diverse and highly structured microenvironments resulting from a combination of microbial metabolism and transport limitations (Stewart and Franklin, 2008). Li et al. (2015) demonstrated different patterns of biomineralization in situ with precipitation starting at the base of the biofilm and building upwards which impacts mineralization. Ex situ studies suggest that the extracellular polymeric substances (EPS) produced by biofilms influence precipitation and regulate patterns of mineralization (Ercole et al., 2007). Biofilm morphology also regulates the internal and external solute transport mechanisms, which determines the physiology of the biofilm-resident cells. Previous studies have demonstrated that microbial biofilms surrounding dead and decaying biomass also act as a template for carbonate precipitation and concretion formation (Iniesto et al., 2015, 2016).

Mineralization requires supersaturation of specific ions in the surrounding environment which can be governed by microbial activity in and around the cadaver immediately upon death. Depending upon the availability of organic substrates and cations, different mineralization reactions can occur, including silicification, phosphatization, pyritization or carbonate precipitation (Briggs et al., 1996; Grimes et al., 2001; Dornbos, 2011; Gaines et al., 2012; Farrell, 2014; Liu D. et al., 2020; Janssen et al., 2022). Among these, carbonates are the most commonly precipitated biominerals (Thompson et al., 1997; Grotzinger and Knoll, 1999; Zhu and Dittrich, 2016).

Microbial function and metabolic activity in biomineral precipitation (especially carbonates) can be grouped into three categories (Figure 4):

• Precipitation of microbial metabolic pathway by-products. Metabolic pathways like photosynthesis, sulfate reduction, denitrification, anaerobic sulfide oxidation, ureolysis and methanogenesis might circumstantially lead to mineralization (Konhauser et al., 2005; Zhu and Dittrich, 2016; Zeng and Tice, 2018). The significance of SRB, iron reducing bacteria and methanogens has been widely recorded in calcite and siderite concretions (Coleman and Raiswell, 1981; Curtis et al., 1986; Coleman, 1993; Melendez et al., 2013a,b; Zeng and Tice, 2014; Cotroneo et al., 2016; Gaines and Vorhies, 2016; Plet et al., 2016; Lengger et al., 2017).

• Interaction of the cell wall with the environment. Carbonate nucleation takes place either through the cell wall via ion exchange, or on the cell wall because of the presence of negatively charged functional groups like carboxyl, phosphate and amine, which can bind to divalent cations (e.g., Ca²⁺, Mg²⁺) when available (Warren et al., 2001; Dittrich and Sibler, 2005; Ercole et al., 2012). Following the increase in concentration of these metal ions in the surrounding microenvironment, and with sufficient availability of bicarbonates/carbonates, an oversaturation of carbonates is achieved, such as in calcite precipitation on cell walls of picocyanobacteria (Warren et al., 2001).

• Entrapment by extracellular polymeric substances (EPS). EPS mainly comprise polysaccharides and proteins along with nucleic acids, lipids, uronic acids (Nichols and Mancuso Nichols, 2008; Ercole et al., 2012; Bains et al., 2015). As EPS contain various acidic residues and sugars, they can trap large divalent cations (e.g., Ca²⁺ and Mg²⁺) and remove free cations from solution. Once EPS degrade, the captured cations remain, and so the local concentration of cations increases and promotes calcium carbonate precipitation.

Figure 4

In the molecular fossil record, metabolic pathways influencing soft tissue preservation have been recorded via biomarker analysis. For example, (Melendez et al., 2013b) reported anaerobic recycling of invertebrate OM via microbial sulfate reduction and photosynthesis. Taphonomic experiments demonstrated the decay of arthropod brains in several Cambrian fossil sites, confirming the role of bacterial activity in mineralization (Parry et al., 2018; Purnell et al., 2018). Further evidence has been recorded in the taphonomic studies of Butler et al. (2015) and Bickel and Tang (2010) on bilaterians. It was found that, in order to counterbalance the rapid gut biota-driven internal decay of bilaterian tissues, gut biota rapidly escape the gut after death and form internal biofilms; these eventually provide a template for, and induce, mineralization, which facilitates concretion formation and the preservation of soft tissue (Bickel and Tang, 2010). The precipitation of siderite concretions has also been attributed to a complex array of sulfate and iron reducing bacteria (Farrell, 2014; McCoy, 2014; Janssen et al., 2022). Bone marrow and skin structures in frogs preserved on microbial mats for 3 years have been recorded in earlier studies (Iniesto et al., 2013, 2016, 2017). Previous studies have also demonstrated that microbes promote concretion formation via mineral precipitation on decaying carcass or within the sediment around decaying tissues (Pye et al., 1990; Briggs et al., 1993; McCoy et al., 2015b). All these investigations provide valuable evidence highlighting the role of microbes in several concretions and fossilization processes, but many other governing factors also play a crucial role.

Physicochemical factors influencing microbially mediated concretions

Numerous physicochemical parameters influence the formation and composition of microbially mediated concretions, a fact attested to by the variable size (both absolute and relative to the concretion nucleus) and geochemistry of concretions (and the fossils they host) in the fossil record. Several of these physicochemical factors are explored below.

Anoxic conditions

Successful fossilization typically correlates with anoxic conditions attributed to rapid burial, which concomitantly prevents scavenging of OM and inhibits aerobic decay processes (Allison, 1988a). Instead, OM decomposition proceeds via anaerobic metabolic pathways (Briggs, 2003b; Janssen et al., 2022). Moreover, under anaerobic conditions, denitrification (e.g., in Pseudomonas sp.), sulfate reduction to H₂S, and anaerobic methane oxidation (coupled with sulfate reduction) are known to increase the alkalinity and change the chemistry around cells leading to carbonate precipitation (van Rijn et al., 2006; Zhu and Dittrich, 2016). In carbonate concretions, early diagenetic decay-induced mineralization is considered responsible for the co-occurrence of concretion formation with soft tissue fossils at their center. Some studies have suggested that anaerobically driven microbial processes, such as sulfate reduction and production of H₂S, have been critical in facilitation of exceptional soft tissue fossil preservation (e.g., Melendez et al., 2013a,b; Schwark, 2013; Plet et al., 2016; Lengger et al., 2017).

pH

The chemistry of pore waters is a significant control in mineral precipitation, and consequently in carbonate concretion formation. Berner (1968a) reported that decaying tissue can increase pH as well as promote precipitation of calcium and magnesium from dissolved ions in solution. This rise in pH is related to the degradative release of bases such as ammonia (Berner, 1968a). However, further work by Berner (1969) showed that calcium carbonate precipitated only when the pH rise coincided with extensive bacterial sulfate reduction (BSR). pH also plays a vital role in the carbonate–phosphate switch that controls carbonate precipitation. Under low-pH conditions (<pH 6.38), and in the presence of free calcium ions and phosphate ions, calcium phosphate precipitates; by contrast, at higher pH (> pH 6.38), and in the presence of free calcium and carbonate ions, calcium carbonate precipitates (Briggs and Kear, 1993c; Briggs and Wilby, 1996; Janssen et al., 2022).

Other physico-chemical variables

Other factors including dissolved oxygen (DO), conductivity and temperature have been demonstrated to be contributing variables in concretion formation (e.g., Briggs, 1995b; Iniesto et al., 2017; Muramiya et al., 2022). Glendonite, a calcite pseudomorph after ikaite (CaCO₃.6H₂O), forms during early diagenesis in marine sediments and under relatively low temperatures ranging from-2°C to 10°C. This biomineral has been widely used as a low-temperature indicator to reconstruct paleoclimate (De Lurio and Frakes, 1999; Muramiya et al., 2022; Rogov et al., 2023). According to a study by Iniesto et al. (2017), DO exhibited a control similar to pH during laboratory based taphonomic experiments on frogs. The DO and pH were stabilized after seven weeks of incubation of a frog, and the drop in DO and pH implies the period of mineralization. This clearly demonstrated that DO and pH has a vital, but as yet unpredictable role in mineralization.

Microbiological controls on carbonate precipitation and concretion formation

Carbonate mineral precipitation is controlled by a number of complex, interrelated chemical processes. This includes alkalinity changes induced by microbiological processes, which can be dictated by the local environment and pore water chemistry (e.g., Berner, 1968b), or influenced by bicarbonate ions sourced from the surrounding pore waters or from decaying OM (Curtis et al., 1986). A source of cations within the substrate and/or porewaters is also required for concretion precipitation, most commonly calcium or iron forming calcite and siderite concretions, respectively (Curtis et al., 1986; Marshall and Pirrie, 2013; McCoy, 2014). Dolomitic concretions can also form in magnesium-rich environments (e.g., Grice et al., 2019; Scheller et al., 2021). Commonly initiated by decay of a central OM-rich nucleus, carbonate cement precipitates within unconsolidated sediment (Raiswell, 1971; Raiswell and Fisher, 2000; McCoy, 2014; Lengger et al., 2017). Carbonate concretions can form either via pervasive growth where nucleation is simultaneous across the concretion and cementation infills pore space later; concentric mineral growth outwards from a central nucleus; or by a combination of both processes (Raiswell and Fisher, 2000). The role of microbiological OM oxidation in concretion initiation and growth has been demonstrated by stable carbon isotope analyses (e.g., Curtis et al., 1972; Hudson, 1978; Coleman and Raiswell, 1981; Gautier, 1982; Raiswell and Fisher, 2000; Cotroneo et al., 2016), as well as biomarker studies (e.g., Melendez et al., 2013a,b; Plet et al., 2016; Lengger et al., 2017). Previous studies have also proven the role of bacterial EPS in mineral precipitation, for example absorbance of iron from iron-rich chlorides and oxides onto the surface of EPS during authigenic precipitation (Spicer, 1991; Dunn et al., 1997).

Calcium carbonate concretions

Calcium carbonate (calcite; CaCO₃) precipitation is a consequence of BSR, wherein sulfate reducing bacteria oxidize OM to CO₂ to obtain energy and reduce sulfate to H₂S (Coleman and Raiswell, 1981; Coleman, 1993; Coleman and Raiswell, 1995; Kiriakoulakis et al., 2000; Melendez et al., 2013b; Plet et al., 2016). BSR is chemically represented by Equations 1, 2 (Raiswell, 1976). Subsequently, reduced sulfide reacts with dissolved iron to form pyrite via solid iron monosulfide (Equations 3, 4; e.g., Berner, 1985), while carbonate reacts to form calcite (e.g., Berner, 1968a; Pye et al., 1990).

Initial stages of calcite concretion formation typically occur within the earliest stages of diagenesis. Anoxic marine settings have abundant dissolved sulfate and therefore favor calcite precipitation (Berner, 1985). H₂S at the photic zone of an anoxic water column promotes photic zone euxinia (PZE), which has been demonstrated to facilitate exceptional OM preservation (see Figure 5) (e.g., Summons and Powell, 1987; Schwark and Püttmann, 1990; Grice et al., 1996, 1997; Schaeffer et al., 1997; Figure 4). Notably, calcite concretions preserving soft tissue and biomolecules have been associated with PZE (e.g., Melendez et al., 2013a,b; Plet et al., 2016; Lengger et al., 2017).

Figure 5

Calcite concretions can display varying morphological and mineralogical properties with different crystalline phases. These include, but are not limited to, calcite, aragonite, vaterite, dolomite, CaCO₃ monohydrate, CaCO₃ hexahydrate and amorphous CaCO₃ (Rodriguez-Navarro et al., 2012; Murugan et al., 2021). The shape and size of CaCO₃ crystal changes during the precipitation process under different physico-chemical conditions and in association with different microbial communities (Wilby et al., 1996; O'Brien et al., 2002; Raff et al., 2008; Dhami et al., 2012; Raff and Raff, 2014; Plet et al., 2016; Zhu and Dittrich, 2016; Iniesto et al., 2018; Grice et al., 2019; Dubey et al., 2022; Murugan et al., 2022). The major factors responsible for microbially induced concretion precipitation include the concentration of calcium, concentration of DIC, pH, and the availability of nucleation sites (Hammes and Verstraete, 2002; Dhami et al., 2013b; Murugan et al., 2021).

Iron carbonate concretions

In contrast to calcite-forming environments, siderite precipitation is associated with sulfate-limited environments (Coleman, 1993), where dissolved sulfate is rapidly utilised forming pyrite (Equations 3, 4), and bacterial metabolic processes mainly occur via microbial iron reduction (Curtis et al., 1986) and methanogenesis (Maynard, 1982; Curtis et al., 1986; Coleman, 1993; Janssen et al., 2022), as per Equations 5, 6, respectively. This is observed in freshwater systems, such as lakes and swamps.

Pyrite formed as a product of early BSR is often identified in relation to siderite concretions; for example, in siderite concretions from Mazon Creek, pyrite can be observed either localized with fossils or in halos around them (e.g., Cotroneo et al., 2016). In the case of Mazon Creek siderite concretions, δ³⁴S isotope data indicated initial bacterial sulfate reduction rapidly gave way to pervasive siderite growth via methanogenesis (Cotroneo et al., 2016).

Lipids released from decaying organisms might also play a potential role in promoting microbial processes (Kamran et al., 2020). Pure cultures of the iron-reducing bacteria Geobacter and Shewanella have precipitated siderite under laboratory conditions (Lin et al., 2020; Janssen et al., 2022). The reduction of the labile iron can raise the pH above optimal conditions (precipitation of calcite and aragonite is favored over pH ~7.2); however, when coupled with low levels of sulfate reduction, pH variation is limited within the range of siderite precipitation (Lin et al., 2020; Janssen et al., 2022). Here, iron (III) is used as an electron source for the oxidation of OM to CO₂ instead of sulfate, by sulfate reducers such as Desulfovibrio (Kamran et al., 2020). A detailed model of iron carbonate concretion formation is shown in Figure 6.

Figure 6

Phosphatic concretions

Marine phosphatic concretions are formed under anoxic conditions near the sediment–water interface, during early diagenesis. Phosphate is sourced from the sediment pore waters with bacteria playing a crucial role in phosphate fixing, with a possible role for bacterial mats in concretion mineralization (Baturin, 1971; Bentor, 1980; Reimers et al., 1990). Large sulfur bacteria like Beggiatoa or Thiomargarita can store phosphate in the form of polyphosphate under oxic conditions (Brock and Schulz-Vogt, 2011). However, these bacteria produce sulfide, and if oxygen supply is insufficient for complete oxidation of the sulfides, the capacity for polyphosphate storage decreases. Increasing sulfide concentrations and anoxia leads to the decomposition of polyphosphate and iron hydroxides, causing the bacteria to release inorganic orthophosphate (Pi) into surrounding pore water (Brock and Schulz-Vogt, 2011). Pi is the precursor for the precipitation of phosphorite minerals and phosphatic replacement of soft tissues (Janssen et al., 2022). Once precipitation begins, the process is estimated to phosphatize soft tissues rapidly, in timescales of days to weeks (Föllmi, 1996).

Most of these phosphatized concretions are triggered by the decomposition of OM by subsurface microbial communities involved in bacterial sulfate reduction and anaerobic methane oxidation, EPS formation, photosynthesis, ureolysis, iron reduction (Equations 3, 4, 7; Plet et al., 2016; Zhu and Dittrich, 2016; Kamran et al., 2020).

The conditions of phosphatization involve phosphate ions (from the decay of animal remains or an allogenic source), Ca²⁺ ions from seawater and low pH from the production of volatile fatty acids and CO₂ (Zoss et al., 2019). Phosphatized concretions are formed from carbonate fluorapatite (Ca₅(PO₄,CO₃)₃F) and occur most in deposits of Jurassic–Cretaceous age, when phosphogenic-favoring environments were particularly prevalent (Martill, 2007; Dornbos, 2011). Phosphatic concretions have been identified in deposits ranging in age from upper Mesoproterozoic [e.g., Diabaig Formation of the Torridon Group, Scotland, UK: Battison and Brasier (2012)] to Miocene, e.g., Riversleigh World Heritage Area, Queensland, Australia (Arena, 2008; Matzke-Karasz et al., 2013) and Funakawa Formation, Japan (Ogihara, 1999). Numerous modern phosphatic-rich deposits are found in organic-rich, offshore environments, e.g., Baja California (Schuffert et al., 1994; Ogihara, 1999), the Namibian coast (Zoss et al., 2019) and the Chilean-Peruvian coastline (Turnbull et al., 1996; Schulz and Schulz, 2005). A famous example from the fossil record is the Lower Cretaceous Santana Group Lagerstätte of Brazil, which preserves an array of fossils including abundant invertebrates, teleost fish, crocodyliforms, pterosaurs, and rare dinosaurs (Smith, 2000; Martill, 2007; Martill and Brito, 2017). Skin, gills, muscles, and collagen are the most frequently phosphatized soft tissues (Vincent et al., 2017; Parry et al., 2018). Phosphatization is also able to preserve cellular and subcellular structures (Bengtson and Budd, 2004; Bengtson et al., 2017; Sun et al., 2020). In bone tissues, the outer compact bone layers are more prone to replacement with fluorapatite, but the inner spongy bone is more prone to be replaced with calcite; however, the timing of phosphatization of bone tissues is still not fully understood (Zoss et al., 2019). The creation of phosphatized tissues and phosphatic concretions in microbial mats is also largely unknown, however there is extensive research on the role of organic-rich substrate in the precipitation of calcium phosphate (Onuma et al., 2000; Heinemann et al., 2011; Janssen et al., 2022). One location reported to contain microbial mat-preserved fossils is the Crato Formation Konservat-Lagerstätte of the Santana Group, Araripe Basin, Brazil (Varejão et al., 2019).

Analytical methods for concretion characterization

A range of sophisticated and multidisciplinary analytical approaches can be utilized in the robust interrogation of fossiliferous concretions and the fossils they contain (Figure 7; Table 2). These methods include: using powerful imaging tools to resolve the physical form and morphologies of concretions and fossils, sometimes at sub-microscopic levels; organic characterization of the nature and molecular speciation of the preserved organisms and the paleoenvironment in which they were formed; inorganic geochemical analysis for depositional information and evaluation of the redox conditions aiding preservation; and the use of microbiological and molecular techniques to study the structure and function of the microbes active in EPS and concretion formation (Figure 8: Approach 1).

Figure 7

Figure 8

Morphological, molecular, and microbiological characterization of concretions

An understanding of the metabolic activities that took place at the time of fossilization can be obtained through various analytical techniques, using either direct (microbial morphotypes, mineralized EPS, etc.) or indirect (microlaminations with OM or micropeloids) microscopic and elemental evidence (Iniesto et al., 2021; Dias and Carvalho, 2022). This understanding can be furthered via investigation of the influence of various metabolic pathways on decay and mineralization through taphonomic experiments in controlled environment (Pye et al., 1990; Briggs and Kear, 1993c; Butler et al., 2015; Wilson et al., 2016; Gäb et al., 2020; Janssen et al., 2022). In the previous taphonomic experiments, Pye et al. (1990) demonstrated at the Norfolk Marsh field setting that concretions form actively in reduced sediments in which sulphate-reducing bacteria are active. The source of carbonate in their study was found out to be partly driven from marine sources and partly from microbial degradation of organic matter. In another study of Briggs and Kear (1993c) on decay of modern shrimps, it was seen that partial mineralization occurred in amorphous calcium phosphate leading to preservation of cellular details of the muscle tissue under anaerobic conditions wherein microbial biofilms played an important role in the inhibition of tissue decomposition. The anaerobic conditions inhibit scavengers and degrading aerobic bacteria and promote various anaerobic metabolic pathways relevant for biologically induced mineralization (Wilson et al., 2016). Gäb et al. (2020) in their taphonomic experiments on fish found that the extreme environmental conditions in the Green River depositional environment could reduce decay and promote mineralization. Understanding the role of microbes and microbial by products in a range of fossilization conditions is therefore imperative and can be unpinned via a range of micrographical, mineralogical and molecular tools as discussed below.

Morphological analysis of real concretion samples

This analysis provides a useful first screening to assess microbial mineral interactions, investigate the role of microbes and biofilms in different fossiliferous concretions and the physical nature of fossils. A range of microscopic and other microanalytical techniques have been utilized in the field of paleomicrobiology, including scanning electron microscopy, optical microscopy, fluorescence and confocal microscopy, atomic force microscopy and various analysis using synchrotron radiation.

Scanning electron microscopy (SEM) and petrographic analysis with coupled X-ray spectroscopy (SEM/EDS) reveals morphological features along with the chemical constituents, thereby providing a comprehensive picture of microenvironments during fossilization (Iniesto et al., 2013, 2016, 2017; Raff and Raff, 2014; Mähler et al., 2020; Dias and Carvalho, 2022). To date, a number of experimental studies on the direct influence of bacteria on mineralization and preservation have been conducted (in marine and non-marine settings) using different scanning electron micrographical and other elemental analysis tools (Briggs and Kear, 1993a,b,c; Hof and Briggs, 1997; Sagemann et al., 1999; Martin et al., 2005; Raff et al., 2008, 2014; Peterson et al., 2010; Butler et al., 2015; Naimark et al., 2016, 2018; Eagan et al., 2017; Mähler et al., 2020). In a recent study of insect fossils from the Lower Cretaceous Crato Formation Lagerstätte (part of the Santana Group of Brazil), SEM imaging revealed direct evidence of microbial morphotypes and textural features of mineralized EPS, thereby providing strong evidence of the influence of microbial mats in the fossilization process (Dias and Carvalho, 2022).

Optical (light) Microscopy helps in visualizing the fine details of an object by creating a magnified image through a series of glass lenses. Optical microscopy has been widely used in the study of concretions (e.g., Iniesto et al., 2015; Dias and Carvalho, 2022; Downen et al., 2022; Lin et al., 2023).

Confocal Scanning laser Microscopy (CSLM) creates sharp and distinctive images of an exact plane of a specimen (Relucenti et al., 2021). It allows the quantitative evaluation of structural parameters, thickness, and roughness. This technique also permits non-destructive analysis of the 3D architecture and 4D visualization of microfossils (Relucenti et al., 2021). This technique is widely used for the identification of bacteria and EPS distribution within the live biofilm matrix (Wagner et al., 2009; Reichhardt and Parsek, 2019). CSLM, in concert with various fluorescent stains, helps in understanding the different classes of macromolecules by calculating their abundance and distribution on biofilms in a very short period of time (Zhang et al., 1998; Hille et al., 2005; Wagner et al., 2009). However, CSLM has been applied and reported sparingly in fossil studies. Studies by Wagner et al. (2009) and Schopf and Kudryavtsev (2009) demonstrated that CSLM, when combined with Raman spectroscopy, enables observation of biofilms in situ, thus providing supplementary information about chemical properties and the distribution of components of EPS.

Fluorescence Microscopy is based on the emission of luminescence because of absorption of photons, when the samples treated with special fluorescent reagents exhibit Stokes shift. This technique can be used to identify structures in fixed and living biological samples (Lichtman and Conchello, 2005; Sanderson et al., 2014), and helps in understanding the viability of living and dead bacterial cells, biofilms, EPS and calcium carbonate precipitates (McMullan, 1995; Vernon-Parry, 2000). This technique has been recently utilized for investigation of internal architecture in steinkern spider fossils from Oligocene Aix-en-Provence Lagerstätte in southern France (Downen et al., 2022), which identified prolific microbial mat communities as likely being responsible for the preservation of infilled spider molds.

Atomic Force Microscopy (AFM) is a form of scanning probe microscopy, which uses a probe or tip to map the contours of the sample (Braga and Ricci, 1998). AFM is the measurement of the variation of force between the probe tip and the sample surface (Braga and Ricci, 1998) and thus helps in achieving a quantitative assessment of various interactive forces on biofilms under ambient conditions, or even on liquid surfaces, without any pre-treatment. This helps in generating a 3D image of surface topography. In general, these advantages make this emerging imaging technique useful for analyzing bacterial morphology, as well as their adhesive and elastic properties (Chatterjee et al., 2014).

Itrax X-Ray Fluorescence (XRF) core scanning extends traditional XRF characterization of the elemental composition of bulk sediment material by providing high-resolution elemental distributions. These have important implications for understanding paleoenvironmental and geochemical records (e.g., Croudace et al., 2006; Rothwell et al., 2006; Thomson et al., 2006), and can enable better understanding of the complex geochemical, redox and microbial conditions controlling carbonate fossilization (Croudace et al., 2006; Hunt et al., 2015; Hussain et al., 2020). The Itrax XRF core scanner simultaneously collects micro-XRF spectrometry elemental profiles, and optical and microradiographic images (Croudace et al., 2006). This provides an opportunity to study the micro-spatial relationship of elemental distributions within sample material. For example, detailed analyses of elemental distributions across carbonate concretions showed steep profiles of important elements (e.g., calcium) that were subsequently used to construct a diffusion model for concretion growth (Yoshida et al., 2015, 2018).

Omic techniques

Omic techniques are a set of high-throughput methods used to study the structure, function, and interactions of microbial communities in different environments. These techniques include DNA metabarcoding, metagenomics, metatranscriptomics, proteomics, and metabolomics, which analyze the genetic material, RNA transcripts, proteins, and metabolites present in a microbial community, respectively (see green pathways in Figure 7; Zarraonaindia et al., 2013; Shaffer et al., 2022). By using these approaches, researchers can gain insights into the diversity and complexity of microbial ecosystems and understand the roles of different microorganisms in these environments, their metabolic pathways, and their interactions with other organisms and their environment. Omic techniques have broad applications in microbiology, ecology, and biotechnology, and are helping to drive discoveries in fields such as environmental science and bioremediation (Garnatje et al., 2017; Gutleben et al., 2018; Zhang et al., 2018; Laczi et al., 2020; McElhinney et al., 2022). In recent years, there has been increasing interest in applying omic techniques to the study of fossils and the processes involved in their formation and preservation (Dong et al., 2019; Janssen et al., 2022). By integrating multiple omic technologies, it is possible to gain a more complete picture of the constituents and functions of microbial communities within concretions, and potentially unravel the mechanisms underlying concretion formation. For example, microbial biofilms have been shown to play a crucial role in the nucleation and growth of concretions (Frankel and Bazylinski, 2003; Grice et al., 2019; Janssen et al., 2022). It is possible to identify the predominant microorganisms and metabolic pathways involved in the formation of concretions by examining the structure of microbial communities and gene expression patterns in biofilms through techniques such as DNA metabarcoding, metagenomics, and metatranscriptomics (Babilonia et al., 2018; Onstott et al., 2019; Campbell et al., 2021). In addition, these techniques can also provide insights into the preservation of fossils within concretions. For instance, proteomic analysis can reveal the proteins and enzymes involved in the preservation of soft tissues in fossils (Boatman et al., 2019), while metabolomic analysis can identify the biochemical pathways responsible for the preservation of organic compounds (Janssen et al., 2022). The use of omic techniques in paleontology and sedimentology is a relatively recent development, and there is still much to be discovered regarding their potential and limitations. However, as the technology continues to improve, these techniques have the potential to revolutionize our understanding of fossil and concretion formation in modern settings.

Ancient DNA

The analysis of ancient DNA (aDNA) provides researchers with innovative ways to study the past (Yang and Watt, 2005). The study of ancient organisms is rapidly growing owing to recent methodological and technological advancement. It is now possible to obtain vast quantities of DNA data from ancient samples in a high-throughput manner and use this information to investigate the dynamics and evolution of past communities (Eisenhofer and Weyrich, 2019). For instance, by analyzing the DNA of microbial communities preserved in sedimentary layers, it is possible to reconstruct the diversity and abundance of past microbial assemblages and identify the environmental factors that influenced their evolution, as well as shed light on their role in mineral formation and biogeochemical cycling over geological time scales (Capo et al., 2022; Dong et al., 2022). The use of aDNA could potentially provide a window into the microorganisms existing at the time of concretion formation and allow for the identification of the original source organism. However, there are several limitations and challenges associated with aDNA analysis, such as the degradation of DNA over time and the risk of contamination from modern sources. Despite these challenges, in the presence of favorable preservation conditions, the application of aDNA analysis holds great potential as a tool for investigating concretions.

Microbiology techniques

Microbial culturing, enzymatic analysis, physico-chemical parameters and viability analysis – Microbial culturing and enrichment is a simple and efficient method to enhance the multiplication of microbes (associated with fossil/sediment samples) by supplementation of nutrients under controlled laboratory conditions (Brock, 1999; Chapin and Lauderdale, 2007; Lewis et al., 2021). This aids in understanding the growth pattern, density, enumeration (colony forming units/ml) and metabolic properties of the enriched cultures along with their concretion/carbonate formation capability (Dhami et al., 2013a, 2017; Murugan et al., 2021). When trying to grow and study a specific microorganism under laboratory conditions (Figure 8, Approach 2), it is important to use a culture medium that closely mimics their natural environment. This helps the microbial colony to grow to its optimum, and enables better understanding of its specific needs and genetic makeup. Such minimal nutrient media have been designed and utilized in previous studies on enrichment of microbes from natural environments (Henson et al., 2016; Rahman et al., 2020; Ramachandran et al., 2020; Rodrigues and de Carvalho, 2022). Artificial sea water (ASW) media is generally used as a substitute for natural seawater to cultivate marine microbes as the latter often suffers from supply issues and seasonal variability and quality (Berges et al., 2001; Henson et al., 2016). Recently, halophilic archaea were cultivated from surface-sterilized middle–upper Eocene rock salt from the Yunying salt mine, China and the key feature that helped in the longevity of these microbes was their ability to keep their genomic DNA intact (Jaakkola et al., 2014).

Microbial community analysis is also conducted via omics tools (discussed above in omics section) followed by characterization of EPS, biofilm properties and any extracellular enzymes (as urease, carbonic anhydrase) produced by the grown cultures as demonstrated in prior studies (Dupraz et al., 2009; Li et al., 2015; Dhami et al., 2016; Al Disi et al., 2019; Murugan et al., 2021). Microbial culture supernatant is also investigated for change in physico-chemical parameters by microbial metabolic activities via a range of elemental analysis tools such as atomic absorption spectroscopy (AAS), Inductively coupled plasma mass spectroscopy (ICP-MS) and Fourier-transform infrared spectroscopy (FT-IR) (Li et al., 2015; Liu R. et al., 2021; Liu X. et al., 2021; Murugan et al., 2021).

In situ characterization of concretion sequestered microfossils

It is advantageous to screen concretion collections with in situ characterization techniques to identify those with the most promising impregnations (e.g., large, exceptional preservation) for more detailed analytical attention. Given the typically limited amounts of fossil sample available and their precious nature, a range of appropriate micro characterization methods are often applied prior to non-destructive chemical analysis.

Many of the micro-graphical techniques described in the previous concretion section (see: Morphological, molecular and microbiological characterization of concretions) can also be applied to the sequestered microfossils. Typically, concretions are opened so that the fossils can be accessed when exposed, but some techniques also allow in situ interrogation of the enclosed fossils. For instance, SEM imaging methods can provide ultrastructural information of fossilized tissues. However, SEM is limited by low electron penetration depth, meaning that it is often more effective on exposed structures, and especially on carefully prepared ultrathin (<100 nm) sections; one drawback, therefore is that these are representative of only a small fraction of the specimen. 3D images of embedded fossils can be achieved through focused ion beam (FIB)-SEM or by combining sequential milling with concurrent Energy Dispersive Spectroscopy (SEM EDS) where despite the destructive milling approach, nanoscale fossil structures can be successfully imaged to provide insights into their chemistry, ultrastructure, taphonomy and biogenicity (Wacey et al., 2012; Brasier et al., 2015).

CSLM and Raman Spectroscopy can also be used for non-intrusive and non-destructive study of the 3D structure and chemical composition of EPS and fossils (Schopf and Kudryavtsev, 2009; Wagner et al., 2009). Schopf et al. (2010) utilized optical microscopy in combination with CSLM and other interdisciplinary approaches to successfully distinguish between authentic microbial fossils and microscopic “look-alikes.”

Atomic Force Microscopy (AFM) is now widely used for fossil observations and imaging in paleontological research (Benítez et al., 2019). AFM studies by Kempe et al. (2002, 2005) on organic-walled fossils from the upper Neoproterozoic Chichkan Formation of Southern Kazakhstan revealed stacked arrays of 200 nm-sized angular platelets of polycyclic aromatic kerogen on their walls. On comparison with SEM, AFM images provided higher resolution and 3D information about the organization of carbon within the cell. AFM has also been used to measure biofilm thickness and the height and “roughness” of EPS (Relucenti et al., 2021), and to identify the crystal structures of biogenic marine calcite and aragonite from fossil corals (Coronado et al., 2015), echinoderms (Stolarski et al., 2009) and mollusks (Casella et al., 2018; Benítez et al., 2019).

Computed tomography (CT) extends the centuries long use of X-Rays to help visualization of geological fossils (Hohenstein, 2004). X-ray computed tomography (XCT) scanners can successfully visualize fossils in un- or partially prepared concretions and has revolutionized the science of paleontology [see Sutton et al. (2014) for an excellent overview]. Applications of XCT to fossils in concretions include the anatomical description of a Devonian shark from Morocco (Klug et al., 2023); the analysis of an ichthyosaur skull from the Triassic of Svalbard (Roberts et al., 2022); and the visualization of trace fossils in driftwood from the Cretaceous–Paleogene Boundary in the USA (Maisch and Becker, 2022). XCT does have its limitations, however, including digital separation of fossils or matrix – in which case other techniques might be more effective (e.g., neutron tomography; see below).

Micro-CT (μCT) scanning, or high resolution XCT, is also now being popularly applied in paleontology. Recent concretion fossil studies include the reinterpretation of a purported Cambrian jellyfish fossil as a pseudofossil (Nolan et al., 2023); the visualization of the musculature and reproductive, digestive, and circulatory systems of a Devonian arthropod (Laville et al., 2023); the revelation in exquisite detail of the anatomy of Carboniferous millipedes from France (Lheritier et al., 2023); and the characterization of a Jurassic pseudoplanktonic community on a fossilized log (Little et al., 2023).

Synchrotron exploration of the X-ray and matter interactions on a range of geological materials can provide insights on morphology, elemental composition, oxidation states, crystalline structure, magnetic properties, and others, which can measurably contribute to the investigation of biogenicity of putative biosignatures (Callefo et al., 2019). Gueriau et al. (2020) utilized synchrotron radiation to generate X-ray fluorescence elemental maps of fossils representative of different taxonomic groups (arthropods, sarcopterygians and actinopterygians), types of preservation (compressed and three-dimensional fossils, including the ones with extensive soft-tissue mineralization), geological ages and depositional environments. Mineralogical maps were also generated in transmission geometry using a two-dimensional area detector placed behind the fossil.

Synchrotron propagation phase contrast micro-CT (PP-SRμCT/PPC SRμCT) identifies and maps mineral phases and their distribution at the microscale over centimeter-sized areas. Elemental information can be collected synchronously, informing on texture (preferential orientation), crystallite size and local strain. The extremely high resolutions (<100 nm; Vorontsov et al., 2023) achievable with PP-SRμCT has possibly led to the greatest paleontological advances when applied to concretions (Sanchez et al., 2012). This sophisticated technique has been applied to a variety of concretion fossils in recent years, including Devonian placoderm fishes from Australia (Trinajstic et al., 2022b), Triassic coprolites from Poland (Qvarnström et al., 2019a,b) and Jurassic cephalopods from France (Rowe et al., 2022). The non-invasive extraction of 3D information from homogeneously dense specimens has proved critical to some paleobiological studies (Tafforeau et al., 2006; Cunningham et al., 2014; Maldanis et al., 2016), revealing even the preservation of soft tissues.

Neutron scattering

Neutron tomography (NT) is similar to CT in as much as it enables digital separation of fossils from rocks (Bevitt, 2018). Advantageously, the contrast and penetration that can be achieved with neutrons is greater than with X-rays: X-rays interact with electrons surrounding an atom, whereas neutrons interact with atomic nuclei (Bevitt, 2018). NT has been used to visualize a variety of fossils in concretions, including Devonian fishes from Australia (Trinajstic et al., 2022b), a Jurassic ammonite from the United Kingdom (Cherns et al., 2022), a Cretaceous fish from Brazil (Pugliesi et al., 2019), a Cretaceous crocodyliform (with part of an ornithopod dinosaur in its body cavity) from Australia (White et al., 2022), a Cretaceous seed cone from New Zealand (Mays et al., 2017), and an Eocene plant from Antarctica (Dawson et al., 2014).

Organic geochemical (and related) analysis of fossil OM

The isolation of the fossil from its concretion host is critical to the success of organic geochemical analysis of fossil OM. Separation is often achieved through physical methods, although these might not fully isolate the fossil and matrix. As a result, pure matrix is commonly analyzed separately from the fossil sample to avoid contamination and accurately determine the contributions of each component.

Sample screening with high throughput bulk analysis

Bulk geochemical and key elemental analysis are common preliminary methods used to chemically screen concretions and their organic fossils. These methods often involve measuring the total organic and inorganic carbon contents of sediments, along with other elements commonly found in organic compounds such as nitrogen, sulphur and oxygen. Elemental analyses can be used to measure these elements in decarbonated sediments treated with hydrochloric acid, providing a total for each element.

Rock-Eval pyrolysis is a widely used method in determining the thermal stability and quality of OM (Espitalié et al., 1977). It measures the thermal evolution of carbon compounds over laboratory applied temperatures (i.e., 300 to 650°C), and can also provide an indication of the carbon, hydrogen and oxygen content of sediments.

Molecular analysis by GC–MS

Natural OM (NOM) samples are typically subject to various wet chemistry and other preparation techniques to provide specific fractions appropriate for separate gas chromatography mass spectrometry (GC–MS) analysis. The most important technique for organic speciation – i.e., identification of organic compounds including biomarkers – in complex samples such as the NOM that can occur in concretions is GC–MS (see Grice and Eiserbeck, 2014 for a review).

Aliphatic and aromatic hydrocarbon speciation

The non-polar moiety of NOM is typically isolated in a solvent extractable or bitumen fraction which can be further resolved by liquid chromatography into saturate and aromatic fractions. These are then analyzed using GC–MS. The compounds detected in NOM samples can include biomarkers that act as molecular fossils of biological compounds like membrane lipids and pigments. After the deposition of organic matter, lipids and other compounds can be preserved and provide insights into past microbial activity (Brocks and Summons, 2014; Grice and Eiserbeck, 2014; Naeher et al., 2022). Molecular fossils can also include (metallo)porphyrins and proteins. These somewhat “functionalized” molecules are also relatively stable and often well-preserved in the rock record. Biomarkers when detected in NOM can provide a link to lipids and pigments of modern organisms (i.e., eukaryotes, bacteria, and archaea; Peters and Moldowan, 1992). In benign settings (e.g., concretions) hydrocarbon biomarkers may remain stable for hundreds of millions of years. Their detection in concretion fossils can therefore provide valuable taxonomic and environmental information about ancient ecosystems (see below).

Analytical pyrolysis of kerogen

The non-solvent soluble or kerogen fraction of NOM can also be interrogated by GC–MS following appropriate thermal (or chemical) treatments. Thermal energy can be used to break macromolecular OM into smaller products which can pass through GC columns, in a process referred to as analytical pyrolysis. An important advantage of kerogen analyses is that its covalently bound lattice is less vulnerable to overprinting from migrating hydrocarbons or other autochthonous inputs than the free hydrocarbon fraction (i.e., bitumen Peters and Moldowan, 1992).

Various pyrolysis devices have been developed for NOM kerogen analysis, but hydropyrolysis (HyPy) is now widely considered the best practice method because of its high detection sensitivity including of ancient biochemical signatures sequestered in inorganic substrates (Reinhardt et al., 2019). This pyrolysis event is conducted in a hydrogen-rich atmosphere to provide hydrogen donors that quench the reactivity of unstable ion and radical pyrolysates. This helps to maintain primary pyrolysate integrity often including the preservation of biomarker stereochemistry (Meredith et al., 2015). The HyPy released fraction is operationally trapped on a bed of silica gel, allowing subsequent isolation of saturate and aromatic hydrocarbon fractions which can be separately analyzed by GC–MS (or GC-isotope ratio-MS for compound specific isotope analysis).

Polar compound speciation and S-biogeochemistry: The polar fraction of solvent extracted (or HyPy liberated) NOM can be isolated by LC elution with polar solvents. Labile biomolecules, like proteins, lipids and sugars, can be in part sequestered through oxidative cross-linking, yielding N-, O-, and S- containing heterocyclic polymers (e.g., Wiemann et al., 2018a, 2020; McCoy et al., 2020). In particular an abundance of sulfides from microbial sulfate reduction (i.e., in low reactive iron/pyrite settings) can aid organic sulfurization during diagenesis, producing organic sulfur-rich macromolecular aggregates which can stabilize and preserve lipid biomarkers (Sinninghe Damsté and de Leeuw, 1990; Schouten et al., 1993; Aizenshtat et al., 1995).

The three-dimensional macromolecules produced by organic sulfurization are not amenable to GC–MS without further treatment. Raney Nickel is commonly used to selectively cleave the carbon-sulfur bonds of polar fractions, releasing a sulfur-bound organic fraction that can be analyzed by GC–MS (Sinninghe Damsté and de Leeuw, 1990). This approach has been widely used to study sulfurized lipids of Phanerozoic sediments. Heteroatomic organic compounds released by this process (or present in other fractions) may not be directly detectable by GC–MS without derivatization of specific chemical functionalities, e.g., acylation or silylation of acid or hydroxyl groups, respectively (Drozd, 1981). Some functionalized and high MW organic species can be detected directly by LC–MS, which can be advantageous for the analysis of thermally unstable or non-volatile species but is limited by increased band broadening effects compared to gas chromatography (Skoog et al., 2018).

Multidimensional GC–MS

Thanks to continued development, optimization and sophistication, GC–MS is being applied at increasing sensitivity and resolution. Both MS and GC detection can now be extended to multiple dimensions to support very high-resolution product detection. Two-dimensional gas chromatography (GC × GC) uses two different columns to separate compounds that co-elute in one-dimensional separations, greatly expanding resolution of complex mixtures (Scarlett et al., 2019). This allows high resolution physical separation which can aid the characterization of particularly complex mixtures. Tandem mass spectrometry (e.g., MS–MS) or Multiple Reaction Monitoring (MRM) can provide particularly selective analysis of target compounds such as molecular biomarkers (Mei et al., 2018). This upward technological trajectory has helped advance our knowledge of the biogeochemical pathways involved in the formation of biomarkers from natural product precursors during eogenesis (in the water column) and diagenesis (sediments and sediment water interface) and the unique palaeoenvironmental conditions required for their exceptional preservation (Grice et al., 2019).

2D surface analysis of NOM by particle bombardment techniques

The ability to correlate organic molecules with spatial and mineralogical sample features is an important consideration when interpreting exceptionally preserved fossils. Detailed molecular biomarker analysis, which typically requires destruction of bulk sample material, would ideally be complemented by spatially informative surface sensitive analytical methods.

Inductively Coupled Plasma Mass Spectrometry (ICP-MS) analysis using a laser probe can be used to create detailed maps of the elements present on the surface of a given sample. For example, Fe and S biochemical gradients measured across in concretion hosting an ichthyosaur fossil (Lower Jurassic Sachrang Formation, Germany) identified much lower microbial activity in the inner part of the concretion, which likely contributed to the excellent fossil preservation (Plet et al., 2016).

Time of Flight-Secondary Ion Mass Spectrometry (ToF-SIMS) is a technique that can analyze organic and inorganic molecules simultaneously with high mass and lateral resolution. Cluster primary ion beams improve the identification of high MW organic compounds with less analyte fragmentation. This technology is useful in various fields such as material science, biology, and surface analysis (Kollmer, 2004; Touboul et al., 2005). Important organic ToF-SIMS studies have included multiple biomarker investigations (e.g., Steele et al., 2001; Toporski et al., 2002; Siljeström et al., 2009, 2010, 2013, 2017, 2022; Thiel and Sjövall, 2011; Greenwalt et al., 2013; Thiel et al., 2014; Gren et al., 2017; Schweitzer et al., 2018). Organic ToF-SIMS analysis of geological and paleontological samples can yield mass spectral data from rare and precious specimens, altering only the uppermost few nanometers of analysis areas (Greenwalt et al., 2013; Lindgren et al., 2018, 2019; Baumgartner et al., 2023). As it employs no analyte separation (such as that provided by GC), it is not capable of resolving stereoisomers, and the isotopic composition of large organic molecules can be difficult to interpret. ToF-SIMS can complement traditional biomarker techniques by spatially correlating trace biomarker detection with organic sources, mineral phases, and structural features.

Raman spectroscopy is a non-destructive analytical method which can be used for chemical characterization of a wide range of sample materials. The incident source is a laser with a wavelength significantly different from the absorption wavelengths of the target analytes. The spectra produced are characteristic to each molecule, representing the energy difference between excitation and emission wavelengths of Raman active bonds. Use of Raman spectroscopy for in situ analysis of fossil specimens can identify preserved molecular functional groups, alongside intermolecular and organo-mineral relationships (Pelletier, 1999), making it a powerful tool for studying preserved organic matter and methods of biomineralization. Recent developments have given rise to widespread applications of Raman spectroscopy for analysis of biomolecular fossilization products (e.g., Yang et al., 2018; Wiemann et al., 2018a,b, 2019, 2020; Boatman et al., 2019; Fabbri et al., 2020; Norell et al., 2020; Steele et al., 2020).

Stable isotope analysis

Analysis of the stable isotopic composition of sedimentary OM can help to distinguish a wide range of source inputs (Hedges and Keil, 1995; Grice and Brocks, 2011). In the case of fossiliferous concretions, these inputs include bacteria involved in concretion formation, the surrounding depositional environment, and the fossilized organism itself (Melendez et al., 2013b; Plet et al., 2017). Stable isotopic composition is controlled by three major factors: the isotopic composition of source elements, the isotopic fractionation during biosynthesis, and isotopic fractionations during burial and diagenesis (Hayes, 2001; Sessions, 2016).

Stable carbon and oxygen measurements of carbonate have helped to classify the source of concretion carbon, e.g., sulfate (or iron) reduction vs. methanogenic CO₂ (Mozley and Burns, 1993; Pearson and Nelson, 2005; Cotroneo et al., 2016), or biogenic vs. abiogenic carbonate (Yoshida et al., 2015). The δ³⁴S of pyrite gives information on the sulfur cycle during concretion formation. Enriched δ³⁴S measurements of pyrite from Mazon Creek concretions suggest formation in sulfate-limited conditions and near total depletion of local dissolved sulfate by SRB during concretion formation (Cotroneo et al., 2016), whereas strongly depleted pyrite in Oligocene Boom Clay concretions (Belgium) indicates abundant dissolved sulfate (De Craen et al., 1999). Stable carbon isotope ratios of bulk organic matter (δ¹³C_org) can be measured after removal of carbonate by reaction with dilute acid. Similarities in δ¹³C_org of Upper Cretaceous Holz Shale concretions (California) and host sediment was interpreted as evidence that OM was not strongly degraded during concretion formation (Loyd, 2017). Tripp et al. (2022) compared δ¹³C_org with compound-specific δ¹³C values of organic compounds from a Mazon Creek concretion (Illinois) preserving a coprolite (see below).

Compound-specific isotope analysis (CSIA) allows the stable isotope analysis of individual compounds in complex mixtures of sedimentary OM (Grice and Brocks, 2011). The technique was first developed for carbon (δ¹³C) and nitrogen (δ¹⁵N) (Matthews and Hayes, 1978), and has since been applied to hydrogen (δ²H, commonly written as δD) (Burgoyne and Hayes, 1998) and sulfur (δ³⁴S) (Amrani et al., 2009). The technical requirements for reliable and reproducible measurements are sufficient peak height for accurate measurement of the minor isotopes, and typically also baseline separation of peaks to allow the entire peak to be integrated without interference (Sessions, 2006; N.B. not necessary for δ34S CSIA).

Challenges and future directions

The investigation of mineral concretions and their capacity to sequester the organic remains of extant organisms is still a relatively new and immature science. The information that concretions can convey about ancient organisms and ecosystems is primarily derived from the detection of molecular biomarkers (or distinctive morphological features) from the well-preserved fossils sequestered within them (Figure 8, Approach 1). Prior to the end goal of biomarker analysis, however, a large number and variety of other analytical approaches can assist the selection and interrogation of concretions with promising fossil targets. Different analytical approaches that can help to exploit this largely untapped biochemical record range from (i) fundamental evaluation of concretion formation controls for a better understanding of the propensity and distribution of those likely to sequester and preserve ancient organisms (Figure 8, Approach 1); to (ii) in situ characterization and imaging techniques able to identify concretions with promising fossil targets for more detailed geochemical analyses; and (iii) detailed geochemical characterization of the microfossils themselves.

This review has outlined promising methodologies utilized in preliminary studies exploring the chemistry of concretion-encapsulated fossils. Despite early advances in the development and application of techniques that have helped define concretion formation processes and characterize their OM record — including at submicroscopic morphologies and biochemical composition levels — this research area is best considered to be at a developmental stage. There is still much to learn about the mechanisms and controls on microbially mediated concretions and their preservation of NOM under different paleoenvironmental conditions. To better exploit the biological and geological information that fossiliferous concretions present, a number of research challenges will need to be addressed:

• More effective literary, analytical and application integration of complementary Earth Science disciplines involved in concretion research, including microbiology, molecular biology, organic and inorganic geochemistry, paleontology and mineralogy. For instance, the role of various biogeochemical factors in the fossilization process (including those that have previously been implicated) can be further elucidated through studies of modern mineralogy, microbes, genes, and surface physicochemistry. Detailed observation and understanding of these parameters and processes will enable a better understanding of the environmental settings that led to concretion formation in deep time.

• Design and develop laboratory simulations and modeling technology to evaluate field-based inferences of fossilization formation mechanisms (Figure 8, Approach 2). These microbial–mineral related processes are complex and often difficult to unravel directly from microbial, mineral and fossil data from the field, but can be systematically evaluated in artificially controlled situations or predicted from intelligent system models. Wide field data collection, including samples from different locations and timescales, will be important to guide the direction of laboratory experiments (Figure 8). The integration of large field, simulated and modeled data sets will provide new insights about microbe–mineral interactions in different concretion-forming environments (e.g., marine and non-marine settings).

• Successful identification and selection of concretions that host the most promising fossils (i.e., the largest and most morphologically intact) will require the development and application of new field tools. Current evaluations of impregnated fossils with traditional imaging and other methods remain challenging. Development of new and accessible methods able to support in situ interrogation of organismic fossils, both in the field and laboratory would be highly beneficial. Appropriate field application will conveniently help to lessen downstream analytical loads.

• Molecular speciation of organic sediments involves sophisticated, time-consuming procedures, restricting timely analytical processing of samples. The analytical challenges are intensified when conducted on trace amounts of organic analyses (well-preserved fossils are often very small) where particularly meticulous protocols need to be implemented to distinguish sample from background signals. This can be exacerbated when baseline organic signals are high (NB. biologically rich paleo-environments can result in highly dispersed organic content), which is the case at several famous sites with fossiliferous concretions, including the Carboniferous deposits at Mazon Creek, Illinois (coincident with a Pennsylvanian coal seam), the Eocene Green River Formation, Utah (oil shale formation); and the Cambrian Alum Shale, Sweden (shale rich; also high uranium concentration contributing to the radiological alteration of OM). New physical separation techniques able to better isolate fossils will be highly beneficial.

• Research scientists are not always the most effective communicators, either within or beyond their direct research communities. Various logistics (e.g., time, lack of training) can challenge the public communication of research outcomes and the engagement of scientists in outreach initiatives. Nevertheless, scientists have an obligation (especially if backed by public funding) to openly communicate and share the results of their work, particularly those which tangibly impact society. The analysis of ancient organisms that are exceptionally preserved within mineral concretions will provide new information about evolutionary processes on Earth. A higher resolution of environmental and biological paleo-dynamics will add valuable context to understanding contemporary environmental and Earth science (ESS) issues, including modern climate change. Paleoenvironmental reconstructions help climate scientists assess the resilience of our planet’s biosphere, as well as its capacity to cope with and regulate widely fluctuating climate conditions. They also enable climate scientists to more accurately predict the environmental and ecological consequences of present-day climate trajectories – some of which are at close to historical highs (e.g., atmospheric temperature and CO₂ rises over the last 200 years). An intensifying community focus on climate change presents an opportunity to improve societal understanding, attitudes, and behavior toward the environment (Bradley et al., 1999; Ballantyne et al., 2001). Effective communication and educational leverage of Earth Science (e.g., concretionary fossil) and climate change research will help to raise the EES literacy of the general public, including students (the next generation of Earth Scientists) who often have soft subject perceptions about ESS due to greater curricula focus on traditional science and mathematics subjects (Burg, 2003; Dawson and Carson, 2013). A basic EES learning will help to balance climate change perceptions, avoiding unwarranted alarm, but also encourage support for the phasing out of harmful industrial activities as societies transition to more environmentally sustainable practices. Effective science outreach programs should incorporate a variety of approaches, including but not limited to digital content, in-person events, workshops, media appearances, school visits, partnered programs and citizen science.

References

• 1

  AhlbergP.TrinajsticK.JohansonZ.LongJ. (2009). Pelvic claspers confirm chondrichthyan-like internal fertilization in arthrodires. Nature460, 888–889. doi: 10.1038/nature08176

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 2

  AizenshtatZ.KreinE. B.VairavamurthyM. A.GoldsteinT. P. (1995). “Role of sulfur in the transformations of sedimentary organic matter: a mechanistic overview” in Geochemical transformations of sedimentary sulfur. eds. VairavamurthyM. A.SchoonenM. A. A. (Washington, D.C.: American Chemical Society), 16–37.

  • Google Scholar

• 3

  Al DisiZ. A.ZouariN.DittrichM.JaouaS.Al-KuwariH. A. S.BontognaliT. R. R. (2019). Characterization of the extracellular polymeric substances (EPS) of Virgibacillus strains capable of mediating the formation of high mg-calcite and protodolomite. Mar. Chem.216:103693. doi: 10.1016/j.marchem.2019.103693

  • CrossRef
  • Google Scholar

• 4

  AllisonP. A. (1988a). The role of anoxia in the decay and mineralization of proteinaceous macro- fossils. Paleobiology14, 139–154. doi: 10.1017/S009483730001188X

  • CrossRef
  • Google Scholar

• 5

  AllisonP. A. (1988b). Taphonomy of the Eocene London clay biota. Palaeontology31, 1079–1100.

  • Google Scholar

• 6

  AllisonP. A.BottjerD. J. (eds.). (2011). Taphonomy: Process and Bias through time. Dordrecht: Springer.

  • Google Scholar

• 7

  AllisonP. A.PyeK. (1994). Early diagenetic mineralization and fossil preservation in modern carbonate concretions. PALAIOS9, 561–575. doi: 10.2307/3515128

  • CrossRef
  • Google Scholar

• 8

  AmraniA.SessionsA. L.AdkinsJ. F. (2009). Compound-specific δ34S analysis of volatile organics by coupled GC/multicollector-ICPMS. Anal. Chem.81, 9027–9034. doi: 10.1021/ac9016538

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 9

  ArcherA. W.KuecherG. J.KvaleE. P. (1995). The role of tidal-velocity asymmetries in the deposition of silty tidal rhythmites (carboniferous, eastern interior Coal Basin, U.S.a.). J. Sediment. Res.65, 408–416. doi: 10.1306/d42680d6-2b26-11d7-8648000102c1865d

  • CrossRef
  • Google Scholar

• 10

  ArenaD. A. (2008). Exceptional preservation of plants and invertebrates by phosphatization, Riversleigh, Australia. PALAIOS23, 495–502. doi: 10.2110/palo.2006.p06-142r

  • CrossRef
  • Google Scholar

• 11

  ArratiaG.SchultzeH.-P. (1999). “Mesozoic fishes from Chile” in Mesozoic fishes 2 – systematics and fossil record. eds. ArratiaG.SchultzeH.-P. (Munich: Verlag Dr. Friedrich Pfeil), 565–593.

  • Google Scholar

• 12

  BabiloniaJ.ConesaA.CasaburiG.PereiraC.LouyakisA. S.ReidR. P.et al. (2018). Comparative metagenomics provides insight into the ecosystem functioning of the Shark Bay stromatolites, Western Australia. Front. Microbiol.9:1359. doi: 10.3389/fmicb.2018.01359

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 13

  BaiY.GuoX.-J.LiY.-Z.HuangT. (2017). Experimental and visual research on the microbial induced carbonate precipitation by Pseudomonas aeruginosa. AMB Express7:57. doi: 10.1186/s13568-017-0358-5

  • CrossRef
  • Google Scholar

• 14

  BainsA.DhamiN. K.MukherjeeA.ReddyM. S. (2015). Influence of exopolymeric materials on bacterially induced mineralization of carbonates. Appl. Biochem. Biotech.175, 3531–3541. doi: 10.1007/s12010-015-1524-3

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 15

  BairdG. C.ShabicaC. W.AndersonJ. L.RichardsonE. S. (1985a). Biota of a Pennsylvanian muddy coast: habitats within the Mazonian delta complex, Northeast Illinois. J. Paleontol.59, 253–281.

  • Google Scholar

• 16

  BairdG. C.SrokaS. D.ShabicaC. W.BeardT. L.ScottA. C.BroadhurstF. M.et al. (1985b). Mazon Creek-type fossil assemblages in the U.S. midcontinent Pennsylvanian: their recurrent character and palaeoenvironmental significance. Philos. T. R. Soc. Lon. B311, 87–99. doi: 10.1098/rstb.1985.0141

  • CrossRef
  • Google Scholar

• 17

  BairdG. C.SrokaS. D.ShabicaC. W.KuecherG. J. (1986). Taphonomy of middle Pennsylvanian Mazon Creek area fossil localities, Northeast Illinois: significance of exceptional fossil preservation in syngenetic concretions. PALAIOS1, 271–285. doi: 10.2307/3514690

  • CrossRef
  • Google Scholar

• 18

  BallantyneR.FienJ.PackerJ. (2001). School environmental education programme impacts upon student and family learning: a case study analysis. Environ. Educ. Res.7, 23–37. doi: 10.1080/13504620124123

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 19

  BattisonL.BrasierM. D. (2012). Remarkably preserved prokaryote and eukaryote microfossils within 1Ga-old lake phosphates of the Torridon group. NW Scotland. Precambrian Res.196-197, 204–217. doi: 10.1016/j.precamres.2011.12.012

  • CrossRef
  • Google Scholar

• 20

  BaturinG. N. (1971). Stages of phosphorite formation on the ocean floor. Nat. Phys. Sci.232, 61–62. doi: 10.1038/physci232061a0

  • CrossRef
  • Google Scholar

• 21

  BaumgartnerR. J.TeeceB. L.RasmussenB.MuhlingJ.RickardW. D. A.PejcicB.et al. (2023). Exceptional preservation of organic matter and iron-organic colloidal mineralization in hydrothermal black smoker-type sulfide mineralization from the Paleoarchean seafloor. Chem. Geol.618:121296. doi: 10.1016/j.chemgeo.2022.121296

  • CrossRef
  • Google Scholar

• 22

  BengtsonS.BuddG. (2004). Comment on small bilaterian fossils from 40 to 55 million years before the Cambrian. Science306:1291. doi: 10.1126/science.1101338

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 23

  BengtsonS.SallstedtT.BelivanovaV.WhitehouseM. (2017). Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae. PLoS Biol.15:e2000735. doi: 10.1371/journal.pbio.2000735

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 24

  BenítezJ. J.Guzman-PuyolS.DomínguezE.HerediaA.Heredia-GuerreroJ. A. (2019). Applications and potentialities of atomic force microscopy in fossil and extant plant cuticle characterization. Rev. Palaeobot. Palyno.268, 125–132. doi: 10.1016/j.revpalbo.2019.06.015

  • CrossRef
  • Google Scholar

• 25

  BentorY. K. (1980). “Phosphorites—the unsolved problems” in Marine Phosphorites—Geochemistry, occurrence, genesis. ed. BentorY. K. (Tulsa, Oklahoma: SEPM Society for Sedimentary Geology), 3–19.

  • Google Scholar

• 26

  BergesJ. A.FranklinD. J.HarrisonP. J. (2001). Evolution of an artificial seawater medium: improvements in enriched seawater, artificial water over the last two decades. J. Phycol.37, 1138–1145. doi: 10.1046/j.1529-8817.2001.01052.x

  • CrossRef
  • Google Scholar

• 27

  BernerR. A. (1968a). Calcium carbonate concretions formed by the decomposition of organic matter. Science159, 195–197. doi: 10.1126/science.159.3811.195

  • CrossRef
  • Google Scholar

• 28

  BernerR. A. (1968b). Rate of concretion growth. Geochim. Cosmochim. Ac.32, 477–483. doi: 10.1016/0016-7037(68)90040-9

  • CrossRef
  • Google Scholar

• 29

  BernerR. A. (1969). Chemical changes affecting dissolved calcium during the bacterial decomposition of fish and clams in sea water. Mar. Geol.7, 253–274. doi: 10.1016/0025-3227(69)90011-5

  • CrossRef
  • Google Scholar

• 30

  BernerR. A. (1985). Sulphate reduction, organic matter decomposition and pyrite formation. Philos. T. R. Soc. Lon. A315, 25–38. doi: 10.1098/rsta.1985.0027

  • CrossRef
  • Google Scholar

• 31

  BevittJ. J. (2018). Discovering dinosaurs with neutrons. Nat. Rev. Mater.3, 296–298. doi: 10.1038/s41578-018-0049-0

  • CrossRef
  • Google Scholar

• 32

  BickelS. L.TangK. W. (2010). Microbial decomposition of proteins and lipids in copepod versus rotifer carcasses. Mar. Biol.157, 1613–1624. doi: 10.1007/s00227-010-1434-4

  • CrossRef
  • Google Scholar

• 33

  BoatmanE. M.GoodwinM. B.HolmanH.-Y. N.FakraS.ZhengW.GronskyR.et al. (2019). Mechanisms of soft tissue and protein preservation in tyrannosaurus rex. Sci. Rep.9:15678. doi: 10.1038/s41598-019-51680-1

  • CrossRef
  • Google Scholar

• 34

  BojanowskiM. J.ClarksonE. N. K. (2012). Origin of siderite concretions in microenvironments of methanogenesis developed in a sulfate reduction zone: an exception or a rule?J. Sediment. Res.82, 585–598. doi: 10.2110/jsr.2012.50

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 35

  BolhuisH.FillingerL.StalL. J. (2013). Coastal microbial mat diversity along a natural salinity gradient. PLoS One8:e63166. doi: 10.1371/journal.pone.0063166

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 36

  BradleyJ. C.WaliczekT. M.ZajicekJ. M. (1999). Relationship between environmental knowledge and environmental attitude of high school students. J. Environ. Educ.30, 17–21. doi: 10.1080/00958969909601873

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 37

  BragaP. C.RicciD. (1998). Atomic force microscopy: application to investigation of Escherichia coli morphology before and after exposure to cefodizime. Antimicrob. Agents Ch.42, 18–22. doi: 10.1128/AAC.42.1.18

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 38

  BrasierM. D.AntcliffeJ.SaundersM.WaceyD. (2015). Changing the picture of Earth's earliest fossils (3.5-1.9 Ga) with new approaches and new discoveries. P. Natl. Acad. Sci. USA112, 4859–4864. doi: 10.1073/pnas.1405338111

  • CrossRef
  • Google Scholar

• 39

  BriggsD. E. G. (1995a). Experimental taphonomy. PALAIOS10, 539–550. doi: 10.2307/3515093

  • CrossRef
  • Google Scholar

• 40

  BriggsD. E. G. (1995b). Preservation of soft tissues in the fossil record. Eclogae Geol. Helv.88, 623–626.

  • Google Scholar

• 41

  BriggsD. E. G. (2003a). “The role of biofilms in the fossilization of non-biomineralized tissues” in Fossil and recent biofilms: A natural history of life on earth. eds. KrumbeinW. E.PatersonD. M.ZavarzinG. A. (Dordrecht: Springer Netherlands), 281–290.

  • Google Scholar

• 42

  BriggsD. E. G. (2003b). The role of decay and mineralization in the preservation of soft-bodied fossils. Annu. Rev. Earth Pl. Sc.31, 275–301. doi: 10.1146/annurev.earth.31.100901.144746

  • CrossRef
  • Google Scholar

• 43

  BriggsD. E. G.KearA. J. (1993a). Decay and preservation of polychaetes: taphonomic thresholds in soft-bodied organisms. Paleobiology19, 107–135. doi: 10.1017/S0094837300012343

  • CrossRef
  • Google Scholar

• 44

  BriggsD. E. G.KearA. J. (1993b). Decay of Branchiostoma: implications for soft-tissue preservation in conodonts and other primitive chordates. Lethaia26, 275–287. doi: 10.1111/j.1502-3931.1993.tb01532.x

  • CrossRef
  • Google Scholar

• 45

  BriggsD. E. G.KearA. J. (1993c). Fossilization of soft tissue in the laboratory. Science259, 1439–1442. doi: 10.1126/science.259.5100.1439

  • CrossRef
  • Google Scholar

• 46

  BriggsD. E. G.KearA. J.MartillD. M.WilbyP. R. (1993). Phosphatization of soft-tissue in experiments and fossils. J. Geol. Soc.150, 1035–1038. doi: 10.1144/gsjgs.150.6.1035

  • CrossRef
  • Google Scholar

• 47

  BriggsD. E. G.MooreR. A.ShultzJ. W.SchweigertG. (2005). Mineralization of soft-part anatomy and invading microbes in the horseshoe crab Mesolimulus from the upper Jurassic Lagerstätte of Nusplingen, Germany. P. Roy. Soc. B-Biol. Sci.272, 627–632. doi: 10.1098/rspb.2004.3006

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 48

  BriggsD. E. G.RaiswellR.BottrellS. H.HatfieldD.BartelsC. (1996). Controls on the pyritization of exceptionally preserved fossils; an analysis of the lower Devonian Hunsrueck slate of Germany. Am. J. Sci.296, 633–663. doi: 10.2475/ajs.296.6.633

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 49

  BriggsD. E. G.WilbyP. R. (1996). The role of the calcium carbonate-calcium phosphate switch in the mineralization of soft-bodied fossils. J. Geol. Soc.153, 665–668. doi: 10.1144/gsjgs.153.5.0665

  • CrossRef
  • Google Scholar

• 50

  BrockT. D. (1999). Robert Koch: A life in medicine and bacteriology. Washington, DC: American Society of Microbiology Press.

  • Google Scholar

• 51

  BrockJ.Schulz-VogtH. N. (2011). Sulfide induces phosphate release from polyphosphate in cultures of a marine Beggiatoa strain. ISME J.5, 497–506. doi: 10.1038/ismej.2010.135

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 52

  BrocksJ. J.SummonsR. E. (2014). “Sedimentary hydrocarbons, biomarkers for early life” in Treatise on geochemistry (second edition) volume 10: Biogeochemistry. eds. KarlD. M.SchlesingerW. H. (Oxford: Elsevier), 61–103.

  • Google Scholar

• 53

  BurgK. (2003). Earth and environmental science: where to from here?Sci. Educ. News52, 61–66. doi: 10.3316/aeipt.129850

  • CrossRef
  • Google Scholar

• 54

  BurgoyneT. W.HayesJ. M. (1998). Quantitative production of H2 by pyrolysis of gas chromatographic effluents. Anal. Chem.70, 5136–5141. doi: 10.1021/ac980248v

  • CrossRef
  • Google Scholar

• 55

  ButlerA. D.CunninghamJ. A.BuddG. E.DonoghueP. C. J. (2015). Experimental taphonomy of Artemia reveals the role of endogenous microbes in mediating decay and fossilization. P. Roy. Soc. B-Biol. Sci.282:20150476. doi: 10.1098/rspb.2015.0476

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 56

  ButtsS. H.BriggsD. E. G. (2011). “Silicification through time” in Taphonomy: Process and Bias through time. eds. AllisonP. A.BottjerD. J. (Dordrecht: Springer Netherlands), 411–434.

  • Google Scholar

• 57

  CallefoF.MaldanisL.TeixeiraV. C.AbansR. A. D. O.MonfrediniT.RodriguesF.et al. (2019). Evaluating biogenicity on the geological record with synchrotron-based techniques. Front. Microbiol.10:2358. doi: 10.3389/fmicb.2019.02358

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 58

  CampbellM. A.CoolenM. J. L.VisscherP. T.MorrisT.GriceK. (2021). Structure and function of Shark Bay microbial communities following tropical cyclone Olwyn: a metatranscriptomic and organic geochemical perspective. Geobiology19, 642–664. doi: 10.1111/gbi.12461

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 59

  CapoE.MonchampM.-E.CoolenM. J. L.DomaizonI.ArmbrechtL.BertilssonS. (2022). Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential. Environ. Microbiol.24, 2201–2209. doi: 10.1111/1462-2920.15913

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 60

  CarpenterK. (2005). Experimental investigation of the role of bacteria in bone fossilization. Neues. Jahrb. Geol. P. M.2005, 83–94. doi: 10.1127/njgpm/2005/2005/83

  • CrossRef
  • Google Scholar

• 61

  CasellaL. A.Simonet RodaM. D. M.AngioliniL.ZieglerA.SchmahlW. W.BrandU.et al. (2018). Archival biogenic micro- and nanostructure data analysis: signatures of diagenetic systems. Data Brief19, 299–311. doi: 10.1016/j.dib.2018.05.041

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 62

  ChapinK. C.LauderdaleT. L. (2007). “Reagents, stains, and media: bacteriology” in Manual of clinical microbiology. eds. MurrayP. R.BaronE. J.JorgensenJ. H.LandryM. L.PfallerM. A.. 9th ed (Washington, D.C.: ASM Press), 334–364.

  • Google Scholar

• 63

  ChatterjeeS.BiswasN.DattaA.DeyR.MaitiP. (2014). Atomic force microscopy in biofilm study. Microscopy63, 269–278. doi: 10.1093/jmicro/dfu013

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 64

  ChernsL.SpencerA. R. T.RahmanI. A.GarwoodR. J.ReedmanC.BurcaG.et al. (2022). Correlative tomography of an exceptionally preserved Jurassic ammonite implies hyponome-propelled swimming. Geology50, 397–401. doi: 10.1130/g49551.1

  • CrossRef
  • Google Scholar

• 65

  ClementsT.PurnellM.GabbottS. (2018). The Mazon Creek Lagerstätte: a diverse late Paleozoic ecosystem entombed within siderite concretions. J. Geol. Soc.176, 1–11. doi: 10.1144/jgs2018-088

  • CrossRef
  • Google Scholar

• 66

  CliftonH. E. (1957). The carbonate concretions of the Ohio shale. Ohio J. Sci.57, 114–124.

  • Google Scholar

• 67

  ColemanM. L. (1993). Microbial processes: controls on the shape and composition of carbonate concretions. Mar. Geol.113, 127–140. doi: 10.1016/0025-3227(93)90154-N

  • CrossRef
  • Google Scholar

• 68

  ColemanM. L.RaiswellR. (1981). Carbon, oxygen and Sulphur isotope variations in concretions from the upper Lias of N.E. England. Geochim. Cosmochim. Acta45, 329–340. doi: 10.1016/0016-7037(81)90243-X

  • CrossRef
  • Google Scholar

• 69

  ColemanM. L.RaiswellR. (1995). Source of carbonate and origin of zonation in pyritiferous carbonate concretions; evaluation of a dynamic model. Am. J. Sci.295, 282–308. doi: 10.2475/ajs.295.3.282

  • CrossRef
  • Google Scholar

• 70

  CoronadoI.Fernández-MartínezE.RodríguezS.TourneurF. (2015). Reconstructing a carboniferous inferred coral–alcyonarian association using a biomineralogical approach. Geobiology13, 340–356. doi: 10.1111/gbi.12133

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 71

  CostertonJ. W.LewandowskiZ.CaldwellD. E.KorberD. R.Lappin-ScottH. M. (1995). Microbial biofilms. Annu. Rev. Microbiol.49, 711–745. doi: 10.1146/annurev.mi.49.100195.003431

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 72

  CotroneoS.SchiffbauerJ. D.McCoyV. E.WortmannU. G.DarrochS. A. F.PengY.et al. (2016). A new model of the formation of Pennsylvanian iron carbonate concretions hosting exceptional soft-bodied fossils in Mazon Creek, Illinois. Geobiology14, 543–555. doi: 10.1111/gbi.12197

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 73

  CroudaceI. W.RindbyA.RothwellR. G. (2006). “ITRAX: description and evaluation of a new multi-function X-ray core scanner” in New techniques in sediment Core analysis. ed. RothwellR. G., vol. 267 (London: Geological Society, London, Special Publications), 51–63.

  • Google Scholar

• 74

  CunninghamJ. A.DonoghueP. C. J.BengtsonS. (2014). Distinguishing biology from geology in soft-tissue preservation. Paleontol. Soc. Papers20, 275–288. doi: 10.1017/S1089332600002898

  • CrossRef
  • Google Scholar

• 75

  CurtisC. D.ColemanM. L.LoveL. G. (1986). Pore water evolution during sediment burial from isotopic and mineral chemistry of calcite, dolomite and siderite concretions. Geochim. Cosmochim. Ac.50, 2321–2334. doi: 10.1016/0016-7037(86)90085-2

  • CrossRef
  • Google Scholar

• 76

  CurtisC. D.PetrowskiC.OertelG. (1972). Stable carbon isotope ratios within carbonate concretions: a clue to place and time of formation. Nature235, 98–100. doi: 10.1038/235098a0

  • CrossRef
  • Google Scholar

• 77

  DangH.LovellC. R. (2016). Microbial surface colonization and biofilm development in marine environments. Microbiol. Mol. Biol. R.80, 91–138. doi: 10.1128/MMBR.00037-15

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 78

  DawsonV.CarsonK. (2013). Science teachers’ and senior secondary schools students’ perceptions of earth and environmental science topics. Aust. J. Environ. Edu.29, 202–220. doi: 10.1017/aee.2014.6

  • CrossRef
  • Google Scholar

• 79

  DawsonM.FrancisJ.CarpenterR. (2014). New views of plant fossils from Antarctica: a comparison of X-ray and neutron imaging techniques. J. Paleontol.88, 702–707. doi: 10.1666/13-124

  • CrossRef
  • Google Scholar

• 80

  De CraenM.SwennenR.KeppensE. M.MacaulayC. I.KiriakoulakisK. (1999). Bacterially mediated formation of carbonate concretions in the Oligocene boom clay of northern Belgium. J. Sediment. Res.69, 1098–1106. doi: 10.2110/jsr.69.1098

  • CrossRef
  • Google Scholar

• 81

  De LurioJ. L.FrakesL. A. (1999). Glendonites as a paleoenvironmental tool: implications for early cretaceous high latitude climates in Australia. Geochim. Cosmochim. Acta63, 1039–1048. doi: 10.1016/S0016-7037(99)00019-8

  • CrossRef
  • Google Scholar

• 82

  DenceW. A. (1956). Concretions of the alewife, Pomolobus pseudoharengus (Wilson), at Onondaga Lake, New York. Copeia1956, 155–158. doi: 10.2307/1439629

  • CrossRef
  • Google Scholar

• 83

  DhamiN. K.AlsubhiW. R.WatkinE.MukherjeeA. (2017). Bacterial community dynamics and biocement formation during stimulation and augmentation: implications for soil consolidation. Front. Microbiol.8:1267. doi: 10.3389/fmicb.2017.01267

  • CrossRef
  • Google Scholar

• 84

  DhamiN. K.ReddyM. S.MukherjeeA. (2012). Improvement in strength properties of ash bricks by bacterial calcite. Ecol. Eng.39, 31–35. doi: 10.1016/j.ecoleng.2011.11.011

  • CrossRef
  • Google Scholar

• 85

  DhamiN. K.ReddyM. S.MukherjeeA. (2013a). Biomineralization of calcium carbonate polymorphs by the bacterial strains isolated from calcareous sites. J. Microbiol. Biotechnol.23, 707–714. doi: 10.4014/jmb.1212.11087

  • CrossRef
  • Google Scholar

• 86

  DhamiN. K.ReddyM. S.MukherjeeA. (2013b). Biomineralization of calcium carbonates and their engineered applications: a review. Front. Microbiol.4:314. doi: 10.3389/fmicb.2013.00314

  • CrossRef
  • Google Scholar

• 87

  DhamiN. K.ReddyM. S.MukherjeeA. (2016). Significant indicators for biomineralisation in sand of varying grain sizes. Constr. Build. Mater.104, 198–207. doi: 10.1016/j.conbuildmat.2015.12.023

  • CrossRef
  • Google Scholar

• 88

  DiasJ. J.CarvalhoI. d. S. (2022). The role of microbial mats in the exquisite preservation of Aptian insect fossils from the Crato Lagerstätte, Brazil. Cretaceous Res.130:105068. doi: 10.1016/j.cretres.2021.105068

  • CrossRef
  • Google Scholar

• 89

  DittrichM.SiblerS. (2005). Cell surface groups of two picocyanobacteria strains studied by zeta potential investigations, potentiometric titration, and infrared spectroscopy. J. Colloid Interf. Sci.286, 487–495. doi: 10.1016/j.jcis.2005.01.029

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 90

  DongH.HuangL.ZhaoL.ZengQ.LiuX.ShengY.et al. (2022). A critical review of mineral–microbe interaction and co-evolution: mechanisms and applications. Natl. Sci. Rev.9:128. doi: 10.1093/nsr/nwac128

  • CrossRef
  • Google Scholar

• 91

  DongY.SanfordR. A.InskeepW. P.SrivastavaV.BuloneV.FieldsC. J.et al. (2019). Physiology, metabolism, and fossilization of hot-spring filamentous microbial mats. Astrobiology19, 1442–1458. doi: 10.1089/ast.2018.1965

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 92

  DornbosS. Q. (2011). “Phosphatization through the Phanerozoic” in Taphonomy: Process and Bias through time. eds. AllisonP. A.BottjerD. J. (Dordrecht: Springer Netherlands), 435–456.

  • Google Scholar

• 93

  DownenM. R.SchiffbauerJ. D.SeldenP. A.OlcottA. N. (2022). Steinkern spiders: a microbial mat-controlled taphonomic pathway in the Oligocene Aix-En-Provence Lagerstätte, France. Palaeoentomology5, 524–536. doi: 10.11646/palaeoentomology.5.6.4

  • CrossRef
  • Google Scholar

• 94

  DrozdJ. (1981). Chemical derivatization in gas chromatography – journal of chromatography library, 19. Amsterdam: Elsevier.

  • Google Scholar

• 95

  DubeyA. A.MuruganR.RaviK.MukherjeeA.DhamiN. K. (2022). Investigation on the impact of cementation media concentration on properties of biocement under stimulation and augmentation approaches. J. Hazard. Tox. Radioact. Waste26:04021050. doi: 10.1061/(ASCE)HZ.2153-5515.0000662

  • CrossRef
  • Google Scholar

• 96

  DunnK. A.McLeanR. J. C.UpchurchG. R.Jr.FolkR. L. (1997). Enhancement of leaf fossilization potential by bacterial biofilms. Geology25, 1119–1122. doi: 10.1130/0091-7613(1997)025<1119:EOLFPB>2.3.CO;2

  • CrossRef
  • Google Scholar

• 97

  DuprazC.ReidR. P.BraissantO.DechoA. W.NormanR. S.VisscherP. T. (2009). Processes of carbonate precipitation in modern microbial mats. Earth-Sci. Rev.96, 141–162. doi: 10.1016/j.earscirev.2008.10.005

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 98

  DuprazC.VisscherP. T. (2005). Microbial lithification in marine stromatolites and hypersaline mats. Trends Microbiol.13, 429–438. doi: 10.1016/j.tim.2005.07.008

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 99

  DworatzekM. (1987). "Sedimentology and petrology of carbonate intercalations in the upper Cambrian Olenid shale facies of southern Sweden". (Uppsala: Sveriges Geologiska Undersökning).

  • Google Scholar

• 100

  EaganJ. L.AndrewsM. E.PearsonR. L.TurnerF. R.RaffE. C.RaffR. A. (2017). Identification and modes of action of endogenous bacteria in taphonomy of embryos and larvae. PALAIOS32, 206–217. doi: 10.2110/palo.2016.071

  • CrossRef
  • Google Scholar

• 101

  EisenhoferR.WeyrichL. S. (2019). Assessing alignment-based taxonomic classification of ancient microbial DNA. PeerJ7:e6594. doi: 10.7717/peerj.6594

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 102

  ErcoleC.BozzelliP.AltieriF.CacchioP.Del GalloM. (2012). Calcium carbonate mineralization: involvement of extracellular polymeric materials isolated from calcifying bacteria. Microsc. Microanal.18, 829–839. doi: 10.1017/S1431927612000426

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 103

  ErcoleC.CacchioP.BottaA. L.CentiV.LepidiA. (2007). Bacterially induced mineralization of calcium carbonate: the role of exopolysaccharides and capsular polysaccharides. Microsc. Microanal.13, 42–50. doi: 10.1017/S1431927607070122

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 104

  ErikssonM. E.De La GarzaR.HornE.LindgrenJ. (2022). A review of ichthyosaur (Reptilia, Ichthyopterygia) soft tissues with implications for life reconstructions. Earth-Sci. Rev.226:103965. doi: 10.1016/j.earscirev.2022.103965

  • CrossRef
  • Google Scholar

• 105

  EspitaliéJ.LaporteJ. L.MadecM.MarquisF.LeplatP.PauletJ.et al. (1977). Méthode rapide de caractérisation des roches mètres, de leur potentiel pétrolier et de leur degré d'évolution. Rev. Inst. Fr. Pét.32, 23–42. doi: 10.2516/ogst:1977002

  • CrossRef
  • Google Scholar

• 106

  FabbriM.WiemannJ.ManucciF.BriggsD. E. G. (2020). Three-dimensional soft tissue preservation revealed in the skin of a non-avian dinosaur. Palaeontology63, 185–193. doi: 10.1111/pala.12470

  • CrossRef
  • Google Scholar

• 107

  FaraE.SaraivaA. Á. F.de Almeida CamposD.MoreiraJ. K. R.de Carvalho SiebraD.KellnerA. W. A. (2005). Controlled excavations in the Romualdo member of the Santana formation (early cretaceous, Araripe Basin, northeastern Brazil): stratigraphic, palaeoenvironmental and palaeoecological implications. Palaeogeogr. Palaeocl.218, 145–160. doi: 10.1016/j.palaeo.2004.12.012

  • CrossRef
  • Google Scholar

• 108

  FarmerJ. D.Des MaraisD. J. (1999). Exploring for a record of ancient Martian life. J. Geophys. Res.-Planet.104, 26977–26995. doi: 10.1029/1998JE000540

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 109

  FarrellÚ. C. (2014). Pyritization of soft tissues in the fossil record: an overview. Paleontol. Soc. Papers20, 35–58. doi: 10.1017/S1089332600002795

  • CrossRef
  • Google Scholar

• 110

  FöllmiK. B. (1996). The phosphorus cycle, phosphogenesis and marine phosphate-rich deposits. Earth-Sci. Rev.40, 55–124. doi: 10.1016/0012-8252(95)00049-6

  • CrossRef
  • Google Scholar

• 111

  FrankelR. B.BazylinskiD. A. (2003). Biologically induced mineralization by bacteria. Rev. Mineral. Geochem.54, 95–114. doi: 10.2113/0540095

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 112

  GäbF.BallhausC.StinnesbeckE.KralA. G.JanssenK.BierbaumG. (2020). Experimental taphonomy of fish – role of elevated pressure, salinity and pH. Sci. Rep.10:7839. doi: 10.1038/s41598-020-64651-8

  • CrossRef
  • Google Scholar

• 113

  GainesR. R.BriggsD. E. G.OrrP. J.Van RoyP. (2012). Preservation of giant anomalocaridids in silica-chlorite concretions from the early Ordovician of Morocco. PALAIOS27, 317–325. doi: 10.2110/palo.2011.p11-093r

  • CrossRef
  • Google Scholar

• 114

  GainesR. R.VorhiesJ. S. (2016). Growth mechanisms and geochemistry of carbonate concretions from the Cambrian wheeler formation (Utah, USA). Sedimentology63, 662–698. doi: 10.1111/sed.12234

  • CrossRef
  • Google Scholar

• 115

  GarnatjeT.PeñuelasJ.VallèsJ. (2017). Ethnobotany, phylogeny, and ‘omics’ for human health and food security. Trends Plant Sci.22, 187–191. doi: 10.1016/j.tplants.2017.01.001

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 116

  GautierD. L. (1982). Siderite concretions; indicators of early diagenesis in the gammon shale (cretaceous). J. Sediment. Res.52, 859–871. doi: 10.1306/212f8076-2b24-11d7-8648000102c1865d

  • CrossRef
  • Google Scholar

• 117

  GehlingJ. G. (1999). Microbial mats in terminal Proterozoic siliciclastics; Ediacaran death masks. PALAIOS14, 40–57. doi: 10.2307/3515360

  • CrossRef
  • Google Scholar

• 118

  GelinF.de LeeuwJ. W.Sinninghe DamstéJ. S.DerenneS.LargeauC.MetzgerP. (1994). The similarity of chemical structures of soluble aliphatic polyaldehyde and insoluble algaenan in the green microalga Botryococcus braunii race a as revealed by analytical pyrolysis. Org. Geochem.21, 423–435. doi: 10.1016/0146-6380(94)90094-9

  • CrossRef
  • Google Scholar

• 119

  GothK.de LeeuwJ. W.PüttmannW.TegelaarE. W. (1988). Origin of Messel oil shale kerogen. Nature336, 759–761. doi: 10.1038/336759a0

  • CrossRef
  • Google Scholar

• 120

  GreenwaltD. E.GorevaY. S.SiljeströmS. M.RoseT.HarbachR. E. (2013). Hemoglobin-derived porphyrins preserved in a middle Eocene blood-engorged mosquito. P. Natl. Acad. Sci. USA110, 18496–18500. doi: 10.1073/pnas.1310885110

  • CrossRef
  • Google Scholar

• 121

  GrenJ. A.SjövallP.ErikssonM. E.SylvestersenR. L.MaroneF.Sigfridsson ClaussK. G. V.et al. (2017). Molecular and microstructural inventory of an isolated fossil bird feather from the Eocene Fur formation of Denmark. Palaeontology60, 73–90. doi: 10.1111/pala.12271

  • CrossRef
  • Google Scholar

• 122

  GriceK.AudinoM.BorehamC. J.AlexanderR.KagiR. I. (2001). Distributions and stable carbon isotopic compositions of biomarkers in torbanites from different palaeogeographical locations. Org. Geochem.32, 1195–1210. doi: 10.1016/S0146-6380(01)00087-0

  • CrossRef
  • Google Scholar

• 123

  GriceK.BrocksJ. J. (2011). “Biomarkers (organic, compound-specific isotopes)” in Encyclopedia of Geobiology. eds. ReitnerJ.ThielV. (Dordrecht: The Netherlands Springer), 167–182.

  • Google Scholar

• 124

  GriceK.EiserbeckC. (2014). “The analysis and application of biomarkers” in Treatise on geochemistry (second edition) volume 12: Organic geochemistry. eds. FalkowskiP. G.FreemanK. H. (Oxford: Elsevier), 47–78.

  • Google Scholar

• 125

  GriceK.HolmanA. I.PletC.TrippM. (2019). Fossilised biomolecules and biomarkers in carbonate concretions from Konservat-Lagerstätten. Fortschr. Mineral.9:158. doi: 10.3390/min9030158

  • CrossRef
  • Google Scholar

• 126

  GriceK.SchaefferP.SchwarkL.MaxwellJ. R. (1996). Molecular indicators of palaeoenvironmental conditions in an immature Permian shale (Kupferschiefer, lower Rhine Basin, north-West Germany) from free and S-bound lipids. Org. Geochem.25, 131–147. doi: 10.1016/S0146-6380(96)00130-1

  • CrossRef
  • Google Scholar

• 127

  GriceK.SchaefferP.SchwarkL.MaxwellJ. R. (1997). Changes in palaeoenvironmental conditions during deposition of the Permian Kupferschiefer (lower Rhine Basin, Northwest Germany) inferred from molecular and isotopic compositions of biomarker components. Org. Geochem.26, 677–690. doi: 10.1016/S0146-6380(97)00036-3

  • CrossRef
  • Google Scholar

• 128

  GriceK.SchoutenS.BlokkerP.DerenneS.LargeauC.NissenbaumA.et al. (2003). Structural and isotopic analysis of kerogens in sediments rich in free sulfurised Botryococcus braunii biomarkers. Org. Geochem.34, 471–482. doi: 10.1016/S0146-6380(02)00187-0

  • CrossRef
  • Google Scholar

• 129

  GrimesS. T.BrockF.RickardD.DaviesK. L.EdwardsD.BriggsD. E. G.et al. (2001). Understanding fossilization: experimental pyritization of plants. Geology29, 123–126. doi: 10.1130/0091-7613(2001)029<0123:UFEPOP>2.0.CO;2

  • CrossRef
  • Google Scholar

• 130

  GrotzingerJ. P.KnollA. H. (1999). Stromatolites in Precambrian carbonates: evolutionary mileposts or environmental dipsticks?Annu. Rev. Earth Pl. Sc.27, 313–358. doi: 10.1146/annurev.earth.27.1.313

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 131

  GueriauP.RéguerS.LeclercqN.CupelloC.BritoP. M.JauvionC.et al. (2020). Visualizing mineralization processes and fossil anatomy using synchronous synchrotron X-ray fluorescence and X-ray diffraction mapping. J. R. Soc. Interface17:20200216. doi: 10.1098/rsif.2020.0216

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 132

  GuptaN. S.BriggsD. E. G.CollinsonM. E.EvershedR. P.MichelsR.JackK. S.et al. (2007). Evidence for the in situ polymerisation of labile aliphatic organic compounds during the preservation of fossil leaves: implications for organic matter preservation. Org. Geochem.38, 499–522. doi: 10.1016/j.orggeochem.2006.06.011

  • CrossRef
  • Google Scholar

• 133

  GutlebenJ.Chaib De MaresM.van ElsasJ. D.SmidtH.OvermannJ.SipkemaD. (2018). The multi-omics promise in context: from sequence to microbial isolate. Crit. Rev. Microb.44, 212–229. doi: 10.1080/1040841X.2017.1332003

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 134

  HammesF.VerstraeteW. (2002). Key roles of pH and calcium metabolism in microbial carbonate precipitation. Rev. Environ. Sci. Bio.1, 3–7. doi: 10.1023/A:1015135629155

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 135

  HayesJ. M. (2001). Fractionation of carbon and hydrogen isotopes in biosynthetic processes. Rev. Mineral. Geochem.43, 225–277. doi: 10.2138/gsrmg.43.1.225

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 136

  HedgesJ. I.KeilR. G. (1995). Sedimentary organic matter preservation: an assessment and speculative synthesis. Mar. Chem.49, 81–115. doi: 10.1016/0304-4203(95)00008-F

  • CrossRef
  • Google Scholar

• 137

  HeinemannS.HeinemannC.JägerM.NeunzehnJ.WiesmannH. P.HankeT. (2011). Effect of silica and hydroxyapatite mineralization on the mechanical properties and the biocompatibility of nanocomposite collagen scaffolds. ACS Appl. Mater. Inter.3, 4323–4331. doi: 10.1021/am200993q

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 138

  HensonM. W.PitreD. M.WeckhorstJ. L.LanclosV. C.WebberA. T.ThrashJ. C. (2016). Artificial seawater media facilitate cultivating members of the microbial majority from the Gulf of Mexico. mSphere1, e00028–e00016. doi: 10.1128/mSphere.00028-16

  • CrossRef
  • Google Scholar

• 139

  HilleA.NeuT. R.HempelD. C.HornH. (2005). Oxygen profiles and biomass distribution in biopellets of aspergillus Niger. Biotechnol. Bioeng.92, 614–623. doi: 10.1002/bit.20628

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 140

  HofC. H. J.BriggsD. E. G. (1997). Decay and mineralization of mantis shrimps (Stomatopoda; Crustacea); a key to their fossil record. PALAIOS12, 420–438. doi: 10.2307/3515381

  • CrossRef
  • Google Scholar

• 141

  HohensteinP. (2004). X-ray imaging for palaeontology. Brit. J. Radiol.77, 420–425. doi: 10.1259/bjr/27832269

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 142

  HudsonJ. D. (1978). Concretions, isotopes, and the diagenetic history of the Oxford clay (Jurassic) of Central England. Sedimentology25, 339–370. doi: 10.1111/j.1365-3091.1978.tb00317.x

  • CrossRef
  • Google Scholar

• 143

  HuggettJ. M. (1994). Diagenesis of mudrocks and concretions from the London clay formation in the London Basin. Clay Miner.29, 693–707. doi: 10.1180/claymin.1994.029.4.22

  • CrossRef
  • Google Scholar

• 144

  HuggettJ. M.GaleA. S.EvansS. (2000). Carbonate concretions from the London clay (Ypresian, Eocene) of southern England and the exceptional preservation of wood-boring communities. J. Geol. Soc.157, 187–200. doi: 10.1144/jgs.157.1.187

  • CrossRef
  • Google Scholar

• 145

  HuntJ. E.CroudaceI. W.MacLachlanS. E. (2015). “Use of calibrated ITRAX XRF data in determining turbidite geochemistry and provenance in Agadir Basin, northwest African passive margin” in Micro-XRF studies of sediment cores: Applications of a non-destructive tool for the environmental sciences. eds. CroudaceI. W.RothwellR. G. (Dordrecht: Springer Netherlands), 127–146.

  • Google Scholar

• 146

  HussainA.HaughtonP. D. W.ShannonP. M.TurnerJ. N.PierceC. S.Obradors-LatreA.et al. (2020). High-resolution X-ray fluorescence profiling of hybrid event beds: implications for sediment gravity flow behaviour and deposit structure. Sedimentology67, 2850–2882. doi: 10.1111/sed.12722

  • CrossRef
  • Google Scholar

• 147

  IniestoM.Blanco-MorenoC.VillalbaA.BuscalioniÁ. D.GuerreroM. C.López-ArchillaA. I. (2018). Plant tissue decay in long-term experiments with microbial mats. Geosciences8:387. doi: 10.3390/geosciences8110387

  • CrossRef
  • Google Scholar

• 148

  IniestoM.BuscalioniÁ. D.Carmen GuerreroM.BenzeraraK.MoreiraD.López-ArchillaA. I. (2016). Involvement of microbial mats in early fossilization by decay delay and formation of impressions and replicas of vertebrates and invertebrates. Sci. Rep.6:25716. doi: 10.1038/srep25716

  • CrossRef
  • Google Scholar

• 149

  IniestoM.Gutiérrez-SilvaP.DiasJ. J.CarvalhoI. S.BuscalioniA. D.López-ArchillaA. I. (2021). Soft tissue histology of insect larvae decayed in laboratory experiments using microbial mats: Taphonomic comparison with cretaceous fossil insects from the exceptionally preserved biota of Araripe, Brazil. Palaeogeogr, Palaeocl.564:110156. doi: 10.1016/j.palaeo.2020.110156

  • CrossRef
  • Google Scholar

• 150

  IniestoM.LagunaC.FlorínM.GuerreroM. C.ChicoteA.BuscalioniA. D.et al. (2015). The impact of microbial mats and their microenvironmental conditions in early decay of fish. PALAIOS30, 792–801. doi: 10.2110/palo.2014.086

  • CrossRef
  • Google Scholar

• 151

  IniestoM.Lopez-ArchillaA. I.Fregenal-MartínezM.BuscalioniA. D.GuerreroM. C. (2013). Involvement of microbial mats in delayed decay: an experimental essay on fish preservation. PALAIOS28, 56–66. doi: 10.2110/palo.2011.p11-099r

  • CrossRef
  • Google Scholar

• 152

  IniestoM.VillalbaI.BuscalioniA. D.GuerreroM. C.López-ArchillaA. I. (2017). The effect of microbial mats in the decay of anurans with implications for understanding taphonomic processes in the fossil record. Sci. Rep.7:45160. doi: 10.1038/srep45160

  • CrossRef
  • Google Scholar

• 153

  IrwinH.CurtisC.ColemanM. (1977). Isotopic evidence for source of diagenetic carbonates formed during burial of organic-rich sediments. Nature269, 209–213. doi: 10.1038/269209a0

  • CrossRef
  • Google Scholar

• 154

  JaakkolaS. T.ZerullaK.GuoQ.LiuY.MaH.YangC.et al. (2014). Halophilic archaea cultivated from surface sterilized middle-late Eocene rock salt are polyploid. PLoS One9:e110533. doi: 10.1371/journal.pone.0110533

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 155

  JanssenK.MählerB.RustJ.BierbaumG.McCoyV. E. (2022). The complex role of microbial metabolic activity in fossilization. Biol. Rev.97, 449–465. doi: 10.1111/brv.12806

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 156

  JohnsonR. G.RichardsonE. S. (1966). A remarkable Pennsylvanian Fauna from the Mazon Creek area, Illinois. J. Geol.74, 626–631.

  • Google Scholar

• 157

  KamranA.SchneiderD.RoddatisV.ThielV.HoppertM. (2020). Formation of siderite in microbial microcosms derived from a marine sediment. Geomicrobiol J.37, 475–485. doi: 10.1080/01490451.2020.1725186

  • CrossRef
  • Google Scholar

• 158

  KempeA.SchopfJ. W.AltermannW.KudryavtsevA. B.HecklW. M. (2002). Atomic force microscopy of Precambrian microscopic fossils. P. Natl. Acad. Sci. USA99, 9117–9120. doi: 10.1073/pnas.142310299

  • CrossRef
  • Google Scholar

• 159

  KempeA.WirthR.AltermannW.StarkR. W.SchopfJ. W.HecklW. M. (2005). Focussed ion beam preparation and in situ nanoscopic study of Precambrian acritarchs. Precambrian Res.140, 36–54. doi: 10.1016/j.precamres.2005.07.002

  • CrossRef
  • Google Scholar

• 160

  KiriakoulakisK.MarshallJ. D.WolffG. A. (2000). Biomarkers in a lower Jurassic concretion from Dorset (UK). J. Geol. Soc.157, 207–220. doi: 10.1144/jgs.157.1.207

  • CrossRef
  • Google Scholar

• 161

  KlugC.CoatesM.FreyL.GreifM.JobbinsM.PohleA.et al. (2023). Broad snouted cladoselachian with sensory specialization at the base of modern chondrichthyans. Swiss J. Palaeo.142:2. doi: 10.1186/s13358-023-00266-6

  • CrossRef
  • Google Scholar

• 162

  KollmerF. (2004). Cluster primary ion bombardment of organic materials. Appl. Surf. Sci.231-232, 153–158. doi: 10.1016/j.apsusc.2004.03.101

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 163

  KonhauserK. O.NewmanD. K.KapplerA. (2005). The potential significance of microbial Fe(III) reduction during deposition of Precambrian banded iron formations. Geobiology3, 167–177. doi: 10.1111/j.1472-4669.2005.00055.x

  • CrossRef
  • Google Scholar

• 164

  KrauseD.JachauK. (2002). Späte leichenveränderungen. Rechtsmedizin12, 175–186. doi: 10.1007/s00194-002-0144-8

  • CrossRef
  • Google Scholar

• 165

  LacziK.Erdeiné KisÁ.SzilágyiÁ.BounedjoumN.BodorA.VinczeG. E.et al. (2020). New frontiers of anaerobic hydrocarbon biodegradation in the multi-omics era. Front. Microbiol.11:590049. doi: 10.3389/fmicb.2020.590049

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 166

  LavilleT.HegnaT. A.ForelM.-B.DarrochS.CharbonnierS. (2023). New look at Concavicaris woodfordi (Euarthropoda: Pancrustacea?) using micro-computed tomography. Palaeontol. Electron.26:26.21.a21. doi: 10.26879/1218

  • CrossRef
  • Google Scholar

• 167

  LenggerS. K.MelendezI. M.SummonsR. E.GriceK. (2017). Mudstones and embedded concretions show differences in lithology-related, but not source-related biomarker distributions. Org. Geochem.113, 67–74. doi: 10.1016/j.orggeochem.2017.08.003

  • CrossRef
  • Google Scholar

• 168

  LewisW. H.TahonG.GeesinkP.SousaD. Z.EttemaT. J. G. (2021). Innovations to culturing the uncultured microbial majority. Nat. Rev. Microbiol.19, 225–240. doi: 10.1038/s41579-020-00458-8

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 169

  LheritierM.PerrouxM.VannierJ.EscarguelG.WesenerT.MoritzL.et al. (2023). Fossils from the Montceau-les-mines Lagerstätte (305 Ma) shed light on the anatomy, ecology and phylogeny of carboniferous millipedes. J. Syst. Palaeontol.21:2169891. doi: 10.1080/14772019.2023.2169891

  • CrossRef
  • Google Scholar

• 170

  LiX.ChoppD. L.RussinW. A.BrannonP. T.ParsekM. R.PackmanA. I. (2015). Spatial patterns of carbonate biomineralization in biofilms. Appl. Environ. Microb.81, 7403–7410. doi: 10.1128/AEM.01585-15

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 171

  LichtmanJ. W.ConchelloJ.-A. (2005). Fluorescence microscopy. Nat. Methods2, 910–919. doi: 10.1038/nmeth817

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 172

  LinL.ChengF.XuJ. (2023). Preservation of molecular fossils in carbonate concretions in cretaceous shales in the songliao basin, Northeast China. Front. Earth Sci.10:1074178. doi: 10.3389/feart.2022.1074178

  • CrossRef
  • Google Scholar

• 173

  LinC. Y.TurchynA. V.KrylovA.AntlerG. (2020). The microbially driven formation of siderite in salt marsh sediments. Geobiology18, 207–224. doi: 10.1111/gbi.12371

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 174

  LindgrenJ.NilssonD.-E.SjövallP.JarenmarkM.ItoS.WakamatsuK.et al. (2019). Fossil insect eyes shed light on trilobite optics and the arthropod pigment screen. Nature573, 122–125. doi: 10.1038/s41586-019-1473-z

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 175

  LindgrenJ.SjövallP.ThielV.ZhengW.ItoS.WakamatsuK.et al. (2018). Soft-tissue evidence for homeothermy and crypsis in a Jurassic ichthyosaur. Nature564, 359–365. doi: 10.1038/s41586-018-0775-x

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 176

  LittleC. T. S.GaleA.WilliamsM.HammerØ.FernandezV. (2023). Bivalve-barnacle pseudoplanktonic colonisation of wood from the Toarcian, lower Jurassic, strawberry Bank Lagerstätte, Somerset, UK. Acta Palaeontol. Pol.68, 133–142. doi: 10.4202/app.01018.2022

  • CrossRef
  • Google Scholar

• 177

  LiuD.FanQ.PapineauD.YuN.ChuY.WangH.et al. (2020). Precipitation of protodolomite facilitated by sulfate-reducing bacteria: the role of capsule extracellular polymeric substances. Chem. Geol.533:119415. doi: 10.1016/j.chemgeo.2019.119415

  • CrossRef
  • Google Scholar

• 178

  LiuR.HuangS.ZhangX.SongY.HeG.WangZ.et al. (2021). Bio-mineralisation, characterization, and stability of calcium carbonate containing organic matter. RCS Adv.11, 14415–14425. doi: 10.1039/D1RA00615K

  • CrossRef
  • Google Scholar

• 179

  LiuA.-Q.TangD.-J.ShiX.-Y.ZhouL.-M.ZhouX.-Q.ShangM.-H.et al. (2019). Growth mechanisms and environmental implications of carbonate concretions from the ~ 1.4 Ga Xiamaling formation, North China. J. Palaeogeogr.8:20. doi: 10.1186/s42501-019-0036-4

  • CrossRef
  • Google Scholar

• 180

  LiuA.TangD.ShiX.ZhouX.ZhouL.ShangM.et al. (2020). Mesoproterozoic oxygenated deep seawater recorded by early diagenetic carbonate concretions from the member IV of the Xiamaling formation, North China. Precambrian Res.341:105667. doi: 10.1016/j.precamres.2020.105667

  • CrossRef
  • Google Scholar

• 181

  LiuX.ZarfelG.van der WeijdenR.LoiskandlW.BitschnauB.DinklaI. J. T.et al. (2021). Density-dependent microbial calcium carbonate precipitation by drinking water bacteria via amino acid metabolism and biosorption. Water Res.202:117444. doi: 10.1016/j.watres.2021.117444

  • CrossRef
  • Google Scholar

• 182

  LongJ. A.TrinajsticK. (2010). The late Devonian Gogo formation Lägerstatte of Western Australia: exceptional early vertebrate preservation and diversity. Annu. Rev. Earth Pl. Sc.38, 255–279. doi: 10.1146/annurev-earth-040809-152416

  • CrossRef
  • Google Scholar

• 183

  LongJ. A.TrinajsticK.JohansonZ. (2009). Devonian arthrodire embryos and the origin of internal fertilization in vertebrates. Nature457, 1124–1127. doi: 10.1038/nature07732

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 184

  LongJ. A.TrinajsticK.YoungG. C.SendenT. (2008). Live birth in the Devonian period. Nature453, 650–652. doi: 10.1038/nature06966

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 185

  LoydS. J. (2017). Preservation of overmature, ancient, sedimentary organic matter in carbonate concretions during outcrop weathering. Geobiology15, 146–157. doi: 10.1111/gbi.12194

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 186

  MabesooneJ. M.TinocoI. M. (1973). Palaeoecology of the Aptian Santana formation (northeastern Brazil). Palaeogeogr. Palaeocl.14, 97–118. doi: 10.1016/0031-0182(73)90006-0

  • CrossRef
  • Google Scholar

• 187

  MackenzieA. S.BrassellS. C.EglintonG.MaxwellJ. R. (1982). Chemical fossils: the geological fate of steroids. Science217, 491–504. doi: 10.1126/science.217.4559.491

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 188

  MaedaH.TanakaG.ShimobayashiN.OhnoT.MatsuokaH. (2011). Cambrian Orsten Lagerstätte from the alum shale formation: fecal pellets as a probable source of phosphorus preservation. PALAIOS26, 225–231. doi: 10.2110/palo.2010.p10-042r

  • CrossRef
  • Google Scholar

• 189

  MählerB.JanssenK.MennekenM.TahounM.LagosM.BierbaumG.et al. (2020). Calcite precipitation forms crystal clusters and muscle mineralization during the decomposition of Cambarellus diminutus (Decapoda: Cambaridae) in freshwater. Palaeontol. Electron.23:a55. doi: 10.26879/992

  • CrossRef
  • Google Scholar

• 190

  MaischH. M.BeckerM. A. (2022). Teredolites driftwood from the Arkadelphia formation–midway group contact (K–Pg), Malvern, Arkansas, USA. Ichnos29, 117–136. doi: 10.1080/10420940.2023.2182298

  • CrossRef
  • Google Scholar

• 191

  MaiseyJ. G. (1991). Santana fossils: An illustrated atlas. New Jersey: T.F.H. Publications.

  • Google Scholar

• 192

  MaldanisL.CarvalhoM.AlmeidaM. R.FreitasF. I.de AndradeJ. A. F. G.NunesR. S.et al. (2016). Heart fossilization is possible and informs the evolution of cardiac outflow tract in vertebrates. elife5:e14698. doi: 10.7554/eLife.14698

  • CrossRef
  • Google Scholar

• 193

  MarshallJ. D.PirrieD. (2013). Carbonate concretions—explained. Geol. Today29, 53–62. doi: 10.1111/gto.12002

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 194

  MartillD. M. (1988). Preservation of fish in the cretaceous Santana formation of Brazil. Palaeontology31, 1–18.

  • Google Scholar

• 195

  MartillD. M. (1989). The medusa effect: instantaneous fossilization. Geol. Today5, 201–205. doi: 10.1111/j.1365-2451.1989.tb00671.x

  • CrossRef
  • Google Scholar

• 196

  MartillD. M. (1990). Macromolecular resolution of fossilized muscle tissue from an elopomorph fish. Nature346, 171–172. doi: 10.1038/346171a0

  • CrossRef
  • Google Scholar

• 197

  MartillD. M. (1993). Fossils of the Santana and Crato formations, Brazil. London: The Palaeontological Association.

  • Google Scholar

• 198

  MartillD. M. (2007). The age of the cretaceous Santana formation fossil Konservat Lagerstätte of north-East Brazil: a historical review and an appraisal of the biochronostratigraphic utility of its palaeobiota. Cretac. Res.28, 895–920. doi: 10.1016/j.cretres.2007.01.002

  • CrossRef
  • Google Scholar

• 199

  MartillD. M.BritoP. M. (2017). “The Santana formation” in Terrestrial conservation Lagerstatten: Windows into the evolution of life on land. eds. FraserN. C.SuesH. D. (Dunedin: Dunedin Academic Press), 215–256.

  • Google Scholar

• 200

  MartinD.BriggsD. E. G.ParkesR. J. (2003). Experimental mineralization of invertebrate eggs and the preservation of Neoproterozoic embryos. Geology31, 39–42. doi: 10.1130/0091-7613(2003)031<0039:EMOIEA>2.0.CO;2

  • CrossRef
  • Google Scholar

• 201

  MartinD.BriggsD. E. G.ParkesR. J. (2005). Decay and mineralization of invertebrate eggs. PALAIOS20, 562–572. doi: 10.2110/palo.2004.p04-67

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 202

  MatthewsD. E.HayesJ. M. (1978). Isotope-ratio-monitoring gas chromatography-mass spectrometry. Anal. Chem.50, 1465–1473. doi: 10.1021/ac50033a022

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 203

  Matzke-KaraszR.NeilJ. V.SmithR. J.GodthelpH.ArcherM.HandS. J. (2013). Ostracods (Crustacea) with soft part preservation from Miocene cave deposits of the Riversleigh world heritage area, NW Queensland, Australia. J. Syst. Palaeontol.11, 789–819. doi: 10.1080/14772019.2012.760007

  • CrossRef
  • Google Scholar

• 204

  MaynardJ. B. (1982). Extension of Berner's "new geochemical classification of sedimentary environments" to ancient sediments. J. Sediment. Res.52, 1325–1331. doi: 10.1306/212F812F-2B24-11D7-8648000102C1865D

  • CrossRef
  • Google Scholar

• 205

  MaysC.BevittJ. J.StilwellJ. D. (2017). Pushing the limits of neutron tomography in palaeontology: three-dimensional modeling of in situ resin within fossil plants. Palaeontol. Electron.20:20.23.57A. doi: 10.26879/808

  • CrossRef
  • Google Scholar

• 206

  McCoyV. E. (2014). Concretions as agents of soft-tissue preservation: a review. Paleontol. Soc. Papers20, 147–162. doi: 10.1017/S1089332600002849

  • CrossRef
  • Google Scholar

• 207

  McCoyV. E.SaupeE. E.LamsdellJ. C.TarhanL. G.McMahonS.LidgardS.et al. (2016). The ‘Tully monster’ is a vertebrate. Nature532, 496–499. doi: 10.1038/nature16992

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 208

  McCoyV. E.WiemannJ.LamsdellJ. C.WhalenC. D.LidgardS.MayerP.et al. (2020). Chemical signatures of soft tissues distinguish between vertebrates and invertebrates from the carboniferous Mazon Creek Lagerstätte of Illinois. Geobiology18, 560–565. doi: 10.1111/gbi.12397

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 209

  McCoyV. E.YoungR. T.BriggsD. E. G. (2015a). Factors controlling exceptional preservation in concretions. PALAIOS30, 272–280. doi: 10.2110/palo.2014.081

  • CrossRef
  • Google Scholar

• 210

  McCoyV. E.YoungR. T.BriggsD. E. G. (2015b). Sediment permeability and the preservation of soft-tissues in concretions: an experimental study. PALAIOS30, 608–612. doi: 10.2110/palo.2015.002

  • CrossRef
  • Google Scholar

• 211

  McElhinneyJ. M. W. R.CatacutanM. K.MawartA.HasanA.DiasJ. (2022). Interfacing machine learning and microbial omics: a promising means to address environmental challenges. Front. Microbiol.13:851450. doi: 10.3389/fmicb.2022.851450

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 212

  McMullanD. (1995). Scanning electron microscopy 1928–1965. Scanning17, 175–185. doi: 10.1002/sca.4950170309

  • CrossRef
  • Google Scholar

• 213

  McNamaraM. E.OrrP. J.KearnsS. L.AlcaláL.AnadónP.Peñalver MolláE. (2009). Soft-tissue preservation in Miocene frogs from Libros, Spain: insights into the genesis of decay microenvironments. PALAIOS24, 104–117. doi: 10.2110/palo.2008.p08-017r

  • CrossRef
  • Google Scholar

• 214

  MeiM.BissadaK. K.MalloyT. B.DarnellL. M.SzymcykE. B. (2018). Improved method for simultaneous determination of saturated and aromatic biomarkers, organosulfur compounds and diamondoids in crude oils by GC–MS/MS. Org. Geochem.116, 35–50. doi: 10.1016/j.orggeochem.2017.09.010

  • CrossRef
  • Google Scholar

• 215

  MelendezI.GriceK.SchwarkL. (2013a). Exceptional preservation of Palaeozoic steroids in a diagenetic continuum. Sci. Rep.3:2768. doi: 10.1038/srep02768

  • CrossRef
  • Google Scholar

• 216

  MelendezI.GriceK.TrinajsticK.LadjavardiM.GreenwoodP.ThompsonK. (2013b). Biomarkers reveal the role of photic zone euxinia in exceptional fossil preservation: an organic geochemical perspective. Geology41, 123–126. doi: 10.1130/g33492.1

  • CrossRef
  • Google Scholar

• 217

  MeredithW.SnapeC. E.LoveG. D. (2015). “Development and use of catalytic hydropyrolysis (HyPy) as an analytical tool for organic geochemical applications” in Principles and practice of analytical techniques in geosciences. ed. GriceK. (Oxford: Royal Society of Chemistry), 171–208.

  • Google Scholar

• 218

  MojarroA.CuiX.ZhangX.JostA. B.BergmannK. D.VintherJ.et al. (2022). Comparative soft-tissue preservation in Holocene-age capelin concretions. Geobiology20, 377–398. doi: 10.1111/gbi.12480

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 219

  MozleyP. S.BurnsS. J. (1993). Oxygen and carbon isotopic composition of marine carbonate concretions; an overview. J. Sediment. Res.63, 73–83. doi: 10.1306/d4267a91-2b26-11d7-8648000102c1865d

  • CrossRef
  • Google Scholar

• 220

  MuramiyaY.YoshidaH.MinamiM.MikamiT.KobayashiT.SekiuchiK.et al. (2022). Glendonite concretion formation due to dead organism decomposition. Sediment. Geol.429:106075. doi: 10.1016/j.sedgeo.2021.106075

  • CrossRef
  • Google Scholar

• 221

  MuruganR.SundararaghavanA.DhamiN. K.MukherjeeA.SuraishkumarG. K. (2022). Importance of carbon to nitrogen ratio in microbial cement production: insights through experiments and genome-scale metabolic modelling. Biochem. Eng. J.186:108573. doi: 10.1016/j.bej.2022.108573

  • CrossRef
  • Google Scholar

• 222

  MuruganR.SuraishkumarG. K.MukherjeeA.DhamiN. K. (2021). Insights into the influence of cell concentration in design and development of microbially induced calcium carbonate precipitation (MICP) process. PLoS One16:e0254536. doi: 10.1371/journal.pone.0254536

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 223

  NaeherS.CuiX.SummonsR. E. (2022). Biomarkers: molecular tools to study life, environment, and climate. Elements18, 79–85. doi: 10.2138/gselements.18.2.79

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 224

  NaimarkE. B.BoevaN. M.KalininaM. A.ZaytsevaL. V. (2018). Complementary transformations of buried organic residues and the ambient sediment: results of long-term taphonomic experiments. Paleontol. J.52, 109–122. doi: 10.1134/S0031030118020053

  • CrossRef
  • Google Scholar

• 225

  NaimarkE.KalininaM.ShokurovA.BoevaN.MarkovA.ZaytsevaL. (2016). Decaying in different clays: implications for soft-tissue preservation. Palaeontology59, 583–595. doi: 10.1111/pala.12246

  • CrossRef
  • Google Scholar

• 226

  NicholsP. D.Mancuso NicholsC. A. (2008). Microbial signature lipid profiling and exopolysaccharides: experiences initiated with Professor David C White and transported to Tasmania, Australia. J. Microbiol. Meth.74, 33–46. doi: 10.1016/j.mimet.2007.06.017

  • CrossRef
  • Google Scholar

• 227

  NipM.TegelaarE. W.BrinkhuisH.De LeeuwJ. W.SchenckP. A.HollowayP. J. (1986). Analysis of modern and fossil plant cuticles by curie point Py-GC and curie point Py-GC-MS: recognition of a new, highly aliphatic and resistant biopolymer. Org. Geochem.10, 769–778. doi: 10.1016/S0146-6380(86)80014-6

  • CrossRef
  • Google Scholar

• 228

  NolanM. R.WalkerS. E.SellyT.SchiffbauerJ. (2023). Is the middle Cambrian Brooksella a hexactinellid sponge, trace fossil or pseudofossil?PeerJ11:e14796. doi: 10.7717/peerj.14796

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 229

  NorellM. A.WiemannJ.FabbriM.YuC.MarsicanoC. A.Moore-NallA.et al. (2020). The first dinosaur egg was soft. Nature583, 406–410. doi: 10.1038/s41586-020-2412-8

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 230

  O'BrienN. R.MeyerH. W.ReillyK.RossA. M.MaguireS. (2002). Microbial taphonomic processes in the fossilization of insects and plants in the late Eocene Florissant formation, Colorado. Rocky Mt. Geol.37, 1–11. doi: 10.2113/gsrocky.37.1.1

  • CrossRef
  • Google Scholar

• 231

  OgiharaS. (1999). Geochemical characteristics of phosphorite and carbonate nodules from the Miocene Funakawa formation, western margin of the Yokote Basin, Northeast Japan. Sediment. Geol.125, 69–82. doi: 10.1016/S0037-0738(98)00136-5

  • CrossRef
  • Google Scholar

• 232

  OnstottT. C.EhlmannB. L.SapersH.ColemanM.IvarssonM.MarlowJ. J.et al. (2019). Paleo-rock-hosted life on earth and the search on Mars: a review and strategy for exploration. Astrobiology19, 1230–1262. doi: 10.1089/ast.2018.1960

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 233

  OnumaK.OyaneA.KokuboT.TrebouxG.KanzakiN.ItoA. (2000). Nucleation of calcium phosphate on 11-mercaptoundecanoic acid self-assembled monolayer in a pseudophysiological solution. J. Phys. Chem. B104, 11950–11956. doi: 10.1021/jp002015p

  • CrossRef
  • Google Scholar

• 234

  ParryL. A.SmithwickF.NordénK. K.SaittaE. T.Lozano-FernandezJ.TannerA. R.et al. (2018). Soft-bodied fossils are not simply rotten carcasses – toward a holistic understanding of exceptional fossil preservation. BioEssays40:1700167. doi: 10.1002/bies.201700167

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 235

  PearsonM. J.NelsonC. S. (2005). Organic geochemistry and stable isotope composition of New Zealand carbonate concretions and calcite fracture fills. New Zeal. J. Geol. Geop.48, 395–414. doi: 10.1080/00288306.2005.9515122

  • CrossRef
  • Google Scholar

• 236

  PelletierM. J. (1999). Analytical applications of Raman spectroscopy. Oxford: Wiley-Blackwell.

  • Google Scholar

• 237

  PercivalS. L.MalicS.CruzH.WilliamsD. W. (2011). “Introduction to biofilms” in Biofilms and veterinary medicine. eds. PercivalS.KnottenbeltD.CochraneC. (Berlin, Heidelberg: Springer Berlin Heidelberg), 41–68.

  • Google Scholar

• 238

  PetersK. E.MoldowanJ. M. (1992). The biomarker guide. New Jersey: Prentice-Hall.

  • Google Scholar

• 239

  PetersonJ. E.LenczewskiM. E.SchererR. P. (2010). Influence of microbial biofilms on the preservation of primary soft tissue in fossil and extant archosaurs. PLoS One5:e13334. doi: 10.1371/journal.pone.0013334

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 240

  PetrovichR. (2001). Mechanisms of fossilization of the soft-bodied and lightly armored faunas of the burgess shale and of some other classical localities. Am. J. Sci.301, 683–726. doi: 10.2475/ajs.301.8.683

  • CrossRef
  • Google Scholar

• 241

  PletC.GriceK.PagèsA.RuebsamW.CoolenM. J. L.SchwarkL. (2016). Microbially-mediated fossil-bearing carbonate concretions and their significance for palaeoenvironmental reconstructions: a multi-proxy organic and inorganic geochemical appraisal. Chem. Geol.426, 95–108. doi: 10.1016/j.chemgeo.2016.01.026

  • CrossRef
  • Google Scholar

• 242

  PletC.GriceK.PagèsA.VerrallM.CoolenM. J. L.RuebsamW.et al. (2017). Palaeobiology of red and white blood cell-like structures, collagen and cholesterol in an ichthyosaur bone. Sci. Rep.7:13776. doi: 10.1038/s41598-017-13873-4

  • CrossRef
  • Google Scholar

• 243

  PlotnickR. E.YoungG. A.HagadornJ. W. (2023). An abundant sea anemone from the carboniferous Mazon Creek Lagerstӓtte, USA. Pap. Palaeontol.9:e1479. doi: 10.1002/spp2.1479

  • CrossRef
  • Google Scholar

• 244

  PugliesiR.PereiraM. A. S.AndradeM. L. G.BassoJ. M. L.VoltaniC. G.GonzalesI. C. (2019). Study of the fish fossil Notelops brama from Araripe-Basin Brazil by neutron tomography. Nucl. Instrum. Meth. A919, 68–72. doi: 10.1016/j.nima.2018.12.001

  • CrossRef
  • Google Scholar

• 245

  PurnellM. A.DonoghueP. J. C.GabbottS. E.McNamaraM. E.MurdockD. J. E.SansomR. S. (2018). Experimental analysis of soft-tissue fossilization: opening the black box. Palaeontology61, 317–323. doi: 10.1111/pala.12360

  • CrossRef
  • Google Scholar

• 246

  PyeK. (1984). SEM analysis of siderite cements in intertidal marsh sediments, Norfolk, England. Mar. Geol.56, 1–12. doi: 10.1016/0025-3227(84)90002-1

  • CrossRef
  • Google Scholar

• 247

  PyeK.DicksonJ. A. D.SchiavonN.ColemanM. L.CoxM. (1990). Formation of siderite-mg-calcite-iron sulphide concretions in intertidal marsh and sandflat sediments, North Norfolk, England. Sedimentology37, 325–343. doi: 10.1111/j.1365-3091.1990.tb00962.x

  • CrossRef
  • Google Scholar

• 248

  QvarnströmM.AhlbergP. E.NiedźwiedzkiG. (2019a). Tyrannosaurid-like osteophagy by a Triassic archosaur. Sci. Rep.9:925. doi: 10.1038/s41598-018-37540-4

  • CrossRef
  • Google Scholar

• 249

  QvarnströmM.WernströmJ. V.PiechowskiR.TałandaM.AhlbergP. E.NiedźwiedzkiG. (2019b). Beetle-bearing coprolites possibly reveal the diet of a late Triassic dinosauriform. Roy. Soc. Open Sci.6:181042. doi: 10.1098/rsos.181042

  • CrossRef
  • Google Scholar

• 250

  RaffR. A.AndrewsM. E.PearsonR. L.TurnerF. R.SaurS. T.ThomasD. C.et al. (2014). Microbial ecology and biofilms in the taphonomy of soft tissues. PALAIOS29, 560–569. doi: 10.2110/palo.2014.043

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 251

  RaffE. C.AndrewsM. E.TurnerF. R.TohE.NelsonD. E.RaffR. A. (2013). Contingent interactions among biofilm-forming bacteria determine preservation or decay in the first steps toward fossilization of marine embryos. Evol. Dev.15, 243–256. doi: 10.1111/ede.12028

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 252

  RaffR. A.RaffE. C. (2014). The role of biology in the fossilization of embryos and other soft-bodied organisms: microbial biofilms and Lagerstätten. Paleontol. Soc. Papers20, 83–100. doi: 10.1017/S1089332600002813

  • CrossRef
  • Google Scholar

• 253

  RaffE. C.SchollaertK. L.NelsonD. E.DonoghueP. C. J.ThomasC.-W.TurnerF. R.et al. (2008). Embryo fossilization is a biological process mediated by microbial biofilms. P. Natl. Acad. Sci. USA105, 19360–19365. doi: 10.1073/pnas.0810106105

  • CrossRef
  • Google Scholar

• 254

  RahmanF. U.AndreeK. B.Salas-MassóN.Fernandez-TejedorM.SanjuanA.FiguerasM. J.et al. (2020). Improved culture enrichment broth for isolation of Arcobacter-like species from the marine environment. Sci. Rep.10:14547. doi: 10.1038/s41598-020-71442-8

  • CrossRef
  • Google Scholar

• 255

  RaiswellR. (1971). The growth of Cambrian and Liassic concretions. Sedimentology17, 147–171. doi: 10.1111/j.1365-3091.1971.tb01773.x

  • CrossRef
  • Google Scholar

• 256

  RaiswellR. (1976). The microbiological formation of carbonate concretions in the upper Lias of NE England. Chem. Geol.18, 227–244. doi: 10.1016/0009-2541(76)90006-1

  • CrossRef
  • Google Scholar

• 257

  RaiswellR.FisherQ. J. (2000). Mudrock-hosted carbonate concretions: a review of growth mechanisms and their influence on chemical and isotopic composition. J. Geol. Soc.157, 239–251. doi: 10.1144/jgs.157.1.239

  • CrossRef
  • Google Scholar

• 258

  RamachandranA. L.PolatP.MukherjeeA.DhamiN. K. (2020). Understanding and creating biocementing beachrocks via biostimulation of indigenous microbial communities. Appl. Microbiol. Biot.104, 3655–3673. doi: 10.1007/s00253-020-10474-6

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 259

  ReichhardtC.ParsekM. R. (2019). Confocal laser scanning microscopy for analysis of Pseudomonas aeruginosa biofilm architecture and matrix localization. Front. Microbiol.10:677. doi: 10.3389/fmicb.2019.00677

  • CrossRef
  • Google Scholar

• 260

  ReimersC. E.KastnerM.GarissonR. E. (1990). “The role of bacterial mats in phosphate mineralization with particular reference to the Monterey formation” in Phosphate deposits of the world Vol. 3: Neogene to modern Phosphorites. eds. BurnettW. C.RiggsS. R. (Cambridge: Cambridge University Press)

  • Google Scholar

• 261

  ReinhardtM.GoetzW.DudaJ. P.HeimC.ReitnerJ.ThielV. (2019). Organic signatures in Pleistocene cherts from Lake Magadi (Kenya) – implications for early earth hydrothermal deposits. Biogeosciences16, 2443–2465. doi: 10.5194/bg-16-2443-2019

  • CrossRef
  • Google Scholar

• 262

  ReitnerJ. (2004). “Organomineralization” in Origins: Genesis, evolution and diversity of life. ed. SeckbachJ. (Dordrecht: Springer Netherlands), 195–212.

  • Google Scholar

• 263

  RelucentiM.FamiliariG.DonfrancescoO.TaurinoM.LiX.ChenR.et al. (2021). Microscopy methods for biofilm imaging: focus on SEM and VP-SEM pros and cons. Biology10:51. doi: 10.3390/biology10010051

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 264

  RileyP. A. (1997). Molecules in focus: melanin. Int. J. Biochem. Cell. B.29, 1235–1239. doi: 10.1016/S1357-2725(97)00013-7

  • CrossRef
  • Google Scholar

• 265

  RobertsA. J.EngelschiønV. S.HurumJ. H. (2022). First three-dimensional skull of the middle Triassic mixosaurid ichthyosaur Phalarodon fraasi from Svalbard, Norway. Acta Palaeontol. Pol.67, 51–62. doi: 10.4202/app.00915.2021

  • CrossRef
  • Google Scholar

• 266

  RodriguesC. J. C.de CarvalhoC. C. C. R. (2022). Cultivating marine bacteria under laboratory conditions: overcoming the “unculturable” dogma. Front. Bioeng. Biotechnol.10:964589. doi: 10.3389/fbioe.2022.964589

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 267

  Rodriguez-NavarroC.JroundiF.SchiroM.Ruiz-AgudoE.González-MuñozM. T. (2012). Influence of substrate mineralogy on bacterial mineralization of calcium carbonate: implications for stone conservation. Appl. Environ. Microbiol.78, 4017–4029. doi: 10.1128/AEM.07044-11

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 268

  RogovM.ErshovaV.GainaC.VereshchaginO.VasilevaK.MikhailovaK.et al. (2023). Glendonites throughout the Phanerozoic. Earth-Sci. Rev241:104430. doi: 10.1016/j.earscirev.2023.104430

  • CrossRef
  • Google Scholar

• 269

  RothwellR. G.HoogakkerB.ThomsonJ.CroudaceI. W.FrenzM. (2006). “Turbidite emplacement on the southern Balearic abyssal plain (western Mediterranean Sea) during marine isotope stages 1–3: an application of ITRAX XRF scanning of sediment cores to lithostratigraphic analysis” in New techniques in sediment Core analysis. ed. RothwellR. G. (London: Geological Society of London), 79–98.

  • Google Scholar

• 270

  RoweA. J.KrutaI.LandmanN. H.VillierL.FernandezV.RougetI. (2022). Exceptional soft-tissue preservation of Jurassic Vampyronassa rhodanica provides new insights on the evolution and palaeoecology of vampyroteuthids. Sci. Rep.12:8292. doi: 10.1038/s41598-022-12269-3

  • CrossRef
  • Google Scholar

• 271

  SagemannJ.BaleS. J.BriggsD. E. G.ParkesR. J. (1999). Controls on the formation of authigenic minerals in association with decaying organic matter: an experimental approach. Geochim. Cosmochim. Ac.63, 1083–1095. doi: 10.1016/S0016-7037(99)00087-3

  • CrossRef
  • Google Scholar

• 272

  SalehF.VaucherR.AntcliffeJ. B.DaleyA. C.El HaririK.KouraissK.et al. (2021). Insights into soft-part preservation from the early Ordovician Fezouata biota. Earth-Sci. Rev.213:103464. doi: 10.1016/j.earscirev.2020.103464

  • CrossRef
  • Google Scholar

• 273

  SanchezS.AhlbergP. E.TrinajsticK. M.MironeA.TafforeauP. (2012). Three-dimensional synchrotron virtual paleohistology: a new insight into the world of fossil bone microstructures. Microsc. Microanal.18, 1095–1105. doi: 10.1017/S1431927612001079

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 274

  SanderP. M. (2021). "Ichthyosauria," in Vertebrate skeletal histology and Paleohistology, eds. BuffrénilV.deRicqlèsA. J.deZylberbergL.PadianK. (Boca Raton: CRC Press), 458–466.

  • Google Scholar

• 275

  SanderP. M.WintrichT. (2021). "Sauropterygia: histology of plesiosauria," in Vertebrate skeletal histology and Paleohistology, eds. BuffrénilV.deRicqlèsA. J.deZylberbergL.PadianK. (Boca Raton: CRC Press), 444–457.

  • Google Scholar

• 276

  SandersonM. J.SmithI.ParkerI.BootmanM. D. (2014). Fluorescence microscopy. Cold Spring Harbor Protoc:pdb.top071795. doi: 10.1101/pdb.top071795

  • CrossRef
  • Google Scholar

• 277

  ScarlettA. G.Despaigne-DiazA. I.WildeS. A.GriceK. (2019). An examination by GC×GC-TOFMS of organic molecules present in highly degraded oils emerging from Caribbean terrestrial seeps of cretaceous age. Geosci. Front.10, 5–15. doi: 10.1016/j.gsf.2018.03.011

  • CrossRef
  • Google Scholar

• 278

  SchaefferP.AdamP.WehrungP.AlbrechtP. (1997). Novel aromatic carotenoid derivatives from sulfur photosynthetic bacteria in sediments. Tetrahedron Lett.38, 8413–8416. doi: 10.1016/S0040-4039(97)10235-0

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 279

  SchellerE. L.SwindleC.GrotzingerJ.BarnhartH.BhattacharjeeS.EhlmannB. L.et al. (2021). Formation of magnesium carbonates on earth and implications for Mars. J. Geophys. Res.-Planet.126:e2021JE006828. doi: 10.1029/2021je006828

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 280

  SchopfJ. W.KudryavtsevA. B. (2009). Confocal laser scanning microscopy and Raman imagery of ancient microscopic fossils. Precambrian Res.173, 39–49. doi: 10.1016/j.precamres.2009.02.007

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 281

  SchopfJ. W.KudryavtsevA. B.SergeevV. N. (2010). Confocal laser scanning microscopy and Raman imagery of the late Neoproterozoic Chichkan microbiota of South Kazakhstan. J. Paleontol.84, 402–416. doi: 10.1666/09-134.1

  • CrossRef
  • Google Scholar

• 282

  SchoutenS.Klein BretelerW. C. M.BlokkerP.SchogtN.RijpstraW. I. C.GriceK.et al. (1998). Biosynthetic effects on the stable carbon isotopic compositions of algal lipids: implications for deciphering the carbon isotopic biomarker record. Geochim. Cosmochim. Ac.62, 1397–1406. doi: 10.1016/S0016-7037(98)00076-3

  • CrossRef
  • Google Scholar

• 283

  SchoutenS.van DrielG. B.Sinninghe DamstéJ. S.de LeeuwJ. W. (1993). Natural sulphurization of ketones and aldehydes: a key reaction in the formation of organic Sulphur compounds. Geochim. Cosmochim. Ac.57, 5111–5116. doi: 10.1016/0016-7037(93)90613-2

  • CrossRef
  • Google Scholar

• 284

  SchuffertJ. D.JahnkeR. A.KastnerM.LeatherJ.SturzA.WingM. R. (1994). Rates of formation of modern phosphorite off western Mexico. Geochim. Cosmochim. Ac.58, 5001–5010. doi: 10.1016/0016-7037(94)90227-5

  • CrossRef
  • Google Scholar

• 285

  SchultzeH.-P. (1989). Three-dimensional muscle preservation in Jurassic fishes of Chile. Rev. Geol. Chile16, 183–215.

  • Google Scholar

• 286

  SchulzH. N.SchulzH. D. (2005). Large sulfur bacteria and the formation of phosphorite. Science307, 416–418. doi: 10.1126/science.1103096

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 287

  SchwarkL. (2013). Exceptional preservation of microbial lipids in Paleozoic to Mesoproterozoic sediments. Geology41, 287–288. doi: 10.1130/focus022013.1

  • CrossRef
  • Google Scholar

• 288

  SchwarkL.PüttmannW. (1990). Aromatic hydrocarbon composition of the Permian Kupferschiefer in the lower Rhine Basin, NW Germany. Org. Geochem.16, 749–761. doi: 10.1016/0146-6380(90)90114-f

  • CrossRef
  • Google Scholar

• 289

  SchweitzerM. H.ZhengW.MoyerA. E.SjövallP.LindgrenJ. (2018). Preservation potential of keratin in deep time. PLoS One13:e0206569. doi: 10.1371/journal.pone.0206569

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 290

  SenterP. J. (2022). Cells and soft tissues in fossil bone: a review of preservation mechanisms, with corrections of misconceptions. Palaeontol. Electron.25:a34. doi: 10.26879/1248

  • CrossRef
  • Google Scholar

• 291

  SessionsA. L. (2006). Isotope-ratio detection for gas chromatography. J. Sep. Sci.29, 1946–1961. doi: 10.1002/jssc.200600002

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 292

  SessionsA. L. (2016). Factors controlling the deuterium contents of sedimentary hydrocarbons. Org. Geochem.96, 43–64. doi: 10.1016/j.orggeochem.2016.02.012

  • CrossRef
  • Google Scholar

• 293

  ShafferJ. P.NothiasL.-F.ThompsonL. R.SandersJ. G.SalidoR. A.CouvillionS. P.et al. (2022). Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity. Nat. Microbiol.7, 2128–2150. doi: 10.1038/s41564-022-01266-x

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 294

  SiljeströmS.HodeT.LausmaaJ.SjövallP.ToporskiJ.ThielV. (2009). Detection of organic biomarkers in crude oils using ToF-SIMS. Org. Geochem.40, 135–143. doi: 10.1016/j.orggeochem.2008.08.010

  • CrossRef
  • Google Scholar

• 295

  SiljeströmS.LausmaaJ.SjövallP.BromanC.ThielV.HodeT. (2010). Analysis of hopanes and steranes in single oil-bearing fluid inclusions using time-of-flight secondary ion mass spectrometry (ToF-SIMS). Geobiology8, 37–44. doi: 10.1111/j.1472-4669.2009.00223.x

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 296

  SiljeströmS.NeubeckA.SteeleA. (2022). Detection of porphyrins in vertebrate fossils from the Messel and implications for organic preservation in the fossil record. PLoS One17:e0269568. doi: 10.1371/journal.pone.0269568

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 297

  SiljeströmS.ParenteauM. N.JahnkeL. L.CadyS. L. (2017). A comparative ToF-SIMS and GC–MS analysis of phototrophic communities collected from an alkaline silica-depositing hot spring. Org. Geochem.109, 14–30. doi: 10.1016/j.orggeochem.2017.03.009

  • CrossRef
  • Google Scholar

• 298

  SiljeströmS.VolkH.GeorgeS. C.LausmaaJ.SjövallP.DutkiewiczA.et al. (2013). Analysis of single oil-bearing fluid inclusions in mid-Proterozoic sandstones (roper group, Australia). Geochim. Cosmochim. Ac.122, 448–463. doi: 10.1016/j.gca.2013.08.010

  • CrossRef
  • Google Scholar

• 299

  Sinninghe DamstéJ. S.de LeeuwJ. W. (1990). Analysis, structure and geochemical significance of organically-bound Sulphur in the geosphere: state of the art and future research. Org. Geochem.16, 1077–1101. doi: 10.1016/0146-6380(90)90145-P

  • CrossRef
  • Google Scholar

• 300

  SiveterD. J.BriggsD. E. G.SiveterD. J.SuttonM. D. (2020). The Herefordshire Lagerstätte: fleshing out Silurian marine life. J. Geol. Soc.177, 1–13. doi: 10.1144/jgs2019-110

  • CrossRef
  • Google Scholar

• 301

  SkoogD. A.HollerF. J.CrouchS. R. (2018). Principles of instrumental analysis7th Edn. Boston: Cengage Learning.

  • Google Scholar

• 302

  SmithR. J. (2000). Morphology and ontogeny of Cretaceous ostracods with preserved appendages from Brazil. Palaeontology43, 63–98. doi: 10.1111/1475-4983.00119

  • CrossRef
  • Google Scholar

• 303

  SondheimerE.DenceW. A.MattickL. R.SilvermanS. R. (1966). Composition of combustible concretions of the alewife, Alosa pseudoharengus. Science152, 221–223. doi: 10.1126/science.152.3719.221

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 304

  SpicerR. (1991). “Plant taphonomic processes” in Taphonomy: Releasing the data locked in the fossil record. eds. AllisonP. A.BriggsD. E. G. (New York: Plenum Press), 71–113.

  • Google Scholar

• 305

  SteeleA.FriesM. D.PasterisJ. D. (2020). Geoscience meets biology: Raman spectroscopy in geobiology and biomineralization. Elements16, 111–116. doi: 10.2138/gselements.16.2.111

  • CrossRef
  • Google Scholar

• 306

  SteeleA.ToporskiJ. K. W.AvciR.GuidryS.McKayD. S. (2001). Time of flight secondary ion mass spectrometry (ToFSIMS) of a number of hopanoids. Org. Geochem.32, 905–911. doi: 10.1016/S0146-6380(01)00048-1

  • CrossRef
  • Google Scholar

• 307

  StewartP. S.FranklinM. J. (2008). Physiological heterogeneity in biofilms. Nat. Rev. Microbiol.6, 199–210. doi: 10.1038/nrmicro1838

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 308

  StolarskiJ.GorzelakP.MazurM.MarrocchiY.MeibomA. (2009). Nanostructural and geochemical features of the Jurassic isocrinid columnal ossicles. Acta Palaeontol. Pol.54, 69–75. doi: 10.4202/app.2009.0108

  • CrossRef
  • Google Scholar

• 309

  SummonsR. E.PowellT. G. (1987). Identification of aryl isoprenoids in source rocks and crude oils: biological markers for the green Sulphur bacteria. Geochim. Cosmochim. Acta51, 557–566. doi: 10.1016/0016-7037(87)90069-X

  • CrossRef
  • Google Scholar

• 310

  SunW.YinZ.CunninghamJ. A.LiuP.ZhuM.DonoghueP. C. J. (2020). Nucleus preservation in early Ediacaran Weng'an embryo-like fossils, experimental taphonomy of nuclei and implications for reading the eukaryote fossil record. Interface Focus10:20200015. doi: 10.1098/rsfs.2020.0015

  • CrossRef
  • Google Scholar

• 311

  SuttonM. D.RahmanI. A.GarwoodR. J. (2014). Techniques for virtual Palaeontology. Chichester, UK: John Wiley & Sons.

  • Google Scholar

• 312

  TafforeauP.BoistelR.BollerE.BravinA.BrunetM.ChaimaneeY.et al. (2006). Applications of X-ray synchrotron microtomography for non-destructive 3D studies of paleontological specimens. Appl. Phys. A Mater. Sci. Process.83, 195–202. doi: 10.1007/s00339-006-3507-2

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 313

  ThielV.BlumenbergM.KielS.LeefmannT.LiebenauK.LindgrenJ.et al. (2014). Occurrence and fate of fatty acyl biomarkers in an ancient whale bone (Oligocene, El Cien formation, Mexico). Org. Geochem.68, 71–81. doi: 10.1016/j.orggeochem.2013.12.006

  • CrossRef
  • Google Scholar

• 314

  ThielV.SjövallP. (2011). Using time-of-flight secondary ion mass spectrometry to study biomarkers. Annu. Rev. Earth Pl. Sc.39, 125–156. doi: 10.1146/annurev-earth-040610-133525

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 315

  ThompsonJ. B.Schultze-LamS.BeveridgeT. J.Des MaraisD. J. (1997). Whiting events: biogenic origin due to the photosynthetic activity of cyanobacterial picoplankton. Limnol. Oceanogr.42, 133–141. doi: 10.4319/lo.1997.42.1.0133

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 316

  ThomsonJ.CroudaceI. W.RothwellR. G. (2006). “A geochemical application of the ITRAX scanner to a sediment core containing eastern Mediterranean sapropel units” in New techniques in sediment Core analysis. ed. RothwellR. G. (London: Geological Society of London), 65–78.

  • Google Scholar

• 317

  TissotB. P.WelteD. H. (1984). Petroleum formation and Occurence. Berlin: Springer-Verlag.

  • Google Scholar

• 318

  ToporskiJ. K. W.SteeleA.WestallF.AvciR.MartillD. M.McKayD. S. (2002). Morphologic and spectral investigation of exceptionally well-preserved bacterial biofilms from the Oligocene Enspel formation, Germany. Geochim. Cosmochim. Acta66, 1773–1791. doi: 10.1016/S0016-7037(01)00870-5

  • CrossRef
  • Google Scholar

• 319

  TouboulD.KollmerF.NiehuisE.BrunelleA.LaprévoteO. (2005). Improvement of biological time-of-flight-secondary ion mass spectrometry imaging with a bismuth cluster ion source. J. Am. Soc. Mass Spectr.16, 1608–1618. doi: 10.1016/j.jasms.2005.06.005

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 320

  TrinajsticK.BriggsD. E. G.LongJ. A. (2022a). The Gogo formation Lagerstätte: a view of Australia's first great barrier reef. J. Geol. Soc.179:jgs2021-2105. doi: 10.1144/jgs2021-105

  • CrossRef
  • Google Scholar

• 321

  TrinajsticK.LongJ. A.SanchezS.BoisvertC. A.SnittingD.TafforeauP.et al. (2022b). Exceptional preservation of organs in Devonian placoderms from the Gogo lagerstätte. Science377, 1311–1314. doi: 10.1126/science.abf3289

  • CrossRef
  • Google Scholar

• 322

  TrinajsticK.MarshallC.LongJ.BifieldK. (2007). Exceptional preservation of nerve and muscle tissues in late Devonian placoderm fish and their evolutionary implications. Biol. Lett.3, 197–200. doi: 10.1098/rsbl.2006.0604

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 323

  TrinajsticK.SanchezS.DupretV.TafforeauP.LongJ.YoungG.et al. (2013). Fossil musculature of the most primitive jawed vertebrates. Science341, 160–164. doi: 10.1126/science.1237275

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 324

  TrippM.WiemannJ.BrocksJ.MayerP.SchwarkL.GriceK. (2022). Fossil biomarkers and biosignatures preserved in coprolites reveal carnivorous diets in the carboniferous Mazon Creek ecosystem. Biology11:1289. doi: 10.3390/biology11091289

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 325

  TurnbullM. J. M.WhitehouseM. J.MoorbathS. (1996). New isotopic age determinations for the Torridonian, NW Scotland. J. Geol. Soc.153, 955–964. doi: 10.1144/gsjgs.153.6.0955

  • CrossRef
  • Google Scholar

• 326

  van RijnJ.TalY.SchreierH. J. (2006). Denitrification in recirculating systems: theory and applications. Aquac. Eng.34, 364–376. doi: 10.1016/j.aquaeng.2005.04.004

  • CrossRef
  • Google Scholar

• 327

  Van RoyP.BriggsD. E. G.GainesR. R. (2015). The Fezouata fossils of Morocco; an extraordinary record of marine life in the early Ordovician. J. Geol. Soc.172, 541–549. doi: 10.1144/jgs2015-017

  • CrossRef
  • Google Scholar

• 328

  VarejãoF. G.WarrenL. V.SimõesM. G.BuatoisL. A.MánganoM. G.Bahniuk RumbelspergerA. M.et al. (2021). Mixed siliciclastic–carbonate sedimentation in an evolving epicontinental sea: Aptian record of marginal marine settings in the interior basins of North-Eastern Brazil. Sedimentology68, 2125–2164. doi: 10.1111/sed.12846

  • CrossRef
  • Google Scholar

• 329

  VarejãoF. G.WarrenL. V.SimõesM. G.FürsichF. T.MatosS. A.AssineM. L. (2019). Exceptional preservation of soft tissues by microbial entombment: insights into the taphonomy of the Crato Konservat-Lagerstätte. PALAIOS34, 331–348. doi: 10.2110/palo.2019.041

  • CrossRef
  • Google Scholar

• 330

  Vernon-ParryK. D. (2000). Scanning electron microscopy: an introduction. III-Vs Rev.13, 40–44. doi: 10.1016/S0961-1290(00)80006-X

  • CrossRef
  • Google Scholar

• 331

  VincentP.AllemandR.TaylorP. D.SuanG.MaxwellE. E. (2017). New insights on the systematics, palaeoecology and palaeobiology of a plesiosaurian with soft tissue preservation from the Toarcian of Holzmaden. Germany. Sci. Nat.104:51. doi: 10.1007/s00114-017-1472-6

  • CrossRef
  • Google Scholar

• 332

  VorontsovD. D.KolesnikovV. B.VoronezhskayaE. E.PerkovskyE. E.BertoM. M.MoweryJ.et al. (2023). Beyond the limits of light: an application of super-resolution confocal microscopy (sCLSM) to investigate Eocene amber microfossils. Life13:865. doi: 10.3390/life13040865

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 333

  WaceyD.MenonS.GreenL.GerstmannD.KongC.McLoughlinN.et al. (2012). Taphonomy of very ancient microfossils from the ∼3400Ma Strelley Pool formation and ∼1900Ma gunflint formation: new insights using a focused ion beam. Precambrian Res.220-221, 234–250. doi: 10.1016/j.precamres.2012.08.005

  • CrossRef
  • Google Scholar

• 334

  WagnerM.IvlevaN. P.HaischC.NiessnerR.HornH. (2009). Combined use of confocal laser scanning microscopy (CLSM) and Raman microscopy (RM): investigations on EPS – matrix. Water Res.43, 63–76. doi: 10.1016/j.watres.2008.10.034

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 335

  WangX.ZhangS.WangH.CanfieldD. E.SuJ.HammarlundE. U.et al. (2017). Remarkable preservation of microfossils and biofilms in Mesoproterozoic silicified bitumen concretions from northern China. Geofluids2017:4818207. doi: 10.1155/2017/4818207

  • CrossRef
  • Google Scholar

• 336

  WarrenL. A.MauriceP. A.ParmarN.FerrisF. G. (2001). Microbially mediated calcium carbonate precipitation: implications for interpreting calcite precipitation and for solid-phase capture of inorganic contaminants. Geomicrobiol J.18, 93–115. doi: 10.1080/01490450151079833

  • CrossRef
  • Google Scholar

• 337

  WeeksL. G. (1953). Environment and mode of origin and facies relationships of carbonate concretions in shales. J. Sediment. Res.23, 162–173. doi: 10.1306/d42695f8-2b26-11d7-8648000102c1865d

  • CrossRef
  • Google Scholar

• 338

  WeeksL. G. (1957). Origin of carbonate concretions in shales, Magdalena Valley. Colombia. GSA Bull.68, 95–102. doi: 10.1130/0016-7606(1957)68[95:Ooccis]2.0.Co;2

  • CrossRef
  • Google Scholar

• 339

  WeinerS.DoveP. M. (2003). An overview of biomineralization processes and the problem of the vital effect. Rev. Mineral. Geochem.54, 1–29. doi: 10.2113/0540001

  • CrossRef
  • Google Scholar

• 340

  WhiteM. A.BellP. R.CampioneN. E.SansaloneG.BroughamT.BevittJ. J.et al. (2022). Abdominal contents reveal cretaceous crocodyliforms ate dinosaurs. Gondwana Res.106, 281–302. doi: 10.1016/j.gr.2022.01.016

  • CrossRef
  • Google Scholar

• 341

  WiemannJ.CrawfordJ. M.BriggsD. E. G. (2020). Phylogenetic and physiological signals in metazoan fossil biomolecules. Sci. Adv.6:eaba6883. doi: 10.1126/sciadv.aba6883

  • CrossRef
  • Google Scholar

• 342

  WiemannJ.FabbriM.YangT.-R.SteinK.SanderP. M.NorellM. A.et al. (2018a). Fossilization transforms vertebrate hard tissue proteins into N-heterocyclic polymers. Nat. Commun.9:4741. doi: 10.1038/s41467-018-07013-3

  • CrossRef
  • Google Scholar

• 343

  WiemannJ.YangT.-R.NorellM. A. (2018b). Dinosaur egg colour had a single evolutionary origin. Nature563, 555–558. doi: 10.1038/s41586-018-0646-5

  • CrossRef
  • Google Scholar

• 344

  WiemannJ.YangT.-R.NorellM. A. (2019). Reply to: egg pigmentation probably has an Archosaurian origin. Nature570, E46–E50. doi: 10.1038/s41586-019-1283-3

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 345

  WilbyP. R.BriggsD. E. G.BernierP.GaillardC. (1996). Role of microbial mats in the fossilization of soft tissues. Geology24, 787–790. doi: 10.1130/0091-7613(1996)024<0787:Rommit>2.3.Co;2

  • CrossRef
  • Google Scholar

• 346

  WilcoxD. A.EfflerS. W. (1981). Formation of alewife concretions in polluted Onondaga Lake. Environ. Pollut. B.2, 203–215. doi: 10.1016/0143-148X(81)90018-5

  • CrossRef
  • Google Scholar

• 347

  WilkinsonM.DampierM. D. (1990). The rate of growth of sandstone-hosted calcite concretions. Geochim. Cosmochim. Ac.54, 3391–3399. doi: 10.1016/0016-7037(90)90293-T

  • CrossRef
  • Google Scholar

• 348

  WilmethD. T.JohnsonH. A.StampsB. W.BerelsonW. M.StevensonB. S.NunnH. S.et al. (2018). Environmental and biological influences on carbonate precipitation within hot spring microbial mats in Little Hot Creek, CA. Front. Microbiol.9:1464. doi: 10.3389/fmicb.2018.01464

  • CrossRef
  • Google Scholar

• 349

  WilsonP.ParryL. A.VintherJ.EdgecombeG. D. (2016). Unveiling biases in soft-tissue phosphatization: extensive preservation of musculature in the cretaceous (Cenomanian) polychaete Rollinschaeta myoplena (Annelida: Amphinomidae). Palaeontology59, 463–479. doi: 10.1111/pala.12237

  • CrossRef
  • Google Scholar

• 350

  WoodlandB. G.StenstromR. C. (1979). “The occurrence and origin of siderite concretions in the Francis Creek shale (Pennsylvanian) of northeastern Illinois” in Mazon Creek fossils (M.H. Nitecki: Academic Press), 69–103.

  • Google Scholar

• 351

  YangT.-R.ChenY.-H.WiemannJ.SpieringB.SanderP. M. (2018). Fossil eggshell cuticle elucidates dinosaur nesting ecology. PeerJ6:e5144. doi: 10.7717/peerj.5144

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 352

  YangD. Y.WattK. (2005). Contamination controls when preparing archaeological remains for ancient DNA analysis. J. Archaeol. Sci.32, 331–336. doi: 10.1016/j.jas.2004.09.008

  • CrossRef
  • Google Scholar

• 353

  YoshidaH.UjiharaA.MinamiM.AsaharaY.KatsutaN.YamamotoK.et al. (2015). Early post-mortem formation of carbonate concretions around tusk-shells over week-month timescales. Sci. Rep.5:14123. doi: 10.1038/srep14123

  • CrossRef
  • Google Scholar

• 354

  YoshidaH.YamamotoK.MinamiM.KatsutaN.Sin-ichiS.MetcalfeR. (2018). Generalized conditions of spherical carbonate concretion formation around decaying organic matter in early diagenesis. Sci. Rep.8:6308. doi: 10.1038/s41598-018-24205-5

  • CrossRef
  • Google Scholar

• 355

  ZarraonaindiaI.SmithD. P.GilbertJ. A. (2013). Beyond the genome: community-level analysis of the microbial world. Biol. Philos.28, 261–282. doi: 10.1007/s10539-012-9357-8

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 356

  ZengZ.TiceM. M. (2014). Promotion and nucleation of carbonate precipitation during microbial iron reduction. Geobiology12, 362–371. doi: 10.1111/gbi.12090

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 357

  ZengZ.TiceM. M. (2018). Electron transfer strategies regulate carbonate mineral and micropore formation. Astrobiology18, 28–36. doi: 10.1089/ast.2016.1560

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 358

  ZhangX.BishopP. L.KupferleM. J. (1998). Measurement of polysaccharides and proteins in biofilm extracellular polymers. Water Sci. Technol.37, 345–348. doi: 10.2166/wst.1998.0661

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 359

  ZhangX.XiaP.WangP.YangJ.BairdD. J. (2018). Omics advances in ecotoxicology. Envir. Sci. Tech.52, 3842–3851. doi: 10.1021/acs.est.7b06494

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 360

  ZhuT.DittrichM. (2016). Carbonate precipitation through microbial activities in natural environment, and their potential in biotechnology: a review. Front. Bioeng. Biotechnol.4:4. doi: 10.3389/fbioe.2016.00004

  • Pubmed Abstract
  • CrossRef
  • Google Scholar

• 361

  ZossR.Medina FerrerF.FloodB. E.JonesD. S.LouwD. C.BaileyJ. (2019). Microbial communities associated with phosphogenic sediments and phosphoclast-associated DNA of the Benguela upwelling system. Geobiology17, 76–90. doi: 10.1111/gbi.12318

  • Pubmed Abstract
  • CrossRef
  • Google Scholar