Microbial Mechanisms of DOM Transformation and Community Dynamics in Soil and Sludge Systems

Dissolved organic matter (DOM) is central to carbon and nutrient cycling in both natural and engineered environments. In soils, DOM comprises a complex mixture of plant and microbial degradation products, making soil one of the planet’s largest carbon reservoirs (containing roughly twice the carbon of the atmosphere and three times that of vegetation). In engineered sludge systems (including drainage and wastewater treatment sludge), DOM originates largely from anthropogenic wastes. Globally, wastewater treatment plants process vast quantities of organic matter, generating substantial sludge byproducts. Microorganisms drive the transformation and remineralization of DOM in these settings, whether in heterogeneous soil matrices or in controlled sludge bioreactors. These microbial processes alter DOM chemistry and ultimately regulate the fate of organic carbon (e.g. stabilization in soil or mineralization to CO2/CH4), thereby influencing global carbon and nutrient fluxes. Conversely, the quantity and quality of DOM profoundly shape microbial community structure and function: different microbes exploit specific organic substrates, so DOM composition can select for metabolic guilds and influence community dynamics. This bidirectional interplay between DOM and microbial communities is fundamental to ecosystem processes in both soils and sludge, yet it remains only partially understood due to DOM’s chemical complexity and the vast microbial diversity involved in its turnover.

Recent advances in analytical chemistry and molecular biology offer new avenues to unravel these DOM-microbe interactions with a mechanistic view. High-resolution spectroscopic and mass spectrometry techniques (e.g., FT-ICR MS) enable detailed characterization of DOM molecules, while multi-omics approaches (metagenomics, metatranscriptomics, metabolomics) and stable isotope tracing illuminate microbial metabolic pathways and the fate of carbon within complex communities. Computational modeling and integrative data analysis further help link biogeochemical process rates with microbial population dynamics. By leveraging such innovative methodologies, researchers can bridge traditionally separate disciplines from soil biogeochemistry and microbial ecology to environmental engineering to gain a more holistic understanding of how DOM transformations proceed and how microbial ecology is shaped in natural and engineered contexts.

This Research Topic will unite interdisciplinary efforts focusing specifically on microbial DOM transformation mechanisms and DOM-driven community dynamics in soil and sludge systems. We emphasize studies that yield a clear mechanistic understanding of microbial processes. Broad surveys of ecosystems or purely engineering, modeling, or omics studies are welcome only if they directly elucidate underlying microbiological mechanisms. We welcome original research articles, reviews, and other formats that address the following themes, including but not limited to:
- Microbial transformation and mineralization of DOM in soils and sludge: mechanistic studies of how microbes degrade, alter, or remineralizer DOM under natural soil conditions and in engineered sludge environments.
- Effects of DOM composition on microbial communities: investigations into how DOM concentration, source, and chemical composition influence microbial community structure and functional activity in soils and sludge.
- Reciprocal feedback between DOM and microbial metabolism: research on how microbial processes generate or modify DOM, and how these microbially derived DOM fractions in turn affect ecosystem function. This includes studies of microbial exudation, secretion of metabolites, or cell lysis in soils or sludge that contribute to the DOM pool, and how such DOM feeds back into microbial activity (e.g., priming effects, substrate-induced shifts in metabolism) and broader carbon/nutrient cycling.
- Microbial mechanisms of particulate organic matter solubilization: investigations into how microbes facilitate the release of DOM from particulate organic substrates in soil and sludge environments. This could involve the role of extracellular enzymes, oxidative radicals, biosurfactants, or cooperative community behaviors (biofilm formation, synergistic consortia) in breaking down detrital plant material or organic waste solids into dissolved forms that microbes can further metabolize.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Editorial
• FAIR² Data
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Editorial
• FAIR² Data
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review
• Technology and Code

Keywords: Dissolved organic matter (DOM), carbon cycling, microbial mechanisms, microbial community, biogeochemistry soil, sludge, wastewater

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.