Livestock manure has become one of the main causes of non-point source environmental pollution due to continuous expansion of livestock and poultry breeding industry (Sun et al., 2012). Correct treatment of livestock and poultry manures is thus required, which could be achieved through composting. Composting is an effective and widely used approach to transform animal manure and other agricultural waste products into high-quality agricultural organic fertilizers (Bernal et al., 2009). As a biological decomposition process, composting relies on the activity of a diverse set of microbes that are important drivers of the depolymerization of organic matter (Xi et al., 2015). Bacteria and fungi are the most abundant and active microbes involved in composting (Rastogi et al., 2020). While bacteria are responsible for a large proportion of decomposition and heat generation in compost (Lopez-Gonzalez et al., 2015), fungi are capable of decomposing complex polymers present in the compost (Yamamoto and Nakai, 2019). While the succession of microbial communities during different composting stages have been studied extensively (Nakasaki et al., 2005; Jiang et al., 2019), there is less information on how the initial manure metataxonomy composition affects composting. The initial compost metataxonomy composition is important because it affects the proliferation of mesophilic microbiota which are responsible for the rapid rise of composting temperature (De Gannes et al., 2013) and creation of a suitable environment for the secondary microorganisms during composting (Ryckeboer et al., 2003). Furthermore, initial composting microbiota could have long-lasting effects for later phases of composting, affecting the maturation and stabilization of composts (Villar et al., 2016). Therefore, information on the initial manure metataxonomy profiles could potentially be used to predict and manage the composting process.

While the activity, metabolism and abundances of microbes is heavily affected by the physicochemical properties of compost (Lopez-Gonzalez et al., 2015; Awasthi et al., 2017; Duan et al., 2019), also the used source materials play an important role important as most of the decomposing microorganisms originate from the raw materials. Of the physicochemical composting properties, temperature is an important indicator for the maturation of compost and reflects microbial activities during composting (Tang et al., 2007; Bernal et al., 2009). Temperature also affects microbial abundances and it has been found that fungi are likely more sensitive to fluctuating temperature and moisture contents than bacteria (Zhang et al., 2011). C/N ratio also reflects the degradation of organic matter by bacteria and fungi (Meng et al., 2019) and the initial C/N ratio can affect the microbial community structure (Lei and Vandergheynst, 2000; Zhang et al., 2011). It is, however, still unclear how different physicochemical compost properties shape the composition and assembly of bacterial and fungal communities, depending on the type of raw materials used for composting.

Livestock manures is one the common raw materials used in composting and microbial communities of livestock and poultry manures have been explored extensively during composting (Awasthi et al., 2019; Chen et al., 2019; Bello et al., 2020). It has been established that different composting systems using manure from different animals are associated with specific microbiota. For example, Firmicutes often dominate in pig manure compost (Wang et al., 2018b), while Proteobacteria are more abundant in cattle manure (Wang et al., 2018a). In case of fungi, Ascomycota and Basidiomycota have been found to be the core phyla in chicken and cow manures (Neher et al., 2013). While such variations could be driven by the composting process, it could also be due to initial differences in manure microbiota composition, determined by the diet of and gut microbiota composition of animals (Hussein et al., 2017; Chen et al., 2019). For example, previous studies have shown that the bovine feed contains more crude fiber, while chicken feed has higher contents of proteins and antibiotics (Sapkota et al., 2007; Chibisa et al., 2016). In general, carnivores consume food with significantly higher protein content than herbivores (Wilder et al., 2013). Such drastic diet differences will likely have consequences for the manure microbiota composition (Carmody et al., 2015), and gut microbiomes of herbivores have been shown to be more diverse compared to omnivores (Ley et al., 2008). While the animal feeding habits are likely to play an important role in determining the microbial composition of their manure, it is not clear if these differences are retained, or if they potentially have effects on the composting process.

Here, we studied this experimentally by comparing the bacterial and fungal communities of four different types of manures (sheep, cattle, pig, and chicken) at the initial and final stages of composting using a trough fermentation approach in the one factory. These four types of manures were selected because sheep and cattle are herbivores, and pig and chicken are omnivores, and hence have significant differences in their diets. Specifically, we investigated the link between physiochemical compost properties and bacterial and fungal communities using correlative analyses. We hypothesized that microbial communities should cluster according the feeding habits of animals, resulting pairing between the herbivore (sheep and cattle) and omnivore (pig and chicken) manure compost treatments. Moreover, we expected that such clustering would be clearer at the initial phase of composting, while community assembly could lead to either clearer divergence or convergence between manure compost treatments during composting.

In this study, we investigated the link between the type of livestock manure, physiochemical compost properties and microbial community composition and assembly. We expected that microbial communities should cluster according the feeding habits of animals. In support for this, we found that both physical compost properties and microbial communities clustered closely depending if the manure originated from herbivores (sheep and cattle) or omnivores (pig and chicken). While clear reduction in bacterial and fungal diversity, and drastic changes in community composition, were observed during composting, microbial communities still retained clustering based on animal feeding habitats. Together, our results suggest that the type of manure used in composting raw materials is strongly linked with both physicochemical compost properties and microbial community composition and assembly during composting.

Based on our analysis, the physicochemical properties of different livestock manure composts clustered into two groups: herbivores (sheep and cattle) and omnivores (pig and chicken). As most nutrients ingested by animals are excreted into feces (Yano et al., 1999), the physicochemical properties of manure used in composting raw materials can reflect the feeding habits of livestock. As a result, observed differences were likely due to the animal dietary as herbivores consume more crude fiber in roughage-based diets, while omnivores have more crude proteins in their diets (Chen et al., 2019). The higher content of TN in pig and chicken manure composts was likely due to high protein contents in their feed (Chen et al., 2019), while higher TC contents and C/N ratios observed in sheep and cattle manure composts could be indicative of the presence of cellulose substances or unutilized complex nitrogen substrates in their feed (Pan et al., 2012). Relative higher TP content in pig and chicken manures was likely due to high phosphorus contents present in commercial feed to meet poultry’s phosphorus requirements (Yano et al., 1999; Sharpley and Moyer, 2000), while phosphorus contents were lower in herbivore manure composts. Animal feeding habits thus clearly affected the physicochemical properties of manure composts. Interestingly, while clear changes were observed during the composting, manure compost treatments still clustered according to herbivory and omnivory at the final phase of composting. This suggest that initial physicochemical differences between manure composts can persist throughout the composting.

Similar to physicochemical composting properties, bacterial and fungal metataxonomy clustered to two groups based on animal diets: herbivores (sheep and cattle) and omnivores (pig and chicken). Previous studies have showed that the differences in diets can affect the gut microbiome composition (Carmody et al., 2015; Hussein et al., 2017; Chen et al., 2019), possibly resulting in different composition of microbial communities in the manure of herbivores and omnivores. While microbial diversity decreased during composting, sheep and cattle manure compost retained significantly higher bacterial and fungal diversity compared to pig and chicken manure composts. These results are consistent with previous studies found that fecal microbiota of herbivores had a higher microbial diversity compared to omnivores and carnivores (Ley et al., 2008). Our analyses also revealed that the composition of both bacterial and fungal communities shifted considerably during composting in all manure compost treatments. However, paired clustering between herbivores (sheep and cattle) and omnivores (pig and chicken) was retained based on Bray-Curtis distances. Our data thus suggests that relative initial differences in manure compost community composition remained similar throughout the composting, and that selection by the composting conditions (Villar et al., 2016) was not strong enough to drive converging of different manure compost communities.

Sheep and cattle manure composts were initially dominated by Proteobacteria that encompass a huge morphological and physiological diversity, playing a critical role in the global cycles of carbon, nitrogen and sulfur (Spain et al., 2009). Interestingly, Chloroflexi became the most dominant phyla in these communities, which suggest that they had selective advantage over Proteobacteria during composting. In contrast, Firmicutes initially predominated in pig and chicken manure composts and increased in their relative abundance during composting. This could be explained by ability to form endospores that can help Firmicutes to survive high temperatures and harsh environment, which has also been shown in previous studies (Hartmann et al., 2014; Bello et al., 2020). At the genera level, bacterial community profiles in pig and chicken manure composts differed initially but converged toward the final phase of composting. This suggest that also the composting conditions were important in determining bacterial community assembly.

In case of fungi, Ascomycota dominated in all manure treatments during the whole composting process, which is in line with previous reports (Zhang et al., 2015; Akyol et al., 2019). One explanation for this is that Ascomycota can secrete a variety of cellulase and hemicellulase enzymes and hence can easily grow during composting by degrading organic materials available (Singh et al., 2003; Meng et al., 2019). The relative abundance of other two phyla, Mucoromycota and Basidiomycota, was initially higher in herbivore compared to omnivore manure composts and they both have been shown to play a vital role in decomposition of organic matter (Li et al., 2020) and straw residue (Ma et al., 2013). However, it is unclear why they were replaced by other species by the final phase of composting. At the genera level, Aspergillus dominated in pig and chicken manure composts initially. This could have been due to their innate ability to resist to bactericidal antibiotics, which are typically observed at high concentrations in pig and chicken manure (Liu et al., 2016). At the final composting phase, the relative abundance of Mycothermus was higher in sheep and cattle manure composts, while Melanocarpus dominated in pig and chicken manure composts. Mycothermus, a thermophilic genus, was reported can produce amylases, cellulases, lipases and xylanases (Aquino et al., 2003; Basotra et al., 2016), while Melanocarpus is able to produce alkaline active thermostable xylanases (Saraswat and Bisaria, 1997) that are important for degrading cellulose and hemicelluloses. Their ability to drive composting process thus likely explain increase in their relative abundances. Moreover, the four types of fermented manure composts which were dominated by different microbiota can be used as microbial inoculant to regulate the soil microbial community that promoting crop growth or stress resistance.

Previous research has reported that the bacterial and fungal communities are influenced by various physiochemical properties of composts (Duan et al., 2019). In our study, RDA analysis revealed that both the compositions of bacterial and fungal communities were significantly affected by NH₄-N and TP contents, suggesting that compost metataxonomy were involved in the nitrogen and phosphorus metabolism. Pearson correlation showed that the abundance of Ignatzschineria and Aspergillus were positively correlated with NH₄-N content, while Cerasibacillus, Bacillus, and Novibacillus positively correlated with TP content. Ignatzschineria, a Gram-negative genus, has been found in aerobic composts (Wang et al., 2017), but its function in the microbial community remains unclear. The success of Aspergillus could be due to its ability to utilize a huge range of nitrogen sources (Krappmann and Braus, 2005), while Cerasibacillus, Bacillus, and Novibacillus were possibly involved in the biodegradation of organic matters during composting (Wang et al., 2020) and potential P solubilization and mobilization via release of carboxylates (Arif et al., 2017; Saeid et al., 2018). These results indicated that both bacteria and fungi were sensitive to the changes of physiochemical properties of composts.

The diversity and composition of bacterial and fungal communities before and after composting were distinct and clustered into two groups based on animal feeding habits: herbivores (sheep and cattle) and omnivores (pig and chicken) manure composts. Despite identical composting conditions, relative differences in community composition did not change much between different manure treatments. Furthermore, the shifts in both bacterial and fungal communities were closely related to physicochemical changes in compost properties, which could be mainly attributed to TN and TC contents of manure composts. Together, our results suggest that the initial physicochemical and biological properties of manure can predict the compost metataxonomy composition and assembly, potentially affecting the composting process efficacy and outcome. This study offers a new insight on how livestock manures with different physiochemical and microbiological properties could potentially be used steer and manage composting process and outcome on an industrial scale.

The original contributions presented in the study are publicly available. This data can be found here: NCBI Sequence Read Archive (SRA) database and accession number is PRJNA675153.

YX and ZW designed the experiments. JW conducted the experiments. XW and TY conducted the data analysis and wrote the manuscript with ZW, SB, and V-PF. All authors read and approved the final manuscript.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.