The co-occurrence network patterns and keystone species of microbial communities in cattle manure-corn straw composting

Tracing microbial community across endophyte-to-saprotroph continuum of Cinnamomum camphora (L.) Presl leaves considering priority effect of endophyte on litter decomposition

Endophytes typically coexist with plants in symbiosis and transition into the saprobic system as plant tissues senesce, participating in the decomposition process of litter. However, the dynamic changes of endophytic communities during this process and their role in litter decomposition remain unclear. This study tracked the microbial composition across the transition from live leaves to litter in Cinnamomum camphora (L.) Presl (C. camphora), evaluating the contribution of endophytes to litter decomposition by examining microbial diversity, community assembly, and co-occurrence networks along the endophyte-to-saprotroph spectrum. The results revealed increasing bacterial diversity but stable fungal diversity, and the diversity of endogenous microbes is mirrored this in the saprophytic phase. Bacterial community assembly was characterized by deterministic processes during the symbiotic phase, shifted to stochastic processes during the saprophytic phase. In contrast, fungal community assembly was predominantly driven by stochastic processes throughout the continuum. Out of the 49 keystone taxa identified, only Pseudorhodoplanes sinuspersici demonstrated a significant positive correlation with community assembly. All identified bacterial keystone taxa during the saprophytic phase originated from endophytic sources, and around 80% of the fungal keystone taxa in the initial stages of decomposition were similarly endophytic in origin. Additionally, 60% of the dominant bacterial taxa and 28% of the dominant fungal taxa at the commencement of decomposition were of endophytic descent. This suggests that endogenous microbes possess the potential to evolve into both keystone and dominant taxa during the saprophytic phase. Endogenous keystone and dominant microbes both exhibited significant correlations with microbial network, indicating their substantial ecological presence in microbial community. Both endogenous keystone and dominant taxa exerted significant potential influences on litter decomposition. Overall, during the saprophytic phase, endophytes are likely to influence the assemblage of microbial communities, the network structure, and decomposition-related functions. Specifically, it appears that bacterial endophytes may possess a greater adaptability to the decomposition processes of leaf litter compared to their fungal counterparts.

Characteristics of the effects of Polygonati Rhizoma on gut microbiota and metabolites in vitro associated with poor dietary habits in pregnant women

Poor dietary habits have been associated with dysbiosis and microbial imbalance in pregnant women. Such imbalances can pose health risks during pregnancy. This study aimed to explore the impact of Polygonati Rhizoma on the gut microbiota of pregnant women through In vitro simulated fermentation. Interestingly, significant differences in microbial community richness and structure were found between the control and the treatment with Polygonati Rhizoma. Analysis of composition and variability indicated that the treatment with Polygonati Rhizoma group showed higher levels of Lactobacillus and Bifidobacterium, but lower levels of Parabacteroides and Lachnoclostridium. The study also investigated specific genera differences between groups using the co-occurrence network analysis and their correlations with microbial metabolites by the redundancy analysis (RDA), Mantel-test network heatmap, and heatmap highlighting the relationships among gut microbiota, short-chain fatty acids (SCFAs), and gases in the absence or presence of Polygonati Rhizoma supplementation. Functional predictions from BugBase phenotype prediction indicated changes in potentially pathogenic and aerobic bacteria in Polygonati Rhizoma supplementation. Overall, the findings provide valuable insights into the influence of Polygonati Rhizoma on the gut microbiota in pregnant women associated with poor dietary habits.

Chromium contamination affects the fungal community and increases the complexity and stability of the network in long-term contaminated soils

Chromium (Cr) contamination can adversely affect soil ecology, yet our knowledge of how fungi respond to Cr contamination at heavily contaminated field sites remains relatively limited. This study employed high-throughput sequencing technology to analyze fungal community characteristics in soils with varying Cr concentrations. The results showed that Cr contamination significantly influenced soil fungi's relative abundance and structure. Mantel test analysis identified hexavalent chromium (Cr(VI)) as the primary factor affecting the structure of the soil fungal community. In addition, FUNGuild functional prediction analysis exhibited that Cr contamination reduced the relative abundance of Pathotroph and Symbiotroph trophic types. High concentrations of Cr may lead to a drop in the relative abundance of Animal Pathogens. Molecular ecological network analysis showed that Cr contamination increased interactions among soil fungi, thereby enhancing the stability and complexity of the network. Within these networks, specific keystone taxa, such as the genus Phanerochaete, exhibited properties capable of removing or reducing the toxicity of heavy metals. Our studies suggest that Cr contamination can alter indigenous fungal communities in soil systems, potentially impacting soil ecosystem function.

Contributions of the bacterial communities to the microcystin degradation and nutrient transformations during aerobic composting of algal sludge

Aerobic composting is a useful method for managing and disposing of salvaged algal sludge. To optimize the composting process and improve compost quality, it is necessary to understand the functions and responses of microbial communities therein. This work studied the degradation process of organic matter and the assemblage of bacterial communities in algal sludge composting via 16S rRNA amplicon sequencing. The results showed that 77.08% of the microcystin was degraded during the thermophilic stage of composting, which was the main period for microcystin degradation. Bacterial community composition and diversity changed significantly during the composting, and gradually stabilized as the compost matured. Different composting stages may be dominated by different module groups separately, as shown in the co-occurrence networks of composting bacterial communities. In the networks, all bacteria associated with microcystin degradation were identified as connectors between different module groups. The algal sludge composting process was driven primarily by deterministic processes, and the main driving forces for bacterial community assembly were temperature, dissolved organic carbon, ammonium, and microcystin. At last, by applying the structural equation modeling method, the bacterial communities under influences of physiochemical properties were proved as the main mediators for the microcystin degradation. This study provides valuable insights into the optimization of bacterial communities in composting to improve the efficiency of microcystin degradation and the quality of the compost product.

Fungi play a crucial role in sustaining microbial networks and accelerating organic matter mineralization and humification during thermophilic phase of composting

Fungi play an important role in the mineralization and humification of refractory organic matter such as lignocellulose during composting. However, limited research on the ecological role of fungi in composting system hindered the development of efficient microbial agents. In this study, six groups of lab-scale composting experiments were conducted to reveal the role of fungal community in composting ecosystems by comparing them with bacterial community. The findings showed that the thermophilic phase was crucial for organic matter degradation and humic acid formation. The Richness index of the fungal community peaked at 1165 during this phase. PCoA analysis revealed a robust thermal stability in the fungal community. Despite temperature fluctuations, the community structure, predominantly governed by Pichia and Candida, remained largely unaltered. The stability of fungal community and the complexity of ecological networks were 1.26 times and 5.15 times higher than those observed in bacterial community, respectively. Fungi-bacteria interdomain interaction markedly enhanced network complexity, contributing to maintain microbial ecological functions. The core fungal species belonging to the family Saccharomycetaceae drove interdomain interaction during thermophilic phase. This study demonstrated the key role of fungi in the composting system, which would provide theoretical guidance for the development of high efficiency composting agents to strengthen the mineralization and humification of organic matter.

Investigating fungal community characteristics in co-composted cotton stalk and various livestock manure products

Agricultural wastes, comprising cotton straw and livestock manure, can be effectively managed through aerobic co-composting. Nevertheless, the quality and microbial characteristics of co-composting products from different sources remain unclear. Therefore, this study utilized livestock manure from various sources in Xinjiang, China, including herbivorous sheep manure (G), omnivorous pigeon manure (Y), and pigeon-sheep mixture (GY) alongside cotton stalks, for a 40-day co-composting process. We monitored physicochemical changes, assessed compost characteristics, and investigated fungal community. The results indicate that all three composts met established composting criteria, with compost G exhibiting the fastest microbial growth and achieving the highest quality. Ascomycota emerged as the predominant taxon in three compost products. Remarkably, at the genus level, the biomarker species for G, Y, and GY are Petromyces and Cordyceps, Neurospora, and Neosartorya, respectively. Microorganisms play a pivotal role in organic matter degradation, impacting nutrient composition, demonstrating significant potential for the decomposition and transformation of compost components. Redundancy analysis indicates that potassium, total organic carbon, and C:N are key factors influencing fungal communities. This study elucidates organic matter degradation in co-composting straw and livestock manure diverse sources, optimizing treatment for efficient agricultural waste utilization and sustainable practices.

Biodiversity and core microbiota of key-stone ecological clusters regulate compost maturity during cow-dung-driven composting

The primary objectives of this study were to explore the community-level succession of bacteria, fungi, and protists during cow-dung-driven composting and to elucidate the contribution of the biodiversity and core microbiota of key-stone microbial clusters on compost maturity. Herein, we used high-throughput sequencing, polytrophic ecological networks, and statistical models to visualize our hypothesis. The results showed significant differences in the richness, phylogenetic diversity, and community composition of bacteria, fungi, and eukaryotes at different composting stages. The ASV191 (Sphingobacterium), ASV2243 (Galibacter), ASV206 (Galibacter), and ASV62 (Firmicutes) were the core microbiota of key-stone bacterial clusters relating to compost maturity; And the ASV356 (Chytridiomycota), ASV470 (Basidiomycota), and ASV299 (Ciliophora) were the core microbiota of key-stone eukaryotic clusters relating to compost maturity based on the data of this study. Compared with the fungal taxa, the biodiversity and core microbiota of key-stone bacterial and eukaryotic clusters contributed more to compost maturity and could largely predict the change in the compost maturity. Structural equation modeling revealed that the biodiversity of total microbial communities and the biodiversity and core microbiota of the key-stone microbial clusters in the compost directly and indirectly regulated compost maturity by influencing nutrient availability (e.g., NH4+-N and NO3--N), hemicellulose, humic acid content, and fulvic acid content, respectively. These results contribute to our understanding of the biodiversity and core microbiota of key-stone microbial clusters in compost to improve the performance and efficiency of cow-dung-driven composting.

Study on the accelerated biodegradation of PAHs in subsurface soil via coupled low-temperature thermally treatment and electron acceptor stimulation based on metagenomic sequencing

In situ anoxic bioremediation is a sustainable technology to remediate PAHs contaminated soils. However, the limited degradation rate of PAHs under anoxic conditions has become the primary bottleneck hindering the application of this technology. In this study, coupled low-temperature thermally treatment (<50 °C) and EA biostimulation was used to enhance PAH removal. Anoxic biodegradation of PAHs in soil was explored in microcosms in the absence and presence of added EAs at 3 temperatures (15 °C, 30 °C, and 45 °C). The influence of temperature, EA, and their interaction on the removal of PAHs were identified. A PAH degradation model based on PLSR analysis identified the importance and the positive/negative role of parameters on PAH removal. Soil archaeal and bacterial communities showed similar succession patterns, the impact of temperature was greater than that of EA. Soil microbial community and function were more influenced by temperature than EAs. Close and frequent interactions were observed among soil bacteria, archaea, PAH-degrading genes and methanogenic genes. A total of 15 bacterial OTUs, 1 PAH-degrading gene and 2 methanogenic genes were identified as keystones in the network. Coupled low-temperature thermally treatment and EA stimulation resulted in higher PAH removal efficiencies than EA stimulation alone and low-temperature thermally treatment alone.

Role of keystone drives polycyclic aromatic hydrocarbons degradation and humification especially combined with aged contaminated soil in co-composting

Accumulation of persistent organic pollutants polycyclic aromatic hydrocarbons (PAHs) in soil has become a global problem. Composting is considered one of the more economical methods of soil remediation and is important for the resourceful use of wastes. Agroforestry waste is produced in huge amounts and is utilized at low rates, hence there is an urgent need to manage it. Here, leaf (LVS) or rice straw (SVS) was co-composting with aged contaminated soil to investigate bacteria interaction to PAHs degradation and humus formation. The degradation rate of high molecular weight PAHs (HMW-PAHs) in LVS and SVS reached 58.9% and 52.5%, and the low molecular weight PAHs (LMW-PAHs) were 77.5% and 65%. Meanwhile, the humus increased by 44.8% and 60.5% in LVS and SVS at the end of co-composting. The topological characteristics and community assembly of the bacterial community showed that LVS had higher complexity and more keystones than SVS, suggesting that LVS might more beneficial for the degradation of PAHs. The stability of the co-occurrence network and stochastic processes (dispersal limitation) dominated community assembly made SVS beneficial for humus formation. Mantel test and structural equation models indicated that the transformation of organic matter was important for PAHs degradation and humus formation. Degradation of HMW-PAHs led to bacterial succession, which affected the formation of precursors and ultimately increased the humus content. This study provided potential technology support for improving the quality of agroforestry organic waste composting and degrading PAHs in aged contaminated soil.

Contrasting fertilization response of soil phosphorus forms and functional bacteria in two newly reclaimed vegetable soils

Fertilization is a pervasive approach to agricultural production enhancing vegetable nutrients such as phosphorus (P) absorption. However, unreasonable fertilization strategies result in high levels of residual P in vegetable planting systems. To better understand the mechanisms of soil phosphorus dynamics responding to inorganic/organic fertilization, we conducted a 3-year field experiment in two newly reclaimed vegetable fields in southern China. The results revealed that soil Olsen-P in CF (mineral fertilization) and OF (Combined application of organic and inorganic fertilizers) increased by approximately 210.6 % and 183.6 %, respectively, while stable P proportion decreased by approximately 9.2 % and 18.1 %, respectively, compared with CK. Combined application of organic and inorganic fertilizer increased the proportion of moderately labile P (NaOH-P) by 1-6 % in comparison with chemical fertilizer and facilitated the conversion from diester-P to monoester-P, indicating that applying pig manure enhanced the potential soil P bioavailability. Besides, organic-inorganic fertilization shaped a bacterial community with more connectivity and stability and changed keystone taxa related to the P transformation of the network. Phenylobacterium, Solirubrobacter, and Modestobacter were regarded as core genera for mobilizing soil phosphorus. However, residual P content in newly reclaimed soils under fertilization, especially for chemical fertilizer, remained non-negligible and may cause potential environmental risks. The partial least squares path modeling results demonstrated that fertilization management had both direct and indirect positive effects on P fraction through the improvement of soil nutrients e.g. total N and soil organic carbon, and bacterial community, while soil properties mainly determined the variation of soil P species. Our results provide comprehensive insights into the current status of legacy P forms and the vital role of fertilizer, key soil properties and bacteria in P dynamics in newly reclaimed vegetable field.

Comparison of bacterial and fungal communities structure and dynamics during chicken manure and pig manure composting

Composting is a sustainable and eco-friendly technology that turns animal waste into organic fertilizers. It remains unclear whether differences exist in the structure of microbial communities during different livestock manure composting. This study analyzed the dynamic change of bacterial and fungal communities, metabolic function, and trophic mode during chicken manure (CM) and pig manure (PM) composting based on 16S rRNA and ITS sequencing. Environmental factors were investigated for their impact on microbial communities. During composting, bacterial diversity decreased and then increased, while fungal diversity slightly increased and then decreased. Saccharomonospora and Aspergillus were the dominant genera and key microorganisms in CM and PM, respectively, which played crucial roles in sustaining the stability of the ecological network structure in the microbial ecology and participating in metabolism. Saccharomonospora gradually increased, while Aspergillus increased at first and then decreased. PM had better microbial community stability and more keystone taxa than CM. In CM and PM, the primary function of bacterial communities was metabolism, while saprotroph was the primary trophic mode of fungal communities. Dissolved organic carbon (DOC) was the primary factor influencing the structure and function of microbial communities in CM and PM. In addition to DOC, pH and moisture were important factors affecting the fungal communities in CM and PM, respectively. These results show that the succession of bacteria and fungi in CM and PM proceeded in a similar pattern, but there are still some differences in the dominant genus and their responses to environmental factors.