Future climate conditions accelerate wheat straw decomposition alongside altered microbial community composition, assembly patterns, and interaction networks

Modeling microbial impact on macrophyte debris decomposition in macrophyte-dominated eutrophic lakes

The decomposition of macrophytes plays a crucial role in the nutrient cycles of macrophyte-dominated eutrophication lakes. While research on plant decomposition mechanisms and microbial influences has rapid developed, it is curious that plant decomposition models have remained stagnant at the single-stage model from 50 years ago, without endeavor to consider any important factors. Our research conducted in-situ experiments and identified the optimal metrics for decomposition-related microbes, thereby establishing models for microbial impacts on decomposition rates (k_RDR). Using backward elimination in stepwise regression, we found that the optimal subset of independent variables-specifically Gammaproteobacteria-Q-L, Actinobacteriota-Q-L, and Ascomycota-Q-L-increased the adjusted R-squared (Ra2) to 0.93, providing the best modeling for decomposition rate (p = 0.002). Additionally, k_RDR can be modeled by synergic parameters of ACHB-Q-L, LDB-Q-L, and AB-Q-L for bacteria, and SFQ for fungi, albeit with a slightly lower Ra2 of 0.7-0.9 (p < 0.01). The primary contribution of our research lies in two key aspects. Firstly, we introduced optimal metrics for modeling microbes, opting for debris surface microbes over sediment microbes, and prioritizing absolute abundance over relative abundance. Secondly, our model represents a noteworthy advancement in debris modeling. Alongside elucidating the focus and innovative aspects of our work, we also addressed existing limitations and proposed directions for future research. SYNOPSIS: This study explores optimum metrics for decomposition-related microbes, offering precise microbial models for enhanced lake nutrient cycle simulation.

Differential responses of soil bacteria, fungi and protists to root exudates and temperature

The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.

Heterogenetic mechanism in high-temperature Daqu fermentation by traditional craft and mechanical craft: From microbial assembly patterns to metabolism phenotypes

The mechanical process has a widely usage in large-scale high-temperature Daqu (HTD) enterprises, however, the quality of the mechanical HTD is gapped with the HTD by traditional process. Currently, the understanding of the mechanism behind this phenomenon is still over-constrained. To this end, the discrepancies in fermentation parameters, enzymatic characteristics, microbial assembly and succession patterns, metabolic phenotypes were compared between traditional HTD and mechanical HTD in this paper. The results showed that mechanical process altered the temperature ramping procedure, resulting in a delayed appearance of the peak temperature. This alteration shifted the assembly pattern of the initial bacterial community from determinism to stochasticity, while having no impact on the stochastic assembly pattern of the fungal community. Concurrently, mechanical pressing impeded the accumulation of arginase, tetramethylpyrazine, trimethylpyrazine, 2-methoxy-4-vinylphenol, and butyric acid, as the target dissimilarities in metabolism between traditional HTD and mechanical HTD. Pearson correlation analysis combined with the functional prediction further demonstrated that Bacillus, Virgibacillus, Oceanobacillus, Kroppenstedtia, Lactobacillus, and Monascus were mainly contributors to metabolic variances. The Redundancy analysis (RDA) of fermented environmental factors on functional ASVs indicated that high temperature, high acid and low moisture were key positive drivers on the microbial metabolism for the characteristic flavor in HTD. Based on these results, heterogeneous mechanisms between traditional HTD and mechanical HTD were explored, and controllable metabolism targets were as possible strategies to improve the quality of mechanical HTD.

Distinct microbial communities under different rock-associated microhabitats in the Qaidam Desert

Hypolithic communities, which occupy highly specialised microhabitats beneath translucent rocks in desert and arid environments, have assembly mechanisms and ecosystem functions are not fully understood. Thus, in this study, we aimed to examine the microbial community structure, assembly, and function of light-accessible (under quartz, calcite, and hypolithic lichen-dominated biocrusts) and light-inaccessible microhabitats (under basalt and adjacent soil) in the Qaidam Desert, China. The results showed that hypolithic communities have different characteristics compared with microbial communities of light-inaccessible microhabitats. Notably, hypolithic bacterial communities were dominated by Cyanobacteria, whereas light-inaccessible microhabitats showed a predominance of Bacteroidetes and Proteobacteria. Although the class Dothideomycetes (phylum: Ascomycota) dominated the fungal communities between the two microhabitat types, Sordariomycetes were more prevalent in light-accessible microhabitats. Network and robustness analyses showed that hypolithic communities were less complex and more resilient than microbial communities in light-inaccessible microhabitats. Our results indicated that deterministic processes, specifically homogeneous selection, govern the establishment of bacterial and fungal communities in light-accessible and light-inaccessible microhabitats. The hypolithic community showed an increased frequency of phylotypes that exhibited increased tolerance to functional stress response pathways. In contrast to light-inaccessible microhabitats, light-accessible microhabitats showed a slight decrease and a notable increase in the prevalence of carbon fixation pathways in prokaryotes and carbon fixation in photosynthetic organisms, respectively. For fungi, light-accessible microhabitats enriched saprotrophic and ectomycorrhizal groups. These results highlight the importance of complex and diverse microhabitats in desert regions, which serve as vital shelters for microbes. Combining future research on interactions between hypolithic communities and environments may enhance our current understanding of their pivotal roles in sustaining desert ecosystems. This knowledge then be applied to design and implement informed conservation efforts to preserve these unique rock-associated microhabitats in desert ecosystems.

Pre-exposure of Triclosan compromise tetracycline-derived antibiotic resistance in methanogenic digestion microbiome

Triclosan (TCS) and tetracycline (TC) are commonly detected antibacterial agents in sewage and environment matrices. Nonetheless, the impact of sequential exposure to TCS and TC on the methanogenic digestion microbiome remains unknown. In this study, TCS was shown to reduce COD removal efficiency to 69.8%, but alleviated the inhibitive effect of consequent TC-amendment on the digestion microbiome. Interestingly, TCS pre-exposure resulted in abundance increase of acetotrophic Methanosaeta to 2.68%, being 2.91 folds higher than that without TCS amendment. Microbial network analyses showed that TCS pre-exposure caused microorganisms to establish a co-ecological relationship against TC disturbance. Further analyses of total antibiotic resistance genes (ARGs) showed the TCS-derived compromise of TC-induced ARGs enrichment in digestion microbiomes, e.g., 238.2% and 152.1% ARGs increase upon TC addition in digestion microbiomes without and with TCS pre-exposure, respectively. This study provides new insights into the impact of antibacterial agents on the methanogenic digestion microbiome.

Core bacteria and fungi in response to residue retention and their contribution to soil multifunctionality in maize agroecosystem

Core microbiome has been proven to play crucial roles in soil function. However, we still lack knowledge on how core microbiome responds to crop residue retention, and whether they contribute to this process. Consequently, we examined the effect of residue retention on soil core and non-core microbial communities in maize seedling, mature stage and freezing period based on a multi-site field experiment in Sanjiang Plain, Northeast China. Totally, 247 bacterial amplicon sequence variants (ASVs) and 109 fungal ASVs were identified as core microbiota. Both core and non-core bacterial/fungal community composition were significantly influenced by residue retention across all study sites. Especially, the core fungal community shifted towards a saprotroph-dominated community. Normalized stochastic ratio pattern revealed that that deterministic process dominated both core and non-core microbial community assembly processes. Residue retention enhanced the deterministic process of core microbial community assembly, while exhibited opposite effect on non-core microbial community. This study also revealed that soil fungi were more sensitive to residue retention than bacteria, with a larger proportion of core fungi were enriched or depleted by residue retention. In addition, residue retention complicated core bacterial co-occurrence network, while simplified fungal network. Our results pointed out both no reduction in microbial diversity or collapse in microbial network structure after repeated freezing-thawing cycles. The potential function of core microbiome was evaluated through random forest analysis and structural equation model, the results indicated core microbiome contributed more to multifunctionality than non-core microbiome. Overall, this study strengthened our understanding of soil core microbiome in response to residue retention, and highlighted their importance in maintaining soil multifunctionality.

Degradation of agricultural waste is dependent on chemical fertilizers in long-term paddy-dry rotation field

The practice of returning straw to agricultural fields is a globally employed technique. Such agricultural fields also receive a significant amount of nitrogen (N) and phosphorus (P) fertilizers, because these two macronutrients are essential for plant growth and development. However, the consequences of such macronutrients input on straw decomposition, soil dissolved organic matter (DOM), key microbes, and lignocellulolytic enzymes are still unclear. In a similar aim, we designed a long-term straw returning study without and with different N and P nutrient supplementation: CK (N0P0), T1 (N120P0), T2 (N120P60), T3 (N120P90), T4 (N120P120), T5 (N0P90), T6 (N60P90), and T7 (N180P90), and evaluated their impact on rice and oilseed rape yield, soil DOM, enzymes, lignocellulose content, microbial diversity, and composition. We found straw returning improved overall yield in all treatments and T7 showed the highest yield for oilseed rape (30.31-38.87 g/plant) and rice (9.14-9.91 t/ha) during five-years of study. The fertilizer application showed a significant impact on soil physicochemical properties, such as water holding capacity and soil porosity decreased, and bulk density increased in fertilized treatments, as compared to CK. Similarly, significantly low OM, cellulose, hemicellulose, and lignin content were found in T7, T4, T3, and T2, while high values were found in CK and T5, respectively. The fluorescence excitation-emission matrix spectra of DOM of different treatments revealed that T3, T7, T4, and T6 showed high peak M (microbial by-products), peak A and peak C (humic acid-like) as compared to others. The microbial composition was also distinctive in each treatment and a high relative abundance of Chloroflexi, Actinobacteriota, Ascomycota, and Basidiomycota were found in T2 and T3 treatments, respectively. These findings indicate that the decomposition of straw in the agricultural field was dependent on nutrients input, which facilitated key microbial growth and impacted positively on lignocellulolytic enzymes, which further aided the breakdown of all components of straw in the field efficiently. On the other hand, high input of chemical based fertilizers to soil can lead to several environmental issues, such as nutrient imbalance, nutrient runoff, soil pH change and changes in microbial activities. Keeping that in consideration, we recommend moderate fertilizer dosage (N120P90) in such fields to achieve higher decomposition of crop straw with a small yield compromise.

Insight into the enhancement effect of humic acid on microbial degradation of triclosan in anaerobic sediments

Humic acid (HA) as one class of macromolecular substances plays important roles in mediating environmental behaviors of pollutants in sediments, but its effect on microbial degradation of triclosan (TCS), a common antibacterial drug, remains unclear. In this study, the effects of HA addition with different dosages (0-5%) on TCS degradation in anaerobic sediment slurries and the underlying microbial mechanisms were investigated. The results showed that HA addition significantly accelerated the TCS removal and the maximum removal percentage (30.2%) was observed in the sediment slurry with 5% HA addition. The iron reduction rate, relative abundances of the genera Comamonas, Pseudomonas and Geobacter, and bacterial network complexity in sediment slurry were significantly enhanced due to HA addition. Based on the partial least squares path modeling analysis, the enhancement effect of HA on TCS degradation was mainly explained by Fe(II):Fe(III) ratio with the highest influence on TCS removal (total effect: 0.723), followed by dominant genera abundances (total effect: 0.391), module relative abundance (total effect: 0.272), and network topological features (total effect: 0.263). This finding enhanced our understanding of the role of HA in TCS biodegradation in contaminated sediments for bioremediation purposes.

Seasonal changes driving shifts in microbial community assembly and species coexistence in an urban river

Microbial communities play a vital role in urban river biogeochemical cycles. However, the seasonal variations in microbial community characteristics, particularly phylogenetic group-based community assembly and species coexistence, have not been extensively investigated. Here, we systematically explored the microbiome characteristics and assembly mechanisms of urban rivers in different seasons using 16S rRNA gene sequencing and multivariate statistical methods. The results indicated that the microbial community presented significant temporal heterogeneity in different seasons, and the diversity decreased from spring to winter. The phylogenetic group-based microbial community assembly was governed by dispersal limitation and drift in spring, summer, and autumn but was structured by homogeneous selection in winter. Moreover, the main functions of nitrification, denitrification, and methanol oxidation were susceptible to dispersal limitation and drift processes, whereas sulfate respiration and aromatic compound degradation were controlled by dispersal limitation and homogeneous selection. Network analyses indicated that network complexity decreased and then increased with seasonal changes, while network stability showed the opposite trend, suggesting that higher complexity and diversity reduced community stability. Temperature was determined to be the primary driver of microbial community structure and assembly processes in different seasons based on canonical correspondence analysis and linear regression analysis. In conclusion, seasonal variation drives the dynamics of microbial community assembly and species coexistence patterns in urban rivers. This study provides new insights into the generation and maintenance of microbial community diversity in urban rivers under seasonal change conditions.

Linking ecological niches to bacterial community structure and assembly in polluted urban aquatic ecosystems

Introduction

Bacterial communities play crucial roles in the functioning and resilience of aquatic ecosystems, and their responses to water pollution may be assessed from ecological niches. However, our understanding of such response patterns and the underlying ecological mechanisms remains limited.

Methods

In this study, we comprehensively investigated the effects of water pollution on the bacterial structure and assembly within different ecological niches, including water, sediment, submerged plant leaf surfaces, and leaf surfaces, using a 16S high-throughput sequencing approach.

Results

Ecological niches had a greater impact on bacterial community diversity than pollution, with a distinct enrichment of unique dominant phyla in different niches. This disparity in diversity extends to the bacterial responses to water pollution, with a general reduction in α-diversity observed in the niches, excluding leaf surfaces. Additionally, the distinct changes in bacterial composition in response to pollution should be correlated with their predicted functions, given the enrichment of functions related to biogeochemical cycling in plant surface niches. Moreover, our study revealed diverse interaction patterns among bacterial communities in different niches, characterized by relatively simply associations in sediments and intricate or interconnected networks in water and plant surfaces. Furthermore, stochastic processes dominated bacterial community assembly in the water column, whereas selective screening of roots and pollution events increased the impact of deterministic processes.

Discussion

Overall, our study emphasizes the importance of ecological niches in shaping bacterial responses to water pollution. These findings improve our understanding of the complicated microbial response patterns to water pollution and have ecological implications for aquatic ecosystem health.

Bacterial community structure and assembly dynamics hinge on plant litter quality

Litter decomposition is a fundamental ecosystem process controlling the biogeochemical cycling of energy and nutrients. Using a 360-day lab incubation experiment to control for environmental factors, we tested how litter quality (low C/N deciduous vs. high C/N coniferous litter) governed the assembly and taxonomic composition of bacterial communities and rates of litter decomposition. Overall, litter mass loss was significantly faster in soils amended with deciduous (DL) rather than coniferous (CL) litter. Communities degrading DL were also more taxonomically diverse and exhibited stochastic assembly throughout the experiment. By contrast, alpha-diversity rapidly declined in communities exposed to CL. Strong environmental selection and competitive biological interactions induced by molecularly complex, nutrient poor CL were reflected in a transition from stochastic to deterministic assembly after 180 days. Constraining how the diversity and assembly of microbial populations modulates core ecosystem processes, such as litter decomposition, will become increasingly important under novel climate conditions, and as policymakers and land managers emphasize soil carbon sequestration as a key natural climate solution.

Microbial Community Colonization Process Unveiled through eDNA-PFU Technology in Mesocosm Ecosystems

Microbial communities are essential components of aquatic ecosystems and are widely employed for the detection, protection, and restoration of water ecosystems. The polyurethane foam unit (PFU) method, an effective and widely used environmental monitoring technique, has been improved with the eDNA-PFU method, offering efficiency, rapidity, and standardization advantages. This research aimed to explore the colonization process of microbial communities within PFUs using eDNA-PFU technology. To achieve this, we conducted ten-day monitoring and sequencing of microbial communities within PFUs in a stable and controlled artificial aquatic ecosystem, comparing them with water environmental samples (eDNA samples). Results showed 1065 genera in eDNA-PFU and 1059 in eDNA, with eDNA-PFU detecting 99.95% of eDNA-identified species. Additionally, the diversity indices of bacteria and eukaryotes in both methods showed similar trends over time in the colonization process; however, relative abundance differed. We further analyzed the colonization dynamics of microbes in eDNA-PFU and identified four clusters with varying colonization speeds. Notably, we found differences in colonization rates between bacteria and eukaryotes. Furthermore, the Molecular Ecological Networks (MEN) showed that the network in eDNA-PFU was more modular, forming a unique microbial community differentiated from the aquatic environment. In conclusion, this study, using eDNA-PFU, comprehensively explored microbial colonization and interrelationships in a controlled mesocosm system, providing foundational data and reference standards for its application in aquatic ecosystem monitoring and beyond.

Ribosomal RNA gene operon copy number, a functional trait indicating the hydrocarbon degradation level of bacterial communities

The lack of universal indicators for predicting microbial biodegradation potential and assessing remediation effects limits the generalization of bioremediation. The community-level ribosomal RNA gene operon (rrn) copy number, an important functional trait, has the potential to serve as a key indicator of the bioremediation of organic pollutants. A meta-analysis based on 1275 samples from 26 hydrocarbon-related studies revealed a positive relationship between the microbial hydrocarbon biodegradation level and the community-level rrn copy number in soil, seawater and culture. Subsequently, a microcosm experiment was performed to decipher the community-level rrn copy number response mechanism during total petroleum hydrocarbon (TPH) biodegradation. The treatment combining straw with resuscitation-promoting factor (Rpf) exhibited the highest community-level rrn copy number and the most effective biodegradation compared with other treatments, and the initial TPH content (20,000 mg kg-1) was reduced by 67.67% after 77 days of incubation. TPH biodegradation rate was positively correlated with the average community-level rrn copy number (p = 0.001, R2 = 0.5781). Both meta and community analyses showed that rrn copy number may reflect the potential of hydrocarbon degradation and microbial dormancy. Our findings provide insight into the applicability of the community-level rrn copy number to assess bacterial biodegradation for pollution remediation.

Impact of conservation tillage on wheat performance and its microbiome

Winter wheat is an important cereal consumed worldwide. However, current management practices involving chemical fertilizers, irrigation, and intensive tillage may have negative impacts on the environment. Conservation agriculture is often presented as a sustainable alternative to maintain wheat production, favoring the beneficial microbiome. Here, we evaluated the impact of different water regimes (rainfed and irrigated), fertilization levels (half and full fertilization), and tillage practices (occasional tillage and no-tillage) on wheat performance, microbial activity, and rhizosphere- and root-associated microbial communities of four winter wheat genotypes (Antequera, Allez-y, Apache, and Cellule) grown in a field experiment. Wheat performance (i.e., yield, plant nitrogen concentrations, and total nitrogen uptake) was mainly affected by irrigation, fertilization, and genotype, whereas microbial activity (i.e., protease and alkaline phosphatase activities) was affected by irrigation. Amplicon sequencing data revealed that habitat (rhizosphere vs. root) was the main factor shaping microbial communities and confirmed that the selection of endophytic microbial communities takes place thanks to specific plant-microbiome interactions. Among the experimental factors applied, the interaction of irrigation and tillage influenced rhizosphere- and root-associated microbiomes. The findings presented in this work make it possible to link agricultural practices to microbial communities, paving the way for better monitoring of these microorganisms in the context of agroecosystem sustainability.

Decreased soil multifunctionality is associated with altered microbial network properties under precipitation reduction in a semiarid grassland

Our results reveal different responses of soil multifunctionality to increased and decreased precipitation. By linking microbial network properties to soil functions, we also show that network complexity and potentially competitive interactions are key drivers of soil multifunctionality.

The Succession of the Cellulolytic Microbial Community from the Soil during Oat Straw Decomposition

The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil microbiome can serve as a source of potentially active cellulolytic microorganisms. Here, we performed an experiment on the de novo colonization of oat straw by the soil microbial community by placing nylon bags with sterilized oat straw in the pots filled with chernozem soil and incubating them for 6 months. The aim was to investigate the changes in decomposer microbiota during this process using conventional sequencing techniques. The bacterial succession during straw decomposition occurred in three phases: the early phase (first month) was characterized by high microbial activity and low diversity, the middle phase (second to third month) was characterized by low activity and low diversity, and the late phase (fourth to sixth months) was characterized by low activity and high diversity. Analysis of amplicon sequencing data revealed three groups of co-changing phylotypes corresponding to these phases. The early active phase was abundant in the cellulolytic members from Pseudomonadota, Bacteroidota, Bacillota, and Actinobacteriota for bacteria and Ascomycota for fungi, and most of the primary phylotypes were gone by the end of the phase. The second intermediate phase was marked by the set of phylotypes from the same phyla persisting in the community. In the mature community of the late phase, apart from the core phylotypes, non-cellulolytic members from Bdellovibrionota, Myxococcota, Chloroflexota, and Thermoproteota appeared. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major bacterial and fungal members of this consortium had genes of glycoside hydrolases (GH) connected to cellulose and chitin degradation. The real-time analysis of the selection of these genes showed that their representation varied between phases, and this occurred under the influence of the host, and not the GH family factor. Our findings demonstrate that soil microbial community may act as an efficient source of cellulolytic microorganisms and that colonization of the cellulolytic substrate occurs in several phases, each characterized by its own taxonomic and functional profile.