Dominant role of abundant rather than rare bacterial taxa in maintaining agro-soil microbiomes under environmental disturbances

Bacterial abundant taxa exhibit stronger environmental adaption than rare taxa in the Arctic Ocean sediments

Marine bacteria influence Earth's environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. However, little is known about the survival strategies of their abundant and rare taxa, especially in polar marine environments. Here, bacterial environmental adaptation, community assembly processes, and co-occurrence patterns between abundant and rare taxa were compared in the Arctic Ocean sediments. Results indicated that the diversity of rare taxa is significantly higher than that of abundant taxa, whereas the distance-decay rate of rare taxa community similarity is over 1.5 times higher than that of abundant taxa. Furthermore, abundant taxa exhibited broader environmental breadth and stronger phylogenetic signals compared to rare taxa. Additionally, the community assembly processes of the abundant taxa were predominantly governed by 81% dispersal limitation, while rare taxa were primarily influenced by 48% heterogeneous selection. The co-occurrence network further revealed the abundant taxa formed a more complex network to enhance their environmental adaptability. This study revealed the differences in environmental responses and community assembly processes between bacterial abundant and rare taxa in polar ocean sediments, providing some valuable insights for understanding their environmental adaptation strategies in marine ecosystems.

Spatial distribution and community composition of endophytic fungi within Mussaenda pubescens stems

Endophytic fungi, pivotal in facilitating plant co-evolution, significantly enhance plant growth, stress resistance, and environmental adaptability. Despite their importance, the spatial distribution of stem endophytic fungi (SEF) within host plants remains poorly characterized. Here, we employed high-throughput sequencing to conduct a comparative analysis of SEF communities in Mussaenda pubescens on a regional scale. Our findings reveal that whole-SEF communities were overwhelmingly dominated by members of the phylum Ascomycota, accounting for 85.9 %, followed by Basidiomycota at 13.9 %, and that alpha diversity within the whole-SEF community of M. pubescens remains relatively consistent across sampling sites. However, significant variation was observed within conditionally abundant taxa (CAT), conditionally rare or abundant taxa (CRAT), and conditionally rare taxa (CRT). Climatic factors emerged as the primary influence on SEF community distribution, followed by spatial distance and stem chemical properties. Neutral community modeling results suggested that both stochastic and deterministic processes play a role in shaping whole-SEF communities, with deterministic processes having a stronger influence on CRT subcommunities. Furthermore, the CRT co-occurrence network exhibited a more complex structure, characterized by higher values of network betweenness and degree relative to CAT and CRAT subcommunities. These findings enhance our understanding of community assembly and ecological interactions between stem fungal endophytes, presenting opportunities for harnessing fungal resources for the benefit of humanity.

Leafcutter ants enhance microbial drought resilience in tropical forest soil

We conducted a research campaign in a neotropical rainforest in Costa Rica throughout the drought phase of an El-Nino Southern Oscillation event to determine microbial community dynamics and soil C fluxes. Our study included nests of the leafcutter ant Atta cephalotes, as soil disturbances made by these ecosystem engineers may influence microbial drought response. Drought decreased the diversity of microbes and the abundance of core microbiome taxa, including Verrucomicrobial bacteria and Sordariomycete fungi. Despite initial responses of decreasing diversity and altered composition, 6 months post-drought the microbiomes were similar to pre-drought conditions, demonstrating the resilience of soil microbial communities to drought events. A. cephalotes nests altered fungal composition in the surrounding soil, and reduced both fungal mortality and growth of Acidobacteria post-drought. Drought increased CH4 consumption in soils due to lower soil moisture, and A. cephalotes nests decrease the variability of CH4 emissions in some soil types. CH4 emissions were tracked by the abundance of methanotrophic bacteria and fungal composition. These results characterize the microbiome of tropical soils across both time and space during drought and provide evidence for the importance of leafcutter ant nests in shaping soil microbiomes and enhancing microbial resilience during climatic perturbations.

Synthesis of recovery patterns in microbial communities across environments

BACKGROUND

Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns.

RESULTS

To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50 days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle.

CONCLUSIONS

This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective. Video Abstract.

Biological Interactions Mediate Soil Functions by Altering Rare Microbial Communities

Soil microbes, the main driving force of terrestrial biogeochemical cycles, facilitate soil organic matter turnover. However, the influence of the soil fauna on microbial communities remains poorly understood. We investigated soil microbiota dynamics by introducing competition and predation among fauna into two soil ecosystems with different fertilization histories. The interactions significantly affected rare microbial communities including bacteria and fungi. Predation enhanced the abundance of C/N cycle-related genes. Rare microbial communities are important drivers of soil functional gene enrichment. Key rare microbial taxa, including SM1A02, Gammaproteobacteria, and HSB_OF53-F07, were identified. Metabolomics analysis suggested that increased functional gene abundance may be due to specific microbial metabolic activity mediated by soil fauna interactions. Predation had a stronger effect on rare microbes, functional genes, and microbial metabolism compared to competition. Long-term organic fertilizer application increased the soil resistance to animal interactions. These findings provide a comprehensive understanding of microbial community dynamics under soil biological interactions, emphasizing the roles of competition and predation among soil fauna in terrestrial ecosystems.

Resource diversity disturbs marine Vibrio diversity and community stability, but loss of Vibrio diversity enhances community stability

Vibrio is a salt-tolerant heterotrophic bacterium that occupies an important ecological niche in marine environments. However, little is known about the contribution of resource diversity to the marine Vibrio diversity and community stability. In this study, we investigated the association among resource diversity, taxonomic diversity, phylogenetic diversity, and community stability of marine Vibrio in the Beibu Gulf. V. campbellii and V. hangzhouensis were the dominant groups in seawater and sediments, respectively, in the Beibu Gulf. Higher alpha diversity was observed in the sediments than in the seawater. Marine Vibrio community assembly was dominated by deterministic processes. Pearson's correlation analysis showed that nitrite (NO 2 - -N), dissolved inorganic nitrogen (DIN), ammonium (NH 4 + -N), and pH were the main factors affecting marine Vibrio community stability in the surface, middle, and bottom layers of seawater and sediment, respectively. Partial least-squares path models (PLS-PM) demonstrated that resource diversity, water properties, nutrients, and geographical distance had important impacts on phylogenetic and taxonomic diversity. Regression analysis revealed that the impact of resource diversity on marine Vibrio diversity and community stability varied across different habitats, but loss of Vibrio diversity increases community stability. Overall, this study provided insights into the mechanisms underlying the maintenance of Vibrio diversity and community stability in marine environments.

Epigallocatechin gallate (EGCG) nanoselenium application improves tea quality (Camellia sinensis L.) and soil quality index without losing microbial diversity: A pot experiment under field condition

Applying selenium (Se) fertilizer is the only way to alleviate soil Se deficiency. Although effects of nanoselenium foliar application on plant growth and stress resistance have been extensively investigated, soil application of nanoselenium on soil microorganisms and their relationship with crop quality and soil health remains unclear. In this study, a steady-state homogeneous nanoparticle of epigallocatechin gallate Se (ESe) was synthesized, and a pot experiment was conducted applying ESe at five concentrations (0, 1, 10, 50, and 100 mg kg-1) to the tea planattion soil. The study revealed a significant increase in Se concentration in soil and tea with ESe application and identified 2.43-7.8 mg kg-1 as the safe and optimal range for soil application. Specifically, the moderate dose of ESe improved the tea quality [reduced tea polyphenols (TP), increased free amino acids (AA), and reduced TP/AA] and soil quality index (SQI). Besides, in marure tea leaves, antioxidant enzyme activities [promote catalase (CAT) superoxide dismutase (SOD), and peroxidase (POD)] increased, while level of oxidative stress [malondialdehyde (MDA), hydrogen peroxide (H2O2) and superoxide anion (O2-)] decreased with ESe application. The 16S rRNA of the soil bacteria showed that ESe application significantly changed the community structure of soil bacteria but did not alter the diversity of the bacteria and the abundance of dominant taxa (phylum and genus levels). Statistical analysis of the taxonomic and functional profiles (STAMP) detected 21 differential taxa (genus level), mainly low-abundance ones, under the ESe application. Linear regression and random forest (RF) modeling revealed that the low-abundance bacterial taxa were significantly correlated with SQI (R2 = 0.28, p < 0.01) and tea quality (R2 = 0.23-0.37, p < 0.01). Thus, the study's findings suggest that ESe application affects soil and tea quality by modulating the low-abundance taxa in soil. The study also highlights the crucial role of low-abundance bacterial taxa of the rhizosphere in regulating soil functions under the ESe application.

Unraveling the spatial-temporal distribution patterns of soil abundant and rare bacterial communities in China's subtropical mountain forest

Introduction

The pivotal roles of both abundant and rare bacteria in ecosystem function are widely acknowledged. Despite this, the diversity elevational patterns of these two bacterial taxa in different seasons and influencing factors remains underexplored, especially in the case of rare bacteria.

Methods

Here, a metabarcoding approach was employed to investigate elevational patterns of these two bacterial communities in different seasons and tested the roles of soil physico-chemical properties in structuring these abundant and rare bacterial community.

Results and discussion

Our findings revealed that variation in elevation and season exerted notably effects on the rare bacterial diversity. Despite the reactions of abundant and rare communities to the elevational gradient exhibited similarities during both summer and winter, distinct elevational patterns were observed in their respective diversity. Specifically, abundant bacterial diversity exhibited a roughly U-shaped pattern along the elevation gradient, while rare bacterial diversity increased with the elevational gradient. Soil moisture and N:P were the dominant factor leading to the pronounced divergence in elevational distributions in summer. Soil temperature and pH were the key factors in winter. The network analysis revealed the bacteria are better able to adapt to environmental fluctuations during the summer season. Additionally, compared to abundant bacteria, the taxonomy of rare bacteria displayed a higher degree of complexity. Our discovery contributes to advancing our comprehension of intricate dynamic diversity patterns in abundant and rare bacteria in the context of environmental gradients and seasonal fluctuations.

Intermediate irrigation with low fertilization promotes soil nutrient cycling and reduces CO2 and CH4 emissions via regulating fungal communities in arid agroecosystems

The field practices, including irrigation and fertilization, strongly affect greenhouse gas emissions and soil nutrient cycling from agriculture. Understanding the underlying mechanism of greenhouse gas emissions, soil nutrient cycling, and their impact factors (fungal diversity, network characteristics, soil pH, salt, and moisture) is essential for efficiently managing global greenhouse gas mitigation and agricultural production. By considering abundant and rare taxa, we determine the identities and relative importance of ecological processes that modulate the fungal communities and identify whether they are crucial contributors to soil nutrient cycling and greenhouse gas emissions. The research is based on a 4-year field fertigation experiment with low (300 kg/ha P2O5 with 150 kg/ha urea) and high (600 kg/ha P2O5 with 300 kg/ha urea) fertilization level and three irrigation levels, that is, low (200 mm), medium (300 mm), and high (400 mm). The α-diversity (richness and Shannon index) of fungal subcommunities was significantly higher under medium irrigation (300 mm) and low fertilization (300 kg/ha P2O5 with 150 kg/ha urea) than under other treatments. Intermediate irrigation with low fertilization treatment yielded the most significant higher multinutrient cycling index and the lowest CO2 and CH4 emissions. The null model indicated that abundant taxa are mainly regulated by stochastic processes (dispersal limitation), and rare taxa are mainly regulated by environmental selection, especially by soil salinity. The co-occurrence network of rare taxa explained the changes in the entire fungal network stability. The abundant taxa played vital roles in regulating soil nutrient status, owing to the stronger association between their network and multinutrient cycling index. Furthermore, we have confirmed that soil moisture and fungal network stability are crucial factors affecting greenhouse gas emissions. Together, these results provide a deep understanding of the mechanisms that reveal fungal community assembly and soil fungal-driven variations in nutrient status and network stability, link fungal network characteristics to ecosystem functions, and reveal the factors that influence greenhouse gas emissions.

Soil rare microorganisms mediated the plant cadmium uptake: The central role of protists

Plants and microorganisms symbiotically mediate and/or catalyse the turnover of elements in rhizosphere soils, thus directly influencing the effectiveness of phytoremediation in addressing heavy metal contamination. Soil rare microbial communities are diverse but not well understood in terms of their importance for phytoremediation. In this study, we simulated the loss of rare microorganisms through dilution-to-extinction approach, and investigated the effects on integrated rhizosphere microbiome with soil microcosm experiments, including bacteria, fungi, protists, and microfauna. Additionally, we explored the implications for ryegrass (Lolium multiflorum Lam.) growth and its uptake of Cd (cadmium). Compared with the undiluted group, ryegrass exhibited a significant decrease in Cd uptake ranging from 52.34 % to 73.71 % in the rare species-loss soils, indicating a lack of functional redundancy in rhizosphere soil microbial community following rare species loss. Interestingly, these soils displayed a remarkable 1.79-fold increase in plant biomass and a 41.02 % increase in plant height. By sequencing the 16S, 18S, and ITS rRNA gene amplicons of rhizosphere microbes, we found that soil rare species loss decreased the rhizosphere microbial α-diversity, changed the community structures, and shifted the functional potential. Protists were particularly affected. Through the analysis of species co-occurrence networks, along with the partial least squares path modeling, we found that the diversity of protists and bacteria and the co-occurring network connectivity of protists and fungi contributed most to plant Cd uptake and growth. These results highlighted the potential significance of rare microorganisms, particularly protists, in phytoextraction of Cd-contaminated soils, owing to their central role in the microbial food web.

Dominant role of rare bacterial taxa rather than abundant taxa in driving the tailing primary succession

Primary ecological succession is imperative for tailing vegetation, driven notably by microbes that enhance tailing nutrient status. Yet, the roles of abundant and rare taxa in tailing primary succession remain underexplored. This study investigates these subcommunities across three succession stages (i.e., original tailing, biological crusts, grasslands). Throughout primary succession, alpha diversity and functional gene abundances of the rare taxa (RT) group consistently rise from bare tailings to grasslands. Conversely, the abundant taxa (AT) group displays an opposing trend. Intriguingly, employing co-occurrence networks, keystone taxa, mantel tests, similarity percentage analysis, and structural equation model, the study uncovers that RT wields a more pivotal role than AT in driving tailing primary succession. Community assembly analysis reveals stochastic control of AT and deterministic control of RT. Additionally, primary succession reinforces stochastic processes in AT, while RT's deterministic process remains unaffected. By unveiling these dynamics, the research enriches our understanding of primary ecological succession in tailings. Recognition of unique diversity patterns and community assembly mechanisms for rare and abundant subcommunities advances tailing ecosystem comprehension and informs ecological restoration strategies. This study thus contributes valuable insights to the complex interplay of microbial taxa during tailing primary succession.

Land management shapes drought responses of dominant soil microbial taxa across grasslands

Soil microbial communities are dominated by a relatively small number of taxa that may play outsized roles in ecosystem functioning, yet little is known about their capacities to resist and recover from climate extremes such as drought, or how environmental context mediates those responses. Here, we imposed an in situ experimental drought across 30 diverse UK grassland sites with contrasting management intensities and found that: (1) the majority of dominant bacterial (85%) and fungal (89%) taxa exhibit resistant or opportunistic drought strategies, possibly contributing to their ubiquity and dominance across sites; and (2) intensive grassland management decreases the proportion of drought-sensitive and non-resilient dominant bacteria-likely via alleviation of nutrient limitation and pH-related stress under fertilisation and liming-but has the opposite impact on dominant fungi. Our results suggest a potential mechanism by which intensive management promotes bacteria over fungi under drought with implications for soil functioning.

Risk characteristics of resistome coalescence in irrigated soils and effect of natural storage of irrigation materials on risk mitigation

Irrigation and fertilization are the routinely agricultural practices but also cause resistome coalescence, by which the entire microbiomes from irrigation materials invade soil microbial community, to transfer antibiotic resistance genes (ARGs) in the coalesced soils. Although studies have reported the effect of irrigation or fertilization on the prevalence and spread of ARGs in soils, risk characteristics of resistome coalescence in irrigation system remain to be demonstrated and few has shown whether natural storage of irrigation materials will reduce resistance risks. To fill the gaps, two microscopic experiments were conducted for deeply exploring resistance risks in the soils irrigated with wastewater and manure fertilizer from a perspective of community coalescence by metagenomic analysis, and to reveal the effect of natural storage of irrigation materials on the reduction of resistance risks in the coalesced soils. Results showed irrigation and coalescence significantly increased the abundance and diversity of ARGs in the soils, and introduced some emerging resistance genes into the coalesced community, including mcr-type, tetX, qacB, and an array of genes conferring resistance to carbapenem. Procrustes analysis demonstrated microbial community was significantly correlated with the ARGs in coalesced soils, and variance partitioning analysis quantified its dominant role on shaping resistome profile in the environment. Besides ARGs, abundant and diverse mobile genetic elements (MGEs) were also identified in the coalesced soils and co-existed on the ARG-carrying contigs, implying potential transfer risk of ARGs in the irrigation system. Further, the analysis of metagenome-assembled genomes (MAGs) confirmed the risk by recovering 358 ARGs-carrying MAGs and identifying the resistant bacteria that co-carried multiple ARGs and MGEs. As expected, the natural storage of irrigation water and manure fertilizer reduced about 27%-54% of ARGs, MGEs and virulence factors in the coalesced soils, thus caused the soils to move towards lower resistance risks to a certain extent.

Regulatory mechanisms of submerged macrophyte on bacterial community recovery in decabromodiphenyl ether contaminated sediment: Microbiological and metabolomic perspectives

Polybrominated diphenyl ether contamination in sediments poses serious threats to human health and ecological safety. Despite the broad application of submerged macrophytes for remediating pollutants, their regulatory influence on bacterial communities in contaminated sediments remains unclear. Herein, we analyzed the effects of decabromodiphenyl ether (BDE-209) and Hydrilla verticillata on sediment bacterial community and function using 16S rRNA gene sequencing and sediment metabolomics. Results showed that BDE-209 significantly inhibited sediment bacterial diversity and metabolic functions. It also enhanced bacterial interactions and altered both the bacterial community and metabolite composition. Uridine and inosine were critical metabolites that positively co-occurred with bacterial taxa inhibited by BDE-209. Notably, planting H. verticillata effectively alleviated the adverse impacts of BDE-209 by reducing its residuals, increasing the total organic carbon, and modifying metabolic profiles. Such mitigation was evidenced by enhancing bacterial diversity, restoring metabolic functions, and attenuating bacterial interactions. However, mitigation effectiveness depended on treatment time. Additionally, propionic acid, palmitic acid, and palmitoleic acid may facilitate the restoration of phylum Proteobacteria and class Planctomycetacia in H. verticillata planted sediment. Together, these findings improve understanding of BDE-209's impacts on aquatic ecosystems and provide valuable insights for ecological restoration using submerged macrophytes.

Exposure to three herbicide mixtures influenced maize root-associated microbial community structure, function and the network complexity

Herbicide mixtures are a new and effective agricultural strategy for managing suppress weed resistance and have been widely used in controlling weeding growth in maize fields. However, the potential ecotoxicological impact of these mixtures on the microbial community structure and function within various root-associated niches, remains inadequately understood. Here, the effects of nicosulfuron, mesotrione and atrazine on soil enzyme activity and microbial community structure and function were investigated when applied alone and in combination. The findings indicated that herbicide mixtures exhibit a prolonged half-life compared to single herbicides. Ecological niches are the major factor influencing the structure and functions of the microbial community, with the rhizosphere exhibiting a more intensive response to herbicide stress. Herbicides significantly inhibited the activities of soil functional enzymes, including dehydrogenase, urease and sucrose in the short-term. Single herbicide did not drastically influence the alpha or beta diversity of the soil bacterial community, but herbicide mixtures significantly increased the richness of the fungal community. Meanwhile, the key functional microbial populations, such as Pseudomonas and Enterobacteriaceae, were significantly altered by herbicide stress. Both individual and combined use of the three herbicides reduced the complexity and stability of the bacterial network but increased the interspecific cooperations of fungal community in the rhizosphere. Moreover, by quantification of residual herbicide concentrations in the soil, we showed that the degradation period of the herbicide mixture was longer than that of single herbicides. Herbicide mixtures increased the contents of NO3--N and NH4+-N in the soil in the short-term. Overall, our study provided a comprehensive insight into the response of maize root-associated microbial communities to herbicide mixtures and facilitated the assessment of the ecological risks posed by herbicide mixtures to the agricultural environment from an agricultural sustainability perspective.

Distinct responses of airborne abundant and rare microbial communities to atmospheric changes associated with Chinese New Year

Airborne microorganisms, including pathogens, would change with surrounding environments and become issues of global concern due to their threats to human health. Microbial communities typically contain a few abundant but many rare species. However, how the airborne abundant and rare microbial communities respond to environmental changes is still unclear, especially at hour scale. Here, we used a sequencing approach based on bacterial 16S rRNA genes and fungal ITS2 regions to investigate the high time-resolved dynamics of airborne bacteria and fungi and to explore the responses of abundant and rare microbes to the atmospheric changes. Our results showed that air pollutants and microbial communities were significantly affected by human activities related to the Chinese New Year (CNY). Before CNY, significant hour-scale changes in both abundant and rare subcommunities were observed, while only abundant bacterial subcommunity changed with hour time series during CNY. Air pollutants and meteorological parameters explained 61.5%-74.2% variations of abundant community but only 13.3%-21.6% variations of rare communities. These results suggested that abundant species were more sensitive to environmental changes than rare taxa. Stochastic processes predominated in the assembly of abundant communities, but deterministic processes determined the assembly of rare communities. Potential bacterial pathogens during CNY were the highest, suggesting an increased health risk of airborne microbes during CNY. Overall, our findings highlighted the "holiday effect" of CNY on airborne microbes and expanded the current understanding of the ecological mechanisms and health risks of microbes in a changing atmosphere.

Elevational characteristics of soil bacterial community and their responses to soil translocation at a mountainside in northwest Sichuan, China

How the soil bacterial communities vary with elevation is context-dependent, and the effect of soil translocation between elevations on bacterial community structure and metabolic function was not fully understood yet. Here, the bacterial community composition and diversity at five elevations along a 1600-3000 m elevation gradient on a mountainside in northwest Sichuan were characterized, and the responses of soil bacterial community to simulated climate changes were further studied by soil translocation reciprocally at three elevations for 12 months. Significant differences were found in soil temperature and moisture at different elevations, but there was no observed change in bacterial alpha diversity. The relative abundance of bacterial phyla was significantly different among the five elevations except for Proteobacteria (the dominant bacterial phyla in five elevation), and most bacterial phyla correlated with soil temperature, moisture, pH and soil bulk density. The direct effect of soil properties (pH, soil nutrients and soil bulk density) on soil bacterial community was stronger than the direct effect of temperature and moisture. Soil translocation changed the relative abundance of some bacterial phyla, and taxonomic groups with significant changes were mainly non-dominant phyla rather than the dominant phyla. Metabolism was the primary function of bacterial community at all elevations, which accounted for ~ 80% of relative abundance, and soil translocation had little effect on metabolic function. These findings indicated that soil bacterial dominant taxa and soil bacterial metabolic functions are relatively stable, which contribute to the stability of the ecosystem when response to the climate change in the future.

Long-term effects on liver metabolism induced by ceftriaxone sodium pretreatment

Ceftriaxone is an emerging contaminant due to its potential harm, while its effects on liver are still need to be clarified. In this study, we first pretreated the 8-week-old C57BL/6J mice with high dose ceftriaxone sodium (Cef, 400 mg/mL, 0.2 mL per dose) for 8 days to prepare a gut dysbiosis model, then treated with normal feed for a two-month recovery period, and applied non-targeted metabolomics (including lipidomics) to investigate the variations of fecal and liver metabolome, and coupled with targeted determination of fecal short-chain fatty acids (SCFAs) and bile acids (BAs). Lastly, the correlations and mediation analysis between the liver metabolism and gut metabolism/microbes were carried, and the potential mechanisms of the mal-effects on gut-liver axis induced by Cef pretreatment were accordingly discussed. Compared to the control group, Cef pretreatment reduced the rate of weight gain and hepatosomatic index, induced bile duct epithelial cells proliferated around the central vein and appearance of binucleated hepatocytes, decreased the ratio of total branching chains amino acids (BCAAs) to total aromatic amino acids (AAAs) in liver metabolome. In fecal metabolome, the total fecal SCFAs and BAs did not change significantly while butyric acid decreased and the primary BAs increased after Cef pretreatment. Correlation and mediation analysis revealed one potential mechanism that Cef may first change the intestinal microbiota (such as destroying its normal structure, reducing its abundance and the stability of the microbial network or certain microbe abundance like Alistipes), and then change the intestinal metabolism (such as acetate, caproate, propionate), leading to liver metabolic disorder (such as spermidine, inosine, cinnamaldehyde). This study proved the possibility of Cef-induced liver damage, displayed the overall metabolic profile of the liver following Cef pretreatment and provided a theoretical framework for further research into the mechanism of Cef-induced liver damage.

Distinct assembly processes and environmental adaptation of abundant and rare archaea in Arctic marine sediments

Revealing the ecological processes and environmental adaptation of abundant and rare archaea is a central, but poorly understood, topic in ecology. Here, abundant and rare archaeal diversity, community assembly processes and co-occurrence patterns were comparatively analyzed in Arctic marine sediments. Our findings revealed that the rare taxa exhibited significantly higher diversity compared to the abundant taxa. Additionally, the abundant taxa displayed stronger environmental adaptation than the rare taxa. The co-occurrence network analysis demonstrated that the rare taxa developed more interspecies interactions and modules in response to environmental disturbance. Furthermore, the community assembly of abundant and rare taxa in sediments was primarily controlled by stochastic and deterministic processes, respectively. These findings provide valuable insights into the archaeal community assembly processes and significantly contribute to a deeper understanding of the environmental adaptability of abundant and rare taxa in Arctic marine sediments.

16S rDNA Sequencing-Based Insights into the Bacterial Community Structure and Function in Co-Existing Soil and Coal Gangue

Coal gangue is a solid waste emitted during coal production. Coal gangue is deployed adjacent to mining land and has characteristics similar to those of the soils of these areas. Coal gangue-soil ecosystems provide habitats for a rich and active bacterial community. However, co-existence networks and the functionality of soil and coal gangue bacterial communities have not been studied. Here, we performed Illumina MiSeq high-throughput sequencing, symbiotic network and statistical analyses, and microbial phenotype prediction to study the microbial community in coal gangue and soil samples from Shanxi Province, China. In general, the structural difference between the bacterial communities in coal gangue and soil was large, indicating that interactions between soil and coal gangue are limited but not absent. The bacterial community exhibited a significant symbiosis network in soil and coal gangue. The co-occurrence network was primarily formed by Proteobacteria, Firmicutes, and Actinobacteria. In addition, BugBase microbiome phenotype predictions and PICRUSt bacterial functional potential predictions showed that transcription regulators represented the highest functional category of symbiotic bacteria in soil and coal gangue. Proteobacteria played an important role in various processes such as mobile element pathogenicity, oxidative stress tolerance, and biofilm formation. In general, this work provides a theoretical basis and data support for the in situ remediation of acidified coal gangue hills based on microbiological methods.

Significant roles of core prokaryotic microbiota across soil profiles in an organic contaminated site: Insight into microbial assemblage, co-occurrence patterns, and potentially key ecological functions

Extreme environmental disturbances induced by organic contaminated sites impose serious impacts on soil microbiomes. However, our understanding of the responses of the core microbiota and its ecological roles in organic contaminated sites is limited. In this study, we took a typical organic contaminated site as an example and investigated the composition and structure, assembly mechanisms of core taxa and their roles in key ecological functions across soil profiles. Results presented that core microbiota with a considerably lower number of species (7.93%) than occasional taxa presented comparatively high relative abundances (38.04%) yet, which was mainly comprised of phyla Proteobacteria (49.21%), Actinobacteria (12.36%), Chloroflexi (10.63%), and Firmicutes (8.21%). Furthermore, core microbiota was more influenced by geographical differentiation than environmental filtering, which possessed broader niche widths and stronger phylogenetic signals for ecological preferences than occasional taxa. Null modelling suggested that stochastic processes dominated the assembly of the core taxa and maintained a stable proportion along soil depths. Core microbiota had a greater impact on microbial community stability and possessed higher functional redundancy than occasional taxa. Additionally, the structural equation model illustrated that core taxa played pivotal roles in degrading organic contaminants and maintaining key biogeochemical cycles potentially. Overall, this study deepens our knowledge of the ecology of core microbiota under complicated environmental conditions in organic contaminated sites, and provides a fundamental basis for preserving and potentially utilizing core microbiota to maintain soil health.

Potential long consequences from internal and external ecology: loss of gut microbiota antifragility in children from an industrialized population compared with an indigenous rural lifestyle

Human health is strongly mediated by the gut microbiota ecosystem, which, in turn, depends not only on its state but also on its dynamics and how it responds to perturbations. Healthy microbiota ecosystems tend to be in criticality and antifragile dynamics corresponding to a maximum complexity configuration, which may be assessed with information and network theory analysis. Under this complex system perspective, we used a new analysis of published data to show that a children's population with an industrialized urban lifestyle from Mexico City exhibits informational and network characteristics similar to parasitized children from a rural indigenous population in the remote mountainous region of Guerrero, México. We propose then, that in this critical age for gut microbiota maturation, the industrialized urban lifestyle could be thought of as an external perturbation to the gut microbiota ecosystem, and we show that it produces a similar loss in criticality/antifragility as the one observed by internal perturbation due to parasitosis by the helminth A. lumbricoides. Finally, several general complexity-based guidelines to prevent or restore gut ecosystem antifragility are discussed.

Microplastics drive microbial assembly, their interactions, and metagenomic functions in two soils with distinct pH and heavy metal availability

Microplastics (MPs) have emerged as widely existing global environmental concerns in terrestrial ecosystems. However, the mechanisms that how MPs are affecting soil microbes and their metagenomic functioning is currently uncertain. Herein, we investigated the response mechanisms of bacterial and fungal communities as well as the metagenomic functions to the addition of MPs in two soils with distinct pH and heavy metals. In this study, the acidic soil (Xintong) and the neutral soil (Huanshan) contaminated by heavy metals were incubated with Polyvinyl Chloride (PVC) MPs at ratios of 2.5% and 5% on 60 and 120 days. We aimed to evaluate the responding, assembly, and interactions of the metagenomic taxonomy and function. Results showed that only in the acidic soil, PVC MPs significantly increased soil pH and decreased CaCl₂-extractable heavy metals, and also reduced bacterial alpha diversity and interaction networks. The relative proportions of Proteobacteria and Bacteroidota in bacteria, and Mortierellomycota in fungi, were increased, but Chloroflexi and Acidobacteriota in bacteria, Ascomycota and Basidiomycota in fungi, were significantly decreased by PVC MPs. Metagenomic functions related to C cycling were repressed but the nutrient cycles were enriched with PVC MPs. In conclusion, our study suggests that the addition of PVC MPs could shift soil microbial community and metagenomic functioning, as well as increasing soil pH and reduced heavy metal availability.

Controls on diversity of core and indicative microbial subcommunities in Tibetan Plateau grassland soils

Core subcommunity represents the less diversity but high abundance, while indicative subcommunity is highly diverse but low abundance in soils. The core subcommunity fundamentally maintains ecosystem stability, while the indicative plays important roles in vital ecosystem functions and is more sensitive to environmental change. However, their environmental driving factors and responses to human disturbances remain less defined. Herein, we explored the patterns of core and indicative soil microbes and their responses to animal grazing in dry grasslands across the Tibetan Plateau, using the Illumina sequencing of 16S rRNA gene. The results revealed that the core subcommunity diversity and richness were lower than the indicative in soils. The indicative subcommunity diversity exhibited substantially stronger correlations with nutrient-associated factors than the core diversity, including soil organic carbon, nitrogen, and plant biomass. The core and indicative microbial subcommunities both strongly varied with grassland ecosystems, while the latter was also significantly influenced by grazing. The variation partitioning analysis revealed that indicative microbial subcommunity was explained less by environmental factors than core subcommunity (34.5% vs 73.0%), but more influenced by grazing (2.6% vs 0.1%). Our findings demonstrated that the indicative microbes were particularly sensitive to soil nutrient-associated factors and human disturbances in alpine dry grasslands.

Assessing the efficacy of bleaching powder in disinfecting marine water: Insights from the rapid recovery of microbiomes

Single-bleaching powder disinfection is a highly prevalent practice to disinfect source water for marine aquaculture to prevent diseases. However, due to the decay of active chlorine and the presence of disinfectant resistance bacteria (DRB), the effects of bleaching powder on prokaryotic community compositions (PCCs) and function in marine water remain unknown. In the present study, the source water in a canvas pond was treated with the normal dose of bleaching powder, and the impact on PCCs and functional profiles was investigated using 16S rRNA gene amplicon sequencing. The bleaching powder strongly altered the PCCs within 0.5 h, but they began to recover at 16 h, eventually achieving 76% similarity with the initial time at 72 h. This extremely rapid recovery was primarily driven by the decay of Bacillus and the regrowth of Pseudoalteromonas, both of which are DRB. Abundant community not only help PCCs recover but also provide larger functional redundancy than rare community. During the recovery of PCCs, stochastic processes drove the community assembly. After 72 h, five out of seven identified disinfectant resistance genes related to efflux pump systems were highly enriched, primarily in Staphylococcus and Bacillus. However, 15 out of the 16 identified antibiotic resistance genes (ARGs) remained unchanged compared to the initial time, indicating that bleaching powder does not contribute to ARGs removal. Overall, the findings demonstrate that single-bleaching powder disinfection cannot successfully meet the objective of disease prevention in marine aquaculture water due to the extremely rapid recovery of PCCs. Hence, secondary disinfection or novel disinfection strategies should be explored for source water disinfection.

Shifts of understory vegetation induced by thinning drive the expansion of soil rare fungi

The gap formation due to forest thinning regulates the understorey microclimate, ground vegetation, and soil biodiversity. However, little is known about abundant and rare taxa's various patterns and assemblage mechanisms under thinning gaps. Thinning gaps with increasing sizes (0, 74, 109, and 196 m2) were established 12 years ago in a 36-year-old spruce plantation in a temperate mountain climate. Soil fungal and bacterial communities were analyzed by MiSeq sequencing and related to soil physicochemical properties and aboveground vegetation. The functional microbial taxa were sorted by FAPROTAX and Fungi Functional Guild database. The bacterial community stabilized under varied thinning intensities and was not different from the control plots, whereas the richness of the rare fungal taxa was at least 1.5-fold higher in the large gaps than in the small ones. Total phosphorus and dissolved organic carbon were the main factors influencing microbial communities in soil under various thinning gaps. The diversity and richness of the entire fungal community and rare fungal taxa increased with the understorey vegetation coverage and shrub biomass after thinning. Gap formation by thinning stimulated the understorey vegetation, the rare saprotroph (Undefined Saprotroph), and mycorrhizal fungi (Ectomycorrhizal-Endophyte-Ericoid Mycorrhizal-Litter Saprotroph-Orchid Mycorrhizal and Bryophyte Parasite-Lichen Parasite-Ectomycorrhizal-Ericoid Mycorrhizal-Undefined Saprotroph), which may accelerate nutrient cycling in forest ecosystems. However, the abundance of Endophyte-Plant Pathogens increased by eight times, which showed the potential risk for the artificial spruce forests. Thus, fungi may be the driving force of forest restoration and nutrient cycling under the increasing intensity of thinning and may induce plant diseases. Therefore, vegetation coverage and microbial functional diversity should be considered to evaluate the sustainability of the artificial forest ecosystem and forest restoration.

Distinct distribution patterns and functional potentials of rare and abundant microorganisms between plastisphere and soils

The increasing application of plastic film has caused the "white pollution" of farmlands in greenhouses. To date, most studies on the ecology of the plastisphere have focused on the whole microbial community, with few on the rare and abundant taxa, especially in the terrestrial ecosystems. To understand the plastisphere rare and abundant taxa of bacterial and fungal communities, we collected residues of plastic film from plastic-covered soils in the greenhouse. The plastisphere was significantly different from surrounding soils in terms of alpha- and beta-diversities of abundant and rare taxa. Such discrepancies were greater in rare taxa than in abundant taxa. Besides, the enrichment of soil-borne plant pathogenic fungi in the plastisphere implied that plastic film residues can act as vectors for pathogen transmission. In the plastisphere, the stochastic process governed the assemblies of rare taxa, while deterministic assemblies dominated that of abundant taxa. However, in surrounding soils, the stochastic process played a larger role in abundant taxa as compared to rare taxa. The plastisphere showed a network of less complexity, more competitive connections, and more modules compared to surrounding soils, and rare taxa played greater roles than abundant taxa. There existed obvious discrepancies in the microbial functions between surrounding soils and plastisphere, including carbon, sulfur, nitrogen, and phosphorus cycling, and rare taxa contribute large proportions to the above cycling processes. Altogether, the findings advance our understanding of ecological mechanisms of abundant and rare taxa in the plastisphere in terrestrial ecosystems.

Deciphering the distinct successional patterns and potential roles of abundant and rare microbial taxa of urban riverine plastisphere

Microbial colonization on microplastics has provoked global concern; however, many studies have not considered the successional patterns and potential roles of abundant and rare taxa of the plastisphere during colonization. Hence, we investigate the taxonomic composition, assembly, interaction and function of abundant and rare taxa in the riverine plastisphere by conducting microcosm experiments. Results showed that rare taxa occupied significantly high community diversity and niche breadth than the abundant taxa, which implies that rare taxa are essential components in maintaining the community stability of the plastisphere. However, the abundant taxa played a major role in driving the succession of plastisphere communities during colonization. Both stochastic and deterministic processes signally affected the plastisphere community assemblies; while, the deterministic patterns (heterogeneous selection) were especially pronounced for rare biospheres. Plastisphere microbial networks were shaped by the enhancement of network modularity and reinforcement of positive interactions. Rare taxa played critical roles in shaping stable plastisphere by occupying the key status in microbial networks. The strong interaction of rare and non-rare taxa suggested that multi-species collaboration might be conducive to the formation and stability of the plastisphere. Both abundant and rare taxa were enriched with plentiful functional genes related to carbon, nitrogen, phosphorus and sulfur cycling; however, their potential metabolic functions were significantly discrepant, implying that the abundant and rare microbes may play different roles in ecosystems. Overall, this study strengthens our comprehending of the mechanisms regarding the formation and maintenance of the plastisphere.

Weak environmental adaptation of rare phylotypes sustaining soil multi-element cycles in response to decades-long fertilization

Deciphering the ecological role of soil communities in the maintenance of multiple ecosystem functions is pivotal for the conservation and sustainability of soil biodiversity. However, few studies have investigated niche differentiation of abundant and rare microbiota, as well as their contributions to multiple soil elemental cycles, particularly in agroecosystems that have received decades of intense fertilization. Here, we characterized the environmental thresholds and phylogenetic signals for the environmental adaptation of both abundant and rare microbial subcommunities via amplicon sequencing and metagenomic sequencing and explored their importance in sustaining soil multiple nutrient cycling in agricultural fields that were fertilized for two decades. The results showed that rare taxa exhibited narrower niche breadths and weaker phylogenetic signals than abundant species. The assembly of abundant subcommunity was shaped predominantly by dispersal limitation (explained 71.1 % of the variation in bacteria) and undominated processes (explained 75 % of the variation in fungi), whereas the assembly of rare subcommunity was dominated by homogeneous selection process (explained 100 % of the variation in bacteria and 60 % of the variation in fungi). Soil ammonia nitrogen was the leading factor mediating the balance between stochastic and deterministic processes in both abundant (R² = 0.15, P < 0.001) and rare (R² = 0.08, P < 0.001) bacterial communities. Notably, the rare biosphere largely contributed to key soil processes such as carbon (R²_bacteria = 0.03, P < 0.05; R²_fungi = 0.05, P < 0.05) and nitrogen (R²_bacteria = 0.03, P < 0.05; R²_fungi = 0.17, P < 0.001) cycling. Collectively, these findings facilitate our understanding of the maintenance of rhizosphere bacterial and fungal diversity in response to agricultural fertilization and highlight the key role of rare taxa in sustaining agricultural ecosystem functions.

Core root-associated prokaryotic community and its relationship to host traits across wheat varieties

The root-associated microbiomes play important roles in plant growth. However, it is largely unknown how wheat variety evolutionary relatedness shapes each subcommunity in the root microbiome and, in turn, how these microbes affect wheat yield and quality. Here we studied the prokaryotic communities associated with the rhizosphere and root endosphere in 95 wheat varieties at regreening and heading stages. The results indicated that the less diverse but abundant core prokaryotic taxa occurred among all varieties. Among these core taxa, we identified 49 and 108 heritable amplicon sequence variants, whose variations in relative abundances across the root endosphere and rhizosphere samples were significantly affected by wheat variety. The significant correlations between phylogenetic distance of wheat varieties and prokaryotic community dissimilarity were only observed in non-core and abundant subcommunities in the endosphere samples. Again, wheat yield was only significantly associated with root endosphere microbiota at the heading stage. Additionally, wheat yield could be predicted using the total abundance of 94 prokaryotic taxa as an indicator. Our results demonstrated that the prokaryotic communities in the root endosphere had higher correlations with wheat yield and quality than those in the rhizosphere; thus, managing root endosphere microbiota, especially core taxa, through agronomic practices and crop breeding, is important for promoting wheat yield and quality.

Abundant fungi dominate the complexity of microbial networks in soil of contaminated site: High-precision community analysis by full-length sequencing

During the past decade, the characterization of microbial community in soil of contaminated sites was primarily done by high-throughput short-read amplicon sequencing. However, due to the similarity of 16S rRNA and ITS genes amplicon sequences, the short-read approach often limits the microbial composition analysis at the species level. Here, we simultaneously performed full-length and short-read amplicon sequencing to clarify the community composition and ecological status of different microbial taxa in contaminated soil from a high-resolution perspective. We found that (1) full-length 16S rRNA gene sequencing gave better resolution for bacterial identification at all levels, while there were no significant differences between the two sequencing platforms for fungal identification in some samples. (2) Abundant taxa were vital for microbial co-occurrences network constructed by both full-length and short-read sequencing data, and abundant fungal species such as Mortierella alpine, Fusarium solani, Mrakia frigida, and Chaetomium homopilatum served as the keystone species. (3) Heavy metal correlated with the microbial community significantly, and bacterial community and its abundant taxa were assembled by deterministic process, while the other taxa were dominated by stochastic process. These findings contribute to the understanding of the ecological mechanisms and microbial interactions in site soil ecosystems and demonstrate that full-length sequencing has the potential to provide more details of microbial community.

Distinct Responses of Abundant and Rare Soil Bacteria to Nitrogen Addition in Tropical Forest Soils

Soil microbial responses to anthropogenic nitrogen (N) enrichment at the overall community level has been extensively studied. However, the responses of community dynamics and assembly processes of the abundant versus rare bacterial taxa to N enrichment have rarely been assessed. Here, we present a study in which the effects of short- (2 years) and long-term (13 years) N additions to two nearby tropical forest sites on abundant and rare soil bacterial community composition and assembly were documented. The N addition, particularly in the long-term experiment, significantly decreased the bacterial α-diversity and shifted the community composition toward copiotrophic and N-sensitive species. The α-diversity and community composition of the rare taxa were more affected, and they were more closely clustered phylogenetically under N addition compared to the abundant taxa, suggesting the community assembly of the rare taxa was more governed by deterministic processes (e.g., environmental filtering). In contrast, the abundant taxa exhibited higher community abundance, broader environmental thresholds, and stronger phylogenetic signals under environmental changes than the rare taxa. Overall, these findings illustrate that the abundant and rare bacterial taxa respond distinctly to N addition in tropical forests, with higher sensitivity of the rare taxa, but potentially broader environmental acclimation of the abundant taxa. IMPORTANCE Atmospheric nitrogen (N) deposition is a worldwide environmental problem and threatens biodiversity and ecosystem functioning. Understanding the responses of community dynamics and assembly processes of abundant and rare soil bacterial taxa to anthropogenic N enrichment is vital for the management of N-polluted forest soils. Our sequence-based data revealed distinct responses in bacterial diversity, community composition, environmental acclimation, and assembly processes between abundant and rare taxa under N-addition soils in tropical forests. These findings provide new insight into the formation and maintenance of bacterial diversity and offer a way to better predict bacterial responses to the ongoing atmospheric N deposition in tropical forests.

Destabilized microbial networks with distinct performances of abundant and rare biospheres in maintaining networks under increasing salinity stress

Global changes such as seawater intrusion and freshwater resource salinization increase environmental stress imposed on the aquatic microbiome. A strong predictive understanding of the responses of the aquatic microbiome to environmental stress will help in coping with the "gray rhino" events in the environment, thereby contributing to an ecologically sustainable future. Considering that microbial ecological networks are tied to the stability of ecosystem functioning and that abundant and rare biospheres with different biogeographic patterns are important drivers of ecosystem functioning, the roles of abundant and rare biospheres in maintaining ecological networks need to be clarified. Here we showed that, with the increasing salinity stress induced by the freshwater-to-seawater transition, the microbial diversity reduced significantly and the taxonomic structure experienced a strong succession. The complexity and stability of microbial ecological networks were diminished by the increasing stress. The composition of the microorganisms supporting the networks underwent sharp turnovers during the freshwater-to-seawater transition, with the abundant biosphere behaving more robustly than the rare biosphere. Notably, the abundant biosphere played a much more important role than the rare biosphere in stabilizing ecological networks under low-stress environments, but the difference between their relative importance narrowed significantly with the increasing stress, suggesting that the environmental stress weakened the "Matthew effect" in the microbial world. With in-depth insights into the aquatic microbial ecology under stress, our findings highlight the importance of adjusting conservation strategies for the abundant and rare biospheres to maintain ecosystem functions and services in response to rising environmental stress.

Grass-microbial inter-domain ecological networks associated with alpine grassland productivity

Associations between grasses and soil microorganisms can strongly influence plant community structures. However, the associations between grass productivity and diversity and soil microbes, as well as the patterns of co-occurrence between grass and microbes remain unclear. Here, we surveyed grass productivity and diversity, determined soil physicochemical, and sequenced soil archaea, bacteria and fungi by metabarcoding technology at 16 alpine grasslands. Using the Distance-decay relationship, Inter-Domain Ecological Network (IDEN), and Mantel tests, we investigated the relationship between grass productivity, diversity and microbial diversity, and the patterns of co-occurrence between grass and microbial inter-domain network in alpine grassland. We found the archaea richness, bacteria richness and Shannon, and fungi α-diversity were significantly negatively correlation with grass diversity, but archaea and bacteria diversity were positively correlation with grass productivity. Moreover, an increase in microbial β-diversity was observed along with increased discrepancy in grass diversity and productivity and soil variables. Variance partitioning analysis suggested that the contribution of grass productivity on microbial community was higher than that of soil variables and grass diversity, which implies that microbial community was more related to grass productivity. Inter-Domain Ecological Network showed that the grass species formed complex and stable ecological networks with some bacterial, archaeal, and fungal species, and the grass-fungal ecological networks showed the highest robustness, which indicated that soil fungi could better co-coexist with aboveground grass in alpine grasslands. Besides, the connectivity degrees of the grass-microbial network were significantly positively correlated with grass productivity, suggesting that the coexistence pattern of grasses and microbes had a positive feedback effect on the grass productivity. The results are important for establishing the regulatory mechanisms between plants and microorganisms in alpine grassland ecosystems.

Cooperation of arbuscular mycorrhizal fungi and bacteria to facilitate the host plant growth dependent on soil pH

Almost all plants grow well in their native soils. We hypothesized that soil microbes promote the growth of their hosts in native soils by the example of soil pH. Here, bahiagrass (Paspalum notatum Flugge) indigenous to subtropical soils was grown in the native soil (the original pH = 4.85) or in pH-adjusted soils with sulfur (pH = 3.14 or 3.34) or calcium hydroxide (pH = 6.85, 8.34, 8.52 or 8.59). Plant growth, soil chemical property, and microbial community composition were characterized to reveal the microbial taxa promoting plant growth in the native soil. Results showed that shoot biomass was the highest in the native soil, while both the decrease and increase in the soil pH reduced the biomass. Compared with other soil chemical properties, soil pH was the top edaphic factor contributing to the differentiation in arbuscular mycorrhizal (AM) fungal and bacterial communities. The top 3 most abundant AM fungal OTUs belonged to Glomus, Claroideoglomus, and Gigaspora, while the top 3 most abundant bacterial OTUs belonged to Clostridiales, Sphingomonas, and Acidothermus, respectively. Regression analyses between microbial abundances and shoot biomass revealed that the most abundant Gigaspora sp. and Sphingomonas sp. were the most promotive fungal and bacterial OTUs, respectively. The application of these two isolates to bahiagrass solely or in combination indicated that Gigaspora sp. was more promotive than Sphingomonas sp. across the soil pH gradient, and they positively interacted to enhance biomass only in the native soil. We demonstrate that microbes cooperate to facilitate host plants to grow well in their native soils with the original pH. Meanwhile, a high-throughput sequencing-guided pipeline to efficiently screen for beneficial microbes is established.

Factors driving the halophyte rhizosphere bacterial communities in coastal salt marshes

Introduction

Root-associated microorganisms promote plant growth and provide protection from stresses. Halophytes are the fundamental components maintaining ecosystem functions of coastal salt marshes; however, it is not clear how their microbiome are structured across large spatial scales. Here, we investigated the rhizosphere bacterial communities of typical coastal halophyte species (Phragmites australis and Suaeda salsa) in temperate and subtropical salt marshes across 1,100 km in eastern China.

Methods

The sampling sites were located from 30.33 to 40.90°N and 119.24 to 121.79°E across east China. A total of 36 plots were investigated in the Liaohe River Estuary, the Yellow River Estuary, Yancheng, and Hangzhou Bay in August 2020. We collected shoot, root, and rhizosphere soil samples. the number of pakchoi leaves, total fresh and dry weight of the seedlings was counted. The soil properties, plant functional traits, the genome sequencing, and metabolomics assay were detected.

Results

The results showed that soil nutrients (total organic carbon, dissolved organic carbon, total nitrogen, soluble sugars, and organic acids) are high in the temperate marsh, while root exudates (measured by metabolite expressions) are significantly higher in the subtropical marsh. We observed higher bacterial alpha diversity, more complex network structure, and more negative connections in the temperate salt marsh, which suggested intense competition among bacterial groups. Variation partitioning analysis showed that climatic, edaphic, and root exudates had the greatest effects on the bacteria in the salt marsh, especially for abundant and moderate subcommunities. Random forest modeling further confirmed this but showed that plant species had a limited effect.

Conclutions

Taken together, the results of this study revealed soil properties (chemical properties) and root exudates (metabolites) had the greatest influence on the bacterial community of salt marsh, especially for abundant and moderate taxa. Our results provided novel insights into the biogeography of halophyte microbiome in coastal wetlands and can be beneficial for policymakers in decision-making on the management of coastal wetlands.

Effect of temperature variation on phosphorus flux at the sediment-water interface of the steppe wetlands

Environmental factors are generally considered to be important factors affecting the release process of phosphorus (P) in sediments. However, little is known about the effect of temperature increased at first and then decreased with the season change on the P flux rate and flux amount at the sediment-water interface in the steppe wetlands. The effects of the temperature variation on P flux at the sediment-water interface in the steppe wetlands during the vegetation growing season under simulated wetland habitat were studied. The results showed that the release of P from sediments to overlying water was greatly affected by temperature changes. When the temperature rose, P was released from the sediment into the overlying water, while P was precipitated from the water into the sediment with the temperature dropped. During simulation period, the total P in water flux rates between sediment and overlying water (FP) was ranged from - 4.51 to 4.99 mg·m^-2·day^-1, while the dissolved reactive P in water flux rates between sediment and overlying water (FDP) was changed from - 5.37 to 5.14 mg·m^-2·day^-1. The FP and FDP were negatively correlated with the content of total P in water (WTP), dissolved reactive P in water (WDRP), pH of sediment (pH), and microbial biomass P (MBP), but increased with temperature (T), aluminum phosphate (Al.P), and occluded phosphate (Oc.P). The P flux rates were affected by temperature variation both directly and indirectly; the mechanism of how temperature influenced the fate of P in the wetland is still not clear. Therefore, the physicochemical properties and kinetic, thermodynamic, and microbiology characteristics should be combined together to clarify the mechanism in future research.

How elevated nitrogen load affects bacterial community structure and nitrogen cycling services in coastal water

Nutrient pollution in the coastal environment has been accelerated by progressively intensifying aquaculture activities. Excessive nutrients can lead to coastal eutrophication with serious economic and ecological consequences. In this study, we studied coastal planktonic microbial community over a year to understand the aquaculture impact on coastal water quality and function. We observed increased total inorganic nitrogen concentrations in active fish farms to favor the diverse Alpha- and Gammaproteobacteria. Bacterial community alpha diversity in fish farms was positively correlated with total inorganic nitrogen, and active fish farming co-influenced the bacterial structural composition and regional beta diversity. By analyzing the nitrogen cycle-related functional compositions and pathways using PICRUSt2 prediction on inferred genomes, we identified the contribution of over 600 bacterial species to four major pathways. Enhanced nitrogen load in active fish farms was positively correlated with elevated dissimilatory nitrate reduction and denitrification pathway abundances. Fallowed fish farms were characterized by a predicted high abundance of nirA and narB genes contributing to assimilatory nitrate reduction pathway due to the prevalence of Cyanobacteria. Overall, these results suggested active operation and short hiatus in coastal aquaculture practices could rapidly impact planktonic bacterial communities and further influence nitrogen cycling and associated processes. These findings will improve the understanding of the responses and interactions between microbiome and aquaculture activities. In a world of increasing aquaculture demands, this work has important implications for sustainable water resource management and development.

Responses of abundant and rare prokaryotic taxa in a controlled organic contaminated site subjected to vertical pollution-induced disturbances

Soil microbiota as the key role mediates the natural attenuation process of organic contaminated sites, and therefore illuminating the mechanisms underlying the responses of abundant and rare species is essential for understanding ecological processes, maintaining ecosystem stability, and regulating natural attenuation well. Here, we explored the distributional characteristics, ecological diversities, and co-occurrence patterns of abundant and rare prokaryotic subcommunities using 16S rRNA high-throughput sequencing in vertical soil profiles of a controlled organic contaminated site. Results showed that abundant prokaryotic taxa were widespread across all soil samples, whereas rare counterparts were unbalancedly distributed. Rare subcommunity had more taxonomic groups and higher α- and β-diversities than abundant subcommunity. Both of these two subcommunities surviving in the organic polluted site possessed the potential of degrading organic contaminants. Abundant subcommunity was little affected by abiotic factors and mainly shaped by soil depth, while rare one was sensitive to environmental disturbances and presented a non-depth-dependent structure. Co-occurrence analysis revealed that rare taxa were more situated at the center of the network and more inclined to cooperate with non-abundant species than abundant taxa, which might play crucial roles in enhancing the resilience and resistance of prokaryotic community and maintaining its structure and stability. Overall, our results suggest that abundant and rare prokaryotic subcommunities present different responses to physicochemical factors and pollution characteristics along vertical soil profiles of organic contaminated sites undergoing natural attenuation.

The effects of g-C3N4/biochar and g-C3N4 on bacterial community in riverbed sediment

Biochar had been widely used to improve the activity of photocatalysts, the biochar-based photocatalysts had more potential for environmental pollution remediation, but their effect on the sediment remained unknown. To understand these, the typical photocatalyst g-C₃N₄ was modified by biochar to develop g-C₃N₄/biochar with enhanced photocatalytic ability. Riverbed sediment was exposed to g-C₃N₄ and g-C₃N₄/biochar respectively for 30 days, and Illumina sequencing was utilized to examine the changes in the bacterial community in the sediment. The results showed that in riverbed sediment, g-C₃N₄ exposure had a concentration-dependent effect on the diversity of bacteria, while g-C₃N₄/biochar exposure had a slight influence on the bacterial diversity and the diversity almost maintained stable with different g-C₃N₄/biochar concentration. The application of g-C₃N₄ exhibited an inhibition influence on the growth of Acidobacteria, Gemmatimonadetes, and Rokubacteria in sediment, whose relative abundance increased when g-C₃N₄ was 25 mg/kg, and then decreased when g-C₃N₄ beyond this concentration. The presence of g-C₃N₄/biochar increased the relative abundance of Cyanobacteria in sediment and showed no obvious impact on other dominant phyla. Both g-C₃N₄ and g-C₃N₄/biochar could alter the levels of TP, NN, and AN in the sediment, but the magnitude of the changes of these physicochemical factors caused by g-C₃N₄/biochar was much smaller than those caused by g-C₃N₄. In addition, the complexity of the bacterial community network was reduced in a high concentration of g-C₃N₄, while it remained stable with different concentrations of g-C₃N₄/biochar treatments. Totally, this study demonstrated that, compared to g-C₃N₄, g-C₃N₄/biochar was able to maintain the relative stability of the bacterial community in riverbed sediment and mitigate the negative effects of photocatalysts to some extent, making biochar an ecological remediation agent with great potential for application.

Response of microbiota to exogenous inoculation improved the enzymatic activities of medium-temperature Daqu

To explore the potential mechanism of improving enzymatic activities in medium-temperature Daqu (MTD) by inoculation functional isolates, we inoculated a single strain of Bacillus licheniformis, and the microbiota composed of Bacillus velezensis and Bacillus subtilis in MTD to investigate the association between the response of the functional microbiota and the enzymatic activity. The results showed that the bacterial community of MTD might be more sensitive to bioturbation than the fungal community, and the indigenous microbiota responded to the single strain more than to the microbiota. Moreover, the differential microorganisms mainly included Lactobacillales, Bacillales, and Saccharomycetales between the conventional and fortified samples. Notably, the composition of functional microbiota related to liquefying activity (LA) and saccharifying activity (SA) were significantly different, changing from Lactobacillus and Rhizomucor to Bacillus, Weissella, and Hyphopichia. That might be closely related to the effect of the bioturbation on LA (31.33%) and SA (43.54%) associated microorganisms was more tellingly. Furthermore, the relative abundance changes of bioturbation-sensitive modules in the co-occurrence network might also lead to the difference in enzymatic activities. Therefore, the LA and SA of MTD were improved by bioturbation significantly. These results provide diverse insights into the exogenous functional isolates to regulate the MTD microbiota and improve enzymatic activities.

Characteristics of soil carbon emissions and bacterial community composition in peatlands at different stages of vegetation succession

Microorganisms are important components of soil ecosystems and play an important role in material cycles. Northern peatlands are important ecosystems in middle-high latitude regions. In peatlands, different vegetation successions occur with changes in groundwater levels. The overall carbon emission of peat bogs is related to the carbon stability of the surrounding environment. Unraveling the assembly and distribution of bacterial communities at different succession stages in peatland is essential to understanding the soil nutrient cycle. In this study, we investigated the characteristics of soil carbon emissions and the composition of subsurface microorganisms under six different succession stages. The highest carbon emission was observed in mossy peatlands, and their soil enzyme activity was closely related to the aboveground vegetation cover type. The succession pattern of ground vegetation was the main driver of soil microorganisms. The abundance of the dominant Proteobacteria decreased with increasing soil depth, while the opposite trend was observed for Chloroflexi. Furthermore, the community structure of microorganisms became progressively simpler and looser as soil water content decreased. The bacterial alpha diversity was driven by soil dissolved organic carbon and Fe, and the beta diversity was driven mainly by soil water content. The bacteria presented a random distribution in a nutrient-rich soil environment and shifted to deterministic distribution with decreasing water and nutrient contents. The balance between taxonomic diversity and dispersal limitation mediates species coexistence in the soil microbiome. This study provides new insights into the soil environment at different stages of succession in peatlands.

Microbial mechanism of zinc fertilizer input on rice grain yield and zinc content of polished rice

Zinc is an essential minor element for rice growth and human health, which can also change the structure of the microorganisms. However, it remains unclear for the effects of zinc fertilizer on microbiome function in agricultural soils and crops. To solve this research gap, we investigated the relationship between improving rice (Oryza sativa L.) yield, Zn concentration, soil microbial community diversity, and function by the application of Zn fertilizer. The field trials included three rice varieties (Huanghuazhan, Nanjing9108, and Nuodao-9925) and two soil Zn levels (0 and 30 kg ha^-1) in Jiangsu province, China. As a test, we studied the variety of soil bacterial composition, diversity, and function using 16S rRNA gene sequencing. The results showed that soil Zn application reduced the diversity of microbial community, but the bacterial network was more closely linked, and the metabolic function of bacterial community was improved, which increased the grain yield (17.34-19.52%) and enriched the Zn content of polished rice (1.40-20.05%). Specifically, redundancy analysis (RDA) and Mantel's test results revealed soil total nitrogen (TN) was the primary driver that led to a community shift in the rice rhizosphere bacterial community, and soil organic carbon (SOC) was considered to have a strong influence on dominant phyla. Furthermore, network analysis indicated the most critical bacterial taxa were identified as Actinobacteria, Bacteroidetes, Proteobacteria, and Chloroflexi based on their topological roles of microorganisms. KEGG metabolic pathway prediction demonstrated that soil Zn application significantly (p < 0.05) improved lipid metabolism, amino acid metabolism, carbohydrate metabolism, and xenobiotic biodegradation. Overall, their positive effects were different among rice varieties, of which Nanjing-9108 (NJ9108) performed better. This study opens new avenues to deeply understand the plant and soil-microbe interactions by the application of fertilizer and further navigates the development of Zn-rich rice cultivation strategies.

Discrepancy strategies of sediment abundant and rare microbial communities in response to floating microplastic disturbances: Study using a microcosmic experiment

Floating microplastics (FMPs) in surface water have been extensively studied, but their influence on sedimentary microbial ecosystems is poorly understood. Here, we investigated response patterns of abundant and rare sedimentary microbes to FMP disturbances by performing microcosmic experiments using fluvial sediment with polyethylene (PE), polylactic acid (PLA), polystyrene (PS) and polyvinyl chloride (PVC) MPs. The results indicated that FMPs altered sediment microbial community diversity and composition. Some organic-degrading, nitrifying and denitrifying bacteria significantly decreased in response to FMP disturbances, which may affect the sediment carbon and nitrogen cycles. Rare taxa persisted under FMP disturbances, whereas abundant taxa were more susceptible to FMP disturbances, suggesting a higher sensitivity of abundant taxa to FMP disturbances. Although stochastic processes governed the assembly of the overall microbial communities, the assembly mechanisms of abundant and rare populations have significantly different responses to FMP interference. The relative contribution of deterministic processes was reinforced by enhanced homogenous selection in abundant populations, while it markedly decreased in rare populations under FMP disturbances. Furthermore, FMPs substantially decreased the network complexity, loosened the coexistence relationships, and increased the negative correlations. Rare species play an important role in reshaping complex microbial interactions and coexistence networks in response to FMP disturbances. This research broadens our perspectives for comprehensively evaluating the ecological effects of FMPs in the aquatic environment to formulate further policy controls.

Soil microbial distribution and assembly are related to vegetation biomass in the alpine permafrost regions of the Qinghai-Tibet Plateau

It is generally believed that there is a vegetation succession sequence from alpine marsh meadow to desert in the alpine ecosystem of the Qinghai-Tibet Plateau. However, we still have a limited understanding about distribution patterns and community assemblies of microorganisms' response to such vegetation changes. Hence, across a gradient represented by three types of alpine vegetation from swamp meadow to meadow to steppe, the soil bacterial, fungal and archaeal diversity was evaluated and then associated with their assembly processes, and glacier foreland vegetation was also surveyed as a case out of this gradient. Vegetation biomass was found to decrease significantly along the vegetation gradient. In contrast to irregular shifts in alpha diversity, bacterial and fungal beta diversities that were dominated by species replacement components (71.07-79.08%) significantly increased with the decreasing gradient in vegetation biomass (P < 0.05). These trends of increase were also found in the extent of stochastic bacterial and fungal assembly. Moreover, an increase in microbial beta diversity but a decrease in beta nearest taxon index were observed along with increased discrepancy in vegetation biomass (P < 0.001). Stepwise regression analyses and structural equation models suggested that vegetation biomass was the major variable that was related to microbial distribution and community assembly, and there might be associations between the dominance of species replacements and stochastic assembly. These findings enhanced our recognition of the relationship between vegetation and soil microorganisms and would facilitate the development of vegetation-microbe feedback models in alpine ecosystems.

How do inundation provoke the release of phosphorus in soil-originated sediment due to nitrogen reduction after reclaiming lake from polder

Different N and P fractions in microcosm incubation experiment was measured using high-resolution in-situ Peeper and DGT techniques combining with sequential extraction procedure. The results showed the synchronous desorption and release of PO₄^3-, S^2- and Fe²⁺ from the solid soil-originated sediment. This trend indicated that the significant reduction of Fe-P and SO₄^2- occurred in the pore water during the inundation. The concentrations of PO₄^3- in the overlying water and pore water increased to more than 0.1 and 0.2 mg/L at the beginning of the incubation experiment. Decreased NO₃^-concentrations from more than 1.5 mg/L to less than 0.5 mg/L combining with increasing NH₄⁺ concentrations from less than 1 mg/L to more than 5 mg/L suggested the remarkable NO₃^- reduction via dissimilatory nitrate reduction to ammonia (DNRA) pathway over time. High NH₄⁺ concentrations in the pore water aggravated the release of Fe²⁺ through reduction of Fe(III)-P as electric acceptors under anaerobic conditions. This process further stimulated the remarkable releasing of labile PO₄^3- from the solid phase to the solution and potential diffusion into overlying water. Additionally, high S^2- concentration at deeper layer indicated the reduction and releasing of S^2- from oxidation states, which can stimulated the NO₃^- reduction and the accumulation of NH₄⁺ in the pore water. This process can also provoke the reduction of Fe-P as electric acceptors following the release of labile PO₄^3- into pore water. Generally, inundation potentially facilitate the desorption of labile P and attention should be paid during the reclaiming lake from polder.

Characterization of the rare microbiome of rice paddy soil from arsenic contaminated hotspot of West Bengal and their interrelation with arsenic and other geochemical parameters

Rare microbial taxa [bacterial and archaeal operational taxonomic units (OTUs) with mean relative abundance ≤ 0.001%] were critical for ecosystem function, yet, their identity and function remained incompletely understood, particularly in arsenic (As) contaminated rice soils. In the present study we have characterized the rare populations of the As-contaminated rice soil microbiomes from West Bengal (India) in terms of their identity, interaction and potential function. Major proportion of the OTUs (73% of total 38,289 OTUs) was represented by rare microbial taxa (henceforth mentioned as rare taxa), which covered 4.5-15.7% of the different communities. Taxonomic assignment of the rare taxa showed their affiliation to members of Gamma-, Alpha-, Delta- Proteobacteria, Actinobacteria, and Acidobacteria. SO₄^2-, NO₃^-, NH₄⁺and pH significantly impacted the distribution of rare taxa. Rare taxa positively correlated with As were found to be more frequent in relatively high As soil while the rare taxa negatively correlated with As were found to be more frequent in relatively low As soil. Co-occurrence-network analysis indicated that rare taxa whose abundance were correlated strongly (R > 0.8) with As also had strong association (R > 0.8) with PO₄^2-, NO₃^-, and NH₄⁺. Correlation analysis indicated that the rare taxa were likely to involved in two major guilds one, involved in N-metabolism and the second involved in As/Fe as well as other metabolisms. Role of the rare taxa in denitrification and dissimilatory NO₃^- reduction (DNRA), As biotransformation, S-, H-, C- and Fe-, metabolism was highlighted from 16S rRNA gene-based predictive analysis. Phylogenetic analysis of rare taxa indicated signatures of inhabitant rice soil microorganisms having significant roles in nitrogen (N) cycle and As-Fe metabolism. This study provided critical insights into the taxonomic identity, metabolic potentials and importance of the rare taxa in As biotransformation and biogeochemical cycling of essential nutrients in As-impacted rice soils.

Plant invasion reconstructs soil microbial assembly and functionality in coastal salt marshes

Microbiologically driven ecosystem processes can be profoundly altered by alien plant invasions. The understanding of ecological mechanisms orchestrating different microbial constituents and their roles in emerging functional properties under plant invasions is limited. Here, we investigated soil microbial communities and functions using high-throughput amplicon sequencing and GeoChip technology, respectively, along a chronological gradient of smooth cordgrass invasion in salt marshes located in the Yellow River Estuary, China. We found a positive correlation between microbial diversity and the duration age of invasion, and both bacterial and fungal communities exerted orderly changes with invasion. Soil microbial metabolic potential, as indicated by the abundance of microbial functional genes involved in biogeochemical cycling, decreased in response to invasion. As a consequence, declined soil microbial metabolisms by plant invasion facilitated the carbon accumulation in invaded salt marshes. Bacteria and fungi exhibited distinct contributions to assembly processes along the invasion gradient: bacterial communities were mainly driven by selection and dispersal limitation, while fungi were dramatically shaped by stochastic processes. Soil microbial-mediated functions were taxon-specific, as indicated by community-function relationships. This study demonstrates the distinct contributions of microbial constituents to microbial community assembly and functions and sheds light on the implications of plant invasion on microbiologically driven ecosystem processes in coastal wetlands.

Fallow Land Enhances Carbon Sequestration in Glomalin and Soil Aggregates Through Regulating Diversity and Network Complexity of Arbuscular Mycorrhizal Fungi Under Climate Change in Relatively High-Latitude Regions

Soil aggregation and aggregate-associated carbon (C) play an essential function in soil health and C sequestration. Arbuscular mycorrhizal fungi (AMF) are considered to be primary soil aggregators due to the combined effect of extraradical hyphae and glomalin-related soil proteins (GRSPs). However, the effects of diversity and network complexity of AMF community on stability of soil aggregates and their associated C under long-term climate change (CC) and land-use conversion (LUC) in relatively high-latitude regions are largely unexplored. Therefore, an 8-year soil plot (with a 30-year cropping history) transplantation experiment was conducted to simulate CC and LUC from cropland to fallow land. The results showed that Glomus, Paraglomus, and Archaeospora were the most abundant genera. The diversity of AMF community in fallow land was higher than cropland and increased with increasing of mean annual temperature (MAT) and mean annual precipitation (MAP). Fallow land enhanced the network complexity of AMF community. The abundance families (Glomeraceae and Paraglomeraceae) exhibited higher values of topological features and were more often located in central ecological positions. Long-term fallow land had a significantly higher hyphal length density, GRSP, mean weight diameter (MWD), geometric mean diameter (GMD), and C concentration of GRSP (C-GRSP) than the cropland. The soil aggregate associated soil organic carbon (SOC) was 16.8, 18.6, and 13.8% higher under fallow land compared to that under cropland at HLJ, JL, and LN study sites, respectively. The structural equation model and random forest regression revealed that AMF diversity, network complexity, and their secreted GRSP mediate the effects of CC and LUC on C-GRSP and aggregate-associated SOC. This study elucidates the climate sensitivity of C within GRSP and soil aggregates which response symmetry to LUC and highlights the potential importance of AMF in C sequestration and climate change mitigation.

Differential Microbial Communities in Paddy Soils Between Guiyang Plateaus and Chengdu Basins Drive the Incidence of Rice Bacterial Diseases

Southwest China has the most complex rice-growing regions in China. With great differences in topography, consisting mainly of basins and plateaus, ecological factors differ greatly between regions. In this study, bulk paddy soils collected from long-term rice fields in Chengdu (basins) and Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared >70% of the dominant genera (abundance >1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites, especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively correlated with the higher incidence of rice bacterial foot rot in Guiyang, whereas temperature had a greater effect on soil microbial functions and positively correlated with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.