Distinct Functions and Assembly Mechanisms of Soil Abundant and Rare Bacterial Taxa Under Increasing Pyrene Stresses

Accumulated temperature dictates the regional structural variation of prokaryotic periphyton at soil-water interface in paddy fields

As a pervasive microbial aggregate found at the water-soil interface in paddy fields, periphyton plays crucial roles in modulating nutrient biogeochemical cycling. Consequently, it effectively mitigates non-point source pollution due to its diverse composition. Despite its significance, the mechanisms governing periphyton diversity across different rice planting regions remain poorly understood. To bridge this gap, we investigated periphyton grown in 200 paddy fields spanning 25° of latitude. Initially, we analyzed local diversity and latitudinal variations in prokaryotic communities within paddy field periphyton, identifying 7 abundant taxa, 42 moderate taxa, and 39 rare taxa as the fundamental prokaryotic framework. Subsequently, to elucidate the mechanisms governing periphyton diversity across large scales, we constructed interaction models illustrating triangular relationships among local richness, assembly, and regional variation of prokaryotic subcommunities. Our findings suggest that accumulated temperature-driven environmental filtering partially influences the assembly process of prokaryotes, thereby impacting local species richness and ultimately governing regional structural variations in periphyton. Furthermore, we determined that a latitude of 39° represents the critical threshold maximizing local species richness of periphyton in paddy fields. This study advances our understanding of the factors shaping periphyton geo-imprints and provides valuable insights into predicting their responses to environmental changes, potentially influencing rice production outcomes.

Microbial perspective on restoration of degraded urban soil using ornamental plants

The urban soil where abandoned buildings are demolished is barren and structurally poor, and this degraded soil requires restoration. Ornamental plants enhance the urban environment, increase biodiversity, and affect soil physicochemical properties, microbial diversity; however, their effects remain unclear. Thus, in this study, a mixed-planting meadow consisting of 14 perennial ornamental flower species, including Iris tectorum, Iris lacteal, and Patrinia scabiosaefolia, etc. Was planted at a demolition site with sewage-contaminated soil in Beijing. Simultaneously, a single-planting lawn of I. tectorum was established in a nearby park. We aimed to examine soil physicochemical properties, sequence soil bacterial 16S rRNA and fungal ITS amplicons, and analyze soil microbial diversity and community structure at both sites at five time points in the year after planting, To explore the effect of herbaceous ornamental plants on degraded urban soil, we used FAPROTAX and FUNGuild to predict bacterial and fungal functions, the bin-based null model to evaluate the soil microbial community, and random matrix theory to construct soil microbial molecular networks. The mixed-planting meadow produced a visually appealing landscape and dynamic seasonal enrichment, significantly increasing soil total nitrogen (TN) and organic matter (SOM) contents by 1.99 and 1.21 times, respectively. TN had a positive correlation with soil microbial α diversity and community structure. Dominant phyla at both sites included Proteobacteria, Actinobacteria, and Ascomycota. Although soil microorganisms were primarily influenced by stochastic processes, stochasticity was notably higher in the mixed-planting meadow than in the single-planting lawn. The mixed-planting meadow significantly increased the relative abundance of beneficial microorganisms, improving nitrification and aerobic ammonium oxidation of soil bacteria, as well as symbiotroph of fungi. No significant changes were observed in the single-planting lawn. The mixed-planting meadow established a complex soil microbial molecular network, enhancing the correlation between bacteria and fungi and increasing the number of key microorganisms. Our findings suggest the potential of mixed-planting meadow in restoring degraded urban soils by influencing the soil microbial community and enhancing the ecological service function. Our study provides theoretical support for applying mixed-planting meadow communities to improve the soil environment of urban green spaces.

Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments

The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.

Association between Soil Physicochemical Properties and Bacterial Community Structure in Diverse Forest Ecosystems

Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to explore the association between soil physicochemical properties and the composition, diversity, co-occurrence network topological features, and assembly mechanisms of the soil bacterial community. Four typical forest types from Liziping Nature Reserve, representing evergreen coniferous forest, deciduous coniferous forest, mixed conifer-broadleaf forest, and its secondary forest, were selected for this study. The soil bacterial community was analyzed using Illumina MiSeq sequencing of 16S rRNA genes. Nonmetric multidimensional scaling was used to illustrate the clustering of different samples based on Bray-Curtis distances. The associations between soil physicochemical properties and bacterial community structure were analyzed using the Mantel test. The interactions among bacterial taxa were visualized with a co-occurrence network, and the community assembly processes were quantified using the Beta Nearest Taxon Index (Beta-NTI). The dominant bacterial phyla across all forest soils were Proteobacteria (45.17%), Acidobacteria (21.73%), Actinobacteria (8.75%), and Chloroflexi (5.06%). Chao1 estimator of richness, observed ASVs, faith-phylogenetic diversity (faith-PD) index, and community composition were distinguishing features of the examined four forest types. The first two principal components of redundancy analysis explained 41.33% of the variation in the soil bacterial community, with total soil organic carbon, soil moisture, pH, total nitrogen, carbon/nitrogen (C/N), carbon/phosphorous (C/P), and nitrogen/phosphorous (N/P) being the main soil physicochemical properties shaping soil bacterial communities. The co-occurrence network structure in the mixed forest was more complex compared to that in pure forests. The Beta-NTI indicated that the bacterial community assembly of the four examined forest types was collaboratively influenced by deterministic and stochastic ecological processes.

An in-depth evaluation of metagenomic classifiers for soil microbiomes

BACKGROUND

Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy.

RESULTS

In this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database.

CONCLUSION

This study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.

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.

The Effects and Toxicity of Different Pyrene Concentrations on Escherichia coli Using Transcriptomic Analysis

Pyrene is a pollutant in the environment and affects the health of living organisms. It is important to understand microbial-mediated pyrene resistance and the related molecular mechanisms due to its toxicity and biodegradability. Due to the unclear response mechanisms of bacteria to PAHs, this study detected the transcriptional changes in Escherichia coli under different pyrene concentrations using transcriptome sequencing technology. Global transcriptome analysis showed that the number of differentially expressed genes (DEGs) in multiple metabolic pathways increased with increasing concentrations of pyrene. In addition, the effects and toxicity of pyrene on Escherichia coli mainly included the up-regulation and inhibition of genes related to carbohydrate metabolism, membrane transport, sulfate reduction, various oxidoreductases, and multidrug efflux pumps. Moreover, we also constructed an association network between significantly differentially expressed sRNAs and key genes and determined the regulatory relationship and key genes of Escherichia coli under pyrene stress. Our study utilized pyrene as an exogenous stress substance to investigate the possible pathways of the bacterial stress response. In addition, this study provides a reference for other related research and serves as a foundation for future research.

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.

The unique climate shapes distinct life-history traits of abundant bacteria in Tibetan Plateau grassland soil

The unique geographical patterns of the Qinghai-Tibet Plateau have shaped the different climatic characteristics of the Lhasa and Nyang River watersheds. However, our understanding of climate-dependent life history strategies in riparian grasslands is very limited. In this research, we have compared the causes and consequences of variations in the composition of soil abundant and rare bacterial taxa in the Nyang and Lhasa River watersheds. The results showed that the abundant bacteria, rather than the rare bacteria, exhibited distinct life history strategies between the Lhasa and Nyang watersheds that were a consequence of climate patterns. The wetter climate of the Nyang watershed led to a high ratio of r-strategists among the abundant bacteria (Abundant K:r = 0.323), while in the less favourable climate of the Lhasa watershed, K-strategists were more common among the soil abundant bacteria (Abundant K:r = 0.542). The assembly processes of abundant and rare bacteria in the Lhasa region under relatively harsh climatic conditions seemed to be more affected by variable selection than those in the Nyang region. Moreover, abundant bacteria in the Lhasa region developed stronger potentially cooperative relationships and exhibited a stronger metabolic capacity than those in the Nyang region. The 26 different functional genes identified in LS were highly associated with 38 abundant bacterial species. In contrast, the 16 identified functional genes in NY were highly correlated with 16 abundant bacterial species. These results provide new insights into climate-dependent life history strategies of soil bacterial communities with different abundances in riparian grasslands of the Tibetan Plateau. Contrasting the life history strategies of bacterial taxa with different abundances contributes to a better mechanistic knowledge of their impact on ecosystem functioning under current and future effects of global climate change.

Oxygen-driven divergence of marine group II archaea reflected by transitions of superoxide dismutases

IMPORTANCE

Reactive oxygen species (ROS), including superoxide anion, is a series of substances that cause oxidative stress for all organisms. Marine group II (MGII) archaea are mainly live in the surface seawater and exposed to considerable ROS. Therefore, it is important to understand the antioxidant capacity of MGII. Our research found that Fe/Mn- superoxide dismutase (Fe/MnSOD) may be more suitable for MGII to resist oxidative damage, and the changes in oxygen concentrations and SOD metallic cofactors play an important role in the selection of SOD by the 17 clades of MGII, which in turn affects the species differentiation of MGII. Overall, this study provides insight into the co-evolutionary history of these uncultivated marine archaea with the earth system.

Community assembly patterns and processes of bacteria in a field-scale aquaculture wastewater treatment system

Microbial communities are responsible for the biological treatment of wastewater, however, our comprehension of their diversity, assembly patterns, and functions remains limited. In this study, we analyzed bacterial communities in both water and sediment samples. These samples were gathered from a novel field-scale aquaculture wastewater treatment system (FAWTS), which employs a multi-stage purification process to eliminate nutrients from pond culture wastewater. Significant variations were observed in bacterial diversity and composition across various ponds within the system and at different stages of the culture. Notably, the bacterial community in the FAWTS displayed a distinct species abundance distribution. The influence of dispersal-driven processes on shaping FAWTS communities was found to be relatively weak. The utilization of neutral and null models unveiled that the assembly of microbial communities was primarily governed by stochastic processes. Moreover, environmental factors variables such as total nitrogen (TN), dissolved oxygen (DO), and temperature were found to be associated with both the composition and assembly of bacterial communities, influencing the relative significance of stochastic processes. Furthermore, we discovered a close relationship between that bacterial community composition and system functionality. These findings hold significant implications for microbial ecologists and environmental engineers, as they can collaboratively refine operational strategies while preserving biodiversity. This, in turn, promotes the stability and efficiency of the FAWTS. In summary, our study contributes to an enhanced mechanistic understanding of microbial community diversity, assembly patterns, and functionality within the FAWTS, offering valuable insights into both microbial ecology and wastewater treatment processes.

Different effects of taproot and fibrous root crops on pore structure and microbial network in reclaimed soil

Understanding the effects of plant roots on the pore structure and microbial community of soil is crucial to recovery and improve soil productivity in mining areas. This study aims to assess the impact of taproot (TR) and fibrous root (FR) crops on the physicochemical properties, pore structure, and microbial communities and networks in reclaimed mine soil. Results showed that reclamation positively influenced pore structure and microbial diversity. Tillage with TR and FR crops significantly increased porosity, total pore volume, and area of mining soil (p < 0.05). Compared with TR, FR produced more macropores, mesopores, and micropores. In addition, the module group, average degree, density, and connectivity of microbial network in FR cultivated soil were higher than those in TR cultivated soil. The microbial network map showed that FR had more keystone taxa than TR, and mainly consisted of Acidobacteria and Proteobacteria. In the FR microbial network, Rhizobiales, Betaproteobacteria, and Acidobacteria_Gp11 play critical roles as module hubs and Noviherbaspirillum and Zavarzinella as connectors. Furthermore, most of the key microbes were significantly correlated (p < 0.05) with the total pore area and probably tended to live in pores >75 μm and 0.1-5 μm in size. Therefore, FR crops were more effective than TR crops in improving pore structure and enhancing the development of microbial network in reclaimed soil.

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.

The response of microbial compositions and functions to chronic single and multiple antibiotic exposure by batch experiment

Understanding the response of the microbial community to external disturbances such as micropollutants is vital for ecological risk evaluation. In this study, the effect of chronic antibiotic exposure on community compositions and functions was investigated by two batch experiments. The first experiment investigated the effect of chronic sulfamethoxazole (SMX) exposure, while the second investigated the combined effect of dissolved organic matter (DOM) sources and multi-antibiotic exposure. The results showed that the community responses to chronic antibiotic exposure depended on the dynamic balance among community resistance, adaptation, recovery, and selection, leading to nonlinear composition diversity variations. The disturbance strength of chronic SMX exposure increased with concentration (0.5-50 μg/L). However, complex sources and structures of coexisting organic matter might delay the disturbance by elevating metabolic activity and generating functional redundancy. Especially, when nutrient was a limiting factor, the disturbance strength by DOM source was greater than that by chronic antibiotic exposure. The resistance of abundant taxa to external distributions resulted in a low explanation of community diversity, while rare taxa played key roles in response to community variation and thereby affected community assembly. Long-term SMX exposure reduced the number of key species and favored the deterministic assembly process by 21%. However, elevated community adaptability might weaken the influence of antibiotic selection. Chronic SMX exposure elevated the relative abundance of sulfonamide resistance genes (sul1, sul2) by a factor of 1.2-4.3, while that of nitrogen-fixing genes (nifH, nifK) and the metabolic pathways related to the toluene, ethylbenzene, and dioxin degradation decreased. However, the combined influence of DOM sources and multi-antibiotic exposure barely caused the difference in the genes linking to element metabolism and drug resistance of microbial communities between blank and exposed groups. This study suggested that more concern should be given to the chronic environmental effect of organic micropollutants.

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.

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.

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.

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.

Increase in Cd Tolerance through Seed-Borne Endophytic Fungus Epichloë gansuensis Affected Root Exudates and Rhizosphere Bacterial Community of Achnatherum inebrians

Soil cadmium (Cd) pollution is a serious environmental problem imperiling food safety and human health. The endophyte Epichloë gansuensis can improve the tolerance of Achnatherum inebrians to Cd stress. However, it is still unknown whether and how the endophyte helps host plants build up a specific bacterial community when challenged by CdCl2. In this study, the responses of the structure and function of bacterial community and root exudates of E+ (E. gansuensis infected) and E- (E. gansuensis uninfected) plants to Cd stress were investigated. Analysis of bacterial community structure indicated that the rhizosphere bacterial community predominated over the root endosphere bacterial community in enhancing the resistance of CdCl2 in a host mediated by E. gansuensis. E+ plant strengthened the interspecific cooperation of rhizosphere bacterial species. Moreover, the analysis of root exudates demonstrated E. gansuensis and increased the contents of organic acids and amino acids under Cd stress, and most root exudates were significantly correlated with rhizosphere bacteria. These results suggested that E. gansuensis employed a specific strategy to recruit distinct rhizosphere bacterial species and relevant functions by affecting root exudates to improve the tolerance of the host to Cd stress. This study provides a firm foundation for the potential application of symbionts in improving phytostabilization efficiency.

Groundwater depth regulates assembly processes of abundant and rare bacterial communities across arid inland river basin

Although numerous studies on bacterial biogeographic patterns in dryland have been conducted, bacterial community assembly across arid inland river basins is unclear. Here, we assessed the ecological drivers that regulate the assembly processes of abundant (ABS) and rare (RBS) bacterial subcommunities based on 162 soil samples collected in an arid inland river basin of China. The results showed that: (1) ABS exhibited a steeper distance-decay slope, and were more strongly affected by dispersal limitation (75.5% and 84.5%), than RBS in surface and subsurface soil. RBS were predominantly controlled by variable selection (54.6% and 50.2%). (2) Soil electric conductivity played a decisive role in mediating the balance between deterministic and stochastic processes of ABS and RBS in surface soil, increasing soil electric conductivity increased the importance of deterministic process. For subsurface soil, soil available phosphorus (SAP) and soil pH drove the balance in the assembly processes of ABS and RBS, respectively. The RBS shifted from determinism to stochasticity with decreased pH, while the dominance of deterministic processes was higher in low-SAP sites. (3) Groundwater depth seasonality had substantial effects on the assembly processes of ABS and RBS, but groundwater depth seasonality affected them indirectly mainly by regulating soil properties. Collectively, our study provides robust evidence that groundwater-driven variations in soil properties mediates the community assembly process of soil bacteria in arid inland river basins. This finding is of importance for forecasting the dynamics of soil microbial community and soil process in response to current and future depleted groundwater.

Biochar rebuilds the network complexity of rare and abundant microbial taxa in reclaimed soil of mining areas to cooperatively avert cadmium stress

Understanding the interactions between the soil microbial communities and species is critical in the remediation of heavy metal-contaminated soil. Biochar has been widely applied as a stabilizer in the in situ remediation of cadmium (Cd)-contaminated soils in mining areas. However, the rebuilding of the microbial taxa of rare and abundant species by biochar and their cooperative resistance to Cd stress remains elusive. In this pursuit, the present study envisaged the effects of two types of biochars viz., poplar bark biochar (PB) and thiourea-modified poplar bark biochar (TP) on the rare and abundant bacterial and fungal taxa by using pot experiments. The results demonstrated that the PB and TP treatments significantly reduced the leached Cd content, by 35.13 and 68.05%, respectively, compared with the control group (CK), in the reclaimed soil of the mining area. The application of biochar significantly improved the physicochemical properties like pH and Soil Organic Matter (SOM) of the soil. It was observed that TP treatment was superior to the PB and CK groups in increasing the diversity of the soil abundant and rare species of microbial taxa. Compared with the CK group, the application of PB and TP enhanced and elevated the complexity of the microbial networks of rare and abundant taxa, increased the number and types of network core microorganisms, reshaped the network core microorganisms and hubs, and boosted the microbial resistance to Cd stress. Our results indicate the response of rare and abundant microbial taxa to biochar application and the mechanism of their synergistic remediation of Cd-contaminated soil, thereby providing technical feasibility for in situ remediation of Cd-contaminated soil in mining areas.

Microplastics reduce soil microbial network complexity and ecological deterministic selection

Microplastics have been proposed as emerging threats for terrestrial systems as they may potentially alter the physicochemical/biophysical soil environments. Due to the variety of properties of microplastics and soils, the microplastic-induced effects in soil ecosystems are greatly manifold. Here, we studied effects of three polymer microplastics (polyamide-6 (PA), polyethylene (PE), and polyethylene terephthalate (PET)) on soil properties with four different soil types. The success patterns, interaction relationships, and assembly processes of soil bacterial communities were also studied. Microplastics have the potential to promote CO₂ emissions and enhance soil humification. Even though microplastics did not significantly alter the diversity and composition of the soil microbial community, the application of microplastics decreased the network complexity and stability, including network size, connectivity, and the number of module and keystone species. The bacterial community assembly was governed by deterministic selection (77.3% - 90.9%) in all treatments, while microplastics increased the contribution of stochastic processes from 9.1% in control to 13.6% - 22.7%. The neutral model results also indicated most of the bacterial taxa were present in the predicted neutral region (approximately 98%), suggesting the importance of stochastic processes. These findings provided a fundamental insight in understanding the effects of microplastics on soil ecosystems. This article is protected by copyright. All rights reserved.

Snowstorm Enhanced the Deterministic Processes of the Microbial Community in Cryoconite at Laohugou Glacier, Tibetan Plateau

Cryoconites harbor diverse microbial communities and are the metabolic hotspot in the glacial ecosystem. Glacial ecosystems are subjected to frequent climate disturbances such as precipitation (snowing), but little is known about whether microbial communities in cryoconite can maintain stability under such disturbance. Here, we investigated the bacterial community in supraglacial cryoconite before and after a snowfall event on the Laohugou Glacier (Tibetan Plateau), based on Illumina MiSeq sequencing of the 16S rRNA gene. Our results showed that the diversity of the microbial community significantly decreased, and the structure of the microbial community changed significantly after the disturbance of snowfall. This was partly due to the relative abundance increased of cold-tolerant bacterial taxa, which turned from rare into abundant sub-communities. After snowfall disturbance, the contribution of the deterministic process increased from 38 to 67%, which is likely due to the enhancement of environmental filtering caused by nitrogen limitation. These findings enhanced our understanding of the distribution patterns and assembly mechanisms of cryoconite bacterial communities on mountain glaciers.