Bacterial Community Assembly Research Articles

Rhizosphere bacterial community is mainly determined by soil environmental factors, but the active bacterial diversity is mainly shaped by plant selection.

The assembly of the rhizosphere community, even the diazotroph community, is mainly shaped by soil environmental factors (including soil climate and physiochemical characteristics) and plant selection. To better understand the driving forces on the active overall and nitrogen-fixing bacterial community compositions, we characterized the communities of tobacco rhizosphere soil collected from three sampling sites with a large geographic scale (> 600km). The results indicate that the diversity and community composition of the overall bacterial and diazotroph communities are obviously differed according to the sampling sites. Still, no significant difference is found between the communities in rootzone and rhizosphere samples. Climate variables including mean annual precipitation (MAP) and mean annual temperature (MAT), soil physiochemical characteristics including available nitrogen (AN), available potassium (AK) and pH are main factors that affect the bacterial and diazotroph community structures in the three sampling sites. Furthermore, MAP and MAT, AN and available phosphorus (AP), total nitrogen (TN) and organic carbon (OC), AK and electrical conductivity (EC) showed similar effects, but pH showed independent effect on the composition of the overall bacteria and diazotroph communities. However, the alpha diversity indices of active overall and nitrogen-fixing bacteria in the rhizosphere are obviously higher than in the rootzone samples, and no significant differences are observed among different sampling sites. Proteobacteria is the predominant active phylum of all samples for overall and nitrogen-fixing bacteria. Escherichia-Shigella, Achromobacter, Streptomyces and Sphingomonas are the dominant active bacterial genera, and Bradyrhizobium, Skermanella and Extensimonas are dominant active nitrogen-fixing bacteria genera in rhizosphere. Furthermore, the high active abundance of Escherichia-Shigella but low abundance of Ralstonia in all three sampling sites indicate high root-knot nematode infection and low wilt disease endemic risk. These results indicate that soil environmental factors contribute more to the tobacco rhizosphere bacterial community assemblage, but the rhizosphere contributes more to the diversity of active overall bacteria and nitrogen-fixing bacteria in the community. Our study provides novel knowledge for the assemble of rhizosphere bacterial and active bacteria communities across a large geographical scale.

Planting density effect on poplar growth traits and soil nutrient availability, and response of microbial community, assembly and function

BackgroundThe interaction between soil characteristics and microbial communities is crucial for poplar growth under different planting densities. Yet, little is understood about their relationships and how they respond to primary environmental drivers across varying planting densities.ResultsIn this study, we investigated poplar growth metrics, soil characteristics, and community assembly of soil bacterial and fungal communities in four poplar genotypes (M1316, BT17, S86, and B331) planted at low, medium, and high densities. Our findings reveal that planting density significantly influenced poplar growth, soil nutrients, and microbial communities (P < 0.05). Lower and medium planting densities supported superior poplar growth, higher soil nutrient levels, increased microbial diversity, and more stable microbial co-occurrence networks. The assembly of bacterial communities in plantation soils was predominantly deterministic (βNTI < -2), while fungal communities showed more stochastic assembly patterns (-2 < βNTI < 2). Soil available phosphorus (AP) and potassium (AK) emerged as pivotal factors shaping microbial communities and influencing bacterial and fungal community assembly. Elevated AP levels promoted the recruitment of beneficial bacteria such as Bacillus and Streptomyces, known for their phosphate-solubilizing abilities. This facilitated positive feedback regulation of soil AP, forming beneficial loops in soils with lower and medium planting densities.ConclusionsOur study underscores the critical role of planting density in shaping soil microbial communities and their interaction with poplar growth. This research carries significant implications for enhancing forest management practices by integrating microbiological factors to bolster forest resilience and productivity.

Stochastic Processes Dominate the Assembly of Soil Bacterial Communities of Land Use Patterns in Lesser Khingan Mountains, Northeast China

To meet the demands of a growing population, natural wetlands are being converted to arable land, significantly impacting soil biodiversity. This study investigated the effects of land use changes on bacterial communities in wetland, arable land, and forest soils in the Lesser Khingan Mountains using Illumina MiSeq 16S rRNA sequencing. Soil physicochemical properties and enzyme activities were measured using standard methods, while microbial diversity was assessed through sequencing analysis. Our findings revealed that forest soils had significantly higher levels of total potassium (2.62 g·kg−1), electrical conductivity (8.22 mS·cm−1), urease (0.18 mg·g−1·d−1), and nitrate reductase (0.13 mg·g−1·d−1), attributed to rich organic matter and active microbial communities. Conversely, arable soils showed lower total potassium (1.94 g·kg−1), reduced electrical conductivity, and suppressed enzyme activities due to frequent tilling and fertilization. Wetland soils exhibited the lowest values primarily due to water saturation, which limits organic matter decomposition and microbial activity. Land use changes notably reduced microbial diversity, with conversion from forest to arable land leading to habitat loss. Forest soils supported higher abundances of Proteobacteria (37.59%) and Actinobacteriota (34.73%), while arable soils favored nitrogen-fixing bacteria. Wetlands were characterized by chemoheterotrophic and anaerobic bacteria. Overall, these findings underscore the profound influence of land use on soil microbial communities and their functional roles, highlighting the need for sustainable management practices.

Synergistic effects of microplastics and sulfonamide on greenhouse gas emissions in agricultural ditch sediments: Insights into microbial interactions

Recently, concerns have been raised regarding concurrent pollution by microplastics and antibiotics in agricultural aquatic ecosystems. However, knowledge gaps remain regarding their combined effects on greenhouse gas (GHG) emissions and bacterial community assembly mechanisms. To address this, a microcosm experiment was performed to investigate the GHG (CH4, CO2, and N2O) emission characteristics and bacterial community assembly mechanisms in agricultural ditch sediments under co-exposure to different microplastics (polythene (PE), polylactic acid (PLA)), and sulfanilamide (SA). The global warming potential (GWP) of the different treatments was ranked as follows: SA+PLA (162.96 mg/m2/h) > PLA (123.49 mg/m2/h) > SA (121.75 mg/m2/h) > SA+PE (102.33 mg/m2/h) > CK (without microplastics or antibiotics, 84.67 mg/m2/h) > PE (78.29 mg/m2/h). Additionally, a phylogenetic bin-based null model and molecular ecological network analysis indicated that SA-induced selective pressures reduced compositional turnover, whereas microplastics enhanced drift effects and decreased network robustness. The co-contamination of SA with different microplastics exhibited the opposite effect on the network and assembly process, suggesting that disturbance-mediated species dominance alters the colonization of rare species. Collectively, these findings provide valuable evidence that the synergistic effects of biodegradable microplastic and SA can promote GHG emissions and influence the mechanisms underlying community assembly processes.

Ecological processes shaping highly connected bacterial communities along strong environmental gradients.

Along the river-sea continuum, microorganisms are directionally dispersed by water flow while being exposed to strong environmental gradients. To compare the two assembly mechanisms that may strongly and differently influence metacommunity dynamics, namely homogenizing dispersal and heterogeneous selection, we characterized the total (16S rRNA gene) and putatively active (16S rRNA transcript) bacterial communities in the Pearl River-South China Sea Continuum, during the wet (summer) and dry (winter) seasons using high-throughput sequencing. Moreover, well-defined sampling was conducted by including freshwater, oligohaline, mesohaline, polyhaline, and marine habitats. We found that heterogeneous selection exceeded homogenizing dispersal in both the total and active fractions of bacterial communities in two seasons. However, homogeneous selection was prevalent (the dominant except in active bacterial communities during summer), which was primarily due to the bacterial communities' tremendous diversity (associated with high rarity) and our specific sampling design. In either summer or winter seasons, homogeneous and heterogeneous selection showed higher relative importance in total and active communities, respectively, implying that the active bacteria were more responsive to environmental gradients than were the total bacteria. In summary, our findings provide insight into the assembly of bacterial communities in natural ecosystems with high spatial connectivity and environmental heterogeneity.

Assembly of phyllosphere bacterial community with PsnWRKY70 in poplar

Plant microbiome plays an important role in growth and development, biotic and abiotic stresses, and genotype is one of the key factors in shaping the microbiome. In this study, the effect of PsnWRKY70 on the synthetic bacterial community of poplar was investigated. To explore the assembly mechanism of poplar phyllosphere bacteria. we used 39 strains of bacteria isolated from the phyllosphere of poplar to construct a synthetic bacterial community. The leaves of aseptic poplar tissue culture seedlings were inoculated with synthetic bacterial community, and the bacterial communities of poplar leaves inoculated with synthetic bacterial community for 0 d, 5 d, 10 d and 15d were sequenced for 16 s. Bacterial community composition, PCoA, and Lefse analyses were performed. The results showed that the bacterial community in the phyllosphere of poplar tended to be in a stable equilibrium state after inoculation with the synthetic bacterial community. The results of β diversity analysis showed that there were significant differences in the bacterial community structure of OE, RE and WT leaves at 5d and 10 d after inoculation with Syncom. It is mainly composed of Methylobacteriaceae, Enterbacteriaceae, Agrobacterium, Rhizobium, Pseudoxanthomonas and Stenotrophomonas. The results of differential bacterial analysis showed that Paracoccus, Arthrobacter and Rhodococcus had higher relative abundance and stability in OE line. PsnWRKY70 gene plays an important role in recruiting Paracoccus, Arthrobacter and Rhodococcus strains in poplar leaves.

Contribution of environmental and biological factors to bacterial community structure and stability in a subalpine lake

AbstractBacterial community play an essential role in regulating water quality and the global biogeochemical cycle in aquatic ecosystems. However, how trophic interactions (i.e., biotic factors) regulate the diversity and composition of bacterial community in lake ecosystems remains unknown. Here, we employed DNA meta-barcoding of water samples to explore the impact of bacterivorous protozoans on the bacterial community. The results showed significant seasonal variations in the diversity and composition of both bacterial and protist communities. The composition of bacterivorous protozoans was identified as the primary predictor for the bacterial community alpha diversity in spring and summer, and for beta diversity in spring and autumn, indicating that biotic interactions play a greater role in driving the diversity of bacterial community across different seasons. Biological factors were more important than environmental factors for explaining the variations in the relative abundance of several bacterial genera (i.e., Pseudoxanthomonas, hgcI_clade, and Pseudorhodobacter). Network analyses showed that bacterial networks differed among seasons, and the autumn network exhibited the highest stability. Our findings indicated that the bacterial community stability was significantly affected by environmental factors, specifically SO42–and PO43–, rather than bacterivorous protozoans. Overall, our findings provide new perspectives on the role of trophic interactions in maintaining the structure of bacterial community in different seasons, and enhance our understanding of the bacterial community assembly in lake ecosystems.

Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities.

Associations with soil microorganisms are crucial for plants' overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, climate, soil properties, and plant genetics remains unclear, as results have been mixed and comprehensive studies across many sites and genotypes are limited. Rhizosphere microbiomes are crucial for crop resistance to pathogens, stress tolerance, nutrient availability, and ultimately yield. Here, we quantify the relative roles of plant genotype, environment, and their interaction in shaping soil rhizosphere communities, using 16S and ITS gene sequencing of rhizosphere soils from 10 genotypes of cultivated sunflower (Helianthus annuus) at 15 sites across the Great Plains of the United States. While site generally outweighed genotype overall in terms of effects on archaeal, bacterial, and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a significant influence on archaeal, bacterial, and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Microbial taxa that were previously associated with resistance to the fungal necrotrophic pathogen Sclerotinia were present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and agronomic microbiome manipulations for agricultural improvement across different geographic regions.IMPORTANCEDespite the importance of plant breeding in agriculture, we still have a limited understanding of how plant genetic variation shapes soil microbiome composition across broad geographic regions. Using 15 sites across the Great Plains of North America, we show that cultivated sunflower rhizosphere archaeal, bacterial, and fungal communities are driven primarily by site soil and climatic differences, but genotype can interact with site to influence the composition, especially in warmer and drier sites with lower overall microbial richness. We also show that all taxa that were previously found to be associated with resistance to the fungal pathogen Sclerotinia sclerotiorum were widespread but significantly affected by site, while a subset was also significantly affected by genotype. Our results contribute to a broader understanding of rhizosphere archaeal, bacterial, and fungal community assembly and provide foundational knowledge for plant breeding efforts and potential future microbiome manipulations in agriculture.

Depth-dependent effects of forest diversification on soil functionality and microbial community characteristics in subtropical forests

Soil microbes are critical to the maintenance of forest ecosystem function and stability. Forest diversification, such as monocultures versus mixed forests stands, can strongly influence microbial community patterns and processes, as well as their role in soil ecosystem multifunctionality, such as in subtropical forest ecosystems. However, less is known about these patterns and processes vary with soil depth. Here, we investigated the results of an eight-year forest diversification field experiment comparing the soil ecosystem multifunctionality, bacterial and fungal community assembly, and network patterns in mixed versus monoculture plantations along vertical profiles (0–80 cm depth) in a subtropical region. We found that the introduction of broadleaf trees in coniferous monocultures led to enhanced synergies between multiple functions, thus improving soil multifunctionality. The effects of mixed plantations on the functional potential in top soils were greater than in deep soils, especially for carbon degradation genes (apu, xylA, cex, and glx). Microbial community assembly in the top layer, particularly in mixed plantations, was dominated by stochastic processes, whereas deterministic were more important in the deep layer. Soil microbial network complexity and stability were higher in the top layer of mixed plantations, but in the deep layer was monoculture. Interestingly, the changes in microbial communities and multifunctionality in the top layer were mainly related to variation in nutrients, whereas those in the deep were more influenced by soil moisture. Overall, we reveal positive effects of mixed forest stands on soil microbial characteristics and functionality compared to that of monocultures. Our findings highlighted the importance of enhancing functional diversity through the promotion of tree species diversity, and managers can better develop forest management strategies to promote soil health under global change scenarios.

Diversity and interactions of rhizobacteria determine multinutrient traits in tomato host plants under nitrogen and water disturbances

Abstract Coevolution within the plant holobiont extends the capacity of host plants for nutrient acquisition and stress resistance. However, the role of the rhizospheric microbiota in maintaining multinutrient utilization (i.e., multinutrient traits) in the host remains to be elucidated. Multinutrient cycling index (MNC), analogous to the widely used multifunctionality index, provides a straightforward and interpretable measure of the multinutrient traits in host plants. Using tomato as a model plant, we characterized MNC (based on multiple aboveground nutrient contents) in host plants under different nitrogen and water supply regimes and explored the associations between rhizospheric bacterial community assemblages and host-plant multinutrient profiles. Rhizosphere bacterial community diversity, quantitative abundance, predicted function, and key topological features of the co-occurrence network were more sensitive to water supply than to nitrogen supply. A core bacteriome comprising 61 genera, such as Candidatus Koribacter and Streptomyces, persisted across different habitats and served as a key predictor of host-plant nutrient uptake. The MNC index increased with greater diversity and higher core taxon abundance in the rhizobacterial community, while decreasing with higher average degree and graph density of rhizobacterial co-occurrence network. Multinutrient absorption by host plants was primarily regulated by community diversity and rhizobacterial network complexity under the interaction of nitrogen and water. The high biodiversity and complex species interactions of the rhizospheric bacteriome play crucial roles in host-plant performance. This study supports the development of rhizosphere microbiome engineering, facilitating effective manipulation of the microbiome for enhanced plant benefits, which supports sustainable agricultural practices and plant health.

The contribution of seasonal variations and Zostera marina presence to the bacterial community assembly of seagrass bed sediments

BackgroundMicroorganisms play pivotal roles in seagrass ecosystems by facilitating material and elemental cycling as well as energy flux. However, our understanding of how seasonal factors and seagrass presence influence the assembly of bacterial communities in seagrass bed sediments is limited. Employing high-throughput sequencing techniques, this study investigates and characterizes bacterial communities in the rhizosphere of eelgrass (Zostera marina) and the bulk sediments across different seasons. The research elucidates information on the significance of seasonal variations and seagrass presence in impacting the microbial communities associated with Zostera marina.ResultsThe results indicate that seasonal variations have a more significant impact on the bacterial community in seagrass bed sediments than the presence of seagrass. We observed that the assembly of bacterial communities in bulk sediments primarily occurs through stochastic processes. However, the presence of seagrass leading to a transition from stochastic to deterministic processes in bacterial community assembly. This shift further impacts the complexity and stability of the bacterial co-occurrence network. Through LEfSe analysis, different candidate biomarkers were identified in the bacterial communities of rhizosphere sediments in different seasons, indicating that seagrass may possess adaptive capabilities to the environment during different stages of growth and development.ConclusionsSeasonal variations play a significant role in shaping these communities, while seagrass presence influences the assembly processes and stability of the bacterial community. These insights will provide valuable information for the ecological conservation of seagrass beds.

Comparative metagenomic study unveils new insights on bacterial communities in two pine-feeding Ips beetles (Coleoptera: Curculionidae: Scolytinae).

Climate change has recently boosted the severity and frequency of pine bark beetle attacks. The bacterial community associated with these beetles acts as "hidden players," enhancing their ability to infest and thrive on defense-rich pine trees. There is limited understanding of the environmental acquisition of these hidden players and their life stage-specific association with different pine-feeding bark beetles. There is inadequate knowledge on novel bacterial introduction to pine trees after the beetle infestation. Hence, we conducted the first comparative bacterial metabarcoding study revealing the bacterial communities in the pine trees before and after beetle feeding and in different life stages of two dominant pine-feeding bark beetles, namely Ips sexdentatus and Ips acuminatus. We also evaluated the bacterial association between wild and lab-bred beetles to measure the deviation due to inhabiting a controlled environment. Significant differences in bacterial amplicon sequence variance (ASVs) abundance existed among different life stages within and between the pine beetles. However, Pseudomonas, Serratia, Pseudoxanthomonas, Taibaiella, and Acinetobacter served as core bacteria. Interestingly, I. sexdentatus larvae correspond to significantly higher bacterial diversity and community richness and evenness compared to other developmental stages, while I. acuminatus adults displayed higher bacterial richness with no significant variation in the diversity and evenness between the life stages. Both wild and lab-bred I. sexdentatus beetles showed a prevalence of the bacterial family Pseudomonadaceae. In addition, wild I. sexdentatus showed dominance of Yersiniaceae, whereas Erwiniaceae was abundant in lab-bred beetles. Alternatively, Acidobacteriaceae, Corynebacteriaceae, and Microbacteriaceae were highly abundant bacterial families in lab-bred, whereas Chitinophagaceae and Microbacteriaceae were highly abundant in wild I. accuminatus. We validated the relative abundances of selected bacterial taxa estimated by metagenomic sequencing with quantitative PCR. Our study sheds new insights into bacterial associations in pine beetles under the influence of various drivers such as environment, host, and life stages. We documented that lab-breeding considerably influences beetle bacterial community assembly. Furthermore, beetle feeding alters bacteriome at the microhabitat level. Nevertheless, our study revisited pine-feeding bark beetle symbiosis under the influence of different drivers and revealed intriguing insight into bacterial community assembly, facilitating future functional studies.

Unique ecology of biofilms and flocs: Bacterial composition, assembly, interaction, and nitrogen metabolism within deteriorated bioreactor inoculated with mature partial nitrification-anammox sludge

This work unraveled discrepant ecological patterns between biofilms and flocs in a deteriorated bioreactor inoculated with mature partial nitrification-anammox (PN/A) sludge. Based on 16S rRNA analysis, a comprehensive evaluation of neutral and null models, along with niche width, delineated that the bacterial community assembly in biofilms and flocs was dominantly driven by the stochastic process, and dispersal limitation critically shaped the community assembly. Co-occurrence network analysis revealed that environmental stress caused decentralized and fragmented bacterial colonies, and anammox bacteria were mainly peripheral in biofilms network and less involved in interspecific interactions. Simultaneous PN/A and partial denitrification-anammox (PD/A) processes were identified, whereas PN and PD process primarily occurred in the biofilms and flocs, respectively, as evidenced by metagenomics. Collectively, these outcomes are expected to deepen the basic understanding of complex microbial community and nitrogen metabolism under environmental disturbance, thereby better characterizing and serving the artificial ecosystems.

Bacterial community and antibiotic resistance genes assembly processes were shaped by different mechanisms in the deep-sea basins of the Western Pacific Ocean.

As the intrinsic property of microorganisms, antibiotic resistance genes (ARGs) are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, human activities often obscure the natural distribution of ARGs through deterministic selective pressures. The deep-sea basin of the western Pacific Ocean is one of the least disturbed areas globally by human activities, providing a natural laboratory to investigate the intrinsic mechanisms governing ARGs in natural environments. In this study, we analyzed bacterial community and ARG diversity in 15 surface sediment samples from three deep-sea basins in the western Pacific Ocean. The relative abundance of ARGs in the surface sediments ranged from 3.10 × 10-3 to 5.37 × 10-2 copies/16S rRNA copies, with multidrug and β-lactam resistance genes dominated in all samples (49.06%-100%). The bacteria were mainly dominated by the Proteobacteria. The principal coordinate analysis (PCoA) showed significant spatial heterogeneity of ARGs and bacteria among the three basins. Null model, neutral community models (NCM), and normalized stochasticity ratio (NST) indicated that bacterial community was dominated by stochastic assembly, driven by geographic barriers leading to independent evolution. Conversely, the NST revealed that the ARGs profile was mainly shaped by deterministic processes. Environmental factors are more crucial than geographical factors and bacterial community for ARG occurrence among the selected factors. Meanwhile, we found that the spread of ARGs was mainly through vertical gene transfer in the pre-antibiotic era. The disparity between the assembly processes of bacterial community and ARGs may be attributed to the fact that ARG hosts were not the dominant bacteria in the community. This study first reported the distribution and assembly processes of ARGs and bacterial community in surface sediments of the western Pacific.

Biofilm formation dynamics in long-distance water conveyance pipelines: Impacts of nutrient levels and metal stress

Biofilm formation in long-distance water conveyance pipelines poses significant risks to water quality, particularly under varying nutrient levels and heavy metal stress. However, the impacts of pipeline material on biofilm formation dynamics under different raw water conditions remain elusive. This study investigated the effects of nutrient availability and Fe-Mn stress on biofilm development, structural stability, bacterial community composition, and the occurrence of viable but non-culturable (VBNC) bacteria. Using reactors with different nutrient conditions, we observed that increased nutrient levels promote biofilm growth but lead to greater instability, heightening the risk of secondary contamination. Notably, nutrient escalation beyond a critical threshold had a diminishing impact on biofilm community composition. Additionally, Fe-Mn stress, while initially enhancing microbial adhesion and metabolic activity, ultimately inhibited biofilm formation over time and increases the prevalence of VBNC bacteria, particularly on stainless steel (SS) surfaces. Our findings also highlighted the importance of material selection for pipelines, with polyvinyl chloride (PVC) showing reduced biofilm formation compared to SS, making it a more suitable option for transporting raw water in environments with high metal content. Dispersal limitation determined the bacterial community assembly during the biofilm formation, accounting for 64.53–90.67 % of the variability in different scenarios. These insights offer valuable guidance for managing biofilm-related issues in water distribution systems, emphasizing the need for careful control of nutrient levels and material choice to ensure water safety over long distances.

Pb pollution altered bacterial community assembly and predicted functions in aggregate-size fractions of agricultural soil near a smelter

In order to investigate the impact of Pb smelter pollution on bacterial community structure, diversity and function at the microenvironment scale, the maize rhizosphere soils subjected to long-term (over 20 years) Pb smelter pollution were collected, and bacterial communities and putative functions associated with different aggregate-size fractions were identified by 16S rRNA sequencing, KEGG and FAPROTAX. The results showed that Pb pollution significantly diminished bacterial diversity, and prompted a shift in the bacterial communities toward more oligotrophic taxa, including Firmicutes, Chloroflexi, and Gemmatimonadetes. Furthermore, the functional subcategories related to cell motility and energy metabolism, as well as the functional groups involved in carbon (C), nitrogen (N), and sulfur (S) cycles, exhibited a marked decline under Pb pollution. At the aggregate scale, distinct differences were observed in the composition of bacterial communities across silt and clay (<250 μm), micro-aggregates (250∼1000 μm), and macro-aggregates (1000∼2000 μm and >2000 μm) in uncontaminated soils. However, Pb pollution disrupted these original distinctions among bacterial communities in various aggregate-size fractions, with a decreased abundance of dominant Proteobacteria and an increased abundance of Firmicutes in large aggregates. While the differences in bacterial functional groups in aggregate-size fractions were also detected. The functional groups associated with carbon (C) and nitrogen (N) cycles were significantly enriched in the macro-aggregates (1000∼2000 μm) in uncontaminated soils. However, similar with the change of bacterial community structure, most functional groups (except for chemoheterotrophy) in aggregate-size fractions exhibited no significant differences under Pb exposure. Our results suggested that Pb pollution altered bacterial community structure and predicted functions at the aggregate level, and showed greater negative effects on bacterial functions in macro-aggregates (1000∼2000 μm). This study can provide a new perspective for the influence of Pb smelter pollution on soil aggregate microenvironment.

Deciphering soil environmental regulation on reassembly of the soil bacterial community during wetland restoration

Soil bacteria are vital to regulate biogeochemical processes in wetlands, however, little is known about the patterns and mechanisms of soil bacterial re-organization during wetland restoration. Here, we used a space-for-time substitution approach and examined the ecological processes that drive soil bacterial assembly from cultivated to restored to natural wetlands. Results showed a decrease of soil bacterial α diversity and increase of bacterial community similarity and bacterial interaction (cooperation vs. competition) with years of restoration, which was dominantly influenced by deterministic processes. Identified bacterial keystone taxa (e.g. Variibacter, Acidibacter) with nutrient metabolism capacity exerted strong positive effect on bacterial interaction. Furthermore, changes of soil water condition and nutrient status showed dominantly direct positive effects on soil bacterial reassembly, while falling soil pH significantly promoted bacterial reassembly by increasing keystone taxa and bacterial interaction during wetland restoration. Overall, findings highlighted the crucial role of environmental filtering and its pathway in influencing keystone bacterial taxa that promotes the reassembly of bacterial community during wetland restoration. Our work thus provides a new crucial and timely insight for improving the management of soil bacterial community assembly within the plethora of current and future wetland restoration projects.

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

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

Differential spatial responses and assembly mechanisms of soil microbial communities across region-scale Taiga ecosystems

Different soil microbial communities play distinct key roles in regulating forest ecosystem processes and functions. However, the differences in spatial variability and assembly mechanisms of various taiga forest soil microbial taxa remain poorly understood. Here, we assessed the spatial patterns of bacterial and fungal communities, their assembly processes, and the influencing factors in taiga forest ecosystems in Xinjiang, China. A significant distance decay pattern was observed in the similarity of bacterial and fungal communities, with bacterial communities exhibiting a more pronounced pattern than fungal communities. Stochastic and deterministic processes governed together to drive soil bacterial community assembly, whereas stochastic processes dominated fungal community assembly. The coexistence networks revealed that the interactions of bacterial and fungal networks in the four regions are primarily based on interspecies symbiosis, with fungal coexistence networks demonstrating greater stability than bacterial networks. Additionally, the study identified a positive relationship between the modularity of bacterial networks and dispersal limitation. Analysis of environmental factors revealed that soil pH primarily affects the characteristics and assembly mechanisms of bacterial communities, while vegetation conditions primarily affect fungal diversity and composition, with other unconsidered environmental variables influencing the fungal community assembly process. This study emphasized the distinct ways in which bacteria and fungi respond to environmental factors and interspecies interactions. Our results suggested that distinct restoration measures should be implemented for bacteria and fungi in future conservation efforts for forest soil microorganisms.

Agricultural management reshaped the diversity patterns and community assembly of rhizosphere bacterial communities in a desert farming system

Desert farming represents human intervention in previously untouched desert landscapes, transforming natural desert areas into managed agricultural farmland. Despite the growing prevalence of desert farming, the effects of agricultural management on soil and microbial dynamics in desert environments are not well understood. This study analyzed rhizosphere bacterial community from crops (corn and wheat) in desert farms and desert plants (Artemisia desertorum) in natural desert environments to explore how bacterial communities respond to agricultural management in desert farming systems. Our results showed that the composition and diversity of rhizosphere bacterial communities were influenced more by the sampling region than by plant type. Bacterial species richness, phylogenetic diversity, and functional traits were significantly affected by moisture and temperature, whereas pH and nitrogen-related factors (total nitrogen, NO3-N, and NH4-N) were stronger correlates of functional differences in the microbial community. We found that the co-occurrence network of bacterial communities exhibited tighter and more positive interactions in natural desert, but was more stable in desert farm. Deterministic processes predominantly governed bacterial community assembly in both desert farms and natural desert, but the importance of stochastic processes increased in desert farms due to reduced environmental stress from agricultural management. These findings provide valuable insights into the impacts of agricultural management on rhizosphere bacterial communities, highlighting the roles of temperature, moisture, and nutrient supply in predicting microbial diversity, function, species interactions, and community assembly. Given the crucial functional roles of rhizosphere microbes, our conclusions can inform desert farm management practices to better manipulate microbial communities for optimized crop production.