Deterministic Assembly Processes Research Articles

Nonlinear responses of biofilm bacteria to alkyl-chain length of parabens by DFT calculation

Parabens can particularly raise significant concerns regarding the disruption of microbial ecology due to their antimicrobial properties. However, the responses of biofilm bacteria to diverse parabens with different alkyl-chain length remains unclear. Here, theoretical calculations and bioinformatic analysis were performed to decipher the influence of parabens varying alkyl-chain lengths on the biofilm bacteria. Our results showed that the disturbances in bacterial community did not linearly response to the alkyl-chain length of parabens, and propylparaben (PrP), with median chain length, had more severe impact on bacterial community. Despite the fact that paraben lethality linearly increased with chain length, the PrP had a higher chemical reactions potential than parabens with shorter or longer alkyl-chain. The chemical reactions potential was critical in the nonlinear responses of bacterial community to alkyl-chain length of parabens. PrP could impose selective pressure to disturb the bacterial community, because it had a more profound contribution to deterministic assembly process. Furthermore, N-acyl-homoserine lactones was also significantly promoted under PrP exposure, confirming that PrP could affect the bacterial community by influencing the quorum-sensing system. Overall, our study reveals the nonlinear responses of bacterial communities to the alkyl-chain lengths of parabens and provides insightful perspectives for the better regulation of parabens. Environmental ImplicationParabens are recognized as emerging organic pollutants, which specially raise great concerns due to their antimicrobial properties disturbing microbial ecology. However, few study have addressed the relationship between bacterial community responses and the molecular structural features of parabens with different alkyl-chain length. This investigation revealed nonlinear responses of the bacterial community to the alkyl-chain length of parabens through DFT calculation and bioinformatic analysis and identified the critical roles of chemical reactions potential in nonlinear responses of bacterial community. Our results benefit the precise evaluation of ecological hazards posed by parabens and provide useful insights for better regulation of parabens.

Enriched rhizospheric functional microbiome may enhance adaptability of Artemisia lavandulaefolia and Betula luminifera in antimony mining areas.

Dominant native plants are crucial for vegetation reconstruction and ecological restoration of mining areas, though their adaptation mechanisms in stressful environments are unclear. This study focuses on the interactions between dominant indigenous species in antimony (Sb) mining area, Artemisia lavandulaefolia and Betula luminifera, and the microbes in their rhizosphere. The rhizosphere microbial diversity and potential functions of both plants were analyzed through the utilization of 16S, ITS sequencing, and metabarcoding analysis. The results revealed that soil environmental factors, rather than plant species, had a more significant impact on the composition of the rhizosphere microbial community. Soil pH and moisture significantly affected microbial biomarkers and keystone species. Actinobacteria, Proteobacteria and Acidobacteriota, exhibited high resistance to Sb and As, and played a crucial role in the cycling of carbon, nitrogen (N), phosphorus (P), and sulfur (S). The genes participating in N, P, and S cycling exhibited metabolic coupling with those genes associated with Sb and As resistance, which might have enhanced the rhizosphere microbes' capacity to endure environmental stressors. The enrichment of these rhizosphere functional microbes is the combined result of dispersal limitations and deterministic assembly processes. Notably, the genes related to quorum sensing, the type III secretion system, and chemotaxis systems were significantly enriched in the rhizosphere of plants, especially in B. luminifera, in the mining area. The phylogenetic tree derived from the evolutionary relationships among rhizosphere microbial and chloroplast whole-genome resequencing results, infers both species especially B. luminifera, may have undergone co-evolution with rhizosphere microorganisms in mining areas. These findings offer valuable insights into the dominant native rhizosphere microorganisms that facilitate plant adaptation to environmental stress in mining areas, thereby shedding light on potential strategies for ecological restoration in such environments.

Impacts of ammoniacal odour removal bioagent on air bacterial community

While biotechnologies offer eco-friendly solutions for eliminating air contaminants, there is a scarcity of research examining the impacts of microbial purification of air pollutants on the structure and function of air microbial communities. In this study, we explored a Lactobacillus paracasei B1 (LAB) agent for removing ammoniacal odour. The impacts of LAB on air bacterial community were revealed. by analyzing the air samples before (BT) and after (AT) LAB bioagent treatment. Remarkably, the LAB bioagent significantly reduced the air ammonia concentration by 96.8%. This reduction was associated with a notable decline in bacterial diversity and a significant shift in community composition. The relative abundance of Staphylococcus, a common pathogen, plummeted from 1.91% to 0.03%. Moreover, other potential pathogens decreased by over 87%, signifying the bioagent's impactful role in diminishing health risks. The dominance of OTU-4 (Lactobacillus) highlighted its crucial role not only in competitive interactions but also potentially in shaping the metabolic pathways or community dynamics within the treated air microbial ecosystem. This shift towards deterministic assembly processes post-treatment, as highlighted by the normalized stochasticity ratio (NST), sheds light on the underlying mechanisms dictating the microbial community's response to bioagent interventions. The bioagent-purified air microbial community showed a strong preference for variable selection (88.9%), likely due to the acidity generated by the LAB. In conclusion, our findings emphasized the positive impact of LAB bioagent in enhancing air quality, which associated with the changes in microbial community.

Stochastic and deterministic assembly processes of microbial communities in relation to natural attenuation of black stains in Lascaux Cave.

Community assembly processes are complex and understanding them represents a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains of life in relation to an anthropogenic disturbance that had resulted in the side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains), and a resilient community (attenuated stains). Metabarcoding data showed that the microbial communities of attenuated stains, black stains, and unstained surfaces differed, with attenuated stains being in an intermediate position. We found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of a fourth, not-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance but are replaced by deterministic processes during post-disturbance recovery. This suggests a major role of always-rare taxa in resilience, perhaps because they might provide key functions required for ecosystem recovery.IMPORTANCEThe importance of stochastic vs deterministic processes in cave microbial ecology has been a neglected topic so far, and this work provided an opportunity to do so in a context related to the dynamics of black-stain alterations in Lascaux, a UNESCO Paleolithic cave. Of particular significance was the discovery of a novel scenario for always-rare microbial taxa in relation to disturbance, in which stochastic processes are replaced later by deterministic processes during post-disturbance recovery, i.e., during attenuation of black stains.

Ecological succession of abundant and rare subcommunities during aerobic composting in the presence of residual amoxicillin

Aerobic composting increases the content of soluble nutrients and facilitates the safe treatment of livestock manure. Although different taxa play crucial roles in maintaining ecological functionality, the succession patterns of community composition and assembly of rare and abundant subcommunities during aerobic composting under antibiotic stress and their contributions to ecosystem functionality remain unclear. Therefore, this study used 16 S rRNA gene sequencing technology to reveal the response mechanisms of diverse microbial communities and the assembly processes of abundant and rare taxa to amoxicillin during aerobic composting. The results indicated that rare taxa exhibited distinct advantages in terms of diversity, community composition, and ecological niche width compared with abundant taxa, highlighting their significance in maintaining ecological community dynamics. In addition, deterministic (heterogeneous selection) and stochastic processes (dispersal limitation) play roles in the community succession and functional dynamics of abundant and rare subcommunities. The findings of this study may contribute to a better understanding of the relative importance of deterministic and stochastic assembly processes in composting systems, and the ecological functions of diverse microbial communities, ultimately leading to improved ecological environment.

Rare subcommunity maintains the stability of ecosystem multifunctionality by deterministic assembly processes in subtropical estuaries.

Microorganisms, especially rare microbial species, are crucial in estuarine ecosystems for driving biogeochemical processes and preserving biodiversity. However, the understanding of the links between ecosystem multifunctionality (EMF) and the diversity of rare bacterial taxa in estuary ecosystems remains limited. Employing high-throughput sequencing and a variety of statistical methods, we assessed the diversities and assembly process of abundant and rare bacterioplankton and their contributions to EMF in a subtropical estuary. Taxonomic analysis revealed Proteobacteria as the predominant phylum among both abundant and rare bacterial taxa. Notably, rare taxa demonstrated significantly higher taxonomic diversity and a larger species pool than abundant taxa. Additionally, our findings highlighted that deterministic assembly processes predominantly shape microbial communities, with heterogeneous selection exerting a stronger influence on rare taxa. Further analysis reveals that rare bacterial beta-diversity significantly impacts to EMF, whereas alpha diversity did not. The partial least squares path modeling (PLS-PM) analysis demonstrated that the beta diversity of abundant and rare taxa, as the main biotic factor, directly affected EMF, while temperature and total organic carbon (TOC) were additional key factors to determine the relationship between beta diversity and EMF. These findings advance our understanding of the distribution features and ecological knowledge of the abundant and rare taxa in EMF in subtropical estuaries, and provide a reference for exploring the multifunctionality of different biospheres in aquatic environments.

Bacterial and Microeukaryotic Community Compositions and Their Assembly Processes in Lakes on the Eastern Qinghai-Tibet Plateau.

Bacterial and microeukaryotic community compositions and their assembly processes have remained challenging and remained unclear in lake ecosystems on the Qinghai-Tibet Plateau (QTP). We revealed the diversity and community compositions, driving factors, ecological assembly processes, and co-occurrence networks of bacterial and microeukaryotic communities in water bodies of the eight lake ecosystems across the Eastern QTP. The results demonstrated that the predominant bacteria in most samples were Proteobacteria, with an average relative abundance of 41.78%, whereas the most abundant of microeukaryotes differed among the sample sites. The redundancy analysis revealed that latitude and pH were the most important driving factors in shaping the bacterial and microeukaryotic community compositions. Homogeneous selection (56.40%) was the dominant process in assembling the bacterial communities, whereas dispersal limitation (67.24%) was the major process in governing the microeukaryotic communities. Furthermore, dissolved organic carbon and salinity were the major factors mediating the balance of deterministic and stochastic assembly processes in the bacterial and microeukaryotic communities. Both the bacterial and microeukaryotic community co-occurrence networks exhibited topological features of modularity and non-random topological features. The results offer insights into the mechanisms underpinning bacterial and microeukaryotic diversities and communities in the lake ecosystems on the QTP.

Residual effects of chlorinated organic pollutants on microbial community and natural redox processes in coastal wetlands

Chlorinated organic pollutants (COPs) are common in flooded environments. To examine the residual status and effects of COPs on flooded environments, a survey of 7 coastal wetlands in Zhejiang, East China was conducted. Total COP concentrations detected from 95.69 to 412.76 ng g-1 dw. Gamma-HCH and o,p'-DDT posed the greatest risk with exceedance rates of 100% according to sediment quality guidelines. Samples with higher COP pollution had higher microbial diversity, more complex microbial networks, more deterministic community assembly processes and lower microbiome stability, indicating an improved soil function for balance cycle of substances, especially for COP degradation. Further analysis using quantitative real-time PCR suggested COP-dechlorination interacted with natural redox processes, especially sulfate reduction and methanogenesis. The positive correlation between CH4 and pentachlorobenzene indicated a potential increase in greenhouse gas emissions caused by COP pollution. Correlation between dsr gene and COPs demonstrated the ability of sulfate-reducing bacteria to degrade COPs. Particularly, facultative OHRB such as sulfate-reducing bacteria hold significant importance in the process of COP-dechlorination. This finding provides a reference for COP pollution remediation. Collectively, our study offers new insight into the residual effect of COPs in coastal wetlands and contributes to an improved understanding of bioremediation strategies for COP pollution.

Resilience of tropical invertebrate community assembly processes to a gradient of land use intensity

Understanding how community assembly processes drive biodiversity patterns is a central goal of community ecology. While it is generally accepted that ecological communities are assembled by both stochastic and deterministic processes, quantifying their relative importance remains challenging. Few studies have investigated how the relative importance of stochastic and deterministic community assembly processes vary among taxa and along gradients of habitat degradation. Using data on 1645 arthropod species across seven taxonomic groups in Malaysian Borneo, we quantified the importance of ecological stochasticity and of a suite of community assembly processes across a gradient of logging intensity. The relationship between logging and community assembly varied depending on the specific combination of taxa and stochasticity metric used, but, in general, the processes that govern invertebrate community assembly were remarkably robust to changes in land use intensity.

Stochastic and deterministic assembly processes of bacterial communities in different soil aggregates

Soil bacterial community assembly determined by both the niche-based deterministic and the stochastic process. However, at aggregate scale, the contribution and limitation of those theories in soil bacterial community assembly process still unknown. In this study, different aggregate fractions with a water-controllable unit were performed to build a simple system, aiming to (i) exhibit a contrasting bacterial community assembly pattern of aggregate fractions after incubation under different water content, (ii) quantify the variations of bacterial community during incubation caused by niches or deterministic factors of physic-chemical characteristics, and (iii) assess the pore water driven immigration rates of neutral or stochastic processes caused by different aggregate fractions on bacterial community assembly by neutral community model (NCM). We found a significantly time-decay of bacteria community of different soil aggregate fractions during the incubation period. Despite of the decrease of the total OTU amounts, the proportion of the unique OTUs in the aggregates of <0.25 mm and shared OTUs in three soil aggregate fractions increased under both saturated and unsaturated conditions. Microbial communities in aggregates of <0.25 mm were more distinctive enriched the core microbiota of Firmicutes and Proteobacteria than other aggregates, which might relate to the higher availability N and pH value. Under water saturated situation, bacterial migration rate of 0.25–1 mm at the early-stage was higher than others indicated the ineligible role of water-driven bacterial dispersal on bacterial community assembly process. Those results revealed the deterministic and stochastic mechanism of soil bacterial community assembly at aggregate scale, which helps to unravel the mysterious soil habitat.

Deterministic assembly processes shaping habitat‐specific glycoside hydrolase composition

AbstractAimGlycoside hydrolases (GHs) encoded by prokaryotes play a crucial role in the degradation of carbohydrates, which is a key step in the carbon cycle. However, their global distribution remains poorly understood. Here, we conducted a comprehensive investigation of the global biogeographic patterns of prokaryotic‐encoded GHs.LocationGlobal.Time periodPresent.Major taxa studiedProkaryotes.MethodsWe conducted a global survey of GH distribution based on 10,000 samples from the Earth Microbiome Project (EMP) and 17,923 completely sequenced prokaryotic genomes. The samples were retrieved from seven continents, covering all 17 EMP Ontology environments. We evaluated the assembly process and influencing factors of GH functional genes within prokaryotic communities, and analysed the rank abundance distributions (RADs), occupancy frequency distributions (OFDs), and taxonomic sources of GH families across various environments.ResultsThe median number of GH genes per thousand genes encoded by global prokaryotic communities was 9.11 (7.16–11.58), with a higher GH abundance in host‐associated communities than in free‐living communities. The median number of GH families in prokaryotic communities was 105 (86–121), with fewer families but tighter functional connections between families in host‐associated communities compared to free‐living communities. In any environment, the RAD of GH families followed a lognormal model, and their OFD was bimodal, with a strong positive correlation between the two. In addition, most GH families had complex and diverse taxonomic sources across different environments.Main conclusionsThis study provides a panoramic view of the functional potentials for carbohydrate degradation across prokaryotic communities under diverse environmental conditions. The composition of GHs encoded by prokaryotic communities exhibits clear habitat specificity, which is driven by a combination of biotic and abiotic factors and generated through highly deterministic assembly processes.

Mechanisms shaping dissolved organic matter and microbial community in lake ecosystems

Lakes are active components of the global carbon cycle and host a range of processes that degrade and modify dissolved organic matter (DOM). Through the degradation of DOM molecules and the synthesis of new compounds, microbes in aquatic environments strongly and continuously influence chemodiversity, which can feedback to influence microbial diversity. Developing a better understanding of the biodiversity patterns that emerge along spatial and environmental gradients is one of the key objectives of community ecology. A changing climate may affect ecological feedback, including those that affect microbial communities. To maintain the function of a lake ecosystem and predict carbon cycling in the environment, it is increasingly important to understand the coupling between microbial and DOM diversity. To unravel the biotic and abiotic mechanisms that control the structure and patterns of DOM and microbial communities in lakes, we combined high-throughput sequencing and ultra-high resolution mass spectrometry together with a null modeling approach. The advantage of null models is their ability to evaluate the relative influences of stochastic and deterministic assembly processes in both DOM and microbial community assemblages. The present study includes spatiotemporal signatures of DOM and the microbial community in six temperate lakes contrasting continental and Mediterranean climates during the productive season. Different environmental conditions and nutrient sources characterized the studied lakes. Our results have shown high covariance between molecular-level DOM diversity and the diversity of individual microbial communities especially with diversity of microeukaryotes and free-living bacteria indicating their dynamic feedback. We found that the differences between lakes and climatic regions were mainly reflected in the diversity of DOM at the molecular formula-level and the microeukaryota community. Furthermore, using null models the DOM assembly was governed by deterministic variable selection operating consistently and strongly within and among lakes. In contrast, microbial community assembly processes were highly variable across lakes with different trophic status and climatic regions. Difference in the processes governing DOM and microbial composition does not indicate weak coupling between these components, rather it suggests that distinct factors may be influencing microbial communities and DOM assemblages separately. Further understanding of the DOM-microbe coupling (or lack thereof) is key to formulating predictive models of future lake ecology and function.

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.

Adaptability of agricultural soil microbial nutrient utilization regulates community assembly under mulching measures on the Loess Plateau

Soil microbial nutrients and resource availability improve with mulching in agroecosystems, resulting in changes of soil microbial nutrient utilization strategies. However, the responses of soil microorganisms to nutrient utilization processes to regulate community assembly and thus maintain resource availability have not been clarified. Here, we performed a long-term field experiment with mulching measures, including no-mulching (NM), straw mulching (SM), plastic mulching (PM), and ridge mulching (RM), conducted on the Loess Plateau of China, to explore the community assembly process in response to microbial nutrient utilization. Microbial nutrient utilization strategies were analysed by measuring soil nutrients, microbial biomass, and extracellular enzyme activities. The results showed that PM and RM acquired C and N nutrients by secreting C- and N-extracellular enzymes in response to C:N- and C:P imbalances in soil chemistry, thereby reducing the nutrient limitation on microbial metabolism and improving microbial C utilization efficiency (CUE). Soil extracellular enzymatic stoichiometry increased and N utilization efficiency (NUE) decreased under mulching and drove an increase in beta-diversity and dominant species abundance in fungal communities. Mulching measures promoted the modular distribution of sensitive microorganisms and aggregation of fungal networks under PM and RM by reducing the stoichiometric imbalance and extracellular enzymatic N:P. At the same time, the microbial community assembly gradually changed from a stochastic to a deterministic process in response to the alleviation of soil C:P imbalance and changes in microbial nutrient utilization, in which the fungal community was dominant. In conclusion, soil microorganisms adaptively responded to changes in soil microbial nutrient utilization through the enhancement of aggregation of fungal co-occurrence networks and deterministic assembly processes. This study provides a better understanding of the impact of mulching on microbial nutrient utilization strategies from a community assembly perspective.

Elevational microbial β diversity and community assembly processes in subarctic ponds

Abstract Knowledge about elevational β diversity patterns and processes is limited for microorganisms, especially in sensitive aquatic ecosystems at high latitudes. Our aim is to investigate elevational β diversity patterns and underlying assembly processes for three biofilm microbial groups in subarctic freshwater ponds. We sampled 89 ponds covering an elevational gradient from 10 to 1038 m above sea level in subarctic Finland and Norway. The microbial groups studied included benthic diatoms, cyanobacteria, and bacteria (i.e., bacteria other than cyanobacteria). We expected to find elevational distance decay in community similarity, driven primarily by variation in the local environment. We further tested whether the level of β diversity decreased towards higher elevations, and whether the relative influence of deterministic and stochastic processes on community assembly changed along the elevational gradient, with increasing effect of deterministic processes at higher elevations under more extreme environmental conditions. As statistical methods, we used generalised dissimilarity modelling, Mantel tests, and a null model with Raup–Crick dissimilarities. For all microbial groups, community dissimilarities increased with increasing environmental or elevational distances. The pure effects of environment were significant for all groups, and pH was the most important variable affecting community dissimilarities. Mean community dissimilarities generally decreased with elevation for all microbial groups. The communities were influenced by both deterministic and stochastic processes, the former of which was stronger towards higher elevations. The influence of deterministic processes was strongest for bacteria. Generally, the communities under deterministic control were more similar to each other than expected by chance. Elevational β diversity patterns of subarctic pond microorganisms primarily reflected environmental effects, showing decreasing β diversity towards high elevations owing to stronger environmental filtering. The relative effects of deterministic or stochastic assembly processes varied among microbial groups, highlighting the need for including multiple groups when studying biodiversity patterns and underlying ecological processes.

Assembly and co-occurrence patterns of rhizosphere bacterial communities are closely linked to soil fertility during continuous cropping of cut chrysanthemum (Chrysanthemum morifolium Ramat).

Continuous cropping is known to have profound effects on the soil microbial community in different planting systems. However, we lack an understanding of how different years of continuous cropping affects rhizosphere soil bacterial community co-occurrence pattern and assembly processes in the cut chrysanthemum (Chrysanthemum morifolium Ramat.) field. We collected the soils from cut chrysanthemum rhizospheres with planting for 1 year (PY1) and continuous cropping for 6 years (CY6) and 12 years (CY12). Real-time quantitative PCR and flow cytometry (FCM) techniques were used to test the 16S rRNA gene copy number and bacterial cell count, respectively. The bacterial community structure was analysed by using high-throughput sequencing technology. The CY12 had a significantly decreased soil fertility index and rhizosphere bacterial living cell counts and gene copy numbers compared to CY6 and PY1 (P <0.05). The rhizosphere bacterial community dissimilarity increased as the continuous cropping years increased. Three main ecological clusters (modules #1, #2, and #3) were observed in the bacterial co-occurrence network across all samples, and only the relative abundance of module #1 (enriched in the CY12) was significantly correlated with soil fertility (P <0.05). Moreover, the rhizosphere bacterial community assembly was primarily governed by the deterministic process under 12 years of continuous cropping. Soil fertility decline correlates with ecological network modularization and the deterministic assembly process of the rhizosphere bacterial community of cut chrysanthemum during continuous cropping.

Conservation tillage and moderate nitrogen application changed the composition, assembly pattern and interaction network of abundant and rare microbial community on straw surface

Microbial-driven straw decomposition is important for soil organic carbon accumulation, nutrient uptake, and crop utilization. However, the mechanism by which tillage and fertilization interactions form the abundant and rare microbial communities that mediate straw degradation in dry farmland remains unclear. Based on an interaction experiment between three tillage practices (zero-till, chisel-till, and conventional plow-till) and three levels of nitrogen fertilizer (180, 240, and 300 kg·N·ha−1), we aimed to understand the community assembly process of abundant and rare microbe in the decomposition of maize straw. We found that the abundant bacterial and fungal communities were governed by stochastic processes, whereas the rare bacterial communities were dominated by deterministic processes. Furthermore, the relative importance of deterministic assembly of all microbial communities was higher in conservation tillage; in addition, the deterministic assembly process of the abundant bacterial and fungal communities was significantly increased by the medium level of nitrogen fertilizer (240 kg·N·ha−1), but the rare microbial community was not significantly affected. Redundancy analysis (RDA) and threshold indicator taxa analysis (TITAN) indicated that soil temperature, pH, and NO3− are the key influencing factors for the abundant and rare microbial communities. Overall, conservation tillage and a medium level of nitrogen fertilizer (240 kg·ha−1) in dry farmland promoted straw decomposition by regulating the development and turnover of straw-decomposing communities, in which they regulated bacterial community succession rather than fungi within a short decomposition time. These findings highlight the distinct responses to conservation tillage and N fertilization in the community assembly of abundant and rare biospheres in maize straw decomposition, and provide additional evidence for the development of conservation tillage applications in drylands.

Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities.

Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.

Microplastics degradation stimulated by in-situ bioelectric field in agricultural soils

Bioelectric field is a stimulated force to degrade xenobiotic pollutants in soils. However, the effect of bioelectric field on microplastics (MPs) aging is unclear. The degradation behavior of polyvinyl chloride (PVC), polyethylene (PE) and polylactic acid (PLA) was investigated in an agricultural soil microbial electrochemical system in which bioelectric field was generated in-situ by native microbes. Based on the density function theory, the energy gaps between the highest and the lowest occupied molecular orbitals of the three polymers with periodic structure were 4.20, 7.24 and 10.09 eV respectively, and further decreased under the electric field, indicating the higher hydrolysis potential of PLA. Meanwhile, the mass loss of PLA in the closed-circuit group (CC) was the highest on day 120, reaching 8.94%, which was 3.01–3.54 times of that without bioelectric field stimulation. This was mainly due to the enrichment of plastic-degrading bacteria and a robust co-occurrence network as the deterministic assembly process, e.g., the abundance of potential plastic-degrading bacteria on the surface of PLA and PVC in the CC increased by 1.92 and 1.30 times, respectively, compared to the open-circuit group. In terms of functional genes, the xenobiotic biodegradation and metabolism capacity of plasticsphere in the CC were stronger than that in soil, and determined by the bioaccessibility of soil nitrogen and carbon. Overall, this study explored the promoting effect of bioelectric field on the degradation of MPs and reveled the mechanism from quantum chemical calculations and microbial community analysis, which provides a novel perception to the in-situ degradation of MPs.

Phylogenetic distance-decay patterns are not explained by local community assembly processes in freshwater lake microbial communities.

While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance-decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance-decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance-decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.