Microbial Community Assembly Processes Research Articles

Selection, drift and community interactions shape microbial biogeographic patterns in the Pacific Ocean

Despite accumulating data on microbial biogeographic patterns in terrestrial and aquatic environments, we still lack a comprehensive understanding of how these patterns establish, in particular in ocean basins. Here we show the relative significance of the ecological mechanisms selection, dispersal and drift for shaping the composition of microbial communities in the Pacific Ocean over a transect of 12,400 km between subantarctic and subarctic regions. In the epipelagic, homogeneous selection contributes 50–60% and drift least to the three mechanism for the assembly of prokaryotic communities whereas in the upper mesopelagic, drift is relatively most important for the particle-associated subcommunities. Temperature is important for the relative significance of homogeneous selection and dispersal limitation for community assembly. The relative significance of both mechanisms was inverted with increasing temperature difference along the transect. For eukaryotes >8 µm, homogeneous selection is also the most important mechanisms at two epipelagic depths whereas at all other depths drift is predominant. As species interactions are essential for structuring microbial communities we further analyzed co-occurrence-based community metrics to assess biogeographic patterns over the transect. These interaction-adjusted indices explained much better variations in microbial community composition as a function of abiotic and biotic variables than compositional or phylogenetic distance measures like Bray–Curtis or UniFrac. Our analyses are important to better understand assembly processes of microbial communities in the upper layers of the largest ocean and how they adapt to effectively perform in global biogeochemical processes. Similar principles presumably act upon microbial community assembly in other ocean basins.

Terrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield

The deep terrestrial biosphere encompasses the life below the photosynthesis-fueled surface that perseveres in typically nutrient and energy depleted anoxic groundwaters. The composition and cycling of this vast dissolved organic matter (DOM) reservoir relevant to the global carbon cycle remains to be deciphered. Here we show that recent Baltic Sea-influenced to ancient pre-Holocene saline Fennoscandian Shield deep bedrock fracture waters carried DOM with a strong terrigenous signature and varying contributions from abiotic and biotic processes. Removal of easily degraded carbon at the surface-to-groundwater transition and corresponding microbial community assembly processes likely resulted in the highly similar DOM signatures across the notably different water types that selected for a core microbiome. In combination with the aliphatic character, depleted δ13C signatures in DOM indicated recent microbial production in the oldest, saline groundwater. Our study revealed the persistence of terrestrially-sourced carbon in severely energy limited deep continental groundwaters supporting deep microbial life.

Soil mesofauna alter the balance between stochastic and deterministic processes in the plastisphere during microbial succession

Plastic debris, as a novel substrate, provides an avenue for enriching microbial growth. Although the structure of the aquatic plastisphere microbial community is well-characterised, linkages between microbial community assembly and species co-existence in the soil plastisphere vary and remain poorly understood, particularly when soil fauna is involved. This study investigated the soil plastisphere community, including bacteria, fungi, and protists, focusing on microbial succession and community assembly processes impacted by soil mesofauna. Certain soil plastisphere microbial taxa thrived at particular time points (e.g. Actinobacteria at 60 d), indicating the irreplaceable role of microplastic selection for time-sensitive taxa. Additionally, the biodiversity of keystone ecological clusters in the soil plastisphere was significantly associated with incubation time. Furthermore, the slopes of bacterial and fungal time-decay curves in soil plastisphere were steeper when treated with soil mesofauna than without soil mesofauna, whereas protist time-decay curves (total and abundant taxa) exhibited the opposite trend. Soil mesofauna increased the relative importance of determinacy in the soil plastisphere bacterial assembly process, while enhancing the stochasticity of fungal and protistan community assemblages. The study demonstrates the complex assembly patterns of soil plastisphere microbial communities, emphasising the importance of interactions between the plastisphere and local soil fauna from an ecological perspective.

Host Species Influence the Gut Microbiota of Endemic Cold-Water Fish in Upper Yangtze River

The fish gut microbiome plays an important role in nutrition absorption and energy metabolism. Studying the gut microbes of cold-water fish is important to understand the dietary adaptation strategies in extreme environments. In this study, the gut samples of Schizothorax wangchiachii (SW, herbivorous), Schizothorax kozlovi (SK, omnivorous), and Percocypris pingi (PP, carnivorous) in the upper Yangtze River were collected, and we sequenced 16S rRNA amplicon to study the potential relationship between gut microbes and host species. The results showed that gut microbial composition and diversity were significantly different between the three cold-water fishes. These fishes had different key taxa in their gut microbes, including bacteria involved in the breakdown of food (e.g., Cetobacterium, Aeromonas, and Clostridium sensu stricto 10). The highest alpha diversity indices (e.g., Chao 1 index) were identified in the herbivore (SW), followed by the carnivore (PP), and the lowest in the omnivore (SK). Non-metric multidimensional scaling (NMDS) results revealed that the gut microbial community of these species was different between host species. The neutral community model (NCM) showed that the microbial community structure of SW was shaped by stochastic processes, and the highest species dispersal was found in SW, followed by PP, and the lowest in SK. The results of niche breadth agreed with these findings. Our results demonstrated that host species influenced the gut microbiome composition, diversity, and microbial community assembly processes of the three cold-water fishes. These findings implied that the variation of gut microbiome composition and function plays a key role in digesting and absorbing nutrients from different foods in cold-water fish.

Machine Learning Prediction of Nitrification From Ammonia- and Nitrite-Oxidizer Community Structure.

Accurately modeling nitrification and understanding the role specific ammonia- or nitrite-oxidizing taxa play in it are of great interest and importance to microbial ecologists. In this study, we applied machine learning to 16S rRNA sequence and nitrification potential data from an experiment examining interactions between cropping systems and rhizosphere on microbial community assembly and nitrogen cycling processes. Given the high dimensionality of microbiome datasets, we only included nitrifers since only a few taxa are capable of ammonia and nitrite oxidation. We compared the performance of linear and nonlinear algorithms with and without qPCR measures of bacterial and archaea ammonia monooxygenase subunit A (amoA) gene abundance. Our feature selection process facilitated the identification of taxons that are most predictive of nitrification and to compare habitats. We found that Nitrosomonas and Nitrospirae were more frequently identified as important predictors of nitrification in conventional systems, whereas Thaumarchaeota were more important predictors in diversified systems. Our results suggest that model performance was not substantively improved by incorporating additional time-consuming and expensive qPCR data on amoA gene abundance. We also identified several clades of nitrifiers important for nitrification in different cropping systems, though we were unable to detect system- or rhizosphere-specific patterns in OTU-level biomarkers for nitrification. Finally, our results highlight the inherent risk of combining data from disparate habitats with the goal of increasing sample size to avoid overfitting models. This study represents a step toward developing machine learning approaches for microbiome research to identify nitrifier ecotypes that may be important for distinguishing ecotypes with defining roles in different habitats.

Soil aggregate modulates microbial ecological adaptations and community assemblies in agricultural soils

Soil aggregates provide spatially heterogeneous microenvironments for soil microbiome and ecological processes. Revealing the nuances of assembly processes in aggregates is critical for understanding the fine-scale organization of the soil microbiome and associated biogeochemistry. However, the effect of aggregate sizes on microbial assemblies remains poorly explored. In this study, we investigated the mechanism underlying the assembly processes of microbial communities within three different aggregates sizes across five long-term fertilization experimental stations throughout eastern China. Our results showed that although geographic sites explained most of the variations in microbial composition in aggregates, aggregates of the same size selected phylogenetically closely related microbial species with similar ecological preferences for specific nutrient variables. Null model analysis showed that environmental selection and dispersal limitation primarily governed the assembly of aggregate bacterial and fungal communities, respectively. The relative importance of deterministic processes on microbial communities increased with the increasing aggregate size across all sites. Multiple stepwise regression analysis indicated that nutrient variables associated with community assembly are distinct in different aggregate-size fractions. Bacterial assembly is mainly affected by total carbon and soil organic carbon in macro- and micro-aggregates, whereas it is influenced by the C/P ratio in the silt + clay fraction. For fungal community assembly, the C/N ratio was the major factor in macroaggregate and silt + clay fractions, while N/P ratio had stronger effects in the microaggregates. Furthermore, fertilization effects on the microbial community assembly processes varied across aggregate sizes. Organic fertilization led to a decrease for bacteria while an increase for fungi in the sorting/dispersal effect ratio. The magnitude of such an impact was higher for macro- and micro-aggregates. GeoChip and enzymatic results further demonstrated the regulation of ecological clusters and functions by nutrient variables across aggregates. Our findings highlight that microbial assembly and functional traits in large aggregate-size fractions are susceptible to nutrient changes, and thus can act as potential biological indicators for sustainable management of agricultural soils.

Geographic Dispersal Limitation Dominated Assembly Processes of Bacterial Communities on Microplastics Compared to Water and Sediment.

Microplastics provide new microbial niches in aquatic environments. Nevertheless, information on the assembly processes and potential ecological mechanisms of bacterial communities on microplastics from reservoirs is lacking. Here, we investigated the assembly processes and potential ecological mechanisms of bacterial communities on microplastics through full-length 16S rRNA sequencing in the Three Gorges Reservoir area of the Yangtze River, compared to water and sediment. The results showed that the Burkholderiaceae were the dominant composition of bacterial communities in microplastics (9.95%), water (25.14%), and sediment (7.22%). The niche width of the bacterial community on microplastics was lower than those in water and sediment. For the microplastics and sediment, distance-decay relationship results showed that the bacterial community similarity was significantly decreased with increasing geographical distance. In addition, the spatial turnover rate of the bacterial community on microplastics along the ~662-km reaches of the Yangtze River in the Three Gorges Reservoir area was higher than that in sediment. Null model analysis showed that the assembly processes of the bacterial community on microplastics were also different from those in water and sediments. Dispersal limitation (52.4%) was the primary assembly process of the bacterial community on microplastics, but variable selection was the most critical assembly process of the bacterial communities in water (47.6%) and sediment (66.7%). Thus, geographic dispersal limitation dominated the assembly processes of bacterial communities on microplastics. This study can enhance our understanding of the assembly mechanism of bacterial communities caused by the selection preference for microplastics from the surrounding environment. IMPORTANCE In river systems, microplastics create new microbial niches that significantly differ from those of the surrounding environment. However, the potential relationships between the biogeographic distribution and assembly processes of microbial communities on microplastics were still not well understood. This study could help us address the lack of knowledge about the assembly processes of bacterial communities on microplastics caused by selection from the surrounding environment. In this study, strong geographic dispersal limitation dominated assembly processes of bacterial communities on microplastics, compared to water and sediment, which may be responsible for the microplastic bacterial richness, and the niche distance was lower than those in water and sediment. In addition, sediment may be the main potential source of bacterial communities on microplastics in the Three Gorges Reservoir area, which makes higher community similarity between microplastics and sediment than between microplastics and water.

Changes of the Freshwater Microbial Community Structure and Assembly Processes during Different Sample Storage Conditions.

A long-standing dilemma for microbial analyses is how to handle and store samples, as it is widely assumed that the microbial diversity and community patterns would be affected by sample storage conditions. However, it is quite challenging to maintain consistency in field sampling, especially for water sample collection and storage. To obtain a comprehensive understanding of how sample storage conditions impact microbial community analyses and the magnitude of the potential storage effects, freshwater samples were collected and stored in bottles with lid closed and without lid at room temperature for up to 6 days. We revealed the dynamics of prokaryotic and eukaryotic microbial communities under different storage conditions over time. The eukaryotic microbial communities changed at a faster rate than the prokaryotic microbial communities during storage. The alpha diversity of the eukaryotic microbial communities was not substantially influenced by container status or storage time for up to 12 h, but the beta diversity differed significantly between the control and all treatment samples. By contrast, no significant changes of either the alpha or beta diversity of the prokaryotic microbial communities were observed within 12 h of room-temperature storage, regardless of the container status. The potential interactions between microbial taxa were more complex when samples were stored in sealed bottles, and the deterministic processes played an increasingly important role in shaping the freshwater microbial communities with storage time. Our results suggest that water samples collected and stored without refrigeration for no more than 12 h may still be useful for downstream analyses of prokaryotic microbial communities. If the eukaryotic microbial communities are desired, storage of water samples should be limited to 3 h at room temperature.

Environmental selection dominates over dispersal limitation in shaping bacterial biogeographical patterns across different soil horizons of the Qinghai-Tibet Plateau

Soil microbial biogeographical patterns have been widely explored from horizontal to vertical scales. However, studies of microbial vertical distributions were still limited (e.g., how soil genetic horizons influence microbial distributions). To shed light on this question, we investigated soil bacterial communities across three soil horizons (topsoil: horizon A; midsoil: horizon B; subsoil: horizon C) of 60 soil profiles along a 3500 km transect in the Qinghai-Tibet Plateau. We found that bacterial diversity was highest in the topsoil and lowest in the subsoil, and community composition significantly differed across soil horizons. The network complexity decreased from topsoil to subsoil. There were significant geographical/environmental distance-decay relationships (DDR) in three soil horizons, with a lower slope from topsoil to subsoil due to the decreased environmental heterogeneity. Variation partitioning analysis (VPA) showed that bacterial community variations were explained more by environmental than spatial factors. Although environmental selection processes played a dominant role, null model analysis revealed that deterministic processes (mainly variable selection) decreased with deeper soil horizons, while stochastic processes (mainly dispersal limitation) increased from topsoil to subsoil. These results suggested that microbial biogeographical patterns and community assembly processes were soil horizon dependent. Our study provides new insights into the microbial vertical distributions in large-scale alpine regions and highlights the vital role of soil genetic horizons in affecting microbial community assembly, which has implications for understanding the pedogenetic process and microbial responses to extreme environment under climate change.

Tree Size Drives Diversity and Community Structure of Microbial Communities on the Bark of Beech (Fagus sylvatica)

Tree bark constitutes an ideal habitat for microbial communities, because it is a stable substrate, rich in micro-niches. Bacteria, fungi, and terrestrial microalgae together form microbial communities, which in turn support more bark-associated organisms, such as mosses, lichens, and invertebrates, thus contributing to forest biodiversity. We have a limited understanding of the diversity and biotic interactions of the bark-associated microbiome, as investigations have mainly focused on agriculturally relevant systems and on single taxonomic groups. Here we implemented a multi-kingdom metabarcoding approach to analyze diversity and community structure of the green algal, bacterial, and fungal components of the bark-associated microbial communities of beech, the most common broadleaved tree of Central European forests. We identified the most abundant taxa, hub taxa, and co-occurring taxa. We found that tree size (as a proxy for age) is an important driver of community assembly, suggesting that environmental filtering leads to less diverse fungal and algal communities over time. Conversely, forest management intensity had negligible effects on microbial communities on bark. Our study suggests the presence of undescribed, yet ecologically meaningful taxa, especially in the fungi, and highlights the importance of bark surfaces as a reservoir of microbial diversity. Our results constitute a first, essential step toward an integrated framework for understanding microbial community assembly processes on bark surfaces, an understudied habitat and neglected component of terrestrial biodiversity. Finally, we propose a cost-effective sampling strategy to study bark-associated microbial communities across large spatial or environmental scales.

Changes in diversity, composition and assembly processes of soil microbial communities during Robinia pseudoacacia L. restoration on the Loess Plateau, China

Changes in diversity, composition and assembly processes of soil microbial communities during Robinia pseudoacacia L. restoration on the Loess Plateau, China

Brassica napus Bacterial Assembly Processes Vary with Plant Compartment and Growth Stage but Not between Lines.

ABSTRACTHolobiont bacterial community assembly processes are an essential element to understanding the plant microbiome. To elucidate these processes, leaf, root, and rhizosphere samples were collected from eight lines of Brassica napus in Saskatchewan over the course of 10 weeks. We then used ecological null modeling to disentangle the community assembly processes over the growing season in each plant part. The root was primarily dominated by stochastic community assembly processes, which is inconsistent with previous studies that suggest of a highly selective root environment. Leaf assembly processes were primarily stochastic as well. In contrast, the rhizosphere was a highly selective environment. The dominant rhizosphere selection process leads to more similar communities. Assembly processes in all plant compartments were dependent on plant growth stage with little line effect on community assembly. The foundations of assembly in the leaf were due to the harsh environment, leading to dominance of stochastic effects, whereas the stochastic effects in the root interior likely arise due to competitive exclusion or priority effects. Engineering canola microbiomes should occur during periods of strong selection assuming strong selection could promote beneficial bacteria. For example, engineering the microbiome to resist pathogens, which are typically aerially born, should focus on the flowering period, whereas microbiomes to enhance yield should likely be engineered postflowering as the rhizosphere is undergoing strong selection.IMPORTANCE In order to harness the microbiome for more sustainable crop production, we must first have a better understanding of microbial community assembly processes that occurring during plant development. This study examines the bacterial community assembly processes of the leaf, root, and rhizosphere of eight different lines of Brassica napus over the growing season. The influence of growth stage and B. napus line were examined in conjunction with the assembly processes. Understanding what influences the assembly processes of crops might allow for more targeted breeding efforts by working with the plant to manipulate the microbiome when it is undergoing the strongest selection pressure.

Conversion of mangrove forests to shrimp ponds in southeastern China destabilizes sediment microbial networks

Within the ecosystem, mangroves serve diverse functions by acting as a carbon sink, removing nitrogen, providing habitats for marine organisms, and regulating climate. Nowadays, many mangrove forests are being converted to shrimp ponds across the world, and several studies have quantified the effects of this conversion on soil carbon stocks and greenhouse gas emissions. However, its effects on the soil microbial community structure and assembly processes remain unclear. In the present study, high-throughput sequencing and multivariate statistical analyses were used to quantify the characteristics of soil microbial communities in common mangrove types in southeastern China and the adjacent converted shrimp ponds. The relative abundance of Verrucomicrobia, Cyanobacteria, and Firmicutes was significantly increased in the shrimp pond sediment compared with that in the mangrove sediment, whereas the archaea, represented by Crenarchaeota and Euryarchaeota, exhibited the opposite patterns. Moreover, the sediment microbial communities in the shrimp ponds exhibited more obvious biogeographical distributions than those in the mangrove habitat. Null model analysis revealed that variable selection (via deterministic processes) governed the microbial community assembly in the mangrove sediments, while dispersal limitation (via stochastic processes) shaped the microbial community structure in the shrimp pond sediments. Our findings suggest that converting mangrove forest habitats to shrimp ponds significantly alters the sediment microbial networks, rendering them unstable (by disrupting the network topology parameters such as modularity, total cohesion, and negative cohesion). This may in turn lead to alterations in various ecosystem functions in response to habitat conversion, highlighting the need for better preserving mangroves through appropriate climate change mitigation measures.

Precipitation balances deterministic and stochastic processes of bacterial community assembly in grassland soils

Microbial biodiversity is crucial for maintaining ecosystem functions. As climate change progresses at both global and regional scales, there is a need to understand microbial community assembly processes and diversity to predict changes in soil function in different regions. However, our knowledge of the mechanisms that shape bacterial β diversity at multiple spatial scales with complex environmental gradients is very limited. To investigate the mechanisms driving bacterial β diversity at regional (across transects) and local (within transect) scales, soil samples were collected from 30 grassland ecosystems in three east-west transects in northern China. The regional species pools influenced β diversity by mediating rare taxa migration across the three transects. After correcting for regional differences in species, the importance of local community assembly processes in controlling bacterial diversity was independent of spatial scales. Homogeneous selection (HoS, 39%–60%) and dispersal limitation (DL, 31%–54%) proved to be the most important community assembly processes for soil bacteria. Two dominant bacterial taxa accounting for 65% of the total abundance were identified, mainly including Acidobacteria, Actinobacteria, and Proteobacteria, with 63% and 64% contributions for the HoS and DL, respectively. Mean annual precipitation (MAP) mediated the relative importance of deterministic and stochastic assembly in bacterial communities. Consistently across all spatial scales, the relative importance of DL increased with aridity, and the contribution of HoS decreased. Importantly, the relative abundance of the two dominant bacterial taxa controlled by the HoS and DL varied with MAP. Collectively, our results provide clear evidence that water availability mediates the community assembly process of soil bacteria. This conclusion is of utmost importance for predicting the dynamics of soil microbial diversity and nutrient cycling in natural ecosystems in drylands.

Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns.

Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.

土壤动物肠道微生物多样性研究进展

PDF HTML阅读 XML下载 导出引用 引用提醒 土壤动物肠道微生物多样性研究进展 DOI: 10.5846/stxb202009182433 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金面上项目（42071059，41671259） A review on gut microbial diversity of soil animals Author: Affiliation: Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:随着分子生物学技术方法的快速发展，动物肠道微生物已成为医学、动物生理学与微生物生态学等研究领域热点。土壤动物种类繁多，分布广泛，其作为陆地生态系统重要组分，是驱动生态系统功能的关键因子。土壤动物体内的微生物由于与宿主长期共存，在与宿主协同进化中形成了丰富多样的群落结构，能够影响土壤动物本身的健康，进而介导土壤动物生态功能的实现。近些年，土壤动物肠道微生物工作方兴未艾，日渐得到重视。总结了四个部分内容：1）首先总结了土壤动物肠道微生物多样性领域的研究现状，该领域年发文量逐年增长，且近十年增长快速。土壤模式生物肠道微生物多样性研究较多且更为深入。土壤动物肠道微生物多样性组成与驱动机制、共存机制及群落构建的理论研究是该领域前沿；2）进而展示了土壤动物肠道微生物多样性组成和研究方法，土壤动物肠道菌群组成以变形菌门、厚壁菌门、放线菌门和拟杆菌门为主。早期工作基于传统分离培养，近年来新一代测序技术推动了该领域发展；3）接着关注了土壤动物肠道微生物的生态学功能，总体上体现在肠道微生物能帮助宿主分解食物基质、参与营养利用、影响寿命和繁殖及提高宿主免疫能力，且其能够影响土壤动物的气体排放及介导其对生态系统的元素转化循环；4）最后重点阐述了影响土壤动物肠道微生物的主要因素（包含宿主和环境因素），土壤动物肠道微生物群落与宿主肠道形态、系统发生、食性、发育阶段及栖息生境和环境污染物息息相关。研究可增加人们对土壤动物肠道微生物的组成和多样性的认识，并帮助深入思考肠道微生物及其同宿主互作机制对土壤生物多样性及生态系统功能的影响。 Abstract:With the rapid development of molecular techniques, gut microbiota of animals have become a hot topic in the fields of medicine, animal physiology and microbial ecology. Soil animals, with high species diversity and wild distribution, are important organisms playing significantly functional roles in terrestrial ecosystems. Associations of microbiota with their animal hosts are evolutionary products of interactions between the two parties. The animal-associated microbiota may indirectly regulate ecosystem functions by influencing host physiological functions. In the recent years, studies on gut microbiota of soil animals have gained much attention. Here, 1) we summarized the current research progresses in studies on microbial community associated with soil animals:Number of publications of this research field increased, especially in the past decade; most of the gut microbial studies focused on soil model animals; frontiers of the research topics included species composition, co-existence and assembly processes of gut microbial communities. 2) We described microbial compositions in soil animal gut, and introduced the common approaches used in the field:Dominant microbial taxa included Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes; while early work was mainly based on culturing methods, new sequencing technology had advanced the field recently. 3) We described biological and ecological functions provided by gut microbiota:Gut microbiota could help soil animals in digesting compound food resources, participate in host nutrient assimilation, affect host lifetime and reproduction and adjust host immune capacity; they may also indirectly affect gas emission and mediate nutrient cycling in soil ecosystems. 4) We discussed the main drivers, including host attributes and environmental factors, that influenced gut microbiota of soil animals:The gut microbial community was closely related to host intestinal morphology, phylogeny, feeding habits and developmental stages, as well as habitat and environmental pollutants. This review can help to understand composition and diversity of gut microbiota of soil animals and advance our knowledge on the roles played by gut microbiota in soil biodiversity and ecosystem functioning. 参考文献 相似文献 引证文献

Season and Nh3-N Significantly Affect the Microbial Community Structure and Assembly Processes in an Agricultural Drainage Receiving Lake

Season and Nh3-N Significantly Affect the Microbial Community Structure and Assembly Processes in an Agricultural Drainage Receiving Lake

Bacterial rather than fungal diversity and community assembly drive soil multifunctionality in a subtropical forest ecosystem.

Microbial diversities are key drivers of soil multifunctionality in terrestrial ecosystems and are important for stability and productivity of ecosystems. However, the relationships among microbial diversity, community assembly and soil multifunctionality in forest ecosystems remained unclear. Here, soil samples were collected from a subtropical forest ecosystem, Lushan Mountain, China. High-throughput sequencing was employed to reveal the bacterial/fungal community assembly and biodiversity, as well as 10 enzyme activities were measured to assess soil multifunctionality. We found that soil multifunctionality was negatively regulated by bacterial and fungal alpha diversity, implying a higher potential functional redundancy in this forest soil. The null model indicated that deterministic processes (variable selection) and stochastic processes (dispersal limitation) govern bacterial and fungal phylogenetic turnover, respectively. Correlation analysis revealed that bacterial rather than fungal community assembly processes have a significant linkage to soil multifunctionality. These observations projected that soil variables could regulate multifunctionality by shaping the phylogenetic and taxonomic turnover of bacteria rather than fungi. In summary, our study highlighted that soil multifunctionality is mainly driven by bacterial diversity and community assembly processes while not fungal, presenting different views and knowledge of microbial diversity and community assembly processes in ecosystem functioning.

Actinobacterial biofertilizer improves the yields of different plants and alters the assembly processes of rhizosphere microbial communities

Biofertilizers are not always applicable for the local environment or specific plant species. Therefore, it is necessary to assess the universal effects of a biofertilizer when applied to different plants across regions. Particularly, how actinobacteria-based biofertilizers affect the assembly of rhizosphere microbial communities remains unknown. Here, we assessed the universal validity and regulatory role of a biofertilizer containing Streptomyces pactum Act12 and Streptomyces rochei D74 in reshaping the rhizosphere microbial communities associated with different plants grown in Shaanxi, Inner Mongolia, and Xinjiang of northwest China. A greenhouse pot experiment was conducted with cucumber, and field experiments were conducted with tomato, pepper, sunflower, and jujube. Compared with the control, biofertilizer application improved the yield of the different plants by 7.7%–55.6%. The community composition of rhizosphere fungi shifted in biofertilizer-treated soils, despite no significant differences in the species diversity or richness of bacteria and fungi. For single plant species, the alpha diversity indices of rhizosphere microbial communities showed distinctly different trends in response to biofertilizer application. Following biofertilizer application, the relative abundance of some plant beneficial taxa (such as Chitinophaga, Dokdonella, Pseudoxanthomonas, and Coprinellus) increased, while the relative abundance of some phytopathogenic taxa (such as Cladosporium and Gibberella) decreased. Stochastic processes contributed predominantly to the bacterial community assembly, whereas the relative contribution of stochastic processes to fungal community assembly increased by 6.3% under biofertilizer treatment. Biofertilizer application reduced the average connectivity and density of microbial co-occurrence networks and changed some of the keystone genera. The results of this study may provide direction for the use of biofertilizers containing Streptomyces strains.

Changes in assembly processes of soil microbial communities in forest-to-cropland conversion in Changbai Mountains, northeastern China

In response to human-induced changes in the environment, it is crucial to assess the underlying factors of the impacts of forest conversion on ecosystem function. However, research is limited on bacteria and fungi diversity, functional properties, and community assembly mechanisms in response to forest-to-cropland conversion. We categorized soil bacterial and fungal communities from primary forest, secondary forest, and cropland in Changbai Mountains, China. We found that forest-to-cropland conversion altered the structure and composition of bacterial and fungal communities and might be associated with potential changes in function. The null models indicated that the conversion from forest to cropland enhanced the bacterial dispersal limitation process and weakened the fungal dispersal limitation processes. Furthermore, ecological drift dominates the ecological processes of cropland fungi. Both edaphic properties (the content of C: N ratio, available phosphorus, nitrate) significantly impacted on soil bacterial and fungal community structures. In addition, there were significant functional variations in the fungal community between forest-to-cropland. The ectomycorrhizal and saprotrophic fungi showed increased abundance in the forest microbial communities, whereas the endophytic and pathogenic fungal abundance was increased in cropland soil. Taken together, our data illustrate the differences in the response of bacteria and fungi to forest-to-cropland conversion in temperate forest areas and deepen our understanding of the effects of forest conversion on microbial functions and community assembly processes.