土壤细菌网络互作调控线虫肠道细菌群落

动物肠道细菌群落在联系宿主与生态系统功能中发挥着至关重要的作用。【目的】本研究旨在评估绿肥翻压和水稻生长不同时期对土壤细菌和线虫肠道细菌群落组成和结构的影响,并探究土壤细菌和线虫肠道细菌群落间的潜在关联关系。【方法】基于盆栽试验,结合16S rRNA基因高通量测序技术,分析黑麦草翻压和对照处理下水稻生长的前期(返青期)和后期(收获期)土壤细菌和线虫肠道细菌群落,结合网络分析研究土壤细菌网络互作对线虫肠道细菌群落的潜在影响。【结果】黑麦草翻压对土壤细菌和线虫肠道细菌群落组成和结构没有显著影响(P>0.05);水稻生长后期样品比前期样品具有更高的α多样性。基于随机森林机器学习法获得的土壤细菌和线虫肠道细菌生物标志物之间存在广泛的显著相关关系,为土壤细菌群落变化调控线虫肠道细菌群落组成提供了有力的证据。共现网络分析表明土壤细菌之间的正相互作用显著促进了土壤细菌和线虫肠道细菌之间的正相互作用(P<0.01),进而影响了线虫肠道细菌之间的网络互作。结构方程模型进一步表明土壤养分含量的降低主要通过降低土壤细菌之间正相互作用,从而间接影响线虫肠道细菌之间的互作。【结论】土壤细菌互作可能在...     

Atmospheric N deposition alters connectance,but not functional potential among saprotrophic bacterial communities

The use of co‐occurrence patterns to investigate interactions between micro‐organisms has provided novel insight into organismal interactions within microbial communities. However, anthropogenic impacts on microbial co‐occurrence patterns and ecosystem function remain an important gap in our ecological knowledge. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. This ecosystem‐level response occurred concomitantly with compositional changes in saprophytic fungi and bacteria. Here, we investigated the influence of experimental N deposition on biotic interactions among forest floor bacterial assemblages by employing phylogenetic and molecular ecological network analysis. When compared to the ambient treatment, the forest floor bacterial community under experimental N deposition was less rich, more phylogenetically dispersed and exhibited a more clustered co‐occurrence network topology. Together, our observations reveal the presence of increased biotic interactions among saprotrophic bacterial assemblages under future rates of N deposition. Moreover, they support the hypothesis that nearly two decades of experimental N deposition can modify the organization of microbial communities and provide further insight into why anthropogenic N deposition has reduced decomposition, increased soil C storage and accelerated phenolic DOC production in our field experiment.     

Disentangling the effect of hybrid interactions and of the constant effort hypothesis on ecological community stability

In the last years, a remarkable theoretical effort has been made in order to understand the relation between stability and complexity in ecological communities. Yet, what maintains species diversity in real ecological communities is still an open question. The non‐random structures of ecological interaction networks have been recognized as one key ingredient impacting the maximum number of coexisting species within the ecological community. However most of the earlier theoretical studies have considered communities with only one interaction type (either antagonistic, competitive or mutualistic). Recently, it has been proposed that multiple interaction types might stabilize ecosystems and that, in this hybrid case, increasing complexity increases stability. Here we show that these results depend on ad hoc hypothesis that the authors used in their model and we highlight the need to disentangle the role of multiple interaction types and constant interaction effort allocation on community stability. Indeed, we find that mixing of mutualistic and predator–prey interaction types does not stabilize the community dynamics and we demonstrate that a positive correlation between complexity and stability is observed only if a constant effort allocation is imposed in the ecological interactions. Synthesis In recent years a sparkling research has been devoted to the search of new theoretical mechanisms to explain way ecosystems may persist despite their complexity. Here we show that, contrary to what recently suggested (Mougi et al. 2012), the mismatch between theoretical results and empirical evidences on the stability of ecological community is still there also for communities with both mutualistic and antagonistic interactions, and the ‘complexity‐stability’ paradox is still alive. Indeed, we demonstrate that their results arise as an artifact of the peculiar rescaling of the interaction strengths they imposed. Our study suggests that further theoretical studies and experimental evidences are still needed to better understand the role of interaction strengths in real ecological communities.     

Phylogenetic Analysis of Bacterial Communities in Different Regions of the Gastrointestinal Tract of Agkistrodon piscivorus,the Cottonmouth Snake

Vertebrates are metagenomic organisms in that they are composed not only of their own genes but also those of their associated microbial cells. The majority of these associated microorganisms are found in the gastrointestinal tract (GIT) and presumably assist in processes such as energy and nutrient acquisition. Few studies have investigated the associated gut bacterial communities of non-mammalian vertebrates, and most rely on captive animals and/or fecal samples only. Here we investigate the gut bacterial community composition of a squamate reptile, the cottonmouth snake, Agkistrodon piscivorus through pyrosequencing of the bacterial 16S rRNA gene. We characterize the bacterial communities present in the small intestine, large intestine and cloaca. Many bacterial lineages present have been reported by other vertebrate gut community studies, but we also recovered unexpected bacteria that may be unique to squamate gut communities. Bacterial communities were not phylogenetically clustered according to GIT region, but there were statistically significant differences in community composition between regions. Additionally we demonstrate the utility of using cloacal swabs as a method for sampling snake gut bacterial communities.     

Unraveling negative biotic interactions determining soil microbial community assembly and functioning

Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.Subject terms: Soil microbiology, Ecology     

Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer,multi-species spread and geographical clustering

The human gut microbiota is a dense microbial ecosystem with extensive opportunities for bacterial contact-dependent processes such as conjugation and Type VI secretion system (T6SS)-dependent antagonism. In the gut Bacteroidales, two distinct genetic architectures of T6SS loci, GA1 and GA2, are contained on Integrative and Conjugative Elements (ICE). Despite intense interest in the T6SSs of the gut Bacteroidales, there is only a superficial understanding of their evolutionary patterns, and of their dissemination among Bacteroidales species in human gut communities. Here, we combine extensive genomic and metagenomic analyses to better understand their ecological and evolutionary dynamics. We identify new genetic subtypes, document extensive intrapersonal transfer of these ICE to Bacteroidales species within human gut microbiomes, and most importantly, reveal frequent population fixation of these newly armed strains in multiple species within a person. We further show the distribution of each of the distinct T6SSs in human populations and show there is geographical clustering. We reveal that the GA1 T6SS ICE integrates at a minimal recombination site leading to their integration throughout genomes and their frequent interruption of genes, whereas the GA2 T6SS ICE integrate at one of three different tRNA genes. The exclusion of concurrent GA1 and GA2 T6SSs in individual strains is associated with intact T6SS loci and with an ICE-encoded gene. By performing a comprehensive analysis of mobile genetic elements (MGE) in co-resident Bacteroidales species in numerous human gut communities, we identify 74 MGE that transferred to multiple Bacteroidales species within individual gut microbiomes. We further show that only three other MGE demonstrate multi-species spread in human gut microbiomes to the degree demonstrated by the GA1 and GA2 ICE. These data underscore the ubiquity and dissemination of mobile T6SS loci within Bacteroidales communities and across human populations.     

In vitro interaction network of a synthetic gut bacterial community

A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM¹²) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM¹² interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, Enterococcus faecalis KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM¹² interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies.Subject terms: Microbiome, Microbial ecology     

Negative interactions determine Clostridioides difficile growth in synthetic human gut communities

Understanding the principles of colonization resistance of the gut microbiome to the pathogen Clostridioides difficile will enable the design of defined bacterial therapeutics. We investigate the ecological principles of community resistance to C. difficile using a synthetic human gut microbiome. Using a dynamic computational model, we demonstrate that C. difficile receives the largest number and magnitude of incoming negative interactions. Our results show that C. difficile is in a unique class of species that display a strong negative dependence between growth and species richness. We identify molecular mechanisms of inhibition including acidification of the environment and competition over resources. We demonstrate that Clostridium hiranonis strongly inhibits C. difficile partially via resource competition. Increasing the initial density of C. difficile can increase its abundance in the assembled community, but community context determines the maximum achievable C. difficile abundance. Our work suggests that the C. difficile inhibitory potential of defined bacterial therapeutics can be optimized by designing communities featuring a combination of mechanisms including species richness, environment acidification, and resource competition.     

The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics

Multiple forces structure natural microbial communities, but the relative roles and interactions of these drivers are poorly understood. Gradients of physical and chemical parameters can be especially influential. In traditional ecological theory, variability in environmental conditions across space and time represents habitat heterogeneity, which may shape communities. Here we used aquatic microbial communities as a model to investigate the relationship between habitat heterogeneity and community composition and dynamics. We defined spatial habitat heterogeneity as vertical temperature and dissolved oxygen (DO) gradients in the water column, and temporal habitat heterogeneity as variation throughout the open-water season in these environmental parameters. Seasonal lake mixing events contribute to temporal habitat heterogeneity by destroying and re-creating these gradients. Because of this, we selected three lakes along a range of annual mixing frequency (polymictic, dimictic, meromictic) for our study. We found that bacterial community composition (BCC) was distinct between the epilimnion and hypolimnion within stratified lakes, and also more variable within the epilimnia through time. We found stark differences in patterns of epilimnion and hypolimnion dynamics over time and across lakes, suggesting that specific drivers have distinct relative importance for each community.     

Ecological drift and local exposures drive enteric bacterial community differences within species of Galápagos iguanas

Diet strongly influences the intestinal microbial communities through species sorting. Alternatively, these communicates may differ because of chance variation in local microbial exposures or species losses among allopatric host populations (i.e. ecological drift). We investigated how these forces shape enteric communities of Galápagos marine and land iguanas. Geographically proximate populations shared more similar communities within a host ecotype, suggesting a role for ecological drift during host colonization of the islands. Additionally, evidence of taxa sharing between proximate heterospecific host populations suggests that contemporary local exposures also influence the gut community assembly. While selective forces such as host-bacterial interactions or dietary differences are dominant drivers of intestinal community differences among hosts, historical and contemporary processes of ecological drift may lead to differences in bacterial composition within a host species. Whether such differences in community structure translate into geographic variation in benefits derived from these intimate microbial communities remains to be explored.     

Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function

We have investigated microbial mats of alkaline siliceous hot springs in Yellowstone National Park as natural model communities to learn how microbial populations group into species-like fundamental units. Here, we bring together empirical patterns of the distribution of molecular variation in predominant mat cyanobacterial populations, theory-based modelling of how to demarcate phylogenetic clusters that correspond to ecological species and the dynamic patterns of the physical and chemical microenvironments these populations inhabit and towards which they have evolved adaptations. We show that putative ecotypes predicted by the theory-based model correspond well with distribution patterns, suggesting populations with distinct ecologies, as expected of ecological species. Further, we show that increased molecular resolution enhances our ability to detect ecotypes in this way, though yet higher molecular resolution is probably needed to detect all ecotypes in this microbial community.     

Interactions retain the co‐phylogenetic matching that communities lost

Both species and their interactions are affected by changes that occur at evolutionary time‐scales, and these changes shape both ecological communities and their phylogenetic structure. That said, extant ecological community structure is contingent upon random chance, environmental filters and local effects. It is therefore unclear how much ecological signal local communities should retain. Here we show that, in a host–parasite system where species interactions vary substantially over a continental gradient, the ecological significance of individual interactions is maintained across different scales. Notably, this occurs despite the fact that observed community variation at the local scale frequently tends to weaken or remove community‐wide phylogenetic signal. When considered in terms of the interplay between community ecology and coevolutionary theory, our results demonstrate that individual interactions are capable and indeed likely to show a consistent signature of past evolutionary history even when woven into communities that do not.     

Eco-evolutionary feedbacks drive species interactions

In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the key to understanding biological communities, it is important to know how species interactions arise and evolve. Here, we show that the feedback between ecological and evolutionary processes has a fundamental role in the emergence and dynamics of species interaction. Using a two-species artificial community, we demonstrate that ecological processes and rapid evolution interact to influence the dynamics of the symbiosis between a eukaryote (Saccharomyces cerevisiae) and a bacterium (Rhizobium etli). The simplicity of our experimental design enables an explicit statement of causality. The niche-constructing activities of the fungus were the key ecological process: it allowed the establishment of a commensal relationship that switched to ammensalism and provided the selective conditions necessary for the adaptive evolution of the bacteria. In this latter state, the bacterial population radiates into more than five genotypes that vary with respect to nutrient transport, metabolic strategies and global regulation. Evolutionary diversification of the bacterial populations has strong effects on the community; the nature of interaction subsequently switches from ammensalism to antagonism where bacteria promote yeast extinction. Our results demonstrate the importance of the evolution-to-ecology pathway in the persistence of interactions and the stability of communities. Thus, eco-evolutionary dynamics have the potential to transform the structure and functioning of ecosystems. Our results suggest that these dynamics should be considered to improve our understanding of beneficial and detrimental host–microbe interactions.     

Spatial heterogeneity of eukaryotic microbial communities in an unstudied geothermal diatomaceous biological soil crust: Yellowstone National Park, WY, USA

Knowledge of microbial communities and their inherent heterogeneity has dramatically increased with the widespread use of high-throughput sequencing technologies, and we are learning more about the ecological processes that structure microbial communities across a wide range of environments, as well as the relative scales of importance for describing bacterial communities in natural systems. Little work has been carried out to assess fine-scale eukaryotic microbial heterogeneity in soils. Here, we present findings from a bar-coded 18S rRNA survey of the eukaryotic microbial communities in a previously unstudied geothermal diatomaceous biological soil crust in Yellowstone National Park, WY, USA, in which we explicitly compare microbial community heterogeneity at the particle scale within soil cores. Multivariate analysis of community composition showed that while subsamples from within the same soil core clustered together, community dissimilarity between particles in the same core was high. This study describes a novel soil microbial environment and also adds to our growing understanding of microbial heterogeneity and the scales relevant to the study of soil microbial communities.     

Geographical and ecological stability of the symbiotic mid‐gut microbiota in European firebugs,Pyrrhocoris apterus (Hemiptera,Pyrrhocoridae)

Symbiotic bacteria often play an essential nutritional role for insects, thereby allowing them to exploit novel food sources and expand into otherwise inaccessible ecological niches. Although many insects are inhabited by complex microbial communities, most studies on insect mutualists so far have focused on single endosymbionts and their interactions with the host. Here, we provide a comprehensive characterization of the gut microbiota of the red firebug (Pyrrhocoris apterus, Hemiptera, Pyrrhocoridae), a model organism for physiological and endocrinological research. A combination of several culture‐independent techniques (454 pyrosequencing, quantitative PCR and cloning/sequencing) revealed a diverse community of likely transient bacterial taxa in the mid‐gut regions M1, M2 and M4. However, the completely anoxic M3 region harboured a distinct microbiota consisting of facultative and obligate anaerobes including Actinobacteria (Coriobacterium glomerans and Gordonibacter sp.), Firmicutes (Clostri‐dium sp. and Lactococcus lactis) and Proteobacteria (Klebsiella sp. and a previously undescribed Rickettsiales bacterium). Characterization of the M3 microbiota in different life stages of P. apterus indicated that the symbiotic bacterial community is vertically transmitted and becomes well defined between the second and third nymphal instar, which coincides with the initiation of feeding. Comparing the mid‐gut M3 microbial communities of P. apterus individuals from five different populations and after feeding on three different diets revealed that the community composition is qualitatively and quantitatively very stable, with the six predominant taxa being consistently abundant. Our findings suggest that the firebug mid‐gut microbiota constitutes a functionally important and possibly coevolved symbiotic community.     

Cross-kingdom interactions matter: fungal-mediated interactions structure an insect community on oak

Although phytophagous insects and plant pathogens frequently share the same host plant, interactions among such phylogenetically distant taxa have received limited attention. Here, we place pathogens and insects in the context of a multitrophic-level community. Focusing on the invasive powdery mildew Erysiphe alphitoides and the insect community on oak (Quercus robur), we demonstrate that mildew-insect interactions may be mediated by both the host plant and by natural enemies, and that the trait-specific outcome of individual interactions can range from negative to positive. Moreover, mildew affects resource selection by insects, thereby modifying the distribution of a specialist herbivore at two spatial scales (within and among trees). Finally, a long-term survey suggests that species-specific responses to mildew scale up to generate landscape-level variation in the insect community structure. Overall, our results show that frequently overlooked cross-kingdom interactions may play a major role in structuring terrestrial plant-based communities.     

The effects of space and diversity of interaction types on the stability of complex ecological networks

The relationship between structure and stability in ecological networks and the effect of spatial dynamics on natural communities have both been major foci of ecological research for decades. Network research has traditionally focused on a single interaction type at a time (e.g. food webs, mutualistic networks). Networks comprising different types of interactions have recently started to be empirically characterized. Patterns observed in these networks and their implications for stability demand for further theoretical investigations. Here, we employed a spatially explicit model to disentangle the effects of mutualism/antagonism ratios in food web dynamics and stability. We found that increasing levels of plant-animal mutualistic interactions generally resulted in more stable communities. More importantly, increasing the proportion of mutualistic vs. antagonistic interactions at the base of the food web affects different aspects of ecological stability in different directions, although never negatively. Stability is either not influenced by increasing mutualism—for the cases of population stability and species’ spatial distributions—or is positively influenced by it—for spatial aggregation of species. Additionally, we observe that the relative increase of mutualistic relationships decreases the strength of biotic interactions in general within the ecological network. Our work highlights the importance of considering several dimensions of stability simultaneously to understand the dynamics of communities comprising multiple interaction types.     

Effect of livestock grazing in the partitions of a semiarid plant–plant spatial signed network

In recent times, network theory has become a useful tool to study the structure of the interactions in ecological communities. However, typically, these approaches focus on a particular kind of interaction while neglecting other possible interactions present in the ecosystem. Here, we present an ecological network for plant communities that consider simultaneously positive and negative interactions, which were derived from the spatial association and segregation between plant species. We employed this network to study the structure and the association strategies in a semiarid plant community of Cabo de Gata-Níjar Natural Park, SE Spain, and how they changed in 4 sites that differed in stocking rate. Association strategies were obtained from the partitions of the network, built based on a relaxed structural balance criterion. We found that grazing simplified the structure of the plant community. With increasing stocking rate species with no significant associations became dominant and the number of partitions decreased in the plant community. Independently of stocking rate, many species presented an associative strategy in the plant community because they benefit from the association to certain ‘nurse’ plants. These ‘nurses’ together with species that developed a segregating strategy, intervened in most of the interactions in the community. Ecological networks that combine links with different signs provide a new insight to analyze the structure of natural communities and identify the species which play a central role in them.     

Floral fungal-bacterial community structure and co-occurrence patterns in four sympatric island plant species

Flowers’ fungal and bacterial communities can exert great impacts on host plant wellness and reproductive success—both directly and indirectly through species interactions. However, information about community structure and co-occurrence patterns in floral microbiome remains scarce. Here, using culture-independent methods, we investigated fungal and bacterial communities associated with stamens and pistils of four plant species (Scaevola taccada, Ipomoea cairica, Ipomoea pes-caprae, and Mussaenda kwangtungensis) growing together under the same environment conditions in an island located in South China. Plant species identity significantly influenced community composition of floral fungi but not bacteria. Stamen and pistil microbiomes did not differ in community composition, but differed in co-occurrence network topological features. Compared with the stamen network, pistil counterpart had fewer links between bacteria and fungi and showed more modular but less concentrated and connected structure. In addition, degree distribution of microbial network in each host species and each microhabitat (stamen or pistil) followed a significant power-law pattern. These results enhance our understanding in the assembly principles and ecological interactions of floral microbial communities.