Species matter: the role of competition in the assembly of congeneric bacteria

Intraspecies dynamics underlie the apparent stability of two important skin microbiome species

Adult human facial skin microbiomes are remarkably similar at the species level, dominated by Cutibacterium acnes and Staphylococcus epidermidis, yet each person harbors a unique community of strains. Understanding how person-specific communities assemble is critical for designing microbiome-based therapies. Here, using 4,055 isolate genomes and 356 metagenomes, we reconstruct on-person evolutionary history to reveal on- and between-person strain dynamics. We find that multiple cells are typically involved in transmission, indicating ample opportunity for migration. Despite this accessibility, family members share only some of their strains. S. epidermidis communities are dynamic, with each strain persisting for an average of only 2 years. C. acnes strains are more stable and have a higher colonization rate during the transition to an adult facial skin microbiome, suggesting this window could facilitate engraftment of therapeutic strains. These previously undetectable dynamics may influence the design of microbiome therapeutics and motivate the study of their effects on hosts.

Ecological processes shaping highly connected bacterial communities along strong environmental gradients

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

Idiosyncratic invasion trajectories of human bacterial pathogens facing temperature disturbances in soil microbial communities

Current knowledge about effects of disturbance on the fate of invaders in complex microbial ecosystems is still in its infancy. In order to investigate this issue, we compared the fate of Klebsiella pneumoniae (Kp) and Listeria monocytogenes (Lm) in soil microcosms. We then used environmental disturbances (freeze-thaw or heat cycles) to compare the fate of both invaders and manipulate soil microbial diversity. Population dynamics of the two pathogens was assessed over 50 days of invasion while microbial diversity was measured at times 0, 20 and 40 days. The outcome of invasion was strain-dependent and the response of the two invaders to disturbance differed. Resistance to Kp invasion was higher under the conditions where resident microbial diversity was the highest while a significant drop of diversity was linked to a higher persistence. In contrast, Lm faced stronger resistance to invasion in heat-treated microcosms where diversity was the lowest. Our results show that diversity is not a universal proxy of resistance to microbial invasion, indicating the need to properly assess other intrinsic properties of the invader, such as its metabolic repertoire, or the array of interactions between the invader and resident communities.

An overview of Parafrankia (Nod+/Fix+) and Pseudofrankia (Nod+/Fix-) interactions through genome mining and experimental modeling in co-culture and co-inoculation of Elaeagnus angustifolia

In many frankia, the ability to nodulate host plants (Nod+) and fix nitrogen (Fix+) is a common strategy. However, some frankia within the Pseudofrankia genus lack one or two of these traits. This phenomenon has been consistently observed across various actinorhizal nodule isolates, displaying Nod- and/or Fix- phenotypes. Yet, the mechanisms supporting the colonization and persistence of these inefficient frankia within nodules, both with and without symbiotic strains (Nod+/Fix+), remain unclear. It is also uncertain whether these associations burden or benefit host plants. This study delves into the ecological interactions between Parafrankia EUN1f and Pseudofrankia inefficax EuI1c, isolated from Elaeagnus umbellata nodules. EUN1f (Nod+/Fix+) and EuI1c (Nod+/Fix-) display contrasting symbiotic traits. While the prediction suggests a competitive scenario, the absence of direct interaction evidence implies that the competitive advantage of EUN1f and EuI1c is likely contingent on contextual factors such as substrate availability and the specific nature of stressors in their respective habitats. In co-culture, EUN1f outperforms EuI1c, especially under specific conditions, driven by its nitrogenase activity. Iron-depleted conditions favor EUN1f, emphasizing iron's role in microbial competition. Both strains benefit from host root exudates in pure culture, but EUN1f dominates in co-culture, enhancing its competitive traits. Nodulation experiments show that host plant preferences align with inoculum strain abundance under nitrogen-depleted conditions, while consistently favoring EUN1f in nitrogen-supplied media. This study unveils competitive dynamics and niche exclusion between EUN1f and EuI1c, suggesting that host plant may penalize less effective strains and even all strains. These findings highlight the complex interplay between strain competition and host selective pressure, warranting further research into the underlying mechanisms shaping plant-microbe-microbe interactions in diverse ecosystems.

IMPORTANCE

While Pseudofrankia strains typically lack the common traits of ability to nodulate the host plant (Nod-) and/or fix nitrogen (Fix-), they are still recovered from actinorhizal nodules. The enigmatic question of how and why these unconventional strains establish themselves within nodule tissue, thriving either alongside symbiotic strains (Nod+/Fix+) or independently, while considering potential metabolic costs to the host plant, remains a perplexing puzzle. This study endeavors to unravel the competitive dynamics between Pseudofrankia inefficax strain EuI1c (Nod+/Fix-) and Parafrankia strain EU1Nf (Nod+/Fix+) through a comprehensive exploration of genomic data and empirical modeling, conducted both in controlled laboratory settings and within the host plant environment.

Microbial Intervention: An Approach to Combat the Postharvest Pathogens of Fruits

Plants host diverse microbial communities, which undergo a complex interaction with each other. Plant-associated microbial communities provide various benefits to the host directly or indirectly, viz. nutrient acquisition, protection from pathogen invaders, mitigation from different biotic and abiotic stress. Presently, plant-associated microbial strains are frequently utilized as biofertilizers, biostimulants and biocontrol agents in greenhouse and field conditions and have shown satisfactory results. Nowadays, the plant/fruit microbiome has been employed to control postharvest pathogens and postharvest decay, and to maintain the quality or shelf life of fruits. In this context, the intervention of the natural fruit microbiome or the creation of synthetic microbial communities to modulate the functional attributes of the natural microbiome is an emerging aspect. In this regard, we discuss the community behavior of microbes in natural conditions and how the microbiome intervention plays a crucial role in the postharvest management of fruits.

Host Dependence of Zooplankton-Associated Microbes and Their Ecological Implications in Freshwater Lakes

Zooplankton is colonized by quite different microbes compared with free-living and particle-associated bacteria, serving as a non-negligible niche of bacteria in aquatic ecosystems. Yet detailed analysis of these bacterial groups is still less known, especially in freshwater lakes. To widen our knowledge of host-microbe interaction and bacterial ecosystem functions, we chose two specific populations of zooplankton, i.e., cladoceran Moina and copepod Calanoids, as hosts from five natural lakes, and illustrated detailed features of their associated bacteria. Through 16S rRNA gene sequencing, we found microbes colonized on Calanoids presented significantly higher α-diversity, stronger bacterial interaction and metabolic function potentials than for Moina. It was also notable that zooplankton-associated bacteria showed a high potential of fatty acid metabolism, which is beneficial for host’s development. Moreover, we found that zooplankton-associated microbes may exert profound effects on biogeochemical cycles in freshwater lakes, since several bacterial members able to participate in carbon and nitrogen cycles were found abundant. Overall, our study expands current understanding of the host-microbe interaction and underlying ecological dynamics in freshwater ecosystem.

Metabolic potential of microbial community and distribution mechanism of Staphylococcus species during broad bean paste fermentation

Although the microbial diversity and structure in bean-based fermented foods have been widely studied, systematic studies on functional microbiota and mechanism of community forms in multi-microbial fermentation systems were still lacking. In this work, the metabolic pathway and functional potential of microbial community in broad bean paste (BBP) were investigated by metagenomics approach, and Staphylococcus, Bacillus, Weissella, Aspergillus and Zygosaccharomyces were found to be the potential predominant populations responsible for substrate alteration and flavor biosynthesis. Among them, Staphylococcus was the most abundant and widespread functional microbe, and closely related Staphylococcus species were diverse and ubiquitously distributed, with the opportunistic pathogen S. gallinarum being the most abundant Staphylococcus specie isolated from BBP. To explain the dominance status of S. gallinarum and species distributions of Staphylococcus genus, we tested the effects of abiotic and biotic factors on three Staphylococcus species using a tractable BBP model, demonstrating that adaptation to environmental conditions (environmental parameters and other functional microbes) led to the dominant position and species coexistence of Staphylococcus, and congeneric competition among Staphylococcus species further shaped ecological distributions of closely related Staphylococcus species. In general, this work revealed the metabolic potential of microbial community and distribution mechanism of Staphylococcus species during BBP fermentation, which could help traditional factories to more precisely control the safety and quality of bean-based fermented foods.

Role of Phylogenetic Structure in the Dynamics of Coastal Viral Assemblages

Marine microbes, including viruses, are an essential part of the marine ecosystem, forming the base of the food web and driving biogeochemical cycles. Within this system, the composition of viral assemblages changes markedly with time, and some of these changes are repeatable through time; however, the extent to which these dynamics are reflected within versus among evolutionarily related groups of viruses is largely unexplored. To examine these dynamics, changes in the composition of two groups of ecologically important viruses and communities of their potential hosts were sampled every 2 weeks for 13 months at a coastal site in British Columbia, Canada. We sequenced two marker genes for viruses-the gene encoding the major capsid protein of T4-like phages and their relatives (gp23) and the RNA-dependent RNA polymerase (RdRp) gene of marnavirus-like RNA viruses-as well as marker genes for their bacterial and eukaryotic host communities, the genes encoding 16S rRNA and 18S rRNA. There were strong lagged correlations between viral diversity and community similarity of putative hosts, implying that the viruses influenced the composition of the host communities. The results showed that for both viral assemblages, the dominant clusters of phylogenetically related viruses shifted over time, and this was correlated with environmental changes. Viral clusters contained many ephemeral taxa and few persistent taxa, but within a viral assemblage, the ephemeral and persistent taxa were closely related, implying ecological dynamics within these clusters. Furthermore, these dynamics occurred in both the RNA and DNA viral assemblages surveyed, implying that this structure is common in natural viral assemblages.IMPORTANCE Viruses are major agents of microbial mortality in marine systems, yet little is known about changes in the composition of viral assemblages in relation to those of the microbial communities that they infect. Here, we sampled coastal seawater every 2 weeks for 1 year and used high-throughput sequencing of marker genes to follow changes in the composition of two groups of ecologically important viruses, as well as the communities of bacteria and protists that serve as their respective hosts. Different subsets of genetically related viruses dominated at different times. These results demonstrate that although the genetic composition of viral assemblages is highly dynamic temporally, for the most part the shuffling of genotypes occurs within a few clusters of phylogenetically related viruses. Thus, it appears that even in temperate coastal waters with large seasonal changes, the highly dynamic shuffling of viral genotypes occurs largely within a few subsets of related individuals.

Phenotypic Clumping Decreases With Flock Richness in Mixed-Species Bird Flocks

Animals that live in groups may experience positive interactions such as cooperative behavior or negative interactions such as competition from group members depending on group size and similarity between individuals. The effect of group size and phenotypic and ecological similarity on group assembly has not been well-studied. Mixed-species flocks are important subsets of bird communities worldwide. We examined associations within these in relation to flock size, to understand rules of flock assembly, in the Western Ghats of India. We examined the relationship between phenotypic clumping and flock richness using four variables—body size, foraging behavior, foraging height and taxonomic relatedness. Using a null model approach, we found that small flocks were more phenotypically clumped for body size than expected by chance; however, phenotypic clumping decreased as flocks increased in size and approached expected phenotypic variation in large flocks. This pattern was not as clear for foraging height and foraging behavior. We then examined a dataset of 55 flock matrices from 24 sites across the world. We found that sites with smaller flocks had higher values of phenotypic clumping for body size and sites with larger flocks were less phenotypically clumped. This relationship was weakly negative for foraging behavior and not statistically significant for taxonomic relatedness. Unlike most single-species groups, participants in mixed-species flocks appear to be able to separate on different axes of trait similarity. They can gain benefits from similarity on one axis while mitigating competition by dissimilarity on others. Consistent with our results, we speculate that flock assembly was deterministic up to a certain point with participants being similar in body size, but larger flocks tended to approach random phenotypic assemblages of species.

The biogeography of Streptomyces in New Zealand enabled by high-throughput sequencing of genus-specific rpoB amplicons

We evaluated Streptomyces biogeography in soils along a 1200 km latitudinal transect across New Zealand (NZ). Streptomyces diversity was examined using high-throughput sequencing of rpoB amplicons generated with a Streptomyces specific primer set. We detected 1287 Streptomyces rpoB operational taxonomic units (OTUs) with 159 ± 92 (average ± SD) rpoB OTUs per site. Only 12% (n = 149) of these OTUs matched rpoB sequences from cultured specimens (99% nucleotide identity cutoff). Streptomyces phylogenetic diversity (Faith's PD) was correlated with soil pH, mean annual temperature and plant community richness (Spearman's r: 0.77, 0.64 and -0.79, respectively; P < 0.05), but not with latitude. In addition, soil pH and plant community richness both explained significant variation in Streptomyces beta diversity. Streptomyces communities exhibited both high dissimilarity and strong dominance of one or a few species at each site. Taken together, these results suggest that dispersal limitation due to competitive interactions limits the colonization success of spores that relocate to new sites. Cultivated Streptomyces isolates represent a major source of clinically useful antibiotics, but only a small fraction of extant diversity within the genus have been identified and most species of Streptomyces have yet to be described.

Facilitative pollinator sharing decreases with floral similarity in multiple systems

Investigating the factors that determine whether interactions are competitive or facilitative is essential to understanding community structure and trait evolution. Co-flowering plants interact indirectly through shared pollinators, and meta-analyses suggest that phylogenetic relatedness and floral trait similarity may predict the outcome of these interactions. In a comparative approach, we manipulated the floral community across five focal species to assess how floral similarity and phylogenetic relatedness affect the outcome of interactions. To assess the extent of pollinator-mediated competition versus facilitation, we compared pollen limitation in five focal species growing with floral neighbors (either congeners or neighbors from a different family) relative to a control (growing alone). We measured floral morphology, color, and nectar traits to calculate multivariate floral similarity between species pairs and inferred a phylogeny to calculate phylogenetic distance. Pollinator-mediated interaction values were regressed against floral similarity and phylogenetic distance. We found evidence of pollinator-mediated facilitation in nine of 13 species pairs. Furthermore, floral similarity and phylogenetic distance reduced facilitative interactions, but the latter relationship was not significant when controlling for the identity of the focal species. Our results suggest that facilitative pollinator sharing is more common than reported in the literature, but co-flowering plant species with similar floral traits are less likely to facilitate pollination. A better understanding of the factors that promote facilitation versus competition has important potential applications for managing rare and invasive species.

Niche Separation Increases With Genetic Distance Among Bloom-Forming Cyanobacteria

Bacterial communities are composed of distinct groups of potentially interacting lineages, each thought to occupy a distinct ecological niche. It remains unclear, however, how quickly niche preference evolves and whether more closely related lineages are more likely to share ecological niches. We addressed these questions by following the dynamics of two bloom-forming cyanobacterial genera over an 8-year time-course in Lake Champlain, Canada, using 16S amplicon sequencing and measurements of several environmental parameters. The two genera, Microcystis (M) and Dolichospermum (D), are frequently observed simultaneously during bloom events and thus have partially overlapping niches. However, the extent of their niche overlap is debated, and it is also unclear to what extent niche partitioning occurs among strains within each genus. To identify strains within each genus, we applied minimum entropy decomposition (MED) to 16S rRNA gene sequences. We confirmed that at a genus level, M and D have different preferences for nitrogen and phosphorus concentrations. Within each genus, we also identified strains differentially associated with temperature, precipitation, and concentrations of nutrients and toxins. In general, niche similarity between strains (as measured by co-occurrence over time) declined with genetic distance. This pattern is consistent with habitat filtering - in which closely related taxa are ecologically similar, and therefore tend to co-occur under similar environmental conditions. In contrast with this general pattern, similarity in certain niche dimensions (notably particulate nitrogen and phosphorus) did not decline linearly with genetic distance, and instead showed a complex polynomial relationship. This observation suggests the importance of processes other than habitat filtering - such as competition between closely related taxa, or convergent trait evolution in distantly related taxa - in shaping particular traits in microbial communities.

The human microbiome in evolution

The trillions of microbes living in the gut-the gut microbiota-play an important role in human biology and disease. While much has been done to explore its diversity, a full understanding of our microbiomes demands an evolutionary perspective. In this review, we compare microbiomes from human populations, placing them in the context of microbes from humanity's near and distant animal relatives. We discuss potential mechanisms to generate host-specific microbiome configurations and the consequences of disrupting those configurations. Finally, we propose that this broader phylogenetic perspective is useful for understanding the mechanisms underlying human-microbiome interactions.

Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions

Phytotelmata in tank-forming Bromeliaceae plants are regarded as potential miniature models for aquatic ecology, but detailed investigations of their microbial communities are rare. Hence, the biogeochemistry in bromeliad tanks remains poorly understood. Here we investigate the structure of bacterial and archaeal communities inhabiting the detritus within the tanks of two bromeliad species, Aechmea nudicaulis and Neoregelia cruenta, from a Brazilian sand dune forest. We used metagenomic sequencing for functional community profiling and 16S sequencing for taxonomic profiling. We estimated the correlation between functional groups and various environmental variables, and compared communities between bromeliad species. In all bromeliads, microbial communities spanned a metabolic network adapted to oxygen-limited conditions, including all denitrification steps, ammonification, sulfate respiration, methanogenesis, reductive acetogenesis and anoxygenic phototrophy. Overall, CO2 reducers dominated in abundance over sulfate reducers, and anoxygenic phototrophs largely outnumbered oxygenic photoautotrophs. Functional community structure correlated strongly with environmental variables, between and within a single bromeliad species. Methanogens and reductive acetogens correlated with detrital volume and canopy coverage, and exhibited higher relative abundances in N. cruenta. A comparison of bromeliads to freshwater lake sediments and soil from around the world, revealed stark differences in terms of taxonomic as well as functional microbial community structure.

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks

Fire alters ecosystems by changing the composition and community structure of soil microbes. The phylogenetic structure of a community provides clues about its main assembling mechanisms. While environmental filtering tends to reduce the community phylogenetic diversity by selecting for functionally (and hence phylogenetically) similar species, processes like competitive exclusion by limiting similarity tend to increase it by preventing the coexistence of functionally (and phylogenetically) similar species. We used co-occurrence networks to detect co-presence (bacteria that co-occur) or exclusion (bacteria that do not co-occur) links indicative of the ecological interactions structuring the community. We propose that inspecting the phylogenetic structure of co-presence or exclusion links allows to detect the main processes simultaneously assembling the community. We monitored a soil bacterial community after an experimental fire and found that fire altered its composition, richness and phylogenetic diversity. Both co-presence and exclusion links were more phylogenetically related than expected by chance. We interpret such a phylogenetic clustering in co-presence links as a result of environmental filtering, while that in exclusion links reflects competitive exclusion by limiting similarity. This suggests that environmental filtering and limiting similarity operate simultaneously to assemble soil bacterial communities, widening the traditional view that only environmental filtering structures bacterial communities.

Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool

Microdiversification of a planktonic freshwater bacterium was studied by comparing 37 Polynucleobacter asymbioticus strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome is clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located. These positions are occupied strain specifically from a set of 28 GI variants, classified according to similarities in their gene content. One variant, present in 62% of the isolates, encodes a pathway for the degradation of aromatic compounds, and another, found in 78% of the strains, contains an operon for nitrate assimilation. Both variants were shown in ecophysiological tests to be functional, thus providing the potential for microniche partitioning. In addition, detected interspecific horizontal exchange of GIs indicates a large gene pool accessible to Polynucleobacter species. In contrast to core genes, GIs are spread more successfully across spatially separated freshwater habitats. The mobility and functional diversity of GIs allow for rapid evolution, which may be a key aspect for the ubiquitous occurrence of Polynucleobacter bacteria.

IMPORTANCE

Assessing the ecological relevance of bacterial diversity is a key challenge for current microbial ecology. The polyphasic approach which was applied in this study, including targeted isolation of strains, genome analysis, and ecophysiological tests, is crucial for the linkage of genetic and ecological knowledge. Particularly great importance is attached to the high number of closely related strains which were investigated, represented by genome-wide average nucleotide identities (ANI) larger than 97%. The extent of functional diversification found on this narrow phylogenetic scale is compelling. Moreover, the transfer of metabolically relevant genomic islands between more distant members of the Polynucleobacter community provides important insights toward a better understanding of the evolution of these globally abundant freshwater bacteria.

Reduced Diversity in the Bacteriome of the Phytophagous Mite Brevipalpus yothersi (Acari: Tenuipalpidae)

Tenuipalpidae comprises mites that transmit viruses to agriculturally important plants. Several tenuipalpid species present parthenogenesis, and in Brevipalpus yothersi, the endosymbiont Cardinium has been associated with female-only colonies. It is unclear what the bacterial composition of B. yothersi is, and how common Cardinium is in those microbiomes. We performed a comparative analysis of the bacteriomes in three populations of B. yothersi and three additional Tetranychoidea species using sequences from V4-fragment of 16S DNA. The bacteriomes were dominated by Bacteroidetes (especially Cardinium) and Proteobacteria, showing a remarkably low alpha diversity. Cardinium was present in about 22% of all sequences; however, it was not present in R. indica and T. evansi. In B. yothersi, the proportion of Cardinium was higher in adults than eggs, suggesting that proliferation of the bacteria could be the result of selective pressures from the host. This hypothesis was further supported because colonies of B. yothersi from different populations showed different bacterial assemblages, and bacteriomes from different mite species showed similar abundances of Cardinium. A phylogenetic analysis of Cardinium revealed that not only specialization but horizontal transmission has been important for this symbiosis. Together, these results represent a glimpse into the evolution of the Tetranychoidea and Cardinium.

High taxonomic variability despite stable functional structure across microbial communities

Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.

Decreases in average bacterial community rRNA operon copy number during succession

Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.

Synthetic Ecology of Microbes: Mathematical Models and Applications

As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Finally, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.

Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas

Acid mine drainage (AMD) is a highly toxic environment for most living organisms due to the presence of many lethal elements including arsenic (As). Thiomonas (Tm.) bacteria are found ubiquitously in AMD and can withstand these extreme conditions, in part because they are able to oxidize arsenite. In order to further improve our knowledge concerning the adaptive capacities of these bacteria, we sequenced and assembled the genome of six isolates derived from the Carnoulès AMD, and compared them to the genomes of Tm. arsenitoxydans 3As (isolated from the same site) and Tm. intermedia K12 (isolated from a sewage pipe). A detailed analysis of the Tm. sp. CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs) were found in each of these three genomes. We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7). Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments.

Biogeographic patterns of bacterial microdiversity in Arctic deep-sea sediments (HAUSGARTEN, Fram Strait)

Marine bacteria colonizing deep-sea sediments beneath the Arctic ocean, a rapidly changing ecosystem, have been shown to exhibit significant biogeographic patterns along transects spanning tens of kilometers and across water depths of several thousand meters (Jacob et al., 2013). Jacob et al. (2013) adopted what has become a classical view of microbial diversity – based on operational taxonomic units clustered at the 97% sequence identity level of the 16S rRNA gene – and observed a very large microbial community replacement at the HAUSGARTEN Long Term Ecological Research station (Eastern Fram Strait). Here, we revisited these data using the oligotyping approach and aimed to obtain new insight into ecological and biogeographic patterns associated with bacterial microdiversity in marine sediments. We also assessed the level of concordance of these insights with previously obtained results. Variation in oligotype dispersal range, relative abundance, co-occurrence, and taxonomic identity were related to environmental parameters such as water depth, biomass, and sedimentary pigment concentration. This study assesses ecological implications of the new microdiversity-based technique using a well-characterized dataset of high relevance for global change biology.

Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological interactions?

BACKGROUND

Since the landmark Santa Rosalia paper by Hutchinson, niche theory addresses the determinants of biodiversity in terms of both environmental and biological aspects. Disentangling the role of habitat filtering and interactions with other species is critical for understanding microbial ecology. Macroscopic biogeography explores hypothetical ecological interactions through the analysis of species associations. These methods have started to be incorporated into microbial ecology relatively recently, due to the inherent experimental difficulties and the coarse grained nature of the data.

RESULTS

Here we investigate the influence of environmental preferences and ecological interactions in the tendency of bacterial taxa to either aggregate or segregate, using a comprehensive dataset of bacterial taxa observed in a wide variety of environments. We assess significance of taxa associations through a null model that takes into account habitat preferences and the global distribution of taxa across samples. The analysis of these associations reveals a surprisingly large number of significant aggregations between taxa, with a marked community structure and a strong propensity to aggregate for cosmopolitan taxa. Due to the coarse grained nature of our data we cannot conclusively reject the hypothesis that many of these aggregations are due to environmental preferences that the null model fails to reproduce. Nevertheless, some observations are better explained by ecological interactions than by habitat filtering. In particular, most pairs of aggregating taxa co-occur in very different environments, which makes it unlikely that these associations are due to habitat preferences, and many are formed by cosmopolitan taxa without well defined habitat preferences. Moreover, known cooperative interactions are retrieved as aggregating pairs of taxa. As observed in similar studies, we also found that phylogenetically related taxa are much more prone to aggregate than to segregate, an observation that may play a role in bacterial speciation.

CONCLUSIONS

We hope that these results stimulate experimental verification of the putative cooperative interactions between cosmopolitan bacteria, and we suggest several groups of aggregated cosmopolitan bacteria that are interesting candidates for such an investigation.

The cryptic role of biodiversity in the emergence of host-microbial mutualisms

The persistence of mutualisms in host-microbial - or holobiont - systems is difficult to explain because microbial mutualists, who bear the costs of providing benefits to their host, are always prone to being competitively displaced by non-mutualist 'cheater' species. This disruptive effect of competition is expected to be particularly strong when the benefits provided by the mutualists entail costs such as reduced competitive ability. Using a metacommunity model, we show that competition between multiple cheaters within the host's microbiome, when combined with the spatial structure of host-microbial interactions, can have a constructive rather than a disruptive effect by allowing the emergence and maintenance of mutualistic microorganisms within the host. These results indicate that many of the microorganisms inhabiting a host's microbiome, including those that would otherwise be considered opportunistic or even potential pathogens, play a cryptic yet critical role in promoting the health and persistence of the holobiont across spatial scales.

River organic matter shapes microbial communities in the sediment of the Rhône prodelta

Microbial-driven organic matter (OM) degradation is a cornerstone of benthic community functioning, but little is known about the relation between OM and community composition. Here we use Rhône prodelta sediments to test the hypothesis that OM quality and source are fundamental structuring factors for bacterial communities in benthic environments. Sampling was performed on four occasions corresponding to contrasting river-flow regimes, and bacterial communities from seven different depths were analyzed by pyrosequencing of 16S rRNA gene amplicons. The sediment matrix was characterized using over 20 environmental variables including bulk parameters (for example, total nitrogen, carbon, OM, porosity and particle size), as well as parameters describing the OM quality and source (for example, pigments, total lipids and amino acids and δ(13)C), and molecular-level biomarkers like fatty acids. Our results show that the variance of the microbial community was best explained by δ(13)C values, indicative of the OM source, and the proportion of saturated or polyunsaturated fatty acids, describing OM lability. These parameters were traced back to seasonal differences in the river flow, delivering OM of different quality and origin, and were directly associated with several frequent bacterial operational taxonomic units. However, the contextual parameters, which explained at most 17% of the variance, were not always the key for understanding the community assembly. Co-occurrence and phylogenetic diversity analysis indicated that bacteria-bacteria interactions were also significant. In conclusion, the drivers structuring the microbial community changed with time but remain closely linked with the river OM input.