The abundance of different SSU rRNA ("16S") gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. ...However, the genomic copy number of the 16S gene varies greatly - from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data.
Research on biodiversity and ecosystem functioning has demonstrated links between plant diversity and ecosystem functions such as productivity. At other trophic levels, the plant microbiome has been ...shown to influence host plant fitness and function, and host-associated microbes have been proposed to influence ecosystem function through their role in defining the extended phenotype of host organisms However, the importance of the plant microbiome for ecosystem function has not been quantified in the context of the known importance of plant diversity and traits. Here, using a tree biodiversity-ecosystem functioning experiment, we provide strong support for the hypothesis that leaf bacterial diversity is positively linked to ecosystem productivity, even after accounting for the role of plant diversity. Our results also show that host species identity, functional identity and functional diversity are the main determinants of leaf bacterial community structure and diversity. Our study provides evidence of a positive correlation between plant-associated microbial diversity and terrestrial ecosystem productivity, and a new mechanism by which models of biodiversity-ecosystem functioning relationships can be improved.
Patterns of phylogenetic relatedness within communities have been widely used to infer the importance of different ecological and evolutionary processes during community assembly, but little is known ...about the relative ability of community phylogenetics methods and null models to detect the signature of processes such as dispersal, competition and filtering under different models of trait evolution. Using a metacommunity simulation incorporating quantitative models of trait evolution and community assembly, I assessed the performance of different tests that have been used to measure community phylogenetic structure. All tests were sensitive to the relative phylogenetic signal in species metacommunity abundances and traits; methods that were most sensitive to the effects of niche-based processes on community structure were also more likely to find non-random patterns of community phylogenetic structure under dispersal assembly. When used with a null model that maintained species occurrence frequency in random communities, several metrics could detect niche-based assembly when there was strong phylogenetic signal in species traits, when multiple traits were involved in community assembly, and in the presence of environmental heterogeneity. Interpretations of the causes of community phylogenetic structure should be modified to account for the influence of dispersal.
Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial ...biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome.
Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure.
Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our health and well-being.
Motivation: The increasing availability of phylogenetic and trait data for communities of co-occurring species has created a need for software that integrates ecological and evolutionary analyses. ...Capabilities: Phylocom calculates numerous metrics of phylogenetic community structure and trait similarity within communities. Hypothesis testing is implemented using several null models. Within the same framework, it measures phylogenetic signal and correlated evolution for species traits. A range of utility functions allow community and phylogenetic data manipulation, tree and trait generation, and integration into scientific workflows. Availability: Open source at: http://phylodiversity.net/phylocom/ Contact: cwebb@oeb.harvard.edu
There is an increasing interest in applying trait-based approaches to microbial ecology, but the question of how and why to do it is still lagging behind. By anchoring our discussion of these ...questions in a framework derived from epistemology, we broaden the scope of trait-based approaches to microbial ecology from one oriented mostly around explanation towards one inclusive of the predictive and integrative potential of these approaches. We use case studies from macro-organismal ecology to concretely show how these goals for knowledge development can be fulfilled and propose clear directions, adapted to the biological reality of microbes, to make the most of recent advancements in the measurement of microbial phenotypes and traits.
There is increasing interest in the use of trait-based approaches to microbial ecology, and the study of microbes is becoming more and more multidisciplinary.The development of new technologies and methodologies for studying microbial biodiversity have increased the availability of large-scale datasets on microbial functional traits from diverse habitats.Trait-based approaches to macro-organismal ecology have improved our capacity to formulate testable hypotheses on ecological dynamics and to foster the exchange of data, methods, and explanations across research teams.Trait-based approaches to microbial ecology have improved our understanding of mechanisms driving microbial adaptation and coexistence across different environments and offer the possibility to link microbial traits with evolutionary fitness and ecological dynamics.
The phyllosphere—the aerial surfaces of plants, including leaves—is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to ...influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density–growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant–microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.
Significance In this study we sequenced bacterial communities present on tree leaves in a neotropical forest in Panama, to quantify the poorly understood relationships between bacterial biodiversity on leaves (the phyllosphere) vs. host tree attributes. Bacterial community structure on leaves was highly correlated with host evolutionary relatedness and suites of plant functional traits related to host ecological strategies for resource uptake and growth/mortality tradeoffs. The abundance of several bacterial taxa was correlated with host growth, mortality, and function. Our study quantifies the drivers of variation in plant-associated microbial biodiversity; our results suggest that incorporating information on plant-associated microbes will improve our understanding of the functional biogeography of plants and plant–microbe interactions.
Phyllosphere bacterial diversity is shaped through interactions between hosts and microbes. Most studies having focused on pairwise associations between host taxa and their symbionts, little is yet ...understood about the influence of the host community as a whole in shaping these interactions. Envisioning phyllosphere bacterial communities as a spatially structured network of communities linked by dispersal (i.e., metacommunities) can help us better understand the relative importance of species sorting among host populations and species versus dispersal from the neighboring host community for bacterial community assembly in forest ecosystems. Here we investigate drivers of metacommunity structure of epiphytic bacteria of the phyllosphere among 33 tree host species distributed across a large-scale transition from deciduous to boreal forest. We expect the identity and traits of hosts to play an important role in determining phyllosphere bacterial composition. We further hypothesize that bacterial dispersal from neighboring host species will modulate the match between a focal host species and its microbiota, and shape opportunities for host specialization of phyllosphere bacteria at local and regional scales. We defined specialization as the level of phylogenetic similarity among hosts that a bacterial symbiont associates with. We found that host taxonomic identity and traits were important drivers of bacterial community turnover and variation in host specialization across the landscape. Dispersal from neighboring communities further played a role in homogenizing bacterial communities. The microbiota of focal hosts such as sugar maple was thus increasingly similar to that of neighboring host species along the transition from deciduous to boreal forest. Specialization of bacterial taxa on sugar maple was further positively correlated with the relative abundance of this host in the landscape, revealing a role for the host community context in shaping evolutionary relationships between phyllosphere bacteria and their tree hosts. These results overall suggest that the dispersal of phyllosphere bacteria from the dominant tree community members may be constraining the match between tree species and their symbionts, particularly at their range limits. We also demonstrate that considering host-associated microbial communities as part of metacommunities within the host landscape is a promising tool for improving our understanding of host-symbiont matching.
In this study, we used data from temperate grassland plant communities in Alberta, Canada to test two longstanding hypotheses in ecology: 1) that there has been correlated evolution of the leaves and ...roots of plants due to selection for an integrated whole-plant resource uptake strategy, and 2) that trait diversity in ecological communities is generated by adaptations to the conditions in different habitats. We tested the first hypothesis using phylogenetic comparative methods to test for evidence of correlated evolution of suites of leaf and root functional traits in these grasslands. There were consistent evolutionary correlations among traits related to plant resource uptake strategies within leaf tissues, and within root tissues. In contrast, there were inconsistent correlations between the traits of leaves and the traits of roots, suggesting different evolutionary pressures on the above and belowground components of plant morphology. To test the second hypothesis, we evaluated the relative importance of two components of trait diversity: within-community variation (species trait values relative to co-occurring species; α traits) and among-community variation (the average trait value in communities where species occur; β traits). Trait diversity was mostly explained by variation among co-occurring species, not among-communities. Additionally, there was a phylogenetic signal in the within-community trait values of species relative to co-occurring taxa, but not in their habitat associations or among-community trait variation. These results suggest that sorting of pre-existing trait variation into local communities can explain the leaf and root trait diversity in these grasslands.
Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities. The package calculates phylogenetic diversity ...metrics, performs trait comparative analyses, manipulates phenotypic and phylogenetic data, and performs tests for phylogenetic signal in trait distributions, community structure and species interactions. Availability: Picante is a package for the R statistical language and environment written in R and C, released under a GPL v2 open-source license, and freely available on the web (http://picante.r-forge.r-project.org) and from CRAN (http://cran.r-project.org). Contact: skembel@uoregon.edu
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