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Genomic approaches to characterizing bacterial communities are revealing significant differences in diversity and composition between environments. But bacterial distributions have not been mapped at a global scale. Although current community surveys are way too sparse to map global diversity patterns directly, there is now sufficient data to fit accurate models of how bacterial distributions vary across different environments and to make global scale maps from these models. We apply this approach to map the global distributions of bacteria in marine surface waters. Our spatially and temporally explicit predictions suggest that bacterial diversity peaks in temperate latitudes across the world's oceans. These global peaks are seasonal, occurring 6 months apart in the two hemispheres, in the boreal and austral winters. This pattern is quite different from the tropical, seasonally consistent diversity patterns observed for most macroorganisms. However, like other marine organisms, surface water bacteria are particularly diverse in regions of high human environmental impacts on the oceans. Our maps provide the first picture of bacterial distributions at a global scale and suggest important differences between the diversity patterns of bacteria compared with other organisms.

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.

Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?

Phylogenetic diversity--patterns of phylogenetic relatedness among organisms in ecological communities--provides important insights into the mechanisms underlying community assembly. Studies that measure phylogenetic diversity in microbial communities have primarily been limited to a single marker gene approach, using the small subunit of the rRNA gene (SSU-rRNA) to quantify phylogenetic relationships among microbial taxa. In this study, we present an approach for inferring phylogenetic relationships among microorganisms based on the random metagenomic sequencing of DNA fragments. To overcome challenges caused by the fragmentary nature of metagenomic data, we leveraged fully sequenced bacterial genomes as a scaffold to enable inference of phylogenetic relationships among metagenomic sequences from multiple phylogenetic marker gene families. The resulting metagenomic phylogeny can be used to quantify the phylogenetic diversity of microbial communities based on metagenomic data sets. We applied this method to understand patterns of microbial phylogenetic diversity and community assembly along an oceanic depth gradient, and compared our findings to previous studies of this gradient using SSU-rRNA gene and metagenomic analyses. Bacterial phylogenetic diversity was highest at intermediate depths beneath the ocean surface, whereas taxonomic diversity (diversity measured by binning sequences into taxonomically similar groups) showed no relationship with depth. Phylogenetic diversity estimates based on the SSU-rRNA gene and the multi-gene metagenomic phylogeny were broadly concordant, suggesting that our approach will be applicable to other metagenomic data sets for which corresponding SSU-rRNA gene sequences are unavailable. Our approach opens up the possibility of using metagenomic data to study microbial diversity in a phylogenetic context.

Alternative states defined by tree‐canopy dominance result in different ecosystem functioning and shape habitat conditions for the understory vegetation. One example in the boreal forest is the alternation between broadleaf deciduous and coniferous forests. Disturbances related to natural fires and human land uses have produced changes in tree‐canopy dominance in the boreal region where coniferous forests change to broadleaved forests, affecting understory community dynamics and their related ecosystem processes and functions. To analyze the factors driving changes in understory vegetation and the resistance of its vegetation to shifts between alternative states, we compared the effects of changes in the system between two contrasting boreal forest types (black spruce vs. trembling aspen) in adjacent stands with similar topoedaphic conditions. We performed a 5‐year in situ experiment using alternative states as a theoretical framework including two approaches: (1) the ecosystem approach, manipulating environmental conditions of light, litter, and nutrients in each forest type to determine the main mechanisms associated with tree‐canopy dominance that affect the diversity and composition of understory communities; and (2) the community approach, physically exchanging understory communities between alternative states, to determine their resistance under a new tree‐canopy dominance through time, as well as the resilience of the forest understory after a small‐scale disturbance. Results indicate that the understory vegetation of trembling aspen forests were resistant through time both after changes in local conditions in the ecosystem approach and in the new black spruce‐dominated alternative state in the community approach. In contrast, mosses and ericaceous plants that typically dominate the forest floor of black spruce forests were negatively affected by the physical effect of broadleaf litter addition in our ecosystem approach and they were not resistant when transplanted to trembling aspen forests in the community approach, as they decreased in abundance and were invaded by aspen understory community species over time. The understory vegetation is a key forest ecosystem driver that can contribute to maintain the resilience of the boreal system and help to preserve their ecosystem services, which is a key aspect to consider in forest management faced with the effects of climate change. [ABSTRACT FROM AUTHOR]

The soil microbiome plays major roles in the below-ground processes and productivity of forest ecosystems. Atmospheric nitrogen (N) deposition is predicted to increase globally and might create disturbances in soil microbial communities, essentially by modifying soil chemistry. However, the impacts of higher N deposition on the soil microbiome in N-limited northern forests are still unclear. For 16 years, we simulated N deposition by adding ammonium nitrate at rates of 3 and 10 times the ambient N deposition directly into soils located in three bioclimatic domains of the eastern Canadian forest (i.e., sugar maple–yellow birch, balsam fir–white birch, and black spruce–feather moss). We identified changes in the microbial communities by isolating the DNA of the L, F, and H soil horizons, as well as by sequencing amplicons of the bacterial 16S rRNA gene and the fungal ITS region. We found that long-term increased N deposition had no effect on soil microbial diversity, but had moderate impacts on the composition of the bacterial and fungal communities. The most noticeable change was the increase in ectomycorrhizal fungi ASV abundance, potentially due to increased tree root growth on fertilized plots. Our work suggests that, in N-limited northern forests, extra N is rapidly mobilized by vegetation, thus minimizing impacts on the soil microbiome. [ABSTRACT FROM AUTHOR]

Author(s): Isabelle Laforest-Lapointe (corresponding author) [1, 2]; Alain Paquette [1, 2]; Christian Messier [1, 2, 3]; Steven W. Kembel [1, 2] Research on biodiversity and ecosystem functioning has demonstrated links [...]