Iterative Subtractive Binning of Freshwater Chronoseries Metagenomes Identifies of over Four Hundred Novel Species and their Ecologic Preferences

AbstractRecent advances in sequencing technology and accompanying bioinformatic pipelines have allowed unprecedented access to the genomes of yet-uncultivated microorganisms from a wide array of natural and engineered environments. However, the catalogue of available genomes from uncultivated freshwater microbial populations remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted few specific taxa. Here, we present a novel genome recovery pipeline, which incorporates iterative subtractive binning and apply it to a time series of metagenomic datasets from seven connected locations along the Chattahoochee River (Southeastern USA). Our set of Metagenome-Assembled Genomes (MAGs) represents over four hundred genomospecies yet to be named, which substantially increase the number of high-quality MAGs from freshwater lakes and represent about half of the total microbial community sampled. We propose names for two novel species that were represented by high-quality MAGs: “CandidatusElulimicrobium humile” (“Ca. Elulimicrobiota” in the “Patescibacteria” group) and “CandidatusAquidulcis frankliniae” (“Chloroflexi”). To evaluate the prevalence of these species in the chronoseries, we introduce novel approaches to estimate relative abundance and a habitat-preference score that control for uneven quality of the genomes and sample representation. Using these metrics, we demonstrate a high degree of habitat-specialization and endemicity for most genomospecies observed in the Chattahoochee lacustrine ecosystem, as well as wider species ecological ranges associated with smaller genomes and higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions.</jats:p

Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics

Studies assessing the effects of anthropogenic inputs on the taxonomic and functional diversity of bacterioplankton communities in lotic ecosystems are limited. Here, we applied 16S rRNA gene amplicon and whole-genome shotgun sequencing to examine the microbial diversity in samples from the Kalamas River (Northwest Greece), a mid-size river that runs through agricultural and NATURA-protected areas, but also receives urban sewage from a large city through a manmade ditch. Samples from three different locations between the exit of the ditch and the estuary, during three different months showed that temporal differences of taxonomic and functional diversity were more pronounced than spatial ones, and <1% of total taxa were shared among all samples, revealing a highly dynamic ecosystem. Comparisons of gene diversity with other aquatic habitats showed that only the high flow winter samples resembled more to freshwater environments while samples during the decreased water flow months were dominated by sewage inputs and soil-related organisms. Notably, microbial human gut signals were detectable over background freshwater and soil/runoff related signals, even at tens of kilometers downstream the city. These findings revealed the significance of allochthonous inputs on the composition and dynamics of river bacterial communities, and highlighted the potential of metagenomics for source tracking purposes. © 2016 Society for Applied Microbiology and John Wiley & Sons Lt

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient

Recent diversity studies have revealed that microbial communities of natural environments are dominated by species-like, sequence-discrete populations. However, how stable the sequence and gene-content diversity are within these populations and especially in highly dynamic lotic habitats remain unclear. Here we quantified the dynamics of intra-population diversity in samples spanning two years and five sites in the Kalamas River (Northwest Greece). A significant positive correlation was observed between higher intra-population sequence diversity and longer persistence over time, revealing that more diverse populations tended to represent more autochthonous (vs. allochthonous) community members. Assessment of intra-population gene-content changes caused by strain replacement or gene loss over time revealed different profiles with the majority of populations exhibiting gene-content changes close to 10% of the total genes, while one population exhibited ~21% change. The variable genes were enriched in hypothetical proteins and mobile elements, and thus, were probably functionally neutral or attributable to phage predation. A few notable exceptions to this pattern were also noted such as phototrophy-related proteins in summer vs. winter populations. Taken together, these results revealed that some freshwater genomes are remarkably dynamic, even across short time and spatial scales, and have implications for the bacterial species concept and microbial source tracking. © 2018, International Society for Microbial Ecology

SAR11 bacteria linked to ocean anoxia and nitrogen loss

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N-2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted similar to 40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group