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

Abstract

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 intrapopulation 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.

The Evolutionary Success of the Marine Bacterium SAR11 Analyzed through a Metagenomic Perspective

“…Mapping metagenomic reads against reference genomes has been applied to capture the heterogeneity at the genomic level within natural populations (17,18). These reads are derived from strains closely related to the strain of the reference genome that are concurrent within a sample.…”

“…In addition, intrapopulation microdiversity has also been proposed as a measure of evolutionary success. High diversity corresponds to populations with high temporal persistence and therefore greater adaptive success in their environment (17,27). In contrast, less diversity is associated with populations that have undergone a recent clonal sweep (18,27).…”

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

“…Recent efforts to recover metagenome-assembled genomes (MAGs) from freshwater environments have largely targeted specific taxa [6–10]. A few recent attempts recovered MAGs from all Bacteria and Archaea present in freshwater communities and resulted in three collections of MAGs from a lake in Siberia (Lake Baikal) and three lakes in North America (Lake Mendota, Trout Bog Lake, and Upper Mystic Lake) [11–13], as well as two collections from rivers in India (Ganges River) and Greece (Kalamas River) [14, 15]. The fraction of the communities captured by these MAGs or other reference genomes is typically moderate to low due to the high diversity of freshwater communities as well as the limitations of the underlying binning methods, which are not optimized for chronoseries datasets from natural habitats but rather for single or small sets of samples from the exact same microbial community.…”

Diversity of Bacteria in Lakes with Different Chlorophyll Content and Investigation of Their Respiratory Activity through a Long-Term Microcosm Experiment

“…Ziros is a deep, dimictic, mesotrophic lake which is exposed to diffuse agricultural pollution [22] while Pamvotis is a shallow, polymictic, eutrophic/hypereutrophic lake impacted by point and non-point pollution related to the extended urbanization and intense agricultural activity in its catchment area [23]. Bacterioplankton diversity has been investigated in a limited number of freshwater ecosystems in the broader geographic area i.e., north-western Greece, e.g., [24][25][26], and to our knowledge, this is the first attempt to reveal the diversity of bacterioplankton communities in Greek lakes using high throughput sequencing. We hypothesize that bacterial community composition will converge in lakes/samplings with similar chlorophyll-a content and that taxa richness and diversity will increase in the more eutrophic waters.…”