Microcoleus (Cyanobacteria) form watershed‐wide populations without strong gradients in population structure

Abstract

The relative importance of separation by distance and by environment to population genetic diversity can be conveniently tested in river networks, where these two drivers are often independently distributed over space. To evaluate the importance of dispersal and environmental conditions in shaping microbial population structures, we performed genome‐resolved metagenomic analyses of benthic Microcoleus‐dominated cyanobacterial mats collected in the Eel and Russian River networks (California, USA). The 64 Microcoleus genomes were clustered into three species that shared >96.5% average nucleotide identity (ANI). Most mats were dominated by one strain, but minor alleles within mats were often shared, even over large spatial distances (>300 km). Within the most common Microcoleus species, the ANI between the dominant strains within mats decreased with increasing spatial separation. However, over shorter spatial distances (tens of kilometres), mats from different subwatersheds had lower ANI than mats from the same subwatershed, suggesting that at shorter spatial distances environmental differences between subwatersheds in factors like canopy cover, conductivity, and mean annual temperature decreases ANI. Since mats in smaller creeks had similar levels of nucleotide diversity (π) as mats in larger downstream subwatersheds, within‐mat genetic diversity does not appear to depend on the downstream accumulation of upstream‐derived strains. The four‐gamete test and sequence length bias suggest recombination occurs between almost all strains within each species, even between populations separated by large distances or living in different habitats. Overall, our results show that, despite some isolation by distance and environmental conditions, sufficient gene‐flow occurs among cyanobacterial strains to prevent either driver from producing distinctive population structures across the watershed.

Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps

“…To identify them, we screened the 1261 MAGs for the presence of three functional genes: the particulate methane monooxygenase marker gene pmoA encoding for MOB, the methyl-coenzyme-M reductase marker gene mcrA for ANME archaea, and the dissimilatory sulfite reductase marker gene dsrA for SRB. To facilitate the microdiversity analyses of key functional taxa, we kept only species-cluster representative MAGs with an estimated quality score ≥50 (defined as the estimated completeness of a genome minus five times its estimated contamination) 40 and at least 10× coverage 15, 22, 41, 42 .…”

Microbial Populations Are Shaped by Dispersal and Recombination in a Low Biomass Subseafloor Habitat

“…1 ; Data set S3). This level of population diversity is approximately equivalent to that observed for soils in grassland meadows (ranging between 4.7 and 43.0 SNVs kbp −1 ) and higher than single species-dominated photosynthetic mats in a connected watershed (ranging between 0.01 and 8.7 SNVs kbp −1 ) ( 11 , 24 ). Based on the observed nucleotide diversity of the North Pond MAGs across all relevant time points (π = 0.002 to 0.01), each population is diverse and shares minor alleles.…”

“…The mean H4 frequencies for each population ranged from 0.44% to 14.84%. Several of the MAG populations (NORP83, NORP147, and NORP169) had H4 frequencies (0.44%, 1.17%, and 1.45%, respectively) below the lowest values estimated for single species photosynthetic mats (3.4% H4 frequency [ 11 ]; Table 2 ). NORP147 did not display decay of the linkage disequilibrium values as genetic distance increased for any of the mutation type pairs, indicating a lack of recombination within the population (S-S, N-S, or N-N; Fig.…”

“…Linkage decay, a signal of recombination, was observed by plotting r 2 against the distance between linked SNVs; where distance between linked SNVs were grouped into 10-bp ranges and separated by the type of mutation within the coding region (synonymous-synonymous [S-S], synonymous-nonsynonymous [S-N], and nonsynonymous-nonsynonymous [N-N]). Additionally, the four-gamete test, another signal of recombination, was performed for all biallelic (AB and ab haplotypes) linked SNV locations ( 11 ). Under the infinite-site model, the presence of all four haplotypes (AB, ab, Ab, aB) can only be explained by at least one recombination event ( 63 , 64 ).…”

“…Population size can have important consequences for how microbial populations evolve over time, and factors such as genetic drift can have an exaggerated impact on small microbial populations compared to habitats in which microbial populations are larger. Most previous studies of adaptation in natural microbial communities have focused on habitats with high biomass and thus larger population sizes, such as the surface ocean, deep-sea hydrothermal vents, and freshwater lakes ( 8 – 11 ). It is unclear how natural selection and genetic drift shape the evolution of microbial communities in low-biomass habitats, despite the fact that a substantial fraction of global microbial biomass is found in such habitats.…”