Differential Functional Constraints Cause Strain-Level Endemism in
            <i>Polynucleobacter</i>
            Populations

Sangwan, Naseer; Zarraonaindia, Iratxe; Hampton-Marcell, Jarrad; Ssegane, Herbert; Eshoo, Tifani W.; Rijal, Geeta; Negri, M. Cristina; Gilbert, Jack A.

doi:10.1128/msystems.00003-16

Cited by 23 publications

(15 citation statements)

References 41 publications

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“…In freshwater systems, transporters are important for cyanobacterial phosphorus acquisition ( 40 ). More recently, amino acid and amine transporter genes were among those found to be associated with various environmental conditions in Polynucleobacter populations in the CAWS ( 41 ). Here, we identified transporter genes that were more abundant following the observed rain event and were primarily related to transmembrane and substrate-specific transporter activity ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community

Chaudhary

Kauser

Ray

et al. 2018

mSphere

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Urban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced storm flow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high-rainfall event, with potential environment and public health implications. Previous work in this area has focused on specific genes/organisms or has not assessed immediate storm flow impact.

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Section: Resultsmentioning

confidence: 99%

Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community

Chaudhary

Kauser

Ray

et al. 2018

mSphere

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“…Several studies have described the existence of ecotypes within microbial species in several environments such as host-associated microbiomes [20-22, 28, 29, 75], granular biofilms [76], marshes [22], the ocean [12,34,77,78], oil spills [30,31] or freshwater lakes [79][80][81][82]. Moreover, it has been claimed that a rich biodiversity guarantees the long-lasting maintenance of bacterial populations [33,39,83,84].…”

Section: Discussionmentioning

confidence: 99%

Intra-species diversity ensures the maintenance of functional microbial communities under changing environmental conditions

García-García

Tamames

Linz

et al. 2019

Preprint

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Intra-species diversity comprises different ecotypes within the same species. These are assumed to provide stability in time and space to those species. However, the role that microdiversity plays in the stability of whole microbial communities remains underexplored. Understanding the drivers of microbial community stability is necessary to predict community response to future disturbances. Here, we analyzed 16S rRNA gene amplicons from eight different temperate bog lakes at OTU-97% and amplicon sequence variant (ASV) levels, and we found ecotypes within the same species with different distribution patterns in space and time. We observed that these ecotypes are adapted to different values of environmental factors such as water temperature and oxygen concentration. Our results showed that the existence of several ASVs within a species favored its persistence across changing environmental conditions. We propose that microdiversity aids the stability of microbial communities in the face of fluctuations in environmental factors.2 15 20 After this step, we retained 26,128 ASVs from 1,108 samples. These ASV sequences are equivalent to OTUs (Operational Taxonomic Units) that differ in as little as one base out of 140 base pairs, therefore corresponding to more than 99.3% identity. The final result was a table containing the abundance of each ASV in each sample. The sequences were taxonomically classified against the FreshTrain database [45] using mothur v.1.39.1 [56]. More detailed information about the successive steps of the procedure can be found in Supplementary Table 1S.

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“…That is, lineages with relatively uniform population compositions among lakes (e.g., CL500-11) may harbor a few widespread genotypes that can dominate a broad range of habitats, whereas highly diversified lineages (e.g., Iluma-A2 and acI-A1) may be composed of many specialist genotypes that collectively colonize a wide range of environments. The latter case assumes partitioning of functional capabilities among genotypes within a lineage to minimize the amount of genetic material required per cell in a given niche [14,41,76]. Indeed, a high degree of microdiversification, mainly related to carbon metabolism, was reported among closely related acI-A1 strains with 100% identical 16S rRNA gene sequences, and even within the ANI>95% species boundary (e.g.…”

Section: Comparison Of Diversification Patterns Among Lineagesmentioning

confidence: 99%

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

Okazaki

Fujinaga

Salcher

et al. 2020

Preprint

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Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on >97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. Our single nucleotideresolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7-101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages.

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Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter Populations

Cited by 23 publications

References 41 publications

Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community

Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community

Intra-species diversity ensures the maintenance of functional microbial communities under changing environmental conditions

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

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