Dataset Information

Exploring the Microdiversity Within Marine Bacterial Taxa: Toward an Integrated Biogeography in the Southern Ocean.

ABSTRACT: Most of the microbial biogeographic patterns in the oceans have been depicted at the whole community level, leaving out finer taxonomic resolution (i.e., microdiversity) that is crucial to conduct intra-population phylogeographic study, as commonly done for macroorganisms. Here, we present a new approach to unravel the bacterial phylogeographic patterns combining community-wide survey by 16S rRNA gene metabarcoding and intra-species resolution through the oligotyping method, allowing robust estimations of genetic and phylogeographic indices, and migration parameters. As a proof-of-concept, we focused on the bacterial genus Spirochaeta across three distant biogeographic provinces of the Southern Ocean; maritime Antarctica, sub-Antarctic Islands, and Patagonia. Each targeted Spirochaeta operational taxonomic units were characterized by a substantial intrapopulation microdiversity, and significant genetic differentiation and phylogeographic structure among the three provinces. Gene flow estimations among Spirochaeta populations support the role of the Antarctic Polar Front as a biogeographic barrier to bacterial dispersal between Antarctic and sub-Antarctic provinces. Conversely, the Antarctic Circumpolar Current appears as the main driver of gene flow, connecting sub-Antarctic Islands with Patagonia and maritime Antarctica. Additionally, historical processes (drift and dispersal limitation) govern up to 86% of the spatial turnover among Spirochaeta populations. Overall, our approach bridges the gap between microbial and macrobial ecology by revealing strong congruency with macroorganisms distribution patterns at the populational level, shaped by the same oceanographic structures and ecological processes.

SUBMITTER: Schwob G

PROVIDER: S-EPMC8317501 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundProkaryotic CRISPR-Cas systems confer resistance to viral infection and thus mediate bacteria-phage interactions. However, the distribution and functional diversity of CRISPRs among environmental bacteria remains largely unknown. Here, comparative genomics of 75 Salinispora strains provided insight into the diversity and distribution of CRISPR-Cas systems in a cosmopolitan marine actinomycete genus.ResultsCRISPRs were found in all Salinispora strains, with the majority containing multiple loci and different Cas array subtypes. Of the six subtypes identified, three have not been previously described. A lower prophage frequency in S. arenicola was associated with a higher fraction of spacers matching Salinispora prophages compared to S. tropica, suggesting differing defensive capacities between Salinispora species. The occurrence of related prophages in strains from distant locations, as well as spacers matching those prophages inserted throughout spacer arrays, indicate recurring encounters with widely distributed phages over time. Linkages of CRISPR features with Salinispora microdiversity pointed to subclade-specific contacts with mobile genetic elements (MGEs). This included lineage-specific spacer deletions or insertions, which may reflect weak selective pressures to maintain immunity or distinct temporal interactions with MGEs, respectively. Biogeographic patterns in spacer and prophage distributions support the concept that Salinispora spp. encounter localized MGEs. Moreover, the presence of spacers matching housekeeping genes suggests that CRISPRs may have functions outside of viral defense.ConclusionsThis study provides a comprehensive examination of CRISPR-Cas systems in a broadly distributed group of environmental bacteria. The ubiquity and diversity of CRISPRs in Salinispora suggests that CRISPR-mediated interactions with MGEs represent a major force in the ecology and evolution of this cosmopolitan marine actinomycete genus.

Project description:Spatial distribution of zooplankton communities depends on numerous factors, especially temperature and salinity conditions (hydrological factor), sampled depth, chlorophyll concentration, and diel cycle. We analyzed and compared the impact of these factors on mesoplankton abundance, biodiversity, quantitative structure based on proportion of taxa and qualitative structure based on presence/absence of taxa in the Southern Ocean. Samples (43 stations, three vertical strata sampled at each station, 163 taxa identified) were collected with a Juday net along the SR02 transect in December 2009. Mesoplankton abundance in discrete vertical layers ranged from 0.2 to 13,743.6 ind. m-3, i.e., five orders of magnitude, maximal and minimal values were recorded in the upper mixed and in the deepest layer, respectively. Within the combined 300-m layer, abundances ranged from 16.0 to 1,455.0 ind. m-3, i.e., two orders of magnitude suggesting that integral samples provide little information about actual variations of mesoplankton abundances. A set of analyses showed that depth was the major driver of mesoplankton distribution (abundance, biodiversity, quantitative structure), hydrological factors influenced two of them (quantitative and qualitative structure), chlorophyll concentration strongly affected only quantitative structure, and diel cycle had an insignificant effect on mesoplankton distribution. Using our current knowledge of the fine structure of the Antarctic Circumpolar Current, we compared effects of four hydrological fronts, i.e., boundaries between different water-masses with distinct environmental characteristics, and eight dynamic jets (narrow yet very intense currents) on mesoplankton distribution. Subtropical, Polar, and Subantarctic Fronts drove quantitative and qualitative structure of mesoplankton assemblages (decreasing in order of influence), while the Southern Boundary affected only qualitative structure. Effects of dynamic jets were insignificant. We suggest that mesoplankton composition is driven by hydrological parameters and further maintained through compartmentalization by fronts. Impact of local eddies and meanders on biodiversity, abundance, qualitative and quantitative structure of mesoplankton is comparable to that of hydrological fronts. Qualitative structure of mesoplankton assemblages mirrors hydrological structure of the Southern Ocean better than quantitative structure and may be recommended for biogeographic analyses of the Southern Ocean. Comparisons with previous reports from the same area retrieved no significant changes in mesoplankton distribution during the period 1992-2009.

Dataset Information

Exploring the Microdiversity Within Marine Bacterial Taxa: Toward an Integrated Biogeography in the Southern Ocean.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets