Community structure and distribution of benthic Bacteria and Archaea in a stratified coastal lagoon in the Southern Gulf of Mexico

Coastal lagoons are important aquatic systems with strong physicochemical gradients, where the participation of microorganisms in biogeochemical cycles has been well recognised; however, to date, the microbial diversity and distribution in these environments remains under-investigated. Here, three distinguished regions (oligohaline, marine and the mixing) of a transitional coastal lagoon were explored to characterise the structure and composition of benthic microbial communities through 16S rRNA gene Illumina-sequencing, for both Bacteria and Archaea domains. Principal coordinate analysis showed differences in the community structure according to the analysed zones. PERMANOVA analysis evidenced that, of the measured variables, sample zonation and salinity were the main environmental factors explaining the variance of the prokaryotic assemblages. Differentially abundant microbial taxa were detected for each region of the lagoon by LEfSe analysis. Representative members of anaerobic methanogens/methanotrophs (Methanosaetaceae, ANME 1-b and WSA2) were enriched in the oligohaline sediments, while the coastal marine zone had a community represented mainly by Sandaracinaceae, Aminicenantes and Thaumarchaeota (Group-C3). The sediments in the mixing zone had higher abundance of Flavobacteriaceae, Syntrophobacteraceae and uncultured Thermoplasmatales, Bathyarchaeota and Lokiarchaeota. This study expands the available information of the composition and distribution of uncultured Bacteria and Archaea in transitional coastal lagoons, contributing to a systematic understanding of the functioning of these ecosystems. [Display omitted] •Benthic bacterial and archaeal communities were assessed in a stratified coastal lagoon in the Southern Gulf of Mexico.•Statistical analysis evidenced that sample zonation and salinity could explain the variance of the prokaryotic assemblages.•Differentially abundant benthic microbial taxa were evidenced for each stratified region of the lagoon.•This study contributes with the repertoire of uncultured Bacteria and Archaea for transitional coastal lagoons.