A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups

Abstract

During the last five decades, the Aral Sea has gradually changed from a saline water body to a hypersaline lake. Microbial community inhabiting the Aral Sea has been through a succession and continuous adaptation during the last 50 years of increasing salinization, but so far, the microbial diversity has not been explored. Prokaryotic diversity of the Large Aral Sea using cultivation-independent methods based on determination of environmental 16S rRNA gene sequences revealed a microbial community related to typical marine or (hyper) saline-adapted Bacteria and Archaea. The archaeal sequences were phylogenetically affiliated with the order Halobacteriales, with a large number of operational taxonomic units constituting a novel cluster in the Haloferacaceae family. Bacterial community analysis indicated a higher diversity with representatives belonging to Proteobacteria, Actinobacteria and Bacteroidetes. Many members of Alphaproteobacteria and Gammaproteobacteria were affiliated with genera like Roseovarius, Idiomarina and Spiribacter which have previously been found in marine or hypersaline waters. The majority of the phylotypes was most closely related to uncultivated organisms and shared less than 97% identity with their closest match in GenBank, indicating a unique community structure in the Large Aral Sea with mostly novel species or genera.

Keywords: archaea; bacteria; halophiles; phylogeny; prokaryotic diversity; salt lake.

Figure 1

Location of study site. (a) Map of the Aral Sea in 2014 showing location of sampling site in the Large Aral Sea with red mark. (b) Close‐up photograph of the Large Aral Sea beach where sampling was done (44°25′41.5″N, 58°14′34.7″E). Source of map: https://www.google.com/maps

Figure 2

Neighbor‐Joining phylogenetic tree showing the phylogenetic positions of the bacterial 16S rRNA clone sequences (B1–B25). The closest cultivated bacteria are indicated in bold. The Aral Sea sequences comprising OTUs are collapsed. Closest related environmental sequences are also included. Database accession numbers are given in brackets. Bootstrap values ≥63% are indicated at branch nodes and based on 500 iterations. Positions containing gaps or missing data were excluded from the analysis. The tree was rooted using the deep‐branching Aquifex aeolicus as outgroup. The bar indicates the number of base substitutions per site

Figure 3

Neighbor‐Joining phylogenetic tree showing the position of the archaeal 16S rRNA clone sequences (the Aral Sea cluster) within the Haloferacaceae family as defined by Gupta et al. (2015). Only type strains of type species are included as references, with accession numbers shown in brackets. Bootstrap values ≥51% are indicated at branch nodes and based on 500 iterations. Positions containing gaps or missing data were excluded from the analysis. Natronolimnobius baerhuensis, belonging to the closest related family, Natrialbaceae, was used as outgroup. The bar indicates the number of base substitutions per site