Functional profiling of bacterial communities in Lake Tuz using 16S rRNA gene sequences

Abstract

The 16S rRNA amplicon sequencing technique is a key aspect of studies of microbial communities but does not provide direct evidence of a community's functional capabilities. This work aimed to assess the structure of the uncultured bacterial communities from two locations in Lake Tuz in Turkey to provide information on their roles in the lake ecosystem. The most abundant phyla in the lake water were Firmicutes (84%) for lake sample site 1 (TG1), 70% for lake sample site 2 (TG2), Fusobacteria (9% for TG1, 22% for TG2) and Proteobacteria (6% for TG1, 7% for TG2). The most abundant genera were Romboutsia (45% for TG1, 35% for TG2), Clostridium sensu stricto 1 (8% for TG1, 8% for TG2), Cetobacterium (9% for TG1, 22% for TG2) and Photobacterium (2% for TG1, 3% for TG2). PICRUSt constitutes a novel bioinformatics tool to establish profiles for bacterial protein functions based on metagenomic 16S rRNA data for a community of unculturable bacteria. PICRUSt also provides information on whole-community metabolic functions related to adaptation, bioremediation potential and the ability of various groups of microorganisms to survive in highly saline water. The overall results provide an effective strategy for assessing the metabolic capacities of microbes in situ in a high-salt aquatic environment such as Lake Tuz and the potential of these microbes to serve as bioremediation agents. This approach provides useful insights into predictive metagenomics of an unculturable microbial community for which only marker-gene surveys are currently available.

Functional and Molecular Characterization of the Halomicrobium sp. IBSBa Inulosucrase

“…In line with the neutral to moderate alkaline pH in Tuz Lake [ 64 ], the pH optimum of Hmc Isc (7.0–7.5) was situated in this region, with rapid activity loss in the acidic region ( Figure 3 a). Such a pH optimum is rather unusual among the inulosucrases so far characterized [ 65 ], suggesting it may be an adaptation towards the specific environmental conditions in certain salt lakes, such as Tuz Lake.…”

“…The main ions in Tuz Lake are Na + (114.25 g/L) and Cl − (201.67 g/L), being much higher than SO 4 2− (19.85 g/L), Mg 2+ (11.44 g/L), K + (6.55 g/L) and Ca 2+ (0.32 g/L) [ 64 ]. When comparing the effect of the salt type on the Hmc Isc activity ( Figure 4 a), it is striking that the K + salts resulted in a tremendous inhibition as compared to NaCl, suggesting that the Na + ion, being the most abundant in Tuz Lake, is one of the most essential factors to preserve the enzyme stability and function.…”

Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S rRNA Amplicon Sequencing

“…The prokaryotic diversity of Tuz Lake has been mostly investigated using culture-dependent methods, permitting the isolation of moderately halophilic bacterial and extremely halophilic archaeal strains that produced lipases and proteases, and to a lower extent cellulase and β-galactosidase enzymes [ 22 , 25 , 26 , 27 , 28 ]. More recently, the archaeal and bacterial diversity of the lake, using culture-independent methods, has been investigated [ 18 , 29 , 30 , 31 , 32 ]. A higher percentage of the archaeal community than that of the bacterial community was detected by FISH.…”

“…Moreover, the bacterial composition of Tuz Lake was examined by the V3–V4 variable regions of bacterial 16S rRNA gene. Firmicutes , Fusobacteria , and Proteobacteria were determined as the most abundant bacterial phyla in two brine samples of the lake [ 31 ].…”

“…Overall, previous microbiological studies using culture-independent analyses were limited to a small number of samples and sampling areas compared to the great extent of the lake or were restricted to the study of bacteria or sediments of Tuz Lake [ 18 , 29 , 30 , 31 ]. In this study, we have determined the composition and abundance of prokaryotic communities present in the brines of different sampling sites of Tuz Lake, including the Deep Zone, as well as the three salterns, Kayacik, Kaldirim, and Yavsan that are associated with the lake, through 16S rRNA gene amplicon sequencing.…”