Unveiling microbial life in the new deep‐sea hypersaline Lake Thetis. Part II: a metagenomic study

Abstract

So far only little is known about the microbial ecology of Mediterranean deep-sea hypersaline anoxic lakes (DHALs). These brine lakes were formed by evaporite dissolution/brine seeps and are important model environments to provide insights into possible metabolisms and distributions of microorganisms on the early Earth. Our study on the Lake Thetis, a new thalassohaline DHAL located South-East of the Medriff Corridor, has revealed microbial communities of contrasting compositions with a high number of novel prokaryotic candidate divisions. The major finding of our present work is co-occurrence of at least three autotrophic carbon dioxide fixation pathways in the brine-seawater interface that are likely fuelled by an active ramified sulphur cycle. Genes for the reductive acetyl-CoA and reductive TCA pathways were also found in the brine suggesting that these pathways are operational even at extremely elevated salinities and that autotrophy is more important in hypersaline environments than previously assumed. Surprisingly, genes coding for RuBisCo were found in the highly reduced brine. Three types of sulphide oxidation pathways were found in the interface. The first involves a multienzyme Sox complex catalysing the complete oxidation of reduced sulphur compounds to sulphate, the second type recruits SQR sulphide:quinone reductase for oxidation of sulphide to elemental sulphur, which, in the presence of sulphide, could further be reduced by polysulphide reductases in the third pathway. The presence of the latter two allows a maximal energy yield from the oxidation of sulphide and at the same time prevents the acidification and the accumulation of S(0) deposits. Amino acid composition analysis of deduced proteins revealed a significant overrepresentation of acidic residues in the brine compared with the interface. This trait is typical for halophilic organisms as an adaptation to the brine's extreme hypersalinity. This work presents the first metagenomic survey of the microbial communities of the recently discovered Lake Thetis whose brine constitutes one of saltiest water bodies ever reported.

Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin

“…In contrast to a previous metagenome study of Thetis interface (Ferrer et al, 2012), we detected transcripts for ribulose 1,5-bisphosphate carboxylase (RuBisCo), the indicative enzyme for the Calvin-Benson-Bassham cycle (CBB) in the UI. Transcripts for RuBisCo were also retrieved to a lesser extent from the LI (Figure 3a).…”

“…The recently discovered Thetis DHAB was selected because a detailed description of the environmental setting, the diversity of its prokaryotes and eukaryotes, selected functional activities, and the genetic potential of the prokaryotic communities existed (La Cono et al, 2011;Ferrer et al, 2012;Stock et al, 2012). For the present study we examined the UI, from 7.0% to 16.3% salinity, and dissolved oxygen from 9.5 mmol l À 1 to 0, and the anoxic LI, with a salinity of 21.4% to 27.6%.…”

“…A pronounced stratification of both prokaryotic and eukaryotic communities was observed over the B2 m thick interface, as was a distinction between halocline and brine communities (La Cono et al, 2011;Stock et al, 2012). A recent metagenomics study of the Thetis brine and halocline (Ferrer et al, 2012) provided increased understanding of the metabolic potential of microbial communities of these habitats. However, [ 14 C]-bicarbonate assimilation rates and reverse transcriptase-PCR of a few functional genes in samples from the same Thetis habitats detected activities not suggested by the metagenome (La Cono et al, 2011), including the expression of ribulose 1,5-bisphosphate carboxylase.…”

Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes

“…However, most of these anaerobic bacteria were identified in marine and estuarine sediments and are capable of using Fe 3+ , Mn 4+ , nitrate or sulfur as electron acceptors, playing a role in the organic matter diagenesis (Roden and Lovley, 1993). In spite of the fact that 16S rRNA gene sequences belonging to Deferribacteres were identified in other hypersaline habitats (Ferrer et al, 2012), no evidence that these iron reducers could function under high-salt concentration was shown to date.…”

Inter-comparison of the potentially active prokaryotic communities in the halocline sediments of Mediterranean deep-sea hypersaline basins

“…While new cell morphologies and ecophysiological traits have been assigned to some of these microorganisms, only recently a more specific picture of the metabolic activities of DHAB microorganisms has started to emerge, e.g. S--oxidizing chemolithotrophy, microaerophilic autotrophy, heterotrophic sulfate reduction, methanogenesis and anaerobic methane oxidation (Borin et al 2009;La Cono et al 2011;Ferrer et al 2012;Pachiadaki et al 2014;Yakimov et al 2013;Alcaide et al 2015). In spite of these recent advances, we still know little about how these microorganisms survive and grow under the prevailing conditions of the DHABs.…”