Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea

Abstract

Oceanic deep hypersaline anoxic basins (DHABs) are characterized by drastic changes in physico-chemical conditions in the transition from overlaying seawater to brine body. Brine-seawater interfaces (BSIs) of several DHABs across the Mediterranean Sea have been shown to possess methanogenic and sulfate-reducing activities, yet no systematic studies have been conducted to address the potential functional diversity of methanogenic and sulfate-reducing communities in the Red Sea DHABs. Here, we evaluated the relative abundance of Bacteria and Archaea using quantitative PCR and conducted phylogenetic analyses of nearly full-length 16S rRNA genes as well as functional marker genes encoding the alpha subunits of methyl-coenzyme M reductase (mcrA) and dissimilatory sulfite reductase (dsrA). Bacteria predominated over Archaea in most locations, the majority of which being affiliated with Deltaproteobacteria, while Thaumarchaeota were the most prevalent Archaea in all sampled locations. The upper convective layers of Atlantis II Deep, which bear increasingly harsh environmental conditions, were dominated by members of the class Thermoplasmata (Marine Benthic Group E and Mediterranean Sea Brine Lakes Group 1). Our study revealed unique microbial compositions, the presence of niche-specific groups, and collectively a higher diversity of the sulfatereducing communities compared to the methanogenic communities in all five studied locations. Dear Dr. Jebbar, Please find attached our revised version of RESMIC-D-15-00081 for publication in Research in Microbiology. The only comment from the referee was on the measurements of CO 2 in our samples. As these were done by a commercial service provide by GEOMAR in Germany, we now refer to their website.We hope that you will find the manuscript now suitable for publication in Research in Microbiology. were dominated by members of the class Thermoplasmata (Marine Benthic Group E and 37Mediterranean Sea Brine Lakes Group 1). Our study revealed unique microbial compositions, the 38 presence of niche-specific groups, and collectively a higher diversity of the sulfate-reducing 39 communities compared to the methanogenic communities in all five studied locations. 40

Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge

“…Sponges can be found in a variety of habitats such as deep-sea cold seeps. The deep-sea seeps studied so far include the Shaban Deep (3), the Discovery Deep (4), the Atlantis II Deep (5), and the Kebrit Deep (6). The seeps are diverse, with varied fluid flow regimes that support ecosystems with different structures (7).…”

Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool

“…Studies of microbial lifestyles in brine pools are less common than those of hydrothermal vents. The brine pools studied so far include the Shaban Deep (Ferrer et al, 2012), Discovery Deep (Wang et al, 2013), Atlantis II Deep (Ngugi et al, 2015), and Kebrit Deep (Guan et al, 2015) of the Red Sea, which contains more than 25 deep hypersaline anoxic pools (Antunes et al, 2011). Previous investigations of other deep-sea brine pools included those in the Mediterranean Sea (van der Wielen et al, 2005) and the Gulf of Mexico (Formolo and Lyons, 2013).…”

“…As a consequence, the prevalent processes in the microbial inhabitants are anaerobic oxidation of methane and sulfite and sulfate reduction (Antunes et al, 2011). Surveys of brine pools identified a few widespread groups including Proteobacteria, Actinobacteria, Cyanobacteria, and Deferribacteres, and showed a higher diversity of bacteria over the archaea (Ferrer et al, 2012; Guan et al, 2015; Ngugi et al, 2015). Despite the common origin and shared features of the investigated brine pools, regional variation may lead to distinct combinations of physicochemical parameters and sustains microorganisms with unique adaptive strategies.…”

Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria

“…The high salinity of the brine pools prevents mixing with the overlying seawater creating a brine-seawater interface (BSI) featuring steep salt and, in the case of hot brines, temperature gradients. Several studies using 16S rRNA gene amplicon community profiling and shotgun metagenomics have recently revealed the abundant presence of Planctomycetes (5–35%) in the BSI above the Discovery Deep, Atlantis II Deep, and Kebrit Deep brine pools [2–4]. As these are low-oxygen environments, detection of Planctomycetes likely indicates the presence of anammox bacteria.…”

“…Two 16S rRNA genes matching the Scalindua clade, with coverage 52× and 14×, and two hzsA sequences, with coverage 37× and 16×, could be reconstructed. The 16S sequence obtained from the former, dominant Scalindua species (5.7% of all 16S rRNA gene reads in our dataset), hereafter referred to as Candidatus Scalindua rubra, is only 94% identical to Candidatus Scalindua brodae and clusters with sequences obtained from the Atlantis II Deep BSI, the brine adjacent to the Discovery Deep [4] (Fig. 1a).…”