Primary producing prokaryotic communities of brine, interface and seawater above the halocline of deep anoxic lake L'Atalante, Eastern Mediterranean Sea

Abstract

Meso-and bathypelagic ecosystems represent the most common marine ecological niche on Earth and contain complex communities of microorganisms that are for the most part ecophysiologically poorly characterized. Gradients of physico-chemical factors (for example, depth-related gradients of light, temperature, salinity, nutrients and pressure) constitute major forces shaping ecosystems at activity 'hot spots' on the ocean floor, such as hydrothermal vents, cold seepages and mud volcanoes and hypersaline lakes, though the relationships between community composition, activities and environmental parameters remain largely elusive. We report here results of a detailed study of primary producing microbial communities in the deep Eastern Mediterranean Sea. The brine column of the deep anoxic hypersaline brine lake, L'Atalante, the overlying water column and the brine-seawater interface, were characterized physico-and geochemically, and microbiologically, in terms of their microbial community compositions, functional gene distributions and [ 14 C]bicarbonate assimilation activities. The depth distribution of genes encoding the crenarchaeal ammonia monooxygenase a subunit (amoA), and the bacterial ribulose-1,5-biphosphate carboxylase/ oxygenase large subunit (RuBisCO), was found to coincide with two different types of chemoautotrophy. Meso-and bathypelagic microbial communities were enriched in ammoniaoxidizing Crenarchaeota, whereas the autotrophic community at the oxic/anoxic interface of L'Atalante lake was dominated by Epsilonproteobacteria and sulfur-oxidizing Gammaproteobacteria. These autotrophic microbes are thus the basis of the food webs populating these deep-sea ecosystems.

Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea)

“…Before cDNA synthesis, RNA-containing extracts were purified from DNA by incubation with DNAse I (DNA-free-Kit, Ambion, Austin, TX, USA) at 37 1C for 30 min and the RNA concentrations determined using a NanoDrop ND 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). Each RNA sample was immediately converted into cDNA with SuperScript II Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and random primers as described elsewhere (Yakimov et al, 2007). The reaction was carried out in a MasterCycler 5331 Gradient (Eppendorf, Hamburg, Germany).…”

“…The experiment was performed using DNA templates originating from all depths sampled in triplicates along with a 'no template control'. Mixtures for Q-PCRs and the reaction conditions were as previously described (Yakimov et al, 2007). Q-PCR amplification was analyzed using an automatic setting of the baseline and threshold values.…”

“…Phylogenetic analysis was performed as previously described (Yakimov et al, 2007(Yakimov et al, , 2009. Briefly, all sequences were edited and aligned with MacVector Software version 11.0.2 (Accelrys, San Diego, CA, USA) (Rajagopal, 2000).…”

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

“…Studies of Discovery, L'Atalante, Urania, Thetis and Bannock basins revealed that DHAB interfaces harbor abundant and diverse microbial communities that include numerous novel candidate divisions that are more productive than most pelagic marine systems (see, for example, Sass et al, 2001;Van Der Wielen et al, 2005;Yakimov et al, 2007;Edgcomb et al, 2009;Stock et al, 2012). Functional analyses of these communities based on PCR amplification of key functional genes as well as activity measurements revealed sulfur cycling and methanogenesis to be dominant prokaryotic metabolic processes supporting life in DHABs and contributing to observed elevated biomass in DHAB haloclines (Daffonchio et al, 2006;Yakimov et al, 2007;Borin et al, 2009). Recent advances in RNA isolation, amplification and high-throughput sequencing make it possible to acquire millions of sequences of transcribed genes from microbial communities.…”

Marine Microorganisms as Source of Stereoselective Esterases and Ketoreductases: Kinetic Resolution of a Prostaglandin Intermediate

“…Deep-sea hypersaline anoxic basins (DHABs) of the Eastern Mediterranean are extreme environments characterized by high salinity and corresponding density, high hydrostatic pressure, absence of light, anoxia, and the presence of a sharp chemocline between brines and the above seawater. Moreover, DHABs contain brines with different composition, and hence each of them constitutes an independent environment, which hosts a peculiar and stratified prokaryotic community, highly adapted to the extreme geosetting (Van der Wielen et al 2005;Daffonchio et al,2006;Yakimov et al 2007). These habitats resulted, therefore, in the selection of unusual microorganisms with peculiar enzyme endowment, i.e.…”