The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

Abstract

Background The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salinity and temperature. Despite its well-known hydrology and physicochemical features, this enormous water mass remains poorly studied at the microbial genomics level. Results We have sampled its different water masses and analyzed the microbiome by shotgun and genome-resolved metagenomics, generating a large number of metagenome-assembled genomes (MAGs) from them. We found various similarities with previously described Black Sea metagenomic datasets, that show remarkable stability in its microbiome. Our datasets are also comparable to other marine anoxic water columns like the Cariaco Basin. The oxic zone resembles to standard marine (e.g. Mediterranean) photic zones, with Cyanobacteria (Synechococcus but a conspicuously absent Prochlorococcus), and photoheterotrophs domination (largely again with marine relatives). The chemocline presents very different characteristics from the oxic surface with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. The euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy-generating metabolism, a few (but detectable) methanogenesis marker genes, and a large number of “dark matter” streamlined genomes of largely unpredictable ecology. Conclusions The Black Sea oxic zone presents many similarities to the global ocean while the redoxcline and euxinic water masses have similarities to other similar aquatic environments of marine (Cariaco Basin or other Black Sea regions) or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environment. We are adding critical information about this unique and important ecosystem and its microbiome.

New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient

“…The other clade, provisionally named 'oxycline', is better resolved phylogenetically (Figure 3) and functionally (Figure 2b) than the other new clades and overlaps with the order GCA_002731375. This taxonomic unit is most likely overranked, since its two taxa represented in GTDB [14] closely cluster with those found in the Saanich Inlet [18] and other marine environments [19,38] (Figure 3 and Supplementary Table S1). About 80 MAGs in the OceanDNA repository [15] appear to be members of the same clade and in the majority of cases (74%) have been recovered from OMZ or equivalent niches with very low oxygen concentrations-probably the highest percentage for GTDB-classified marine MAGs [15].…”

“…This large soluble enzyme is part of the 120 protein markers used for GTDB taxonomy [12] and reacts with nucleotides as the majority of the same proteins. In the absence of sequence data for the 16S RNA in MAGs [17][18][19]38], CTP synthase can provide a valuable marker for taxonomic classification of Alphaproteobacteria, having features complementary with those of NuoL [10]. Figure 3 shows a representative ML tree of this protein from Alphaproteobacterial taxa spanning deep branching Rhodospirillales to early branching Rhizobiales, therefore encompassing the phylogenetic space of the new clades (Figure 1).…”

“…Such subdivisions could be retained under the super-order Rhodospirillales, despite the fact that they have been defined solely by phylogenomic analysis [12,14], which contrasts with traditional classifications based upon multiple phenotypic and genotypic features (multiphasic taxonomy) [13,16]. A clear advantage of GTDB taxonomy is that it provides a detailed set of subdivisions to automatically classify many MAGs derived from large assembly studies of marine or other environments [12,14,15,[17][18][19]. The limits of this phylogenomics-based classification are not only the incongruencies with the NCBI taxonomy (Table 1), but also the number and type of protein markers that can be assigned to a given MAG to estimate its taxonomic placement [12].…”

Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake

“…In the deeper Framvaren Fjord, Norway (180 m), PSB are found directly beneath the chemocline but within the redox transition zone, and GSB are found just below (Behnke et al, , 2006 , 2010 ; Sorensen, 1988 ), similar to FGL. In contrast, in the Black Sea (maximum depth >2200 m), GSB are observed, but the presence of PSB in the water column has not been confirmed (Cabello‐Yeves et al, 2021 ; Overmann & Manske, 2006 ). Like FGL, the Black Sea GSB consist largely of Chl .…”

“…Like FGL, the Black Sea GSB consist largely of Chl . phaeobacteroides and are found beneath the chemocline, and Synechococcus are the dominant cyanobacterium above the chemocline (Cabello‐Yeves et al, 2021 ).…”