Microbiome of the Black Sea water column analyzed by 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 (mostly) temperature. In spite of its well-known hydrology and physico chemistry, 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 classic and genome-resolved metagenomics generating a large number of metagenome-assembled genomes (MAGs) from them. The oxic zone presents many similarities to the global ocean while the euxinic water mass has similarities to other similar aquatic environments of marine or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environments and includes Cyanobacteria (Synechococcus), photoheterotrophs (largely with marine relatives), facultative/microaerophilic microbes again largely marine, chemolithotrophs (N and S oxidizers) and a large number of anaerobes, mostly sulfate reducers but also a few methanogens and a large number of 'dark matter' streamlined genomes of largely unpredictable ecology. Conclusions: The Black Sea presents a mixture of similarities to other water bodies. The photic zone has many microbes in common with that of the Mediterranean with the relevant exception of the absence of Prochlorococcus. The chemocline already presents very different characteristics with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. Finally 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 and a small but detectable methanogenesis.We are adding critical information about this unique and important ecosystem and its microbiome.

mebipred: identifying metal-binding potential in protein sequences.

“…The difference between 5 consecutive depths until 1,000m is in line with the changes in the environment described by the pH chemocline, changes in reduction potential, and reduced light [89]; i.e. the deeper one goes the lower the pH, the less calcium, and the more Fe 1,000m and 2,000m likely accompanies a change in the microbial community [82].…”

“…Mebipred can predict metal-binding from metagenome read translations. We compared the metal-binding profiles of the Black Sea metagenomic (assembled and not assembled) samples obtained at different depths in a water column [82] (which was not certified by peer review) is the author/funder. All rights reserved.…”

“…oxygen, and light gradients have been characterized [84]. The sea surface layers 1,000m and 2,000m likely accompanies a change in the microbial community [82].…”

Carbon fixation pathways across the bacterial and archaeal tree of life

“…4 show six representative MAGs and for the remainder see Tables S1, S4, and S6 ). Similarly, organisms assigned to the order GCA-2,400,775 have been predicted to be chemolithotrophic, even though no CFP had been proposed ( 51 ). In our analysis, 96 MAGs assigned to this taxon have genes for the CBB cycle and have the predicted capacity to oxidise ammonia, carbon monoxide, hydrogen, sulfide, sulfite, or thiosulfate (Fig.…”

The importance of environmental parameters and mixing zone in shaping estuarine microbial communities along a freshwater-marine gradient

“…Dehalococcoidia (SAR202 clade) are known to be key players in carbon and sulfur cycling in aphotic zones, contributing to the degradation of recalcitrant organic compounds forming syntrophic networks with organic matter degraders (Landry et al, 2017; Yang et al, 2020; Cabello-Yeves et al, 2021). Nitrite oxidizers, Nitrospinaceae , are one of the important players in the nitrogen cycle, as observed at the redoxcline and in oxygen minimum zones of the Black Sea and the eastern tropical North Pacific Ocean, respectively (Beman et al, 2013; Cabello-Yeves et al, 2020), where metabolic coupling with NH 4 -oxidizing Archaea can also occur (Mincer et al, 2007; Santoro et al, 2010). The association of these zOTUs with high nitrate concentration, along with low DO in the intermediate waters, indicates that these microorganisms are likely key players in nutrient cycling and further raises the possibility that they may play a role in the oxygen demand inside the harbour.…”