Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2–0.8 µm) and up to 45% in the largest particles (20–200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.

Strain ISS155^T, isolated from surface Mediterranean seawater, has cells that are Gram-reaction-negative, motile, strictly aerobic chemoorganotrophic, oxidase-positive, unable to reduce nitrate to nitrite, and able to grow with cellulose as the sole carbon and energy source. It is mesophilic, neutrophilic, slightly halophilic and has a requirement for sodium and magnesium ions. Its 16S rRNA gene sequence places the strain among members of Cellvibrionaceae , in the Gammaproteobacteria , with Agarilytica rhodophyticola 017^T as closest relative (94.3 % similarity). Its major cellular fatty acids are C_18 : 1, C_16 : 0 and C_16 : 1; major phospholipids are phosphatidyl glycerol, phosphatidyl ethanolamine and an unidentified lipid, and the major respiratory quinone is Q8. The genome size is 6.09 Mbp and G+C content is 45.2 mol%. A phylogenomic analysis using UBCG merges strain ISS155^T in a clade with A. rhodophyticola , Teredinibacter turnerae , Saccharophagus degradans and Agaribacterium haliotis type strain genomes, all of them possessing a varied array of carbohydrate-active enzymes and the potential for polysaccharide degradation. Average amino acid identity indexes determined against available Cellvibrionaceae type strain genomes show that strain ISS155^T is related to them by values lower than 60 %, with a maximum of 58 % to A. rhodophyticola 017^T and 57 % to T. turnerae T7902^T and S. degradans 2-40^T. These results, together with the low 16S rRNA gene sequence similarities and differences in phenotypic profiles, indicate that strain ISS155^T represents a new genus and species in Cellvibrionaceae , for which we propose the name Thalassocella blandensis gen. nov., sp. nov., and strain ISS155^T (=CECT 9533^T=LMG 31237^T) as the type strain.

Microbial reduction of inorganic divalent mercury (Hg²⁺) and methylmercury (MeHg) demethylation is performed by the mer operon, specifically by merA and merB genes, respectively, but little is known about the mercury tolerance capacity of marine microorganisms and its prevalence in the ocean. Here, combining culture-dependent analyses with metagenomic and metatranscriptomic data, we show that marine bacteria that encode mer genes are widespread and active in the global ocean. We explored the distribution of these genes in 290 marine heterotrophic bacteria (Alteromonas and Marinobacter spp.) isolated from different oceanographic regions and depths, and assessed their tolerance to diverse concentrations of Hg²⁺ and MeHg. In particular, the Alteromonas sp. ISS312 strain presented the highest tolerance capacity and a degradation efficiency for MeHg of 98.2% in 24 h. Fragment recruitment analyses of Alteromonas sp. genomes (ISS312 strain and its associated reconstructed metagenome assembled genome MAG-0289) against microbial bathypelagic metagenomes confirm their prevalence in the deep ocean. Moreover, we retrieved 54 merA and 6 merB genes variants related to the Alteromonas sp. ISS312 strain from global metagenomes and metatranscriptomes from Tara Oceans. Our findings highlight the biological reductive MeHg degradation as a relevant pathway of the ocean Hg biogeochemical cycle.

The ocean's mercury (Hg) content has tripled due to anthropogenic activities, and although the dark ocean (>200 m) has become an important Hg reservoir, concentrations of the toxic and bioaccumulative methylmercury (MeHg) are low and therefore very difficult to measure. As a consequence, the current understanding of the Hg cycle in the deep ocean is severely data-limited, and the factors controlling MeHg, as well as its transformation rates, remain largely unknown. By analyzing 52 globally distributed bathypelagic deep-ocean metagenomes and 26 new metatranscriptomes from the Malaspina Expedition, our study reveals the widespread distribution and expression of bacterial-coding genes merA and merB in the global bathypelagic ocean (∼4000 m depth). These genes, associated with Hg^II reduction and MeHg demethylation, respectively, are particularly prevalent within the particle-attached fraction. Moreover, our results indicate that water mass age and the organic matter composition shaped the structure of the communities harboring merA and merB genes living in different particle size fractions, their abundance, and their expression levels. Members of the orders Corynebacteriales, Rhodobacterales, Alteromonadales, Oceanospirillales, Moraxellales, and Flavobacteriales were the main taxonomic players containing merA and merB genes in the deep ocean. These findings, together with our previous results of pure culture isolates of the deep bathypelagic ocean possessing the metabolic capacity to degrade MeHg, indicated that both methylmercury demethylation and Hg^II reduction likely occur in the global dark ocean, the largest biome in the biosphere.

Strain ISS653^T, isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bacterium, strictly aerobic and chemoorganotrophic, slightly halophilic (1–15 % NaCl) and mesophilic (4–37 °C), oxidase- and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C_15 : 0, iso-C_15 : 0 2-OH, and iso-C_17 : 0 3-OH; the major identified phospholipid is phosphatidylethanolamine and the major respiratory quinone is MK6. Genome size is 4.28 Mbp and DNA G+C content is 34.9 mol%. 16S rRNA gene sequence similarity places the strain among members of the family Flavobacteriaceae, with the type strains of Mesonia phycicola (93.2 %), Salegentibacter mishustinae (93.1 %) and Mesonia mobilis (92.9 %) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with M. mobilis (81 % AAI; 78.9 % ANI), M. phycicola (76 % AAI; 76.3 % ANI), Mesonia maritima (72 % AAI, 74.9 % ANI), Mesonia hippocampi (64 % AAI, 70.8 % ANI) and Mesonia algae (68 % AAI; 72.2 % ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653^T in a clade with species of the genus Mesonia . We conclude that strain ISS653^T represents a novel species of the genus Mesonia for which we propose the name Mesonia oceanica sp. nov., and strain ISS653^T (=CECT 9532^T=LMG 31236^T) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the Tara oceans expedition indicate that the species is more abundant in the mesopelagic dark ocean than in the photic layer and it is more frequent in the South Pacific, Indian and North Atlantic oceans.

Cork matrices biofunctionalized with Moringa oleifera seed extracts (MoSe) have potential for use as a biofilter with antibacterial properties to reduce waterborne pathogens. The aim of this study was to evaluate the effect of cork biofunctionalized with active antimicrobial compounds of MoSe (f-cork) on the inhibition of Escherichia coli (InhEc). The LacZ gene from a strain of E. coli was used as the target sequence using viability quantification Polymerase Chain Reaction (qPCR) and differentiation of viable and dead bacteria through selective cell viability PMA staining. To perform this, a 2⁷⁻⁴ fractional factorial design and a biofiltration system were used to evaluate the effect of the active protein in MoSe immobilized in granulated cork on InhEc. We found that the potential for antimicrobial activity increased with f-cork for an effective maximal bacterial reduction (99.99%; p < 0.05). The effect of f-cork functionalized with MoSe on E. coli viability was of 0.024% and 0.005% for the cells exposed to PMA, respectively, being the relevant conditions in treatment 2: (0 L/min) without aeration, (5%) MoSe and (5 mm) cork particle. In conclusion, the f-cork functionalized with MoSe presented biosorbent and antibacterial properties that effectively reduced the E. coli growth.