Marinobacter salinexigens sp. nov., a marine bacterium isolated from hadal seawater of the Mariana Trench

Albibacterium profundi sp. nov., isolated from sediment of the Challenger Deep of Mariana Trench, and reclassification of Pedobacter indicus as Albibacterium indicum comb. nov

A rod-shaped, white-pigmented, non-motile, Gram-stain-negative bacterium, designated RHL897T, was isolated from sediments collected at the Mariana Trench Challenger Deep (10,816 m). Strain RHL897T was strictly aerobic and grew at 4-37 °C, pH 6.0-10.0 and in the presence of 0-11.0 % (w/v) NaCl. Its genomic DNA G+C content was 41.2%. Metabolic analysis revealed mechanisms for salt tolerance, abundant metal ion transport proteins and stronger resistance to heavy metals such as arsenic and mercury compared to the closest reference strains, likely linked to adaptation to the hadal sediment environment. The predominant menaquinone was MK-7, and the major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified glycolipid. The main fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and iso-C17 : 0 3OH. Strain RHL897T exhibited the highest 16S rRNA gene sequence similarity to the type strain of Pedobacter indicus (97.9%) and Albibacterium bauzanense (96.1%). Phylogenetic trees constructed based on 16S rRNA gene sequences and a 549 core gene set indicated that strain RHL897T was closely related to P. indicus and A. bauzanense, with all three species clustering within a distinct clade. Combined with the analyses of average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization, strain RHL897T represented a novel species of the genus Albibacterium, for which the name Albibacterium profundi sp. nov. is proposed. The type strain is RHL897T (=MCCC 1K09221T=KCTC 102276T). Furthermore, the revised phylogeny with the inclusion of RHL897T suggested that P. indicus should be reclassified under the genus Albibacterium and renamed Albibacterium indicum.

Changes in the structure of the microbial community within the phycospheric microenvironment and potential biogeochemical effects induced in the demise stage of green tides caused by Ulva prolifera

Green tides caused by Ulva prolifera occur annually in the Yellow Sea of China, and the massive amount of biomass decomposing during the demise stage of this green tide has deleterious ecological effects. Although microorganisms are considered key factors influencing algal bloom demise, an understanding of the microbial-algae interactions within the phycospheric microenvironment during this process is still lacking. Here, we focused on the variations in phycospheric microbial communities during the late stage of the green tide in three typically affected areas of the Yellow Sea via metagenomic sequencing analysis. In total, 16.9 million reads obtained from 18 metagenome samples were incorporated into the assembled contigs (13.4 Gbp). The phycosphere microbial community composition and diversity changed visibly during the demise of U. prolifera. The abundances of algae-lysing bacteria, Flavobacteriaceae at the family level and Alteromonas, Maribacter, and Vibrio at the genus level increased significantly in the phycosphere. In addition, the levels of glycoside hydrolases (GHs) and polysaccharide lyases (PLs) enzymes, which decompose U. prolifera polysaccharides in the phycosphere, were greater. Therefore, the degradation of algal polysaccharides can increase the efficiency of carbon metabolism pathways in the phycospheric microenvironment. Most of the genes detected in the phycosphere, especially norC, nrfA, and nasA, were associated with nitrogen metabolism pathways and showed dynamics related to the demise of the large amount of organic matter released by a green tide. Therefore, the demise of green tide algae may affect the potential carbon and nitrogen cycles of the phycospheric microenvironment by driving changes in the structure and diversity of microbial communities. Our research provides a novel perspective to better understand the ecological impact of U. prolifera during the green tide demise stage.

Marinobacter qingdaonensis sp. nov., a moderately halotolerant bacterium isolated from intertidal sediment

A Gram-stain-negative, aerobic, rod-shaped and halotolerant bacterium, designated as strain ASW11-75T, was isolated from intertidal sediments in Qingdao, PR China, and identified using a polyphasic taxonomic approach. Growth of strain ASW11-75T occurred at 10-45 °C (optimum, 37 °C), pH 6.5-9.0 (optimum, pH 8.0) and 0.5-18.0 % NaCl concentrations (optimum, 2.5 %). Phylogenetic analyses based on 16S rRNA gene sequences and 1179 single-copy orthologous clusters indicated that strain ASW11-75T is affiliated with the genus Marinobacter. Strain ASW11-75T showed highest 16S rRNA gene sequence similarity to 'Marinobacter arenosus' CAU 1620T (98.5 %). The digital DNA-DNA hybridization and average nucleotide identity values between strain ASW11-75T and its closely related strains (Marinobacter salarius R9SW1T, Marinobacter similis A3d10T, 'Marinobacter arenosus' CAU 1620T, Marinobacter sediminum R65T, Marinobacter salinus Hb8T, Marinobacter alexandrii LZ-8T and Marinobacter nauticus ATCC 49840T) were 19.8-24.5 % and 76.6-80.7 %, respectively. The predominant cellular fatty acids were C16 : 0, C18 : 1  ω9c and C16 : 0 N alcohol. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid and two unidentified lipids. The major isoprenoid quinone was ubiquinone-9. The genomic DNA G+C content was 62.2 mol%. Based on genomic and gene function analysis, strain ASW11-75T had lower protein isoelectric points with higher ratios of acidic residues to basic residues and possessed genes related to ion transport and organic osmoprotectant uptake, implying its potential tolerance to salt. The results of polyphasic characterization indicated strain ASW11-75T represents a novel Marinobacter species, for which the name Marinobacter qingdaonensis sp. nov. with the type strain ASW11-75T is proposed. The type strain is ASW11-75T (=KCTC 82497T=MCCC 1K05587T).

Glucosylglycerol phosphorylase, a potential novel pathway of microbial glucosylglycerol catabolism

Glucosylglycerol (GG) is a natural compatible solute that can be synthesized by many cyanobacteria and a few heterotrophic bacteria under high salinity conditions. In cyanobacteria, GG is synthesized by GG-phosphate synthase and GG-phosphate phosphatase, and a hydrolase GGHA catalyzes its degradation. In heterotrophic bacteria (such as some Marinobacter species), a fused form of GG-phosphate phosphatase and GG-phosphate synthase is present, but the cyanobacteria-like degradation pathway is not available. Instead, a phosphorylase GGP, of which the coding gene is located adjacent to the gene that encodes the GG-synthesizing enzyme, is supposed to perform the GG degradation function. In the present study, a GGP homolog from the salt-tolerant M. salinexigens ZYF650T was characterized. The recombinant GGP catalyzed GG decomposition via a two-step process of phosphorolysis and hydrolysis in vitro and exhibited high substrate specificity toward GG. The activity of GGP was enhanced by inorganic salts at low concentrations but significantly inhibited by increasing salt concentrations. While the investigation on the physiological role of GGP in M. salinexigens ZYF650T was limited due to the failed induction of GG production, the heterologous expression of ggp in the living cells of the GG-producing cyanobacterium Synechocystis sp. PCC 6803 significantly reduced the salt-induced GG accumulation. Together, these data suggested that GGP may represent a novel pathway of microbial GG catabolism. KEY POINTS: • GGP catalyzes GG degradation by a process of phosphorolysis and hydrolysis • GGP-catalyzed GG degradation is different from GGHA-based GG degradation • GGP represents a potential novel pathway of microbial GG catabolism.

Massilia litorea sp. nov., Marinobacter salinisoli sp. nov. and Rhodobacter xanthinilyticus sp. nov., isolated from coastal environments

Three bacterial strains, namely LPB0304T, LPB0319T and LPB0142T, were isolated from coastal environments. The 16S rRNA gene sequences of the three isolates were found to show the highest sequence similarities to Massilia litorea (98.44 %), Marinobacter salinisoli (97.55 %) and Rhodobacter lacus (97.60 %), respectively. The low (<98.7 %) sequence similarities and tree topologies implied the novelty of the three isolates, representing novel genomic species of the genus Massilia, Marinobacter and Rhodobacter. Numerous biochemical and physiological features also supported the distinctiveness of the isolates from previously known species. Based on the phenotypic and phylogenetic data presented in this study, three novel species are suggested with the following names: Massilia litorea sp. nov. (LPB0304T=KACC 21523T=ATCC TSD-216T), Marinobacter salinisoli sp. nov. (LPB0319T=KACC 21522T=ATCC TSD-218T) and Rhodobacter xanthinilyticus sp. nov. (LPB0142T=KACC 18892T=JCM 31567T).

Marinobacter panjinensis sp. nov., a moderately halophilic bacterium isolated from sea tidal flat environment

Two moderately halotolerant bacterium strains, designated PJ-16^T and PJ-38, were isolated from a tidal flat of the red beach in Panjin City, Liaoning Province, PR China. Cells were found to be Gram-stain-negative, aerobic, motile, rod-shaped with a single polar flagellum. Optimum growth of strain PJ-16^T occurred at 30 °C, pH 7.0 and 0.2-8.0  % (w/v) NaCl, and strain PJ-38 at 30 °C, pH 6.0-7.0 and 0.2-8.0  % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PJ-16^T was most closely related to Marinobacter denitrificans KCTC 62941^T (99.2 % 16S rRNA gene sequence similarity), Marinobacter algicola DSM 16394^T (98.6 %), Marinobacter salarius JCM 19399^T (98.4 %) and Marinobacter confluentis KCTC 42705^T (98.2 %), and strain PJ-38 was most closely related to M. denitrificans KCTC 62941^T (99.1 %), M. algicola DSM 16394^T (98.6 %), M. salarius JCM 19399^T (98.4 %) and M. confluentis KCTC 42705^T (98.1 %). The G+C content of the genomic DNA of strain PJ-16^T based on its draft genomic sequence was 57.4 mol%. The major cellular fatty acids of strain PJ-16^T were C_16 : 0, C_16 : 1  ω7c/C_16 : 1  ω6c and C_18 : 1  ω9c. The major respiratory quinone of PJ-16^T was ubiquinone-9 and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The results of the phenotypic, phylogenetic and genomic analyses revealed that strains PJ-16^T and PJ-38 represent a novel species of the genus Marinobacter, and the name Marinobacter panjinensis sp. nov. is proposed. The type strain is PJ-16^T (= CGMCC 1.13694^T= KCTC 72023^T).

Draft Genome Sequence of the Planctobacterium marinum Type Strain K7

Planctobacterium marinum strain K7 is a Gram-negative gammaproteobacterium of the Alteromonadaceae family and is the sole type strain in the genus Planctobacterium. Presented here is the draft whole-genome sequence of P. marinum strain K7.

Diversity and distribution of viruses inhabiting the deepest ocean on Earth

As the most abundant biological entities on the planet, viruses significantly influence the overall functioning of marine ecosystems. The abundance, distribution, and biodiversity of viral communities in the upper ocean have been relatively well studied, but our understanding of viruses in the hadal biosphere remains poor. Here, we established the oceanic trench viral genome dataset (OTVGD) by analysing 19 microbial metagenomes derived from seawater and sediment samples of the Mariana, Yap, and Kermadec Trenches. The trench viral communities harbored remarkably high novelty, and they were predicted to infect ecologically important microbial clades, including Thaumarchaeota and Oleibacter. Significant inter-trench and intra-trench exchange of viral communities was proposed. Moreover, viral communities in different habitats (seawater/sediment and depth-stratified ocean zones) exhibited distinct niche-dependent distribution patterns and genomic properties. Notably, microbes and viruses in the hadopelagic seawater seemed to preferably adopt lysogenic lifestyles compared to those in the upper ocean. Furthermore, niche-specific auxiliary metabolic genes were identified in the hadal viral genomes, and a novel viral D-amino acid oxidase was functionally and phylogenetically characterized, suggesting the contribution of these genes in the utilization of refractory organic matter. Together, these findings highlight the genomic novelty, dynamic movement, and environment-driven diversification of viral communities in oceanic trenches, and suggest that viruses may influence the hadal ecosystem by reprogramming the metabolism of their hosts and modulating the community of keystone microbes.

Marinobacter alexandrii sp. nov., a novel yellow-pigmented and algae growth-promoting bacterium isolated from marine phycosphere microbiota

The marine phycosphere harbors unique cross-kingdom associations with ecological relevance. During investigating the diversity of phycosphere microbiota of marine harmful algal blooms dinoflagellates, a faint yellow-pigmented bacterium, designated as strain LZ-8, was isolated from paralytic shellfish poisoning toxin-producing dinoflagellate Alexandrium catenella LZT09. The new isolate appeared to have growth-promoting potential toward its algal host. Molecular analysis using 16S rRNA gene, housekeeping rpoD gene and whole-genome sequence comparison indicated that strain LZ-8^T was a novel gammaproteobacterium of the family Alteromonadaceae. The major fatty acids of strain LZ-8^T were C_16:0, C_18:1 ω9c, C_12:0 3-OH, summed feature 3, C_16:1 ω9c, C_12:0 and summed feature 9. The major isoprenoid quinone was Q-9. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid, two unidentified aminolipids and six unidentified polar lipids. The genomic DNA G+C content was 57.36 mol%. Based on genome sequencing, several biosynthetic gene clusters responsible for bacterial biosynthesis of carotenoids and siderophores that may involve in algae-bacterial interactions were identified in the genome of strain LZ-8^T. The polyphasic characterization indicated that strain LZ-8^T represents a novel Marinobacter species. The name Marinobacter alexandrii sp. nov., type strain LZ-8^T (= CCTCC AB 2018386^T = KCTC 72198^T) is proposed.