Phylogenetically and metabolically diverse autotrophs in the world's deepest blue hole.

The world's deepest yongle blue hole (YBH) is characterized by sharp dissolved oxygen (DO) gradients, and considerably low-organic-carbon and high-inorganic-carbon concentrations that may support active autotrophic communities. To understand metabolic strategies of autotrophic communities for obtaining carbon and energy spanning redox gradients, we presented finer characterizations of microbial community, metagenome and metagenome-assembled genomes (MAGs) in the YBH possessing oxic, hypoxic, essentially anoxic and completely anoxic zones vertically. Firstly, the YBH microbial composition and function shifted across the four zones, linking to different biogeochemical processes.

sp. nov., a marine bacterium isolated from the coast of Qingdao.

A Gram-stain-negative, facultative anaerobic, rod-shaped strain, named SDRW27, was isolated from offshore seawater collected near Qingdao. Strain SDRW27 was able to grow at 16-37 °C (optimum, 28 °C), pH 6.0-9.

Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole.

The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted.

An IncN-ST7 epidemic plasmid mediates the dissemination of carbapenem-resistant Klebsiella pneumoniae in a neonatal intensive care unit in China over 10 years.

Objectives: Carbapenem-resistant Klebsiella pneumoniae (CRKP) has widely disseminated globally, but its epidemiological characterization and clinical significance in paediatric patients are not well understood. In this study, we aimed to trace the dissemination dynamics of CRKP in the neonatal intensive care unit (NICU) of a tertiary hospital over a 10-y period.

Methods: We collected 67 non-duplicate K.

A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China.

Adaptation to selective pressures is crucial for clinically important pathogens to establish epidemics, but the underlying evolutionary drivers remain poorly understood. The current epidemic of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant threat to public health. In this study we analyzed the genome sequences of 794 CRKP bloodstream isolates collected in 40 hospitals in China between 2014 and 2019.

Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater.

Background: Ubiquitous and diverse marine microorganisms utilise the abundant organosulfur molecule dimethylsulfoniopropionate (DMSP), the main precursor of the climate-active gas dimethylsulfide (DMS), as a source of carbon, sulfur and/or signalling molecules. However, it is currently difficult to discern which microbes actively catabolise DMSP in the environment, why they do so and the pathways used.

Results: Here, a novel DNA-stable isotope probing (SIP) approach, where only the propionate and not the DMS moiety of DMSP was C-labelled, was strategically applied to identify key microorganisms actively using DMSP and also likely DMS as a carbon source, and their catabolic enzymes, in North Sea water.

Frequent convergence of and carbapenemase genes in complex driven by epidemic plasmids and host incompatibility.

Convergence of and carbapenemase genes has been sporadically detected in complex (ECC) with an upward trend. However, the state of the epidemic and underlying mechanism of such convergence has been poorly understood. In this study, the co-occurrence of MCR and carbapenemases was systematically analyzed in 230 clinical ECC isolates collected between 2000 and 2018 together with a global dataset consisting of 3,559 ECC genomes compiled from GenBank.

DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data.

Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date.

Succession of marine bacteria in response to Ulva prolifera-derived dissolved organic matter.

Increasing macroalgal blooms as a consequence of climate warming and coastal eutrophication have profound effects on the marine environment. The outbreaks of Ulva prolifera in the Yellow Sea of China occurring every summer since 2007 to present have formed the world's largest green tide. The green tide releases huge amounts of dissolved organic matter (DOM) to the seawater, causing an organic overload.

Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench.

Microbial eukaryotes are widespread and play important roles in marine ecosystems. However, their ecological characteristics in the deep sea (>1,000 m), especially hadal trenches, were largely unknown. Here, we investigated the diversity and metabolic potentials of microbial eukaryotes along the whole water column of the Mariana Trench by metagenomics.

sp. nov., an agar-digesting marine bacterium isolated from coastal seawater in Daya Bay (Guangdong, China).

A Gram-strain-negative, facultatively anaerobic, motile, rod-shaped and flagellated marine bacterium, designated SM6, was isolated from surface seawater collected in Daya Bay (Guangdong, China). Phylogenetic analysis based on 16S rRNA gene sequences, multilocus sequence analysis, phylogenomic analysis of single-copy gene families and whole genome data showed that strain SM6 belonged to the genus . The closest phylogenetic relatives of SM6 were MSSRF60 (97.

sp. nov., an agar-digesting marine bacterium isolated from surface seawater.

A Gram-stain-negative, aerobic, gliding, reddish-orange-coloured, rod-shaped strain, designated SR4, was isolated from surface seawater sampled at Luhuitou fringing reef (South China Sea). Phylogenetic analyses based on the 16S rRNA gene, phylogenomic analysis of single-copy gene families and whole genome data affiliated it to the genus . It was most closely related to NBRC 100898 (97.

Bacteria are important dimethylsulfoniopropionate producers in marine aphotic and high-pressure environments.

Dimethylsulfoniopropionate (DMSP) is an important marine osmolyte. Aphotic environments are only recently being considered as potential contributors to global DMSP production. Here, our Mariana Trench study reveals a typical seawater DMSP/dimethylsulfide (DMS) profile, with highest concentrations in the euphotic zone and decreased but consistent levels below.

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth.

The Earth's oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored. Here, we used metagenomics to investigate the microbial communities and their potential to drive biogeochemical cycling in seven different water layers down the vertical profile of the Challenger Deep (0-10,500 m) in the Mariana Trench, the deepest natural point in the Earth's oceans.

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

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterium, designated ZYF650, was isolated from the hadal seawater (9600 m) of the Mariana Trench. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that ZYF650 formed a lineage within the family that was distinct from the most closely related species and with 16S rRNA gene sequences similarities of 98.0 and 97.

Ancestral niche separation and evolutionary rate differentiation between sister marine flavobacteria lineages.

Marine flavobacteria are specialists for polysaccharide degradation. They dominate in habitats enriched with polysaccharides, but are also prevalent in pelagic environments where polysaccharides are less available. These niches are likely occupied by distinct lineages, but evolutionary processes underlying their niche differentiation remain elusive.

Comparative genomic and metabolic analysis of manganese-oxidizing mechanisms in Celeribacter manganoxidans DY25: Its adaptation to the environment of polymetallic nodules.

Manganese (Mn) nodule is one of the ubiquitous polymetallic concretions and mainly consists of Mn - Fe oxi-hydroxide precipitations. A primary oxidation of Mn(II) to MnO, in which microorganisms may play important roles, is followed by agglomeration of MnO into nodules. Celeribater manganoxidans DY25, belonging to family Rhodobacteraceae, has ability to catalyze the formation of MnO [1].

sp. nov. and sp. nov., two marine bacteria isolated from the East China Sea.

Two Gram-staining-negative, facultatively anaerobic, motile, short clavate and flagellated marine bacteria, designated strains BEI233 and LJC006, were isolated from the East China Sea. On the basis of the results of 16S rRNA gene sequencing and multilocus sequence analysis, BEI233 and LJC006 should be assigned to the genus . The closest phylogenetic relatives of BEI233 are LMG 19158 (98.

Biogenic production of DMSP and its degradation to DMS-their roles in the global sulfur cycle.

Dimethyl sulfide (DMS) is the most abundant form of volatile sulfur in Earth's oceans, and is mainly produced by the enzymatic clevage of dimethylsulfoniopropionate (DMSP). DMS and DMSP play important roles in driving the global sulfur cycle and may affect climate. DMSP is proposed to serve as an osmolyte, a grazing deterrent, a signaling molecule, an antioxidant, a cryoprotectant and/or as a sink for excess sulfur.

Photobacterium chitinilyticum sp. nov., a marine bacterium isolated from seawater at the bottom of the East China Sea.

A Gram-stain-negative, facultative aerobic, motile by a polar flagellum, rod-shaped strain, designated BEI247, was isolated from seawater at the bottom of the East China Sea. Phylogenetic analysis of the 16S rRNA gene and whole genome data affiliated it with the genus Photobacterium. It was most closely related to Photobacterium alginatilyticum P03D4 (97.

Carbohydrate catabolic capability of a Flavobacteriia bacterium isolated from hadal water.

Flavobacteriia are abundant in many marine environments including hadal waters, as demonstrated recently. However, it is unclear how this flavobacterial population adapts to hadal conditions. In this study, extensive comparative genomic analyses were performed for the flavobacterial strain Euzebyella marina RN62 isolated from the Mariana Trench hadal water in low abundance.