Marinobacterium profundum sp. nov., a marine bacterium from deep-sea sediment

Direct Production of Bio-Recalcitrant Carboxyl-Rich Alicyclic Molecules Evidenced in a Bacterium-Induced Steroid Degradation Experiment

Carboxyl-rich alicyclic molecules (CRAM) are highly unsaturated compounds extensively distributed throughout aquatic environments and sediments. This molecular group is widely referred to as a major proxy of recalcitrant organic materials, but its direct biosynthesis remains unclear. Steroids are a typical anthropogenic contaminant and have been previously suggested to be precursors of CRAM; however, experimental evidence to support this hypothesis is lacking. Here, a steroid-degrading bacterium, Comamonas testosteroni ATCC 11996, was incubated in a liquid medium supplemented with testosterone (a typical steroid) as the sole carbon source for 90 days. Testosterone-induced metabolites (TIM) were extracted for molecular characterization and to examine the bioavailability during an additional 90-day incubation after inoculation with a natural coastal microbial assemblage. The results showed that 1,775 molecular formulas (MFs) were assigned to TIM using ultrahigh-resolution mass spectrometry, with 66.99% categorized as CRAM-like constituents. A large fraction of TIM was respired or transformed during the additional 90-day seawater incubation; nevertheless, 638 MFs of the TIM persisted or increased during incubation. Among the 638 MFs, 394 were commonly assigned in natural deep seawater samples (depths of 500 to 2,000 m) from the South China Sea. Compared to the catabolites of the well-established testosterone degradation pathway, we compiled a list of bio-refractory MFs and potential chemical structures, some of which shared structural homology with CRAM. These results demonstrated direct microbial production of bio-refractory CRAM from steroid hormones and indicated that some of the biogenic CRAM resisted microbial decomposition, potentially contributing to the aquatic refractory dissolved organic matter (DOM) pool. IMPORTANCE CRAM are an operationally defined DOM group comprising a complex mixture of carboxylated and fused alicyclic structures. This DOM group is majorly characterized as refractory DOM in the marine environment. However, the origins of the complex CRAM remain unclear. In this study, we demonstrated that testosterone (a typical steroid) could be transformed into bio-refractory CRAM by a single bacterial strain and observed that some of the CRAM highly resisted microbial degradation. Through molecular comparison and screening, potential chemical structures of steroid-induced CRAM were suggested. This study established the biological connection between steroids and bio-refractory CRAM, and it provides a novel perspective explaining the fate of terrestrial contaminants in aquatic environments.

Systematic assessment of mineral distribution and diversity of microbial communities and its interactions in the Taiwan subduction zone of mud volcanoes

Mud volcanoes are the most dynamic and unstable sedimentary structures in the areas of tectonic compression like the subduction zones. In this study, we comprehensively analyzed the distribution of minerals as well as diversity, abundance and metabolic potential of the microbial communities of major mud volcanic groups across Taiwan namely Chu-kou Fault (CKF), Gu-ting-keng Anticline (GTKA), Chi-shan Fault (CSF), and Longitudinal Valley Fault (LVF). The mud volcano fluids recorded relatively higher Na and Cl contents than the other elements, particularly in the CKF and GTKA groups. The highest microbial diversity and richness were observed in the CSF group, followed by the GTKA group, whereas the lowest microbial diversity was observed in the CKF and LVF groups. Proteobacteria were common in all the sampling sites, except WST-7 and WST-H (Wu-Shan-Ting) of the CSF group, which were abundant in Chloroflexi. The halophilic genus Alterococcus was abundant in the Na-and Cl-rich CL-A sites of the CKF group. Sulfurovum was dominant in the CLHS (Chung-Lun hot spring) site of the CKF group and was positively correlated with sulfur/thiosulfate respiration, which might have resulted in a higher expression of these pathways in the respective group. Aerobic methane-oxidizing microbial communities, such as Methylobacter, Methylomicrobium, Methylomonas, and Methylosoma, constituted a dominant part of the LVF and CSF groups, except for the YNH-A and YNH-B (Yang-Nyu-Hu) sites. The WST-7 and JS sites were abundant in both methane-producing and methane-oxidizing microbial communities. The LGH-F1 (Lei-Gong-Huo) site was dominated by both methanotrophic and methylotrophic genera, such as Methylomicrobium and Methylophaga, respectively. Methylotrophy, methanotrophs, and hydrocarbon-degrading pathways were more abundant in the LVF and CSF groups but not in the remaining groups. The results of this study extend our knowledge of the diversity, abundance, and metabolic functions of prokaryotes in major terrestrial mud volcanoes in Taiwan.

Inputs don't equal outputs: bacterial microbiomes of the ingesta, gut, and feces of the keystone deposit feeder Ilyanassa obsoleta

Bacteria drive energy fluxes and geochemical processes in estuarine sediments. Deposit-feeding invertebrates alter the structure and activity of microbial communities through sediment ingestion, gut passage, and defecation. The eastern mud snail, Ilyanassa obsoleta, is native to estuaries of the northwestern Atlantic, ranging from Nova Scotia, Canada, to Florida in the USA. Given extremely high densities, their deposit-feeding and locomotory activities exert ecological influence on other invertebrates and microbes. Our aim was to characterize the bacterial microbiome of this 'keystone species' and determine how its feeding alters the native bacterial microbiota. We gathered snails from both mudflat and sandflat habitats and collected their fresh fecal pellets in the laboratory. Dissection of these same snails allowed us to compare bacterial assemblages of ingested sediments, shell surfaces, gut sections (esophagus, stomach, intestine), and feces using DNA metabarcoding. Our findings indicate a diverse, resident gut microbiota. The stomach and intestines were dominated by bacteria of the genus Mycoplasma. Comparison of ingesta and feces revealed digestion of several bacterial taxa, introduction of gut residents during passage, in addition to unique bacterial taxa within the feces of unknown provenance. Our results demonstrate that I. obsoleta has the potential to modify microbial community structure in estuarine sediments.

Taxogenomic and Metabolic Insights into Marinobacterium ramblicola sp. nov., a New Slightly Halophilic Bacterium Isolated from Rambla Salada, Murcia

A Gram-negative, motile, rod-shaped bacteria, designated D7^T, was isolated by using the dilution-to-extinction method, from a soil sample taken from Rambla Salada (Murcia, Spain). Growth of strain D7^T was observed at 15–40 °C (optimum, 37 °C), pH 5–9 (optimum, 7) and 0–7.5% (w/v) NaCl (optimum, 3%). It is facultatively anaerobic. Phylogenetic analysis based on 16S rRNA gene sequence showed it belongs to the genus Marinobacterium. The in silico DDH and ANI against closest Marinobacterium relatives support its placement as a new species within this genus. The major fatty acids of strain D7^T were C_16:0, summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) and summed feature 8 (C_18:1 ω7c/C_18:1 ω6c). The polar lipid profile consists of phosphatidylethanolamine, phosphatidylglycerol and two uncharacterized lipids. Ubiquinone 8 was the unique isoprenoid quinone detected. The DNA G + C content was 59.2 mol%. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genomic characterization, strain D7^T (= CECT 9818^T = LMG 31312^T) represents a novel species of the genus Marinobacterium for which the name Marinobacterium ramblicola sp. nov. is proposed. Genome-based metabolic reconstructions of strain D7^T suggested a heterotrophic and chemolitotrophic lifestyle, as well as the capacity to biosynthetize and catabolize compatible solutes, and to degrade hydrocarbon aromatic compounds.

Marinobacterium boryeongense sp. nov., isolated from seawater

A Gram-stain-negative and strictly aerobic bacterium, designated DMHB-2^T, was isolated from a sample of seawater collected off the Yellow Sea coast of the Republic of Korea. Cells were short rods and motile by means of a single polar flagellum. Catalase and oxidase activities were positive. Growth occurred at pH 5.5-10.0 (optimum, pH 6.0), 15-45 °C (optimum, 25 °C) and with 1-9 % NaCl (optimum, 3 %). The respiratory quinone was ubiquinone-8 and the major fatty acids were C16 : 0 (17.9 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 26.1 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 37.4 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DMHB-2^T belong to the genus Marinobacterium, with the highest 16S rRNA gene sequence similarity of 95.2 % to Marinobacterium zhoushanense KCTC 42782^T. The genomic DNA G+C content of strain DMHB-2^T was 60.8 mol%. On the basis of the phenotypic, chemotaxonomic and genotypic characteristics presented in this study, strain DMHB-2^T is suggested to represent a novel species of the genus Marinobacterium, for which the name Marinobacteriumboryeongense sp. nov. is proposed. The type strain is DMHB-2^T (=KACC 19225^T=JCM 31902^T).

Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica

The genus Marinobacterium belongs to the family Alteromonadaceae within the class Gammaproteobacteria and was reported in 1997. Currently the genus Marinobacterium contains 16 species. Marinobacterium rhizophilum CL-YJ9^T was isolated from sediment associated with the roots of a plant growing in a tidal flat of Youngjong Island, Korea. The genome of the strain CL-YJ9^T was sequenced through the Genomic Encyclopedia of Type Strains, Phase I: KMG project. Here we report the main features of the draft genome of the strain. The 5,364,574 bp long draft genome consists of 58 scaffolds with 4762 protein-coding and 91 RNA genes. Based on the genomic analyses, the strain seems to adapt to osmotic changes by intracellular production as well as extracellular uptake of compatible solutes, such as ectoine and betaine. In addition, the strain has a number of genes to defense against oxygen stresses such as reactive oxygen species and hypoxia.

Marinobacterium zhoushanense sp. nov., isolated from surface seawater

A Gram-stain-negative, facultatively anaerobic bacterium, designated WM3T, was isolated from surface seawater collected from the East China Sea. Cells were catalase- and oxidase-positive, short rods and motile by means of a single polar flagellum. Growth occurred at 15-43 °C (optimum 37-40 C), pH 5.5-9.5 (optimum pH 6.5-7.5) and with 0.25-9.0 % (w/v) NaCl (optimum 1.0-1.5 %). Chemotaxonomic analysis showed that the respiratory quinone was ubiquinone-8, the major fatty acids included C16 : 0 (23.6 %), C18 : 1ω7c (26.2 %) and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH, 22.1 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain WM3T was most closely related to the genus Marinobacterium, sharing the highest 16S rRNA gene sequence similarity of 95.5 % with both Marinobacterium litorale KCTC 12756T and Marinobacterium mangrovicola DSM 27697T. The genomic DNA G+C content of the strain WM3T was 55.8 mol%. On the basis of phenotypic, chemotaxonomic and genotypic characteristics presented in this study, strain WM3T is suggested to represent a novel species of the genus Marinobacterium, for which the name Marinobacterium zhoushanense sp. nov. is proposed. The type strain is WM3T (=KCTC 42782T=CGMCC 1.15341T).