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The use of un-utilized feedstock and seawater for material and/or energy production using marine microbial catalysts is one potential option toward contributing to the development of a more sustainable society. Ethanol production from alginate, which is an oxidized polysaccharide present in brown seaweed, is extremely difficult due to the imbalance of reducing power in the microbial cells. Production of ethanol by such means has so far been unsuccessful using marine microbial biocatalysts. To produce ethanol from alginate, an alternative pathway consisting of a pyruvate decarboxylase gene (pdc) and an alcohol dehydrogenase II gene (adhII) derived from Zymomonas mobilis strain ZM4 was implemented into a metabolically engineered bacterium, Vibrio halioticoli, which is a representative marine alginate decomposer. No ethanol from alginate was produced in the wild-type V. halioticoli; however, the engineered V. halioticoli harboring the pdc and adhII operon (Pet operon), designated to the V. halioticoli (Pet), was able to produce 880 mg/L ethanol in maximum from 1.5% alginate for 72 h. The Pet operon also worked on the other marine alginolytic vibrios for ethanol production from alginate. This is the first case of ethanol production from alginate using marine bacterial biocatalysts under seawater-based media.

Vibrionaceae is one of the most diverse bacterial families and is currently classified into over 50 clades, some members of which play an important role in the symbiotic relationships with humans and animals. Halioticoli clade, which currently consists of 10 species: 8 species associated with the gut of abalone (symbiotic), 1 species (V. breoganii) from bivalves, and 1 species (V. ishigakensis) from subtropical seawater (planktonic). To accelerate studies in the evolution, ecogenomics, and biotechnology of Halioticoli clade species, the genomic backbones and pangenome analyses based on complete genome sequences are needed. Genome sizes of Halioticoli clade species ranged from 3.5 Mb to 4.8 Mb, with V. ishigakensis the biggest. The evolutionary relationships using multilocus sequence analysis based on eight housekeeping genes and 125 single-copy core genes revealed a division of five sub-clades in this clade; 1) V. breoganii, V. comitans, V. inusitatus and V. superstes, 2) V. ezurae, V. neonatus, and V. halioticoli, 3) V. rarus, 4) V. gallicus, and 5) V. ishigakensis. The pan-genomic analysis combined with function and metabolism estimations showed that the planktonic group (sub-clade 5) contained the greatest number of specific genes, and more genes responsible for carbohydrate metabolisms, especially the genes encoding D-galactonate degradation. These results demonstrated that the genome expanded by acquiring more abilities for utilizing various carbohydrates during the evolution from symbiotic to a planktonic lifestyle. Moreover, according to Carbohydrate-Active enZYmes (CAZy) profiling, genes encoding alginate degrading enzymes (aly), classified into PL6, PL7, PL15, and PL17 were common in the ten genomes, but sub-clade 1 had the most. Meanwhile, sub-clade 1and 5 also possessed abundant genes related to macroalgae substrates degradation (GHs), which are also responsible for the genome expansion of sub-clade 1 and 5.

There is a lot of evidence indicating pioneer microbes in early life having various effects on later host biology. Because of the influential phylogenetic position of sea cucumber, which is a deep branching clade in Deuterostomia, the attention on the microbiome in sea cucumber has been increasing. Although microbes in sea cucumber have been reported in several studies, there is a lack of knowledge regarding the pioneer microbiota in the early life stages of sea cucumber. In this study, microbiota changes during the larval development of sea cucumber were assessed using a laboratory rearing system. Microbial community structure was likely to be related to the developmental stage and significant alterations were detected in the late auricularia stage. The relative abundances of Oceanospirillales, Alteromonadales, and Rhodobacterales significantly varied after gut formation. A total of 257 strains were isolated from larval developmental stages of sea cucumber and affiliated to 124 ASVs in the metagenomic analysis. This data demonstrates for the first-time dynamic changes of sea cucumber microbiota in the developmental stages in early life.

Vibriosis accounts for 66.7% of diseases reported in groupers' cultures and affects almost all stages of growth. The disease could lead up to mortality up to 50% mortality, and it was reported that high stocking density and poor fish handling were among the factors that contributed to the disease dissemination. V. harveyi has been reported to be among the causative agent and has caused acute mortality in cage groupers. In this study, we report the genome of V. harveyi VH1 isolated from a diseased tiger grouper Epinephelus fuscoguttatus, reared in a cage farm located in the coastal area of Langkawi. (c) 2022 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)

Light is one of the most critical stimuli in the majority of living organisms. In the last two decades, blue light (BL) has become a major subject of attention because of developments in light-emitting diodes (LED). The effects of BL on eukaryotic organisms and phototrophic prokaryotes have been well studied, but the knowledge of its effects on non-phototrophic prokaryotes remains unclear. Since BL can penetrate seawater, it is expected that most prokaryotes living in the ocean possess molecular mechanisms which protect against BL. The aim of this study is to assess the molecular mechanisms of Vibrio parahaemolyticus cells against BL as a marine bacterial model compared to other wavelength light exposures. Physiological and transcriptomic analyses of BL-exposed cells compared to other light treated cells revealed the highest ROS fold change, the highest number of differentially expressed genes (DEGs), and up-regulation in the gene responsible to not only compatible solute such as glycine betaine and ectoine but also iron-sulfur biosynthesis related to ROS formation. Furthermore, red light (RL) up-regulated the expression of cryptochrome DASH, a protein known to be excited by BL, and orange light (OL) decreased the expression of thermostable direct hemolysin (TDH), suggesting that OL attenuates the virulence of V. parahaemolyticus. In addition, the expression of VtrA (V. parahaemolyticus type III secretion system 2 (T3SS2) regulator A) but not VtrB (V. parahaemolyticus T3SS2 regulator B) increased under both light treatments, indicating that light exposure is unlikely to be involved in T3SS2-mediated pathogenicity. These results expand our knowledge on unique light responses in non-phototrophic marine prokaryotes.

Sea urchin is an indicator of coastal environmental changes in the global warming era, and is also a model organism in developmental biology and evolution. Due to the depletion of wild resources, new aquaculture techniques for improving stocks have been well studied. The gut microbiome shapes various aspects of a host's physiology. However, these microbiome structures and functions on sea urchins, particularly Mesocentrotus nudus and Strongylocentrotus intermedius which are important marine bioresources commonly found in Japan, have not been fully investigated yet. Using metagenomic approaches including meta16S and shotgun metagenome sequencings, the structures, functions, and dynamics of the gut microbiome of M. nudus and S. intermedius, related to both habitat environment and host growth, were studied. Firstly, a broad meta16S analysis revealed that at the family level, Psychromonadaceae and Flavobacteriaceae reads (38-71%) dominated in these sea urchins, which is a unique feature observed in species in Japan. Flavobacteriaceae reads were more abundant in individuals after rearing in an aquarium with circulating compared to one with running water. Campylobacteraceae and Vibrionaceae abundances increased in both kinds of laboratory-reared sea urchins in both types of experiments. 2-weeks feeding experiments of M. nudus and S. intermedius transplanted from the farm to laboratory revealed that these gut microbial structures were affected by diet rather than rearing environments and host species. Secondly, further meta16S analysis of microbial reads related to M. nudus growth revealed that at least four Amplicon Sequence Variant (ASV) affiliated to Saccharicrinis fermentans, which is known to be a nitrogen (N-2) fixing bacterium, showed a significant positive correlation to the body weight and test diameter. Interestingly, gut microbiome comparisons using shotgun metagenome sequencing of individuals showing higher and lower growth rates revealed a significant abundanc

The Splendidus clade is the largest clade in Vibrionaceae, and its members are often related to mortality of marine animals with huge economic losses. The molecular bases of their pathogenicity and virulence, however, remain largely unknown. In particular, the complete genome sequences of the Splendidus clade species are rarely registered, which is one of the obstacles to predict core and/or unique genes responsible for their adaptation and pathogenicity, and to perform a fine scale meta-transcriptome during bacterial infection to their hosts. In this study, we obtained the complete genomes of all type strains in the Splendidus clade and revealed that (1) different genome sizes (4.4-5.9 Mb) with V. lentus the biggest and most of them had several big plasmids, likely because of the different features on mobilome elements; (2) the Splendidus clade consists of 19 species except V. cortegadensis, and 3 sub-clades (SC) were defined with the 15 most closely related members as SC1; (3) different carbohydrate degradation preferences may be the result of environmental adaptation; and (4) a broad prediction of virulence factors (VFs) revealed core and species unique VF genes.

We report the complete genome sequence of Vibrio parahaemolyticus strain C5A causing an acute hepatopancreatic necrosis disease (AHPND) in Penaeus vannamei sampled from a culture pond in the east of peninsular Malaysia isolated in 2017.

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Shiotani, T., Mino, S., Sato, W., Nishikawa, S., Yonezawa, M., Sievert, S. M., & Sawabe, T. Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum "Campylobacterota". Plos One, 15(12), (2020): e0241366, doi:10.1371/journal.pone.0241366., A novel bacterium, strain EPR55-1T, was isolated from a deep-sea hydrothermal vent on the East Pacific Rise. The cells were motile rods. Growth was observed at temperatures between 50 and 60°C (optimum, 60°C), at pH values between 5.4 and 8.6 (optimum, pH 6.6) and in the presence of 2.4–3.2% (w/v) NaCl (optimum, 2.4%). The isolate used molecular hydrogen as its sole electron donor, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and thiosulfate, sulfite (0.01 to 0.001%, w/v) or elemental sulfur as its sole sulfur source. Nitrate, nitrous oxide (33%, v/v), thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur could serve as the sole electron acceptor to support growth. Phylogenetic analyses based on both 16S rRNA gene sequences and whole genome sequences indicated that strain EPR55-1T belonged to the family Nitratiruptoraceae of the class “Campylobacteria”, but it had the distinct phylogenetic relationship with the genus Nitratiruptor. On the basis of the physiological and molecular characteristics of the isolate, the name Nitrosophilus alvini gen. nov. sp. nov. is proposed, with EPR55-1T as the type strain (= JCM 32893T = KCTC 15925T). In addition, it is shown that “Nitratiruptor labii” should be transferred to the genus Nitrtosophilus; the name Nitrosophilus labii comb. nov. (JCM 34002T = DSM 111345T) is proposed for this organism. Furthermore, 16S rRNA gene-based and genome-based analyses showed that Cetia pacifica is phylogenetically associated with Caminibacter species. We therefore propose the reclassification of Cetia pacifica as Caminibacter pacificus comb. nov. (DSM 27783T = JCM 19563T). Additionally, AAI thresholds for genus classification and the reclassification of subordinate taxa within “Campylobacteria” are also evaluated, based on the analyses using publicly available genomes of all the campylobacterial species., This study was partially supported by the JSPS KAKENHI (No. 12J03037 and No. 15H05991), the Takahashi Industrial and Economic Research Foundation, and US National Science Foundation grant OCE-1559198 and the WHOI Investment in Science Fund to S.M.S. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

A novel thermophilic bacterium, strain SSM-sur55(T), was isolated from a chimney structure at the Urashima site on the Southern Mariana Trough in the Pacific Ocean. Growth was observed at temperatures between 25 and 60 degrees C (optimum, 55 degrees C; 180 min doubling time), at pH values between 5.3 and 7.2 (optimum, pH 5.9) and in the presence of between 1.6 and 5.6% (w/v) NaCl (optimum, 3.2%). The isolate used molecular hydrogen as its sole energy source, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and elemental sulfur as its sole sulfur source. Thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur was utilized as its sole electron acceptor. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SSM-sur55(T) belonged to the genus Hydrogenimonas of the class "Campylobacteria", and its closest relative was Hydrogenimonas thermophila EP1-55-1%(T) (94.9%). On the basis of the phylogenetic, physiological and molecular characteristics, strain SSM-sur55(T) represents a novel species within the genus Hydrogenimonas, for which the name Hydrogenimonas urashimensis sp. nov. is proposed, with the type strain SSM-sur55(T) (JCM 19825 = KCTC 15926).

A novel thermophilic bacterium, strain SSM-sur55(T), was isolated from a chimney structure at the Urashima site on the Southern Mariana Trough in the Pacific Ocean. Growth was observed at temperatures between 25 and 60 degrees C (optimum, 55 degrees C; 180 min doubling time), at pH values between 5.3 and 7.2 (optimum, pH 5.9) and in the presence of between 1.6 and 5.6% (w/v) NaCl (optimum, 3.2%). The isolate used molecular hydrogen as its sole energy source, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and elemental sulfur as its sole sulfur source. Thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur was utilized as its sole electron acceptor. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SSM-sur55(T) belonged to the genus Hydrogenimonas of the class "Campylobacteria", and its closest relative was Hydrogenimonas thermophila EP1-55-1%(T) (94.9%). On the basis of the phylogenetic, physiological and molecular characteristics, strain SSM-sur55(T) represents a novel species within the genus Hydrogenimonas, for which the name Hydrogenimonas urashimensis sp. nov. is proposed, with the type strain SSM-sur55(T) (JCM 19825 = KCTC 15926).