[Show abstract][Hide abstract] ABSTRACT: Advances in genomic microbial taxonomy have opened the way to create a more universal and transparent concept of species but is still in a transitional stage towards becoming a defining robust criteria for describing new microbial species with minimum features obtained using both genome and classical polyphasic taxonomies. Here we performed advanced microbial taxonomies combined with both genome-based and classical approaches for new agarolytic vibrio isolates to describe not only a novel Vibrio species but also a member of a new Vibrio clade. Two novel vibrio strains (Vibrio astriarenae sp. nov. C7 T and C20) showing agarolytic, halophilic and fermentative metabolic activity were isolated from a seawater sample collected in a coral reef in Okinawa. Intraspecific similarities of the isolates were identical in both sequences on the 16S rRNA and pyrH genes, but the closest relatives on the molecular phylogenetic trees on the basis of 16S rRNA and pyrH gene sequences were V. hangzhouensis JCM 15146 T (97.8% similarity) and V. agarivorans CECT 5085 T (97.3% similarity), respectively. Further multilocus sequence analysis (MLSA) on the basis of 8 protein coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) obtained by the genome sequences clearly showed the V. astriarenae strain C7 T and C20 formed a distinct new clade protruded next to V. agarivorans CECT 5085 T. The singleton V. agarivorans has never been included in previous MLSA of Vibrionaceae due to the lack of some gene sequences. Now the gene sequences are completed and analysis of 100 taxa in total
PLoS ONE 08/2015; 10(8). DOI:10.1371/journal.pone.0136279 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Vibrio tritonius strain AM2 shows high-yield hydrogen production even under saline conditions (1.7 mol hydrogen/mol mannitol). However, the molecular mechanism of efficient hydrogen production has never been studied in the genus Vibrio. The aim of this study is to identify the genes responsible for hydrogen evolution in V. tritonius and the gene expression pattern. Complete genome analysis revealed an existence of a single 24-kb gene cluster containing 21 genes, which are essential for the formation of an energy-conserving formate hydrogen lyase (FHL) complex, to be more specific the vibrio FHL was structurally rather similar to the hyf (hydrogenase four) gene cluster found in Escherichia coli. Moreover, genes responsible to the formate dehydrogenase (FDH-H), fhlA-type transcriptional activator and hydrogenase maturation proteins (hyp) were also located downstream of the vibrio hyf gene cluster to form a “super-gene-set” of the FHL complex gene cluster. The vibrio gene for the large subunit of the FHL complex hyfG possessed typical motifs coordinating the [NiFe] center at the active site, which indicates the V. tritonius hydrogenase was able to be classified as a [NiFe]-hydrogenase. Furthermore, transcriptional analysis revealed that the expression level of the hyfG gene slightly increased upon pH decrease, which correlates to the pH-dependent hydrogen production of V. tritonius. Therefore, we can conclude that the FHL complex of V. tritonius is key enzyme in the hydrogen production under acidic conditions. Moreover hyfABCDEFGHIJ-hycI-hydN-fdhF and hyp genes could be co-transcribed respectively during the efficient hydrogen production state. Details of the gene cluster are discussed here.
International Journal of Hydrogen Energy 08/2015; 40(30):9137. DOI:10.1016/j.ijhydene.2015.05.137 · 3.31 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In deep-sea hydrothermal environments, most invertebrates associate with dense populations of symbiotic microorganisms in order to obtain nutrition. The molecular interactions between deep-sea animals and environmental microbes, including their symbionts, have not yet been elucidated in detail. Hemagglutinins/lectins, which are carbohydrate-binding proteins, have recently been reported to play important roles in a wide array of biological processes, including the recognition and control of non-self materials. We herein assessed hemagglutination activity in the serum of a deep-sea vent endemic crab, Shinkaia crosnieri, which harbors chemosynthetic epibionts on its plumose setae. Horse and rabbit erythrocytes were agglutinated using this serum (opt. pH 7.5 and opt. temperature 15°C). Agglutinating activity was inhibited by eight kinds of sugars and several divalent cations, did not require any divalent metal ions, and remained detectable even after heating the serum at 100°C for 30 min. By using fluorescently labeled serum, we demonstrated that deep-sea crab serum components bound to the epibionts even in the presence of sugars. This study represents the first immunological assessment of a deep-sea vent endemic crab and demonstrated the possibility of a non-lectin-mediated symbiont-host interaction.
Microbes and Environments 07/2015; 30(3). DOI:10.1264/jsme2.ME15066 · 2.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Gillisia limnaea strain DSM 15749 (=R-8282T, =LMG21470,=CIP108418) is a Gram-negative, strictly aerobic, psychrophilic, and non-photosynthetic bacterium that belongs to the family Flavobacteriaceae, which was isolated from a microbial mat in Lake Fryxell, Antarctica (Van Trappen et al., 2004). The bacterium shows yellow colored colony, but the carotenoid composition has never been determined yet. In this study, we elucidated the structure of carotenoids produced by the strain DSM 15749. G. limnaea strain DSM 15749 synthesized a novel monocyclic-type carotenoid, 3″-hydroxy-2′-isopentenylsaproxanthin ((3R, 2′S)-2′-(3-hydroxy-3-methylbutyl)-3′, 4′-didehydro-1′, 2′-dihydro-β, ψ-carotene-3, 1′-diol), as well as (3R, 3′R)-zeaxanthin. Furthermore, another monocyclic carotenoid, 2′-isopentenylsaproxanthin, was also detected in the strain DSM 15749. 3″-Hydroxy-2′-isopentenylsaproxanthin is “Chimera”-like unique structures, in that one end group forms the same structure of zeaxanthin, and the other end group is the same as bacterioruberin which is produced by several extremophilic bacteria and archaea. This structure involved the hydroxy derivative of 2′-isopentenylsaproxanthin. The present study is the first report about the carotenoids produced by the genus Gillisia, of the family Flavobacteriaceae.
Biocatalysis and Agricultural Biotechnology 03/2015; 4(2). DOI:10.1016/j.bcab.2015.02.005
[Show abstract][Hide abstract] ABSTRACT: Biofuels represent a viable alternative to the use of fossil fuels. They contribute to the reduction of greenhouse gas emission and do not compete with agricultural land. However, biofuels are not yet capable of replacing the current energy matrix based on fossil fuels because they cannot compete with standard fuels such as diesel and gasoline. Therefore, innovation is necessary to promote technical, economical, and environmental viability of biofuels. For this purpose, the marine realm is a promising source of bioresources to promote innovation in biofuel production. The marine biomass can be converted into biofuels such as biodiesel, bioethanol, and biogases (i. e., methane and hydrogen) through microbial activity. Microbial diversity plays a fundamental role in marine ecosystems by recycling of organic matter, which is a reflection of the vast genetic diversity associated to the marine microbial species available for biotechnological exploitation. The present study provides an overview of the importance of microbial fuels and presents innovative findings which can be applied to the production of biofuels in the near future.
Handbook of Marine Biotechnology, 02/2015: chapter Biofuel Innovation by Microbial Diversity; Springer., ISBN: 978-3-642-53971-8
[Show abstract][Hide abstract] ABSTRACT: Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.
Archives of Microbiology 12/2014; 197(3). DOI:10.1007/s00203-014-1071-2 · 1.67 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Here, we present the draft genome sequence of a novel carotenoid 2′-isopentenylsaproxanthin producer, Jejuia pallidilutea strain 11shimoA1, isolated from the surface of seaweed in Japan, and the ethyl methanesulfonate-induced pigmentation mutants.
This genomic information will help to not only elucidate the 2′-isopentenylsaproxanthin biosynthetic pathway but also understand
the evolution of flavobacteria.
[Show abstract][Hide abstract] ABSTRACT: Here, we present the draft genome sequences of a zeaxanthin-producing flavobacterium, Algibacter lectus strains SS8 and NR4, isolated from coastal sediment and rock surfaces in Hakodate, Japan, respectively. This genomic information
represents the first Algibacter genome sequences, which will help us to elucidate the biology and evolution of Flavobacteriaceae bacteria.
[Show abstract][Hide abstract] ABSTRACT: Here, we present the draft genome sequences of six carotenoid producers affiliated with Nonlabens spp. isolated from marine environments in both the northern and southern parts of Japan. The genomic information will help
to elucidate the function and evolution of carotenoid synthetic gene clusters not only in the genus Nonlabens but also in the family Flavobacteriaceae.
[Show abstract][Hide abstract] ABSTRACT: Microbial oceanography studies have demonstrated the central role of microbes in functioning and nutrient cycling of the global ocean. Most of these former studies including at Southwestern Atlantic Ocean (SAO) focused on surface seawater and benthic organisms (e.g., coral reefs and sponges). This is the first metagenomic study of the SAO. The SAO harbors a great microbial diversity and marine life (e.g., coral reefs and rhodolith beds). The aim of this study was to characterize the microbial community diversity of the SAO along the depth continuum and different water masses by means of metagenomic, physical-chemical and biological analyses. The microbial community abundance and diversity appear to be strongly influenced by the temperature, dissolved organic carbon, and depth, and three groups were defined [1. surface waters; 2. sub-superficial chlorophyll maximum (SCM) (48-82 m) and 3. deep waters (236-1,200 m)] according to the microbial composition. The microbial communities of deep water masses [South Atlantic Central water, Antarctic Intermediate water and Upper Circumpolar Deep water] are highly similar. Of the 421,418 predicted genes for SAO metagenomes, 36.7 % had no homologous hits against 17,451,486 sequences from the North Atlantic, South Atlantic, North Pacific, South Pacific and Indian Oceans. From these unique genes from the SAO, only 6.64 % had hits against the NCBI non-redundant protein database. SAO microbial communities share genes with the global ocean in at least 70 cellular functions; however, more than a third of predicted SAO genes represent a unique gene pool in global ocean. This study was the first attempt to characterize the taxonomic and functional community diversity of different water masses at SAO and compare it with the microbial community diversity of the global ocean, and SAO had a significant portion of endemic gene diversity. Microbial communities of deep water masses (236-1,200 m) are highly similar, suggesting that these water masses have very similar microbiological attributes, despite the common knowledge that water masses determine prokaryotic community and are barriers to microbial dispersal. The present study also shows that SCM is a clearly differentiated layer within Tropical waters with higher abundance of phototrophic microbes and microbial diversity.
Archives of Microbiology 09/2014; 197(2). DOI:10.1007/s00203-014-1035-6 · 1.67 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Two non-pigmented, motile, Gram-negative marine bacteria designated R9SW1T and A3d10T were isolated from sea water samples collected from Chazhma Bay, Gulf of Peter the Great, Sea of Japan, Pacific Ocean, Russia and St. Kilda Beach, Port Phillip Bay, the Tasman Sea, Pacific Ocean, respectively. Both organisms were found to grow between 4°C and 40°C, between pH 6 to 9, and are moderately halophilic, tolerating up to 20% (w/v) NaCl. Both strains were found to be able to degrade Tween 40 and 80, but only strain R9SW1T was found to be able to degrade starch. The major fatty acids were characteristic for the genus Marinobacter including C16:0, C16:1ω7c, C18:1ω9c and C18:1ω7c. The G+C content of the DNA for strains R9SW1T and A3d10T were determined to be 57.1 mol% and 57.6 mol%, respectively. The two new strains share 97.6% of their 16S rRNA gene sequences, with 82.3% similarity in the average nucleotide identity (ANI), 19.8% similarity in the in silico genome-to-genome distance (GGD), 68.1% similarity in the average amino acid identity (AAI) of all conserved protein-coding genes, and 31 of the Karlin's genomic signature dissimilarity. A phylogenetic analysis showed that R9SW1T clusters with M. algicola DG893T sharing 99.40%, and A3d10T clusters with M. sediminum R65T sharing 99.53% of 16S rRNA gene sequence similarities. The results of the genomic and polyphasic taxonomic study, including genomic, genetic, phenotypic, chemotaxonomic and phylogenetic analyses based on the 16S rRNA, gyrB and rpoD gene sequence similarities, the analysis of the protein profiles generated using MALDI-TOF mass spectrometry, and DNA-DNA relatedness data, indicated that strains R9SW1T and A3d10T represent two novel species of the genus Marinobacter. The names Marinobacter salarius sp. nov., with the type strain R9SW1T ( = LMG 27497T = JCM 19399T = CIP 110588T = KMM 7502T) and Marinobacter similis sp. nov., with the type strain A3d10T ( = JCM 19398T = CIP 110589T = KMM 7501T), are proposed.
PLoS ONE 09/2014; 9(9):e106514. DOI:10.1371/journal.pone.0106514 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Here, the draft genome sequences of two Vibrionaceae, Vibrio ponticus C121 and Photobacterium aphoticum C119, which were isolated from the coral reef vicinity in Okinawa, Japan, are reported. The genome provides further insight
into the genomic plasticity, biocomplexity, and ecophysiology, including pathogenicity and evolution, of these genera.
[Show abstract][Hide abstract] ABSTRACT: A novel mesophilic, strictly hydrogen-oxidizing, sulfur-, nitrate- and thiosulfate-reducing bacterium, designated strain Monchim33(T), was isolated from a deep-sea hydrothermal vent chimney at the Central Indian Ridge. The non-motile, rod-shaped cells were Gram-negative and non-sporulating. Growth was observed between 15 and 37 °C (optimum 33 °C; 3.2 h doubling time) and between pH 5.4 and 8.6 (optimum pH 6.0). The isolate was a strictly anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. The G + C content of genomic DNA was 42.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate belonged to the genus Sulfurovum and was closely related to Sulfurovum sp. NBC37-1 and S. lithotrophicum 42BKT(T) (95.6 % and 95.4 % sequence similarity, respectively). DNA-DNA hybridization demonstrated that the novel isolate could be differentiated genotypically from Sulfurovum sp. NBC37-1 and S. lithotrophicum 42BKT(T). On the basis of the molecular and physiological traits of the new isolate, the name Sulfurovum aggregans sp. nov. is proposed, with the type strain Monchim33(T) (=JCM 19824(T) =DSM 27205(T)).
International Journal of Systematic and Evolutionary Microbiology 06/2014; 64(Pt 9). DOI:10.1099/ijs.0.065094-0 · 2.51 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Here, we present the draft genomes of Marinobacter similis A3d10(T), a potential plastic biodegrader, and Marinobacter salarius R9SW1(T), isolated from radioactive waters. This genomic information will contribute information on the genetic basis of the metabolic pathways for the degradation of both plastic and radionuclides.
[Show abstract][Hide abstract] ABSTRACT: To achieve more stable bio-hydrogen (bioH2) production from non-food feedstocks, stable feedstock preparations of marine biomass and an efficient bioH2 system using marine bacteria under saline conditions are two important key technologies that needed to be developed. Vibrio tritonius strain AM2, which was isolated from the gut of a marine invertebrate, was cultured under various conditions in marine broth (at initial 2.25% (w/v) NaCl) supplemented with mannitol, a seaweed carbohydrate, to evaluate its hydrogen production. The maximum molar yield of bioH2 was recorded as 1.7 mol H2/mol mannitol at pH 6 and 37 °C. The mannitol-grown cells had higher yields of bioH2 than the glucose-grown cells in the pH range 5.5–7.5. Compared to glucose, mannitol might be a better substrate for bioH2 production using strain AM2. Fermentation product profiling revealed that strain AM2 might be utilising the formate-hydrogen pathway for bioH2 production. Furthermore, strain AM2 was able to produce hydrogen from powdered brown macroalgae containing 31.1% dry weight of mannitol. The molar yield of hydrogen reached 1.6 mol H2/mol mannitol contained in the seaweed feedstock. In conclusion, strain AM2 has the ability to produce hydrogen from mannitol with high yields even under saline conditions.
International Journal of Hydrogen Energy 05/2014; 39(14):7270–7277. DOI:10.1016/j.ijhydene.2014.02.164 · 3.31 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Carotenoids are a class of naturally occurring pigment, carrying out important biological functions in photosynthesis and involved in environmental responses including nutrition in organisms. Saproxanthin and myxol, which have monocyclic carotenoids with a γ-carotene skeleton, have been reported to show a stronger antioxidant activity than those with β-carotene and zeaxanthin. In this research, a yellow-orange bacterium of strain 11shimoA1 (JCM19538) was isolated from a seaweed collected at Nabeta Bay (Shizuoka, Japan). The 16S rRNA gene sequence of strain 11shimoA1 revealed more than 99.99 % similarity with those of Jejuia pallidilutea strains in the family Flavobacteriaceae. Strain 11shimoA1 synthesized two types of carotenoids. One of them was (3R, 3'R)-zeaxanthin with dicyclic structure and another was identified as (3R, 2'S)-2'-isopentenylsaproxanthin, a novel monocyclic carotenoid with pentenyl residue at C-2' position of saproxanthin, using FAB-MS, (1)H NMR, and CD analyses. Culturing strain 11shimoA1 in an alkaline medium at pH 9.2 resulted in a markedly increased in production of 2'-isopentenylsaproxanthin per dry cell weight, but a decreased in zeaxanthin production as compared to their respective production levels in medium with pH 7.0. These carotenoids are likely to play some roles in the adaptation of the bacterium to the environmental conditions.
[Show abstract][Hide abstract] ABSTRACT: Deep-sea vents harbor dense populations of various animals that have their specific symbiotic bacteria. Scaly-foot gastropods, which are snails with mineralized scales covering the sides of its foot, have a gammaproteobacterial endosymbiont in their enlarged esophageal glands and diverse epibionts on the surface of their scales. In this study, we report the complete genome sequencing of gammaproteobacterial endosymbiont. The endosymbiont genome displays features consistent with ongoing genome reduction such as large proportions of pseudogenes and insertion elements. The genome encodes functions commonly found in deep-sea vent chemoautotrophs such as sulfur oxidation and carbon fixation. Stable carbon isotope ((13)C)-labeling experiments confirmed the endosymbiont chemoautotrophy. The genome also includes an intact hydrogenase gene cluster that potentially has been horizontally transferred from phylogenetically distant bacteria. Notable findings include the presence and transcription of genes for flagellar assembly, through which proteins are potentially exported from bacterium to the host. Symbionts of snail individuals exhibited extreme genetic homogeneity, showing only two synonymous changes in 19 different genes (13 810 positions in total) determined for 32 individual gastropods collected from a single colony at one time. The extremely low genetic individuality in endosymbionts probably reflects that the stringent symbiont selection by host prevents the random genetic drift in the small population of horizontally transmitted symbiont. This study is the first complete genome analysis of gastropod endosymbiont and offers an opportunity to study genome evolution in a recently evolved endosymbiont.The ISME Journal advance online publication, 8 August 2013; doi:10.1038/ismej.2013.131.
The ISME Journal 01/2014; 8(1):40-51. DOI:10.1038/ismej.2013.131 · 9.30 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the "Porteresiae" clade.
Frontiers in Microbiology 12/2013; 4:414. DOI:10.3389/fmicb.2013.00414 · 3.99 Impact Factor