Vibrio aerogenes sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production

Acute Ammonia Causes Pathogenic Dysbiosis of Shrimp Gut Biofilms

Acute ammonia exposure has detrimental effects on shrimp, but the underlying mechanisms remain to be fully explored. In the present study, we investigated the impact of acute ammonia exposure on the gut microbiota of the white shrimp Litopenaeus vannamei and its association with shrimp mortality. Exposure to a lethal concentration of ammonia for 48 h resulted in increased mortality in L. vannamei, with severe damage to the hepatopancreas. Ammonia exposure led to a significant decrease in gut microbial diversity, along with the loss of beneficial bacterial taxa and the proliferation of pathogenic Vibrio strains. A phenotypic analysis revealed a transition from the dominance of aerobic to facultative anaerobic strains due to ammonia exposure. A functional analysis revealed that ammonia exposure led to an enrichment of genes related to biofilm formation, host colonization, and virulence pathogenicity. A species-level analysis and experiments suggest the key role of a Vibrio harveyi strain in causing shrimp disease and specificity under distinct environments. These findings provide new information on the mechanism of shrimp disease under environmental changes.

Rise and metabolic roles of Vibrio during the fermentation of crab paste

Microbial community may systematically promote the development of fermentation process of foods. Traditional fermentation is a spontaneous natural process that determines a unique nutritional characteristic of crab paste of Portunus trituberculatus, However, rare information is available regarding the development pattern and metabolic role of bacterial community during the fermentation of crab paste. Here, using a 16S rRNA gene amplicon sequencing technology, we investigated dynamics of bacterial community and its relationship with metabolites during the fermentation of crab paste. The results showed that bacterial community changed dynamically with the fermentation of crab paste which highlighted by consistently decreased α-diversity and overwhelming dominance of Vibrio at the later days of fermentation. Vibrio had a positive correlation with trimethylamine, hypoxanthine, formate, and alanine while a negative correlation with inosine and adenosine diphosphate. In contrast, most of other bacterial indicators had a reverse correlation with these metabolites. Moreover, Vibrio presented an improved function potential in the formation of the significantly increased metabolites. These findings demonstrate that the inexorable rise of Vibrio not only drives the indicator OTUs turnover in the bacterial community but also has incriminated the quality of crab paste from fresh to perished.

Comparative Physiology and Genomics of Hydrogen-Producing Vibrios

The Hyf-type formate hydrogen lyase (FHL) complex was first proposed based on sequence comparisons in Escherichia coli in 1997 (Andrews et al. in Microbiology 143:3633-3647, 1997). The hydrogenase in the Hyf-type FHL was estimated to be a proton-translocating energy-conserving [NiFe]-hydrogenase. Although the structure of FHL is similar to that of complex I, silent gene expression in E. coli has caused delays in unveiling the genetic and biochemical features of the FHL. The entire set of genes required for Hyf-type FHL synthesis has also been found in the genome sequences of Vibrio tritonius in 2015 (Matsumura et al. in Int J Hydrog Energy 40:9137-9146, 2015), which produces more hydrogen (H₂) than E. coli. Here we investigate the physiological characteristics, genome comparisons, and gene expressions to elucidate the genetic backgrounds of Hyf-type FHL, and how Hyf-type FHL correlates with the higher H₂ production of V. tritonius. Physiological comparisons among the seven H₂-producing vibrios reveal that V. porteresiae and V. tritonius, grouped in the Porteresiae clade, show greater capacity for H₂ production than the other species. The structures of FHL-Hyp gene clusters were closely related in both Porteresiae species, but differed from those of the other species with the presence of hupE, a possible nickel permease gene. Interestingly, deeper genome comparisons revealed the co-presence of nickel ABC transporter genes (nik) with the Hyf-type FHL gene only on the genome of the Porteresiae clade species. Therefore, active primary Ni transport might be one of the key factors characterizing higher H₂ production in V. tritonius. Furthermore, the expression of FHL gene cluster was significantly up-regulated in V. tritonius cells stimulated with formate, indicating that formate is likely to be a control factor for the gene expression of V. tritonius FHL in a similar way to the formate regulon encoding the E. coli FHL.

Emerging Research Topics in the Vibrionaceae and the Squid-Vibrio Symbiosis

The Vibrionaceae encompasses a cosmopolitan group that is mostly aquatic and possesses tremendous metabolic and genetic diversity. Given the importance of this taxon, it deserves continued and deeper research in a multitude of areas. This review outlines emerging topics of interest within the Vibrionaceae. Moreover, previously understudied research areas are highlighted that merit further exploration, including affiliations with marine plants (seagrasses), microbial predators, intracellular niches, and resistance to heavy metal toxicity. Agarases, phototrophy, phage shock protein response, and microbial experimental evolution are also fields discussed. The squid-Vibrio symbiosis is a stellar model system, which can be a useful guiding light on deeper expeditions and voyages traversing these "seas of interest". Where appropriate, the squid-Vibrio mutualism is mentioned in how it has or could facilitate the illumination of these various subjects. Additional research is warranted on the topics specified herein, since they have critical relevance for biomedical science, pharmaceuticals, and health care. There are also practical applications in agriculture, zymology, food science, and culinary use. The tractability of microbial experimental evolution is explained. Examples are given of how microbial selection studies can be used to examine the roles of chance, contingency, and determinism (natural selection) in shaping Earth's natural history.

Vibrio salinus sp. nov., a marine nitrogen-fixing bacterium isolated from the lagoon sediment of an islet inside an atoll in the western Pacific Ocean

A marine, facultatively anaerobic, nitrogen-fixing bacterium, designated strain DNF-1^T, was isolated from the lagoon sediment of Dongsha Island, Taiwan. Cells grown in broth cultures were Gram-negative rods that were motile by means of monotrichous flagella. Cells grown on plate medium produced prosthecae and vesicle-like structures. NaCl was required and optimal growth occurred at about 2-3% NaCl, 25-30 °C and pH 7-8. The strain grew aerobically and was capable of anaerobic growth by fermenting D-glucose or other carbohydrates as substrate. Both the aerobic and anaerobic growth could be achieved with NH₄Cl as a sole nitrogen source. When N₂ served as the sole nitrogen source only anaerobic growth was observed. Major cellular fatty acids were C_14:0, C_16:0 and C_16:1 ω7c, while major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 42.2 mol% based on the genomic DNA data. Phylogenetic analyses based on 16S rRNA genes and the housekeeping genes, gapA, pyrH, recA and gyrB, revealed that the strain formed a distinct lineage at species level in the genus Vibrio of the family Vibrionaceae. These results and those from genomic, chemotaxonomic and physiological studies strongly support the assignment of a novel Vibrio species. The name Vibrio salinus sp. nov. is proposed for the novel species, with DNF-1^T (= BCRC 81209^T = JCM 33626^T) as the type strain. This newly proposed species represents the second example of the genus Vibrio that has been demonstrated to be capable of anaerobic growth by fixing N₂ as the sole nitrogen source.

Flavobacterium taihuense sp. nov., a bacterium isolated from lake sediment

A novel bacterium, designated NAS39T, was isolated from the interfacial sediment of Taihu Lake in PR China and its taxonomic position was investigated by using a polyphasic approach. Cells of the isolate were Gram-stain-negative, aerobic, non-motile, catalase-positive, yellow and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences supported that strain NAS39T formed a cluster within the genus Flavobacterium , and was most closely related to Flavobacterium laiguense LB2P30T (98.4 %), followed by Flavobacterium tiangeerense 0563T (97.4 %). The average nucleotide identity values between strain NAS39T and F. laiguense LB2P30T and F. tiangeerense 0563T were 82.5 and 75.3 %, respectively. The digital DNA–DNA hybridization values between strain NAS39T and F. laiguense LB2P30T and F. tiangeerense 0563T were 40.9 and 18.6 %, respectively. The genomic DNA G+C content was 34.1 mol%. The major respiratory quinone was menaquinone-6. The dominant cellular fatty acids were iso-C15 : 0 and summed feature 3 comprising C16 : 1 ω7c/C16 : 1 ω6c. The polar lipids comprised phosphatidyl ethanolamine, two amino lipids, three amino phospholipids and two unidentified lipids. Based on the phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, strain NAS39T (=MCCC 1K06094T=KACC 22328T) represents a novel species of the genus Flavobacterium , for which the name Flavobacterium taihuense sp. nov. is proposed.

Vibrio nitrifigilis sp. nov., a marine nitrogen-fixing bacterium isolated from the lagoon sediment of an islet inside an atoll

A nitrogen-fixing isolate of facultatively anaerobic, marine bacterium, designated strain NFV-1^T, was recovered from the lagoon sediment of Dongsha Island, Taiwan. It was a Gram-negative rod which exhibited motility with monotrichous flagellation in broth cultures. The strain required NaCl for growth and grew optimally at about 25-35 °C, 3% NaCl and pH 7-8. It grew aerobically and could achieve anaerobic growth by fermenting D-glucose or other carbohydrates as substrates. NH₄Cl could serve as a sole nitrogen source for growth aerobically and anaerobically, whereas growth with N₂ as the sole nitrogen source was observed only under anaerobic conditions. Cellular fatty acids were predominated by C_16:1 ω7c, C_16:0, and C_18:1 ω7c. The major polar lipids consisted of phosphatidylethanolamine and phosphatidylserine. Strain NFV-1^T had a DNA G + C content of 42.5 mol%, as evaluated according to the chromosomal DNA sequencing data. Analyses of sequence similarities and phylogeny based on the 16S rRNA genes, together with the housekeeping genes, gyrB, ftsZ, mreB, topA and gapA, indicated that the strain formed a distinct species-level lineage in the genus Vibrio of the family Vibrionaceae. These phylogenetic data and those from genomic and phenotypic characterisations support the establishment of a novel Vibrio species, for which the name Vibrio nitrifigilis sp. nov. (type strain NFV-1^T = BCRC 81211^T = JCM 33628^T) is proposed.

Rufibacter hautae sp. nov., a red-pigmented bacterium from freshwater lake sediment, and proposal of Rufibacter quisquiliarum as a latter heterotypic synonym of Rufibacter ruber

A taxonomic identification using a polyphasic approach was performed on strain NBS58-1^T, which was isolated from the interfacial sediment of Taihu Lake in China. Strain NBS58-1^T was Gram-stain-negative, aerobic, non-spore-forming and catalase-positive. Phylogenetic analyses based on 16S rRNA gene and three housekeeping genes (rpoB, gyrB and dnaK) sequences supported the position that strain NBS58-1^T should be classified within the genus Rufibacter. The 16S rRNA gene sequence of strain NBS58-1^T possessed the highest similarity to Rufibacter sediminis H-1^T (96.60 %), followed by Rufibacter glacialis MDT1-10-3^T (96.17 %). And the ANI value between strain NBS58-1^T and R. glacialis MDT1-10-3^T was 79.3 %. The respiratory quinone was menaquinone 7 (MK-7). The major cellular fatty acids comprised iso-C_15 : 0 and summed feature 3. Phosphatidylethanolamine, two unidentified phospholipids and four unidentified lipids were the main polar lipids. The genomic DNA G+C content was 51.3 mol%. Based on phenotypic features and phylogenetic position, a novel species with the name Rufibacter hautae sp. nov. is proposed. The type strain is NBS58-1^T=(KACC 21309^T=MCCC 1K04037^T). We also proposed Rufibacter quisquiliarum as a latter heterotypic synonym of Rufibacter ruber.

Gemmobacter caeruleus sp. nov., a novel species originating from lake sediment

An aerobic, Gram-stain-negative, non-spore-forming and rod-shaped bacterial strain, designated N8T, was isolated from the interfacial sediment of Taihu Lake in PR China. The strain formed white to blue colonies on R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain N8T represented a member of the genus Gemmobacter and was most closely related to Gemmobacter aquaticus A1-9T (97.97 %). The average nucleotide identity and digital DNA–DNAhybridization values between strain N8T and G. aquaticus A1-9T based on their whole genomes were 78.8 and 21.7 %, respectively. Q-10 was the main predominant ubiquinone. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C18 : 0 and C16 : 0. The G+C content of the genomic DNA was 66.1 mol%. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid, two unidentified glycolipids and two unidentified lipids. Based on its physiological, biochemical and chemotaxonomic characteristics, strain N8T represents a novel species of the genus Gemmobacter , for which the name Gemmobacter caeruleus sp. nov. is proposed. The type strain is N8T=(KACC 21307T=MCCC 1K04036T).

Altererythrobacter amylolyticus sp. nov., isolated from lake sediment

An aerobic, motile, Gram-stain-negative bacterium, designated strain NS1T, was isolated from interfacial sediment from Taihu Lake, China. The strain formed yellow colonies on R2A medium. Cells were ovoid to rod-shaped and non-spore-forming. Growth occurred at 15–40 °C (optimum, 28 °C), at pH 5.0–10.5 (optimum, 6.5–7.5) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). Phylogenetic trees based on 16S rRNA gene sequences showed that strain NS1T represented a member of the genus Altererythrobacter and had the highest sequence similarity to Altererythrobacter troitsensis CCTCC AB 2015180T (97.1 %). The average nucleotide identity value between strain NS1T and the closest related strain based on their genomes was 78.6 %. The predominant ubiquinone was Q-10. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid, an unidentified glycolipid and six unidentified lipids. The genomic DNA G+C content was 66.6 mol%. On the basis of phenotypic and genotypic characteristics, strain NS1T represents a novel species of the genus Altererythrobacter , for which the name Altererythrobacter amylolyticus sp. nov. is proposed. The type strain is NS1T (=CGMCC 1.13679T=NBRC 113553T).

Dongshaea marina gen. nov., sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production

Two isolates of heterotrophic, facultatively anaerobic, marine bacteria, designated DM1 and DM2^T, were recovered from a lagoon sediment sample of Dongsha Island, Taiwan. Cells were Gram-reaction-negative rods. Nearly all of the cells were non-motile and non-flagellated during the late exponential to early stationary phase of growth, while a few of the cells exhibited motility with monotrichous flagellation. The two isolates required NaCl for growth and grew optimally at about 30 °C, 2-3 % NaCl and pH 7-8. They grew aerobically and could achieve anaerobic growth by fermenting d-glucose or other carbohydrates with production of acids and the gases, including CO₂ and H₂. Ubiquinone Q-8 was the only respiratory quinone. Cellular fatty acids were predominated by C_16 : 0, C_18 : 1ω7c and C_16 : 1ω7c. The major polar lipid was phosphatidylethanolamine. Strains DM1 and DM2^T had DNA G+C contents of 52.0 and 51.8 mol%, respectively, as determined by HPLC analysis. Phylogenetic analyses based on 16S rRNA gene sequences clearly indicated that the two isolates formed a distinct genus-level lineage in the family Aeromonadaceae of the class Gammaproteobacteria and was an outgroup with respect to a stable supragenic clade comprising species of the genera Oceanimonas, Oceanisphaera and Zobellella. The phylogenetic data and those from chemotaxonomic, physiological and morphological characterizations support the establishment of a novel species and genus inside the family Aeromonadaceae, for which the name Dongshaea marina gen. nov., sp. nov. is proposed. The type strain is DM2^T (=BCRC 81069^T=JCM 32096^T).

Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov

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.

Rhizobium pongamiae sp. nov. from root nodules of Pongamia pinnata

Pongamia pinnata has an added advantage of N2-fixing ability and tolerance to stress conditions as compared with other biodiesel crops. It harbours “rhizobia” as an endophytic bacterial community on its root nodules. A gram-negative, nonmotile, fast-growing, rod-shaped, bacterial strain VKLR-01^T was isolated from root nodules of Pongamia that grew optimal at 28°C, pH 7.0 in presence of 2% NaCl. Isolate VKLR-01 exhibits higher tolerance to the prevailing adverse conditions, for example, salt stress, elevated temperatures and alkalinity. Strain VKLR-01^T has the major cellular fatty acid as C_18:1   ω7c (65.92%). Strain VKLR-01^T was found to be a nitrogen fixer using the acetylene reduction assay and PCR detection of a nifH gene. On the basis of phenotypic, phylogenetic distinctiveness and molecular data (16S rRNA, recA, and atpD gene sequences, G + C content, DNA-DNA hybridization etc.), strain VKLR-01^T = (MTCC 10513^T = MSCL 1015^T) is considered to represent a novel species of the genus Rhizobium for which the name Rhizobium pongamiae sp. nov. is proposed. Rhizobium pongamiae may possess specific traits that can be transferred to other rhizobia through biotechnological tools and can be directly used as inoculants for reclamation of wasteland; hence, they are very important from both economic and environmental prospects.

Vibrio zhuhaiensis sp. nov., isolated from a Japanese prawn (Marsupenaeus japonicus)

A Gram-negative, oxidase-positive, facultatively anaerobic bacterium, designated strain E20121, was isolated from the digestive tract of a Japanese prawn (Marsupenaeus japonicus) collected from the coastal sea water area of Zhuhai, Guangdong province, China. The new isolate was determined to be closely related to Vibrio ponticus DSM 16217(T), having 97.6 % 16S rRNA gene sequence similarity. Phylogenetic analysis based on recA, pyrH and rpoA also showed low levels of sequence similarities (72.6-96.6 %) with all species of the genus Vibrio. A multigene phylogenetic tree using concatenated sequences of the four genes (16S rRNA, rpoA, recA and pyrH) clearly showed that the new isolate is different from the currently known Vibrio species. DNA-DNA hybridization experiments revealed similarity values below 70 % with the closest related species V. ponticus DSM 16217(T). Several phenotypic traits enabled the differentiation of strain E20121 from the closest phylogenetic neighbours. The DNA G+C content of strain E20121 was determined to be 47.6 mol % and the major fatty acid components identified were C16:1ω7c and/or C16:1ω6c (39.8 %), C18:1ω7c (13.6 %) and C16:0 (9.6 %). Based on genotypic, phenotypic, chemotaxonomic, phylogenetic and DNA-DNA hybridization analyses, strain E20121 is proposed to represent a novel species of the genus Vibrio for which the name Vibrio zhuhaiensis sp. nov. is proposed. The type strain is E20121(T)(=DSM 25602(T) = CCTCC AB 2011174(T)).

Kangiella taiwanensis sp. nov. and Kangiella marina sp. nov., marine bacteria isolated from shallow coastal water

Two Gram-negative, heterotrophic, aerobic, marine bacteria, designated strains KT1T and KM1T, were isolated from seawater samples collected from the shallow coastal regions of northern Taiwan. Cells grown in broth cultures were non-flagellated rods. NaCl was required for growth. Optimal growth occurred with 2–5 % NaCl, at 25–30 °C and at pH 8. They grew aerobically and were not capable of anaerobic growth by fermenting d-glucose or other carbohydrates. Q-8 was the only isoprenoid quinone. The major polar lipid detected in strain KT1T was phosphatidylmonomethylethanolamine, whereas those detected in KM1T were phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and an unidentified phospholipid. Cellular fatty acids were nearly all iso-branched, with iso-C15 : 0 as the most abundant component (54.6–57.2 % of the total). Strains KT1T and KM1T had DNA G+C contents of 43.9 and 46.3 mol%, respectively. The two strains shared 98.1 % 16S rRNA gene sequence similarity; levels of similarity with the type strains of species of the genus Kangiella were 95.6–98.4 %. Data from the present taxonomic study conducted using a polyphasic approach revealed that the isolates could be classified as representatives of two novel species of the genus Kangiella , for which the names Kangiella taiwanensis sp. nov. (type strain KT1T = BCRC 80330T = JCM 17727T) and Kangiella marina sp. nov. (type strain KM1T = BCRC 80329T = JCM 17728T) are proposed.

A comprehensive and quantitative review of dark fermentative biohydrogen production

Biohydrogen production (BHP) can be achieved by direct or indirect biophotolysis, photo-fermentation and dark fermentation, whereof only the latter does not require the input of light energy. Our motivation to compile this review was to quantify and comprehensively report strains and process performance of dark fermentative BHP. This review summarizes the work done on pure and defined co-culture dark fermentative BHP since the year 1901. Qualitative growth characteristics and quantitative normalized results of H2 production for more than 2000 conditions are presented in a normalized and therefore comparable format to the scientific community.Statistically based evidence shows that thermophilic strains comprise high substrate conversion efficiency, but mesophilic strains achieve high volumetric productivity. Moreover, microbes of Thermoanaerobacterales (Family III) have to be preferred when aiming to achieve high substrate conversion efficiency in comparison to the families Clostridiaceae and Enterobacteriaceae. The limited number of results available on dark fermentative BHP from fed-batch cultivations indicates the yet underestimated potential of this bioprocessing application. A Design of Experiments strategy should be preferred for efficient bioprocess development and optimization of BHP aiming at improving medium, cultivation conditions and revealing inhibitory effects. This will enable comparing and optimizing strains and processes independent of initial conditions and scale.

Simiduia areninigrae sp. nov., an agarolytic bacterium isolated from sea sand

During a study intended to screen for agar-degrading bacteria, strain M2-5T was isolated from black sand off the shore of Jeju Island, Republic of Korea. Strain M2-5T exhibited agarase activity; the β-agarase gene of the isolate had 62 % amino acid sequence identity to the β-agarase gene of Microbulbifer thermotolerans JAMB A94T. The isolate was closely related to members of the genus Simiduia but was clearly discernible from reported Simiduia species, based on a polyphasic analysis. Cells of strain M2-5T were Gram-negative, catalase- and oxidase-positive, motile rods. The DNA G+C content was 53.3 mol%. The predominant isoprenoid quinone was Q-8. The major cellular fatty acids were C17 : 1ω8c (25.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c; 17.2 %) and C17 : 0 (15.0 %). Phylogenetic analysis using 16S rRNA gene sequences showed that strain M2-5T had 96.6 % gene sequence similarity to Simiduia agarivorans SA1T, the most closely related type strain of the genus Simiduia . These results suggest that strain M2-5T represents a novel species in the genus Simiduia , for which the name Simiduia areninigrae sp. nov. is proposed; the type strain is M2-5T ( = KCTC 23293T = NCAIM B 02424T).

Aliidiomarina taiwanensis gen. nov., sp. nov., isolated from shallow coastal water

A Gram-negative, heterotrophic, aerobic, marine bacterium, designated AIT1T, was isolated from a seawater sample collected in the shallow coastal region of Bitou Harbour, New Taipei City, Taiwan. Cells grown in broth cultures were straight or slightly curved rods that were motile by means of a single polar flagellum. Strain AIT1T required NaCl for growth, grew optimally at 30–40 °C and with 1.5–5.0 % NaCl, and was incapable of anaerobic growth by fermentation of glucose or other carbohydrates. The isoprenoid quinones consisted of Q-8 (95.2 %) and Q-9 (4.8 %). The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cellular fatty acids were predominantly iso-branched and included iso-C17 : 0 (26.5 %), summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0; 25.9 %) and iso-C15 : 0 (20.5 %). The DNA G+C content was 51.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AIT1T formed a distinct lineage within the class Gammaproteobacteria and was most closely related to members of the genus Idiomarina in the family Idiomarinaceae (91.5–93.9 % 16S rRNA gene sequence similarity). The phylogenetic data, together with chemotaxonomic, physiological and morphological data, revealed that the isolate should be classified as a representative of a novel species in a new genus in the family Idiomarinaceae, for which the name Aliidiomarina taiwanensis gen. nov., sp. nov. is proposed. The type strain is AIT1T ( = JCM 16052T = BCRC 80035T = NCCB 100321T).

Photobacterium atrarenae sp. nov. a novel bacterium isolated from sea sand

The gram-reaction-negative, motile, facultatively anaerobic, catalase-positive, oxidase-positive bacterial strain M3-4(T) was isolated from black sea sand and subjected to a taxonomic study. Cells of strain M3-4(T) have monotrichous flagella, grow optimally at 37°C and at pH 7-8 in the presence of 1-4% (w/v) NaCl and hydrolyze casein, starch and L: -tyrosine. According to phylogenetic analyses using 16S rRNA gene sequences, strain M3-4(T) belongs to the genus Photobacterium and is most closely related to Photobacterium rosenbergii LMG 22223(T) (97.4%) and P. gaetbulicola KCTC 22804(T) (96.6%). The DNA-DNA relatedness value between M3-4(T) and P. rosenbergii LMG 22223(T) was 21.5%. The DNA G+C mol% of strain M3-4(T) was 53.6. The major cellular fatty acid of strain M3-4(T) was a summed feature 3 consisting of C(16:1) ω7c and/or iso-C(15:0) 2-OH (35.0%), followed by C(16:0) (25.4%) and C(18:1)ω7c (16.8%). These data suggest that strain M3-4(T) represents a novel species in genus Photobacterium, for which the name P. atrarenae sp. nov. is proposed. The type strain is M3-4(T) (= KCTC 23265(T) = NCAIM B 02414(T)).

Aliagarivorans marinus gen. nov., sp. nov. and Aliagarivorans taiwanensis sp. nov., facultatively anaerobic marine bacteria capable of agar degradation

Two agarolytic strains of Gram-negative, heterotrophic, facultatively anaerobic, marine bacteria, designated AAM1T and AAT1T, were isolated from seawater samples collected in the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. Cells grown in broth cultures were straight rods that were motile by means of a single polar flagellum. The two isolates required NaCl for growth and grew optimally at about 25-30 degrees C, in 2-4% NaCl and at pH 8. They grew aerobically and could achieve anaerobic growth by fermenting D-glucose or other sugars. The major isoprenoid quinone was Q-8 (79.8-92.0%) and the major cellular fatty acids were summed feature 3 (C16:1omega7c and/or iso-C15:0 2-OH; 26.4-35.6%), C18:1omega7c (27.1-31.4%) and C16:0 (14.8-16.3%) in the two strains. Strains AAM1T and AAT1T had DNA G+C contents of 52.9 and 52.4 mol%, respectively. The two strains had a 16S rRNA gene sequence similarity of 98.6% and shared 84.9-92.4% sequence similarity with the type strains of Agarivorans albus (91.2-92.4%), eight Alteromonas species (84.9-87.1%), two Aestuariibacter species (86.0-87.0%), Bowmanella denitrificans (86.1-86.7%), eight Glaciecola species (85.0-87.9%) and Salinimonas chungwhensis (85.9-86.1%). Despite their high sequence similarity, strains AAM1T and AAT1T had a DNA-DNA relatedness value of only 4.5%. The data obtained from these polyphasic taxonomic studies revealed that the two agarolytic isolates could be classified as representatives of two novel species in a new genus, Aliagarivorans gen. nov., with Aliagarivorans marinus sp. nov. [type strain is AAM1T (=BCRC 17888T=JCM 15522T)] as the type species and Aliagarivorans taiwanensis sp. nov. [type strain is AAT1T (=BCRC 17889T=JCM 15537T)] as a second species.

Pseudidiomarina marina sp. nov. and Pseudidiomarina tainanensis sp. nov. and reclassification of Idiomarina homiensis and Idiomarina salinarum as Pseudidiomarina homiensis comb. nov. and Pseudidiomarina salinarum comb. nov., respectively

Two Gram-negative strains of heterotrophic, aerobic, marine bacteria, designated PIM1T and PIN1T, were isolated from seawater samples collected from the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. Cells grown in broth cultures were straight rods and non-motile. The two isolates required NaCl for growth and grew optimally at 30-35 degrees C and 2-5 % NaCl. They grew aerobically and were not capable of anaerobic growth by fermentation of glucose or other carbohydrates. The cellular fatty acids were predominantly iso-branched, with iso-C(15 : 0) (17.0-21.4 %), iso-C(17 : 0) (18.2-21.0 %) and iso-C(17 : 1)omega9c (15.7-16.6 %) as the most abundant components. The predominant isoprenoid quinone was Q-8 (95.2-97.1 %). Strains PIM1T and PIN1T had DNA G+C contents of 46.6 and 46.9 mol%, respectively. Phylogeny based on 16S rRNA gene sequences and DNA-DNA hybridization, together with data from physiological, morphological and chemotaxonomic characterizations, indicated that the two isolates should be classified as representatives of two novel species of the genus Pseudidiomarina of the family Idiomarinaceae, for which the names Pseudidiomarina marina sp. nov. (type strain PIM1T=BCRC 17749T=JCM 15083T) and Pseudidiomarina tainanensis sp. nov. (type strain PIN1T=BCRC 17750T=JCM 15084T) are proposed. In addition, based on the characterization data obtained in this study, it is proposed that Idiomarina homiensis and Idiomarina salinarum should be reclassified as Pseudidiomarina homiensis comb. nov. and Pseudidiomarina salinarum comb. nov., respectively.

Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization

The ability to use lactate as a sole source of carbon and energy is one of the key metabolic signatures of Shewanellae, a diverse group of dissimilatory metal-reducing bacteria commonly found in aquatic and sedimentary environments. Nonetheless, homology searches failed to recognize orthologs of previously described bacterial d- or l-lactate oxidizing enzymes (Escherichia coli genes dld and lldD) in any of the 13 analyzed genomes of Shewanella spp. By using comparative genomic techniques, we identified a conserved chromosomal gene cluster in Shewanella oneidensis MR-1 (locus tag: SO_1522-SO_1518) containing lactate permease and candidate genes for both d- and l-lactate dehydrogenase enzymes. The predicted d-LDH gene (dld-II, SO_1521) is a distant homolog of FAD-dependent lactate dehydrogenase from yeast, whereas the predicted l-LDH is encoded by 3 genes with previously unknown functions (lldEGF, SO_1520-SO_1518). Through a combination of genetic and biochemical techniques, we experimentally confirmed the predicted physiological role of these novel genes in S. oneidensis MR-1 and carried out successful functional validation studies in Escherichia coli and Bacillus subtilis. We conclusively showed that dld-II and lldEFG encode fully functional d-and l-LDH enzymes, which catalyze the oxidation of the respective lactate stereoisomers to pyruvate. Notably, the S. oneidensis MR-1 LldEFG enzyme is a previously uncharacterized example of a multisubunit lactate oxidase. Comparative analysis of >400 bacterial species revealed the presence of LldEFG and Dld-II in a broad range of diverse species accentuating the potential importance of these previously unknown proteins in microbial metabolism.

Altererythrobacter indicus sp. nov., isolated from wild rice (Porteresia coarctata Tateoka)

A Gram-negative, rod-shaped, non-spore-forming organism, strain MSSRF26T, was isolated from mangrove-associated wild rice in India. On the basis of 16S rRNA gene sequence similarities, strain MSSRF26T was shown to belong to the Alphaproteobacteria, most closely related to Altererythrobacter luteolus and Altererythrobacter epoxidivorans (96.1 and 95.9 % similarity to the respective type strains). Chemotaxonomic data [major ubiquinones Q-10 (91 %) and Q-9 (9 %); major polyamine spermidine, with putrescine, cadaverine and spermine detected only in trace amounts; major polar lipids phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid; major fatty acid C18 : 1 omega 7c and C(14 : 0) 2-OH as hydroxylated fatty acid] supported the affiliation of MSSRF26T to the genus Altererythrobacter. Fatty acid data and physiological and biochemical tests allowed phenotypic differentiation of the isolate from described Altererythrobacter species. Strain MSSRF26T therefore represents a novel species, for which the name Altererythrobacter indicus sp. nov. is proposed, with the type strain MSSRF26T (=LMG 23789T =DSM 18604T).

Identification of Vibrio spp. with a set of dichotomous keys

AIMS

To define a binary biochemical key for the identification of all recognized Vibrio spp.

METHODS AND RESULTS

A matrix of phenotypical results was developed based on the previous taxonomical studies and the first description manuscripts. A unification of results from various sources was also performed to integrate different taxonomical studies within the same data matrix. Established criteria for selecting the optimal set of tests yielded the highest discrimination, as well as the lowest number of tests. An initial identification key was defined using arginine dihydrolase, lysine decarboxylase and ornithine decarboxylase tests, as well as defining eight different clusters. This key leads each cluster to a secondary key for species identification. Most of Vibrio spp. presented an identification threshold of 100%.

CONCLUSIONS

A new set of biochemical keys has been determined provides a scheme for the rapid identification of clinical and environmental species of Vibrio. No more than 14 are needed for even the most complicated identifications. This newly defined set of keys updates and improves similar findings published in previous studies.

SIGNIFICANCE AND IMPACT OF THE STUDY

These biochemical keys are designed for use in routine applications, particularly in environmental and clinical studies involving a high number of isolates.

Vibrio rhizosphaerae sp. nov., a red-pigmented bacterium that antagonizes phytopathogenic bacteria

Two novel red-pigmented Vibrio strains, MSSRF3T and MSSRF10, with antibacterial activity against phytopathogens were isolated from the rhizosphere region of mangrove-associated wild rice (Porteresia coarctata Tateoka), in Pichavaram, India. The cells were Gram-negative, facultatively anaerobic and rod-shaped and were motile by means of single polar flagella. The two strains were catalase-positive and oxidase-negative, and were able to grow in 0.1–10 % NaCl (with optimum growth in 2 % NaCl) and at temperatures of 20–42 °C (optimum growth at 25–30 °C). Both strains produced acid and gas from d-glucose under anaerobic conditions and utilized a wide range of compounds as sole carbon and energy sources. The DNA G+C contents determined were 51.3 mol% for strain MSSRF3T and 51.0 mol% for strain MSSRF10. Phylogenetic analysis based on 16S rRNA, rpoA, recA and pyrH gene sequences showed that strains MSSRF3T and MSSRF10 belong to the genus Vibrio and are very closely related to Vibrio ruber JCM 11486T, with which they share 98.3–98.5 % (16S rRNA), 98.3–99.7 % (rpoA), 90.2–99.8 % (recA) and 91.3–99.4 % (pyrH) gene sequence similarities, respectively. Levels of DNA–DNA relatedness were 44 % between strains MSSRF3T and MSSRF10, 80 % between strain MSSRF10 and V. ruber JCM 11486T and 45 % between strain MSSRF3T and V. ruber JCM 11486T. Strain MSSRF3T was phenotypically similar to V. ruber JCM 11486T. However, the inability to reduce nitrate to nitrite, the ability to grow in 0.1 % NaCl and the presence of caseinase were characteristics that allowed differentiation between V. ruber JCM 11486T and strain MSSRF3T. In addition, strain MSSRF3T could be differentiated from strain MSSRF10 and its closest relative V. ruber JCM 11486T with respect to its genomic fingerprinting analysis (random amplified polymorphic DNA, GTG5, BOX, PCR-restriction fragment length polymorphism and ribotyping). Therefore, based on phenotypic, genotypic, phylogenetic and DNA–DNA hybridization analyses, strain MSSRF3T (=LMG 23790T=DSM 18581T) should be classified as representing the type strain of a novel species of the genus Vibrio, for which the name Vibrio rhizosphaerae sp. nov. is proposed.

Alteromonas tagae sp. nov. and Alteromonas simiduii sp. nov., mercury-resistant bacteria isolated from a Taiwanese estuary

Two mercury-resistant strains of heterotrophic, aerobic, marine bacteria, designated AT1T and AS1T, were isolated from water samples collected from the Er-Jen River estuary, Tainan, Taiwan. Cells were Gram-negative rods that were motile by means of a single polar flagellum. Buds and prosthecae were produced. The two isolates required NaCl for growth and grew optimally at about 30 °C, 2–4 % NaCl and pH 7–8. They grew aerobically and were incapable of anaerobic growth by fermenting glucose or other carbohydrates. They grew and expressed Hg2+-reducing activity in liquid media containing HgCl2. Strain AS1T reduced nitrate to nitrite. The predominant isoprenoid quinone was Q8 (91.3–99.9 %). The polar lipids of strain AT1T consisted of phosphatidylethanolamine (46.6 %), phosphatidylglycerol (28.9 %) and sulfolipid (24.5 %), whereas those of AS1T comprised phosphatidylethanolamine (48.2 %) and phosphatidylglycerol (51.8 %). The two isolates contained C16 : 1 ω7c and/or iso-C15 : 0 2-OH (22.4–33.7 %), C16 : 0 (19.0–22.7 %) and C18 : 1 ω7c (11.3–11.7 %) as the major fatty acids. Strains AT1T and AS1T had DNA G+C contents of 43.1 and 45.3 mol%, respectively. Phylogeny based on 16S rRNA gene sequences, together with data from morphological, physiological and chemotaxonomic characterization, indicated that the two isolates could be classified as representatives of two novel species in the genus Alteromonas, for which the names Alteromonas tagae sp. nov. (type strain AT1T=BCRC 17571T=JCM 13895T) and Alteromonas simiduii sp. nov. (type strain AS1T=BCRC 17572T=JCM 13896T) are proposed.

Thalassomonas agarivorans sp. nov., a marine agarolytic bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the genus Thalassomonas

A marine agarolytic bacterium, designated strain TMA1(T), was isolated from a seawater sample collected in a shallow-water region of An-Ping Harbour, Taiwan. It was non-fermentative and Gram-negative. Cells grown in broth cultures were straight or curved rods, non-motile and non-flagellated. The isolate required NaCl for growth and exhibited optimal growth at 25 degrees C and 3 % NaCl. It grew aerobically and was incapable of anaerobic growth by fermenting glucose or other carbohydrates. Predominant cellular fatty acids were C(16 : 0) (17.5 %), C(17 : 1)omega8c (12.8 %), C(17 : 0) (11.1 %), C(15 : 0) iso 2-OH/C(16 : 1)omega7c (8.6 %) and C(13 : 0) (7.3 %). The DNA G + C content was 41.0 mol%. Phylogenetic, phenotypic and chemotaxonomic data accumulated in this study revealed that the isolate could be classified in a novel species of the genus Thalassomonas in the family Colwelliaceae. The name Thalassomonas agarivorans sp. nov. is proposed for the novel species, with TMA1(T) (=BCRC 17492(T) = JCM 13379(T)) as the type strain.

Zobellella denitrificans gen. nov., sp. nov. and Zobellella taiwanensis sp. nov., denitrifying bacteria capable of fermentative metabolism

Two denitrifying strains of heterotrophic, facultatively anaerobic bacteria, designated ZD1T and ZT1T, were isolated from sediment samples collected from mangrove ecosystems in Taiwan. The isolates were Gram-negative. Cells grown in broth cultures were straight rods that were motile by means of a single polar flagellum. The isolates grew optimally in 1–3 % NaCl, but NaCl was not an absolute requirement for growth; only strain ZT1T grew in 13–14 % NaCl. Both isolates grew between 10 and 45 °C, with optimum growth at 30–35 °C. They were capable of anaerobic growth by denitrifying metabolism using nitrate or nitrous oxide as terminal electron acceptors or, alternatively, by fermenting glucose, sucrose or mannitol as substrates. C18 : 1 ω7c was the most abundant fatty acid (32.6–35.7 %). The other major fatty acids included C16 : 1 ω7c (27.5–29.4 %) and C16 : 0 (20.1–22.0 %). The two isolates had 16S rRNA gene sequence similarity of 96.8 % and shared 94.1–96.8 % sequence similarity with the most closely related species, Oceanimonas doudoroffii, Oceanimonas baumannii, Oceanimonas smirnovii and Oceanisphaera litoralis. They could be distinguished from these species in that they were capable of fermentative metabolism, had relatively high DNA G+C contents (62.0–64.0 mol%) and contained C18 : 1 ω7c instead of C16 : 1 ω7c as the most abundant fatty acid. Characterization data accumulated in this study revealed that the two denitrifying isolates could be classified as representatives of two novel species in a new genus, Zobellella gen. nov., with Zobellella denitrificans sp. nov. (type strain ZD1T=BCRC 17493T=JCM 13380T) as the type species and Zobellella taiwanensis sp. nov. (type strain ZT1T=BCRC 17494T=JCM 13381T) as a second species.

Pseudidiomarina taiwanensis gen. nov., sp. nov., a marine bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the family Idiomarinaceae

Two strains of heterotrophic, aerobic, marine bacteria, designated strains PIT1T and PIT2, were isolated from sea-water samples collected at the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. Both strains were Gram-negative. Cells grown in broth cultures were straight rods that were non-motile, lacking flagella. Both strains required NaCl for growth and exhibited optimal growth at 30–35 °C, 1–4 % NaCl and pH 8. They grew aerobically and were incapable of anaerobic growth by fermentation of glucose or other carbohydrates. Cellular fatty acids were predominantly iso-branched, with C15 : 0 iso and C17 : 0 iso representing the most abundant components. The DNA G+C contents of strains PIT1T and PIT2 were 49·3 and 48·6 mol%, respectively. Phylogeny based on 16S rRNA gene sequences, together with data from phenotypic and chemotaxonomic characterization, revealed that the two isolates could be assigned to a novel genus in the family Idiomarinaceae, for which the name Pseudidiomarina gen. nov. is proposed. Pseudidiomarina taiwanensis sp. nov. is the type species of the novel genus (type strain PIT1T=BCRC 17465T=JCM 13360T).

Vibrio neonatus sp. nov. and Vibrio ezurae sp. nov. Isolated from the Gut of Japanese Abalones

Five alginolytic, facultative anaerobic, non-motile bacteria were isolated from the gut of Japanese abalones (Haliotis discus discus, H. diversicolor diversicolor and H. diversicolor aquatilis). Phylogenetic analyses based on 16S rRNA gene and gap gene sequences indicated that these strains are closely related to V. halioticoli. DNA-DNA hybridizations, FAFLP fingerprintings, and phylogenies of gap and 16S rRNA gene sequences showed that the five strains represent two species different from all currently described vibrios. The names Vibrio neonatus sp. nov. (IAM 15060T = LMG 19973T = HDD3-1T; mol% G+C of DNA is 42.1-43.9), and Vibrio ezurae sp. nov. (IAM 15061T = LMG 19970T = HDS1-1T; mol% G+C of DNA is 43.6-44.8) are proposed to encompass these new taxa. The two new species can be differentiated from V. halioticoli on the basis of several features, including beta-galactosidase activity, assimilation of glycerol, D-mannose and D-gluconate.

Pseudovibrio denitrificans gen. nov., sp. nov., a marine, facultatively anaerobic, fermentative bacterium capable of denitrification

Two denitrifying strains of heterotrophic, facultatively anaerobic, marine bacteria, designated DN34T and DN33, were isolated from sea-water samples collected in Nanwan Bay, Kenting National Park, Taiwan. They were Gram-negative. Cells in late exponential to early stationary phase of growth were predominantly straight or curved rods, but Y- or V-shaped forms were also observed. They were motile by means of one to several lateral or subpolar flagella. Both strains required NaCl for growth and exhibited optimal growth at about 30 °C, pH 8 and 3 % NaCl. They were capable of anaerobic growth by carrying out denitrifying metabolism using nitrate, nitrite or nitrous oxide as terminal electron acceptors or, alternatively, by fermenting glucose, mannose, sucrose or trehalose as substrates. Anaerobic fermentative growth on glucose resulted in formation of various organic acids, including formate, lactate, acetate, pyruvate and fumarate. The major cellular fatty acids were 2-OH-14 : 0, 3-OH-14 : 0 and 16 : 0. DN34T and DN33 had DNA G+C contents of 51·7 and 51·6 mol%, respectively. Physiological characterization, together with phylogenetic analysis based on 16S rRNA gene sequence analysis, revealed that the two denitrifying strains could be accommodated in a novel genus, for which the name Pseudovibrio gen. nov. is proposed. Pseudovibrio denitrificans sp. nov. is the type species, with DN34T (=BCRC 17323T=JCM 12308T) as the type strain.

Characterization of Vibrio strains isolated from turbot (Scophthalmus maximus) culture by phenotypic analysis, ribotyping and 16S rRNA gene sequence comparison

AIM

The aim of the present study was to clarify the taxonomic status of Vibrio strains isolated from an aquaculture system and to compare the results of the identifications made by phenotypic and molecular methods.

METHODS AND RESULTS

Fifty-one Vibrio strains isolated from a turbot (Scophthalmus maximus) aquaculture system were characterized by ribotyping and 16S rRNA gene sequencing. The strains had been identified phenotypically in a previous numerical taxonomy analysis as Vibrio anguillarum, V. mediterranei, V. splendidus, V. aestuarianus, V. ordalii, V. fischeri and V. scophthalmi. Cluster analysis of ribotype patterns showed that the strains were separated into two main groups: V. splendidus-V. lentus and V. scophthalmi groups. The use of 16S rRNA gene sequence allowed differentiation among V. splendidus biovar I and V. lentus strains.

CONCLUSIONS

The molecular methods identified strains of V. splendidus biovar I, V. lentus and V. scophthalmi, showing discrepancies with phenotypic characterization.

SIGNIFICANCE AND IMPACT OF THE STUDY

The molecular methods, as 16S rRNA gene sequence analysis, are necessary for the identification of phenotypically close species to avoid mis-identifications. Interestingly, this is the first report of V. lentus strains associated to turbot culture.

New methods for the analysis of binarized BIOLOG GN data of Vibrio species: minimization of stochastic complexity and cumulative classification

We apply minimization of stochastic complexity and the closely related method of cumulative classification to analyse the extensively studied BIOLOG GN data of Vibrio spp. Minimization of stochastic complexity provides an objective tool of bacterial taxonomy as it produces classifications that are optimal from the point of view of information theory. We compare the outcome of our results with previously published classifications of the same data set. Our results both confirm earlier detected relationships between species and discover new ones.