Spongiibacter taiwanensis sp. nov., a marine bacterium isolated from aged seawater.

A Gram-reaction-negative, heterotrophic, marine bacterium, designated strain SPT1T, was isolated from an aged seawater sample which was collected from the shallow coastal region of Nanya, Keelung, Taiwan and stored at room temperature for more than 7 years. Strain SPT1T was a motile rod which exhibited monotrichous flagellation. It required NaCl for growth and exhibited optimal growth at 30-35 °C, 1-3 % NaCl and pH 7-8. The strain was a strictly aerobic bacterium, incapable of anaerobic growth by nitrate reduction or denitrification, or by fermenting glucose or other carbohydrates. Cellular fatty acids were dominated by C16 : 1ω7c and/or C16 : 1ω6c (23.4 %), C17 : 1ω8c (18.1 %), C16 : 0 (8.5 %), C18 : 1ω7c (8.4 %) and C10 : 0 3-OH (6.3 %). The predominant isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and phosphatidic acid. The DNA G+C content was 57.9 mol%. Phylogeny based on 16S rRNA gene sequences showed that strain SPT1T formed a distinct species-level lineage within the genus Spongiibacter of the class Gammaproteobacteria and shared sequence similarities of 94.4-96.2 % with Spongiibacter marinusand Spongiibacter tropicus, the only two species of the genus Spongiibacterwith validly published names. The 16S rRNA gene sequence similarities between strain SPT1T and other species were less than 93.1 %. Polyphasic taxonomic data obtained in this study indicated that strain SPT1T could be classified as a novel species of the genus Spongiibacter, for which the name Spongiibacter taiwanensis sp. nov. is proposed. The type strain is SPT1T (=JCM 31012T=BCRC 80916T).

Reclassification of [Glaciecola] lipolytica and [Aestuariibacter] litoralis in Aliiglaciecola gen. nov., as Aliiglaciecola lipolytica comb. nov. and Aliiglaciecola litoralis comb. nov., respectively.

Following phylogenetic analysis based on 16S rRNA gene sequences, together with DNA G+C contents and differential chemotaxonomic and physiological characteristics, a new genus with the name Aliiglaciecola gen. nov. is proposed to more appropriately accommodate two recognized species of the genera Glaciecola and Aestuariibacter. Accordingly, [Glaciecola] lipolytica and [Aestuariibacter] litoralis should be reassigned to the novel genus as Aliiglaciecola lipolytica comb. nov. (type strain, E3(T) = JCM 15139(T) = CGMCC 1.7001(T)) and Aliiglaciecola litoralis comb. nov. (type strain, KMM 3894(T) = JCM 15896(T) = NRIC 0754(T)), respectively. Aliiglaciecola lipolytica is proposed as the type species of this new genus. Physiologically, the combined characteristics of positive reactions for nitrate reduction and growth at 4 °C and 36 °C distinguish the new genus from the genera Aestuariibacter and Glaciecola by one to three traits. Moreover, the new genus is also distinguished from the genus Glaciecola by the fatty acid profile and distinguished from the genus Aestuariibacter by the differences of major isoprenoid quinone (MK-7 vs Q-8) and DNA G+C content (40.8-43.0 mol% vs 48.0-54.0 mol%).

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 KT1(T) and KM1(T), 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 KT1(T) was phosphatidylmonomethylethanolamine, whereas those detected in KM1(T) were phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and an unidentified phospholipid. Cellular fatty acids were nearly all iso-branched, with iso-C(15 : 0) as the most abundant component (54.6-57.2 % of the total). Strains KT1(T) and KM1(T) 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 KT1(T) = BCRC 80330(T) = JCM 17727(T)) and Kangiella marina sp. nov. (type strain KM1(T) = BCRC 80329(T) = JCM 17728(T)) are proposed.

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

A Gram-negative, heterotrophic, aerobic, marine bacterium, designated AIT1(T), 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 AIT1(T) 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-C(17:0) (26.5%), summed feature 9 (comprising iso-C(17:1)ω9c and/or 10-methyl C(16:0); 25.9%) and iso-C(15:0) (20.5%). The DNA G+C content was 51.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AIT1(T) 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 AIT1(T) (=JCM 16052(T)=BCRC 80035(T)=NCCB 100321(T)).

Isolation and characterization of marine luminous bacteria from shallow coastal waters of Taiwan.

BACKGROUND AND PURPOSE: Marine luminous bacteria were isolated and identified from samples in shallow coastal waters of Taiwan during the relatively warm seasons. METHODS: Identification of the luminous isolates was performed based on differences of phenotypic and genotypic characteristics together with data from phylogenetic analysis. RESULTS: Twenty seven strains of marine luminous bacteria were isolated. They were divided into five types based on differences of phenotypic characteristics. However, they could be clustered into only two genotypes according to the analysis of restriction patterns of polymerase chain reaction-amplified 16S rRNA genes digested with various restriction enzymes. The characterization data together with the 16S rRNA gene-based phylogenetic analysis revealed that the isolates included in phenotype I (seven isolates) could be Photobacterium leiognathi, and those included in phenotypes II-V (twenty isolates) might be classified as Vibrio harveyi. However, phylogeny based on gyrB sequences indicated that phenotypes II-V could be classified into two species, V. harveyi and Vibrio campbellii. CONCLUSION: Culturable luminous bacteria in the shallow coastal waters of Taiwan during the sampling period are dominated by V. harveyi/campbellii and P. leiognathi, and the former species appeared to be more prevalent and numerous than the latter species in general.

Effects of Host Phylogeny and Habitats on Gut Microbiomes of Oriental River Prawn (Macrobrachium nipponense).

The gut microbial community is one of the richest and most complex ecosystems on earth, and the intestinal microbes play an important role in host development and health. Next generation sequencing approaches, which rapidly produce millions of short reads that enable the investigation on a culture independent basis, are now popular for exploring microbial community. Currently, the gut microbiome in fresh water shrimp is unexplored. To explore gut microbiomes of the oriental river prawn (Macrobrachium nipponense) and investigate the effects of host genetics and habitats on the microbial composition, 454 pyrosequencing based on the 16S rRNA gene were performed. We collected six groups of samples, including M. nipponense shrimp from two populations, rivers and lakes, and one sister species (M. asperulum) as an out group. We found that Proteobacteria is the major phylum in oriental river prawn, followed by Firmicutes and Actinobacteria. Compositional analysis showed microbial divergence between the two shrimp species is higher than that between the two populations of one shrimp species collected from river and lake. Hierarchical clustering also showed that host genetics had a greater impact on the divergence of gut microbiome than host habitats. This finding was also congruent with the functional prediction from the metagenomic data implying that the two shrimp species still shared the same type of biological functions, reflecting a similar metabolic profile in their gut environments. In conclusion, this study provides the first investigation of the gut microbiome of fresh water shrimp, and supports the hypothesis of host species-specific signatures of bacterial community composition.

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.

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.

Simiduia agarivorans gen. nov., sp. nov., a marine, agarolytic bacterium isolated from shallow coastal water from Keelung, Taiwan.

A Gram-negative, heterotrophic, agarolytic, marine bacterium, designated strain SA1T, was isolated from a seawater sample collected in the shallow coastal region of Keelung, Taiwan. Cells were straight to slightly curved rods. Nearly all of the cells were non-motile and non-flagellated during the exponential phase of growth in broth cultures; a few cells (<1 %) were motile and were considered to have monotrichous flagella. The isolate required NaCl for growth and grew optimally at 30-35 degrees C and 2-3 % (w/v) NaCl. It grew aerobically and was incapable of anaerobic growth by fermentation of glucose or other carbohydrates. However, anaerobic growth could be achieved by reduction of nitrate to nitrite. Polar lipids comprised phosphatidylethanolamine (71.8 %), diphosphatidylglycerol (12.7 %), phosphatidylglycerol (12.2 %) and phosphatidylserine (3.3 %). Isoprenoid quinones consisted of Q-10 (87.5 %), MK-9 (6.6 %) and MK-7 (5.9 %). Major cellular fatty acids were C16 : 1 omega 7c and/or iso-C15 : 0 2-OH (28.6 %), C17 : 1 omega 8c (22.8 %), C16 : 0 (14.5 %), C18 : 1 omega 7c (11.0 %) and C17 : 0 (6.4 %). The DNA G+C content was 55.6 mol%. Phylogeny based on 16S rRNA gene sequence analysis showed that strain SA1T formed a distinct lineage within the class Gammaproteobacteria. Strain SA1T was related most closely to Teredinibacter turnerae, Cellvibrio spp., Saccharophagus degradans, Pseudomonas spp. and Microbulbifer spp., strains of these species sharing <93 % 16S rRNA gene sequence similarity with strain SA1T. The phylogenetic data and those from physiological, morphological and chemotaxonomic characterizations indicated that strain SA1T represents a novel species and genus, for which the name Simiduia agarivorans gen. nov., sp. nov. is proposed. The type strain is SA1T (=BCRC 17597T=JCM 13881T).

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 degrees 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 C(15 : 0) iso and C(17 : 0) iso representing the most abundant components. The DNA G+C contents of strains PIT1(T) 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).

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.

Bowmanella denitrificans gen. nov., sp. nov., a denitrifying bacterium isolated from seawater from An-Ping Harbour, Taiwan.

A heterotrophic, non-fermentative, denitrifying isolate, designated strain BD1(T), was obtained from a seawater sample collected in the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. The cells of strain BD1(T) were Gram-negative. Cells grown in broth cultures were curved rods that were motile by means of a single polar flagellum. Growth occurred between 10 and 40 degrees C, with an optimum at 30-35 degrees C. Strain BD1(T) grew in NaCl levels of 0-10 %, with better growth occurring at 1-3 %. It grew aerobically and could achieve anaerobic growth by adopting a denitrifying metabolism with nitrate or nitrous oxide as the terminal electron acceptor. The major fatty acids were C(16 : 0), C(18 : 1)omega7c and summed feature 3 (C(16 : 1)omega7c and/or C(15 : 0) iso 2-OH). The polar lipids consisted of phosphatidylethanolamine (56.6 %) and phosphatidylglycerol (43.4 %). The isoprenoid quinones were Q-8 (81.5 %), Q-9 (11.1 %) and Q-10 (7.4 %). The DNA G+C content was 50.0 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain BD1(T) formed a distinct lineage in the Gammaproteobacteria and that it exhibited the highest level of sequence similarity with species of the genera Alteromonas (92.8-93.7 %), Aestuariibacter (93.0 %), Glaciecola (90.4-92.7 %) and Salinimonas (91.8 %). Strain BD1(T) was distinguishable from species of these genera by the presence of Q-9 and Q-10. Phenotypically, strain BD1(T) was also distinguishable from species of these genera in that it did not require NaCl for growth and was capable of denitrification. On the basis of the polyphasic data from this study, the isolate represents a novel species within a novel genus, for which the name Bowmanella denitrificans gen. nov., sp. nov. is proposed. The type strain of Bowmanella denitrificans is BD1(T) (=BCRC 17491(T)=JCM 13378(T)).

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 DN34(T) 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 degrees 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. DN34(T) 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 DN34(T) (=BCRC 17323(T)=JCM 12308(T)) as the type strain.

Marinobacter lutaoensis sp. nov., a thermotolerant marine bacterium isolated from a coastal hot spring in Lutao, Taiwan.

A heterotrophic and thermotolerant marine bacterium, designated strain T5054, was isolated from a hot spring on the coast of Lutao, Taiwan. It was a strictly aerobic, Gram-negative rod. Cells grown in broth cultures were non-spore-forming and motile by means of one to several polar flagella. It seems that pilus-like structures were produced from both poles of the cells. Strain T5054 required Na+ for growth and exhibited optimal growth at about 45 degrees C, pH 7, and 3-5% NaCl. It contained iso-C15:0 as the most abundant fatty acid and ubiquinone-8 as the only isoprenoid quinone. Its genomic DNA G+C content was 63.5 mol%. The strain did not require vitamins or other organic growth factors, and it grew on glucose, mannitol, and a variety of organic acids and amino acids as sole carbon sources. Characterization data, together with the results of a 16S rDNA-based phylogenetic analysis, indicated that strain T5054 could be classified as a new species in the genus Marinobacter. The name Marinobacter lutaoensis sp. nov. is proposed for this new bacterium. The type strain is T5054 (CCRC 17087; JCM 11179).