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-1T, 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 C14:0, C16:0 and C16:1 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-1T (= BCRC 81209T = JCM 33626T) 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.

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-1T, 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 C16:1 ω7c, C16:0, and C18:1 ω7c. The major polar lipids consisted of phosphatidylethanolamine and phosphatidylserine. Strain NFV-1T 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-1T = BCRC 81211T = JCM 33628T) is proposed.

Glaciimonas soli sp. nov., a soil bacterium isolated from the forest of a high elevation mountain.

A Gram-negative, psychrophilic bacterium, designated strain GS1T, was isolated from a forest soil sample collected from the West Peak of Mt. Yushan, Yushan National Park, Taiwan. Cells grown in broth cultures were mostly non-motile and non-flagellated, whereas motile cells with monotrichous, subpolar flagella were also observed. The novel strain grew over a temperature range of 4-25 °C with optimum growth at 10-15 °C. It grew aerobically and was not capable of anaerobic growth by fermentation of D-glucose or other carbohydrates. Ubiquinone 8 was the predominant isoprenoid quinone. The major polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol and dimethylaminoethanol. Cellular fatty acids were dominated by C16:1ω7c (35.2%), C16:0 (19.5%), C18:1ω7c (18.8%) and C17:0ω7c cyclo (15.5%). The DNA G + C content was 49.2 mol% evaluated according to the genomic sequencing data. Strain GS1T shared more than 96.5% 16S rRNA gene sequence similarities with type strains of four Collimonas species (97.2-97.5%), three Glaciimonas species (97.3% for each of the three) and Oxalicibacterium solurbis (96.5%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GS1T formed a stable genus-level clade with type strains of species in the genus Glaciimonas in the family Oxalobacteraceae and GS1T was an outgroup with respect to these Glaciimonas species. Characteristically, strain GS1T could be easily distinguished from the recognised Glaciimonas species by exhibition of swimming motility with monotrichous, subpolar flagellum in some of the cells, ability to grow in NaCl at 2% but not at 3% and the distinguishable fatty acid profiles. On the basis of the polyphasic taxonomic data from this study, strain GS1T is considered to represent a novel species of the genus Glaciimonas, for which the name Glaciimonas soli sp. nov. is proposed. The type strain is GS1T (= JCM 33275T = BCRC 81091T).

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 DM2T, 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 C16 : 0, C18 : 1ω7c and C16 : 1ω7c. The major polar lipid was phosphatidylethanolamine. Strains DM1 and DM2T 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 DM2T (=BCRC 81069T=JCM 32096T).

Tagaea marina gen. nov., sp. nov., a marine bacterium isolated from shallow coastal water.

A Gram-negative, heterotrophic, marine bacterium, designated strain TT1T, was isolated from seawater collected from the shallow coastal region of Anping Harbour, Tainan, Taiwan. Cells grown in broth cultures were straight rods that were motile by means of a single polar flagellum. The isolate required NaCl for growth and exhibited optimal growth at 30-35 °C, 2-4 % NaCl and pH 7-8. Strain TT1T grew aerobically and was not capable of anaerobic growth by fermentation of glucose or other carbohydrates. Q-10 was the sole major isoprenoid quinone. Cellular fatty acids were dominated by C18 : 1ω7c (47.5 %), C18 : 1 2-OH (16.3 %) and C19 : 0ω8c cyclo (10.6 %). The DNA G+C content was 56.4 mol%. Phylogeny based on 16S rRNA gene sequences showed that strain TT1T formed a distinct genus-level lineage in the family Rhodospirillaceae of the class Alphaproteobacteria and exhibited the highest sequence similarity with species of the genera Thalassobaculum (89.9-90.0 % 16S rRNA gene sequence similarity), Oceanibaculum (89.4-89.9 %) and Nisaea (89.1-89.7 %). Strain TT1T could be distinguished from species of these phylogenetically closest genera based on differences in DNA G+C contents (56.4 mol% vs 60.0-68.0 mol%), fatty acid profiles and some physiological characteristics. On the basis of the polyphasic taxonomic data from this study, strain TT1T is considered to represent a novel species of a new genus in the family Rhodospirillaceae, for which the name Tagaea marina gen. nov., sp. nov. is proposed. The type strain of the type species is TT1T ( = JCM 18659T = BCRC 80493T).

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).

Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea.

BACKGROUND: Prokaryotic microbes, the most abundant organisms in the ocean, are remarkably diverse. Despite numerous studies of marine prokaryotes, the zonation of their communities in pelagic zones has been poorly delineated. By exploiting the persistent stratification of the South China Sea (SCS), we performed a 2-year, large spatial scale (10, 100, 1000, and 3000 m) survey, which included a pilot study in 2006 and comprehensive sampling in 2007, to investigate the biological zonation of bacteria and archaea using 16S rRNA tag and shotgun metagenome sequencing. RESULTS: Alphaproteobacteria dominated the bacterial community in the surface SCS, where the abundance of Betaproteobacteria was seemingly associated with climatic activity. Gammaproteobacteria thrived in the deep SCS, where a noticeable amount of Cyanobacteria were also detected. Marine Groups II and III Euryarchaeota were predominant in the archaeal communities in the surface and deep SCS, respectively. Bacterial diversity was higher than archaeal diversity at all sampling depths in the SCS, and peaked at mid-depths, agreeing with the diversity pattern found in global water columns. Metagenomic analysis not only showed differential %GC values and genome sizes between the surface and deep SCS, but also demonstrated depth-dependent metabolic potentials, such as cobalamin biosynthesis at 10 m, osmoregulation at 100 m, signal transduction at 1000 m, and plasmid and phage replication at 3000 m. When compared with other oceans, urease at 10 m and both exonuclease and permease at 3000 m were more abundant in the SCS. Finally, enriched genes associated with nutrient assimilation in the sea surface and transposase in the deep-sea metagenomes exemplified the functional zonation in global oceans. CONCLUSIONS: Prokaryotic communities in the SCS stratified with depth, with maximal bacterial diversity at mid-depth, in accordance with global water columns. The SCS had functional zonation among depths and endemically enriched metabolic potentials at the study site, in contrast to other oceans.

Gemella parahaemolysans sp. nov. and Gemella taiwanensis sp. nov., isolated from human clinical specimens.

Four Gram-staining-positive, catalase-negative, coccoid isolates, designated NTUH_1465(T), NTUH_2196, NTUH_4957 and NTUH_5572(T), were isolated from human specimens. The four isolates displayed more than 99.6% 16S rRNA gene sequence similarity with Gemella haemolysans ATCC 10379(T), and 96.7 to 98.6% similarity with Gemella sanguinis ATCC 700632(T), Gemella morbillorum ATCC 27824(T) or Gemella cuniculi CCUG 42726(T). However, phylogenetic analysis of concatenated sequences of three housekeeping genes, groEL, rpoB and recA, suggested that the four isolates were distinct from G. haemolysans ATCC 10379(T) and other species. Isolates NTUH_2196, NTUH_4957 and NTUH_5572(T) clustered together and formed a stable monophyletic clade. DNA-DNA hybridization values among strains NTUH_1465(T) and NTUH_5572(T) and their phylogenetically related neighbours were all lower than 49%. The four isolates could be distinguished from G. haemolysans and other species by phenotypic characteristics. Based on the phylogenetic and phenotypic results, two novel species Gemella parahaemolysans sp. nov. (type strain NTUH_1465(T) = BCRC 80365(T) = JCM 18067(T)) and Gemella taiwanensis sp. nov. (type strain NTUH_5572(T) = BCRC 80366(T) = JCM 18066(T)) are proposed.

Aliidiomarina shirensis sp. nov., a halophilic bacterium isolated from Shira Lake in Khakasia, southern Siberia, and a proposal to transfer Idiomarina maris to the genus Aliidiomarina.

Strain AIS(T), an aerobic halophilic, Gram-reaction-negative, heterotrophic bacterium isolated from the water of Shira Lake in Khakasia, southern Siberia, was characterized using a polyphasic approach. Our analysis of the 16S rRNA gene sequences showed that 'Aliidiomarina haloalkalitolerans', 'Aliidiomarina sanyensis', Idiomarina maris and AIS(T) formed a distinct lineage. The sequence similarities between AIS(T) and the type strains of species of the genera Idiomarina and Aliidiomarina were 91.6-95.1 % and 94.0-96.9 %, respectively. The major isoprenoid quinone of AIS(T) was ubiquinone 8 (Q-8). Predominant cellular fatty acids were iso-C17 : 0, iso-C15 : 0 and summed feature 9. The genomic DNA G+C content was 45.8 mol%. It is concluded that AIS(T) represents a novel species of the genus Aliidiomarina, and the name Aliidiomarina shirensis sp. nov. is herein proposed for it. The type strain is AIS(T) ( = JCM 17761(T) = BCRC 80327(T)). Based on its fatty acid profile and our phylogenetic analysis, we propose that Idiomarina maris be transferred to the genus Aliidiomarina.

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.

Complete Genome Sequence of Simiduia agarivorans SA1(T), a Marine Bacterium Able To Degrade a Variety of Polysaccharides.

Simiduia agarivorans strain SA1(T) is able to degrade a variety of polysaccharides found in marine algae, plants, and animals. The genome of S. agarivorans SA1(T) consists of a single chromosome (4,309,711 bp), and its information may provide insights into the polysaccharide-degrading capability, cell division, flagellar motility, and chemotaxis of this bacterium.

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).

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 AT1(T) and AS1(T), 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 degrees 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 Hg(2+)-reducing activity in liquid media containing HgCl(2). Strain AS1(T) reduced nitrate to nitrite. The predominant isoprenoid quinone was Q(8) (91.3-99.9 %). The polar lipids of strain AT1(T) consisted of phosphatidylethanolamine (46.6 %), phosphatidylglycerol (28.9 %) and sulfolipid (24.5 %), whereas those of AS1(T) comprised phosphatidylethanolamine (48.2 %) and phosphatidylglycerol (51.8 %). The two isolates contained C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH (22.4-33.7 %), C(16 : 0) (19.0-22.7 %) and C(18 : 1)omega7c (11.3-11.7 %) as the major fatty acids. Strains AT1(T) and AS1(T) 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 AT1(T)=BCRC 17571(T)=JCM 13895(T)) and Alteromonas simiduii sp. nov. (type strain AS1(T)=BCRC 17572(T)=JCM 13896(T)) are proposed.

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 ZD1(T) and ZT1(T), 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 ZT1(T) grew in 13-14 % NaCl. Both isolates grew between 10 and 45 degrees C, with optimum growth at 30-35 degrees 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. C(18 : 1)omega7c was the most abundant fatty acid (32.6-35.7 %). The other major fatty acids included C(16 : 1)omega7c (27.5-29.4 %) and C(16 : 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 C(18 : 1)omega7c instead of C(16 : 1)omega7c 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 ZD1(T) = BCRC 17493(T) = JCM 13380(T)) as the type species and Zobellella taiwanensis sp. nov. (type strain ZT1(T) = BCRC 17494(T) = JCM 13381(T)) as a second species.