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

Microbial dynamics and quality characteristics of spontaneously fermented salamis produced by replacing pork fat with avocado pulp

The aim of this study was to develop a novel and healthier fermented meat product by replacing pork fat with avocado pulp (AVP) during salami production. Experimental salamis were produced under laboratory conditions by substituting pork fat with AVP partially (10-AVP) and totally (20-AVP), while control salamis (CTR) remained AVP-free. The microbial composition of control and experimental salamis was assessed using a combined culture-dependent and -independent approach. Over a 20-days ripening period, lactic acid bacteria, coagulase-negative staphylococci, and yeasts dominated the microbial community, with approximate levels of 9.0, 7.0 and 6.0 log CFU/g, respectively. Illumina technology identified 26 taxonomic groups, with leuconostocs being the predominant group across all trials [constituting 31.26-59.12 % of relative abundance (RA)]. Gas Chromatography-Mass Spectrometry (GC-MS) analysis revealed changes in fatty acid composition and volatile organic compounds due to the substitution of pork fat with AVP. Specifically, monounsaturated fatty acids and terpene compounds increased, while saturated fatty acids and lipid oxidation products decreased. Although AVP influenced the sensory characteristics of the salamis, the highest overall satisfaction ratings were observed for the 10-AVP salamis. Consequently, substituting pork fat with AVP emerges as a viable strategy for producing healthier salamis and diversifying the meat product portfolio.

Pseudidiomarina fusca sp. nov., Isolated from the Surface Seawater of the Western Pacific Ocean

The Gram-negative marine bacterium GXY010T, which has been isolated from the surface seawater of the western Pacific Ocean, is aerobic, non-motile and non-flagellated. Strain GXY010T exhibits growth across a temperature range of 10-42 °C (optimal at 37 °C), pH tolerance from 7.0 to 11.0 (optimal at 7.5) and a NaCl concentration ranging from 1.0 to 15.0% (w/v, optimal at 5.0%). Ubiquinone-8 (Q-8) was the predominant isoprenoid quinone in strain GXY010T. The dominant fatty acids (>10%) of strain GXY010T were iso-C15:0 (14.65%), summed feature 9 (iso-C17:1ω9c and/or 10-methyl C16:0) (12.41%), iso-C17:0 (10.85%) and summed feature 3 (C16:1ω7c and/or C16:1ω6c) (10.41%). Phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), unidentifiable glycolipid (GL) and four non-identifiable aminolipids (AL1-AL4) were the predominant polar lipids of strain GXY010T. The genomic DNA G+C content was identified as a result of 48.0% for strain GXY010T. The strain GXY010T genome consisted of 2,766,857 bp, with 2664 Open Reading Frames (ORFs), including 2586 Coding sequences (CDSs) and 78 RNAs. Strain GXY010T showed Average Nucleotide Identity (ANI) values of 73.4% and 70.6% and DNA-DNA hybridization (DDH) values of 19.2% and 14.5% with reference species Pseudidiomarina tainanensis MCCC 1A02633T (=PIN1T) and Pseudidiomarina taiwanensis MCCC 1A00163T (=PIT1T). From the results of the polyphasic analysis, a newly named species, Pseudidiomarina fusca sp. nov. within the genus Pseudidiomarina, was proposed. The type strain of Pseudidiomarina fusca is GXY010T (=JCM 35760T = MCCC M28199T = KCTC 92693T).

The Hypersaline Soils of the Odiel Saltmarshes Natural Area as a Source for Uncovering a New Taxon: Pseudidiomarina terrestris sp. nov

The hypersaline soils of the Odiel Saltmarshes Natural Area are an extreme environment with high levels of some heavy metals; however, it is a relevant source of prokaryotic diversity that we aim to explore. In this study, six strains related to the halophilic genus Pseudidiomarina were isolated from this habitat. The phylogenetic study based on the 16S rRNA gene sequence and the fingerprinting analysis suggested that they constituted a single new species within the genus Pseudidiomarina. Comparative genomic analysis based on the OGRIs indices and the phylogeny inferred from the core genome were performed considering all the members of the family Idiomarinaceae. Additionally, a completed phenotypic characterization, as well as the fatty acid profile, were also carried out. Due to the characteristics of the habitat, genomic functions related to salinity and high heavy metal concentrations were studied, along with the global metabolism of the six isolates. Last, the ecological distribution of the isolates was studied in different hypersaline environments by genome recruitment. To sum up, the six strains constitute a new species within the genus Pseudidiomarina, for which the name Pseudidiomarina terrestris sp. nov. is proposed. The low abundance in all the studied hypersaline habitats indicates that it belongs to the rare biosphere in these habitats. In silico genome functional analysis suggests the presence of heavy metal transporters and pathways for nitrate reduction and nitrogen assimilation in low availability, among other metabolic traits.

Comparative genomics of seven genomes of genus Idiomarina reveals important halo adaptations and genes for stress response

The genus Idiomarina consists of halophilic and/or haloalkaliphilic organisms. We compared the complete genomes of seven strains of the genus Idiomarina to investigate its adaptation to saline environment. A total of 1,313 core genes related to salinity tolerance, stress response, antibiotic resistance genes, virulence factors, and drug targets were found. Comparative genomics revealed various genes involved in halo adaptations of these organisms, including transporters and influx or efflux systems for elements such as Fe, Cu, Zn, Pb, and Cd. In agreement with their isolation sources (such as hydrothermal vents and marine sediments) and environments abundant in heavy metals, various resistance proteins and transporters associated with metal tolerance were also identified. These included copper resistance proteins, zinc uptake transcriptional repressor Zur, MerC domain-containing protein, Cd(II)/Pb(II)-responsive transcriptional regulator, Co/Zn/Cd efflux system protein, and mercuric transporter. Interestingly, we observed that the carbohydrate metabolism pathways were incomplete in all the strains and transporters used for absorption of small sugars were also not found in them. Also, the presence of higher proportion of genes involved in protein metabolism than carbohydrate metabolism indicates that proteinaceous substrates act as the major food substrates for these bacterial strains than carbohydrates. Genomic islands were detected in some species, highlighting the role of horizontal gene transfer for acquisition in novel genes. Genomic rearrangements in terms of partially palindromic regions were detected in all strains. To our knowledge, this is the first comprehensive comparative genomics study among the genus Idiomarina revealing unique genomic features within bacterial species inhabiting different ecological niches.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03887-3.

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.

In-Depth Investigation of the Safety of Wooden Shelves Used for Traditional Cheese Ripening

The main goal of this research was to characterize the bacterial diversity of the wooden boards used for aging traditional Sicilian cheeses and to evaluate whether pathogenic bacteria are associated with these surfaces. Eighteen cheese dairy factories producing three traditional cheese typologies (PDO Pecorino Siciliano, PDO Piacentinu Ennese, and Caciocavallo Palermitano) were selected within the region of Sicily. The wooden shelf surfaces were sampled by a destructive method to detach wood splinters as well as by a nondestructive brushing to collect microbial cells. Scanning electron microscopy showed the presence of almost continuous bacterial formations on the majority of the shelves analyzed. Yeasts and fungal hyphae were also visualized, indicating the complexity of the plank communities. The amplicon library of the 16S rRNA gene V3-V4 region was paired-end sequenced using the Illumina MiSeq system, allowing the identification of 14 phyla, 32 classes, 52 orders, 93 families, and 137 genera. Staphylococcus equorum was identified from all wooden surfaces, with a maximum abundance of 64.75%. Among cheese-surface-ripening bacteria, Brevibacterium and Corynebacterium were detected in almost all samples. Several halophilic (Halomonas, Tetragenococcus halophilus, Chromohalobacter, Salimicrobium, Marinococcus, Salegentibacter, Haererehalobacter, Marinobacter, and Idiomarinaceae) and moderately halophilic (Salinicoccus, Psychrobacter, and Salinisphaera) bacteria were frequently identified. Lactic acid bacteria (LAB) were present at low percentages in the genera Leuconostoc, Lactococcus, Lactobacillus, Pediococcus, and Streptococcus. The levels of viable microorganisms on the wooden shelves ranged between 2.4 and 7.8 log CFU/cm2. In some cases, LAB were counted at very high levels (8.2 log CFU/cm2). Members of the Enterobacteriaceae family were detected in a viable state for only six samples. Coagulase-positive staphylococci, Salmonella spp., and Listeria monocytogenes were not detected. Seventy-five strains belonged to the genera Leuconostoc, Lactococcus, Pediococcus, Enterococcus, Lactobacillus, and Weissella. IMPORTANCE This study provides evidence for the lack of pathogenic bacteria on the wooden shelves used to ripen internal bacterially ripened semihard and hard cheeses produced in Sicily. These three cheeses are not inoculated on their surfaces, and surface ripening is not considered to occur or, at least, does not occur at the same extent as surface-inoculated smear cheeses. Several bacterial groups identified from the wooden shelves are typically associated with smear cheeses, strongly suggesting that PDO Pecorino Siciliano, PDO Piacentinu Ennese, and Caciocavallo Palermitano cheese rind contributes to their final organoleptic profiles.

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.

Pseudidiomarina piscicola sp. nov., isolated from cultured European seabass, Dicenthrarchus labrax

Strain CECT 9734 ^T, a Gram-negative, aerobic, chemoorganotrophic bacterium, motile by polar flagella, was isolated from cultured European seabass, Dicenthrarchus labrax, in Spain. It grows from 5 to 42 ºC, 6–9 pH and 1–12% total salinity. Major cellular fatty acids are C_15:0 iso, summed feature 9 (C_17:1 iso w9c/C_16:0 10-methyl) and C_17:0 iso. The genome size is 2.5 Mbp and G + C content is 49.5 mol%. Comparative analysis of the 16S rRNA gene sequence shows that the strain is a member of Pseudidiomarina, with highest similarities with Pseudidiomarina halophila (97.0%) and Pseudidiomarina salinarum (96.9%). Phylogenomic tree based on UBCG program shows P. halophila as its closest relative. ANI and in-silico DDH with other Pseudidiomarina spp. are lower than 87 and 20%, respectively, suggesting that strain CECT 9734 ^T represents a new species, for which we propose the name Pseudidiomarina piscicola sp. nov. and CECT 9734 ^T (= LUBLD50 7a^T = LMG 31044 ^T) as type strain.

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

A Gram-negative, psychrophilic bacterium, designated strain GS1^T, 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 C_16:1ω7c (35.2%), C_16:0 (19.5%), C_18:1ω7c (18.8%) and C_17:0ω7c cyclo (15.5%). The DNA G + C content was 49.2 mol% evaluated according to the genomic sequencing data. Strain GS1^T 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 GS1^T formed a stable genus-level clade with type strains of species in the genus Glaciimonas in the family Oxalobacteraceae and GS1^T was an outgroup with respect to these Glaciimonas species. Characteristically, strain GS1^T 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 GS1^T 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 GS1^T (= JCM 33275^T = BCRC 81091^T).

Marinobacter denitrificans sp. nov., isolated from marine sediment of southern Scott Coast, Antarctica

A novel bacterium, designated JB02H27^T, was isolated from marine sediment collected from the southern Scott Coast, Antarctica. Cells were Gram-stain-negative, facultatively anaerobic, polar-flagellated and motile rods. Growth occurred at 4-45 °C, at pH 7.0-9.0 and with 3-25 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain JB02H27^T consistently fell within the genus Marinobacter and formed a clade together with Marinobacter algicola DG893^T (98.8 % similarity), Marinobacter confluentis KCTC 42705^T (98.4 %), Marinobacter salarius R9SW1^T (98.4%) and Marinobacter halotolerans CP12^T (97.9 %), which were subsequently used as reference strains for comparisons of phenotypic and chemotaxonomic characteristics. Average nucleotide identity values between strain JB02H27^T and the four related type strains were 80.9, 76.6, 81.9 and 76.3 %, respectively. The major fatty acids were summed feature 3, C_16 : 0, C_18 : 1 ω9c and C_16 : 0 N alcohol. The polar lipids included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified phospholipid, aminolipid, aminophospholipid and glycolipids. The sole respiratory quinone was ubiquinone-9. The DNA G+C content was 56.9 mol%. Based on the genomic, phylogenetic, phenotypic and chemotaxonomic analysis, we propose that strain JB02H27^T represents a novel species of the genus Marinobacter, for which the name Marinobacter denitrificans sp. nov. is proposed. The type strain is JB02H27^T (=GDMCC 1.1528^T=KCTC 62941^T).

Idiomarina mangrovi sp. nov., isolated from rhizosphere soil of a mangrove Avicennia marina forest

A Gram-staining negative, aerobic, motile and rod-shaped bacterium, designated ZQ330^T, was isolated from rhizosphere soil of a mangrove (Avicennia marina) forest of Zhangzhou, Fujian Province, China. The growth range of NaCl concentration was 0.5-10.0 % (w/v), with an optimum at 2.5-3.0 % (w/v), the temperature range for growth was 10-40 °C, with an optimum at 28-30 °C, the pH range for growth was pH 6.0-9.5, with an optimum at pH 7.5. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZQ330^T exhibited less than 97.0 % sequence similarity to all type strains with validly published names and revealed that strain ZQ330^T formed a distinct lineage in the genus Idiomarina. The average nucleotide identity, and in silico DNA-DNA hybridization values between strain ZQ330^T and the reference strains were 64.8-69.9 % and 27.5-28.4 %, respectively. Chemotaxonomic analysis indicated that the main respiratory quinone was Q-8, the predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0, summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c), iso-C15 : 1F, C16 : 0, C18 : 0, summed feature 3 (C16 : 1ω8c and/or iso-C16 : 1 2-OH) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid, an unidentified aminolipid, an unidentified phospholipid and two unidentified lipids. Based on the genotypic, phenotypic, chemotaxonomic and phylogenetic features, strain ZQ330^T is considered to represent a novel species, for which the name Idiomarina mangrovi sp. nov. is proposed. The type strain is ZQ330^T (=MCCC 1K03495^T=KCTC 62455^T).

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).

Genome-Based Analysis Reveals the Taxonomy and Diversity of the Family Idiomarinaceae

Idiomarinaceae is a family of Gram-stain negative, mesophilic euryhalophiles. To provide a robust framework for the evolutionary and taxonomic relationships of bacteria of this family, we compared herein the genomes of 36 type strains and 43 non-type strains using 16S rRNA gene sequences, core genome based 78 single-copy orthologous proteins, digital DNA-DNA hybridization and average nucleotide identity (ANI) estimation. The 79 bacteria of this family were consistently divided into taxon I, taxon II, and taxon III corresponding to the three genera Idiomarina, Pseudidiomarina, and Aliidiomarina, which contained 13 putative new genospecies in addition to 35 well-defined species represented by each type strain. Furthermore, genetic diversity of this family was evident at the genus- and species levels, and exceeded that which is defined currently by the named species. In view of multiple genotypic characteristics clearly distinct from the other two genera, we propose reinstating the genus Pseudidiomarina as a monophyletic taxon. Taken together, this is the first genome-based study of the taxonomy and diversity of bacteria within the family Idiomarinaceae, and will contribute to further insights into microbial evolution and adaptation to saline environments.

Idiomarina andamanensis sp. nov., an alkalitolerant bacterium isolated from Andaman Sea water

Two closely related aerobic, Gram-negative rod shaped bacteria (strain W5^T and W3) were isolated from Andaman Sea. Heterotrophic growth on marine agar was observed at 15-45 °C and pH 6-10. Strain W5^T showed maximum 16S rRNA sequence similarity of 99.58% with Idiomarina marina JCM 15083^T. DNA fingerprinting analysis by ERIC-REP PCR, PFGE and MLSA revealed differences in banding patterns, also DNA-DNA hybridization values were well below 70% confirming W5^T to be a new species. DNA G+C content was 46.7 mol%. Major fatty acids were iso-C15:0, iso-C17:0, iso-C17:1 ω9c, iso-C13:0 3OH, iso-C11:0 3OH and C16:0. Polar lipids included phosphatidylglycerol (PG) and phosphatidylethanolamine (PE) diphosphatidylglycerol (DPG) phospholipid (PL) two aminolipids (AL) and two unidentified lipids (L1-2). Q-8 is the predominant ubiquinone. On the basis of polyphasic taxonomic study, strain W5^T is considered to be representative of a new species of the genus Idiomarina, for which the name Idiomarina andamanensis sp. nov. is being proposed. The type strain W5^T (= LMG 29773^T = JCM 31645^T) was isolated from Andaman Sea.

Aliidiomarina sedimenti sp. nov., a haloalkaliphilic bacterium in the family Idiomarinaceae

A novel Gram-staining-negative straight or curved rod-shaped, moderately halophilic and alkaliphilic bacterium, designated strain GBSy1T, was isolated from a sediment sample from the coastal-marine wetland Gomishan in Iran. GBSy1T was motile, and formed non-pigmented, mucoid colonies. Growth occurred with between 1 and 15 % (w/v) NaCl and the isolate grew optimally with 5 % (w/v) NaCl. The optimum pH and temperature for growth were 8.5 and 34 °C, while the strain was able to grow at pH 7.0-10 and 4-40 °C. On the basis of the results of 16S rRNA gene sequence analysis, GBSy1T was shown to represent a member of the genus Aliidiomarina within the class Gammaproteobacteria, family Idiomarinaceae and showed closest phylogenetic similarity to Aliidiomarina marisCF12-14T (97.7 %). The DNA G+C content of GBSy1T was 51.2 mol%. The cells of GBSy1T contained the isoprenoid ubiquinones Q-8, Q-9 and Q-10 (92, 2 and 2 %, respectively). The major cellular fatty acids of the isolate were iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and three unknown phospholipids. The level of DNA-DNA relatedness between GBSy1T and Aliidiomarina marisDSM 22154T was 31 %. All these features confirmed the placement of GBSy1T within the genus Aliidiomarina. On the basis of evidence from this study, a novel species of the genus Aliidiomarina, Aliidiomarina sedimenti sp. nov., is proposed, with GBSy1T (=IBRC-M 10764T=CECT 8340T) as the type strain.

Emended description of the family Chromatiaceae, phylogenetic analyses of the genera Alishewanella, Rheinheimera and Arsukibacterium, transfer of Rheinheimera longhuensis LH2-2T to the genus Alishewanella and description of Alishewanella alkalitolerans sp. nov. from Lonar Lake, India

Phylogenetic analyses were performed for members of the family Chromatiaceae, signature nucleotides deduced and the genus Alishewanella transferred to Chromatiaceae. Phylogenetic analyses were executed for the genera Alishewanella, Arsukibacterium and Rheinheimera and the genus Rheinheimera is proposed to be split, with the creation of the Pararheinheimera gen. nov. Furthermore, the species Rheinheimera longhuensis, is transferred to the genus Alishewanella as Alishewanella longhuensis comb. nov. Besides, the genera Alishewanella and Rheinheimera are also emended. Strain LNK-7.1^T was isolated from a water sample from the Lonar Lake, India. Cells were Gram-negative, motile rods, positive for catalase, oxidase, phosphatase, contained C_16:0, C_17:1ω8c, summed feature3 (C_16:1ω6c and/or C_16:1ω7c) and summed feature 8 (C_18:1ω7c) as major fatty acids, PE and PG as the major lipids and Q-8 as the sole respiratory quinone. Phylogenetic analyses using NJ, ME, ML and Maximum parsimony, based on 16S rRNA gene sequences, identified Alishewanella tabrizica RCRI4^T as the closely related species of strain LNK-7.1^T with a 16S rRNA gene sequence similarity of 98.13%. The DNA-DNA similarity between LNK-7.1^T and the closely related species (A. tabrizica) was only 12.0% and, therefore, strain LNK-7.1^T was identified as a novel species of the genus Alishewanella with the proposed name Alishewanella alkalitolerans sp. nov. In addition phenotypic characteristics confirmed the species status to strain LNK-7.1^T. The type strain of A. alkalitolerans is LNK-7.1^T (LMG 29592^T = KCTC 52279^T), isolated from a water sample collected from the Lonar lake, India.

Idiomarina aquatica sp. nov., a moderately halophilic bacterium isolated from salterns

Four bacterial strains, SN-14T, SN-4, M6-46 and M6-58B, were isolated from water of ponds of two salterns located in Huelva (Spain). They were Gram-stain-negative, aerobic and slightly curved rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the four strains belong to the genus Idiomarina, being related most closely to Idiomarina fontislapidosi F23T (98.4–98.0% sequence similarity), Idiomarina seosinensis CL-SP19T (98.3–98.0%), Idiomarina piscisalsi TPS4-2T (97.9–97.4%), Idiomarina baltica OS145T (97.5–97.4%) and Idiomarina zobellii KMM 231T (97.6–97.0%). The level of similarity with the type species of the genus, Idiomarina abyssalis KMM 227T, was 97.2–96.7%. The novel strains exhibited optimal growth at 5–10% (w/v) total salts, pH 7 and 37 °C. The major fatty acids of strain SN-14T were iso-C15 : 0, iso-C17 : 0, C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and iso-C17 : 1ω9c/C16 : 0 10-methyl. The DNA G+C content range was 47.6–50.8 mol%. The level of DNA–DNA relatedness between strain SN-14T and I. fontislapidosi F23T was 13%, while those between strain SN-14T and the other three new isolates were between 77 and 99%. These data demonstrated that the four isolates constitute a novel species of the genus Idiomarina. Based on the phylogenetic, genotypic, phenotypic and chemotaxonomic data, the four strains represent a novel species of the genus Idiomarina, for which the name Idiomarina aquatica sp. nov. is proposed. The type strain is SN-14T ( = CCM 8471T = CECT 8360T = LMG 27613T).

Idiomarina halophila sp. nov., isolated from a solar saltern sediment

A Gram-stain-negative, halophilic bacterium, designated strain BH195T, was isolated from the sediment of the solar saltern pond located in Gomso, Republic of Korea. Strain BH195T was a strictly aerobic, non-motile rod, which grew at pH 3.5–10.5 (optimum, pH 7.5), at 4–55 °C (optimum, 30 °C) and at salinities of 0.5–11 % (w/v) NaCl [optimum, 2–3 % (w/v) NaCl]. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain BH195T belongs to the genus Idiomarina , showing the highest sequence similarity to Idiomarina salinarum ISL-52T (97.4 %), Idiomarina homiensis PO-M2T (96.8 %), Idiomarina aestuarii KYW314T (96.7 %), and Idiomarina tainanensis PIN1T (96.7 %). The major cellular fatty acids of strain BH195T were iso-C11 : 0 3-OH, iso-C15 : 0 and iso-C11 : 0. The DNA G+C content was 51.3 mol% and the major respiratory quinone was ubiquinone 8. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid. DNA–DNA relatedness between strain BH195T and I. salinarum KCTC 12971T was 33 %. On the basis of this polyphasic analysis, strain BH195T represents a novel species of the genus Idiomarina for which the name Idiomarina halophila sp. nov. is proposed. The type strain is BH195T ( = KACC 17610T = NCAIM B 02544T).

Idiomarina planktonica sp. nov., isolated from a saline lake

A Gram-stain-negative bacterium, strain TS-T11(T), was isolated from Tuosu lake, a saline lake (salinity 5.4%, w/v) in the Qaidam basin, Qinghai province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain TS-T11(T) were non-spore-forming rods, 0.6-0.8 µm wide and 0.8-2.2 µm long, and motile by means of a single polar flagellum. Strain TS-T11(T) was strictly heterotrophic and aerobic. Cells were positive for catalase and oxidase. Growth was observed in the presence of 0.5-11.0% (w/v) NaCl (optimum 4.0-6.0%), at 4-40 °C (optimum 30-35 °C) and at pH 6.0-10.5 (optimum pH 7.5-8.5). Strain TS-T11(T) contained iso-C15:0, iso-C17:0 and iso-C17:1ω9c as the predominant fatty acids (>10%). The major respiratory quinone was Q-8. The polar lipids consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and nine uncharacterized phospholipids. The G+C content of genomic DNA was 46.8 mol% (Tm). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T11(T) was associated with the genus Idiomarina, and showed highest 16S rRNA gene sequence similarity to Idiomarina aestuarii KYW314(T) (97.4%) and Idiomarina salinarum ISL-52(T) (97.4%). DNA-DNA relatedness of strain TS-T11(T) to I. aestuarii JCM 16344(T) and I. salinarum DSM 21900(T) was 22.2 ± 2.4 and 11.5 ± 1.6%, respectively. Based on the data presented above, it was concluded that strain TS-T11(T) represents a novel species of the genus Idiomarina, for which the name Idiomarina planktonica sp. nov. is proposed. The type strain is TS-T11(T) ( = CGMCC 1.12458(T) = JCM 19263(T)).

Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural microbial communities.

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 AIST, 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 AIST formed a distinct lineage. The sequence similarities between AIST 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 AIST 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 AIST represents a novel species of the genus Aliidiomarina , and the name Aliidiomarina shirensis sp. nov. is herein proposed for it. The type strain is AIST ( = JCM 17761T = BCRC 80327T). Based on its fatty acid profile and our phylogenetic analysis, we propose that Idiomarina maris be transferred to the genus Aliidiomarina .

Gemmobacter megaterium sp. nov., isolated from coastal planktonic seaweeds

A Gram-stain-negative, non-motile and aerobic bacterium, designated CF17T, was isolated from coastal planktonic seaweeds, East China Sea. The isolate grew at 18–37 °C (optimum 25–28 °C), pH 6.5–9.0 (optimum 7.0–8.0) and with 0–5 % NaCl (optimum 1–2 %, w/v) and 0.5–10 % sea salts (optimum 2–3 %, w/v). Growth of strain CF17T could be stimulated prominently by supplementing the growth medium with the autoclaved supernatant of a culture of strain CF5, which was isolated from the same sample along with strain CF17T. The cell morphology of strain CF17T was a bean-shaped rod consisting of a swollen end and a long prostheca. The phylogenetic analysis of 16S rRNA gene sequences indicated that strain CF17T clustered with Gemmobacter nectariphilus DSM 15620T within the genus Gemmobacter . The DNA G+C content of strain CF17T was 61.4 mol%. The respiratory quinone was ubiquinone Q-10. The major fatty acids included C18 : 1ω7c and C18 : 0. The polar lipids of strain CF17T consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two uncharacterized phospholipids, one uncharacterized aminolipid, three uncharacterized glycolipids and one uncharacterized lipid. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain CF17T ( = CGMCC 1.11024T = JCM 18498T) is considered to represent a novel species of the genus Gemmobacter , for which the name Gemmobacter megaterium sp. nov. is proposed.

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, E3T = JCM 15139T = CGMCC 1.7001T) and Aliiglaciecola litoralis comb. nov. (type strain, KMM 3894T = JCM 15896T = NRIC 0754T), 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%).

Idiomarina indica sp. nov., isolated from seawater

Two Gram-negative, aerobic, rod-shaped bacteria, designated strains SW104T and X07, were isolated from a seawater sample collected from the Indian Ocean. The strains grew at a temperature range of 12–50 °C (optimum, 35–37 °C), and at pH 6.0–9.0 (optimum pH 7.0–7.5). The predominant cellular fatty acids of strain SW104T were iso-C15 : 0 (41.2 %), iso-C17 : 1ω9c (15.2 %) and iso-C17 : 0 (11.1 %). The major respiratory quinone was ubiquinone 8 (Q-8). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C contents of strains SW104T and X07 were 49.8 and 49.5 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the new isolates were related to members of the genus Idiomarina , showing the highest similarity with Idiomarina taiwanensis PIT1T and Idiomarina maritima 908087T (96.1 and 95.9 %, respectively). On the basis of phenotypic, genotypic and phylogenetic characteristics, it is proposed that strains SW104T and X07 should be described as representatives of a novel species of the genus Idiomarina , for which the name Idiomarina indica sp. nov. is proposed. The type strain is SW104T ( = CGMCC 1.10824T = JCM 18138T).

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.

Idiomarina maris sp. nov., a marine bacterium isolated from sediment

A protease-producing marine bacterium, designated CF12-14T, was isolated from sediment of the South China Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain CF12-14T formed a separate lineage within the genus Idiomarina (Gammaproteobacteria). The isolate showed the highest 16S rRNA gene sequence similarity with Idiomarina salinarum ISL-52T (94.7 %), Idiomarina seosinensis CL-SP19T (94.6 %) and other members of the genus Idiomarina (91.9–94.6 %). Cells were Gram-negative, aerobic, flagellated, straight or slightly curved, and often formed buds and prosthecae. Strain CF12-14T grew at 4–42 °C (optimum 30–35 °C) and with 0.1–15 % (w/v) NaCl (optimum 2–3 %). The isolate reduced nitrate to nitrite and hydrolysed DNA, but did not produce acids from sugars. The predominant cellular fatty acids were iso-C15 : 0 (27.4 %), iso-C17 : 0 (16.0 %) and iso-C17 : 1ω9c (15.8 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was ubiquinone 8. The DNA G+C content was 50.4 mol%. The phylogenetic, phenotypic and chemotaxonomic data supported the conclusion that CF12-14T represents a novel species of the genus Idiomarina, for which the name Idiomarina maris sp. nov. is proposed. The type strain is CF12-14T ( = CCTCC AB 208166T = KACC 13974T).

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).

Aliidiomarina haloalkalitolerans sp. nov., a marine bacterium isolated from coastal surface seawater

A novel Gram-negative, rod shaped, motile, non-sporing strictly aerobic bacterium, designated strain AK5(T), was isolated from a sea water sample collected near Visakhapatnam coast, Bay of Bengal, India. Colonies on marine agar were circular, 3-4 mm in diameter, creamish and rose with entire margin. Growth occurred at 10-40°C, 0.5-12% (w/v) NaCl and pH of 7-11. Strain AK5(T) was oxidase and catalase positive. The fatty acids were dominated by iso-branched saturated and unsaturated fatty acids with a high abundance of iso-C(15:0), iso-C(17:0) and summed feature 9 (as defined by MIDI). Q8 was found to be the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and four unidentified phospholipids as polar lipids. The DNA G+C content of strain AK5(T) was 54.7 ± 0.2 mol%. Phylogenetic analysis revealed that strain AK5(T) was a member of the genus Aliidiomarina and closely related to Aliidiomarina taiwanensis with a phylogenetic distance of 5.3% (94.7% 16S rRNA gene sequence similarity) and clustered with the same species. Results from the polyphasic taxonomy study support the conclusion that strain AK5(T) represents a novel Aliidiomarina species, for which the name Aliidiomarina haloalkalitolerans sp. nov. is proposed. The type strain of A. haloalkalitolerans is AK5(T) (= MTCC 11064(T) = JCM 17359(T)).

Idiomarina aquimaris sp. nov., isolated from the reef-building coral Isopora palifera

A bacterial strain designated SW15(T) was isolated from a sample of the reef-building coral Isopora palifera, collected in southern Taiwan. The novel strain was characterized using a polyphasic taxonomic approach. Cells of strain SW15(T) were Gram-negative, aerobic, light yellow, rod-shaped and motile by means of a single polar flagellum. In phylogenetic analyses based on 16S rRNA gene sequences, strain SW15(T) appeared to belong to the genus Idiomarina in the class Gammaproteobacteria and to be most closely related to Idiomarina homiensis PO-M2(T) (97.6% sequence similarity). Strain SW15(T) exhibited optimal growth between 20 and 30 °C, with NaCl between 3% and 4% (w/v) and at a pH value between 7 and 8. Predominant cellular fatty acids were iso-C(15:0) (31.1%), iso-C(17:0) (15.4%), iso-C(17:1)ω9c (10.0%) and C(16:0) (8.8%). The major respiratory quinone was ubiquinone Q-8. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine, an uncharacterized aminolipid and several uncharacterized phospholipids. The DNA G+C content was 51.1 mol%. The level of DNA-DNA relatedness between strain SW15(T) and Idiomarina homiensis PO-M2(T) was 42.6-56.5%. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of the novel strain from established species of the genus Idiomarina. Based on the genotypic, phenotypic and chemotaxonomic data, strain SW15(T) represents a novel species in the genus Idiomarina, for which the name Idiomarina aquimaris sp. nov. is proposed, with SW15(T) (=LMG 25374(T)=BCRC 80083(T)) as the type strain.

Rheinheimera nanhaiensis sp. nov., isolated from marine sediments, and emended description of the genus Rheinheimera Brettar et al. 2002 emend. Merchant et al. 2007

A Gram-negative, facultatively aerobic, oxidase- and catalase-positive, rod-shaped bacterium, designated strain E407-8T, was isolated from a sediment sample from the South China Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain E407-8T was affiliated with the genus Rheinheimera, sharing the highest sequence similarity with Rheinheimera pacifica KMM 1406T (97.5 %) and Rheinheimera aquimaris SW-353T (97.4 %) and showing less than 97 % sequence similarity to the type strains of other recognized Rheinheimera species. Levels of DNA–DNA relatedness of strain E407-8T to R. pacifica DSM 17616T and R. aquimaris JCM 14331T were 25.2 % (25.3 % in the duplicate measurement) and 9.4 % (6.5 %), respectively. The bacterium could grow at 10–48 °C (optimum 37 °C) and in the presence of 0–8 % (w/v) NaCl (optimum 0.5–2.5 %). The major cellular fatty acids of strain E407-8T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C17 : 1ω8c, C16 : 0 and C18 : 1ω7c. The predominant respiratory quinone was ubiquinone Q-8. The DNA G+C content was 51.0 mol%. Based on the results of our polyphasic taxonomic study, strain E407-8T represents a novel species in the genus Rheinheimera, for which the name Rheinheimera nanhaiensis sp. nov. is proposed. The type strain is E407-8T ( = CCTCC AB 209089T  = KACC 14030T). An emended description of the genus Rheinheimera Brettar et al. 2002 emend. Merchant et al. 2007 is also proposed.

Idiomarina xiamenensis sp. nov., isolated from surface seawater, and proposal to transfer Pseudidiomarina aestuarii to the genus Idiomarina as Idiomarina aestuarii comb. nov

A taxonomic study was carried out on strain 10-D-4T, which was isolated from a crude oil-degrading consortium enriched from surface seawater collected around Xiamen Island, PR China. Strain 10-D-4T grew optimally at pH 7.0–8.0 and at 25 °C. The 16S rRNA gene sequence of strain 10-D-4T showed the highest similarity to those of Idiomarina salinarum ISL-52T (94.6 %), Idiomarina tainanensis PIN1T (94.2 %) and Idiomarina seosinensis CL-SP19T (94.1 %), and showed lower similarity (92.3–94.0 %) to other members of the genus Idiomarina. The major isoprenoid quinone was ubiquinone 8 (Q-8). The major fatty acids were iso-C13 : 0 (5.2 %), iso-C15 : 0 (15.3 %), C16 : 0 (14.3 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) (6.6 %), iso-C17 : 0 (15.4 %) and C18 : 1ω7c (13.5 %). The G+C content of the chromosomal DNA was 50.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences, together with data from phenotypic and chemotaxonomic characterization, revealed that strain 10-D-4T represents a novel species of the genus Idiomarina, for which the name Idiomarina xiamenensis sp. nov. is proposed. The type strain is 10-D-4T ( = CCTCC AB 209061T  = LMG 25227T  = MCCC 1A01370T). We also propose the transfer of Pseudidiomarina aestuarii, described recently, to the genus Idiomarina as Idiomarina aestuarii comb. nov. (type strain KYW314T  = KCTC 22740T  = JCM 16344T).

Pseudidiomarina aestuarii sp. nov., a marine bacterium isolated from shallow coastal seawater

A non-motile, rod-shaped and aerobic marine bacterium, designated strain KYW314(T), was isolated from seawater collected from the South Sea, Republic of Korea. Cells were Gram-negative, catalase- and oxidase-positive and had proteolytic activity. The major fatty acids were iso-C(15 : 0) (17.2 %), C(16 : 0) (11.1 %), iso-C(17 : 0) (10.5 %) and C(18 : 1)ω 7c (10.0 %). The DNA G+C content was 56.4 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain KYW314(T) formed a lineage within the genus Pseudidiomarina (95.4-97.3 % sequence similarity) and a distinct branch within the clade containing Pseudidiomarina taiwanensis PIT1(T) and Pseudidiomarina sediminum c121(T). Phenotypic characteristics could distinguish strain KYW314(T) from members of the genus Pseudidiomarina. On the basis of the data presented, strain KYW314(T) represents a novel species, for which the name Pseudidiomarina aestuarii sp. nov. is proposed. The type strain is KYW314(T) (=KCTC 22740(T) =JCM 16344(T)).

Description of Idiomarina insulisalsae sp. nov., isolated from the soil of a sea salt evaporation pond, proposal to transfer the species of the genus Pseudidiomarina to the genus Idiomarina and emended description of the genus Idiomarina

A halophilic, aerobic Gram-negative bacterium, designated strain CVS-6(T), was isolated from a sea salt evaporation pond on the Island of Sal in the Cape Verde Archipelago. Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation of the organism with members of the family Idiomarinaceae. Sequence similarities between CVS-6(T) and the type strains of the species of the genera Pseudidiomarina and Idiomarina ranged from 93.7% to 96.9%. The major isoprenoid quinone was ubiquinone 8 (Q-8). The major cellular fatty acids were 15:0 iso (21.8%), 17:0 iso (12.5%), 17:1 iso omega9c (10.7%), and 16:1 omega7c (10.6%). The DNA G+C content was 51.6 mol%. The species represented by strain CVS-6(T) could be distinguished from the species of the genera Pseudidiomarina and Idiomarina; however, it was not possible to distinguish both genera from each other using the phenotypic or chemotaxonomic characteristics examined. Consequently, we propose that the species classified in the genus Pseudidiomarina should be transferred to the genus Idiomarina. We also propose that, on the basis of physiological and biochemical characteristics, strain CVS-6(T) (=LMG 23123=CIP 108836) represents a new species which we name Idiomarina insulisalsae.

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.

Pseudidiomarina sediminum sp. nov., a marine bacterium isolated from coastal sediments of Luoyuan Bay in China

A strain of heterotrophic, facultatively anaerobic, marine bacterium, designated strain c121T, was isolated from coastal sediment of Luoyuan Bay, in Fujian province, PR China. Analysis of the 16S rRNA gene sequence revealed an affiliation with the genus Pseudidiomarina; the sequence similarity between c121T and Pseudidiomarina taiwanensis PIT1T was 97%. Cells of the novel strain were non-pigmented, Gram-negative rods, 0.3 microm wide and 1.2-1.8 microm long. Cells grown in broth cultures were non-motile, lacking flagella. Growth of the strain was observed at salinities ranging from 0.5 to 15 % NaCl, and the optimal concentration was about 1-8%. The temperature range for growth was rather broad and was high for a marine bacterium: the strain grew at 13-42 degrees C, showed good growth at 20-40 degrees C and had an optimum between 30 and 40 degrees C. The major cellular fatty acids were iso-C15:0 (24.2%), C16:1omega7c/iso-C15:0 2-OH (15.3%) and iso-C17:1omega9c (11.9%). The DNA G+C content was 50.0 mol%. Phylogeny based on 16S rRNA gene sequences, together with data from phenotypic and chemotaxonomic characterization, revealed that strain c121T could be classified within a novel species of the genus Pseudidiomarina, for which the name Pseudidiomarina sediminum sp. nov. is proposed, with the type strain c121T (=CICC 10319T=LMG 24046T).

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.

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 BD1T, was obtained from a seawater sample collected in the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. The cells of strain BD1T 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 °C, with an optimum at 30–35 °C. Strain BD1T 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 C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or C15 : 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 BD1T 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 BD1T was distinguishable from species of these genera by the presence of Q-9 and Q-10. Phenotypically, strain BD1T 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 BD1T (=BCRC 17491T=JCM 13378T).

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.