Hongiella mannitolivorans gen. nov., sp. nov., Hongiella halophila sp. nov. and Hongiella ornithinivorans sp. nov., isolated from tidal flat sediment

Algoriphagus algorifonticola sp. nov., a marine bacterium isolated from cold spring area of South China Sea

A Gram-stain-negative, aerobic, non-motile, short-rod-shaped bacterium, designated strain hg1T, was isolated from marine sediment within the cold spring area of South China Sea and subjected to a polyphasic taxonomic investigation. Colonies were circular and 1.0–2.0 mm in diameter, coral in colour, convex and smooth after growth on marine agar at 28 °C for 3 days. Strain hg1T was found to grow at 4–40 °C (optimum, 35–37 °C), at pH 6.5–9.0 (optimum, pH 7.5) and with 0–8 % (w/v) NaCl (optimum, 1.5–2 %). Chemotaxonomic analysis showed the sole respiratory quinone was MK-7, and the principal fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and iso-C16 : 0. The major polar lipids are phosphatidylethanolamine, an unidentified phospholipid and five unidentified glycolipids. The DNA G+C content of strain hg1T was 39.6 mol% based on the genome sequence. The comparison of 16S rRNA gene sequence similarities showed that hg1T was closely related to Algoriphagus ornithinivorans DSM 15282T (98.6 % sequence similarity), Algoriphagus zhangzhouensis MCCC 1F01099T (97.9 %) and Algoriphagus vanfongensis DSM 17529T (97.2 %); it exhibited 97.0 % or less sequence similarity to the type strains of other species of the genus Algoriphagus with validly published names. Phylogenetic trees reconstructed with the neighbour-joining, maximum-parsimony and maximum-likelihood methods based on 16S rRNA gene sequences showed that strain hg1T constituted a separate branch with A . ornithinivorans , A. zhangzhouensis , A. vanfongensis in a clade of the genus Algoriphagus . OrthoANI values between strain hg1T and A . ornithinivorans , A. zhangzhouensis and A. vanfongensis were 94.3, 74.1, 73.2 %, respectively, and in silico DNA–DNA hybridization values were 56.2, 18.5 and 18.3 %, respectively. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain hg1T is clearly distinct from recognized species of genus Algoriphagus . On the basis of these features, we propose that strain hg1T (=MCCC 1K03570T=KCTC 72111T) represents a novel species of the genus Algoriphagus with the name Algoriphagus algorifonticola sp. nov.

Algoriphagus pacificus sp. nov. and Algoriphagus oliviformis sp. nov., isolated from a mariculture fishpond

Two Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, non-flagellated, non-spore-forming and non-motile strains (YJ13C^T and H41^T) were isolated from a mariculture fishpond in PR China. Comparisons based on 16S rRNA gene sequences indicated that YJ13C^T and H41^T shared 16S rRNA gene sequences similarities between 92.6 and 99.2 % with species of the genus Algoriphagus. YJ13C^T only shared 93.8 % 16S rRNA gene sequence similarity with H41^T. The reconstructed phylogenetic and phylogenomic trees indicated that YJ13C^T and H41^T clustered closely with species of the genus Algoriphagus. The calculated pairwise orthologous average nucleotide identity with usearch (OrthoANIu) values between strains YJ13C^T and H41^T and other related strains were all less than 79.5 %. The OrthoANIu value between YJ13C^T and H41^T was only 69.9 %. MK-7 was the predominant respiratory quinone of YJ13C^T and H41^T and their major cellular fatty acids contained iso-C_15 : 0, C_16 : 1 ω7c and C_17 : 1 ω9c. The polar lipids profiles of YJ13C^T and H41^T consisted of phosphatidylethanolamine and several kinds of unidentified lipids. Combining the above descriptions, strains YJ13C^T and H41^T represent two distinct novel species of the genus Algoriphagus, for which the names Algoriphagus pacificus sp. nov. (type strain YJ13C^T=GDMCC 1.2178^T=KCTC 82450^T) and Algoriphagus oliviformis sp. nov. (type strain H41^T=GDMCC 1.2179^T=KCTC 82451^T) are proposed.

Aequorivita lutea sp. nov., a novel bacterium isolated from the estuarine sediment of the Pearl River in China, and transfer of Vitellibacter todarodis and Vitellibacter aquimaris to the genus Aequorivita as Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov

A Gram-negative, aerobic, rod-shaped, non-motile by gliding bacterium was isolated from the estuarine sediment of the Pearl River in PR China and designated as strain q18^T. Colonies were circular, smooth and yellow on marine agar after 48 h cultivation. Salinity, temperature and pH for optimal growth were 5 % (NaCl), 30 °C and 7, respectively. The 16S rRNA gene sequence of the strain q18^T showed the highest similarity of 97.3 % to the type strain of Aequorivita echinoideorum CC-CZW007^T. 16S rRNA gene-based phylogenetic analysis indicated that strain q18^T grouped into the genus Aequorivita in the family Flavobacteriaceae of the phylum Bacteroidetes, and was distinct from all known species in the genus. Menaquinone (MK-6) was the main respiratory quinone detected in strain q18^T. The major fatty acids were iso-C_15 : 0 and iso-C_17 : 0 3-OH. The polar lipids of strain q18^T mainly comprised phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and one unidentified polar lipid. The G+C content of the genome was ~42.8 mol%. The draft genome size of strain q18^T was 3.3 Mbp. The average nucleotide identity values were around 79.0 % between strain q18^T and reference Aequorivita strains. Based on the polyphasic analysis, strain q18^T was confirmed to represent a novel species of the genus Aequorivita, for which the name Aequorivita lutea sp. nov., is proposed. The type strain is q18^T (=CICC 24821^T=KCTC 72764 ^T). Further, based on the results of phylogenetic, chemotaxonomic and phenotypic analyses, two species previously classified into the genus Vitellibacter, Vitellibacter todarodis Kim et al. 2018 and Vitellibacter aquimaris Thevarajoo et al. 2016, are transferred to the genus Aequorivita as Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov. respectively.

Algoriphagus kandeliae sp. nov., isolated from mangrove rhizosphere soil

Strain XY-J91^T, a Gram-stain-negative, reddish orange, non-spore-forming and short-rod-shaped marine bacterium, was isolated from rhizosphere soil of the mangrove plant Kandelia candel (L.) Druce in Mai Po Nature Reserve, Hong Kong. The strain showed growth at 15-50 °C (optimum 40 °C), at pH 5.5-9.5 (optimum 7.0-8.0) and with 0-8 % (w/v) NaCl (optimum 1-2 %). The only respiratory quinone was MK-7 and the major fatty acids were iso-C_15 : 0 and iso-C_17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified phospholipid. The G+C content of strain XY-J91^T was 40.4 mol%. Strain XY-J91^T exhibited highest 16S rRNA gene sequence similarities to the type strains of Algoriphagus marincola SW-2^T (96.66 %), Algoriphagus taiwanensis CC-PR-82^T (96.21%), Algoriphagus ornithinivorans JC2052^T (96.16%), Algoriphagus confluentis HJM-2^T (95.73%) and Algoriphagus zhangzhouensis 12C11^T (95.52 %). Based on the phylogenetic, phenotypic and chemotaxonomic evidence presented, strain XY-J91^T represents a novel species of the genus Algoriphagus, for which the name Algoriphagus kandeliae sp. nov. is proposed. The type strain is XY-J91^T (=MCCC 1K03612^T=KCTC 72216^T).

Algoriphagus aquimaris sp. nov., isolated from seashore sand

Strain F21^T, a marine, aerobic, Gram-negative, rod-shaped bacterium, was isolated from seashore sand sampled in Pohang, Republic of Korea. Cells of strain F21^T were non-motile, catalase-positive, oxidase-positive, non-spore-forming and formed pinkish-red colonies on marine agar. The strain grew optimally at 37°C, pH 7 and in the presence of 2-3 % NaCl (w/v). Analysis of the 16S rRNA gene sequence of strain F21^T revealed that it belonged to the genus Algoriphagus, family Cyclobacteriaceae, with similarity values of 98.1 and 96.8 % to Algoriphagus marincola DSM 16067^T and Algoriphagus ornithinivorans IMSNU 14014^T, respectively. When comparing the genome sequence of F21 ^T with those of the type strains of six species of the genus Algoriphagus, the values obtained were below the thresholds for analyses of average nucleotide identity (71.8-92.7 %) and in silico DNA-DNA hybridization using the Genome-to-Genome Distance Calculator (14.7-75.2 %). The DNA G+C content of strain F21^T was 42.0 mol%. The chemotaxonomic characteristics of F21^T included MK-7 as the predominant isoprenoid quinone, iso-C_15 : 0, iso-C_17 : 0 3-OH and summed feature 3 (C_16 : 1ω6c and/or C_16 : 1ω7c) as major cellular fatty acids, and phosphatidylcholine and phosphatidylethanolamine as major polar lipids. On the basis of phenotypic and chemotaxonomic properties, phylogenetic distinctiveness, and genomic data, we named strain F21^T as Algoriphagus aquimaris sp. nov. and proposed that strain F21^T (=KEMB 2250-007^T= KCTC 72106^T=JCM 33187^T) in the genus Algoriphagus represents a novel species.

Algoriphagus sanaruensis sp. nov., a member of the family Cyclobacteriaceae, isolated from a brackish lake in Hamamatsu, Japan

Strain M8-2^T, which was isolated from brackish lake water (Lake Sanaru) in Japan, was characterized for representation of a novel species in the genus Algoriphagus. Cells of strain M8-2^T were aerobic, Gram-stain-negative and curved-rod-shaped (0.2-0.5 µm wide and 0.7-1.9 µm long). Strain M8-2^T grew optimally at 30 °C, pH 6.5-7.5 and in the presence of 0.5-1.0 % (w/v) NaCl. MK-7 was the sole isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, an unidentified phospholipid and an unidentified polar lipid. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain M8-2^T belonged to the genus Algoriphagus and was closely related to Algoriphagus aquatilis A8-7^T, Algoriphagus boseongensis BS-R1^T, Algoriphagus aquaeductus T4^T, Algoriphagus olei CC-Hsuan-617^T, Algoriphagusshivajiensis NIO-S3^T and Algoriphagus mannitolivorans DSM 15301^T with sequence similarities of 96.6-97.4 %. Results of average nucleotide identity (<75 %) and digital DNA-DNA hybridization (<19 %) studies showed that M8-2^T was distinct from its phylogenetic relatives. Based on the results of tests for acid production, the predominant cellular fatty acid composition, the DNA G+C content and phylogenetic position, a novel species in the genus Algoriphagus, with the name Algoriphagussanaruensis sp. nov., is proposed for strain M8-2^T (=JCM 31446^T=LMG 29969^T).

Cultivation of activated sludge using sea mud as seed to treat industrial phenolic wastewater with high salinity

A technique is proposed to treat saline hazardous wastewater by using marine activated sludge, cultivated with sea mud as seed. Since the developed marine activated sludge had phenol-tolerant microorganisms (MAS-1, MAS-2 and MAS-3) which originated from the ocean, it was envisaged that these bacteria could survive and breakdown phenol in saline environments. In this work, typical phenol-tolerant microorganisms were isolated from the marine activated sludge and identified. After a hierarchical acclimation process, the marine activated sludge was used to treat the industrial phenolic wastewater with high salinity. The marine activated sludge was able to break down phenol and other organic components effectively and efficiently in treating the wastewater with salinity of 5.7% w/v. The results showed a high removal of phenol (99%), COD (80%) and NH₃-N (68%).

Effect of bioflocculation on fouling-related biofoulants in a membrane bioreactor during saline wastewater treatments

A membrane bioreactor (MBR) was operated in two modes; with and without the inoculation of marine Arthrobacter cells, to investigate the effect of bioflocculation on membrane biofouling during saline wastewater treatments. The MBR-Arthrobacter system showed a higher resistance to membrane fouling than the normal MBR system. Lower concentrations of the fouling-related components and higher removal efficiencies of COD and NH₃-N were observed in the MBR-Arthrobacter system. The bioflocculation of Arthrobacter preferred to settle down the humic acid-like, fulvic acid-like and aromatic proteins components (larger biomolecules) rather than the soluble microbial by-product-like components (smaller biomolecules).

Carboxylicivirga flava sp. nov., isolated from marine surface sediment

A novel bacterial strain, designated Q15T, was isolated from sediments obtained from the Bohai Sea in China and subjected to a polyphasic taxonomic study. Cells of strain Q15T were Gram-stain-negative, strictly aerobic rods that produced circular, flat, orange colonies. Phylogenetic analysis based on 16S rRNA gene sequences revealed that Q15T was affiliated with the genus Carboxylicivirga in the family Marinilabiliaceae of the phylum Bacteroidetes. Strain Q15T differed genotypically from the type strains of the three recognized species of this genus (Carboxylicivirga taeanensis MEBiC 08903T, Carboxylicivirga mesophila MEBiC 07026T and Carboxylicivirga linearis FB218T) and shared 94.0-95.2 % 16S rRNA gene sequence similarity with them. The DNA G+C content of strain Q15T was 44.7 mol%. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH, and menaquinone MK-7 was the main respiratory quinone. Polar lipids contained phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid and other unknown lipids. Based on the data from the current polyphasic analysis, a novel species, Carboxylicivirga flava sp. nov., is hereby proposed with Q15T (=CICC 23923T=KCTC 42707T) as the type strain.

Biodegradation of saline phenolic wastewater in a biological contact oxidation reactor with immobilized cells of Oceanimonas sp

OBJECTIVE

To develop a method to treat saline phenolic wastewater in a biological contact oxidation reactor (BCOR) with immobilized cells of a marine microorganism, Oceanimonas sp., isolated from seawater.

RESULTS

Cells were immobilized on fibre carriers in the BCOR. Saline wastewater with phenol at 1.5 g/l and NaCl at 6 % (w/v) was treated. In continuous assays, 99 % removal of phenol was achieved and a kinetic model for the phenol degradation is presented based on Monod's equation.

CONCLUSION

The BOCR system using immobilized cells of Oceanimonas efficiently treats saline phenolic wastewaters without having decrease the salinity of the wastewater.

Permianibacter aggregans gen. nov., sp. nov., a bacterium of the family Pseudomonadaceae capable of aggregating potential biofuel-producing microalgae

A novel bacterial strain, capable of aggregating potential biofuel-producing microalgae, was isolated from the phycosphere of an algal culture and designated HW001T. The novel bacterial strain was identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics in this study. Cells were aerobic, Gram-negative rods. 16S rRNA gene-based phylogenetic analysis revealed that strain HW001T is affiliated with the family Pseudomonadaceae in the phylum Proteobacteria , but forms a distinct clade within this family. The DNA G+C content of strain HW001T was 55.4 mol%. The predominant cellular fatty acids were iso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c), C16 : 0 and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). Q-8 was the main respiratory quinone. The polar lipid profile contained phosphatidylethanolamine, an unidentified aminophospholipid and some unidentified lipids. Based on the extensive polyphasic analysis, strain HW001T represents a novel species of a new genus in the family Pseudomonadaceae , for which the name Permianibacter aggregans gen. nov., sp. nov., is proposed. The type strain of the type species is HW001T ( = CICC 10856T = KCTC 32485T).

Imperialibacter roseus gen. nov., sp. nov., a novel bacterium of the family Flammeovirgaceae isolated from Permian groundwater

A novel bacterial strain, designated P4T, was isolated from Permian groundwater and identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics. Cells were aerobic, Gram-stain-negative rods. 16S rRNA gene sequence-based phylogenetic analysis revealed that P4T is affiliated with the family Flammeovirgaceae in the phylum Bacteroidetes , but forms a distinct cluster within this family. The DNA G+C content of strain P4T was 45.2 mol%. The predominant cellular fatty acids were C16 : 1ω6c/C16 : 1ω7c and iso-C15 : 0. MK-7 was the main respiratory quinone. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid, unidentified glycolipids and unidentified polar lipids. Based on our extensive polyphasic analysis, a novel species in a new genus, Imperialibacter roseus gen. nov., sp. nov., is proposed. The type strain of Imperialibacter roseus is P4T ( = CICC 10659T = KCTC 32399T).

Algoriphagus zhangzhouensis sp. nov., isolated from mangrove sediment

A Gram-negative, short-rod-shaped and non-motile bacterium, strain 12C11T, was isolated from an oil-degrading consortium, enriched from the Fugong mangrove sediment, Fujian Province of China. Optimum growth was observed at 25 °C, at pH 7.5 and with 4 % (w/v) NaCl. Comparative 16S rRNA gene sequence analysis demonstrated that it shared highest similarity with members of the genus Algoriphagus (97.5–93.4 %), exhibiting 97.5 % sequence similarity to Algoriphagus ornithinivorans IMSNU 14014T, followed by Algoriphagus vanfongensis KMM 6241T (97.2 %); it shared <96.0 % sequence similarity with other members of the genus. Levels of nucleotide sequence similarity between gyrB (DNA gyrase subunit B) genes of strain 12C11T and A. vanfongensis KMM 6241T, A. ornithinivorans IMSNU 14014T, Algoriphagus marincola SW-2T and Algoriphagus hitonicola 7-UAHT were 78.8, 78.6, 75.6 and 77.4 %, respectively. Phylogenetic trees based on these housekeeping genes showed that strain 12C11T and other Algoriphagus strains formed a distinct lineage. The dominant fatty acids were iso-C15 : 0 (32.1 %), C16 : 1ω7c/C16 : 1ω6c (11.6 %), iso-C17 : 1 I/anteiso-C17 : 1 B (10.1 %), iso-C17 : 0 3-OH (9.2 %) and iso-C17 : 1ω9c/C16 : 0 10-methyl (7.1 %), which accounted for 70.0 % of the total fatty acids. DNA–DNA hybridization showed that strain 12C11T shared low DNA–DNA relatedness with A. vanfongensis KMM 6241T and A. ornithinivorans IMSNU 14014T (30.7±0.9 and 30.5±1.8 %, respectively). The G+C content of the chromosomal DNA of strain 12C11T was 38.4 mol%. The major respiratory quinones were MK-7 (96.0 %) and MK-6 (4.0 %). According to its morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, the novel strain most appropriately belongs to the genus Algoriphagus , but can readily be distinguished from known Algoriphagus species. The name Algoriphagus zhangzhouensis sp. nov. is proposed (type strain 12C11T = CGMCC 1.11027T = MCCC 1F01099T = DSM 25035T).

Algoriphagus chungangensis sp. nov., isolated from a tidal flat sediment

A Gram-stain-negative, non-spore-forming, non-motile, strictly aerobic, rod-shaped bacterial strain, designated CAU 1002T, was isolated from a tidal flat sediment and its taxonomic position was investigated using a polyphasic approach. Strain CAU 1002T grew optimally at 30 °C and pH 7.5. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1002T formed a distinct lineage within the genus Algoriphagus and was most closely related to Algoriphagus lutimaris KCTC 22630T and Algoriphagus halophilus KCTC 12051T (97.75 and 97.74 % 16S rRNA gene sequence similarity, respectively). The strain contained MK-7 as the major isoprenoid quinone and iso-C15 : 0 and C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3) as the major fatty acids. The cell-wall peptidoglycan of strain CAU 1002T contained meso-diaminopimelic acids. The major whole-cell sugars were glucose, arabinose, sucrose, and ribose. The polar lipid profile was composed of phosphatidylethanolamine, five unidentified aminolipids, one unidentified aminophospholipid, one unidentified phospholipid, one unidentified aminoglycolipid, one unidentified glycolipid and twelve unidentified lipids. The DNA G+C content of strain CAU 1002T was 38.0 mol%. On the basis of phylogenetic inference, phenotypic, chemotaxonomic and genotypic data, strain CAU 1002T should be classified into the genus Algoriphagus as a member of a novel species, for which the name Algoriphagus chungangensis sp. nov. is proposed. The type strain is CAU 1002T ( = KCTC 23759T = CCUG 61890T). The description of the genus Algoriphagus is emended.

Algoriphagus shivajiensis sp. nov., isolated from Cochin back water, India

Novel orange-pigmented, Gram-negative, rod-shaped, non-motile bacteria, designated strains NIO-S3(T) and NIO-S4, were isolated from a water sample collected from Cochin back waters, Thanneermukkom and Arookutty, Kerala, India. Both strains were positive for oxidase and catalase activities, and hydrolyzed gelatin and Tween 40. The predominant fatty acids were iso-C15:0, anteiso-C15:0, iso-C17:0 3OH, C16:1ω7c/C16:1ω6c (summed feature 3) and iso-C17:1ω9c/C16:0 10-methyl (summed feature 9), whereas MK-7 was the major respiratory quinone, and phosphatidylethanolamine, two unidentified phospholipids and one unidentified lipid were the only polar lipids. The DNA G+C content of the two strains was 43.7 and 43.6mol%, respectively. The 16S rRNA gene sequence analysis indicated that they were members of the genus Algoriphagus and closely related to Algoriphagus olei CC-Hsuan-617(T), Algoriphagus aquatilis A8-7(T), Algoriphagus aquaeductus LMG 24398(T) and Algoriphagus mannitolivorans DSM 15301(T), with pairwise sequence similarities of 96.8, 96.6, 96.2 and 96.2%, respectively. DNA-DNA hybridization between strains NIO-S3(T) and NIO-S4 showed a relatedness of 89%. Based on data from the current polyphasic study, the strains are proposed as a novel species of the genus Algoriphagus, for which the name Algoriphagus shivajiensis sp. nov. is proposed. The type strain of A. shivajiensis is NIO-S3(T) (=JCM 17885(T)=MTCC 11066(T)).

A bacterial sulfonolipid triggers multicellular development in the closest living relatives of animals

Bacterially-produced small molecules exert profound influences on animal health, morphogenesis, and evolution through poorly understood mechanisms. In one of the closest living relatives of animals, the choanoflagellate Salpingoeca rosetta, we find that rosette colony development is induced by the prey bacterium Algoriphagus machipongonensis and its close relatives in the Bacteroidetes phylum. Here we show that a rosette inducing factor (RIF-1) produced by A. machipongonensis belongs to the small class of sulfonolipids, obscure relatives of the better known sphingolipids that play important roles in signal transmission in plants, animals, and fungi. RIF-1 has extraordinary potency (femtomolar, or 10⁻¹⁵ M) and S. rosetta can respond to it over a broad dynamic range—nine orders of magnitude. This study provides a prototypical example of bacterial sulfonolipids triggering eukaryotic morphogenesis and suggests molecular mechanisms through which bacteria may have contributed to the evolution of animals.

DOI:http://dx.doi.org/10.7554/eLife.00013.001

All animals, including humans, evolved in a world filled with bacteria. Although bacteria are most familiar as pathogens, some bacteria produce small molecules that are essential for the biology of animals and other eukaryotes, although the details of the ways in which these bacterial molecules are beneficial are not well understood.

The choanoflagellates are water-dwelling organisms that use their whip-like flagella to move around, feeding on bacteria. They can exist as one cell or a colony of multiple cells and, perhaps surprisingly, are the closest known living relatives of animals. This means that experiments on these organisms have the potential to improve our understanding of animal development and the transition from egg to embryo to adult.

Alegado et al. have explored how the morphology of Salpingoeca rosetta, a colony-forming choanoflagellate, is influenced by its interactions with various species of bacteria. In particular, they find that the development of multicellularity in S. rosetta is triggered by the presence of the bacterium Algoriphagus machipongonensis as well as its close relatives. They also identify the signaling molecule produced by the bacteria to be C₃₂H₆₄NO₇S; this lipid molecule is an obscure relative of the sphingolipid molecules that have important roles in signal transmission in animals, plants, and fungi. Moreover, Alegado et al. show that S. rosetta can respond to this molecule – which they call rosette-inducing factor (RIF-1) – over a wide range of concentrations, including concentrations as low as 10⁻¹⁷ M.

The work of Alegado et al. suggests that interactions between S. rosetta and Algoriphagus bacteria could be a productive model system for studying the influences of bacteria on animal cell biology, and for investigating the mechanisms of signal delivery and reception. Moreover, the molecular mechanisms revealed by this work leave open the possibility that bacteria might have contributed to the evolution of multicellularity in animals.

DOI:http://dx.doi.org/10.7554/eLife.00013.002

Cecembia lonarensis gen. nov., sp. nov., a haloalkalitolerant bacterium of the family Cyclobacteriaceae , isolated from a haloalkaline lake and emended descriptions of the genera Indibacter , Nitritalea and Belliella

A novel Gram-staining-negative, rod-shaped, non-motile bacterium, designated strain LW9T, was isolated from a water sample collected from Lonar Lake of Buldhana district, Maharashtra, India. Colonies and broth cultures were reddish orange due to the presence of carotenoid pigments. Strain LW9T was positive for catalase, ornithine decarboxylase and lysine decarboxylase activities and negative for gelatinase, oxidase, urease and lipase activities. The predominant fatty acids were iso-C15 : 0 (31.3 %), iso-C16 : 0 (9.3 %), anteiso-C15 : 0 (7.3 %), iso-C16 : 1 H (6.1 %), summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c; 5.9 %), iso-C17 : 1ω9c (5.4 %) and iso-C17 : 0 3-OH (5.0 %). Strain LW9T contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids and seven unidentified lipids. The DNA G+C content of strain LW9T was 40.5 mol%. 16S rRNA gene sequence analysis indicated that the type strains of Indibacter alkaliphilus and Aquiflexum balticum , two members of the family Cyclobacteriaceae (phylum ‘ Bacteroidetes ’) were the most closely related strains with sequence similarities of 93.0 and 94.0 %, respectively. Other members of the family Cyclobacteriaceae showed sequence similarities <93.0 %. Based on these phenotypic characteristics and on phylogenetic inference, strain LW9T is proposed as the representative of novel species in a new genus, Cecembia lonarensis gen. nov., sp. nov. The type strain of the type species, Cecembia lonarensis, is LW9T ( = CCUG 58316T = KCTC 22772T). Emended descriptions of the genera Indibacter , Nitritalea and Belliella are also proposed.

Alkalibacillus huanghaiensis Sp. Nov., a New Strain of Moderately Halophilic Bacterias Isolated from Sea Water of the Yellow Sea in China

A Gram-positive, strictly aerobic and moderately halophilic bacterial strain HSD was obtained from the sea water sample collected from International Sea Water Bathing Place in Weihai, a city on the shore of the Yellow Sea. Strain HSD was bacillus. The optimum growth temperature was 32~37°C and the optimum pH was 6.0~9.0. It could grow well at 100 g•L-1 salt mass concentration. The G+C mole fraction of its genomic DNA was 37.5%. 16S rRNA gene sequence indicated a close relationship to Alkalibacillus halophilus (DQ359731) with similarity of 99%. However, they had obvious difference in whole-cell main fatty acid components, cell size, cell morphology, motility, oxidase, gelatine liquefication, nitrate reduction, NaCl tolerance range, pH tolerance range, G+C mole fraction, sole carbon source, sole nitrogen source, antibiotic sensitivity and a source of the strain isolation. Comparing of these taxonomic characters of strain HSD with those of other type strains of the genus Alkalibacillus, the differences were more obvious. In view of multiple identification results, it was proposed that strain HSD was classified as the type strain of a new species of the genus Alkalibacillus under the name Alkalibacillus huanghaiensis sp.nov..

Algoriphagus namhaensis sp. nov., isolated from seawater

A Gram-staining-negative, non-motile, non-spore-forming bacterial strain, DPG-3T, was isolated from seawater from the South Sea in Korea, and its taxonomic position was investigated using a polyphasic approach. Strain DPG-3T grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. In a neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain DPG-3T fell within a clade comprising Algoriphagus species and appeared most closely related to Algoriphagus halophilus JC 2051T (96.1 %16S rRNA gene sequence similarity) and Algoriphagus lutimaris S1-3T (96.4 %). The type strains of other Algoriphagus species showed 16S rRNA gene sequence similarities of 92.9–96.0 % with strain DPG-3T. The predominant menaquinone of strain DPG-3T was MK-7. The major fatty acids were iso-C15 : 0 and iso-C15 : 0 2-OH and/or C16 : 1ω7c (summed feature 3). The major polar lipids detected in strain DPG-3T were phosphatidylcholine, phosphatidylethanolamine and an unidentified lipid. The genomic DNA G+C content was 44.8 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DPG-3T is considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus namhaensis sp. nov. is proposed. The type strain is DPG-3T ( = KCTC 23419T = CCUG 60523T).

Algoriphagus aquaeductus sp. nov., isolated from a freshwater pipe

A Gram-staining-negative, aerobic to microaerophilic, rod-shaped, red-coloured bacterium, strain T4T, was isolated from a freshwater pipe on Tenerife island. A polyphasic taxonomic study was performed in order to characterize the strain in detail. The isolate is surrounded by a slime capsule, occurs singly, in the form of short chains, or in aggregates, and exhibits catalase and oxidase activities. Growth was observed at 15–42 °C. Optimum growth occurred at pH 8 with mono- and disaccharides, followed by polysaccharides and deoxysaccharides, but the bacterium utilized only a restricted spectrum of alcohols, alditols, amides, amines, carboxylic acids and amino acids. Strain T4T tolerated concentrations of 0–4 % (w/v) NaCl and contained MK-7 as predominant isoprenoid quinone as well as carotenoids, but lacked pigments of the flexirubin type. The predominant fatty acids were iso-C15 : 0 (32.2 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 22.5 %), and iso-C17 : 0 3-OH (7.9 %). Major polar lipids were phosphatidylethanolamine, phospholipids, aminophospholipids and other lipids of unknown character. The DNA G+C content was approximately 41.8 mol%. The sequence of the 16S-rRNA gene assigned strain T4T to the CFB group, forming a coherent cluster with species of the genus Algoriphagus with the highest similarity of 98.8 % to Algoriphagus aquatilis A8-7T. DNA–DNA hybridization revealed 37.5 % relatedness to strain A8-7T. Based on morphological, physiological and molecular properties as well as on phylogenetic distinctiveness, strain T4T should be placed into the genus Algoriphagus as a novel species, for which the name Algoriphagus aquaeductus sp. nov. (type strain T4T  = DSM 19759T  = LMG 24398T  = NCIMB 14399T) is proposed.

Algoriphagus machipongonensis sp. nov., co-isolated with a colonial choanoflagellate

A Gram-negative, non-motile, non-spore-forming bacterial strain, PR1(T), was isolated from a mud core sample containing colonial choanoflagellates near Hog Island, Virginia, USA. Strain PR1(T) grew optimally at 30 °C and with 3 % (w/v) NaCl. Strain PR1(T) contained MK-7 as the major menaquinone as well as carotenoids but lacked pigments of the flexirubin-type. The predominant fatty acids were iso-C(15 : 0) (29.4 %), iso-C(17 : 1)ω9c (18.5 %) and summed feature 3 (C(16 : 1)ω6c and/or C(16 : 1)ω7c; 11.3 %). The major polar lipids detected in strain PR1(T) were phosphatidylethanolamine, an unknown phospholipid, an aminophospholipid, an aminolipid and two lipids of unknown character. The DNA G+C content was 38.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PR1(T) fell within the cluster comprising the genus Algoriphagus and was most closely related to Algoriphagus halophilus JC 2051(T) (95.4 % sequence similarity) and Algoriphagus lutimaris S1-3(T) (95.3 % sequence similarity). The 16S rRNA gene sequence similarity between strain PR1(T) and the type strains of other species of the genus Algoriphagus were in the range 91-95 %. Differential phenotypic properties and phylogenetic and genetic distinctiveness of strain PR1(T) demonstrated that this strain was distinct from other members of the genus Algoriphagus, including its closest relative, A. halophilus. Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strain PR1(T) should be placed in the genus Algoriphagus as a representative of a novel species, for which the name Algoriphagus machipongonensis sp. nov. is proposed. The type strain is PR1(T) (= ATCC BAA-2233(T) = DSM 24695(T)).

Algoriphagus jejuensis sp. nov., isolated from seawater

A Gram-negative, pink-pigmented, non-motile, strictly aerobic rod, designated CNU040T, was isolated from seawater from the coast of Jeju Island in Korea. The temperature, pH and NaCl ranges for growth were 4–30 °C, pH 5.5–10.0 and 0–5.0 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CNU040T belonged to a distinct lineage in the genus Algoriphagus and exhibited high sequence similarity with Algoriphagus terrigena DS-44T (98.3 %) and Algoriphagus alkaliphilus AC-74T (96.6 %) and lower sequence similarity (<96.0 %) with all other members of the genus Algoriphagus. DNA–DNA relatedness between strain CNU040T and A. terrigena KCTC 12545T was 44.5 %. The DNA G+C content of the isolate was 48.5 mol% and the major respiratory quinone was menaquinone-7. The major cellular fatty acids were iso-C15 : 0 (28.6 %) and summed feature 3 (consisting of iso-C15 : 0 2-OH and/or C16 : 1ω7c; 24.0 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, one unknown amino lipid, one unknown aminophospholipid and three unknown polar lipids. On the basis of phenotypic, phylogenetic and genotypic data, strain CNU040T represents a novel species within the genus Algoriphagus, for which the name Algoriphagus jejuensis sp. nov. is proposed. The type strain is CNU040T ( = KCTC 22647T  = JCM 16112T).

Algoriphagus faecimaris sp. nov., isolated from coastal sediment

A Gram-negative, non-motile, non-sporulating bacterial strain, designated LYX05(T), was isolated from coastal sediment of Qingdao, China, on the coast of the Yellow Sea. Strain LYX05(T) was aerobic and heterotrophic. The strain grew optimally at 37 °C and pH 7.5 and in the presence of 2% (w/v) NaCl. Colonies were 1-2 mm in diameter, circular, reddish orange and shiny with entire edges on marine agar medium. Cells were rods (0.3-0.5 µm wide and 0.8-1.6 µm long). The dominant fatty acids were iso-C(15:0) (40.82%) and C(16:0) (10.45%). The DNA G+C content was 42.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LYX05(T) was phylogenetically related to the members of the genus Algoriphagus and the closest relative was Algoriphagus hitonicola 7-UAH(T) (95.8% 16S rRNA gene sequence similarity). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain LYX05(T) was considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus faecimaris sp. nov. is proposed. The type strain is LYX05(T) (=JCM 16561(T) =DSM 23095(T) =LMG 25474(T)).

Marinobacterium lutimaris sp. nov., isolated from a tidal flat

A Gram-staining-negative, moderately halophilic bacterium, designated strain AN9T, was isolated from a tidal flat of the Taean coast in South Korea. Cells were catalase- and oxidase-positive short rods that were motile by means of a single polar flagellum. Growth of strain AN9T was observed at 15–40 °C (optimum, 25–30 °C) and at pH 6.0–8.0 (optimum, pH 6.5–7.5). Strain AN9T contained ubiquinone Q-8 as the predominant isoprenoid quinone and C10 : 0 3-OH (31.7 %), C18 : 1 ω7c (24.8 %), C16 : 0 (14.7 %) and summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH, 10.72 %) as the major fatty acids. The G+C content of the genomic DNA of strain AN9T was 58 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AN9T was related to members of the genus Marinobacterium and was related most closely to Marinobacterium litorale IMCC1877T (96.8 % similarity). On the basis of chemotaxonomic and molecular data, strain AN9T is considered to represent a novel species of the genus Marinobacterium, for which the name Marinobacterium lutimaris sp. nov. is proposed. The type strain is AN9T (=KACC 13703T =DSM 22012T).

Algoriphagus lutimaris sp. nov., isolated from a tidal flat sediment

A Gram-negative, non-motile, non-spore-forming bacterial strain, S1-3T, was isolated from a tidal flat sediment on the west coast of Korea and its taxonomic position was investigated. Strain S1-3T grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. Strain S1-3T contained MK-7 as the predominant menaquinone and C16 : 1 ω7c and/or iso-C15 : 0 2-OH and iso-C15 : 0 as the major fatty acids. The DNA G+C content was 41.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain S1-3T fell within the clade comprising Algoriphagus species, clustering with Algoriphagus halophilus IMSNU 14013T, with which it exhibited 99.6 % 16S rRNA gene sequence similarity. The 16S rRNA gene sequence similarity between strain S1-3T and the type strains of other Algoriphagus species was 94.0–97.1 %. Differential phenotypic properties and phylogenetic and genetic distinctiveness of strain S1-3T demonstrated that this strain is distinguishable from the other Algoriphagus species as well as A. halophilus. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strain S1-3T is considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus lutimaris sp. nov. is proposed. The type strain is S1-3T (=KCTC 22630T =CCUG 57608T).

Identification and characterization of metagenomic fragments from tidal flat sediment

Phylogenetic surveys based on cultivation-independent methods have revealed that tidal flat sediments are environments with extensive microbial diversity. Since most of prokaryotes in nature cannot be easily cultivated under general laboratory conditions, our knowledge on prokaryotic dwellers in tidal flat sediment is mainly based on the analysis of metagenomes. Microbial community analysis based on the 16S rRNA gene and other phylogenetic markers has been widely used to provide important information on the role of microorganisms, but it is basically an indirect means, compared with direct sequencing of metagenomic DNAs. In this study, we applied a sequence-based metagenomic approach to characterize uncultivated prokaryotes from tidal flat sediment. Two large-insert genomic libraries based on fosmid were constructed from tidal flat metagenomic DNA. A survey based on end-sequencing of selected fosmid clones resulted in the identification of clones containing 274 bacterial and 16 archaeal homologs in which majority were of proteobacterial origins. Two fosmid clones containing large metagenomic DNAs were completely sequenced using the shotgun method. Both DNA inserts contained more than 20 genes encoding putative proteins which implied their ecological roles in tidal flat sediment. Phylogenetic analyses of evolutionary conserved proteins indicate that these clones are not closely related to known prokaryotes whose genome sequence is known, and genes in tidal flat may be subjected to extensive lateral gene transfer, notably between domains Bacteria and Archaea. This is the first report demonstrating that direct sequencing of metagenomic gene library is useful in underpinning the genetic makeup and functional roles of prokaryotes in tidal flat sediments.

Proposal of Algoriphagus vanfongensis sp. nov., transfer of members of the genera Hongiella Yi and Chun 2004 emend. Nedashkovskaya et al. 2004 and Chimaereicella Tiago et al. 2006 to the genus Algoriphagus, and emended description of the genus Algoriphagus Bowman et al. 2003 emend. Nedashkovskaya et al. 2004

A taxonomic study of a novel marine, heterotrophic, non-gliding, halotolerant and light-pink-pigmented bacterium was carried out using a polyphasic approach. 16S rRNA gene sequence analysis revealed that strain KMM 6241T is a member of the phylum Bacteroidetes. Strain KMM 6241T formed a cluster with the genera Algoriphagus, Chimaereicella and Hongiella with sequence similarities of 94.0–98.2 %. Hongiella ornithinivorans was the closest relative of the novel isolate. Comparative analysis of phenotypic, chemotaxonomic and genotypic characteristics of strain KMM 6241T and representatives of the genera Algoriphagus, Chimaereicella and Hongiella revealed many similar features. Consequently, phylogenetic evidence supported by phenotypic and genotypic similarities support the transfer of members of the genera Chimaereicella and Hongiella to the genus Algoriphagus and the establishment of a novel species, Algoriphagus vanfongensis sp. nov., with strain KMM 6241T (=DSM 17529T=KCTC 12716T) as the type strain.

Pontibacter akesuensis sp. nov., isolated from a desert soil in China

A Gram-negative, non-motile, rod-shaped bacterium, designated strain AKS 1T, was isolated from a desert soil sample collected from Akesu, XinJiang Province, China. A taxonomic study, including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, was performed on the novel isolate. The predominant menaquinone of strain AKS 1T was MK-7. The major fatty acids included i-C15 : 0, ai-C17 : 1 B/i-C17 : 1 I and i-C17 : 0 3-OH. The G+C content of the DNA was 51.4 mol%. Based on the results of phenotypic and genotypic characteristics, strain AKS 1T should be assigned as representing a novel species of the genus Pontibacter, for which the name Pontibacter akesuensis is proposed. The type strain is AKS 1T (=KCTC 12758T=CCTCC AB 206086T).

Marinobacterium halophilum sp. nov., a marine bacterium isolated from the Yellow Sea

A moderately halophilic, aerobic, Gram-negative bacterium was isolated from a tidal flat area of Dae-Chun, Chung-Nam, Korea. The strain, designated mano11T, comprised rod-shaped cells that were motile by means of polar flagella. It grew with 3–12 % NaCl and at 4–37 °C and pH 5.3–9.3. The predominant menaquinone present in this strain was MK-7 and diaminopimelic acid was not found in the cell-wall peptidoglycan. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain mano11T belongs to the genus Marinobacterium. Strain mano11T exhibited 92.8–98.3 % 16S rRNA gene sequence similarity when compared with the type strains of three other species of the genus Marinobacterium. DNA–DNA hybridization between strain mano11T and Marinobacterium georgiense DSM 11526T, its closest relative in terms of 16S rRNA gene sequence similarity, was 13 %. On the basis of the phenotypic, genetic and phylogenetic data, strain mano11T represents a novel species of the genus Marinobacterium, for which the name Marinobacterium halophilum sp. nov. is proposed. The type strain is mano11T (=KCTC 12240T=DSM 17586T).

Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family "Flexibacteraceae"

A Gram-negative bacterial isolate (designated SRC-1(T)) was isolated from an occasional drainage system and characterized by a polyphasic approach to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain SRC-1(T) with the family "Flexibacteraceae" of the phylum Bacteroidetes. It showed greatest sequence similarity to Pontibacter actiniarum KMM 6156(T) (95.5 %) followed by Adhaeribacter aquaticus MBRG1.5(T) (89.0 %) and Hymenobacter roseosalivarius DSM 11622(T) (88.9 %), but it differed from these micro-organisms in many phenotypic characteristics. Strain SRC-1(T) was an obligate aerobe and its cells were non-motile, irregular rods. The major fatty acids included mainly unsaturated and hydroxy fatty acids, including 17 : 1 iso I/anteiso B (36.7 %), 15 : 0 iso (15.8 %) and 17 : 0 iso 3-OH (10.3 %), and the DNA G+C content was 59.5 mol%. From the phenotypic and genotypic analyses it was clear that strain SRC-1(T) was quite different from members other genera in the family '"Flexibacteraceae". Therefore we conclude that strain SRC-1(T) represents a novel genus, for which the name Effluviibacter gen. nov., containing a single species Effluviibacter roseus sp. nov., is proposed. The type species of the genus is Effluviibacter roseus, the type strain of which is strain SRC-1(T) (=MTCC 7260(T)=DSM 17521(T)).

Echinicola pacifica gen. nov., sp. nov., a novel flexibacterium isolated from the sea urchin Strongylocentrotus intermedius

The taxonomic position of three novel marine, heterotrophic, pigmented and agarolytic bacteria with gliding motility, isolated from the sea urchin Strongylocentrotus intermedius, was investigated. 16S rRNA gene sequence analysis revealed that strains KMM 6166, KMM 6172T and KMM 6173 are members of the phylum Bacteroidetes; their nearest neighbours were Belliella baltica and Hongiella marincola (similarities of 94.5 and 93.6 %, respectively). The DNA G+C content of the strains was 44–45 mol%. The predominant fatty acids were C15 : 0 iso, C16 : 1 ω5c, C17 : 1 iso ω9c, C17 : 0 iso 3-OH and summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH). The major respiratory quinone was MK-7. Results of molecular experiments supported by phenotypic and chemotaxonomic data enabled the isolates to be classified as representatives of a novel species in a new genus, for which the name Echinicola pacifica gen. nov., sp. nov. is proposed. Echinicola pacifica is the type species of the genus Echinicola, and its type strain is KMM 6172T (=KCTC 12368T=LMG 23350T).

Algoriphagus terrigena sp. nov., isolated from soil

A Gram-negative, non-motile, non-spore-forming bacterial strain, DS-44T, was isolated from soil from Dokdo in Korea, and its taxonomic position was investigated by using a polyphasic approach. It grew optimally at 25 °C and in the presence of 2 % (w/v) NaCl. Strain DS-44T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The DNA G+C content was 49·0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-44T belongs to the genus Algoriphagus of the phylum Bacteroidetes. Similarity values between the 16S rRNA gene sequences of strain DS-44T and those of the type strains of recognized Algoriphagus species were in the range 93·8–95·7 %, making it possible to categorize strain DS-44T as a species that is separate from previously described Algoriphagus species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DS-44T (=KCTC 12545T=CIP 108837T) was classified in the genus Algoriphagus as the type strain of a novel species, for which the name Algoriphagus terrigena sp. nov. is proposed.

Chimaereicella alkaliphila gen. nov., sp. nov., a Gram-negative alkaliphilic bacterium isolated from a nonsaline alkaline groundwater

A Gram-negative bacterium designated AC-74(T) was isolated from a highly alkaline groundwater environment (pH 11.4). This organism formed rod-shaped cells, is strictly aerobic, catalase and oxidase positive, tolerates up to 3.0% NaCl, has an optimum growth temperature of 30 degrees C, but no growth occurs at 10 or 40 degrees C, and an optimum pH value of 8.0, but no growth occurs at pH 7.0 or 11.3. The predominant fatty acids are iso-15:0, iso-17:1 omega9c and 16:1 omega7c and or iso-15:2OH. The G+C content of DNA was 43.5mol%. The phylogenetic analyses of the sequences of the 16s RNA genes indicated that strain AC-74(T) belongs to the family "Flexibacteriaceae" and is phylogenetically equidistant ( approximately 94.5%) from the majority of the species of the genus Algoriphagus and from the genus Hongiella. Based on the phylogenetic analyses and distinct phenotypic characteristics, we are of the opinion that strain AC-74(T), represents a new species of the novel genus for which we propose the name Chimaereicella alkaliphila gen. nov., sp. nov.

Leadbetterella byssophila gen. nov., sp. nov., isolated from cotton-waste composts for the cultivation of oyster mushroom

A bacterial strain, designated 4M15T, was isolated from cotton-waste composts used as mushroom cultivation in South Korea. Properties of this isolate were studied on the basis of physiological and biochemical characteristics, fatty acid profile, isoprenoid quinone, DNA G+C content and phylogenetic position based on 16S rRNA gene sequence analysis. The strain was found to form a distinct phylogenetic lineage related to the family ‘Flexibacteraceae’ within the phylum ‘Bacteroidetes’. No recognized species showed >85 % 16S rRNA gene sequence similarity to strain 4M15T. The fatty acid profile of strain 4M15T included C16 : 1 ω7c/iso-C15 : 0 2-OH (30·5 %), iso-C15 : 0 (24·2 %), iso-C15 : 0 2-OH/C16 : 1 ω7c (15·9), iso-C17 : 0 3-OH (10·5 %) and C16 : 0 (5·6 %). The major isoprenoid quinone was menaquinone MK-7. The DNA G+C content was 33·0 mol%. Cells were Gram-negative, strictly aerobic, rod-shaped, non-motile, catalase-positive, oxidase-positive and flexirubin-positive. The strain hydrolysed aesculin, gelatin, starch and tyrosine. Several phenotypic tests could be used to differentiate strain 4M15T from other members of the family ‘Flexibacteraceae’. On the basis of the data presented, strain 4M15T should be assigned to the phylum ‘Bacteroidetes’ as a novel genus and species, for which the name Leadbetterella byssophila gen. nov., sp. nov. is proposed. The type strain is 4M15T (=KACC 11308T=DSM 17132T).

Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum ‘Bacteroidetes’, and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003

The taxonomic position of a marine, gliding, pink-pigmented, aerobic, heterotrophic and Gram-negative bacterium was established using a polyphasic approach. 16S rRNA gene sequence analysis indicated that the strain was a member of the phylum ‘Bacteroidetes’ in which it occupied a separate lineage. The predominant cellular fatty acids were C15 : 0 iso, C17 : 0 iso 3-OH, summed feature 3 and summed feature 4. The DNA G+C content was 48·7 mol%. Phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analyses strongly support the assignment of the newly isolated bacterium as a member of a novel genus and species, for which the name Pontibacter actiniarum gen. nov., sp. nov. is proposed. The type strain is KMM 6156T (=KCTC 12367T=LMG 23027T). It is also proposed that the illegitimate names Reichenbachia and Reichenbachia agariperforans are replaced with Reichenbachiella and Reichenbachiella agariperforans, respectively.

Algoriphagus locisalis sp. nov., isolated from a marine solar saltern

Two Gram-negative, rod-shaped, non-motile bacterial strains, MSS-170T and MSS-171, were isolated from sea water of a marine solar saltern of the Yellow Sea, Korea, and characterized by using a polyphasic taxonomic approach. The two isolates grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. They were characterized chemotaxonomically as having MK-7 as the predominant menaquinone and major amounts of fatty acids iso-C15 : 0 and C16 : 1 ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content of each of the two strains was 42 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the two strains fall within the evolutionary radiation enclosed by the genus Algoriphagus. Strains MSS-170T and MSS-171 had identical 16S rRNA gene sequences and exhibited a mean DNA–DNA relatedness level of 93 %. The two strains exhibited 16S rRNA gene sequence similarity levels of 96·4–98·9 % with respect to the type strains of recognized Algoriphagus species. DNA–DNA relatedness levels between the two strains and the type strains of six Algoriphagus species were less than 35 %. On the basis of phenotypic data and phylogenetic and genetic distinctiveness, strains MSS-170T and MSS-171 were classified in the genus Algoriphagus as members of a novel species, for which the name Algoriphagus locisalis sp. nov. is proposed. The type strain is MSS-170T (=KCTC 12310T=JCM 12597T).

Bacterial diversity and carbonate precipitation in the giant microbialites from the highly alkaline Lake Van, Turkey

Lake Van harbors the largest known microbialites on Earth. The surface of these huge carbonate pinnacles is covered by coccoid cyanobacteria whereas their central axis is occupied by a channel through which neutral, relatively Ca-enriched, groundwater flows into highly alkaline (pH approximately 9.7) Ca-poor lake water. Previous microscopy observations showed the presence of aragonite globules composed by rounded nanostructures of uncertain origin that resemble similar bodies found in some meteorites. Here, we have carried out fine-scale mineralogical and microbial diversity analyses from surface and internal microbialite samples. Electron transmission microscopy revealed that the nanostructures correspond to rounded aragonite nanoprecipitates. A progressive mineralization of cells by the deposition of nanoprecipitates on their surface was observed from external towards internal microbialite areas. Molecular diversity studies based on 16S rDNA amplification revealed the presence of bacterial lineages affiliated to the Alpha-, Beta- and Gammaproteobacteria, the Cyanobacteria, the Cytophaga-Flexibacter-Bacteroides (CFB) group, the Actinobacteria and the Firmicutes. Cyanobacteria and CFB members were only detected in surface layers. The most abundant and diverse lineages were the Firmicutes (low GC Gram positives). To the exclusion of cyanobacteria, the closest cultivated members to the Lake Van phylotypes were most frequently alkaliphilic and/or heterotrophic bacteria able to degrade complex organics. These heterotrophic bacteria may play a crucial role in the formation of Lake Van microbialites by locally promoting carbonate precipitation.

Algoriphagus antarcticus sp. nov., a novel psychrophile from microbial mats in Antarctic lakes

A taxonomic study was performed on six strains isolated from microbial mats of lakes Reid, Fryxell and Ace in Antarctica. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belonged to the family 'Flexibacteraceae' and were closely related to the recently described genera Algoriphagus and Hongiella. The isolates were Gram-negative, chemoheterotrophic, aerobic, psychrophilic, orange-red-pigmented bacteria and their DNA G+C content ranged from 39.9 to 41.0 mol%. Whole-cell fatty acid profiles included mainly branched fatty acids and summed feature 3, comprising 15 : 0 iso 2OH, 16 : 1omega7c or both. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenetic results, the novel strains were classified as Algoriphagus antarcticus sp. nov. The type strain is LMG 21980(T) (=DSM 15986(T)=R-10710(T)).

Roseivirga ehrenbergii gen. nov., sp. nov., a novel marine bacterium of the phylum 'Bacteroidetes', isolated from the green alga Ulva fenestrata

The taxonomic position of a novel marine bacterium isolated from the green alga Ulva fenestrata collected in the Sea of Japan was established. Cells of the strain studied, designated KMM 6017T, were strictly aerobic, heterotrophic, pink-pigmented, non-motile by gliding, Gram-negative and oxidase-, catalase-, beta-galactosidase- and alkaline phosphatase-positive. 16S rRNA gene sequence analysis indicated that the strain occupied a distinct lineage within the phylum 'Bacteroidetes' and formed a cluster with [Flexibacter] tractuosus and Reichenbachia agariperforans. The G+C content of the DNA of KMM 6017T was 40.2 mol%. The major respiratory quinone was MK-7. The predominant fatty acids were i15 : 1, i15 : 0 and i17 : 0 3-OH (34.2, 24 and 7.7 %, respectively). On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacterium was assigned to the genus Roseivirga gen. nov., as Roseivirga ehrenbergii gen. nov., sp. nov. The type strain is KMM 6017T (=KCTC 12282T=LMG 22567T).

Adhaeribacter aquaticus gen. nov., sp. nov., a Gram-negative isolate from a potable water biofilm

A Gram-negative bacterium was isolated from a freshwater biofilm developed on a stainless steel surface under a fluid velocity of 0·26 m s−1. The strain, MBRG1.5T, was cultivated on R2A agar and formed pink colonies. Light microscopy and negative staining in a transmission electron microscope showed that the cells were rod-shaped, approximately 2·8–4·1 μm long by 0·9–1·7 μm wide in size and produced large quantities of extracellular fibrillar material. Additionally, following growth in batch culture, transmission electron microscopy showed that many cells plasmolysed. Stationary-phase cells were more variable in size and shape. The DNA G+C content was 40·0 mol%. The most abundant fatty acids were 15 : 0 iso (22·5 %), followed by 16 : 1ω5c (16·9 %) and 15 : 0 iso 2-OH (16·5 %). Phylogenetic analysis of the 16S rRNA gene showed that the strain was a member of the family ‘Flexibacteraceae’ of the Cytophaga–Flavobacterium–Bacteroides group. Phenotypic and genotypic analyses indicated that the strain could not be assigned to any recognized genus; therefore a novel genus and species, Adhaeribacter aquaticus gen. nov., sp. nov., is proposed, with MBRG1.5T (=DSM 16391T=NCIMB 14008T) as the type strain.

Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the Cytophaga–Flavobacterium–Bacteroides group isolated from surface water of the central Baltic Sea

A bacterial isolate from the Baltic Sea, BA160T, was characterized for its physiological and biochemical features, fatty acid profile, G+C content and phylogenetic position based on 16S rRNA gene sequences. The strain was isolated from the surface water of the central Baltic Sea during the decay of a plankton bloom. Phylogenetic analyses of the 16S rRNA gene sequence revealed a clear affiliation with the family ‘Flexibacteraceae’, and showed the closest phylogenetic relationship with the species Belliella baltica and Cyclobacterium marinum. The G+C content of the DNA was 38·4 mol%. The strain was red-coloured due to carotenoids, Gram-negative, rod-shaped, and catalase- and oxidase-positive. Growth was observed at salinities from 0 to 6 %, with an optimum around 1·5 %. Temperature for growth ranged from 4 to 40 °C, with an optimum around 30 °C. The fatty acids were dominated by branched-chain fatty acids (>87 %), with a high abundance of iso-C15 : 0 (23 %) and anteiso-C15 : 0 (19 %). According to its morphology, physiology, fatty acid composition, G+C content and 16S rRNA gene sequence, strain BA160T is considered to represent a new genus of the family ‘Flexibacteraceae’. Due to its aquatic origin, the name Aquiflexum balticum gen. nov, sp. nov. is suggested for the type species (type strain, BA160T=DSM 16537T=LMG 22565T=CIP 108445T) of the new genus.

Description of Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., from sea water and algae, transfer of Hongiella halophila Yi and Chun 2004 to the genus Algoriphagus as Algoriphagus halophilus comb. nov. and emended descriptions of the genera Algoriphagus Bowman et al. 2003 and Hongiella Yi and Chun 2004

Four marine heterotrophic, aerobic, pink-pigmented and non-motile bacterial strains were isolated from sea water and algae collected in the Sea of Japan. In a polyphasic taxonomic study, 16S rRNA gene sequence analysis indicated that the strains were phylogenetically highly related to Algoriphagus ratkowskyi LMG 21435T, a member of the phylum Bacteroidetes. Further phenotypic, chemotaxonomic and genomic analyses revealed that the strains represent three novel species of the genus Algoriphagus, for which the following names are proposed: Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., with type strains KMM 3958T (= LMG 21971T = CCUG 47101T), KMM 3957T (= LMG 21970T = CCUG 47095T) and KMM 3956T (= LMG 21969T = CCUG 47094T), respectively. The species Hongiella halophila Yi and Chun 2004 is transferred to the genus Algoriphagus as Algoriphagus halophilus comb. nov. because of its close phylogenetic relatedness to Algoriphagus species and analogous phenotypic and chemotaxonomic properties. The above-mentioned novel species descriptions and species reclassification justify emended descriptions of the genera Algoriphagus and Hongiella.