A New Family,Alteromonadaceae fam. nov., Including Marine Proteobacteria of the Genera Alteromonas,Pseudoalteromonas, Idiomarina,and Colwellia

The taxonomic positions of the marine genera Alteromonas, Pseudoalteromonas, Idiomarina, and Colwellia within the gamma subclass of the class Proteobacteria were specified on the basis of their phenotypic, genotypic, and phylogenetic characteristics. Gram-negative aerobic bacteria of the genera Alteromonas, Pseudoalteromonas, and Idiomarina and facultatively anaerobic bacteria of the genus Colwellia were found to form a phylogenetic cluster with a 16S rRNA sequence homology of 90% or higher. The characteristics of these genera presented in this paper allow their reliable taxonomic identification. Based on the analysis of our experimental data and analyses available in the literature, we propose to combine the genera Alteromonas, Pseudoalteromonas, Idiomarina, and Colwellia into a new family, Alteromonadaceae fam. nov., with the type genus Alteromonas.     

Description of three new Alteromonas species Alteromonas antoniana sp. nov., Alteromonas lipotrueae sp. nov. and Alteromonas lipotrueiana sp. nov. isolated from marine environments,and proposal for reclassification of the genus Salinimonas as Alteromonas

In the course of a bioprospective study of marine prokaryotes for cosmetic purposes, four strains, MD_567^T, MD_652^T, MD_674 and PS_109^T, were isolated that 16S rRNA gene affiliation indicated could represent three new species within the family Alteromonadaceae. A thorough phylogenetic, genomic and phenotypic taxonomic study confirmed that the isolates could be classified as three new taxa for which we propose the names Alteromonas antoniana sp. nov., Alteromonas lipotrueae sp. nov. and Alteromonas lipotrueiana sp. nov. In addition, the consistent monophyletic nature of the members of the genera Alteromonas and Salinimonas showed that both taxa should be unified, and therefore we also propose the reclassification of the genus Salinimonas within Alteromonas, as well as new combinations for the species of the former. As the specific epithets profundi and sediminis are already used for Alteromonas species, we created the nomina nova “Alteromonas alteriprofundi” nom. nov. and Alteromonas alterisediminis nom. nov. to accommodate the new names for “Salinimonas profundi” and Salinimonas sediminis. Whole genome comparisons also allowed us to detect the unexpected codification of aromatic hydrocarbon biodegradative compounds, such as benzoate and catechol, whose activity was then demonstrated phenotypically. Finally, the high genomic identity between the type strains of Alteromonas stellipolaris and Alteromonas addita indicated that the latter is a junior heterotypic synonym of Alteromonas stellipolaris.     

Truepera radiovictrix gen. nov., sp. nov., a new radiation resistant species and the proposal of Trueperaceae fam. nov

Two isolates, belonging to a new species of a novel genus of the Phylum “Deinococcus/Thermus ”, were recovered from hot spring runoffs on the Island of São Miguel in the Azores. Strains RQ-24^T and TU-8 are the first cultured representatives of a distinct phylogenetic lineage within this phylum. These strains form orange/red colonies, spherical-shaped cells, have an optimum growth temperature of about 50 °C, an optimum pH for growth between about 7.5 and 9.5, and do not grow at pH below 6.5 or above pH 11.2. These organisms grow in complex media without added NaCl, but have a maximum growth rate in media with 1.0% NaCl and grow in media containing up to 6.0% NaCl. The organisms are extremely ionizing radiation resistant; 60% of the cells survive 5.0 kGy. These strains are chemoorganotrophic and aerobic; do not grow in Thermus medium under anaerobic conditions with or without nitrate as electron acceptor and glucose as a source of carbon and energy, but ferment glucose to d-lactate without formation of gas. The organisms assimilate a large variety of sugars, organic acids and amino acids. Fatty acids are predominantly iso- and anteiso-branched; long chain 1,2 diols were also found in low relative proportions; menaquinone 8 (MK-8) is the primary respiratory quinone. Peptidoglycan was not detected. Based on 16S rRNA gene sequence analysis, physiological, biochemical and chemical analysis we describe a new species of one novel genus represented by strain RQ-24^T (CIP 108686^T = LMG 22925^T = DSM 17093^T) for which we propose the name Truepera radiovictrix. We also propose the family Trueperaceae fam. nov. to accommodate this new genus.     

Echinocampidae fam. nov., a new family of Late Jurassic-Early Cretaceous radiolarians of Arctic Siberia

When studying Late Jurassic-Early Cretaceous radiolarians from the Nordvik section (Arctic Siberia), unique morphotypes of multicyrtoid nassellarians with many horns in the apical part of the shell, which continue the rays A, V, 2l, D, and 2L of the cephalic spicule, were recorded. These morphotypes are assigned to a new family, Echinocampidae fam. nov., including three new genera (Echinocampe gen. nov., Nordvikella gen. nov., and Arctocapsula gen. nov.) and eight new species. The family Echinocampidae was probably restricted to high latitudes and belonged to the boreal fauna of the terminal Jurassic and the basal Cretaceous.     

Natranaeroarchaeum sulfidigenes gen. nov., sp. nov., carbohydrate-utilizing sulfur-respiring haloarchaeon from hypersaline soda lakes,a member of a new family Natronoarchaeaceae fam. nov. in the order Halobacteriales

A pure culture of alkaliphilic haloarchaeon strain AArc-S^T capable of anaerobic growth by carbohydrate-dependent sulfur respiration was obtained from hypersaline lakes in southwestern Siberia. According to phylogenetic analysis, AArc-S^T formed a new genus level branch most related to the genus Natronoarchaeum in the order Halobacteriales. The strain is facultatively anaerobic with strictly respiratory metabolism growing either by anaerobic respiration with elemental sulfur and thiosulfate as the electron acceptors or by aerobic respiration at microoxic conditions. Thiosulfate is reduced partially to sulfide and sulfite. It is a first sulfur-reducing alkaliphilic haloarchaeon utilizing sugars, starch and glycerol as substrates for anaerobic growth. It is extremely halophilic (optimum at 3.5 M total Na⁺) and obligately alkaliphilic (optimum at pH 9.5). The dominant polar lipids include PG and PGP-Me with the archaeol (C₂₀-C₂₀) or extended archaeol (C₂₀-C₂₅) cores. The dominant respiratory lipoquinone is MK-8:8. On the basis of unique physiological properties and results of phylogenetic analysis, the soda lake isolate is suggested to be classified into a novel genus and species Natranaeroarchaeum sulfidigenes gen. nov., sp. nov. (=JCM 34033^T = UNIQEM U1000^T). Furthermore, on the bases of phylogenomic reconstruction, a new family Natronoarchaeaceae fam. nov. is proposed within the order Halobacteriales incorporating Natranaeroarchaeum and three related genera: Natronoarchaeum, Salinarchaeum and Halostella.     

Alexandriicola marinus gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from marine phycosphere

Two yellow-pigmented bacterial strains, LZ-14 ^T and ABI-LZ29, were isolated from the cultivable phycosphere microbiota of the highly toxic marine dinoflagellate Alexandrium catenella LZT09 and demonstrated obvious microalgae growth-promoting potentials toward the algal host. To elucidate the taxonomic status of the two bioactive bacterial strains, they were subjected to a polyphasic taxonomic characterization. Both strains were found to be Gram-negative, aerobic, rod-shaped and motile; to contain Q-10 as the predominant ubiquinone; summed feature 8, C_16:0, C_18:1 ω7c 11-methyl and summed feature 3 as the major fatty acids; and diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and two unidentified phospholipids as the predominant polar lipids. Based on the phylogenetic analysis, phylogenomic inferences and phenotypic characteristics, the strains could be clearly distinguished from phylogenetically closely related species and formed a distinct monophyletic lineage in the family Rhodobacteraceae. The size of the draft genome of strain LZ-14 ^T is 4.615 Mb, with a DNA G?+?C content of 63.3 mol%. It contains ten predicted secondary metabolite biosynthetic gene clusters and core genes for bacterial exopolysaccharide biosynthesis. Therefore, strain LZ-14 ^T (= CCTCC AB 2017230 ^T?=?KCTC 62342 ^T) represents a novel species of a new genus, for which the name Alexandriicola marinus gen. nov., sp. nov., is proposed.

     

Defluvibacter lusatiae gen. nov., sp. nov., a new chlorohenol-degrading member of the alpha-2 subgroup of proteobacteria.

The two Gram-negative bacterial strains S1 and S4 were isolated from activated sludge of an industrial waste water treatment plant and exhibited a stable capability to degrade 2,4-dichlorophenol, 4-chloro-2-methylphenol, 4-chlorophenol and phenol. The cells were short rods with a polar flagellum, being mesophilic, strictly aerobic, oxidase-positive, and chemoorganotrophic. They utilized a range of amino acids, but only a restricted number of carbohydrates. Reassociation experiments with DNA from strains S1 and S4 revealed high interstrain similarity, indicating, that both strains belong to the same species. The phylogenetic position was determined by comparison of the almost complete 16S rDNA sequence of strain S1 with sequences of related bacteria. Strain S1 clustered with members of the alpha-2 subgroup of the Proteobacteria by forming a separate lineage within the radiation of Mesorhizobium, Phyllobacterium and Sinorhizobium. Both strains can be differentiated from members of related taxa by a set of physiological and chemotaxonomic properties including the ability to grow with norvaline, L-tryptophan, putrescine, glutarate and malonate, and by the presence of spermidine as major polyamine and of 12:0 3OH as fatty acid. Strain S1 is described as type strain of a new species and assigned to a new genus with the proposed name Defluvibacter lusatiae.     

Natronogracilivirga saccharolytica gen. nov., sp. nov. and Cyclonatronum proteinivorum gen. nov., sp. nov., haloalkaliphilic organotrophic bacteroidetes from hypersaline soda lakes forming a new family Cyclonatronaceae fam. nov. in the order Balneolales

Two heterotrophic bacteroidetes strains were isolated as satellites from autotrophic enrichments inoculated with samples from hypersaline soda lakes in southwestern Siberia. Strain Z-1702^T is an obligate anaerobic fermentative saccharolytic bacterium from an iron-reducing enrichment culture, while Ca. Cyclonatronum proteinivorum Omega^T is an obligate aerobic proteolytic microorganism from a cyanobacterial enrichment. Cells of isolated bacteria are characterized by highly variable morphology. Both strains are chloride-independent moderate salt-tolerant obligate alkaliphiles and mesophiles. Strain Z-1702^T ferments glucose, maltose, fructose, mannose, sorbose, galactose, cellobiose, N-acetyl-glucosamine and alpha-glucans, including starch, glycogen, dextrin, and pullulan. Strain Omega^T is strictly proteolytic utilizing a range of proteins and peptones. The main polar lipid fatty acid in both strains is iso-C_15:0, while other major components are various C₁₆ and C₁₇ isomers. According to pairwise sequence alignments using BLAST Gracilimonas was the nearest cultured relative to both strains (<90% of 16S rRNA gene sequence identity). Phylogenetic analysis placed strain Z-1702^T and strain Omega^T as two different genera in a deep-branching clade of the new family level within the order Balneolales with genus. Based on physiological characteristics and phylogenetic position of strain Z-1702^T it was proposed to represent a novel genus and species Natronogracilivirga saccharolityca gen. nov., sp. nov. (= DSMZ 109061^T =JCM 32930^T =VKM B 3262^T). Furthermore, phylogenetic and phenotypic parameters of N. saccharolityca and C. proteinivorum gen. nov., sp. nov., strain Omega^T (=JCM 31662^T, =UNIQEM U979^T), make it possible to include them into a new family with a proposed designation Cyclonatronaceae fam. nov..     

Morphology and taxonomy of five marine sand-dwelling Thecadinium species (Dinophyceae) from Japan, including four new species: Thecadinium arenarium sp. nov., Thecadinium ovatum sp. nov., Thecadinium striatum sp. nov. and Thecadinium yashimaense sp. nov.

Thecadinium inclinatum Balech and four new marine sand‐dwelling species of the dinoflagellate genus Thecadinium are described from the sandy beaches along the coast of Shikoku, Japan. Thecadinium inclinatum is thecate, bilaterally flattened, elliptical in shape, non‐photosynthetic, and measures 55–75 μ in length and 43–59 μ in depth. The epi‐ and hypotheca theca are semielliptical and the thecal surface is smooth with small pores. The plate formula is Po (pore plate), 3′, 7″,?c,?s, 5″′1″′.Thecadinium ovatum sp. nov. is thecate, non‐photosynthetic, bilaterally flattened and almost oval in lateral view. The cell measures 40–50 μm in length and 33–40 μm in depth. The hypotheca has two or three strong antapical spines. The plate formula is 3′, 6″,6c, 5s?, 5″′, 1″′. Thecadinium striatum sp. nov. is thecate, non‐photosynthetic, bilaterally flattened and somewhat elliptical in lateral view. The cell is 33–41 μm long and 23–30 μm deep. Several striae are present on the hypotheca. The plate formula is 3′, 6″, 6c, 5s?, 5″′, 1″″. Thecadinium yashimaense sp. nov. is bilaterally flattened, photosynthetic and elliptical in ventral view. The cell is 44–65 μm long and 23–36 μm wide. The thecal surface is smooth with small pores. he cingulum forms a steep left–handed spiral. The plate formula is Po, 3′, la, 6″, 5c, 4s, 5″′, 1″′. Thecadinium arenarium sp. nov. is somewhat wedge‐shaped in ventral view, photosynthetic with brownish chloroplasts and almost rounded in cross section. The cingulum forms a steep left‐handed spiral. The cell measures 35–41 μm in length and 25–30 μm in width. The thecal surface is weakly reticulated with small pores. The hypotheca is conical. The plate formula is Po, 3′, la, 6″, 5c, 4s, 5″′, 1″″.     

Staphylococcus lipolyticus sp. nov., a new cold-adapted lipase producing marine species

A cold-adapted lipase producing bacterium, designated SS-33^T, was isolated from sea sediment collected from the Bay of Bengal, India, and subjected to a polyphasic taxonomic study. Strain SS-33^T exhibited the highest 16S rRNA gene sequence similarity with Staphylococcus cohnii subsp. urealyticus (97.18 %), Staphylococcus saprophyticus subsp. bovis (97.16 %) and Staphylococcus cohnii subsp. cohnii (97.04 %). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SS-33^T belongs to the genus Staphylococcus. Cells of strain SS-33^T were Gram-positive, coccus-shaped, non-spore-forming, non-motile, catalase-positive and oxidase-negative. The major fatty acid detected in strain SS-33^T was anteiso-C15:0 and the menaquinone was MK-7. The genomic DNA G + C content was 33 mol%. The DNA-DNA hybridization among strain SS-33^T and the closely related species indicated that strain SS-33^T represents a novel species of the genus Staphylococcus. On the basis of the morphological, physiological and chemotaxonomic characteristics, the results of phylogenetic analysis and the DNA-DNA hybridization, a novel species is proposed for strain SS-33^T, with the name Staphylococcus lipolyticus sp. nov. The strain type is SS-33^T (=MTCC 10101^T?=?JCM 16560^T). Staphylococcus lipolyticus SS-33^T hydrolyzed various substrates including tributyrin, olive oil, Tween 20, Tween 40, Tween 60, and Tween 80 at low temperatures, as well as mesophilic temperatures. Lipase from strain SS-33^T was partially purified by acetone precipitation. The molecular weight of lipase protein was determined 67 kDa by SDS-PAGE. Zymography was performed to monitor the lipase activity in Native-PAGE. Calcium ions increased lipase activity twofold. The optimum pH of lipase was pH 7.0 and optimum temperature was 30 °C. However, lipase exhibited 90 % activity of its optimum temperature at 10 °C and became more stable at 10 °C as compared to 30 °C. The lipase activity and stability at low temperature has wide ranging applications in various industrial processes. Therefore, cold-adapted mesophilic lipase from strain SS-33^T may be used for industrial applications. This is the first report of the production of cold-adapted mesophilic lipase by any Staphylococcus species.     

Halorussus rarus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern

Two halophilic archaeal strains TBN4^T and TBN5 were isolated from Taibei marine solar saltern in Jiangsu, China. Both strains showed light red-pigmented colonies and their cells were rod, motile and Gram-stain-negative. They were able to grow at 25–50°C (optimum 37°C), at 1.4–4.3 M NaCl (optimum 2.1 M NaCl), at 0–1.0 M MgCl₂ (optimum 0.005 M MgCl₂) and at pH 6.0–9.0 (optimum pH 7.0). Their cells lyse in distilled water and minimal NaCl concentration to prevent cell lysis is 8% (w/v). The major polar lipids of the two strains were PG (phosphatidylglycerol), PGP-Me (phosphatidylglycerol phosphate methyl ester), PGS (phosphatidylglycerol sulfate) and five glycolipids chromatographically identical to S-TGD-1 (sulfated galactosyl mannosyl glucosyl diether), S-DGD-1 (sulfated mannosyl glucosyl diether), TGD-1 (galactosyl mannosyl glucosyl diether), DGD-1 (mannosyl glucosyl diether) and DGD-2 (an unknown diglycosyl diether). Phylogenetic analysis revealed that TBN4^T and strain TBN5 formed a distinct clade with genus Haladaptatus (showing 90.0–90.9% 16S rRNA gene similarities). The DNA G + C content of strain TBN4^T and strain TBN5 are 66.1 and 65.4 mol%, respectively. The DNA–DNA hybridization value between strain TBN4^T and strain TBN5 was 94.3%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain TBN4^T and strain TBN5 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Halorussus rarus gen. nov., sp. nov. is proposed. The type strain is TBN4^T (=CGMCC 1.10122^T = JCM 16429^T).     

Spongiimonas flava gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from an unidentified marine sponge

A Gram-negative, strictly aerobic, golden-yellow pigmented, non-motile, rod-shaped strain designated J36A-7^T was isolated from an unidentified yellow-green coloured marine sponge. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (85.6 %) to Nonlabens dokdonensis DSW-6^T. The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain J36A-7^T were identified as iso-C16:0, iso-C17:0 3-OH and summed feature three as defined by the MIDI system (C16:1 ω7c and/or iso-C15:0 2-OH). The DNA G+C content was determined to be 31.2 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a complex polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified glycolipids, one unidentified aminolipid and one unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Spongiimonas flava gen. nov., sp. nov. is proposed. The type strain of S. flava is J36A-7^T (=KCTC 32176^T = NBRC 109319^T).     

Croceibacter atlanticus gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae

A bright, saffron-colored marine bacterium HTCC2559T was isolated from the Bermuda Atlantic Time Series station in the western Sargasso Sea, Atlantic Ocean by high throughput culturing methods and characterized by polyphasic approaches. Phenotypic data and phylogenetic analyses showed that the strain is a member of the family Flavobacteriaceae. The strain was gram-negative, non-motile, chemoheterotrophic, strictly aerobic, NaCl-requiring, rod-shaped cells that contain carotenoid pigments but not flexirubin. Several kinds of macromolecules (gelatin, DNA, starch, casein, and elastin) were degraded and carbohydrates, sugar alcohols, organic acids, and amino acids were utilized as sole carbon sources. The dominant fatty acids were branched or hydroxy acids, and 3-OH i17:0, i15:0, i15:1, and i17:1 omega9c were abundant. The DNA G+C content of the strain is 34.8 mol%. Phylogenetic analyses using three treeing algorithms based on 16S rRNA gene sequences revealed that the strain formed a very distinct lineage that is allied closely with several seawater environmental clones in the family Flavobacteriaceae. Therefore, it is proposed from the polyphasic studies that strain HTCC2559T (=ATCC BAA-628T = KCTC 12090T) belongs to a new genus and species named Croceibacter atlanticus gen. nov., sp. nov.     

Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium.

On the basis of phenotypical characteristics and analysis of 16S rRNA sequence, a new species belonging to a new genus is described, and the name Marinobacter hydrocarbonoclasticus is proposed. This organism, isolated from Mediterranean seawater near a petroleum refinery, is a gram-negative, aerobic, rod-shaped bacterium. It grows at NaCl concentrations of 0.08 to 3.5 M and uses various hydrocarbons as the sole source of carbon and energy. Its DNA has a guanine-plus-cytosine content of 52.7 mol%. The 16S rRNA analysis shows a clear affiliation between M. hydrocarbonoclasticus and the gamma group of the phylum Proteobacteria. A close phylogenetic relationship appears among the species Marinomonas vaga, Oceanospirillum linum, Halomonas elongata, and Pseudomonas aeruginosa. Because of the impossibility of finding a single most closely related species, we suggest that this bacterium be assigned to a new genus, at least temporarily. The possibility of a revision of this status when new data appear is, however, not excluded. The type strain is M. hydrocarbonoclasticus SP.17 (= ATCC 49840).