Biogeography of Lentibacter algarum, description of a new strain isolated from the North Sea and emended genus and species descriptions.

A new heterotrophic, aerobic alphaproteobacterium, designated strain SH36 (=DSM 23330=LMG 25292), was obtained from a seawater sample collected in the open North Sea during a phytoplankton bloom. Analysis of the 16S rRNA gene sequence revealed affiliation of strain SH36 to the species Lentibacter algarum (family Roseobacteraceae), showing 100 and 99.9 % sequence similarity to the 16S rRNA genes of the strains L. algarum ZXM098 and ZXM100T. Digital DNA-DNA hybridization of strain SH36 with the type strain of L. algarum showed 98.0 % relatedness, confirming that strain SH36 can be classified within the same species. All three L. algarum strains were compared by physiological, morphological, chemotaxonomic, and genotypic characteristics. The strains showed only minor differences in the composition of fatty acids and polar lipids, but considerable physiological differences. Comparison of the 16S rRNA gene sequence of SH36 with sequences present in GenBank revealed that phylotypes with ≥98.65 % sequence identity to the type strain of L. algarum were found at different marine and estuarine locations of temperate and subtropic regions. Furthermore, by using a specific PCR approach L. algarum was detected throughout annual cycles at the offshore station at Helgoland Roads in the German Bight, indicating that this species is a permanent member of the microbial community in the North Sea.

Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., of Haloactinobacterium album as Ruania alba comb. nov, with an emended description of the genus Ruania, recognition that the genus names Haloactinobacterium and Ruania are heterotypic synonyms and description of Occultella aeris sp. nov., a halotolerant isolate from surface soil sampled at an ancient copper smelter.

In the course of screening the surface soils of ancient copper mines and smelters (East Harz, Germany) an aerobic, non-motile and halotolerant actinobacterium forming small rods or cocci was isolated. The strain designated F300T developed creamy to yellow colonies on tryptone soy agar and grew optimally at 28 °C, pH 7-8 and with 0.5-2 % (m/v) NaCl. Its peptidoglycan was of type A4α l-Lys-l-Glu (A11.54). The menaquinone profile was dominated by MK-8(II, III-H4) and contained minor amounts of MK-8(H2), MK-8(H6) and MK-9(H4). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, mono and diacylated phosphatidylinositol dimannosides, and components that were not fully characterized, including two phospholipids, two glycolipids and an uncharacterized lipid. Major whole-cell sugars were rhamnose and ribose. The fatty acid profile contained mainly iso and anteiso branched fatty acids (anteiso-C15 : 0, iso-C14 : 0) and aldehydes/dimethylacetals (i.e. not fatty acids). Sequence analysis of its genomic DNA and subsequent analysis of the data placed the isolate in the group currently defined by members of the genera Ruania and Haloactinobacterium (family Ruaniaceae, order Micrococcales) as a sister taxon to the previously described species Haloactinobacterium glacieicola, sharing an average nucleotide identity and average amino acid identity values of 85.3 and 85.7 %, respectively. Genotypic and chemotaxonomic analyses support the view that strain F300T (=DSM 108350T=CIP 111667T) is the type strain of a new genus and new species for which the name Occultella aeris gen. nov., sp. nov. is proposed. Based on revised chemotaxonomic and additional genome based data, it is necessary to discuss and evaluate the results in the light of the classification and nomenclature of members of the family Ruaniaceae, i.e. the genera Haloactinobacterium and Ruania. Consequently, the reclassification of Haloactinobacterium glacieicola as Occultella glacieicola comb. nov. and Haloactinobacterium album as Ruania alba comb. nov., with an emended description of the genus Ruania are proposed.

Recognition of the unsuitability of DSM 12173 as the deposited type strain of Thermocrinis ruber Huber et al. 1999, recognition of DSM 23557 as an authentic sub-culture of strain OC 1/4, the nomenclatural type of Thermocrinis ruber Huber et al. 1999 and an emended description of Thermocrinis ruber Huber et al. 1999.

During the course of growing cell material for the extraction of genomic DNA for the Genomic Encyclopedia of Bacteria and Archaea, strain OC 1/4, the designated type strain of Thermocrinis ruber was cultivated at the Institute for Microbiology and Archaea Center of the University of Regensburg, Regensburg, Germany. Partial sequencing of the 16S rRNA gene indicated that the cell material initially cultivated and the strain held in the DSMZ as DSM 12173 did not correspond with that deposited as AJ005640 and was probably a strain of Thermocrinis albus. A subsequent search of the strain collection of the Institute for Microbiology and Archaea Center of the University of Regensburg held in liquid nitrogen indicated that a strain could be recovered from the liquid nitrogen stocks that corresponded with the properties originally given for strain OC 1/4. We report here on the characterization of this strain that has subsequently been deposited in the DSMZ as DSM 23557.

Anaerohalosphaera lusitana gen. nov., sp. nov., and Limihaloglobus sulfuriphilus gen. nov., sp. nov., isolated from solar saltern sediments, and proposal of Anaerohalosphaeraceae fam. nov. within the order Sedimentisphaerales.

Two strains of anaerobic, coccoid, saccharolytic, Gram-stain-negative bacteria were isolated from samples of anoxic hypersaline sediments of evaporation ponds in Tavira (Portugal) and Mallorca (Spain). Both isolates were moderately halophilic, neutrophilic and had a temperature optimum at 37 °C. The highest 16S rRNA gene sequence identity values were found with members of the genus Sedimentisphaera (84.9-88.2 %) within the order Sedimentisphaerales, class Phycisphaerae. The strain SM-Chi-D1T could be assigned to the family Sedimentisphaeraceae, while phylogenetic analyses based on 16S rRNA gene sequences and genomic data indicate that strain ST-NAGAB-D1T is both a member of a novel genus and a novel family. SM-Chi-D1T could be distinguished from other cultured members of the Sedimentisphaeraceae mainly by the stimulatory effect of sulfur on growth, lack of ethanol production during fermentation and several differences in the cellular fatty acids and polar lipids patterns. Main differential characteristics of ST-NAGAB-D1T were a polytrichous flagellation, the absence of branched chain fatty acids and presence of large proportions of the unsaturated cellular fatty acids C16 : 1 c9 and C18 : 1 c11. On the basis of genomic, chemotaxonomic, biochemical and physiological data, we propose the novel species and genera Anaerohalosphaera lusitana gen. nov., sp. nov., and Limihaloglobus sulfuriphilus gen. nov., sp. nov., represented by the type strains ST-NAGAB-D1T (=DSM 103484T=JCM 31926T=KCTC 15600T) and SM-Chi-D1T (=DSM 100118T=JCM 31927T=KCTC 15601T), respectively. In addition, we propose the novel family Anaerohalosphaeraceae fam. nov. to accommodate the genus Anaerohalosphaera.

Corynebacterium alimapuense sp. nov., an obligate marine actinomycete isolated from sediment of Valparaíso bay, Chile.

A novel Gram-positive, non-motile, non-spore-forming and aerobic bacterium, designated strain VA37-3T, was isolated from a marine sediment sample collected at 19.2 m water depth from Valparaíso bay, Chile. Strain VA37-3T exhibits 97.6 % 16S rRNA gene sequence similarity to Corynebacterium marinum D7015T, 96.4 % to Corynebacterium humireducens MFC-5T and 96 % to Corynebacterium testudinoris M935/96/4T; and a rpoB gene sequence similarity of 85.1 % to Corynebacterium pollutisoli VMS11T, both analyses suggesting that strain VA37-3T represents a novel species of Corynebacterium. Physiological testing indicated that strain VA37-3T requires artificial sea water or sodium-supplemented media for growth, representing the first obligate marine actinomycete of the genus Corynebacterium. The genome of the proposed new species, along with the type strains of its most closely related species were sequenced and characterized. In silico genome-based similarity analyses revealed an ANIb of 72.8 % (C. marinum D7015T), ANIm of 85.0 % (Corynebacterium mustelae DSM 45274T), tetra of 0.90 (Corynebacterium callunae DSM 20147T) and ggdc of 24.7 % (Corynebacterium kutscheri DSM 20755T) when compared with the closest related strains. The genomic DNA G+C content of strain VA37-3T was 57.0 %. Chemotaxonomic assessment of strain VN6-2T showed the major fatty acids were C18 : 1ω9c and C16 : 0. Menaquinones predominantly consisted of MK-8(II-H2). Polar lipids consisted of diphosphatidylglycerol, glycolipids, phosphatidylglycerol, phosphoglycolipid and phosphatidylinositol. Mycolic acids also were present. Overall, the results from phylogenetic, phenotypic and genomic analyses confirmed that strain VA37-3T represents a novel species of the genus Corynebacterium, for which the name Corynebacterium alimapuense sp. nov. is proposed, with VA37-3T as the type strain (=CCUG 69366T=NCIMB 15118T).

Description of Gramella forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of Gramella gaetbulicola Cho et al. 2011.

Strain KT0803T was isolated from coastal eutrophic surface waters of Helgoland Roads near the island of Helgoland, North Sea, Germany. The taxonomic position of the strain, previously known as 'Gramella forsetii' KT0803, was investigated by using a polyphasic approach. The strain was Gram-stain-negative, chemo-organotrophic, heterotrophic, strictly aerobic, oxidase- and catalase-positive, rod-shaped, motile by gliding and had orange-yellow carotenoid pigments, but was negative for flexirubin-type pigments. It grew optimally at 22-25 °C, at pH 7.5 and at a salinity between 2-3 %. Strain KT0803T hydrolysed the polysaccharides laminarin, alginate, pachyman and starch. The respiratory quinone was MK-6. Polar lipids comprised phosphatidylethanolamine, six unidentified lipids and two unidentified aminolipids. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and iso-C17 : 1ω7c, with smaller amounts of iso-C15 : 0 2-OH, C15 : 0, anteiso-C15 : 0 and C17 : 1ω6c. The G+C content of the genomic DNA was 36.6 mol%. The 16S rRNA gene sequence identities were 98.6 % with Gramella echinicola DSM 19838T, 98.3 % with Gramella gaetbulicola DSM 23082T, 98.1 % with Gramella aestuariivivens BG-MY13T and Gramella aquimixticola HJM-19T, 98.0 % with Gramella lutea YJ019T, 97.9 % with Gramella portivictoriae DSM 23547T and 96.9 % with Gramella marina KMM 6048T. The DNA-DNA relatedness values were <35 % between strain KT0803T and type strains with >98.2 % 16S rRNA gene sequence identity. Based on the chemotaxonomic, phenotypic and genomic characteristics, strain KT0803T has been assigned to the genus Gramella, as Gramella forsetii sp. nov. The type strain is KT0803T (=DSM 17595T=CGMCC 1.15422T). An emended description of Gramella gaetbulicolaCho et al. 2011 is also proposed.

Updating Rule 15 of the International Code of Nomenclature of Bacteria.

The wording of Rule 15 as originally published in the 1975 and 1990 revisions of the International Code of Nomenclature of Bacteria with regard to the definition ofnomenclatural typeswas not clearly expressed and was modified by the Judicial Commission in 2008. However, there is a difference between the wording as proposed and that accepted. On reflection there is justification for re-examining both the proposed and the accepted wording.

Reclassification of Angiococcus disciformis, Cystobacter minus and Cystobacter violaceus as Archangium disciforme comb. nov., Archangium minus comb. nov. and Archangium violaceum comb. nov., unification of the families Archangiaceae and Cystobacteraceae, and emended descriptions of the families Myxococcaceae and Archangiaceae.

The species Archangium gephyra, Angiococcus disciformis, Cystobacter minus and Cystobacter violaceus are currently classified in three different genera of the order Myxococcales. The 16S rRNA gene sequences of the respective type strains show a similarity higher than 98.4 % and form a tight phylogenetic group. A dendrogram calculating the similarity of MALDI-TOF spectra confirmed the close relatedness of the four species that grouped in a monophyletic cluster in the neighbourhood of other species of the genus Cystobacter. The type strains shared similar fatty acid patterns of high complexity with iso-C15 : 0, C16 : 1ω5c and iso-C14 : 0 3-OH as the major components. The vegetative cells of these species are uniformly long needle-shaped rods, and the myxospores are short rods, ovoid or irregularly spherical thus differing from the myxospores of species related to Cystobacter fuscus, the type species of this genus. Some enzymic and hydrolysing reactions of the type strains are described. As a result of the high relatedness and similarity of the four species, it is proposed to place them into one genus, and due to phylogenetic and morphological distinctness, the species should be classified in a genus distinct from the genus Cystobacter as Archangium gephyra (type strain M18T = DSM 2261T = ATCC 25201T = NBRC 100087T), Archangium disciforme comb. nov. (type strain CMU 1T = DSM 52716T = ATCC 33172T), Archangium minus comb. nov. (proposed neotype strain Cb m2 = DSM 14751 = JCM 12627) and Archangium violaceum comb. nov. (type strain Cb vi61T = DSM 14727T = CIP 109131T = JCM 12629T). Since the family ArchangiaceaeJahn 1924 AL has priority over the family CystobacteraceaeMcCurdy 1970 AL, it is proposed to assign the genera Archangium, Anaeromyxobacter, Cystobacter, Hyalangium, Melittangium and Stigmatella to the family Archangiaceae. Emended descriptions of the families Myxococcaceae and Archangiaceae are also provided.

Description of Octadecabacter temperatus sp. nov., isolated from the southern North Sea, emended descriptions of the genus Octadecabacter and its species and reclassification of Octadecabacter jejudonensisPark and Yoon 2014 as Pseudooctadecabacter jejudonensis gen. nov., comb. nov.

A heterotrophic, Gram-negative, aerobic bacterium, designated strain SB1T, was isolated from surface water of the southern North Sea. Comparison of 16S rRNA gene sequences revealed that strain SB1T is affiliated to the genus Octadecabacter within the marine Roseobacter clade (family Rhodobacteraceae), with Octadecabacter antarcticus as the closest described species (98.2 % sequence similarity to the type strain). DNA-DNA hybridization indicated that SB1T represents a distinct species within this genus. On marine agar, strain SB1T formed beige, circular and convex colonies. Cells were irregular, motile rods. Growth occurred between 4 and 25 °C and was optimal at 20 °C, and at pH 7-9 (optimum pH 7.5-8.5) and NaCl concentrations between 1 and 6 % (optimum 2-4 %). The DNA G+C content of SB1T was 54.7 mol%. The fatty acids (>1 %) comprised 10 : 0 3-OH, 12 : 1 3-OH, 16 : 1ω7c, 16 : 0, 18 : 2ω7,12, 18 : 1ω7c, 18 : 0 and 11-methyl 18 : 1ω7c. The sole respiratory lipoquinone was ubiquinone Q-10 and the polar lipid pattern indicated the presence of the phospholipids phosphatidylglycerol and phosphatidylcholine, as well as unidentified aminolipid AL1, phospholipids PL1 and PL3 and lipids L1, L2 and L4. On the basis of phylogenetic and phenotypic differences, strain SB1T represents a novel species in the genus Octadecabacter, for which we propose the name Octadecabacter temperatus sp. nov. The type strain is SB1T ( = DSM 26878T = LMG 27946T). Furthermore, our results suggest the reclassification of Octadecabacter jejudonensis as the type species of a new genus, Pseudooctadecabacter gen. nov., as Pseudooctadecabacter jejudonensis comb. nov. (type strain SSK2-1T = KCTC 32535T = CECT 8397T). Finally, emended descriptions of the genus Octadecabacter and its species Octadecabacter antarcticus and Octadecabacter arcticus are also provided.

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic 'phylogenomic' efforts to compile a phylogeny-driven 'Genomic Encyclopedia of Bacteria and Archaea' in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.

Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov.

A Gram-positive staining, rod-shaped, non-motile, spore-forming obligately anaerobic bacterium, designated CRIBT, was isolated from the gastro-intestinal tract of a rat and characterized. The major cellular fatty acids of strain CRIBT were saturated and unsaturated straight-chain C12-C19 fatty acids, with C16:0 being the predominant fatty acid. The polar lipid profile comprised six glycolipids, four phospholipids and one lipid that did not stain with any of the specific spray reagents used. The only quinone was MK-6. The predominating cell-wall sugars were glucose and galactose. The peptidoglycan type of strain CRIBT was A1σ lanthionine-direct. The genomic DNA G+C content of strain CRIBT was 28.1 mol%. On the basis of 16S rRNA gene sequence similarity, strain CRIBT was most closely related to a number of species of the genus Clostridium, including Clostridium lituseburense (97.2%), Clostridium glycolicum (96.2%), Clostridium mayombei (96.2%), Clostridium bartlettii (96.0%) and Clostridium irregulare (95.5%). All these species show very low 16S rRNA gene sequence similarity (<85%) to the type strain of Clostridium butyricum, the type species of the genus Clostridium. DNA-DNA hybridization with closely related reference strains indicated reassociation values below 32%. On the basis of phenotypic and genetic studies, a novel genus, Romboutsia gen. nov., is proposed. The novel isolate CRIBT (=DSM 25109T=NIZO 4048T) is proposed as the type strain of the type species, Romboutsia ilealis gen. nov., sp. nov., of the proposed novel genus. It is proposed that C. lituseburense is transferred to this genus as Romboutsia lituseburensis comb. nov. Furthermore, the reclassification into novel genera is proposed for C. bartlettii, as Intestinibacter bartlettii gen. nov., comb. nov. (type species of the genus), C. glycolicum, as Terrisporobacter glycolicus gen. nov., comb. nov. (type species of the genus), C. mayombei, as Terrisporobacter mayombei gen. nov., comb. nov., and C. irregulare, as Asaccharospora irregularis gen. nov., comb. nov. (type species of the genus), on the basis of additional data collected in this study. In addition, an emendation of the species Peptostreptococcus anaerobius and the order Eubacteriales is provided.

Pelagimonas varians gen. nov., sp. nov., isolated from the southern North Sea.

A heterotrophic, Gram-stain-negative, aerobic bacterium, designated strain SH4-1(T), was obtained from a seawater sample collected from the southern North Sea during a phytoplankton bloom. The 16S rRNA gene sequence comparison revealed affiliation to the Roseobacter clade (class Alphaproteobacteria) with Sulfitobacter marinus SW-265(T) as the most closely related characterized strain, showing 97.2 % 16S rRNA gene sequence similarity. Calculation of phylogenetic trees based on 16S rRNA gene sequences indicated, however, that members of the genus Roseobacter, Roseobacter denitrificans Och 114(T) and Roseobacter litoralis Och 149(T) (95 % and 96 % sequence similarity, respectively) fall between strain SH4-1(T) and the Sulfitobacter cluster including Oceanibulbus indolifex HEL-45(T) (≥95.4 % sequence similarity). Cells of strain SH4-1(T) are irregular rods with at least one flagellum. Optimal growth occurred between 28 and 32 °C and at a pH between 7.0 and 8.5. Cells require the vitamin nicotinic acid amide as well as sodium ions for growth. The DNA G+C content was 55.1 mol%. The fatty acids (>1 %) comprised C10 : 0 3-OH, C12 : 1, C14 : 1 3-OH, C16 : 0, C18 : 0, C18 : 2, C18 : 1ω7c and 11-methyl C18 : 1ω7c. The polar lipid pattern indicated the presence of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, an unidentified aminolipid, one unidentified phospholipid and one other unidentified lipid. On the basis of phenotypic, chemotaxonomic and phylogenetic differences, strain SH4-1(T) represents a novel species in a new genus within the family Rhodobacteraceae, for which we propose the name Pelagimonas varians gen. nov., sp. nov. The type strain of the type species is SH4-1(T) ( = DSM 23678(T) = LMG 26343(T) = CIP 110297(T)).

Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga.

Two Gram-reaction-negative, rod-shaped, motile bacteria, designated strains U82 and U95(T), were isolated from the marine alga Ulva australis collected at Sharks Point, Clovelly, a rocky intertidal zone near Sydney, Australia. Both strains were oxidase- and catalase-positive, formed brown- to black-pigmented colonies and required NaCl for growth. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that these strains belong to the Roseobacter clade within the Alphaproteobacteria. The 16S rRNA genes of both strains were identical across the sequenced 1326 nt, but showed differences in the intergenic spacer region (ITS) between the 16S and the 23S rRNA genes. At the genomic level the DNA G+C contents of strains U82 and U95(T) were identical (52.6 mol%) and they had a DNA-DNA hybridization value of 83.7%, suggesting that these strains belong to the same species. The closest described phylogenetic neighbour to strains U82 and U95(T) was Thalassobius aestuarii DSM 15283(T) with 95.8% 16S rRNA gene sequence similarity. Other close relatives include further species of the genera Thalassobius and Shimia. Strains U82 and U95(T) were negative for bacteriochlorophyll a production, showed antibacterial activity towards other marine bacteria, were resistant to the antibiotics gentamicin and spectinomycin and were unable to hydrolyse starch or gelatin. The major fatty acids (>1%) were 18 : 1ω7c, 16 : 0, 18 : 2, 10 : 0 3-OH, 12 : 0, 20 : 1 2-OH and 18 : 0. The polar lipid pattern indicated the presence of phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and four unidentified phospholipids. Both strains produced ubiquinone 10 (Q-10) as the sole respiratory lipoquinone. Based on their phenotypic and phylogenetic characteristics, it is suggested that strains U82 and U95(T) are members of a novel species within a new genus for which the name Epibacterium ulvae gen. nov., sp. nov. is proposed. The type strain of the type species is U95(T) ( = DSM 24752(T) = LMG 26464(T)).

Phaeobacter leonis sp. nov., an alphaproteobacterium from Mediterranean Sea sediments.

A novel Gram-stain-negative, strictly aerobic, heterotrophic bacterium, designated 306(T), was isolated from near-surface (109 cm below the sea floor) sediments of the Gulf of Lions, in the Mediterranean Sea. Strain 306(T) grew at temperatures between 4 and 32 °C (optimum 17-22 °C), from pH 6.5 to 9.0 (optimum 8.0-9.0) and between 0.5 and 6.0% (w/v) NaCl (optimum 2.0%). Its DNA G+C content was 58.8 mol%. On the basis of 16S rRNA gene sequence similarity, the novel isolate belongs to the class Alphaproteobacteria and is related to the genus Phaeobacter. It shares 98.7% 16S rRNA sequence identity with Phaeobacter arcticus, its closest phylogenetic relative. It contained Q-10 as the only respiratory quinone, C(18:1)ω7c and C(16:0) as major fatty acids (>5%) and phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, two unidentified lipids and an aminolipid as polar lipids. The chemotaxonomic data are consistent with the affiliation of strain 306(T) to the genus Phaeobacter. Results of physiological experiments, biochemical tests and DNA-DNA hybridizations (with P. arcticus) indicate that strain 306(T) is genetically and phenotypically distinct from the five species of the genus Phaeobacter with validly published names. Strain 306(T) therefore represents a novel species, for which the name Phaeobacter leonis sp. nov. is proposed. The type strain is 306(T) ( =DSM 25627(T) =CIP 110369(T) =UBOCC 3187(T)).

Sphingomonas starnbergensis sp. nov., isolated from a prealpine freshwater lake.

A novel type of freshwater bacterium was isolated from the prealpine mesotrophic Starnberger See (Bavaria, southern Germany). Cells of strain 382(T) were Gram-negative and rod-shaped, motile and creamy-white. The isolate was strictly aerobic, catalase- and oxidase-positive, and grew at pH values of 6-9 (optimum, pH 7) and temperatures of 10-37 °C (optimum, 28 °C). The genomic G+C content of strain 382(T) was 64.1 mol%. Based on 16S rRNA gene sequence analyses, strain 382(T) belongs to the family Sphingomonadaceae and clusters within the genus Sphingomonas. Sphingomonas histidinilytica UM 2(T) and Sphingomonas wittichii DSM 6014(T) were the closest relatives, as indicated by the highest 16S rRNA gene sequence similarities (97.1 % and 96.8 %, respectively). Sphingomonas paucimobilis DSM 1098(T) (the type species of the genus Sphingomonas) exhibited 95.3 % sequence similarity. This affiliation of strain 382(T) to the genus Sphingomonas is confirmed by the presence of Q-10 as the major respiratory quinone, two sphingoglycolipids, C14 : 0 2-OH as the major 2-hydroxy fatty acid and sym-homospermidine as the major polyamine. The main cellular fatty acids of strain 382(T) were C18 : 1ω7c (39 %), C16 : 1ω7c (21 %), C16 : 0 (10 %) and C14 : 0 2-OH (10 %). Based on the phylogenetic distance from other species of the genus Sphingomonas and its unusually high C16 : 1ω7c content, strain 382(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas starnbergensis is proposed. The type strain is 382(T) ( = DSM 25077(T)  = LMG 26763(T)).

Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov.

Two novel chemo-organoheterotrophic members of the Sphingomonadaceae were isolated from alpine and pre-alpine lakes. Cells stained gram-negative, were motile and rod-shaped, and formed yellow, circular, convex colonies on different agar media. Strains 301(T) and 469(T) were strictly aerobic, catalase- and oxidase-positive, and grew at temperatures between 10 and 40 °C (optimum, 28 °C), and at pH values between 5 and 10 (optimum, pH 7). Both strains contained Q-10 as the dominant quinone, sphingoglycolipids and 2-hydroxymyristic acid, whereas 3-hydroxy fatty acids were absent. Major fatty acids of strain 301(T) were C(18 : 1)ω7c (53.3 %) and C(16 : 1)ω7c (22.9 %), with C(14 : 0) 2-OH (10.8 %) as the major 2-hydroxy fatty acid. Fatty acids of strain 469(T) were dominated by C(18 : 1)ω7c (34.4 %), C(16 : 1)ω7c (32.0 %) and C(14 : 0) 2-OH (15.2 %) as the major 2-hydroxy fatty acid. The genomic DNA G+C contents of strains 301(T) and 469(T) were 63.4 and 64.6 mol%, respectively. 16S rRNA gene sequence comparison indicated that both strains belonged to the genus Sphingobium. This classification was supported by the presence of spermidine as the major polyamine. The phylogenetically closest relatives of strain 301(T) were Sphingobium amiense DSM 16289(T), Sphingobium vermicomposti DSM 21299(T), Sphingobium yanoikuyae DSM 7462(T) and Sphingobium scionense DSM 19371(T) (98.8, 98.0, 97.9 and 97.4 % sequence similarity, respectively). DNA-DNA hybridization of genomic DNA yielded similarities in the range 43.2-12.1 % between strain 301(T) and the type strains of these four Sphingobium species. Closest relatives of strain 469(T) were Sphingomonas suberifaciens DSM 7465(T) and Sphingobium scionense DSM 19371(T) (97.1 and 96.5 % 16S rRNA gene sequence similarity, respectively). The degree of DNA-DNA hybridization between strain 469(T) and Sphingomonas suberifaciens DSM 7465(T) was 17.9 %. Based on the results of the molecular analyses and their phenotypic characteristics, strains 301(T) and 469(T) represent two novel species of the genus Sphingobium. The name Sphingobium limneticum sp. nov. is proposed for strain 301(T)( = DSM25076(T) = LMG 26659(T)). The name Sphingobium boeckii sp. nov. is proposed for strain 469(T) ( = DSM 25079(T) = LMG 26901(T)). The polyphasic analysis also suggests that Sphingomonas suberifaciens should be reclassified as Sphingobium suberifaciens comb. nov. with Ca1(T) ( = EY 2404(T) = ATCC 49355(T) = CIP 105429(T) = DSM 7465(T) = ICMP 12535(T) = NBRC 15211(T) = JCM 8521(T) = LMG 17323(T) = NCPPB 3629(T)) as the type strain.

Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov.

A previously undescribed aerobic, non-sporulating bacterium, strain G1A_585(T), was isolated from an oligotrophic freshwater lake in Bavaria, Germany. The rod-shaped cells were Gram-stain-negative and non-motile. Based on 16S rRNA gene sequence similarity, strain G1A_585(T) was a member of the family Sphingomonadaceae and shared <95.2 % similarity with type strains of all members of the most closely related genus, Sphingopyxis. Phyogenetically, the isolate shared a root with strains of three marine species, Sphingopyxis flavimaris DSM 16223(T), Sphingopyxis marina DSM 22363(T) and Sphingopyxis litoris DSM 22379(T). The polar lipids of strain G1A_585(T) were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipids, three glycolipids and one unknown lipid. Ubiquinone-10 was the dominant quinone (93.1 %) and ubiquinone-9 (6.5 %) was also detected. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 38.2 %); C16 : 1ω7c (33.6 %) and C14 : 0 2-OH (17.8 %). The major polyamine was spermidine and traces of 1,3-diaminopropane, putrescine and spermine were also detected. The DNA G+C content of strain G1A_585(T) was 55.7 mol% and the isolate was oxidase- and catalase-positive. Based on the phylogenetic relationship, the low DNA G+C content compared with most other members of the genus Sphingopyxis and the presence of signature nucleotides in the 16S rRNA gene sequence, a novel species in a new genus and species, Sphingorhabdus planktonica gen. nov., sp. nov., is proposed; the type strain of Sphingorhabdus planktonica is G1A_585(T) ( = DSM 25081(T)  = LMG 26646(T)). Because Sphingopyxis flavimaris DSM 16223(T), Sphingopyxis marina DSM 22363(T) and Sphingopyxis litoris DSM 22379(T) form a phylogenetic group together with strain G1A_585(T) that is clearly separated from all other known Sphingopyxis strains and share signature nucleotides, these three Sphingopyxis strains are reclassified as members of the proposed novel genus Sphingorhabdus: Sphingorhabdus flavimaris comb. nov. (type strain SW-151(T) = DSM 16223(T) = KCTC 12232(T)), Sphingorhabdus marina comb. nov. (type strain FR1087(T) = DSM 22363(T) = IMSNU 14132(T) = KCTC 12763(T) = JCM 14161(T)) and Sphingorhabdus litoris comb. nov. (type strain FR1093(T) = DSM 22379(T) = IMSNU 14133(T) = KCTC 12764(T) = JCM 14162(T)).

Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium.

A novel non-motile, Gram-staining-negative, yellow-pigmented bacterium, designated AG13(T), isolated from a rain water pond at a plant nursery in Spain and characterized as a plant-growth-promoting bacterium, was investigated to determine its taxonomic status. The isolate grew best over a temperature range of 15-40 °C, at pH 5.0-8.0 and with 0-4 % (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Chryseobacterium. The DNA G+C content of the novel strain was 37.2 mol%. The strain had a polyamine pattern with sym-homospermidine as the major compound and produced flexirubin-type pigments. MK-6 was the dominant menaquinone and the major cellular fatty acids were iso-C15 : 0, C17 : 1ω9c and iso-C17 : 0 3-OH. The main polar lipids were phosphatidylethanolamine, aminolipids and several unidentified lipids. The 16S rRNA gene showed 92.0-97.2 % sequence similarity with those of the members of the genus Chryseobacterium. Based on chemotaxonomic and phenotypic traits, and DNA-DNA hybridizations with the type strains of the most closely related species, the isolate is proposed to represent a novel species, Chryseobacterium hispalense, type strain AG13(T) ( = DSM 25574(T) = CCUG 63019(T)). Emended descriptions of the species Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium are also provided.

Planktomarina temperata gen. nov., sp. nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea.

Four heterotrophic bacterial strains belonging to the globally distributed marine RCA (Roseobacter clade-affiliated) cluster (family Rhodobacteraceae, class Alphaproteobacteria) were obtained from coastal seawater samples. Strain RCA23(T) was isolated from a 10(-7) dilution culture inoculated with seawater from the German Wadden Sea (southern North Sea), reflecting the high abundance of RCA bacteria in this habitat. Strains IMCC1909, IMCC1923 and IMCC1933 were isolated from diluted seawater (10(-3)) of the Yellow Sea, South Korea. Based on 16S rRNA gene sequence comparison, Octadecabacter antarcticus 307(T) is the closest described relative of the RCA strains, with 95.4-95.5 % sequence similarity. Cells of RCA23(T), IMCC1909, IMCC1923 and IMCC1933 are small motile rods requiring sodium ions. Optimal growth of RCA23(T) occurs at 25 °C and within a very narrow pH range (pH 7-8, optimum pH 7.5). The DNA G+C base content of RCA23(T) is 53.67 mol%. The major respiratory lipoquinone is ubiquinone-10 (Q-10) and the dominant fatty acids (>1 %) are 12 : 1 3-OH, 16 : 1ω7c, 16 : 0, 18 : 1ω7c, 18 : 0 and 11-methyl 18 : 1ω7c. The polar lipid pattern indicated the presence of phosphatidylglycerol, two unidentified aminolipids and two unidentified phospholipids. On marine agar, RCA23(T) forms non-pigmented, transparent to light beige, small (<1 mm), circular, convex colonies. Strain RCA23(T) harbours all genes for the production of bacteriochlorophyll a (BChl a). Genes encoding the light-harvesting reaction centre of BChl a (pufM) were identified in all RCA strains. No visible pigmentation was observed for any of the strains under laboratory conditions, but spectrophotometric analysis revealed weak production of BChl a by RCA23(T). Morphological, physiological and genotypic features of strain RCA23(T) suggest that it represents a novel species of a new genus within the Rhodobacteraceae, for which we propose the name Planktomarina temperata gen. nov., sp. nov., described previously by Giebel et al. [ISME J 5 (2011), 8-19] as 'Candidatus Planktomarina temperata'. The type strain of Planktomarina temperata is RCA23(T) ( = DSM 22400(T) = JCM 18269(T)).

Planktotalea frisia gen. nov., sp. nov., isolated from the southern North Sea.

A heterotrophic, aerobic bacterium, designated strain SH6-1(T), was obtained from a seawater sample collected from the open North Sea during a phytoplankton bloom. Strain SH6-1(T) was isolated from a 10(-6) dilution culture, which indicated a high abundance of this organism in the environmental sample. 16S rRNA gene sequence comparison revealed that strain SH6-1(T) belonged to the marine Roseobacter clade (order Rhodobacterales) within the class Alphaproteobacteria. Pelagicola litoralis CL-ES2(T) was the closest phylogenetic neighbour (96.4% 16S rRNA gene sequence similarity). Cells of strain SH6-1(T) were small or elongated irregular rods. Optimal growth occurred between 20 and 25 °C and between pH 7.5 and 9.0 with peptone and yeast extract. On marine agar, the isolate formed non-pigmented, small, circular, convex colonies. For growth, cells required sodium ions and the vitamins pantothenic acid and nicotinic acid amide. The DNA G+C content was 53.8 mol%. The fatty acids (>1%) were C(10:0) 3-OH, C(16:0), C(12:1), C(12:1) 3-OH, C(18:0), C(18:1)ω7c, C(18:2) and 11-methyl C(18:1)ω7c. The polar lipid pattern indicated the presence of phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and one unidentified phospholipid. The major respiratory lipoquinone was ubiquinone Q-10. Strain SH6-1(T) contained the genes pufLM, which code for the bacterial photosynthesis reaction centre; however, no bacteriochlorophyll a could be detected. Physiological, genotypic and phenotypic differences from P. litoralis support the description of a novel genus and species, for which we suggest the name Planktotalea frisia gen. nov., sp. nov; the type strain of the type species is SH6-1(T) (=DSM 23709(T)=LMG 25294(T)).