When should a DDH experiment be mandatory in microbial taxonomy?

Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter

A novel, Gram-negative, non-spore-forming, pleomorphic yellow-orange bacterial strain was isolated from a stadium seat. Strain Coronado^T falls within the Erythrobacteraceae family and the genus Porphyrobacter based on 16S rRNA phylogenetic analysis. This strain has Q-10 as the predominant respiratory lipoquinone, as do other members of the family. The fatty acid profile of this strain is similar to other Porphyrobacter, however Coronado^T contains predominately C18:1ω7cis and C16:0, a high percentage of the latter not being observed in any other Erythrobacteraceae. This strain is catalase-positive and oxidase-negative, can grow from 4 to 28 °C, at NaCl concentrations 0.1–1.5%, and at pH 6.0–8.0. On the basis of phenotypic and phylogenetic data presented in this study, strain Coronado^T represents a novel species in the Porphyrobacter genus for which the name Porphyrobacter mercurialis sp. nov. is proposed; the type strain is Coronado^T (=DSMZ 29971, =LMG 28700).

Salibacterium halotolerans gen. nov., sp. nov., a bacterium isolated from a salt pan, reclassification of Bacillus qingdaonensis as Salibacterium qingdaonense comb. nov. and Bacillus halochares as Salibacterium halochares comb. nov

Two novel Gram-stain-positive, rod-shaped, non-motile, non-endospore-forming bacterial strains, S7T and IB5, were isolated from Khavda, India. Based on 16S rRNA gene sequence analysis they were identified as belonging to the class Bacilli, order Bacillales, family Bacillaceae, and were most closely related to Bacillus qingdaonensis CGMCC 1.6134T (97.3 %, sequence similarity), Bacillus halochares LMG 24571T (96.9 %), Bacillus salarius KCTC 3912T (95.6 %) and Bacillus aidingensis DSM 18341T (95.3 %). However, these strains shared only 88.2 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T, indicating that strains S7T and IB5 might not be members of the genus Bacillus. The DNA–DNA relatedness of these strains with B. qingdaonensis CGMCC 1.6134T was 42.9 ± 0.8. The cell-wall peptidoglycan of strains S7T and IB5 contained meso-diaminopimelic acid, while the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and three unknown lipids. The predominant isoprenoid quinone was MK-7. anteiso-C15 : 0 was the predominant fatty acid. The results of the phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strains S7T and IB5, suggesting that they represent a novel member of the family Bacillaceae, for which the name Salibacterium halotolerans gen. nov., sp. nov. is proposed. The type strain of Salibacterium halotolerans is S7T ( = KCTC 33658T = CGMCC 1.15324T). Based on the results of the present study, it is also suggested that B. qingdaonensis and B. halochares should be transferred to this novel genus, as Salibacterium qingdaonense comb. nov. and Salibacterium halochares comb. nov., respectively.

Bacillus formosensis sp. nov., isolated from pesticide wastewater

A Gram-stain-positive, endospore-forming rod (designated strain CC-LY275T) was isolated from a pesticide wastewater sample. The isolate grew at a temperature 20-45 °C, at pH 7.0-8.0 and tolerated NaCl 6 % (w/v). The most closely related strains in terms of 16S rRNA gene sequence similarity were Bacillus horneckiae (97.1 %) and Bacillus oceanisediminis (96.8 %), respectively. The G+C content of the genomic DNA was 37.9 mol%. Strain CC-LY275T was determined to possess iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0 as predominant fatty acids. The major polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Cell-wall peptidoglycan contained meso-diaminopimelic acid; menaquinone (MK-7) was the predominant respiratory quinone. According to the distinct phylogenetic, phenotypic and chemotaxonomic properties, the name Bacillus formosensis sp. nov. (type strain CC-LY275T = BCRC 80443T = JCM 18448T) is proposed.

Noncontiguous finished genome sequence and description of Weeksella massiliensis sp. nov

Strain FF8(T) (= CSUR P860 = DSM 28259) was isolated in Dakar, Senegal, from the urine of a 65-year-old man with acute cystitis. This strain shows a similarity of sequence of 16S rRNA of 98.38% with Weeksella virosa, and its GenBank accession numbers are HG931340 and CCMH00000000. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis had a poor score, ranging from 1.32 to 1.56, that did not allow identification of the bacterium. Using a polyphasic study made of phenotypic and genomic analyses, strain FF8(T) was a Gram-negative, aerobic rod and a member of the family Flavobacteriaceae. The sequenced genome is 2 562 781 bp with one chromosome but no plasmid. It exhibits a G + C content of 35.9% and contains 2390 protein-coding and 56 RNA genes, including a complete rRNA operon. On the basis of these data, we propose the creation of Weeksella massiliensis sp. nov.

High-quality genome sequence and description of Bacillus ndiopicus strain FF3(T) sp. nov

Strain FF3(T) was isolated from the skin-flora of a 39-year-old healthy Senegalese man. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry did not allow any identification. This strain exhibited a 16S rRNA sequence similarity of 96.8% with Bacillus massiliensis, the phylogenetically closest species with standing nomenclature. Using a polyphasic study made of phenotypic and genomic analyses, strain FF3(T) was Gram-positive, aeroanaerobic and rod shaped and exhibited a genome of 4 068 720 bp with a G+C content of 37.03% that coded 3982 protein-coding and 67 RNA genes (including four rRNA operons). On the basis of these data, we propose the creation of Bacillus ndiopicus sp. nov.

Enterobacter tabaci sp. nov., a novel member of the genus Enterobacter isolated from a tobacco stem

A Gram-stain negative, motile, rod-shaped bacterium, designated strain YIM Hb-3(T), was isolated from the stem of a tobacco plant. The strain was observed to form convex, circular and yellow-colored colonies. The predominant respiratory quinone was identified as Q-8. The major fatty acids (>5%) detected were C(16:1)ω7c and/or C(16:1)ω6c (summed feature 3), C(16:0), C(17:0)cyclo, C(18:1)ω7c and/or C(18:1)ω6c (summed feature 8), C(14:0)3-OH and/or iso-C(16:1)I (summed feature 2), C(14:0) and C(12:0). The genomic DNA G+C content was determined to be 54.8 mol%. Phylogenetic trees based on 16S rRNA gene sequences and multilocus sequence analysis showed that strain YIM Hb-3(T) had the closest phylogenetic relationship with Enterobacter mori LMG 25706(T). DNA-DNA relatedness value between strain YIM Hb-3(T) and E. mori LMG 25706(T) was 46.9 ± 3.8%. On the basis of phenotypic and chemotaxonomic data, phylogenetic analysis, and DNA-DNA relatedness value, strain YIM Hb-3(T) is considered to represent a novel species of the genus Enterobacter, for which the name Enterobacter tabaci sp. nov. is proposed. The type strain is YIM Hb-3(T) (=KACC 17832(T) =KCTC 42694(T)).

Edaphobacter dinghuensis sp. nov., an acidobacterium isolated from lower subtropical forest soil

An aerobic bacterium, designated DHF9T, was isolated from a soil sample collected from the lower subtropical forest of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Cells were Gram-stain-negative, non-motile, short rods that multiplied by binary division. Strain DHF9T was an obligately acidophilic, mesophilic bacterium capable of growth at pH 3.5-5.5 (optimum pH 4.0) and at 10-33 °C (optimum 28-33 °C). Growth was inhibited at NaCl concentrations above 2.0 % (w/v). The major fatty acids were iso-C15 : 0, C16 : 0 and C16 : 1ω7c. The polar lipids consist of phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids, two unidentified polar lipids and an unidentified glycolipid. The DNA G+C content was 57.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs to the genus Edaphobacter in subdivision 1 of the phylum Acidobacteria, with the highest 16S rRNA gene sequence similarity of 97.0 % to Edaphobacter modestus Jbg-1T. Based on phylogenetic, chemotaxonomic and physiological analyses, it is proposed that strain DHF9T represents a novel species of the genus Edaphobacter, named Edaphobacter dinghuensis sp. nov. The type strain is DHF9T ( = DSM 29920T = CGMCC 1.12997T).

Occallatibacter riparius gen. nov., sp. nov. and Occallatibacter savannae sp. nov., acidobacteria isolated from Namibian soils, and emended description of the family Acidobacteriaceae

Three Gram-negative, non-spore-forming, encapsulated bacteria were isolated from a Namibian river-bank soil (strains 277T and 307) and a semiarid savannah soil (strain A2-1cT). 16S rRNA gene sequence analyses placed them within subdivision 1 of the Acidobacteria and revealed 100 % similarity between strains 277T and 307 and 98.2 % similarity between A2-1cT and the former two strains. The closest relatives with validly published names were Telmatobacter bradus, Acidicapsa borealis and Acidicapsa ligni (94.7-95.9 % similarity to the type strains). Cells of all three strains were rod-shaped and motile and divided by binary fission. Ultrastructural analyses revealed a thick cell envelope, resulting mainly from a thick periplasmic space. Colonies of strains 277T and 307 were white to cream and light pink, respectively, while strain A2-1cT displayed a bright pink colour. All three strains were aerobic, chemoheterotrophic mesophiles with a broad temperature range for growth and a moderately acidic pH optimum. Sugars and complex proteinaceous substrates were the preferred carbon and energy sources. A few polysaccharides were degraded. The major quinone in all three strains was MK-8; MK-7 occurred in strain A2-1cT as a minor compound. Major fatty acids were iso-C15 : 0 and iso-C17 : 1ω7c. In addition, iso-C17 : 0 occurred in significant amounts. The DNA G+C contents of strains 277T, 307 and A2-1cT were 59.6, 59.9 and 58.5 mol%, respectively. Based on these characteristics, the three isolates are assigned to two novel species of the novel genus Occallatibacter gen. nov., Occallatibacter riparius sp. nov. [type strain 277T ( = DSM 25168T = LMG 26948T) and reference strain 307 ( = DSM 25169 = LMG 26947)] and Occallatibacter savannae sp. nov. [type strain A2-1cT ( = DSM 25170T = LMG 26946T)]. Together with several other recently described taxa, the novel isolates provide the basis for an emended description of the established family Acidobacteriaceae.

Acidipila dinghuensis sp. nov., an acidobacterium isolated from forest soil

An aerobic, chemoheterotrophic, non-motile, capsule-forming bacterium designated DHOF10T was isolated from a soil sample collected from the forest of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOF10T was able to grow at pH 3.5-8.0 (optimum pH 4.0-4.5) and at 10-37 °C (optimum 28-37 °C). NaCl tolerance was up to 1.0 % (w/v). Major fatty acids consisted of iso-C15 : 0, C18 : 1ω9c and C16 : 1ω7c. The quinone was MK-8 and the DNA G+C content was 56.3 mol%. The polar lipids consisted of phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid, two unidentified aminophospholipids and two unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of genus Acidipila of the phylum Acidobacteria, with the highest 16S rRNA gene sequence similarity of 97.3 % to Acidipila rosea AP8T. On the basis of phylogenetic, phenotypic, physiological and chemotaxonomic distinctiveness, strain DHOF10T represents a novel species of the genus Acidipila, for which the name Acidipila dinghuensis sp. nov. is proposed. The type strain is DHOF10T ( = CGMCC 1.13007T = KCTC 42631T).

Jatrophihabitans fulvus sp. nov., an actinobacterium isolated from grass soil

A Gram-stain-positive, aerobic, non-motile, non-spore-forming, rod-shaped bacterium, designated strain PB158T, was isolated from grass soil sampled in Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies placed the novel isolate in the class Actinobacteria, and most closely related to Jatrophihabitans endophyticus S9-650T and Jatrophihabitans soli KIS75-12T with 98.1 and 97.0 % 16S rRNA gene sequence similarity, respectively. Cells of strain PB158T formed yellow colonies on R2A agar, contained MK-9(H4) as the predominant menaquinone, meso-diaminopimelic acid as the diagnostic diamino acid, and included iso-C16 : 0, C18 : 1ω9c, and C17 : 1ω8c as the major fatty acids (>5 %). The acyl type was found to be N-glycolylated. The G+C content of genomic DNA of strain PB158T was 72.4 mol%. In DNA–DNA hybridizations, the DNA–DNA relatedness value observed between strain PB158T and the type strain of J. endophyticus was 21.8 % indicating that the two strains do not belong to the same species. Thus, the combined genotypic and phenotypic data supported the conclusion that strain PB158T represents a novel species of the genus Jatrophihabitans, for which the name Jatrophihabitans fulvus sp. nov. is proposed. The type strain is PB158T ( = KCTC 33605T = JCM 30448T).

Kordia zhangzhouensis sp. nov., isolated from surface freshwater

An aerobic, Gram-stain-negative, rod-shaped and non-motile bacterium, JS14SB-1T, was isolated from the surface freshwater of the Jiulong River, PR China. Strain JS14SB-1T grew at 15–38 °C (optimum, 28–35 °C), at pH 6.0–9.0 (optimum pH 7.0) and in the presence of 1.0–7.0 % (w/v) NaCl [optimum 3.0–5.0 % (w/v)]. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain JS14SB-1T was affiliated to the genus Kordia, sharing low similarities (95.1–97.1 %) to all type strains of species of this genus. The digital DNA–DNA hybridization (DDH) value between strain JS14SB-1T and the closely related strain Kordia jejudonensis SSK3-3T was 20.70 ± 2.33 % and far below the 70 % DDH value taken as the gold standard for delineation of bacterial species. The major fatty acids were identified as iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipids were phosphatidylethanolamine, glycolipid, aminolipid, several unidentified phospholipids and lipids. The predominant menaquinone was MK-6. The G+C content of the genomic DNA was 33.8 mol%. Based on the phenotypic, phylogenetic and chemotaxonomic distinctiveness, strain JS14SB-1T is considered to represent a novel species of the genus Kordia, for which the name Kordia zhangzhouensis sp. nov. is proposed; the type strain is JS14SB-1T ( = MCCC 1A00726T = KCTC 42140T).

Taxonomic description and genome sequence of Rheinheimera mesophila sp. nov., isolated from an industrial waste site

A novel Gram-staining-negative gammaproteobacterium, designated IITR-13T, was isolated from a pesticide-contaminated soil and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, the strain showed the closest similarity (98.7 %) to Rheinheimera tangshanensis JA3-B52T followed by Rheinheimera texasensis A62-14BT (97.7 %) and Rheinheimera soli BD-d46T (97.3 %). The 16S rRNA gene sequence similarity of the novel strain to other members of the genus Rheinheimera was < 97.3 %. However, DNA–DNA hybridization between strain IITR-13T and the type strains of R. tangshanensis, R. texasensis and R. soli was 47.5 ± 0.6, 42.4 ± 0.4 and 39.8 ± 0.3 %, respectively; these values are less than 70 %, a threshold value for delineation of a novel species. The strain had C12 : 0 3-OH, C16 : 0, C17 : 1ω8c, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and C18 : 1ω6c as the major fatty acids. The major isoprenoid quinones detected for strain IITR-13T were ubiquinone Q-8 and menaquinone MK-7.The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and seven unknown phospholipids. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the novel strain should be assigned to a novel species, for which the name Rheinheimera mesophila sp. nov. is proposed, with the type strain IITR-13T ( = MTCC 12064T = DSM 29723T). Also, we report the draft genome sequence of Rheinheimera mesophila IITR-13T; the draft genome sequence includes 3 749 903 bases and comprises 3449 predicted coding sequences, with a G+C content of 47.8 %. It consists of 102 contigs (>1000 bp).

Noncontiguous finished genome sequence and description of Necropsobacter massiliensis sp. nov

Strain FF6(T) was isolated from the cervical abscess of a 4-year-old Senegalese boy, in Dakar, Senegal. MALDI-TOF MS did not provide any identification. This strain exhibited a 95.17% 16S rRNA sequence identity with Necropsobacter rosorum. Using a polyphasic study including phenotypic and genomic analyses, strain FF6(T) was an aero-anaerobic Gram-negative cocobacillus, oxidase positive, and exhibited a genome of 2,493,927 bp (1 chromosome but no plasmid) with a G+C content of 46.2% that coded 2,309 protein-coding and 53 RNA genes. On the basis of these data, we propose the creation of Necropsobacter massiliensis sp. nov.

Saccharothrix ecbatanensis sp. nov., an actinobacterium isolated from soil

A novel actinomycete, designated HM 537T, was isolated from soil in Hamedan Province, Iran. Cell-wall hydrolysates of strain HM 537T contained meso-diaminopimelic acid, and whole-cell hydrolysates contained ribose, glucose, galactose, rhamnose and traces of mannose. The main phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and an unknown phospholipid. MK-9(H4), an unknown MK and MK-10(H4) were the predominant menaquinones. The major fatty acids included iso-C16 : 0, iso-C15 : 0, iso-C16 : 1 G and 9(?)-methyl C16 : 0. Strain HM 537T had the highest 16S rRNA gene sequence similarity to Saccharothrix hoggarensis DSM 45457T (99.5 %) and Saccharothrix saharensis DSM 45456T (99.0 %). DNA-DNA hybridization studies showed relatedness values of 13.8 ± 3.3 % with S. hoggarensis DSM 45457T and 16.3 ± 3.5 % with S. saharensis DSM 45456T. Based on the results of phenotypic and genotypic studies, strain HM 537T represents a novel species of the genus Saccharothrix, for which the name Saccharothrix ecbatanensis sp. nov. is proposed. The type strain is HM 537T ( = DSM 45486T = UTMC 00537T = CCUG 63021T).

Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum

A Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit at the E. V. Smith Research Center in Tallassee (Macon county), AL, USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6 %) and Novosphingobium barchaimii (98.5 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 98.3 %. DNA–DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low relatedness values of 8 % (reciprocal 7 %), 24 % (reciprocal 26 %) and 19 % (reciprocal 25 %), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid, C14 : 0 2-OH (11.7 %), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a novel species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T ( = LMG 28605T = CCM 8569T = CIP 110884T).

Streptomyces olivicoloratus sp. nov., an antibiotic-producing bacterium isolated from soil

Strain T13T, isolated from forest soil in Jeollabuk-do, South Korea, exhibited antibiotic production on yeast extract-malt extract-glucose (YMG) medium containing magnesium chloride as a trace mineral, and inhibited the growth of Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa, Staphylococcus epidermidis, Paenibacillus larvae, Escherichia coli, Candida albicans and Aspergillus niger. Growth occurred at 15-45 °C, pH 4-11 and in the presence of up to 2 % (w/v) NaCl. Biochemical analyses indicated that the predominant menaquinones produced by this strain were MK-9(H6) and MK-9(H8); small amounts of MK-10(H2) and MK-10(H4) were also detected. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine, and the cell-wall peptidoglycan contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. Whole-cell hydrolysates contained glucose, galactose, ribose and rhamnose. The fatty-acid profile of strain T13T was made up predominantly of iso- and anteiso-branched fatty acids. Genetic analyses demonstrated that strain T13T is closely related to Streptomyces gramineus JR-43T (98.29 % 16S rRNA gene sequence similarity), S. graminisoli JR-19T (97.99 %), S. rhizophilus JR-41T (97.86 %), S. longwoodensis LMG 20096T (97.84 %), S. graminifolii JL-22T (97.79 %) and S. yaanensis Z4T (97.56 %), and DNA-DNA hybridization yielded relatedness values of 35.27-43.42 % when T13T was compared to related strains. The results of morphological, chemotaxonomic, phylogenetic and phenotypic analyses confirm that this strain represents a novel species of the genus Streptomyces, for which the name Streptomyces olivicoloratus sp. nov. is proposed. The type strain is T13T ( = KEMB 9005-210T = KACC 18227T = NBRC 110901T).

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.

Halorussus amylolyticus sp. nov., isolated from an inland salt lake

A halophilic archaeal strain, YC93T, was isolated from Yuncheng salt lake in Shanxi Province, China. Cells were pleomorphic rods, stained Gram-negative and formed light-red-pigmented colonies on agar plates. Strain YC93T was able to grow at 25–50 °C (optimum 37 °C), with 1.4–4.8 M NaCl (optimum 2.0 M), with 0–1.0 M MgCl2 (optimum 0.05 M) and at pH 6.0–9.5 (optimum pH 7.0). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). 16S rRNA gene sequence analysis revealed that strain YC93T had two dissimilar 16S rRNA genes both of which were phylogenetically related to those of the two recognized members of the genus Halorussus (93.0–95.3 % similarity). The rpoB′ gene of strain YC93T was phylogenetically related to the corresponding gene of Halorussus rarus TBN4T (91.3 % similarity) and Halorussus ruber YC25T (90.5 %). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and five glycolipids chromatographically identical to those of Halorussus rarus CGMCC 1.10122T. The DNA G+C content of strain YC93T was 64.6 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain YC93T represents a novel species of the genus Halorussus, for which the name Halorussus amylolyticus sp. nov. is proposed. The type strain is YC93T ( = CGMCC 1.12126T = JCM 18367T).

Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov

Strain JCE(T) was isolated from the fecal sample of a 24-year-old obese man living in Jeddah, Saudi Arabia. It is an aerobic, Gram-positive, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.5 % with Bacillus niacini, the phylogenetically closest species with standing nomenclature. Moreover, the strain JCE(T) presents many phenotypic differences, when it is compared to other Bacillus species, and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,762,944 bp long genome (1 chromosome but no plasmid) contains 4,654 protein-coding and 98 RNAs genes, including 92 tRNA genes. The strain JCE(T) differs from most of the other closely Bacillus species by more than 1 % in G + C content. In addition, digital DNA-DNA hybridization values for the genome of the strain JCE(T) against the closest Bacillus genomes range between 19.5 to 28.1, that confirming again its new species status. On the basis of these polyphasic data made of phenotypic and genomic analyses, we propose the creation of Bacillus jeddahensis sp. nov. that contains the strain JCE(T).

The Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile Is a New Strain of Pseudoalteromonas agarivorans Containing Abundant and Diverse Virulence-Related Genes

Sponge diseases have increased dramatically, yet the causative agents of disease outbreaks have eluded identification. We undertook a polyphasic taxonomic analysis of the only confirmed sponge pathogen and identified it as a novel strain of Pseudoalteromonas agarivorans. 16S ribosomal RNA (rRNA) and gyraseB (gyrB) gene sequences along with phenotypic characteristics demonstrated that strain NW4327 was most closely related to P. agarivorans. DNA-DNA hybridization and in silico genome comparisons established NW4327 as a novel strain of P. agarivorans. Genes associated with type IV pili, mannose-sensitive hemagglutinin pili, and curli formation were identified in NW4327. One gene cluster encoding ATP-binding cassette (ABC) transporter, HlyD and TolC, and two clusters related to the general secretion pathway indicated the presence of type I secretion system (T1SS) and type II secretion system (T2SS), respectively. A contiguous gene cluster of at least 19 genes related to type VI secretion system (T6SS) which included all 13 core genes was found. The absence of T1SS and T6SS in nonpathogenic P. agarivorans S816 established NW4327 as the virulent strain. Serine proteases and metalloproteases of the classes S8, S9, M4, M6, M48, and U32 were identified in NW4327, many of which can degrade collagen. Collagenase activity in NW4327 and its absence in the nonpathogenic P. agarivorans KMM 255(T) reinforced the invasiveness of NW4327. This is the first report unambiguously identifying a sponge pathogen and providing the first insights into the virulence genes present in any pathogenic Pseudoalteromonas genome. The investigation supports a theoretical study predicting high abundance of terrestrial virulence gene homologues in marine bacteria.

High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes

Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in Northern Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA gene sequence phylogeny revealed a clustering of members of the genus Myroides as a monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2^T and its next relatives seem more closely related to the genus Myroides than to the type species of the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391 protein-coding and 65 RNA genes is part of the GenomicEncyclopedia ofBacteria andArchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and one large CAZy rich gene cluster that might enable strain WB 3.3-2^T to decompose plant and algae derived polysaccharides. Based on these results we propose F. rivuli as an interesting candidate for further physiological studies and the role of Bacteroidetes in the decomposition of complex polymers in the environment.

High-quality genome sequence and description of Bacillus dielmoensis strain FF4(T) sp. nov

Strain FF4^T was isolated from the skin flora of a 16-year-old healthy Senegalese female. This strain exhibited a 16S rRNA sequence similarity of 97.5 % with Bacillus fumarioli, the phylogenetically closest species with standing in nomenclature and a poor MALDI-TOF-MS score (1.1 to 1.3) that does not allow any identification. Using a polyphasic study consisting of phenotypic and genomic analyses, strain FF4^T was Gram-positive, aerobic, rod-shaped, and exhibited a genome of 4,563,381 bp (1 chromosome but no plasmid) with a G + C content of 40.8 % that coded 4,308 protein-coding and 157 RNA genes (including 5 rRNA operons). On the basis of these data, we propose the creation of Bacillus dielmoensis sp. nov.

Identification and Antimicrobial Resistance of Bacteria Isolated from Probiotic Products Used in Shrimp Culture

Probiotics are increasingly used in aquaculture to control diseases and improve feed digestion and pond water quality; however, little is known about the antimicrobial resistance properties of such probiotic bacteria and to what extent they may contribute to the development of bacterial resistance in aquaculture ponds. Concerns have been raised that the declared information on probiotic product labels are incorrect and information on bacterial composition are often missing. We therefore evaluated seven probiotics commonly used in Vietnamese shrimp culture for their bacterial species content, phenotypic antimicrobial resistance and associated transferable resistance genes. The bacterial species was established by 16S rRNA sequence analysis of 125 representative bacterial isolates. MIC testing was done for a range of antimicrobials and whole genome sequencing of six multiple antimicrobial resistant Bacillus spp. used to identify resistance genes and genetic elements associated with horizontal gene transfer. Thirteen bacterial species declared on the probiotic products could not be identified and 11 non-declared Bacillus spp. were identified. Although our culture-based isolation and identification may have missed a few bacterial species present in the tested products this would represent minor bias, but future studies may apply culture independent identification methods like pyro sequencing. Only 6/60 isolates were resistant to more than four antimicrobials and whole genome sequencing showed that they contained macrolide (ermD), tetracycline (tetL), phenicol (fexA) and trimethoprim (dfrD, dfrG and dfrK) resistance genes, but not known structures associated with horizontal gene transfer. Probiotic bacterial strains used in Vietnamese shrimp culture seem to contribute with very limited types and numbers of resistance genes compared to the naturally occurring bacterial species in aquaculture environments. Approval procedures of probiotic products must be strengthened through scientific-based efficacy trials and product labels should allow identification of individual bacterial strains and inform the farmer on specific purpose, dosage and correct application measures.

Marmoricola aquaticus sp. nov., an actinomycete isolated from a marine sponge

A novel marine actinomycete, designated B374T, was isolated from a marine sponge, Glodia corticostylifera, which was collected from São Paulo, Brasil. The taxonomic position of B374T was established by using data derived from a polyphasic approach. The organism showed a combination of chemotaxonomic and morphological characteristics consistent with its classification in the genus Marmoricola and it formed a distinct phyletic line in the clade of the genus Marmoricola, based on 16S rRNA gene sequences. Strain B374T was most closely related to Marmoricola aequoreus SST-45T (98.5 % 16S rRNA gene sequence similarity), but was distinguished from this strain and from the other type strains of species of the genus Marmoricola on the basis of a combination of phenotypic properties. The data obtained, therefore, indicates that isolate B374T ( = CBMAI 1089T = DSM 28169T) should be classified as a novel species of the genus Marmoricola, for which the name Marmoricola aquaticus sp. nov. is proposed.

Clostridium amazonense sp. nov. an obliqately anaerobic bacterium isolated from a remote Amazonian community in Peru

A strictly anaerobic Gram-stain positive, spore-forming, rod-shaped bacterium designated NE08V(T), was isolated from a fecal sample of an individual residing in a remote Amazonian community in Peru. Phylogenetic analysis based on the 16S rRNA gene sequence showed the organism belonged to the genus Clostridium and is most closely related to Clostridium vulturis (97.4% sequence similarity) and was further characterized using biochemical and chemotaxonomic methods. The major cellular fatty acids were anteiso C13:0 and C16:0 with a genomic DNA G + C content of 31.6 mol%. Fermentation products during growth with PYG were acetate and butyrate. Based on phylogenetic, phenotypic and chemotaxonomic information, strain NE08V was identified as representing a novel species of the genus Clostridium, for which the name Clostridium amazonense sp. nov. is proposed. The type strain is NE08V(T) (DSM 23598(T) = CCUG 59712(T)).

The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota

Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.

Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil

Strain SB026T was isolated from Brazilian rainforest soil and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological features consistent with its classification in the genus Amycolatopsis and formed a branch in the Amycolatopsis 16S rRNA gene tree together with Amycolatopsis bullii NRRL B-24847T, Amycolatopsis plumensis NRRL B-24324T, Amycolatopsis tolypomycina DSM 44544T and Amycolatopsis vancoresmycina NRRL B-24208T. It was related most closely to A. bullii NRRL B-24847T (99.0 % 16S rRNA gene sequence similarity), but was distinguished from this strain by a low level of DNA–DNA relatedness (~46 %) and discriminatory phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the isolate should be classified in the genus Amycolatopsis as representing a novel species, Amycolatopsis rhabdoformis sp. nov. The type strain is SB026T ( = CBMAI 1694T = CMAA 1285T = NCIMB 14900T).

Flavobacterium nitrogenifigens sp. nov., isolated from switchgrass (Panicum virgatum)

A yellow, nitrogen-fixing bacterial strain, NXU-44(T), isolated from the rhizosphere of switchgrass (Panicum virgatum) in Auburn, Alabama, USA, was studied to determine its taxonomic position. Cells of the isolate were rod-shaped and Gram-stain-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus Flavobacterium with highest sequence similarities to the type strains of Flavobacterium ginsenosidimutans (97.9%), Flavobacterium phragmitis (97.6%) and Flavobacterium anhuiense (97.5%). The 16S rRNA gene sequence similarities to all other species of the genus Flavobacterium were below 97.5%. The fatty acid profile of strain NXU-44(T) consisted of the major fatty acids iso-C15 : 0, iso-C15 : 0 2-OH/C16 : 1ω7c and iso-C17 : 0 3-OH. The major compounds in the polar lipid profile were phosphatidylethanolamine, phosphatidylserine, one aminolipid and two polar lipids. The quinone system was composed exclusively of menaquinone MK-6. The polyamine pattern contained the major compound sym-homospermidine and only minor amounts of other polyamines. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. These data and the differential biochemical and chemotaxonomic properties show that strain NXU-44(T) represents a novel species of the genus Flavobacterium for which the name Flavobacterium nitrogenifigens sp. nov. is proposed. The type strain is NXU-44(T) ( = LMG 28694(T) = CIP 110894(T)).

Modestobacter lapidis sp. nov. and Modestobacter muralis sp. nov., isolated from a deteriorated sandstone historic building in Salamanca, Spain

A polyphasic study was undertaken to establish the taxonomic status of two Modestobacter strains isolated from the surface of deteriorated sandstone of a historic building in Salamanca, Spain. The strains, isolates MDVD1(T) and MON 3.1(T), were found to have chemotaxonomic and morphological properties consistent with their classification in the genus Modestobacter and to form distinct phyletic lines in the Modestobacter 16S rRNA gene tree. Isolate MDVD1(T) was found to be closely related to the type strain of Modestobacter versicolor (98.7 % similarity) and isolate MON 3.1(T) to the type strain of Modestobacter multiseptatus (98.6 % similarity). The isolates were distinguished readily from one another and from the Modestobacter type strains by a broad range of phenotypic properties, by qualitative and quantitative differences in fatty acid profiles and by BOX fingerprint patterns. On the basis of these data, it is proposed that the isolates be classified in the genus Modestobacter as Modestobacter lapidis sp. nov. and Modestobacter muralis sp. nov., with isolates MON 3.1(T) (CECT 8844(T) = DSM 100206(T)) and MDVD1(T) (CECT 8845(T) = DSM 100205(T)) as the respective type strains.

Halomicroarcula salina sp. nov., isolated from a marine solar saltern

Halophilic archaeal strain YGHS18T was isolated from the Yinggehai marine solar saltern near Shanya city of Hainan Province, China. Cells from the strain were observed to be pleomorphic rods, stained Gram-negative, and formed red-pigmented colonies on solid media. Strain YGHS18T was found to be able to grow at 20–50 °C (optimum 37 °C), with 0.9–4.8 M NaCl (optimum 2.1 M) and at pH 5.5–9.0 (optimum pH 7.0). The cells lysed in distilled water and the minimum NaCl concentration to prevent cell lysis was found to be 0.9 M. The major polar lipids of the strain were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, glucosyl mannosyl glucosyl diether and a diglycosyl diether (DGD-2). Strain YGHS18T possessed two heterogeneous 16S rRNA genes (rrnA and rrnB) and both were related to those of members of the genera Haloarcula (93.1–96.9 % sequence similarity) and Halomicroarcula (92.7–96.1 % similarity). The rrnA gene (orthologous gene) of strain YGHS18T clustered phylogenetically with members of the genus Halomicroarcula while the rrnB gene formed a paraphyly with members of the genera Halomicroarcula and Haloarcula . The rpoB′ gene of strain YGHS18T was related phylogenetically to species of the genera Halomicroarcula (91.6–92.7 % sequence similarity) and Haloarcula (91.5–92.4 % similarity). EF-2 gene analysis revealed that strain YGHS18T was related phylogenetically to species of the genus Halomicroarcula (92.2–92.9 % sequence similarity) rather than to those of the genus Haloarcula (90.9–91.7 % similarity). The DNA G+C content of strain YGHS18T was determined to be 64.5 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain YGHS18T ( = CGMCC 1.12128T = JCM 18369T) represents a novel species of the genus Halomicroarcula , for which the name Halomicroarcula salina sp. nov. is proposed.

Tamlana nanhaiensis sp. nov., isolated from surface seawater collected from the South China Sea

A polyphasic taxonomic study was performed on a strain, designated FHC16(T), which was isolated from surface seawater collected from the South China Sea. Cells of strain FHC16(T) are Gram stain-negative, oxidase- and catalase-positive and non-motile rods. Growth was observed at 15-37 °C (optimum, 25-30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0-5 % (w/v) NaCl (optimum, 3%). 16S rRNA gene sequence analysis showed that strain FHC16(T) is most closely related to Tamlana sedimentorum JCM 19808(T) (98.2% sequence similarity). The ANI value between strain FHC16(T) and T. sedimentorum JCM 19808(T) was found to be 81.82-81.81%. The DNA-DNA hybridization estimated value between strain FHC16(T) and T. sedimentorum JCM 19808(T) was determined to be 25.8 ± 2.41%. The principal fatty acids (>5% of the total) were found to be iso-C(15:0), iso G-C(15:1), iso-C(17:0) 3-OH, iso-C(15:0) 3-OH and summed feature 3 (comprising C(16:1)ω7c/C(16:1)ω6c). The strain was found to have MK-6 as the major respiratory menaquinone, which is consistent with the other three recognized Tamlana species, T. sedimentorum, Tamlana crocina and Tamlana agarivorans. The polar lipids were found to comprise phosphatidylethanolamine, one unidentified aminophospholipid, two unidentified aminolipids and seven unidentified lipids. The G+C content of the chromosomal DNA was determined to be 34.2 mol%. On the basis of phenotypic, chemotaxonomic and molecular data, strain FHC16(T) is considered to represent a novel species of the genus Tamlana, for which the name Tamlana nanhaiensis sp. nov. is proposed. The type strain is FHC16(T) (.LMG 27420(T) = CGMCC 1.12469(T) = MCCC 1A06648(T)).

Pseudomonas matsuisoli sp. nov., isolated from a soil sample

An aerobic, Gram-stain-negative, rod-shaped and polar-flagellated bacterium, designated strain CC-MHH0089T, was isolated from a soil sample taken on Matsu Island (Taiwan). Strain CC-MHH0089T grew at 15–30 °C and pH 5.0–10.0 and tolerated ≤8 % (w/v) NaCl. 16S rRNA gene sequence analysis showed high pairwise sequence similarity to Pseudomonas azotifigens 6H33bT (97.3 %) and Pseudomonas balearica SP1402T (96.7 %) and lower sequence similarity to other strains (<96.0 %). In DNA–DNA reassociation experiments, the relatedness of strain CC-MHH0089T to P. azotifigens JCM 12708T was 38.3 % (reciprocal value 19.5 %). Evolutionary trees reconstructed on the basis of 16S rRNA, gyrB and rpoB gene sequences revealed a varying phylogenetic neighbourhood of strain CC-MHH0089T with regard to the most closely related type strains. The predominant quinone system was ubiquinone 9 (Q-9) and the DNA G+C content was 63.6 mol%. The major fatty acids were C12 : 0, C16 : 0, C17 : 0, C19 : 0 cyclo ω8c and summed features 2 (C14 : 0 3-OH/iso-C16 : 1 I), 3 (C16 : 1ω7c/C16 : 1ω6c) and 8 (C18 : 1ω7c/C18 : 1ω6c). The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. According to its distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-MHH0089T is proposed to represent a novel species within the genus Pseudomonas , for which the name Pseudomonas matsuisoli sp. nov. is proposed. The type strain is CC-MHH0089T ( = BCRC 80771T = JCM 30078T).

Red soils harbor diverse culturable actinomycetes that are promising sources of novel secondary metabolites

Red soils, which are widely distributed in tropical and subtropical regions of southern China, are characterized by low organic carbon, high content of iron oxides, and acidity and, hence, are likely to be ideal habitats for acidophilic actinomycetes. However, the diversity and biosynthetic potential of actinomycetes in such habitats are underexplored. Here, a total of 600 actinomycete strains were isolated from red soils collected in Jiangxi Province in southeast China. 16S rRNA gene sequence analysis revealed a high diversity of the isolates, which were distributed into 26 genera, 10 families, and 7 orders within the class Actinobacteria; these taxa contained at least 49 phylotypes that are likely to represent new species within 15 genera. The isolates showed good physiological potentials for biosynthesis and biocontrol. Chemical screening of 107 semirandomly selected isolates spanning 20 genera revealed the presence of at least 193 secondary metabolites from 52 isolates, of which 125 compounds from 39 isolates of 12 genera were putatively novel. Macrolides, polyethers, diketopiperazines, and siderophores accounted for most of the known compounds. The structures of six novel compounds were elucidated, two of which had a unique skeleton and represented characteristic secondary metabolites of a putative novel Streptomyces phylotype. These results demonstrate that red soils are rich reservoirs for diverse culturable actinomycetes, notably members of the families Streptomycetaceae, Pseudonocardiaceae, and Streptosporangiaceae, with the capacity to synthesize novel bioactive compounds.

Streptomyces fractus sp. nov., a novel streptomycete isolated from the gut of a South African termite

An actinobacterial strain, MV32(T), was isolated from the paunch region of the hindgut of a South African termite, Amitermes hastatus, as part of an investigation of the actinobacterial population residing within this higher order termite species. Strain MV32(T) was chosen for further study from amongst the many potentially novel actinomycete isolates because of its strong antibacterial activity against Mycobacterium aurum A+. 16S rRNA gene phylogenetic analyses clearly placed strain MV32(T) within the genus Streptomyces, with 99.3% sequence similarity to its closest relative, Streptomyces endophyticus YIM 65594(T). Despite this high sequence similarity, DNA-DNA hybridisation analysis showed a DNA relatedness value of 62 ± 2%, to S. endophyticus DSM 41984(T) (indicating that strain MV32(T) belongs to a different genomic species), as well as values of 14.4 ± 0.8 and 10.4 ± 2.9%, respectively, to its next closest relatives, Streptomyces kunmingensis NRRL B-16240(T) and Streptomyces cinnabarinus NRRL B-12382(T). Based on these results and supported by both chemotaxonomic data and a number of phenotypic differences, strain MV32(T) is proposed to represent a new species within the genus Streptomyces, with the name Streptomyces fractus (= DSM 42163(T) = NRRL B-59159(T)).

Genome-wide gene order distances support clustering the gram-positive bacteria

Initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a Monte Carlo method to estimate the conservation of gene order. The method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. The raw distances were then corrected for gene order convergence using an adaptation of the Jukes-Cantor model, as well as using the common distance correction D' = -ln(1-D). First, we compared the distances found via the order of six orthologs to distances found based on ortholog gene content and small subunit rRNA sequences. The Jukes-Cantor gene order distances are reasonably well correlated with the divergence of rRNA (R (2) = 0.24), especially at rRNA Jukes-Cantor distances of less than 0.2 (R (2) = 0.52). Gene content is only weakly correlated with rRNA divergence (R (2) = 0.04) over all distances, however, it is especially strongly correlated at rRNA Jukes-Cantor distances of less than 0.1 (R (2) = 0.67). This initial work suggests that gene order may be useful in conjunction with other methods to help understand the relatedness of genomes. Using the gene order distances in 143 genomes, the relations of prokaryotes were studied using neighbor joining and agreement subtrees. We then repeated our study of the relations of prokaryotes using gene order in 172 complete genomes better representing a wider-diversity of prokaryotes. Consistently, our trees show the Actinobacteria as a sister group to the bulk of the Firmicutes. In fact, the robustness of gene order support was found to be considerably greater for uniting these two phyla than for uniting any of the proteobacterial classes together. The results are supportive of the idea that Actinobacteria and Firmicutes are closely related, which in turn implies a single origin for the gram-positive cell.

Actinokineospora spheciospongiae sp. nov., isolated from the marine sponge Spheciospongia vagabunda

A Gram-staining-positive, aerobic organism, isolated from the Red Sea sponge Spheciospongia vagabunda was investigated to determine its taxonomic position. On the basis of results of 16S rRNA gene sequence analysis strain EG49(T) was most closely related to Actinokineospora cibodasensis and Actinokineospora baliensis (both 97.3 % similarity) and Actinokineospora diospyrosa and Actinokineospora auranticolor (both 97.0 % similarity). The 16S rRNA gene sequence similarity to all other species of the genus Actinokineospora was <97.0 %. The quinone system of strain EG49(T) contained the menaquinones MK-9(H4) (47 %), MK-9(H6) (27 %) and MK-9(H2) (15 %) in major amounts. Minor amounts of MK-7(H4) (2 %), MK-9(H0) (1 %), MK-9(H8) (3 %) and MK-10(H4) (3 %) were detected as well in addition to MK-8(H4), MK-8(H6), MK-10(H2) and MK-10(H6) (all <1 %). The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. In the polar lipid profile, diphosphatidylglycerol, phosphatidylethanolamine and hydroxyphosphatidylethanolamine were predominant. Phosphatidylinositol-mannoside, two unidentified phospholipids and two glycoglipids as well as one aminoglycolipid, one aminolipid and one unidentified lipid were found in addition. The fatty acid profile was composed of mainly iso-branched fatty acids: iso-C16 : 0, iso-C14 : 0, iso-C15 : 0 and iso-C16 : 1H. All these findings clearly supported the classification of the strain as representing a member of the genus Actinokineospora. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain EG49(T) from the most closely related species of the genus Actinokineospora. Strain EG49(T) represents a novel species of the genus Actinokineospora, for which we propose the name Actinokineospora spheciospongiae sp. nov., with strain EG49(T) ( = DSM 45935(T) = CCM 8480(T) = LMG 27700(T)) as the type strain.

Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov

A taxonomic study was carried out on strain P73T, which was isolated from deep-sea sediment of the Indian Ocean by enrichment of polycyclic aromatic hydrocarbons. The strain was able to degrade biphenyl, naphthalene, 2-methylnaphthalene, 2,6-dimethylnaphthalene, acenaphthene, anthracene, phenanthrene, dibenzothiophene, dibenzofuran, fluorene, 4-methyldibenzothiophene and fluoranthene, but not pyrene or chrysene. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P73T formed a clade with the genera Celeribacter and Huaishuia within the family Rhodobacteraceae , with highest sequence similarity of 96.98 % to Celeribacter neptunius H 14T, followed by Huaishuia halophila ZXM137T (96.42 %). The bacterium was Gram-stain-negative, oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at salinities from 0.5 to 12 % and at temperatures from 10 to 41 °C. The principal fatty acids (>10 %) of strain P73T were summed feature 8 (C18 : 1ω7c/ω6c) and C19 : 0ω8c cyclo. The sole respiratory quinone was Q-10. The major lipids were phosphatidylglycerol, one unknown aminolipid, one unknown phospholipid and one unknown lipid; a second unknown phospholipid and one unknown glycolipid were present as minor components. The G+C content of the chromosomal DNA was 66.0 mol%. The combined genotypic and phenotypic data show that strain P73T represents a novel species of the genus Celeribacter , for which the name Celeribacter indicus sp. nov. is proposed. The type strain is P73T ( = MCCC 1A01112T = LMG 27600T = DSM 27257T). Phylogenetic study and existing phenotypic information also show that Huaishuia halophila should be transferred to the genus Celeribacter as Celeribacter halophilus comb. nov. (type strain ZXM137T = MCCC 1A06432T = CGMCC 1.8891T = LMG 24854T).

Belliella kenyensis sp. nov., isolated from an alkaline lake

A red-pigmented, Gram-reaction-negative, aerobic bacterial strain, designated No.164(T), was isolated from sediment sample from the alkaline Lake Elmenteita located in the Kenyan Rift Valley. Results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Belliella, with the highest sequence similarity (97 %) to Belliella pelovolcani DSM 46698(T). Optimal growth temperature was 30-35 °C, at pH 7.0-12.0 in the presence of 0-4 % (w/v) NaCl. Flexirubins were absent. The respiratory menaquinone (MK-7), predominant cellular fatty acids (iso-C15 : 0, anteiso-C15 : 0 and a mixture of C16 : 1ω7c and/or iso-C15 : 0 2-OH) and DNA G+C content (38.1 mol%) of strain No.164(T) were consistent with those of other members of the genus Belliella. The polar lipids consisted of phosphatidylethanolamine, eight unspecified lipids and one unspecified phospholipid. Several phenotypic characteristics can be used to differentiate this isolate from those of other species of the genus Belliella. The results of polyphasic analyses presented in this study indicated that this isolate should be classified as representing a novel species of the genus Belliella. The name Belliella kenyensis sp. nov. is therefore proposed; the type strain is strain No.164(T) ( = DSM 46651(T) = CECT 8551(T)).