Ornithinicoccus hortensis gen. nov., sp. nov., a soil actinomycete which contains L-ornithine

Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field

A Gram-stain-positive actinobacterial strain, designated YJ01T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01T was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5–1.9 µm, and was able to grow at 10–37 °C (optimum, 28–30 °C), at pH 4.5–9.0 (optimum, pH 7.0–8.0) and at salinities of 0–7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01T with closely related relatives were in the range 96.2–92.8 %, and the results of phylogenomic analysis indicated that strain YJ01T was clearly separated from species of genera in the family Intrasporangiaceae showing average nucleotide identity values of 84.2–83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn–Gly2–d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01T is considered to represent a novel species of a new genus in the family Intrasporangiaceae , for which the name Segeticoccus rhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccus rhizosphaerae is YJ01T (=KACC 19547T=NBRC 113173T).

Ornithinicoccus soli sp. nov., isolated from farmland soil

A Gram-stain-positive, aerobic, non-motile and coccoid-shaped bacterium, designated XNB-1^T, was isolated from farmland soil in Taian, Shandong province, China. Strain XNB-1^T contained iso-C_15 : 0 and iso-C_16 : 0 as the predominant fatty acids. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn←Gly_{(1, 2)}←d-Glu. The polar lipid profile of strain XNB-1^T consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid and three unidentified phospholipids. The predominant menaquinone of strain XNB-1^T was MK-8(H₄) and the DNA G+C content was 70.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XNB-1^T belonged to the genus Ornithinicoccus, and shared the highest similarity with Ornithinicoccus hortensis HKI 0125^T (96.0 %), followed by Ornithinicoccus halotolerans EGI 80423^T (95.5 %). Genome-based analysis of average nucleotide identity of strain XNB-1^T with O. hortensis HKI 0125^T and O. halotolerans EGI 80423^T yielded values of 73.1 and 73.3 %, respectively, while the digital DNA-DNA hybridization values were 19.5 and 19.9 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain XNB-1^T is considered to represent a novel species of the genus Ornithinicoccus, for which the name Ornithinicoccus soli sp. nov. is proposed. The type strain is XNB-1^T (=CCTCC AB 2019099^T=KCTC 49259^T).

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Ornithinicoccus halotolerans sp. nov., and emended description of the genus Ornithinicoccus

A halotolerant actinobacterial strain, designated EGI 80423T, was isolated from a desert soil of Xinjiang, north-west China, and subjected to a polyphasic taxonomic characterization. Strain EGI 80423T grew at pH 7.0-10.0 and with 0-14.0% (w/v) NaCl, optimally at pH 8.0-9.0 and with 2.0-4.0% (w/v) NaCl. Cells of strain EGI 80423T were Gram-stain-positive, non-motile cocci with diameters of 0.6-0.8 μm. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was Orn ← Glu. The major fatty acids identified were iso-C17:1ω9c, iso-C15:0 and iso-C17:0. The predominant menaquinone was MK-8(H4), while the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unknown phospholipids, two unknown glycolipids, six unknown phosphoglycolipids and five unknown polar lipids. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EGI 80423T clustered with the single member of the genus Ornithinicoccus. Sequence similarity between strain EGI 80423T and Ornithinicoccus hortensis NBRC 16434T. Because the type strain has been provided by NBRC, Japan was 97.7%. The DNA-DNA relatedness value between strain EGI 80423T and O. hortensis NBRC 16434T was 36.84%. Based on morphological, chemotaxonomic and phylogenetic characteristics, and DNA-DNA hybridization data, strain EGI 80423T represents a novel species of the genus Ornithinicoccus, for which the name Ornithinicoccus halotolerans sp. nov. is proposed. The type strain is EGI 80423T (=CGMCC 1.14989T=KCTC 39700T). The description of the genus Ornithinicoccus has also been emended.

Monashia flava gen. nov., sp. nov., an actinobacterium of the family Intrasporangiaceae

A novel actinobacterial strain, MUSC 78^T, was isolated from a mangrove soil collected from Peninsular Malaysia. The taxonomic status of this strain was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain MUSC 78^T represented a novel lineage within the class Actinobacteria. Strain MUSC 78^T formed a distinct clade in the family Intrasporangiaceae and was related most closely to members of the genera Terrabacter (98.3-96.8 % 16S rRNA gene sequence similarity), Intrasporangium (98.2-96.8 %), Humibacillus (97.2 %), Janibacter (97.0-95.3 %), Terracoccus (96.8 %), Kribbia (96.6 %), Phycicoccus (96.2-94.7 %), Knoellia (96.1-94.8 %), Tetrasphaera (96.0-94.9 %) and Lapillicoccus (95.9 %). Cells were irregular rod-shaped or cocci and stained Gram-positive. The cell-wall peptidoglycan type was A3γ, with ll-diaminopimelic acid as the diagnostic diamino acid. The main cell-wall sugar was mannose and lower amounts of galactose and rhamnose were present. The predominant menaquinone was MK-8(H₄). The polar lipid profile consisted of phosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, diphosphatidylglycerol and phosphoglycolipid. The predominant fatty acids were iso-C_15 : 0, anteiso-C_15 : 0 and iso-C_16 : 0. The DNA G+C content was 73.1 mol%. Based on this polyphasic study, MUSC 78^T exhibited phylogenetic and phenotypic differences from members of the genera of the family Intrasporangiaceae, and therefore a novel species of a new genus, Monashia flava gen. nov., sp. nov., is proposed. The type strain of Monashia flava is MUSC 78^T ( = DSM 29621^T = MCCC 1K00454^T = NBRC 110749^T).

Oryzobacter terrae gen. nov., sp. nov., isolated from paddy soil

A bacterial strain, PSGM2-16(T), was isolated from a pot of paddy soil grown with rice in Suwon region, Republic of Korea, and was characterized as having aerobic, Gram-stain-positive, short-rod-shaped cells with one polar flagellum. The 16S rRNA gene sequence of strain PSGM2-16(T) revealed the highest sequence similarities with Knoellia locipacati DMZ1T (97.4%), Fodinibacter luteus YIM C003(T) (97.2%) and Lapillicoccus jejuensis R-Ac013(T) (97.0%), and the phylogenetic tree showed that strain PSGM2-16(T) formed a subgroup with Ornithinibacter aureus HB09001(T) and F. luteus YIM C003(T) within the family Intrasporangiaceae. The major fatty acids (>10% of the total fatty acids) of strain PSGM2-16(T) were iso-C16 : 0, C17 : 1ω8c and iso-C14 : 0. The predominant menaquinone was MK-8(H4). The polar lipids present were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three aminophospholipids and two phospholipids. The peptidoglycan was type A4γ with meso-diaminopimelic acid as the diagnostic diamino acid. DNA-DNA hybridization values between strain PSGM2-16(T) and closely related taxa were much less than 70%. The genomic DNA G+C content of strain PSGM2-16(T) was 70.0 mol%. On the basis of the evidence presented, it is concluded that strain PSGM2-16(T) represents a novel species of a new genus in the family Intrasporangiaceae, for which the name Oryzobacter terrae gen. nov., sp. nov. is proposed. The type strain of the type species is PSGM2-16(T) ( = KACC 17299(T)= DSM 27137(T)= NBRC 109598(T)).

Oryzihumus terrae sp. nov., isolated from soil and emended description of the genus Oryzihumus

A Gram-stain-positive, aerobic, non-flagellated bacterium, designated KIS22-12(T), was isolated from a soil sample of Baengnyeong Island in Onjin county, Republic of Korea. Cells were non-spore-forming cocci showing catalase-positive and oxidase-negative reactions. Growth of strain KIS22-12(T) was observed between 10 and 35 °C (optimum, 28-30 °C), between pH 5.0 and 9.0 (optimum, pH 7.0) and with 0-3% (w/v) NaCl. Strain KIS22-12(T) contained MK-8(H4) as the predominant menaquinone, and C17 : 1ω8c, iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. Strain KIS22-12(T) contained diphosphatidylglycerol, phosphatidylinositol, one unknown aminophospholipid, one unknown aminolipid, two unknown phospholipids and one unknown lipid. The peptidoglycan type was A1γ. The G+C content of the genomic DNA was 75.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KIS22-12(T) formed a phyletic lineage with Oryzihumus leptocrescens KV-628(T). 16S rRNA gene sequence similarity between the two strains was 96.5%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain KIS22-12(T) represents a novel species within the genus Oryzihumus, for which the name Oryzihumus terrae sp. nov. is proposed. The type strain is KIS22-12(T) ( = KACC 16543(T) = DSM 27161(T) = NBRC 109596(T)). An emended description of the genus Oryzihumus is also provided.

Ornithinimicrobium murale sp. nov., isolated from an indoor wall colonized by moulds

A Gram-positive, non-spore-forming actinobacterium (01-Gi-040(T)) isolated from an indoor wall was studied to examine its taxonomic position. The isolate formed a very rudimentary substrate-mycelium that fragmented into rod-shaped to coccoid cells. On the basis of the 16S rRNA gene sequence similarity studies, strain 01-Gi-040(T) was shown to belong to the genus Ornithinimicrobium closely related to Ornithinimicrobium kibberense K22-20(T) (97.1 %), Ornithinimicrobium humiphilum DSM 12362(T) (96.2 %) and Ornithinimicrobium pekingense LW6(T) (96.1 %). A close relationship was also found with Arsenicicoccus bolidensis CCUG 47306(T) (95.9 %) and Arsenicicoccus piscis Kis4-19(T) (95.7 %) and a moderate relationship to the type strains of the genus Serinicoccus (94.0-94.1 %). The predominant menaquinone of strain 01-Gi-040(T) was MK-8(H(4)). The peptidoglycan contained ornithine as the diagnostic diamino acid. The polar lipid profile consisted of the lipids phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid, an unknown aminolipid and two unknown phosphoglycolipids. The major fatty acids iso-C(15 : 0), iso-C(16 : 0) and iso-C(17 : 0) were consistent with the fatty acid patterns reported for members of the genus Ornithinimicrobium. The results of DNA-DNA hybridizations, physiological and biochemical tests allowed phenotypic differentiation of strain 01-Gi-040(T) from the three recognized species of the genus Ornithinimicrobium. Strain 01-Gi-040(T) represents a novel species of the genus Ornithinimicrobium, for which we propose the name Ornithinimicrobium murale sp. nov., with the type strain 01-Gi-040(T) (= DSM 22056(T) = CCM 7610(T)).

Ornithinibacter aureus gen. nov., sp. nov., a novel member of the family Intrasporangiaceae

A novel strain of the class Actinobacteria was isolated from a seawater sample collected in the South China Sea using modified R2A agar plates. The strain was a Gram-stain-positive, non-motile, non-spore-forming, catalase-positive, irregular rod-shaped bacterium. The strain grew at 4–45 °C and pH 5.0–10.2, and tolerated 5 % (w/v) NaCl. Based on its 16S rRNA gene sequence, the organism was related phylogenetically to members of the genera Fodinibacter (96.7 % similarity), Lapillicoccus (96.5 %), Knoellia (95.0–95.8 %), Oryzihumus (95.6 %) and Humibacillus (95.6 %). The cell-wall contained l-ornithine as the major diagnostic diamino acid in the peptidoglycan. MK-8(H4) was the predominant menaquinone. Major cellular fatty acids were iso-C18 : 1 ω9c, iso-C16 : 0, iso-C15 : 0 and C17 : 0. The G+C content of the DNA was 69.6 mol%. Phenotypic and phylogenetic data revealed that this strain represents a novel species in a new genus of the family Intrasporangiaceae, for which the name Ornithinibacter aureus gen. nov., sp. nov. is proposed; the type strain of Ornithinibacter aureus is HB09001T (=CGMCC 1.10341T =DSM 23364T).

Angustibacter luteus gen. nov., sp. nov., isolated from subarctic forest soil

An actinobacterial strain was isolated from subarctic forest soil, and subjected to polyphasic taxonomic characterization. The cell-wall peptidoglycan comprised meso-diaminopimelic acid, alanine and glutamic acid. MK-9(H4) was the predominant isoprenoid quinone, and iso-C17 : 0, iso-C15 : 0 and C16 : 0 were detected as the major cellular fatty acids. Phylogenetic analyses based on 16S rRNA gene sequences showed that this organism was related to members of the suborders Kineosporiineae and Micrococcineae. The phenotypic properties readily differentiated this organism from the phylogenetic neighbours. Based on the phenotypic and genotypic evidence, the strain is assigned to a novel species of a novel genus: Angustibacter luteus gen. nov., sp. nov. with type strain TT07R-79T (=NBRC 105387T =KACC 14249T).

Transfer of Bacillus mucilaginosus and Bacillus edaphicus to the genus Paenibacillus as Paenibacillus mucilaginosus comb. nov. and Paenibacillus edaphicus comb. nov

Bacillus mucilaginosus and Bacillus edaphicus were reclassified based on their 16S rRNA and gyrB gene sequences, DNA–DNA hybridization, fatty acid methyl esters and other taxonomic characteristics. Phylogenetic analysis based on 16S rRNA and gyrB gene sequences indicated that strains of B. mucilaginosus and B. edaphicus were members of the genus Paenibacillus, with over 90.4 % and 70.3 % sequence similarity, respectively. Their DNA G+C contents were 54.5–56.8 mol%. The DNA–DNA relatedness values of B. edaphicus VKPM B-7517T with B. mucilaginosus KNP414 and B. mucilaginosus CGMCC 1.236 were 89.2 % and 88.7 %, respectively. The major isoprenoid quinone of B. mucilaginosus and B. edaphicus was MK-7 (94.1–95.7 %). The peptidoglycan type was A1γ (meso-diaminopimelic acid) and the major polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were anteiso-C15 : 0, C16 : 1 ω11c and C16 : 0. Phenotypic features and fatty acid profiles supported the similarity of B. mucilaginosus and B. edaphicus to Paenibacillus validus CCTCC 95016T and confirmed their relationship with members of the genus Paenibacillus. Therefore, it is proposed that Bacillus mucilaginosus and Bacillus edaphicus be transferred to the genus Paenibacillus as Paenibacillus mucilaginosus comb. nov. (type strain HSCC 1605T=VKPM B-7519T=VKM B-1480DT=CIP 105815T=KCTC 3870T) and Paenibacillus edaphicus comb. nov. (type strain VKPM B-7517T=DSM 12974T=CIP 105814T), respectively.

Fodinibacter luteus gen. nov., sp. nov., an actinobacterium isolated from a salt mine

A Gram-positive-staining, aerobic, catalase- and oxidase-positive, irregular short rod-shaped actinobacterium, designated strain YIM C003T, was isolated from a salt mine in Yunnan, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM C003T was most closely related to strains of the genera Knoellia (94.2-96.0% similarity), Oryzihumus (95.6%), Terrabacter (94.9-95.4%), Janibacter (94.9-95.4%), Kribbia (95.0%), Lapillicoccus (95.0%) and Phycicoccus (94.2-95.0%) of the family Intrasporangiaceae and that it formed an independent monophyletic lineage with three strains of Oryzihumus leptocrescens. The DNA G+C content of strain YIM C003T was 72.0 mol%. The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The predominant menaquinone was MK-8(H4). Mycolic acids were not detected. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. The major cellular fatty acids were C18:1omega9c and C16:0. These chemotaxonomic properties, together with data from phylogenetic analysis, enabled the novel isolate to be differentiated from all other members of the family. A novel species in a new genus, Fodinibacter luteus gen. nov., sp. nov., is proposed, with strain YIM C003T (=DSM 21208T=CCTCC AA 208036T) as the type strain of Fodinibacter luteus.

An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa

The higher ranks of the class Actinobacteria were proposed and described in 1997. At each rank, the taxa were delineated from each other solely on the basis of 16S rRNA gene sequence phylogenetic clustering and taxon-specific 16S rRNA signature nucleotides. In the past 10 years, many novel members have been assigned to this class while, at the same time, some members have been reclassified. The new 16S rRNA gene sequence information and the changes in phylogenetic positions of some taxa influence decisions about which 16S rRNA nucleotides to define as taxon-specific. As a consequence, the phylogenetic relationships of Actinobacteria at higher levels may need to be reconstructed. Here, we present new 16S rRNA signature nucleotide patterns of taxa above the family level and indicate the affiliation of genera to families. These sets replace the signatures published in 1997. In addition, Actinopolysporineae subord. nov. and Actinopolysporaceae fam. nov. are proposed to accommodate the genus Actinopolyspora, Kineosporiineae subord. nov. and Kineosporiaceae fam. nov. are proposed to accommodate the genera Kineococcus, Kineosporia and Quadrisphaera, Beutenbergiaceae fam. nov. is proposed to accommodate the genera Beutenbergia, Georgenia and Salana and Cryptosporangiaceae fam. nov. is proposed to accommodate the genus Cryptosporangium. The families Nocardiaceae and Gordoniaceae are proposed to be combined in an emended family Nocardiaceae. Emended descriptions are also proposed for most of the other higher taxa.

Stability of microbial communities in goat milk during a lactation year: Molecular approaches

The microbial communities in milks from one herd were evaluated during 1-year of lactation, using molecular methods to evaluate their stability and the effect of breeding conditions on their composition. The diversity of microbial communities was measured using two approaches: molecular identification by 16S and 18S rDNA sequencing of isolates from counting media (two milks), and direct identification using 16S rDNA from clone libraries (six milks). The stability of these communities was evaluated by counting on selective media and by Single Strand Conformation Polymorphism (SSCP) analysis of variable region V3 of the 16S rRNA gene and variable region V4 of the 18S rRNA gene. One hundred and eighteen milk samples taken throughout the year were analyzed. Wide diversity among bacteria and yeasts in the milk was revealed. In addition to species commonly encountered in milk, such as Lactococcus lactis, Lactococcus garvieae, Enterococcus faecalis, Lactobacillus casei, Leuconostoc mesenteroides, Staphylococcus epidermidis, Staphylococcus simulans, Staphylococcus caprae, Staphylococcus equorum, Micrococcus sp., Kocuria sp., Pantoea agglomerans and Pseudomonas putida, sequences were affiliated to other species only described in cheeses, such as Corynebacterium variabile, Arthrobacter sp., Brachybacterium paraconglomeratum, Clostridium sp. and Rothia sp. Several halophilic species atypical in milk were found, belonging to Jeotgalicoccus psychrophilus, Salinicoccus sp., Dietza maris, Exiguobacterium, Ornithinicoccus sp. and Hahella chejuensis. The yeast community was composed of Debaryomyces hansenii, Kluyveromyces lactis, Trichosporon beigelii, Rhodotorula glutinis, Rhodotorula minuta, Candida pararugosa, Candida intermedia, Candida inconspicua, Cryptococcus curvatus and Cryptococcus magnus. The analyses of microbial counts and microbial SSCP profiles both distinguished four groups of milks corresponding to four periods defined by season and feeding regime. The microbial community was stable within each period. Milks from winter were characterized by Lactococcus and Pseudomonas, those from summer by P. agglomerans and Klebsiella and those from autumn by Chryseobacterium indologenes, Acinetobacter baumanii, Staphylococcus, Corynebacteria and yeasts. However, the composition of the community can vary according to factors other than feeding. This study opens new investigation fields in the field of raw milk microbial ecology.

Staphylococcus pettenkoferi sp. nov., a novel coagulase-negative staphylococcal species isolated from human clinical specimens

Five coagulase-negative, novobiocin-susceptible staphylococcal strains were isolated from human blood cultures in different German and Belgian medical facilities. A novel species, ‘Staphylococcus pettenkoferi’ was proposed recently to accommodate two of these strains (B3117T and A6664), although the name was not validly published. All five strains belonged to the genus Staphylococcus because they were non-motile, Gram-positive, catalase-positive cocci with peptidoglycan type (A3α type l-lys–gly2–4–l-Ser–Gly), menaquinone pattern (MK-7, MK-6 and MK-8) and major cellular fatty acids (ai-C15 : 0, ai-C17 : 0 and i-C15 : 0) that corresponded to those of staphylococci. Phenotypically, the isolates most closely resembled Staphylococcus capitis subsp. capitis and Staphylococcus auricularis, but they could be distinguished from these species by physiological tests and chemotaxonomic investigations. The results of DNA–DNA hybridization, chemotaxonomic investigations and 16S rRNA gene and RNA polymerase B gene (rpoB) sequence analysis enabled strains B3117T, K6999, 229 and 230 to be differentiated genotypically and phenotypically from known Staphylococcus species, indicating that these isolates are representatives of a novel species. The name Staphylococcus pettenkoferi sp. nov. is proposed for this novel species, with strain B3117T (=CIP 107711T=CCUG 51270T) as the type strain. Due to differences in the results of physiological and chemotaxonomic investigations and DNA–DNA hybridization data, strain A6664 was not included in the description of the novel species.

Ruania albidiflava gen. nov., sp. nov., a novel member of the suborder Micrococcineae

A Gram-positive, coccoid, non-spore-forming bacterium, designated strain 3-6T, was isolated from farmland soil and subjected to a polyphasic taxonomic analysis. Comparative analysis of the 16S rRNA gene sequence revealed that the strain represented a novel member of the suborder Micrococcineae. Its nearest phylogenetic neighbour was the type strain of Georgenia muralis (94.2 % 16S rRNA gene sequence similarity). Chemotaxonomic characteristics of strain 3-6T were as follows: the major menaquinone was MK-8(H4); the polar lipids consisted mainly of diphosphatidylglycerol, phosphatidylglycerol and one unknown glycolipid; the predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0; mycolic acids were absent. A new murein type, l-lys–gly–l-glu–l-Glu (A4α), was found in the peptidoglycan of the cell wall. The DNA G+C content was 69.8 mol%. On the basis of morphological, chemotaxonomic and phylogenetic characteristics, it is suggested that strain 3-6T represents a novel species of a new genus within the suborder Micrococcineae, for which the name Ruania albidiflava gen. nov., sp. nov. is proposed. The type strain of Ruania albidiflava is 3-6T (=CGMCC 4.3142T=DSM 18029T=JCM 13910T=PCM 2644T).

Demequina aestuarii gen. nov., sp. nov., a novel actinomycete of the suborder Micrococcineae, and reclassification of Cellulomonas fermentans Bagnara et al. 1985 as Actinotalea fermentans gen. nov., comb. nov

An actinobacterial strain containing demethylmenaquinone DMK-9(H4) as the diagnostic isoprenoid quinone was isolated from a tidal flat sediment sample, from South Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JC2054T represents a distinct phyletic line within the suborder Micrococcineae of the order Actinomycetales. The closest phylogenetic neighbour was Cellulomonas fermentans, with 94.7 % 16S rRNA gene sequence similarity. The novel isolate was strictly aerobic and slightly halophilic, with optimum growth occurring in 2–4 % (w/v) NaCl. Cells were non-motile, non-sporulating and rod-shaped. The peptidoglycan type was of the A-type of cross-linkage. l-ornithine was the diamino acid and d-glutamate represented the N-terminus of the interpeptide bridge. The predominant fatty acids were anteiso-branched and straight-chain fatty acids. The major polar lipids were phosphatidylinositol, diphosphatidylglycerol and an unknown phospholipid. The menaquinone composition of C. fermentans was determined to be MK-10(H4), MK-9(H4) and MK-8(H4) in the ratio 56 : 2 : 1. On the basis of the polyphasic evidence presented in this study, it is proposed that strain JC2054T should be classified as representing a novel genus and species of the suborder Micrococcineae, with the name Demequina aestuarii gen. nov., sp. nov. The type strain is JC2054T (=IMSNU 14027T=KCTC 9919T=JCM 12123T). In addition, it was clear from the phylogenetic analysis and chemotaxonomic data that C. fermentans does not belong to the genus Cellulomonas or any other recognized genera. Therefore, C. fermentans should be reclassified as representing a novel genus, for which the name Actinotalea fermentans gen. nov., comb. nov. is proposed, with strain DSM 3133T (=ATCC 43279T=CFBP 4259T=CIP 103003T=NBRC 15517T=JCM 9966T=LMG 16154T) as the type strain.

Phycicoccus jejuensis gen. nov., sp. nov., an actinomycete isolated from seaweed

A marine actinomycete strain, designated KSW2-15T, was isolated from a dried seaweed sample collected from a sandy beach on the coast of Jeju in the Republic of Korea. The organism produced non-motile, non-endospore-forming, Gram-positive, coccoid cells. The colonies were circular, translucent and yellow in colour with entire margins. meso-Diaminopimelic acid was present as the diamino acid of the peptidoglycan. The acyl type of the muramic acid was acetyl. Mycolic acids were not present. The predominant menaquinone was MK-8(H4). The polar lipids were phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were of the saturated, unsaturated and iso-branched methyl types. The DNA G+C content was 74 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain KSW2-15T formed a loose association with ‘Candidatus Nostocoida limicola’, within the radiation of the family Intrasporangiaceae of the suborder Micrococcineae. The organism showed the highest levels of sequence similarity with ‘Candidatus Nostocoida limicola’ (96.1 %), Terrabacter tumescens (96.1 %) and Terrabacter terrae (96.0 %). The levels of 16S rRNA gene sequence similarity between the isolate and members of other genera of the family Intrasporangiaceae were in the range 92.1–95.5 %. On the basis of the polyphasic evidence, the isolate should be classified within a novel genus and species, for which the name Phycicoccus jejuensis gen. nov., sp. nov. is proposed. The type strain of Phycicoccus jejuensis is strain KSW2-15T (=KCCM 42315T=NRRL B-24460T).

Isolates of ‘Candidatus Nostocoida limicola’ Blackall et al. 2000 should be described as three novel species of the genus Tetrasphaera, as Tetrasphaera jenkinsii sp. nov., Tetrasphaera vanveenii sp. nov. and Tetrasphaera veronensis sp. nov

Despite differences in their morphologies, comparative analyses of 16S rRNA gene sequences revealed high levels of similarity (>94 %) between strains of the filamentous bacterium ‘Candidatus Nostocoida limicola’ and the cocci Tetrasphaera australiensis and Tetrasphaera japonica and the rod Tetrasphaera elongata, all isolated from activated sludge. These sequence data and their chemotaxonomic characters, including cell wall, menaquinone and lipid compositions and fingerprints of their 16S–23S rRNA intergenic regions, support the proposition that these isolates should be combined into a single genus containing six species, in the family Intrasporangiaceae in the Actinobacteria. This suggestion receives additional support from DNA–DNA hybridization data and when partial sequences of the rpoC1 gene are compared between these strains. Even though few phenotypic characterization data were obtained for these slowly growing isolates, it is proposed, on the basis of the extensive chemotaxonomic and molecular evidence presented here, that ‘Candidatus N. limicola’ strains Ben 17, Ben 18, Ben 67, Ben 68 and Ben 74 all be placed into the species Tetrasphaera jenkinsii sp. nov. (type strain Ben 74T=DSM 17519T=NCIMB 14128T), ‘Candidatus N. limicola’ strain Ben 70 into Tetrasphaera vanveenii sp. nov. (type strain Ben 70T=DSM 17518T=NCIMB 14127T) and ‘Candidatus N. limicola’ strains Ver 1 and Ver 2 into Tetrasphaera veronensis sp. nov. (type strain Ver 1T=DSM 17520T=NCIMB 14129T).

Kribbia dieselivorans gen. nov., sp. nov., a novel member of the family Intrasporangiaceae

Two Gram-positive, catalase-positive, irregular short rod- or coccoid-shaped bacterial strains, N113T and R33, were isolated from an enrichment culture with diesel oil-degradation activity and their taxonomic positions were investigated using a polyphasic approach. Phenotypic, phylogenetic and genetic similarities indicated that strains N113T and R33 were representatives of the same species. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains N113T and R33 form a lineage independent from those of members of the family Intrasporangiaceae. The novel isolates had cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-8(H4) as the predominant menaquinone and 10-methyl-C18 : 0, iso-C16 : 0, C18 : 1 ω9c, C16 : 0 and C18 : 0 as the major cellular fatty acids. The DNA G+C contents were 69.6–69.9 mol%. These chemotaxonomic properties, together with phylogenetic distinctiveness, distinguish the two novel strains from recognized members of the family Intrasporangiaceae. On the basis of phenotypic, phylogenetic and genetic data, strains N113T (=KCTC 19143T=JCM 13585T) and R33 are classified as representatives of a novel genus and species, Kribbia dieselivorans gen. nov., sp. nov., within the family Intrasporangiaceae.

Ornithinimicrobium kibberense sp. nov., isolated from the Indian Himalayas

A buff-yellow-pigmented bacterium, strain K22-20T, which was isolated from a cold desert of the Indian Himalayas, was subjected to a polyphasic taxonomic study. Phenotypic and chemical properties of strain K22-20T were consistent with its classification in the genus Ornithinimicrobium. The major fatty acids of the strain were iso-C17 : 1 ω9c (cis-15-methyl 7-hexadecenoic acid), iso-C15 : 0 (13-methyl tetradecanoic acid), iso-C16 : 0 (14-methyl pentadecanoic acid) and iso-C17 : 0 (15-methyl hexadecanoic acid). The G+C content of the genomic DNA was 71 mol%. According to 16S rRNA gene sequence analysis, strain K22-20T was closely related to Ornithinimicrobium humiphilum HKI 0124T (97.7 %). However, genomic relatedness between strain K22-20T and O. humiphilum MTCC 6406T, as revealed by DNA–DNA hybridization, was 64.5 %. Based on the polyphasic data, strain K22-20T (=MTCC 6545T=DSM 17687T=JCM 12763T) represents a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium kibberense sp. nov. is proposed.

Diverse bacteria associated with root nodules of spontaneous legumes in Tunisia and first report for nifH-like gene within the genera Microbacterium and Starkeya

We characterized 34 endophytic bacterial isolates associated to root nodules collected from spontaneous legumes in the arid zone of Tunisia by 16S rDNA polymerase chain reaction (PCR)-restriction fragment length polymorphism, whole cell protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), 16S rDNA and 16S-23S rDNA internal transcribed spacer sequencing. Phylogenetically, these isolates belong to the branches containing the genera Inquilinus, Bosea, Rhodopseudomonas, Paracraurococcus, Phyllobacterium, Ochrobactrum, Starkeya, Sphingomonas, Pseudomonas, Agromyces, Microbacterium, Ornithinicoccus, Bacillus, and Paenibacillus. These strains did not induce any nodule formation when inoculated on the wide host spectrum legume species M. atropurpureum (Siratro) and no nodA gene could be amplified by PCR. However, nifH sequences, most similar to those of Sinorhizobium meliloti, were detected within strains related to the genera Microbacterium, Agromyces, Starkeya and Phyllobacterium.

Terrabacter terrae sp. nov., a novel actinomycete isolated from soil in Spain

A Gram-positive, aerobic, long-rod-shaped, non-spore-forming bacterium (strain PPLB(T)) was isolated from soil mixed with Iberian pig hair. This actinomycete showed keratinase activity in vitro when chicken feathers were added to the culture medium. Strain PPLB(T) was oxidase-negative and catalase-positive and produced lipase and esterase lipase. This actinomycete grew at 40 degrees C on nutrient agar and in the same medium containing 5 % (w/v) NaCl. Growth was observed with many different carbohydrates as the sole carbon source. On the basis of 16S rRNA gene sequence similarity, strain PPLB(T) was shown to belong to the genus Terrabacter of the family Intrasporangiaceae. Strain PPLB(T) showed 98.8 % 16S rRNA gene sequence similarity to Terrabacter tumescens. Chemotaxonomic data, such as the main ubiquinone (MK-8), the main polar lipids (phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol) and the main fatty acids (i-C(15 : 0), ai-C(15 : 0), i-C(16 : 0) and ai-C(17 : 0)) supported the affiliation of strain PPLB(T) to the genus Terrabacter. The G+C content of the DNA was 71 mol%. The results of DNA-DNA hybridization (36.6 % relatedness between Terrabacter tumescens and strain PPLB(T)) and physiological and biochemical tests suggested that strain PPLB(T) belongs to a novel species of the genus Terrabacter, for which the name Terrabacter terrae sp. nov. is proposed. The type strain is PPLB(T) (=CECT 3379T=LMG 22921T).

Oryzihumus leptocrescens gen. nov., sp. nov

Three novel strains were isolated from a soil sample collected in Japan using GPM agar plates supplemented with superoxide dismutase and/or catalase. The strains were Gram-positive, catalase-positive, irregular rod-shaped bacteria with meso-diaminopimelic acid as a peptidoglycan diagnostic diamino acid, and the acyl type of the peptidoglycan was acetyl. The major menaquinone was MK-8(H4). Mycolic acids were not detected. The G+C content of the DNA was 72–73 mol%. On the basis of morphological and chemotaxonomic properties and a phylogenetic analysis using 16S rRNA gene sequences, these strains were classified as a novel genus and species, Oryzihumus leptocrescens gen. nov., sp. nov., in the family Intrasporangiaceae of the order Actinomycetales. The type strain is KV-628T (=NRRL B-24347T=JCM 12835T=NBRC 100762T).

Six novel Arthrobacter species isolated from deteriorated mural paintings

A group of 21 bacterial strains was isolated from samples of biofilm formation in the Servilia tomb (necropolis of Carmona, Spain) and the Saint-Catherine chapel (castle at Herberstein, Austria). A polyphasic taxonomic study of these isolates, including morphological, biochemical and chemotaxonomic characterization, rep-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA base ratio and DNA-DNA relatedness studies, allocated them to the genus Arthrobacter. The isolates represent six novel species, for which the names Arthrobacter castelli sp. nov., Arthrobacter monumenti sp. nov., Arthrobacter parietis sp. nov., Arthrobacter pigmenti sp. nov., Arthrobacter tecti sp. nov. and Arthrobacter tumbae sp. nov. are proposed. The respective type strains are LMG 22283(T) (=DSM 16402(T)), LMG 19502(T) (=DSM 16405(T)), LMG 22281(T) (=DSM 16404(T)), LMG 22284(T) (=DSM 16403(T)), LMG 22282(T) (=DSM 16407(T)) and LMG 19501(T) (=DSM 16406(T)).

Marinococcus halotolerans sp. nov., isolated from Qinghai, north-west China

An aerobic bacterium was isolated from saline soil located in Qinghai, north-west China. The bacterium, designated YIM 70157T, was investigated using a polyphasic taxonomic approach. The Gram reaction of the organism was positive. Comparative 16S rRNA gene sequence analysis demonstrated the isolate to be a member of the genus Marinococcus, the closest phylogenetic neighbour of the unknown bacterium being Marinococcus halophilus DSM 20408T with a similarity of 99·4 %. The peptidoglycan type of YIM 70157T was A1γ, with meso-diaminopimelic acid as diagnostic diamino acid. The major fatty acids were ai-C15 : 0, ai-C17 : 0 and i-C16 : 0. The menaquinones were MK-7 and MK-6. The phospholipids were diphosphatidylglycerol and phosphatidylinositol. The G+C content of total DNA was 48·5 mol%. On the basis of phylogenetic and phenotypic evidence and DNA–DNA hybridization data, this isolate should be classified as a novel species of Marinococcus, for which the name Marinococcus halotolerans sp. nov. is proposed. The type strain is YIM 70157T (=DSM 16375T=KCTC 19045T).

Cellulomonas bogoriensis sp. nov., an alkaliphilic cellulomonad

An alkaliphilic, slightly halotolerant, chemo-organotrophic, Gram-positive, rod-shaped bacterium, strain 69B4T, was isolated from the sediment of the littoral zone of Lake Bogoria, Kenya. Phylogenetically, it is a member of the genusCellulomonas, showing less than 97·5 % sequence similarity to the type strains of otherCellulomonasspecies. The highest level of similarity, albeit moderate, was found with respect toCellulomonas cellaseaDSM 20118T. Chemotaxonomic properties confirm the 16S rRNA gene-based generic affiliation, i.e. a DNA G+C content of 71·5 mol%, anteiso-C15 : 0and C16 : 0as the major fatty acids, MK-9(H4) as the major isoprenoid quinone, a peptidoglycan containingl-ornithine as the diamino acid andd-aspartic acid in the interpeptide bridge and phosphatidylglycerol as the only identified main polar lipid. The strain is aerobic to facultatively anaerobic, being capable of growth under strictly anaerobic conditions. Optimal growth occurs between pH values 9·0 and 10·0. On the basis of its distinct phylogenetic position and metabolic properties, strain 69B4Trepresents a novel species of the genusCellulomonas, for which the nameCellulomonas bogoriensissp. nov. is proposed. The type strain is 69B4T(=DSM 16987T=CIP 108683T).

Janibacter melonis sp. nov., isolated from abnormally spoiled oriental melon in Korea

Two Gram-positive bacterial strains, CM2104(T) and CM2110, isolated from the inner part of abnormally spoiled oriental melon (Cucumis melo) in Korea, were subjected to a polyphasic taxonomic study. The cell-wall peptidoglycan of strains CM2104(T) and CM2110 contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H(4)). The major fatty acids detected in the two strains were iso-C(16 : 0), C(17 : 1)omega8c and C(18 : 1)omega9c or C(17 : 0). The DNA G+C content of the two strains was 73 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed a coherent cluster with a clade comprising two Janibacter species, Janibacter limosus and Janibacter terrae. Strains CM2104(T) and CM2110 exhibited a 16S rRNA gene sequence similarity value of 99.7 % and a mean DNA-DNA relatedness level of 89 %. Strains CM2104(T) and CM2110 showed 16S rRNA gene sequence similarity levels of 97.8-98.4 % to the type strains of J. limosus and J. terrae. DNA-DNA relatedness between strains CM2104(T) and CM2110 and the type strains of these two Janibacter species was 7-11 %. On the basis of the phenotypic and phylogenetic data and genomic distinctiveness, strains CM2104(T) and CM2110 should be placed within the genus Janibacter as members of a novel species, for which the name Janibacter melonis sp. nov. is proposed. The type strain is CM2104(T) (=KCTC 9987(T)=DSM 16063(T)=JCM 12321(T)).

Development and evaluation of a quality-controlled ribosomal sequence database for 16S ribosomal DNA-based identification of Staphylococcus species

To establish an improved ribosomal gene sequence database as part of the Ribosomal Differentiation of Microorganisms (RIDOM) project and to overcome the drawbacks of phenotypic identification systems and publicly accessible sequence databases, both strands of the 5' end of the 16S ribosomal DNA (rDNA) of 81 type and reference strains comprising all validly described staphylococcal (sub)species were sequenced. Assuming a normal distribution for pairwise distances of all unique staphylococcal sequences and choosing a reporting criterion of > or =98.7% similarity for a "distinct species," a statistical error probability of 1.0% was calculated. To evaluate this database, a 16S rDNA fragment (corresponding to Escherichia coli positions 54 to 510) of 55 clinical Staphylococcus isolates (including those of the small-colony variant phenotype) were sequenced and analyzed by the RIDOM approach. Of these isolates, 54 (98.2%) had a similarity score above the proposed threshold using RIDOM; 48 (87.3%) of the sequences gave a perfect match, whereas 83.6% were found by searching National Center for Biotechnology Information (NCBI) database entries. In contrast to RIDOM, which showed four ambiguities at the species level (mainly concerning Staphylococcus intermedius versus Staphylococcus delphini), the NCBI database search yielded 18 taxon-related ambiguities and showed numerous matches exhibiting redundant or unspecified entries. Comparing molecular results with those of biochemical procedures, ID 32 Staph (bioMerieux, Marcy I'Etoile, France) and VITEK 2 (bioMerieux) failed to identify 13 (23.6%) and 19 (34.5%) isolates, respectively, due to incorrect identification and/or categorization below acceptable values. In contrast to phenotypic methods and the NCBI database, the novel high-quality RIDOM sequence database provides excellent identification of staphylococci, including rarely isolated species and phenotypic variants.

Serinicoccus marinus gen. nov., sp. nov., a novel actinomycete with l-ornithine and l-serine in the peptidoglycan

A Gram-positive bacterial strain containing l-ornithine as the diagnostic diamino acid was isolated from a sea-water-sample from the East Sea, Korea. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain JC1078T represents a phyletic line within the suborder Micrococcineae of the order Actinomycetales, adjacent to the genus Ornithinimicrobium. The highest sequence similarity values to the isolate were observed against Ornithinimicrobium humiphilum (94·3 %) and Kytococcus sedentarius (94·1 %). The strain was strictly aerobic and moderately halophilic with optimal growth at 2–3 % (w/v) NaCl. Cells were non-motile, non-sporulating and coccoid-shaped. The cell wall contains l-ornithine, glutamic acid, alanine, glycine and serine. The major menaquinone was MK-8(H4). The predominant cellular fatty acids were of the iso- and anteiso-methyl-branched types. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unknown glycolipid. The acyl type of the glycan chain of peptidoglycan is acetyl. The DNA G+C content was 72 mol%. The combination of physiological, biochemical and chemotaxonomical data clearly separated the marine isolate from other members of the suborder Micrococcineae. On the basis of polyphasic evidence, it is proposed to classify strain JC1078T in a novel genus and species, for which the name Serinicoccus marinus gen. nov., sp. nov. is proposed. The type strain is JC1078T (=IMSNU 14026T=KCTC 9980T=DSM 15273T).

Reclassification of Promicromonospora pachnodae Cazemier et al. 2004 as Xylanimicrobium pachnodae gen. nov., comb. nov

The recently described facultatively anaerobic Promicromonospora pachnodae is phylogenetically only moderately related to authentic members of Promicromonospora. P. pachnodae is closely related to Xylanibacterium ulmi and slightly less closely related to Xylanimonas cellulosilytica and Isoptericola variabilis (basonym Cellulosimicrobium variabile). Members of the different genera of Promicromonosporaceae have similar chemotaxonomic properties; they share the same peptidoglycan type (A4α) and have similar profiles of polar lipids, menaquinones, fatty acids and whole cell sugars. However, they differ from each other in the detailed amino acid composition of peptidoglycan, a taxonomically significant character that has previously been used in the delineation of actinobacterial genera. Recognized Promicromonospora species and Xylanibacterium ulmi exhibit the l-lys–l-ala–d-Glu type, Xylanimonas cellulosilytica and I. variabilis show the l-lys–d-Asp type, whereas P. pachnodae has the l-lys–l-ser–d-Glu type. This property, together with the distinct phylogenetic position of Promicromonospora pachnodae, suggests a novel genus for the xylanolytic organism Xylanimicrobium pachnodae (Cazemier et al. 2004) gen. nov., comb. nov.

Reclassification of Cellulosimicrobium variabile Bakalidou et al. 2002 as Isoptericola variabilis gen. nov., comb. nov

As already depicted in the original publication, the type strain of the species Cellulosimicrobium variabile Bakalidou et al. 2002, DSM 10177(T), does not cluster unambiguously with the type species, Cellulosimicrobium cellulans DSM 43879(T), in phylogenetic analysis. Strain DSM 10177(T) is moderately related to the recently described species Xylanimonas cellulosilytica, Promicromonospora pachnodae and Xylanibacterium ulmi, forming a lineage that branches between C. cellulans and members of the genus Promicromonospora in most dendrograms generated on the basis of different algorithms and reference strains. The type strains of the two Cellulosimicrobium species resemble each other in morphology, composition of fatty acids, DNA G+C content, phospholipids and the presence of lysine in position 3 of the peptide subunit of peptidoglycan. However, the two strains differ from each other in cell-wall sugars and in the amino acid composition of the A4alpha-type peptidoglycan, which contains serine and aspartic acid in C. cellulans, whereas only aspartic acid is present in the interpeptide bridge of C. variabile. This type is also present in Xylanimonas cellulosilytica XIL07(T), but not in the neighbouring species P. pachnodae DSM 12657(T), which exhibits the L-lys-L-ser-D-Glu type. On the basis of distinct phylogenetic position and the amino acid composition of peptidoglycan, a novel genus and combination for C. variabile, Isoptericola variabilis gen. nov., comb. nov., is proposed.

Arsenicicoccus bolidensis gen. nov., sp. nov., a novel actinomycete isolated from contaminated lake sediment

An unknown Gram-positive, catalase-positive, facultatively anaerobic, non-spore-forming, coccus-shaped bacterium originating from sediment was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on ll-diaminopimelic acid (type ll-Dpm-glycine1), a complex mixture of saturated, monounsaturated and iso- and anteiso-methyl-branched, non-hydroxylated, long-chain cellular fatty acids and tetrahydrogenated menaquinones with eight isoprene units [MK-8(H4)] as the major respiratory lipoquinone. This combination of characteristics somewhat resembled members of the suborder Micrococcineae, but did not correspond to any currently described species. Comparative 16S rRNA gene sequencing confirmed that the unidentified coccus-shaped organism is a member of the Actinobacteria and represents a hitherto-unknown subline related to, albeit different from, a number of taxa including Intrasporangium, Janibacter, Terrabacter, Terracoccus and Ornithinicoccus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium originating from lake sediment be classified as a new genus and species, Arsenicicoccus bolidensis gen. nov., sp. nov. (type strain CCUG 47306T=DSM 15745T).

Search and Discovery Strategies for Biotechnology: the Paradigm Shift

SUMMARY

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology.

Search and discovery strategies for biotechnology: the paradigm shift

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology.