Proposal of the suffix -ota to denote phyla. Addendum to 'Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes'

As an addendum to the earlier proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes (Oren et al., Int J Syst Evol Microbiol 2015;65:4284-4287) we propose the suffix -ota to denote phyla, replacing the somewhat awkward -aeota. We therefore present a new draft modified version of Rule 8 of the International Code of Nomenclature of Prokaryotes and a corrected list of names of phyla to be considered for validation after approval of the proposal to include the rank of phylum in the Code.

Dehalogenimonas formicexedens sp. nov., a chlorinated alkane-respiring bacterium isolated from contaminated groundwater

A strictly anaerobic, Gram-stain-negative, non-spore-forming bacterium designated NSZ-14T, isolated from contaminated groundwater in Louisiana (USA), was characterized using a polyphasic approach. Strain NSZ-14T reductively dehalogenated a variety of polychlorinated aliphatic alkanes, producing ethene from 1,2-dichloroethane, propene from 1,2-dichloropropane, a mixture of cis- and trans-1,2-dichloroethene from 1,1,2,2-tetrachloroethane, vinyl chloride from 1,1,2-trichloroethane and allyl chloride (3-chloro-1-propene) from 1,2,3-trichloropropane. Formate or hydrogen could both serve as electron donors. Dechlorination occurred between pH 5.5 and 7.5 and over a temperature range of 20-37 °C. Major cellular fatty acids included C18 : 1ω9c, C14 : 0 and C16 : 0. 16S rRNA gene sequence-based phylogenetic analysis indicated that the strain clusters within the class Dehalococcoidia of the phylum Chloroflexi, most closely related to but distinct from type strains of the species Dehalogenimonas alkenigignens (97.63 % similarity) and Dehalogenimonas lykanthroporepellens (95.05 %). A complete genome sequence determined for strain NSZ-14T revealed a DNA G+C content of 53.96 mol%, which was corroborated by HPLC (54.1±0.2 mol% G+C). Genome-wide comparisons based on average nucleotide identity by orthology and estimated DNA-DNA hybridization values combined with phenotypic and chemotaxonomic traits and phylogenetic analysis indicate that strain NSZ-14T represents a novel species within the genus Dehalogenimonas, for which the name Dehalogenimonas formicexedens sp. nov. is proposed. The type strain is NSZ-14T (=HAMBI 3672T=JCM 19277T=VKM B-3058T). An emended description of Dehalogenimonas alkenigignens is also provided.

Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes

The International Code of Nomenclature of Prokaryotes covers the nomenclature of prokaryotes up to the rank of class. We propose here modifying the Code to include the rank of phylum so that names of phyla that fulfil the rules of the Code will obtain standing in the nomenclature.

Genome sequence of the organohalide-respiring Dehalogenimonas alkenigignens type strain (IP3-3(T))

Dehalogenimonas alkenigignens IP3-3^T is a strictly anaerobic, mesophilic, Gram negative staining bacterium that grows by organohalide respiration, coupling the oxidation of H₂ to the reductive dehalogenation of polychlorinated alkanes. Growth has not been observed with any non-polyhalogenated alkane electron acceptors. Here we describe the features of strain IP3-3^T together with genome sequence information and its annotation. The 1,849,792 bp high-quality-draft genome contains 1936 predicted protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small unit rRNA (16S) locus. The genome contains 29 predicted reductive dehalogenase genes, a large majority of which lack cognate genes encoding membrane anchoring proteins.

Reassessment of PCR primers targeting 16S rRNA genes of the organohalide-respiring genus Dehalogenimonas

Representatives from the genus Dehalogenimonas have the metabolic capacity to anaerobically transform a variety of environmentally important polychlorinated aliphatic compounds. In light of the recent isolation of additional strains, description of a new species, and an expanded number of uncultured DNA sequences, PCR primers and protocols intended to uniquely target members of this organohalide-respiring genus were reevaluated. Nine of fourteen primer combinations reported previously as genus-specific failed to amplify 16S rRNA genes of recently isolated Dehalogenimonas strains. Use of alternative combinations or modified genus-specific primers, however, allowed detection of all presently known Dehalogenimonas strains. Use of a modified primer set in qPCR revealed an approximately two-order of magnitude increase in concentration of Dehalogenimonas 16S rRNA gene copies following subsurface injection of electron donors at a Louisiana Superfund site, demonstrating the utility of the newly developed protocol and suggesting that the genus Dehalogenimonas can respond to biostimulation remediation strategies in a manner similar to that previously reported for other dechlorinating genera such as Dehalococcoides.

Description of two new thermophilic species of the genus Rubrobacter, Rubrobacter calidifluminis sp. nov. and Rubrobacter naiadicus sp. nov., and emended description of the genus Rubrobacter and the species Rubrobacter bracarensis

Four isolates, designated, RG-1(T), RG-3(T), RG-6 and RG-8 with optimum growth temperatures around 60°C were recovered from a hot stream near Ribeira Grande on the Island of São Miguel in the Azores. These strains were strictly aerobic, catalase and oxidase positive. The organisms could be divided into two groups; one comprising strains RG-1(T) and RG-6, the other formed by strains RG-3(T) and RG-8, with distinctive phenotypic and chemotaxonomic characteristics. Major fatty acids varied between the groups, but all contained iso-branched components such as iso-C16:0 10-methyl and iso-C17:0 10-methyl. Analysis of the 16S rRNA gene shows the strains to cluster with species of the genus Rubrobacter, specifically with Rubrobacter xylanophilus to which they have pairwise sequence similarity in the range of 98.4-98.6%. The DNA-DNA hybridization result show that strains RG-1(T) and RG-3(T) share 72% reassociation. Strains RG-1(T) and RG-3(T) displayed extreme tolerance to desiccation when compared to other species of the genus. Based on genotypic, physiological and biochemical characteristics we describe two new species: Rubrobacter calidifluminis sp. nov., represented by strain RG-1(T) (=CECT 8308(T) =JCM 19154(T)) and Rubrobacter naiadicus sp. nov. represented by strain RG-3(T) (=CECT 8310(T)=JCM 19155(T)). The description of the species Rubrobacter bracarensis[16] is emended to correct the fatty acid composition of these organisms. The discovery of new fatty acids in these species requires emendation of the description of the genus Rubrobacter.

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA-DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12,000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11,000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

Heliimonas saccharivorans gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a mineral water aquifer, and emended description of Filimonas lacunae

Two isolates, with optimum growth temperature and pH of about 30 °C and 6.0–7.0, were recovered from a borehole head of a mineral water aquifer in Portugal. The closest relatives based on 16S rRNA gene sequence analysis were species of genera of the family Chitinophagaceae . Strains L2-4T and L2-109 formed translucent colonies and non-motile pleomorphic cells. Strains were strictly aerobic, and oxidase- and catalase-positive. The major fatty acids of strains L2-4T and L2-109 were 17 : 0 iso 3-OH, 15 : 0 iso and 15 : 1 iso G. The major polar lipids were phosphatidylethanolamine, one unidentified phospholipid, four unidentified aminophospholipids, four unidentified aminolipids and three unidentified polar lipids. Menaquinone 7 was the only respiratory quinone. The G+C content of the DNA of strains L2-4T and L2-109 was 42.0 and 41.4 mol%, respectively. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics, strains L2-4T ( = CECT 8122T = LMG 26919T) and L2-109 ( = CECT 8121 = LMG 26920) are considered to represent a novel species of a new genus, for which the name Heliimonas saccharivorans gen. nov., sp. nov. is proposed. The type strain of Heliimonas saccharivorans is L2-4T. Due to additional results obtained in this study an emended description of Filimonas lacunae is provided.

Dehalogenimonas spp. can Reductively Dehalogenate High Concentrations of 1,2-Dichloroethane, 1,2-Dichloropropane, and 1,1,2-Trichloroethane

The contaminant concentrations over which type strains of the species Dehalogenimonas alkenigignens and Dehalogenimonas lykanthroporepellens were able to reductively dechlorinate 1,2-dichloroethane (1,2-DCA), 1,2-dichloropropane (1,2-DCP), and 1,1,2-trichloroethane (1,1,2-TCA) were evaluated. Although initially isolated from an environment with much lower halogenated solvent concentrations, D. alkenigignens IP3-3T was found to reductively dehalogenate chlorinated alkanes at concentrations comparable to D. lykanthroporepellens BL-DC-9T. Both species dechlorinated 1,2-DCA, 1,2-DCP, and 1,1,2-TCA present at initial concentrations at least as high as 8.7, 4.0, and 3.5 mM, respectively. The ability of Dehalogenimonas spp. to carry out anaerobic reductive dechlorination even in the presence of high concentrations of chlorinated aliphatic alkanes has important implications for remediation of contaminated soil and groundwater.

Dehalogenimonas alkenigignens sp. nov., a chlorinated-alkane-dehalogenating bacterium isolated from groundwater

Two strictly anaerobic bacterial strains, designated IP3-3(T) and SBP-1, were isolated from groundwater contaminated by chlorinated alkanes and alkenes at a Superfund Site located near Baton Rouge, Louisiana (USA). Both strains reductively dehalogenate a variety of polychlorinated aliphatic alkanes, including 1,2-dichloroethane, 1,2-dichloropropane, 1,1,2,2-tetrachloroethane, 1,1,2-trichloroethane and 1,2,3-trichloropropane, when provided with hydrogen as the electron donor. To clarify their taxonomic position, strains IP3-3(T) and SBP-1 were characterized using a polyphasic approach. Both IP3-3(T) and SBP-1 are mesophilic, non-spore-forming, non-motile and Gram-stain-negative. Cells of both strains are irregular cocci with diameters of 0.4-1.1 µm. Both are resistant to ampicillin and vancomycin. The genomic DNA G+C contents of strains IP3-3(T) and SBP-1 are 55.5±0.4 and 56.2±0.2 mol% (HPLC), respectively. Major cellular fatty acids include C18 : 1ω9c, C16 : 0, C14 : 0 and C16 : 1ω9c. 16S rRNA gene sequence based phylogenetic analyses indicated that the strains cluster within the phylum Chloroflexi most closely related to but distinct from the species Dehalogenimonas lykanthroporepellens (96.2 % pairwise similarity) and Dehalococcoides mccartyi (90.6 % pairwise similarity). Physiological and chemotaxonomic traits as well as phylogenetic analysis support the conclusion that these strains represent a novel species within the genus Dehalogenimonas for which the name Dehalogenimonas alkenigignens sp. nov. is proposed. The type strain is IP3-3(T) ( = JCM 17062(T) = NRRL B-59545(T)).

Pelosinus defluvii sp. nov., isolated from chlorinated solvent-contaminated groundwater, emended description of the genus Pelosinus and transfer of Sporotalea propionica to Pelosinus propionicus comb. nov

Two anaerobic bacterial strains, designated SHI-1T and SHI-2, were isolated from chlorinated solvent-contaminated groundwater. They were found to be identical in phenotypic properties and shared high (98.5–99.8 %) pairwise 16S rRNA gene sequence similarity. Multiple 16S rRNA genes were found to be present in the isolates as well as Pelosinus fermentans DSM 17108T and Sporotalea propionica DSM 13327T. Strains SHI-1T and SHI-2 could be differentiated from their closest phylogenetic relatives, P. fermentans DSM 17108T and S. propionica DSM 13327T, on the basis of their phenotypic and phylogenetic properties. The isolates were Gram-negative, spore-forming, motile rods with peritrichous flagella. Growth occurred at 10–42 °C and pH 5.5–8.5. Fermentative growth was observed on Casamino acids, fructose, fumarate, glucose, glycerol, pyruvate and yeast extract. The major organic acids produced from glucose and glycerol fermentation were propionate and acetate. The major organic acids produced from fermentation of fumarate were propionate, acetate and succinate. The major cellular fatty acids were summed feature 4 (consisting of C15 : 1ω8c and/or C15 : 2), summed feature 8 (consisting of C17 : 1ω8c and/or C17 : 2) and C14 : 0 dimethyl aldehyde. The polar lipids comprised aminophospholipids, including phosphatidylethanolamine and phosphatidylserine, and an unknown phospholipid. The genomic DNA G+C content was 39.2 mol%. We propose that strains SHI-1T and SHI-2 are assigned to a novel species of the genus Pelosinus , with the name Pelosinus defluvii sp. nov. (type strain SHI-1T  = NRRL Y-59407T  = LMG 25549T). The description of the genus Pelosinus is emended. We also propose the transfer of S. propionica to the genus Pelosinus as Pelosinus propionicus comb. nov. (type strain TmPN3T = DSM 13327T = ATCC BAA-626T), on the basis of phylogenetic, chemotaxonomic and phenotypic properties.

Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to "Dehalococcoides" strains

Dehalogenimonas lykanthroporepellens is the type species of the genus Dehalogenimonas, which belongs to a deeply branching lineage within the phylum Chloroflexi. This strictly anaerobic, mesophilic, non spore-forming, Gram-negative staining bacterium was first isolated from chlorinated solvent contaminated groundwater at a Superfund site located near Baton Rouge, Louisiana, USA. D. lykanthroporepellens was of interest for genome sequencing for two reasons: (a) an unusual ability to couple growth with reductive dechlorination of environmentally important polychlorinated aliphatic alkanes and (b) a phylogenetic position that is distant from previously sequenced bacteria. The 1,686,510 bp circular chromosome of strain BL-DC-9(T) contains 1,720 predicted protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small subunit rRNA (16S) locus.

Actinomyces naturae sp. nov., the first Actinomyces sp. isolated from a non-human or animal source

Three facultatively anaerobic, Gram-positive staining, rod-shaped, non-spore forming, flagellated bacterial strains, BL-75, BL-79(T) and BL-104, were isolated from chlorinated solvent-contaminated groundwater. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed them to represent a distinct lineage within the genus Actinomyces with sequence identities in the range of <88-95.4% with previously described Actinomyces species. The strains were oxidase and catalase negative. Nitrate was not reduced. Esculin was hydrolyzed. Growth occurred in the temperature range of 20-43°C (optimum 30-37°C) and pH range 4.5-9.0 (optimum pH 6.5). Substrates supporting growth included various mono-, di-, and tri-saccharides. The end products of glucose fermentation were acetate, lactate, succinate and formate. Fermentative growth was observed in the presence of near saturation concentrations of perchloroethene (PCE) and toluene and in the presence of 1,2-dichloroethane and 1,1,2-trichloroethane at concentrations up to at least 24.4 mM and 11.2 mM, respectively. The dominant cellular fatty acids when grown in peptone/yeast extract/glucose (PYG) medium were C(18:1) ω9c, C(16:0), and C(14:0). The peptidoglycan was found to contain the amino acids alanine, glutamic acid, lysine, and ornithine at approximate molar ratios of 1.7 Ala: 2.3 Glu: 1.3 Lys: 1.0 Orn. The cell wall sugars were found to include rhamnose and mannose. The polar lipids were found to include diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phospholipid (PL), phosphoglycolipids (PGL), and glycolipids (GL). The main respiratory quinone of strain BL-79(T) was MK-9(H(4)), with minor components MK-10(H(4)) and MK-8(H(4)). The DNA mol% G+C content of the type strain is 69.8%. On the basis of phylogenetic and phenotypic characteristics, these strains could be differentiated from previously described species of the genus Actinomyces. Strains BL-75, BL-79(T) and BL-104 are designated as a novel species, for which the name Actinomyces naturae sp. nov. is proposed. This is the first Actinomyces species isolated from an environmental rather than human or animal sources. The type strain of Actinomyces naturae is BL-79(T) (= CCUG 56698(T) = NRRL B-24670(T)).

Schleiferia thermophila gen. nov., sp. nov., a slightly thermophilic bacterium of the phylum ‘Bacteroidetes’ and the proposal of Schleiferiaceae fam. nov

A bacterial isolate, with an optimum growth temperature of about 50 °C and an optimum pH for growth between 7.5 and 8.5, was recovered from a hot spring in the Furnas area of the Island of São Miguel in the Azores. The novel isolate is orange-pigmented, forms non-motile, rod-shaped cells that stain Gram-negative, is strictly aerobic, oxidase-positive and catalase-negative. The major fatty acids of strain TU-20T are 16 : 1ω6c, 17 : 0 iso 3-OH and 15 : 0 iso. Menaquinone 6 is the major respiratory quinone. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics, we describe a novel species of a novel genus represented by strain TU-20T ( = DSM 21410T  = LMG 24594T) for which we propose the name Schleiferia thermophila gen nov., sp. nov. We also propose the family Schleiferiaceae fam. nov. to accommodate this new genus.

Hydrotalea sandarakina sp. nov., isolated from a hot spring runoff, and emended descriptions of the genus Hydrotalea and the species Hydrotalea flava

Two bacterial isolates, designated AF-51(T) and AF-50, with an optimum growth temperature of about 45 °C and an optimum pH for growth between 6.0 and 6.5, were recovered from a hot spring in the Furnas, Área da Fonte 1825, on the Island of São Miguel in the Azores. Based on 16S rRNA gene sequence analysis, these strains were related most closely to the type strain of Hydrotalea flava at a pairwise similarity of 95.7%. The two strains were orange-pigmented and formed non-motile, rod-shaped cells that stained Gram-negative and were aerobic and oxidase- and catalase-positive. The major fatty acids were iso-C(15:0), iso-C(17:0) 3-OH and iso-C(16:0). The major respiratory quinone was menaquinone 7. Based on phylogenetic, physiological and biochemical characteristics, these strains from the Azores are considered to represent a single novel species of the genus Hydrotalea, for which the name Hydrotalea sandarakina sp. nov. is proposed. The type strain is AF-51(T) (=DSM 23241(T)=LMG 25526(T)). We provide emended descriptions of the genus Hydrotalea and of H. flava to reflect new results obtained in this study.

Acetogenesis from dichloromethane by a two-component mixed culture comprising a novel bacterium

A strictly anaerobic two-component culture able to grow exponentially with a doubling time of 20 h on a medium containing dichloromethane as the carbon and energy source was characterized. On a medium without sulfate, we observed (per mol of dichloromethane) a mass balance of 2 mol of chloride, 0.26 mol of acetate, 0.05 mol of formate, and 0.25 mol of carbon in biomass. One component of the culture, strain DMB, was identified by a 16S ribosomal DNA analysis as a Desulfovibrio sp. The other component, the gram-positive organism strain DMC, could not be isolated. It was possible, however, to associate strain DMC on a medium containing dichloromethane in a coculture with Acetobacterium woodii or Methanospirillum hungatei. Coculture of strain DMC with the Archaeon M. hungatei allowed us to specifically amplify by PCR the 16S rRNA gene of strain DMC. A phylogenetic analysis of the 16S ribosomal DNA sequence revealed that this organism groups within the radiation of the Clostridium-Bacillus subphylum and exhibits the highest levels of sequence similarity (89%) with Desulfotomaculum orientis and Desulfitobacterium dehalogenans. Since the novel organism strain DMC was able to grow acetogenically with dichloromethane when it was associated with one of three metabolically different partners and since, in contrast to strain DMB, strain DMC contained carbon monoxide dehydrogenase activity, this bacterium is responsible for both the dehalogenation of dichloromethane and the acetogenesis observed in the original two-component culture. The obligatory dependence of strain DMC on a partner during growth with dichloromethane is thought to stem from the need for a growth factor produced by the associated organism.

Tepidamorphus gemmatus gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria

Two isolates, with an optimum growth temperature of about 45-50 degrees C and an optimum pH for growth between 7.5 and 8.5, were recovered from a hot spring in the Furnas area on the Island of São Miguel in the Azores. Strains form irregular rod-shaped cells are motile and stain Gram negative. The cells multiply by budding. These strains are non-pigmented, strictly aerobic, catalase and oxidase positive. These organisms assimilated carbohydrates, organic acids and amino acids. The major fatty acids are 19:0(cyclo omega8c) and 18:0. Ubiquinone 10 is the major respiratory quinone. The major polar lipids are diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine in addition to one unidentified aminolipid and one unidentified glycolipid. Bacteriochlorophyll a, puf genes and RuBisCo genes were not detected. Analysis of the 16SrRNA gene shows the strains to cluster with species of the genera Afifella, Rhodobium, Anderseniella and Amorphus to which they have sequence similarity in the range 93-94%. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics we describe a new species of a novel genus represented by strain CB-27A(T) (=DSM 19345(T)=LMG 24113(T)) for which we propose the name Tepidamorphus gemmatus.

Thiomonas bhubaneswarensis sp. nov., an obligately mixotrophic, moderately thermophilic, thiosulfate-oxidizing bacterium

A novel aerobic, obligately mixotrophic, moderately thermophilic, thiosulfate-oxidizing bacterium, S10T, was isolated from hot-spring sediment samples collected from Atri, Bhubaneswar, India. The cells of this isolate stained Gram-negative and were strictly aerobic, non-sporulating, rod-shaped and motile with a single polar flagellum. Strain S10T was positive for oxidase and catalase activities. It was capable of utilizing thiosulfate under mixotrophic growth conditions. Mixotrophic growth was observed at pH 6.0-8.5 and 25-45 degrees C; optimum growth occurred at pH 7.5-8.0 and 30-37 degrees C. The major cellular fatty acids were C12:0 3-OH, C16:1omega7c, C16:0, C17:0 cyclo, C18:1omega7c and C19:0 cyclo omega8c. The DNA G+C content of strain S10T was 64.8 mol%. 16S rRNA gene sequence analysis indicated that the bacterium clustered within the radiation of the genus Thiomonas and showed 98.0% similarity with Thiomonas perometabolis ATCC 23370T and Thiomonas intermedia ATCC 15466T. However, DNA-DNA reassociation values of strain S10T with Thiomonas perometabolis JCM 20426T and Thiomonas intermedia JCM 20425T, its nearest phylogenetic relatives, were 46 and 39%, respectively. On the basis of phenotypic, physiological and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA-DNA reassociation studies, it is proposed that strain S10T represents a novel species of the genus Thiomonas, Thiomonas bhubaneswarensis sp. nov.; the type strain is S10T (=DSM 18181T=JCM 14806T).

Elioraea tepidiphila gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria

A bacterial isolate, strain TU-7T, with an optimum growth temperature of about 45-50 degrees C and an optimum pH for growth between 8.0 and 8.5, was recovered from a hot spring in the Furnas area of the island of São Miguel in the Azores. The new isolate is non-pigmented, facultatively chemolithoorganotrophic, strictly aerobic and catalase- and oxidase-positive. The organism oxidized thiosulfate to sulfate with enhancement of growth. This organism assimilated organic acids but did not assimilate carbohydrates or polyols. 16S rRNA gene sequence analysis placed strain TU-7T within the radiation of the Alphaproteobacteria as a deep branch of the family Acetobacteriaceae. The major fatty acids of strain TU-7T are 18 : 1 omega 7c, 18 : 0, 19 : 0 cyclo omega 8c and an aliphatic chain with an equivalent chain-length of 20.195, identified as 19 : 0 2-OH cyclo omega 8 (Delta 11 : 12). Ubiquinone 10 is the major respiratory quinone and the major polar lipids are phosphatidylcholine, phosphatidylethanolamine, diphosphosphatidylglycerol and phosphatidylglycerol in addition to two unidentified aminolipids. Bacteriochlorophyll a and puf genes were not detected. Based on 16S rRNA gene sequence analysis and physiological and biochemical characteristics, we describe a novel species of a new genus represented by strain TU-7T, for which we propose the name Elioraea tepidiphila gen. nov., sp. nov. The type strain of Elioraea tepidiphila is strain TU-7T (=DSM 17972T =CIP 109115T).

Description of four novel psychrophilic, ionizing radiation-sensitive Deinococcus species from alpine environments

Five psychrophilic bacterial strains were isolated from soil samples collected above the treeline of alpine environments. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these organisms represent four novel species of the genus Deinococcus; levels of sequence similarity to the type strains of recognized Deinococcus species were in the range 89.3-94.7 %. Strains PO-04-20-132T, PO-04-20-144, PO-04-19-125T, ME-04-01-32T and ME-04-04-52T grew aerobically, with optimum growth at 10 degrees C and at pH 6-9. The major respiratory menaquinone was MK-8. The fatty acid profiles of strains PO-04-20-132T, PO-04-20-144, PO-04-19-125T and ME-04-01-32T were dominated by 16 : 1omega7c, 17 : 0 iso and 15 : 1omega6c, whereas 16 : 1omega7c, 17 : 0 cyclo and 16 : 0 predominated in strain ME-04-04-52T. The DNA G+C contents of strains PO-04-20-132T, PO-04-19-125T, ME-04-01-32T and ME-04-04-52T were 63.2, 63.1, 65.9 and 62.6 mol%, respectively. Strains PO-04-20-132T, PO-04-19-125T, ME-04-01-32T and ME-04-04-52T had gamma radiation D10 (dose required to reduce the bacterial population by 10-fold) values of < or =4 kGy. These four strains showed sensitivity to UV radiation and extended desiccation as compared with Deinococcus radiodurans. On the basis of the phylogenetic analyses, and chemotaxonomic and phenotypic data, it is proposed that strains PO-04-20-132T (=LMG 24019T=NRRL B-41950T; Deinococcus radiomollis sp. nov.), PO-04-19-125T (=LMG 24282T=NRRL B-41949T; Deinococcus claudionis sp. nov.), ME-04-01-32T (=LMG 24022T=NRRL B-41947T; Deinococcus altitudinis sp. nov.) and ME-04-04-52T (=LMG 24283T=NRRL B-41948T; Deinococcus alpinitundrae sp. nov.) represent the type strains of four novel species of the genus Deinococcus.

Thermoanaerobacter sulfurigignens sp. nov., an anaerobic thermophilic bacterium that reduces 1 M thiosulfate to elemental sulfur and tolerates 90 mM sulfite

Two anaerobic thermophilic bacteria, designated strains JW/SL824 and JW/SL-NZ826(T), were isolated from an acidic volcanic steam outlet on White Island, New Zealand. Cells were rod-shaped, spore-forming, motile and Gram-stain negative, but contained Gram-type positive cell wall. Strain JW/SL-NZ826(T) utilized various carbohydrates including xylose and glucose. The fermentation end products produced from glucose in the absence of thiosulfate were lactate, ethanol, acetate, CO(2) and H(2). The temperature range for growth was 34-72 degrees C, with an optimum at 63-67 degrees C. The pH(60 degrees C) range for growth was 4.0-8.0, with an optimum at 5.0-6.5. The doubling time of strain JW/SL-NZ826(T) under optimal growth conditions was 2.4 h. The DNA G+C content was 34-35 mol% (HPLC). The two strains reduced up to 1 M thiosulfate to elemental sulfur without sulfide formation, which is a trend typically observed among species belonging to the genus Thermoanaerobacterium. Sulfur globules containing short and long sulfur chains but no S(8)-ring sulfur were produced inside and outside the cells. Up to 90 mM sulfite was tolerated. This tolerance is assumed to be an adaptation to the geochemistry of the environment of White Island. The 16S rRNA gene sequence analysis, however, indicated that the two strains belonged to the genus Thermoanaerobacter, with similarities in the range 95.6-92.7 %. Therefore, strains JW/SL-NZ824 and JW/SL-NZ826(T) represent a novel taxon, for which the name Thermoanaerobacter sulfurigignens sp. nov. is proposed, with strain JW/SL-NZ826(T) (=ATCC 700320(T)=DSM 17917(T)) as the type strain. Based on this and previous studies, an emended description of the genus Thermoanaerobacter is given.

Deinococcus peraridilitoris sp. nov., isolated from a coastal desert

Three ionizing-radiation-resistant bacterial strains (designated KR-196, KR-198 and KR-200(T)) were isolated from a sample of arid soil collected from a coastal desert in Chile. The soil sample was irradiated before serial dilution plating was performed using one-tenth-strength plate count agar. Phylogenetic analysis of the 16S rRNA gene sequences showed these organisms to represent a novel species of the genus Deinococcus, having sequence similarities of 87.3-90.8 % with respect to recognized Deinococcus species. Strains KR-196, KR-198 and KR-200(T) were aerobic and showed optimum growth at 30 degrees C and pH 6.5-8.0. The major respiratory menaquinone was MK-8. The predominant fatty acids in these strains were 16 : 1 omega 7c, 16 : 0, 15 : 1 omega 6c, 17 : 0 and 18 : 0. The DNA G+C content of strain KR-200(T) was 63.9 mol%. Strains KR-196, KR-198 and KR-200(T) were found to be resistant to >10 kGy gamma radiation. On the basis of the phylogenetic, chemotaxonomic and phenotypic data, strain KR-200(T) represents a novel species of the genus Deinococcus, for which the name Deinococcus peraridilitoris sp. nov. is proposed. The type strain is KR-200(T) (=LMG 22246(T)=CIP 109416(T)).

Salirhabdus euzebyi gen. nov., sp. nov., a Gram-positive, halotolerant bacterium isolated from a sea salt evaporation pond

A low-G+C, Gram-positive bacterium, designated CVS-14T, was recovered from a sea salt evaporation pond on the island of Sal in the Cape Verde Archipelago. This organism was catalase- and oxidase-positive. Cells were motile, spore-forming aerobic rods, with an optimum growth temperature of about 35–40 °C and optimum pH between 7.0 and 8.5. Optimal growth occurred in media containing 4–6 % (w/v) NaCl, although the organism was able to grow in medium without added NaCl and in medium containing 16 % NaCl. The cell-wall peptidoglycan was of A1γ type and the major respiratory quinone was menaquinone 7 (MK-7). Major fatty acids were iso-15 : 0, anteiso-15 : 0, iso-17 : 0 and anteiso-17 : 0. The DNA G+C content was 37.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain CVS-14T formed a distinct new branch within the radiation of the moderately halophilic bacilli group, forming a separate lineage from species of the genera Salinibacillus, Paucisalibacillus, Oceanobacillus, Lentibacillus and Virgibacillus. Strain CVS-14T showed 16S rRNA gene pairwise similarity values of ~95 % with species of the genus Salinibacillus. On the basis of morphological, physiological, chemotaxonomic and phylogenetic characteristics, strain CVS-14T is considered to represent a novel species in a new genus, for which the name Salirhabdus euzebyi gen. nov., sp. nov. is proposed. The type strain is CVS-14T (=LMG 22839T=CIP 108577T).

Description of Azospira restricta sp. nov., a nitrogen-fixing bacterium isolated from groundwater

A novel, Gram-negative bacterial strain, SUA2T, isolated from groundwater, was characterized using a polyphasic approach. Cells are Gram-negative, non-spore-forming, straight to curved rods with a single polar flagellum. Strain SUA2T is oxidase- and catalase-positive and is able to fix nitrogen. Poly-β-hydroxybutyrate storage granules are produced. Dominant fatty acids when grown in R2A and VM ethanol media for 72 h at 37 °C are C16 : 0, C16 : 1 ω7c, C17 : 0 cyclo, C10 : 0 3-OH, C18 : 1 ω7c, C12 : 0 and C15 : 0. DNA G+C content is 67.9 mol%. Phenotypic and phylogenetic data indicate that strain SUA2T is related to, but clearly differentiated from Azospira oryzae. Strain SUA2T is thus proposed as a novel species of the genus Azospira with the name Azospira restricta sp. nov. The description of the genus Azospira is emended to include the characteristics of this novel species. The type strain of Azospira restricta is SUA2T (=NRRL B-41660T=DSM 18626T=LMG 23819T).

Marinobacter salsuginis sp. nov., isolated from the brine–seawater interface of the Shaban Deep, Red Sea

Two moderately halophilic Gram-negative bacteria were isolated from a sample taken from the brine–seawater interface of the Shaban Deep in the Red Sea. Phylogenetic analysis of the 16S rRNA gene sequence showed that these organisms represent a novel species of the genus Marinobacter. Cells of the new isolates formed non-pigmented colonies and were motile by means of a single polar flagellum. Strains SD-14BT and SD-14C grew optimally at 35–37 °C, in 5 % NaCl and at pH 7.5–8.0. The organisms were aerobic, but reduced nitrate to nitrogen under anaerobic conditions. Acid was produced from only a few carbohydrates. Ubiquinone 9 was the major respiratory quinone. The major fatty acids of strains SD-14BT and SD-14C were C16 : 0, C18 : 1 ω9c, summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c) and C12 : 0 3-OH. The DNA G+C contents were 55.9 and 55.7 mol%, respectively. On the basis of the phylogenetic analyses and physiological and biochemical characteristics, it is proposed that strains SD-14BT and SD-14C represent a novel species of the genus Marinobacter, with the name Marinobacter salsuginis sp. nov. The type strain is strain SD-14BT (=DSM 18347T=LMG 23697T).

Bacterial diversity of an acidic Louisiana groundwater contaminated by dense nonaqueous-phase liquid containing chloroethanes and other solvents

Bacterial concentration and diversity was assessed in a moderately acidic (pH 5.1) anaerobic groundwater contaminated by chlorosolvent-containing DNAPL at a Superfund site located near Baton Rouge, Louisiana. Groundwater analysis revealed a total aqueous-phase chlorosolvent concentration exceeding 1000 mg L(-1), including chloroethanes, vinyl chloride, 1,2-dichloropropane, and hexachloro-1,3-butadiene as the primary contaminants. Direct counting of stained cells revealed more than 3 x 10(7) cells mL(-1) in the groundwater, with 58% intact and potentially viable. Universal and 'Dehalococcoides'-specific 16S rRNA gene libraries were created and analyzed. Universal clones were grouped into 18 operational taxonomic units (OTUs), which were dominated by low-G+C Gram-positive bacteria (62%) and included several as yet uncultured or undescribed organisms. Several unique 16S rRNA gene sequences closely related to Dehalococcoides ethenogenes were detected. Anaerobically grown isolates (168 in total) were also sequenced. These were phylogenetically grouped into 18 OTUs, of which only three were represented in the clone library. Phylogenetic analysis of isolates and the clone sequences revealed close relationships with dechlorinators, fermenters, and hydrogen producers. Despite acidic conditions and saturation or near-saturation chlorosolvent concentrations, the data presented here demonstrate that large numbers of novel bacteria are present in groundwater within the DNAPL source zone, and the population appears to contain bacterial components necessary to carry out reductive dechlorination.

Tepidicella xavieri gen. nov., sp. nov., a betaproteobacterium isolated from a hot spring runoff

Strains TU-16T and TU-18, two non-pigmented bacterial isolates with an optimum growth temperature of about 45 degrees C and an optimum pH of about 8.5-9.0, were recovered from the Furnas geothermal area on the Island of São Miguel in the Azores. Phylogenetic analysis of the 16S rRNA gene sequence of these strains indicated that they represent a novel species in a new genus of the phylum Betaproteobacteria. The major fatty acids of strains TU-16T and TU-18 were 16 : 0 and 18 : 1omega7c. Ubiquinone 8 was the major respiratory quinone and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The novel isolates were aerobic; thiosulfate was oxidized to sulfate in the presence of a metabolizable carbon source. The organism assimilated organic acids and amino acids, but did not assimilate carbohydrates or polyols. Based on phylogenetic analyses and physiological and biochemical characteristics, it is proposed that strain TU-16T (=LMG 23030T = CIP 108724T) represents the type strain of a novel species in a new genus, Tepidicella xavieri gen. nov., sp. nov.

Brooklawnia cerclae gen. nov., sp. nov., a propionate-forming bacterium isolated from chlorosolvent-contaminated groundwater

Two novel facultatively anaerobic bacterial strains, BL-34T and BL-35, isolated from groundwater contaminated by a mixture of chlorosolvents were characterized using a polyphasic approach. The two strains exhibited essentially identical taxonomic features except for a vitamin B12 requirement by strain BL-35 for optimal growth. Phylogenetically, the isolates were affiliated with members of the family Propionibacteriaceae and were placed in a phylogenetic branch adjacent to, but distinct from, those of the genera Propionimicrobium, Propionibacterium, Luteococcus, Propioniferax and Tessaracoccus. The cells of the novel strains were Gram-positive, non-motile, non-spore-forming pleomorphic rods. They produced catalase but not oxidase, and nitrate reduction did not occur in peptone/yeast extract/glucose medium. Propionate and acetate were the predominant products of glucose fermentation. Fermentation occurred in the presence of 1,2-dichloroethane and 1,1,2-trichloroethane at concentrations up to at least 9.8 mM. The genomic DNA G+C content was 67.5–67.9 mol%. Menaquinone MK-9(H4) was the predominant respiratory quinone and meso-diaminopimelic acid was present in the cell-wall peptidoglycan layer. The major cellular fatty acids were C15 : 0 and anteiso-C15 : 0. On the basis of the results obtained in this study, strains BL-34T and BL-35 should be classified within a novel taxon, for which the name Brooklawnia cerclae gen. nov., sp. nov. is proposed. The type strain of Brooklawnia cerclae is BL-34T (=LMG 23248T=NRRL B-41418T). An additional strain, BL-35 (=LMG 23249=NRRL B-41419), was also characterized.

Salinicoccus salsiraiae sp. nov.: a new moderately halophilic gram-positive bacterium isolated from salted skate

Two moderately halophilic low G + C Gram-positive bacteria were isolated from a sample of salted skate (Class Chondrychthyes, Genus Raja). Phylogenetic analysis of the 16S rRNA gene sequence of strains RH1(T) and RH4 showed that these organisms represented a novel species of the genus Salinicoccus. The new isolates formed pink-red colonies and flocculated in liquid media, with optimum growth in media containing 4% NaCl and pH of about 8.0. These organisms are aerobic but reduce nitrate to nitrite under anaerobic conditions. Acid is produced from several carbohydrates. Oxidase and catalase were detected. Menaquinone 6 was the major respiratory quinone. The major fatty acids of strains RH1(T) and RH4 were 15:0 anteiso and 15:0 iso. The G + C contents of DNA were 46.2 and 46.0 mol%, respectively. The peptidoglycan was of A3alpha L-Lys-Gly(5-6) type. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we suggest that strain RH1(T) (=LMG 22840 = CIP 108576) represents a new species of the genus Salinicoccus, for which we propose the name Salinicoccus salsiraiae.

Propionicicella superfundia gen. nov., sp. nov., a chlorosolvent-tolerant propionate-forming, facultative anaerobic bacterium isolated from contaminated groundwater

A novel strain, designated as BL-10(T), was characterized using a polyphasic approach after isolation from groundwater contaminated by a mixture of chlorosolvents that included 1,1,2-trichloroethane, 1,2-dichloroethane, and vinyl chloride. Stain BL-10(T) is a facultatively anaerobic bacterium able to ferment glucose to form propionate, acetate, formate, lactate, and succinate. Fermentation occurred in the presence of 1,2-dichloroethane and 1,1,2-trichloroethane at concentrations to at least 9.8 and 5.9 mM, respectively. Cells are Gram-positive, rod-shaped, non-motile, and do not form spores. Oxidase and catalase are not produced and nitrate reduction did not occur in PYG medium. Menaquinone MK-9 is the predominant respiratory quinone and meso-diaminopimelic acid is present in the cell wall peptidoglycan layer. Major cellular fatty acids are C(15:0), iso C(16:0), and anteiso C(15:0). Genomic DNA G + C content is 69.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed strain BL-10(T) to fall within the radiation of genera Propionicimonas and Micropruina. On the basis of the results obtained in this study, it is proposed that strain BL-10(T) should be classified as a novel taxon, for which the name Propionicicella superfundia gen. nov., sp. nov. is proposed. The type strain of Propionicicella superfundia is BL-10(T) (=ATCC BAA-1218(T), =LMG 23096(T)).

Thioclava pacifica gen. nov., sp. nov., a novel facultatively autotrophic, marine, sulfur-oxidizing bacterium from a near-shore sulfidic hydrothermal area

Strain TL 2(T) was isolated on mineral medium with thiosulfate from a near-shore sulfidic hydrothermal area in Matupi Harbour on the island of New Britain, Papua New Guinea. The cells varied from long filaments with swollen ends, often aggregated, to short rods, depending on the growth conditions. The bacterium was obligately aerobic and grew autotrophically with thiosulfate as energy source or heterotrophically with organic acids and sugars. In thiosulfate-limited continuous culture, mu(max) and Y(max) for autotrophic growth were 0.1 h(-1) and 3 g protein mol(-1), respectively. From the various reduced sulfur compounds tested, only thiosulfate and sulfide supported active respiration. Inorganic carbon was assimilated via the Calvin cycle. Presence of the 'green'-type of form I RubisCO gene was detected. Growth was possible from 15 to 47 degrees C with an optimum at 35 degrees C, pH 6.5-8.5 with an optimum at pH 8.0, and between 10 and 90 g NaCl l(-1) with an optimum at 35 g l(-1). Phylogenetic analysis based on 16S rRNA and cbbL gene sequences demonstrated that strain TL 2(T) forms a separate lineage within the alpha-3 subdivision of the Proteobacteria, distantly related to the genera Rhodovulum and Rhodobacter. On the basis of these results, a novel genus and species, Thioclava pacifica gen. nov., sp. nov., is proposed to accommodate strain TL 2(T) (= DSM 10166(T) = UNIQEM 229(T)).

Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of nine new species of the genus Deinococcus obtained from a single soil sample

The ionizing-radiation-resistant fractions of two soil bacterial communities were investigated by exposing an arid soil from the Sonoran Desert and a nonarid soil from a Louisiana forest to various doses of ionizing radiation using a (60)Co source. The numbers of surviving bacteria decreased as the dose of gamma radiation to which the soils were exposed increased. Bacterial isolates surviving doses of 30 kGy were recovered from the Sonoran Desert soil, while no isolates were recovered from the nonarid forest soil after exposure to doses greater than 13 kGy. The phylogenetic diversities of the surviving culturable bacteria were compared for the two soils using 16S rRNA gene sequence analysis. In addition to a bacterial population that was more resistant to higher doses of ionizing radiation, the diversity of the isolates was greater in the arid soil. The taxonomic diversity of the isolates recovered was found to decrease as the level of ionizing-radiation exposure increased. Bacterial isolates of the genera Deinococcus, Geodermatophilus, and Hymenobacter were still recovered from the arid soil after exposure to doses of 17 to 30 kGy. The recovery of large numbers of extremely ionizing-radiation-resistant bacteria from an arid soil and not from a nonarid soil provides further ecological support for the hypothesis that the ionizing-radiation resistance phenotype is a consequence of the evolution of other DNA repair systems that protect cells against commonly encountered environmental stressors, such as desiccation. The diverse group of bacterial strains isolated from the arid soil sample included 60 Deinococcus strains, the characterization of which revealed nine novel species of this genus.

Herminiimonas fonticola gen. nov., sp. nov., a Betaproteobacterium isolated from a source of bottled mineral water

Several yellowish-pigmented bacteria with an optimum growth temperature of about 30 degrees C, were recovered from the source (borehole) of bottled mineral water in the Serra da Estrela in Eastern Portugal. Phylogenetic analyses of the 16S rRNA gene sequence of strains S-94T , S-97, S-99 and S-92 indicated that these organisms represent a new species of the Betaproteobacteria that is not closely related to any other known species. The major fatty acids of the strains are 16:1 omega7c and 16:0. Ubiquinone 8 is the major respiratory quinone. The new isolates are strictly organotrophic and aerobic. The new strains only assimilated organic acids, glycine and alanine. Casamino acids and a mixture of all natural amino acids are not used as sole carbon and nitrogen sources; these are used as nitrogen source in the presence of organic acids. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we are of the opinion that strains S-94T, S-97, S-99 and S-92 represent a new species of a novel genus for which we propose the name Herminiimonas fonticola gen. nov., sp. nov.

Truepera radiovictrixgen. nov., sp. nov., a new radiation resistant species and the proposal ofTrueperaceaefam. nov

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

Gamma-proteobacteria Aquicella lusitana gen. nov., sp. nov., and Aquicella siphonis sp. nov. infect protozoa and require activated charcoal for growth in laboratory media

Several isolates, belonging to two new species of the same novel genus of gamma-proteobacteria, were recovered from drilled well (borehole) and spa water at São Gemil in central Portugal. These organisms are phylogenetically most closely related to the strictly intracellular uncultured species of the genus Rickettsiella, which cause disease in arthropods, and to the facultatively intracellular species of the genus Legionella, some of which cause Legionnaires' disease and Pontiac fever. The São Gemil strains grew only on media containing charcoal, as is also true of the species of the genus LEGIONELLA: Unlike the vast majority of Legionella isolates, the new isolates did not require L-cysteine or ferric pyrophosphate for growth but like the legionellae had an absolute requirement for alpha-ketoglutarate. Strains SGT-39(T) and SGT-56 grew consistently between 30 and 43 degrees C, while strains SGT-108(T) and SGT-109 grew between 30 and 40 degrees C. The pH ranges for growth of these organisms were surprisingly narrow: strains SGT-39(T) and SGT-56 grew between pH 6.3 and 7.3, while strains SGT-108(T) and SGT-109 grew between pH 6.3 and 7.0. Both organisms proliferated in the amoeba Hartmannella vermiformis but did not grow in U937 human cells. Based on 16S rRNA gene sequence analysis and physiological, biochemical, and chemical analysis we describe two new species of one novel genus; one species is represented by strain SGT-39(T), for which we propose the name Aquicella lusitana, while strain SGT-108(T) represents a second species of the same genus, for which we propose the name Aquicella siphonis.

Mars-like soils in the Atacama Desert, Chile, and the dry limit of microbial life

The Viking missions showed the martian soil to be lifeless and depleted in organic material and indicated the presence of one or more reactive oxidants. Here we report the presence of Mars-like soils in the extreme arid region of the Atacama Desert. Samples from this region had organic species only at trace levels and extremely low levels of culturable bacteria. Two samples from the extreme arid region were tested for DNA and none was recovered. Incubation experiments, patterned after the Viking labeled-release experiment but with separate biological and nonbiological isomers, show active decomposition of organic species in these soils by nonbiological processes.

Detection of eubacterial 3-hydroxy-3-methylglutaryl coenzyme a reductases from natural populations of actinomycetes

Three natural populations of actinomycetes were investigated by PCR for the presence of type I 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG CoA), a gene associated with isoprenoid biosynthesis. The populations were obtained from an agricultural site (69 isolates), a coastal salt marsh (220 isolates), and a desert soil (96 isolates). A set (34) of standard actinomycete reference strains were also investigated. The target gene was only detected in 5 of the 419 actinomycetes screened, which represented 4 from the coastal salt marsh and one reference strain. The isolates that contained the gene were taxonomically diverse (4 Streptomyces spp. and 1 Nocardia sp.). These results suggest that type I HMG CoA containing pathways are rare in actinomycetes and their distribution within actinomycetes populations is not random.

Colored moderately thermophilic bacteria in paper-machine biofilms

Biofilms cause several problems in papermaking. This report describes a microbiological survey of colored biofilms in six paper and board machines, including two case studies of outbreaks of colored slimes in which the causative bacteria were found. A total of 95 pink-, red-, orange- or yellow-pigmented strains were isolated. Nearly all (99%) of the strains grew at 52 degrees C, 72% grew at 56 degrees C, but only 30% grew at 28 degrees C, indicating that most of the strains were moderately thermophilic. Biofilm formation potential and biocide susceptibility of the strains were analyzed with a microtiter plate assay. In the presence of 5 ppm of methylene bisthiocyanate or 2,2-dibromo-3-nitrilopropionamide in paper-machine water, 55 strains formed biofims. Moreover, 39 strains increased biofilm production by 5-753% in the presence of biocide, suggesting that biocide concentrations inhibitory to planktonic but not to surface-attached cells may actually promote biofouling. The cells may have inactivated a portion of the biocides, as the cell density in this assay was high, corresponding to the highest cell densities occurring in the circulating waters. Four groups of colored bacteria that were isolated from several mills were identified. Pink-pigmented Deinococcus geothermalis and red-pigmented Meiothermus silvanus occurred as common primary biofilm-formers in paper machines. This report is the first description of the involvement of Meiothermus species in red-slime formation in the paper industry. The third group of bacteria (putative new species related to Roseomonas) contained strains that were not biofilm formers, but which were commonly found in slimes of neutral or alkaline machines. The fourth group contained red-pigmented biofilm-forming strains representing a novel genus of alpha- Proteobacteria related to Rhodobacter. Many colored paper-machine bacteria are species previously known from microbial mats of hot springs. Some characteristics of the bacterial groups are described here in order to facilitate their recognition in future cases of colored-slime outbreaks in the paper industry.

Thermomonas hydrothermalis sp. nov., a new slightly thermophilic gamma-proteobacterium isolated from a hot spring in central Portugal

Several non-pigmented bacterial isolates, with an optimum growth temperature of about 50 degrees C, were recovered from the hot spring at São Gemil in Central Portugal. Phylogenetic analyses of the 16S rRNA gene sequence of strain SGM-6T indicated that this organism represents a new species of the gamma-subclass of the Proteobacteria that is closely related to the newly described slightly thermophilic species Thermomonas haemolytica. The major fatty acids of strains SGM-6T and SGM-7 are C15:0 iso, C16:0 iso, C11:0 iso and C11:0 iso 3OH. Ubiquinone 8 is the major respiratory quinone. The new isolates are strictly organotrophic and aerobic. Strain SGM-6T only assimilated D-glucose, D-maltose, D-cellobiose, D-furanose, L-glutamate, L-glutamine, L-lysine, L-proline, L-ornithine, acetate, L-glutamic acid and pyruvate of sixty-five carbon sources tested. Strain SGM-7 also assimilates L-serine, but does not assimilate L-ornithine. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we propose that strains SGM-6T and SGM-7 represent a new species most closely related to Thermomonas haemolytica for which we propose the name Thermomonas hydrothermalis.