Nitrospira-dominated biofilm within a thermal artesian spring: a case for nitrification-driven primary production in a geothermal setting.

Water chemistry, energetic modeling, and molecular analyses were combined to investigate the microbial ecology of a biofilm growing in a thermal artesian spring within Hot Springs National Park, AR. This unique fresh water spring has a low dissolved chemical load and is isolated from both light and direct terrestrial carbon input - resulting in an oligotrophic ecosystem limited for fixed carbon and electron donors. Evaluation of energy yields of lithotrophic reactions putatively linked to autotrophy identified the aerobic oxidation of methane, hydrogen, sulfide, ammonia, and nitrite as the most exergonic. Small subunit (SSU) rRNA gene libraries from biofilm revealed a low-diversity microbial assemblage populated by bacteria and archaea at a gene copy ratio of 45:1. Members of the bacterial family 'Nitrospiraceae', known for their autotrophic nitrite oxidation, dominated the bacterial SSU rRNA gene library (approximately 45%). Members of the Thaumarchaeota ThAOA/HWCGIII (>96%) and Thaumarchaeota Group I.1b (2.5%), which both contain confirmed autotrophic ammonia oxidizers, dominated the archaeal SSU rRNA library. Archaea appear to dominate among the ammonia oxidizers, as only ammonia monooxygenase subunit A (amoA) genes belonging to members of the Thaumarchaeota were detected. The geochemical, phylogenetic, and genetic data support a model that describes a novel thermophilic biofilm built largely by an autotrophic nitrifying microbial assemblage. This is also the first observation of 'Nitrospiraceae' as the dominant organisms within a geothermal environment.

Uruburuella suis gen. nov., sp. nov., isolated from clinical specimens of pigs.

Five strains of an unusual Gram-negative, catalase-positive, oxidase-positive, coccobacillus-shaped bacterium isolated from the lungs and heart of pigs with pneumonia and pericarditis were characterized by phenotypic and molecular genetic methods. On the basis of cellular morphology and biochemical criteria, the isolates were tentatively assigned to the family Neisseriaceae, although they did not appear to correspond to any recognized genus or species. Comparative 16S rRNA gene sequencing showed that the five unidentified strains were phylogenetically highly related to each other and represent a hitherto unknown subline within the family Neisseriaceae. On the basis of both phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from pigs be classified as a novel genus and species within the family Neisseriaceae, for which the name Uruburuella suis gen. nov., sp. nov. is proposed. The type strain of U. suis is 1258/02(T) (=CCUG 47806(T)=CECT 5685(T)).

Streptococcus entericus sp. nov., isolated from cattle intestine.

Biochemical, molecular chemical and molecular genetic studies were performed on an unknown gram-positive, catalase-negative, coccus-shaped organism isolated from the intestine of a cow affected with catarrhal enteritis. The organism was tentatively identified as a streptococcal species based on results of cellular morphological and biochemical tests. 16S rRNA gene sequencing studies confirmed its provisional identification as a member of the genus Streptococcus, but the organism did not correspond to any recognized species of this genus. The nearest phylogenetic relatives of the unknown coccus from a calf were Streptococcus acidominimus and Streptococcus suis. The unknown bacterium, however, was distinguished from these species and other animal streptococci by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be classified as a novel species of the genus Streptococcus, Streptococcus entericus sp. nov. The type strain is CECT 5353T (= CCUG 44616T).

Actinomyces funkei sp. nov., isolated from human clinical specimens.

Three strains of a previously undescribed Actinomyces-like bacterium were isolated from human clinical specimens. Phenotypic studies indicated that the strains were members of the genus Actinomyces and were presumptively identified as Actinomyces turicensis. Comparative 16S rRNA gene sequencing studies showed that although the bacterium is phylogenetically closely related to Actinomyces turicensis, it nevertheless constitutes a new sub-line within the genus Actinomyces. Based on phenotypic and molecular chemical and molecular genetic evidence, it is proposed that the unknown Actinomyces-like bacterium from human clinical specimens be classified as Actinomyces funkei sp. nov. The type strain of Actinomyces funkei is CCUG 42773T (= CIP 106713T).

Lactobacillus psittaci sp. nov., isolated from a hyacinth macaw (Anodorhynchus hyacinthinus).

A Gram-positive, non-spore-forming, catalase-negative, facultatively anaerobic coccibacillus to rod-shaped bacterium isolated from a parrot was characterized using phenotypic and molecular taxonomic methods. The unknown bacterium phenotypically resembled lactobacilli and comparative 16S rRNA gene sequencing demonstrated that the organism represents a distinct subline within the Lactobacillus delbrueckii rRNA cluster of the genus. 16S rRNA sequence divergence values of > 6% with recognized Lactobacillus species clearly demonstrated the phylogenetic separateness of the parrot bacterium. On the basis of phylogenetic evidence and the phenotypic distinctiveness of the unknown bacterium, a new species, Lactobacillus psittaci sp. nov., is proposed. The type strain of Lactobacillus psittaci is CCUG 42378T (= CIP 106492T).

Filobacillus milensis gen. nov., sp. nov., a new halophilic spore-forming bacterium with Orn-D-Glu-type peptidoglycan.

A spore-forming, halophilic bacterium was isolated from surface sediment located on the beach of Palaeochori Bay near to a shallow water hydrothermal vent area, Milos, Greece. The bacterium, designated SH 714T, consisted of motile, strictly aerobic rods which contained an Orn-D-Glu type murein and a G+C content of 35 mol%. Thin sections showed a cell wall typical for Gram-positive bacteria; the peptidoglycan layer, however, was very thin. The Gram-reaction of the organism was negative. Comparative 16S rRNA gene sequencing demonstrated that the isolate represents a new line of descent within the spore-forming rods branching at the periphery of the rRNA group 1 Bacillus (Bacillus sensu stricto). The nearest phylogenetic neighbours of the unknown bacterium were Bacillus haloalkaliphilus, Marinococcus albus and Halobacillus species. Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium be classified as Filobacillus milensis gen. nov., sp. nov. The type strain is SH 714T (= DSM 13259T = ATCC 700960T).

Aerococcus sanguicola sp. nov., isolated from a human clinical source.

Phenotypic and phylogenetic studies were performed on an unknown, Gram-positive, catalase-negative coccus isolated from human blood. Comparative 16S rRNA gene sequencing demonstrated that the organism represents a new subline within the genus Aerococcus. The unknown bacterium was readily distinguished from the three currently recognized Aerococcus species, Aerococcus christensenii, Aerococcus urinae and Aerococcus viridans, by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that this unknown bacterium from blood be classified as Aerococcus sanguicola sp. nov. The type strain of Aerococcus sanguicola is CCUG 43001T (= CIP 106533T).

Aerococcus urinaehominis sp. nov., isolated from human urine.

Phenotypic and phylogenetic studies were performed on an unknown Gram-positive catalase-negative coccus isolated from human urine. Comparative 16S rRNA gene sequencing demonstrated that the organism represents a new subline within the genus Aerococcus. The unknown bacterium was readily distinguished from the three currently recognized Aerococcus species, Aerococcus christensenii, Aerococcus urinae and Aerococcus viridans, by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from urine be classified as Aerococcus urinaehominis sp. nov. The type strain of Aerococcus urinaehominis is CCUG 42038bT (= CIP 106675T).

Lactobacillus cypricasei sp. nov., isolated from Halloumi cheese.

Four strains of a hitherto unknown bacterium isolated from Halloumi cheese were compared by using phenotypic and phylogenetic studies. Comparative 16S rRNA gene sequencing demonstrated that the strains were identical to each other and represent a new subline within the genus Lactobacillus. The unknown bacterium was readily distinguished from other described Gram-positive catalase-negative taxa by means of biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Lactobacillus cypricasei sp. nov. The type strain of L. cypricasei is CCUG 42961T (= CIP 106393T).

Arcanobacterium pluranimalium sp. nov., isolated from porpoise and deer.

Two strains of a previously undescribed Arcanobacterium-like bacterium were isolated from a dead harbour porpoise and a dead sallow deer. Biochemical testing and PAGE analysis of whole-cell proteins indicated that the strains were phenotypically closely related to each other and distinct from previously described Actinomyces and Arcanobacterium species. Comparative 16S rRNA gene sequencing studies showed the bacterium to be a hitherto unknown subline within the genus Arcanobacterium. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Arcanobacterium pluranimalium sp. nov. The type strain of Arcanobacterium pluranimalium is CCUG 42575T (= CIP 106442T).

Lactobacillus coleohominis sp. nov., isolated from human sources.

Four strains of a hitherto unrecognized gram-positive, catalase-negative, facultatively anaerobic, rod-shaped bacterium isolated from human sources were characterized using phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing demonstrated that the bacterium represents a new subline within the Lactobacillus casei/Pediococcus rRNA group of the genus Lactobacillus. The unknown bacterium was readily distinguished from all other described Lactobacillus species and related taxa by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Lactobacillus coleohominis sp. nov. The type strain of Lactobacillus coleohominis is CCUG 44007T (= CIP 106820T).

Clostridium hathewayi sp. nov., from human faeces.

A strictly anoxic, Gram-positive, sporeforming, rod-shaped bacterium was isolated from a chemostat inoculated with human faeces. The bacterium used carbohydrate as fermentable substrates, producing acetate, ethanol, carbon dioxide and hydrogen as the major products of glucose metabolism, and possessed a G + C content of 50.7 to 50.9 mol%. Comparative 16S rRNA gene sequencing showed that the unidentified bacterium represents a previously unrecognised sub-line within the Clostridium coccoides rRNA group of organisms. The nearest relatives of the unknown bacterium corresponded to Clostridium algidixylanolyticum, C. aerotolerans, C. celerecrescens, C. indolis, C. sphenoides, C. methoxybenzovorans and C. xylanolyticum but 16S rRNA sequence divergence values of >4% demonstrated that it represents a novel species. Based on the presented findings a new species, Clostridium hathewayi, is described. The type strain of Clostridium hathewayi is DSM = 13479T (= CCUG 43506 T).

Meningoencephalitis associated with Globicatella sanguinis infection in lambs.

Thirty lambs displayed symptoms of meningoencephalitis. An unusual gram-positive coccus was isolated in pure culture from the blood and brain samples from one of the affected animals, and phenotypic and phylogenetic characterization showed this to be Globicatella sanguinis. This is the first report of the isolation of G. sanguinis in pure culture from an animal infection.

Atopobacter phocae gen. nov., sp. nov., a novel bacterium isolated from common seals.

Two strains of a Gram-positive, catalase-negative, facultatively anaerobic, rod-shaped bacterium isolated from common seals were characterized using phenotypic and molecular taxonomic methods. The two strains closely resembled each other based on their biochemical characteristics, and PAGE analysis of whole-cell protein patterns confirmed their close phenotypic affinity. 16S rRNA gene sequencing showed that the two strains were genetically highly related (99.8% sequence similarity) and that they constitute a new line of descent within the lactic acid group of bacteria. The nearest phylogenetic neighbours of the unknown bacterium were Granulicatella spp., with related taxa such as enterococci, carnobacteria, Desemzia incerta, Lactosphaera pasteurii, Melissococcus plutonius, tetragenococci and vagococci more distantly related. Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium from seals be classified in a new genus as Atopobacter phocae gen. nov., sp. nov. The type strain of Atopobacter phocae is CCUG 42358T (= CIP 106392T).

New LL-diaminopimelic acid-containing actinomycetes from hypersaline, heliothermal and meromictic Antarctic Ekho Lake: Nocardioides aquaticus sp. nov. and Friedmanniella [correction of Friedmannielly] lacustris sp. nov.

Two Gram-positive, non-motile and aerobic bacteria were isolated from a water sample of the hypersaline Ekho Lake, Antarctica. The cocci or short rods grew well on oligotrophic PYGV agar of pH 7.5 and at 26 degrees C. Strains EL-17KT and EL-17AT both required thiamine and biotin, strain EL-17AT also required nicotinic acid. Carbon sources utilized by both strains were acetate, pyruvate, alpha-D-glucose, glutamate and (weakly) citrate, but succinate, malate or butyrate were utilized only by EL-17KT. Gelatin, starch and DNA were hydrolyzed, NH, was formed from peptone, and nitrate was reduced aerobically by both strains. The isolates had the same temperature tolerance for growth in the range tested (below 3 to above 33.5 degrees C) and pH range (<5.5 to >9.5) and were sensitive to chloramphenicol and penicillin G. Their cell walls contained LL-diaminopimelic acid and had a single glycine residue as interpeptide bridge. Strain EL-17AT contained glycine at position 1 of the peptide subunit (peptidoglycan type A 3gamma'). Isolates EL-17KT and EL-17AT differed in their maximum NaCl tolerance, which was 15% or 6-8%, respectively. The major fatty acid of EL-17KT was C18:1 and that of EL-17AT was ai-C15:0. The major respiratory quinones of EL-17KT and EL-17AT were MK-8(H4) and MK-9(H4), respectively. The former isolate had 69 mol% G+C, the latter had 73 mol% G+C. Comparative 16S rRNA gene sequencing revealed phylogenetic relationships of isolate EL-17KT with the genus Nocardioides, with N. pyridinolyticus and N. plantarum as the closest relatives. Phenotypic and genotypic characteristics support the description of a new species, Nocardioides aquaticus sp. nov., with EL-17KT as the type strain (= DSM 11439T). Isolate EL-17AT is related to the genus Friedmanniella, with E antarctica and E spumicola as the closest relatives. The differentiating characteristics support the description of a new species, Friedmanniella lacustris sp. nov., with EL-17AT as the type strain (= DSM 11465T).

Vagococcus fessus sp. nov., isolated from a seal and a harbour porpoise.

A polyphasic taxonomic study was performed on two strains of an unknown Gram-positive, catalase-negative, coccus-shaped bacterium isolated from a dead seal and a harbour porpoise. Comparative 16S rRNA gene sequencing demonstrated that the unknown bacterium represents a new subline within the genus Vagococcus close to, but distinct from, Vagococcus fluvialis, Vagococcus lutrae and Vagococcus salmoninarum. The unknown bacterium was readily distinguished from the three currently recognized Vagococcus species by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as a new species, Vagococcus fessus. The type strain of Vagococcus fessus is CCUG 41755T.

Lactobacillus fornicalis sp. nov., isolated from the posterior fornix of the human vagina.

Twelve strains isolated from the posterior fornix fluid of the human vagina were identified as Lactobacillus johnsonii, Lactobacillus acidophilus, Lactobacillus gallinarum and Lactobacillus crispatus based on numerical analyses of total soluble cell protein profiles and randomly amplified polymorphic DNA (RAPD)-PCR banding patterns. Five strains grouped with the type strains of Lactobacillus gasseri (DSM 20077T) and Lactobacillus jensenii (DSM 20557T) at r > or = 0.83 in one protein profile cluster, well separated from the other species included in this study. However, numerical analysis of the RAPD-PCR banding patterns of representative strains selected from the L. gasseri-L. jensenii protein cluster clearly indicated that they belong to two different species. Four strains (TV 1010, TG 1013, TV 1018T and TV 1045) grouped into another well separated protein profile cluster at r > or = 0.87. Strains selected from this cluster displayed very similar RAPD-PCR banding patterns and clustered at R2 > or = 0.78, separate from the other strains examined. Sequencing of the 16S rRNA of two representative strains, TV 1018T and TG 1013, of this group indicated that it represents a new member of rRNA group I Lactobacillus, which includes Lactobacillus delbrueckii, the type of the genus, and close relatives Lactobacillus acetotolerans, Lactobacillus kefiranofaciens, Lactobacillus iners, L. jensenii, L. crispatus, L. acidophilus, Lactobacillus helveticus, Lactobacillus amylovorus, Lactobacillus hamsteri, L. johnsonii, L. gasseri and Lactobacillus amylolyticus. The name Lactobacillus fornicalis sp. nov. is proposed for strains TV 1010 (DSM 13172), TG 1013, TV 1018T and TV 1045, with strain TV 1018T (= DSM 13171T = ATCC 700934T) as the type.

Luteococcus peritonei sp. nov., isolated from the human peritoneum.

An unusual catalase-positive pleomorphic Gram-positive rod isolated from a human clinical specimen was subjected to a polyphasic taxonomic analysis. Comparative 16S rRNA gene sequence analysis revealed the unknown bacterium was a member of the high G+C branch of the Gram-positive bacteria (Actinobacteria), and was phylogenetically a member of the family Propionibacteriaceae, with Luteococcus japonicus as its nearest relative. Based on both phenotypic and phylogenetic evidence, it is proposed that the unknown bacterium be classified in the genus Luteococcus, as Luteococcus peritonei sp. nov. The type strain of Luteococcus peritonei is CCUG 38120T.

Staleya guttiformis gen. nov., sp. nov. and Sulfitobacter brevis sp. nov., alpha-3-Proteobacteria from hypersaline, heliothermal and meromictic antarctic Ekho Lake.

Two Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). 16S rRNA gene sequence comparisons show the isolates to be phylogenetically close to the genera Sulfitobacter and Roseobacter. Cells can be motile and contain storage granules. Sulfite addition does not stimulate growth. Isolate EL-38T can produce bacteriochlorophyll a and has a weak requirement for sodium ions; polar lipids include phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified amino lipid, but not diphosphatidylgycerol. The dominant fatty acid is 18:1omega7c; other characteristic fatty acids are 3-OH 10:0, 3-OH 14:1, 16:0, 18:0, 18:2 and 19:1. The DNA base composition is 55.0-56.3 mol% G+C. Isolate EL-162T has an absolute requirement for sodium ions. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified amino lipid are present in the polar lipids. Dominant fatty acids of this isolate are 18:1omega7c and 18:1omega9c as well as 18:2 which is present as two isomers. Other characteristic fatty acids are 3-OH 10:0, 3-OH 14:1, 16:0 and 18:0. The G+C content is 57.9-58.1 mol%. Morphological, physiological and genotypic differences from related, thus far known genera support the description of Staleya guttiformis gen. nov. and sp. nov. with EL-38T (= DSM 11458T) as the type strain and of Sulfitobacter brevis sp. nov. with the type strain EL-162T (= DSM 11443T).

The genus Abiotrophia (Kawamura et al.) is not monophyletic: proposal of Granulicatella gen. nov., Granulicatella adiacens comb. nov., Granulicatella elegans comb. nov. and Granulicatella balaenopterae comb. nov.

The genus Abiotrophia currently includes four species, Abiotrophia defectiva, Abiotrophia adiacens, Abiotrophia balaenopterae and Abiotrophia elegans. Recent 16S rRNA gene sequencing studies have demonstrated that the genus is not monophyletic and is in need of taxonomic revision. Phylogenetically, the genus Abiotrophia consists of two distinct lines, A. defectiva, the type species of the genus, and a robust group consisting of A. adiacens, A. balaenopterae and A. elegans. Therefore, it is formally proposed that the genus Abiotrophia should be restricted to A. defectiva and that A. adiacens, A. balaenopterae and A. elegans should be reclassified in a new genus, Granulicatella, as Granulicatella adiacens comb. nov., Granulicatella balaenopterae comb. nov. and Granulicatella elegans comb. nov.