Characterization of two subsurface H2-utilizing bacteria, Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov., and their ecological roles.

We examined the relative roles of acetogenic and sulfate-reducing bacteria in H2 consumption in a previously characterized subsurface sandstone ecosystem. Enrichment cultures originally inoculated with ground sandstone material obtained from a Cretaceous formation in central New Mexico were grown with hydrogen in a mineral medium supplemented with 0.02% yeast extract. Sulfate reduction and acetogenesis occurred in these cultures, and the two most abundant organisms carrying out the reactions were isolated. Based on 16S rRNA analysis data and on substrate utilization patterns, these organisms were named Desulfomicrobium hypogeium sp. nov. and Acetobacterium psammolithicum sp. nov. The steady-state H2 concentrations measured in sandstone-sediment slurries (threshold concentration, 5 nM), in pure cultures of sulfate reducers (threshold concentration, 2 nM), and in pure cultures of acetogens (threshold concentrations 195 to 414 nM) suggest that sulfate reduction is the dominant terminal electron-accepting process in the ecosystem examined. In an experiment in which direct competition for H2 between D. hypogeium and A. psammolithicum was examined, sulfate reduction was the dominant process.     

Four new species of Chryseobacterium from the rhizosphere of coastal sand dune plants, Chryseobacterium elymi sp. nov., Chryseobacterium hagamense sp. nov., Chryseobacterium lathyri sp. nov. and Chryseobacterium rhizosphaerae sp. nov.

The taxonomic positions of five Gram-negative, non-spore-forming and non-motile bacterial strains isolated from the rhizosphere of sand dune plants were examined using a polyphasic approach. The analysis of the 16S rRNA gene sequence indicated that all of the isolates fell into four distinct phylogenetic clusters belonging to the genus Chryseobacterium of the family Flavobacteriaceae. The 16S rRNA gene sequence similarities of isolates to mostly related type strains of Chryseobacterium ranged from 97.5% to 98.5%. All strains contained MK-6 as the predominant menaquinone, and iso-C_15:0, iso-C_17:0 3-OH and a summed feature of iso-C_15:0 2-OH and/or C_16:1 ω7c as the dominant fatty acids. Combined phenotypic, genotypic and chemotaxonomic data supported that they represented four novel species in the genus Chryseobacterium, for which the names Chryseobacterium hagamense sp. nov. (type strain RHA2-9^T=KCTC 22545^T=NBRC 105253^T), Chryseobacterium elymi sp. nov. (type strain RHA3-1^T=KCTC 22547^T=NBRC 105251^T), Chryseobacterium lathyri sp. nov. (type strain RBA2-6^T=KCTC 22544^T=NBRC 105250^T), and Chryseobacterium rhizosphaerae sp. nov. (type strain RSB3-1^T=KCTC 22548^T=NBRC 105248^T) are proposed.     

The new facultatively chemolithoautotrophic, moderately halophilic, sulfate-reducing bacterium Desulfovermiculus halophilus gen. nov., sp. nov., isolated from an oil field

The new mesophilic, chemolithoautotrophic, moderately halophilic, sulfate-reducing bacterium strain 11-6, could grow at a NaCl concentration in the medium of 30–230 g/l, with an optimum at 80–100 g/l. Cells were vibrios motile at the early stages of growth. Lactate, pyruvate, malate, fumarate, succinate, propionate, butyrate, crotonate, ethanol, alanine, formate, and H₂/CO₂ were used in sulfate reduction. Butyrate was degraded completely, without acetate accumulation. In butyrate-grown cells, a high activity of CO dehydrogenase was detected. Additional growth factors were not required. Autotrophic growth occurred, in the presence of sulfate, on H₂/CO₂ or formate without other electron donors. Fermentation of pyruvate and fumarate was possible in the absence of sulfate. Apart from sulfate, sulfite, thiosulfate, and elemental sulfur were able to serve as electron acceptors. The optimal growth temperature was 37°C; the optimum pH was 7.2. Desulfoviridin was not detected. Menaquinone MK-7 was present. The DNA G+C content was 55.2 mol %. Phylogenetically, the bacterium represented a separate branch within the cluster formed by representatives of the family Desulfohalobiaceae in the class Deltaproteobacteria. The bacterium was assigned to a new genus and species, Desulfovermiculus halophilus gen. nov., sp. nov. The type strain is 11-6^T (= VKM B-2364), isolated from the highly mineralized formation water of an oil field.     

Lithoautotrophic growth of sulfate-reducing bacteria,and description of Desulfobacterium autotrophicum gen. nov., sp. nov.

The capacity of mesophilic sulfate-reducing bacteria to grow lithoautotrophically with H₂, sulfate and CO₂ was investigated with enrichment cultures and isolated species. (a) Enrichments in liquid mineral media with H₂, sulfate and CO₂ consistently yielded mixed cultures of nonautotrophic, acetate-requiring Desulfovibrio species and autotrophic, acetate-producing Acetobacterium species (cell ratio approx. 20:1). (b) By direct dilution of mud samples in agar, various non-sporing sulfate reducers were isolated in pure cultures that did grow autotrophically. Two oval cell types (strains HRM2, HRM4) and one curved cell type (strain HRM6) from marine sediment were studied in detail. The strains grew in mineral medium supplemented only with vitamins (biotin, p-aminobenzoate, nicotinate). Carbon autotrophy was evident (i) from comparative growth experiments with non-autotrophic, acetate-requiring species, (ii) from high cell densities ruling out a cell synthesis from organic impurities in the mineral media, and (iii) by demonstrating that 96–99% of the cell carbon was derived from ¹⁴C-labelled CO₂. Autotrophic growth occurred with a doubling time of 16–20 h at 24–28°C. Formate, fatty acids up to palmitate, ethanol, lactate, succinate, fumarate, malate and other organic acids were also used and completely oxidized. The three strains possessed cytochromes of the b-and c-type, but no desulfoviridin. Strain HRM2 is described as a new species of a new genus, Desulfobacterium autotrophicum. (c) The capacity for autotrophic growth was also tested with sulfate-reducing bacteria that originally had been isolated on organic substrates. The incompletely oxidizing, non-sporing types such as Desulfovibrio and Desulfobulbus species and Desulfomonas pigra were confirmed to be obligate heterotrophs that required acetate for growth with H₂ and sulfate. In contrast, several of the completely oxidizing sulfate reducers were facultative autotrophs, such as Desulfosarcina variabilis, Desulfonema limicola, Desulfococcus niacini, and the newly isolated Desulfobacterium vacuolatum and Desulfobacter hydrogenophilus. The only incompletely oxidizing sulfate reducer that could grow autotrophically was the sporing Desulfotomaculum orientis, which obtained 96% of its cell carbon from ¹⁴C-labelled CO₂. Desulfovibrio baarsii and Desulfococcus multivorans may also be regarded as types of facultative autotrophs; they could not oxidize H₂, but grew on sulfate with formate as the only organic substrate.     

Natronocalculus amylovorans gen. nov., sp. nov., and Natranaeroarchaeum aerophilus sp. nov., dominant culturable amylolytic natronoarchaea from hypersaline soda lakes in southwestern Siberia

Several pure cultures of alkaliphilic haloaloarchaea were enriched and isolated from hypersaline soda lakes in southwestern Siberia using amylopectin and fructans as substrates. Phylogenomic analysis placed the isolates into two distinct groups within the class Halobacteria. Four isolates forming group 1 were closely related to a recently described Natranaeroarchaeum sulfidigenes and the other three strains forming group 2 represent a novel genus-level phylogenetic lineage. All isolates are saccharolytic archaea growing with various starch-like alpha-glucans including soluble starch, amylopectin, dextrin, glycogen, pullulane and cyclodextrin. In addition, group 1 can use levan while group 2 – inulin (plant storage beta-fructans). Group 1 strains can also grow anaerobically with either glucose or maltose using elemental sulfur as the electron acceptor. Both groups are moderately alkaliphilic with a pH range for growth from 7.2 to 9.3 (optimum between 8.0–8.8) and low Mg-demanding extreme halophiles growing optimally at 4 M total Na⁺. The major respiratory menaquinone is MK-8:8 and the core biphytanyl lipids are dominated by archaeol (C₂₀-C₂₀) and a less abundant extended archaeol (C₂₀-C₂₅) with PG and PGP-Me as polar groups. The four isolates of group 1 are suggested to be classified into a new species as Natranaeroarchaeum aerophilus sp. nov. (type strain AArc-St1-1^T = JCM 32519^T). The three isolates of group 2 are proposed to form a new genus and species for which the name Natronocalculus amylovorans gen. nov., sp. nov. is suggested (type strain AArc-St2^T = JCM 32475^T).     

Propionate-Degrading Bacterium, Syntrophobacter wolinii sp. nov. gen. nov., from Methanogenic Ecosystems

A new genus and species of a nonmotile gram-negative rod, Syntrophobacter wolinii, is the first bacterium described which degrades propionate only in coculture with an H₂-using organism and in the absence of light or exogenous electron acceptors such as O₂, sulfate, or nitrate. It was isolated from methanogenic enrichments from an anaerobic municipal sewage digestor, using anaerobic roll tubes containing a medium with propionate as the energy source in association with an H₂-using, sulfate-reducing Desulfovibrio sp. which cannot utilize fatty acids other than formate. S. wolinii produced acetate and, presumably, CO₂ and H₂ (or formate) from propionate. In media without sulfate and with Methanospirillum hungatei, a methanogen that uses only H₂-CO₂ or formate as an energy source, acetate, methane, and, presumably, CO₂ were produced from propionate and only small amounts of Desulfovibrio sp. were present. Isolation in coculture with the methanogen was not successful. S. wolinii does not use other saturated fatty acids as energy sources.     

Enrichment and isolation of Acetitomaculum ruminis,gen. nov., sp. nov.: acetogenic bacteria from the bovine rumen

Five strains of acetogenic bacteria were isolated by selective enrichment from the rumen of a mature Hereford crossbred steer fed a typical high forage diet. Suspensions of rumen bacteria, prepared from contents collected 7 h postfeeding, blended and strained through cheesecloth, were incubated in a minimal medium containing 10% clarified rumen fluid under either H₂:CO₂ (80:20) or N₂:CO₂ (80:20) headspace atmosphere. The selection criterion was an increment of acetate in the enrichments incubated under H₂:CO₂. Periodically, the enrichment broths were plated onto agar media and presumed acetogenic bacteria subsequently were screened for acetate production. Selected acetogenic bacteria utilized a pressurized atmosphere of H₂:CO₂ to form acetate in quantities 2 to 8-fold higher than when grown under N₂:CO₂. All presumptive acetogenic isolates were derived from either the 10^-7 or 10^-8 dilutions of rumen contents. All 5 strains were Gram-positive rods, and all utilized formate, glucose and CO. One strain required, and all were stimulated by, rumen fluid. No spores were observed with phase-contast microscopy and two strains were motile. No methane was detected in the headspace of pure cultures grown under either gas phase. The isolation of these bacteria indicates that acetogenic bacteria are inhabitants of the rumen of the bovine fed a typical diet and suggests that they may be participants in the utilization of hydrogen in the rumen ecosystem. Strain 139B (= ATCC 43876) is named Acetitomaculum ruminis gen. nov., sp. nov. and is the type strain of this new species. Portions of this work were presented previously (Greening RC, Leedle JAZ (1987) Abstr Annu Meet Am Soc Microbiol I 131, pp 194)     

Saccharopolyspora karakumensis sp. nov., Saccharopolyspora elongata sp. nov., Saccharopolyspora aridisoli sp. nov., Saccharopolyspora terrae sp. nov. and their biotechnological potential revealed by genome analysis

Exploration of unexplored habitats for novel actinobacteria with high bioactivity potential holds great promise in the search for novel entities. During the course of isolation of actinobacteria from desert soils, four actinobacteria, designated as 5K548^T, 7K502^T, 16K309^T and 16K404^T, were isolated from the Karakum Desert and their bioactivity potential as well as taxonomic provenances were revealed by comprehensive genome analyses. Pairwise sequence analyses of the 16S rRNA genes indicated that the four strains are representatives of putatively novel taxa within the prolific actinobacterial genus Saccharopolyspora. The strains have typical chemotaxonomic characteristics of the genus Saccharopolyspora by having meso-diaminopimelic acid as diagnostic diaminoacid, arabinose, galactose and ribose as whole-cell sugars. Consistent with this assignment, all of the isolates contained phosphatidylcholine in their polar lipid profiles and MK-9(H₄) as the predominant menaquinone. The sizes of the genomes of the isolates ranged from 6.0 to 10.2 Mb and the associated G + C contents from 69.6 to 69.7 %. Polyphasic characterizations including determination of overall genome relatedness indices revealed that the strains are representatives of four novel species in the genus Saccharopolyspora. Consequently, isolates 5K548^T, 7K502^T, 16K404^T and 16K309^T are proposed as novel Saccharopolyspora species for which the names of Saccharopolyspora karakumensis sp. nov., Saccharopolyspora elongata sp. nov., Saccharopolyspora aridisoli sp. nov. and Saccharopolyspora terrae sp. nov. are proposed, respectively. Comprehensive genome analysis for biosynthetic gene clusters showed that the strains have high potential for novel secondary metabolites. Moreover, the strains harbour many antimicrobial resistance genes providing more evidence for their potentiality for bioactive metabolites.     

Classification of Achromobacter genogroups 2, 5, 7 and 14 as Achromobacter insuavis sp. nov., Achromobacter aegrifaciens sp. nov., Achromobacter anxifer sp. nov. and Achromobacter dolens sp. nov., respectively

The phenotypic and genotypic characteristics of seventeen Achromobacter strains representing MLST genogroups 2, 5, 7 and 14 were examined. Although genogroup 2 and 14 strains shared a DNA–DNA hybridization level of about 70%, the type strains of both genogroups differed in numerous biochemical characteristics and all genogroup 2 and 14 strains could by distinguished by nitrite reduction, denitrification and growth on acetamide. Given the MLST sequence divergence which identified genogroups 2 and 14 as clearly distinct populations, the availability of nrdA sequence analysis as a single locus identification tool for all Achromobacter species and genogroups, and the differential phenotypic characteristics, we propose to formally classify Achromobacter genogroups 2, 5, 7 and 14 as four novel Achromobacter species for which we propose the names Achromobacter insuavis sp. nov. (with strain LMG 26845^T [= CCUG 62426^T] as the type strain), Achromobacter aegrifaciens sp. nov. (with strain LMG 26852^T [= CCUG 62438^T] as the type strain), Achromobacter anxifer sp. nov. (with strain LMG 26857^T [= CCUG 62444^T] as the type strain), and Achromobacter dolens sp. nov. (with strain LMG 26840^T [= CCUG 62421^T] as the type strain).     

First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov

Two moderately halophilic and psychrotolerant new Mycoplasma species were isolated from common cephalopods. Three strains were isolated in pure culture from two individual European flying squid (Todarodes sagittatus), and two individual octopuses (Octopus vulgaris). The strains showed optimal growth at 25 °C and a salinity of 3% (w/v) NaCl. Molecular analyses revealed that the isolates belonged to two new, but phylogenetically related species, divergent from all previously described Mollicutes, representing the first marine isolates of the class, and also the first Mycoplasma strains for which NaCl requirement has been demonstrated. A genome search against all available marine metagenomes and 16S rRNA gene databases indicated that these two species represent a novel non-free-living marine lineage of Mollicutes, specifically associated with marine animals. Morphology and physiology were compatible with other members of this group, and genomic and phenotypic analyses demonstrated that these organisms represent two novel species of the genus Mycoplasma, for which the names Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov. are proposed; the type strains are PE^T (DSM 105487^T, CIP 111404^T) and 5H^T (DSM 105,488^T, CIP 111405^T), respectively.     

Natrarchaeobius chitinivorans gen. nov., sp. nov., and Natrarchaeobius halalkaliphilus sp. nov., alkaliphilic,chitin-utilizing haloarchaea from hypersaline alkaline lakes

Two groups of alkaliphilic haloarchaea from hypersaline alkaline lakes in Central Asia, Egypt and North America were enriched and isolated in pure culture using chitin as growth substrate. These cultures, termed AArcht, were divided into two groups: group 1 which includes eleven isolates from highly alkaline soda lakes and group 2 which contains a single isolate obtained from the alkaline hypersaline Searles Lake. The colonies of chitin-utilizing natronoarchaea were red-pigmented and surrounded by large zones of chitin hydrolysis. The free cells of both groups were mostly flat nonmotile rods, while the cells that attached to chitin or formed colonies on chitin plates were mostly coccoid. The isolates are obligate aerobic saccharolytic archaea utilizing chitin and chitosane (less actively) as the only sugar polymers as well as a few hexoses as their carbon and energy source. Both groups are extremely halophilic, growing optimally at 3.5–4 M total Na⁺, but they differ in their pH profiles: the main group 1 isolates are obligately alkaliphilic, while the single group 2 strain (AArcht-Sl^T) is alkalitolerant. The core archaeal lipids in both groups are dominated by C₂₀–C₂₀ and C₂₀–C₂₅ dialkyl glycerol ethers (DGE) in approximately equal proportion. Phylogenetic analysis indicated that the isolates form an independent genus-level lineage within the family Natrialbaceae with 3 species-level subgroups. The available genomes of the closest cultured relatives of the AArcht strains, belonging to the genera Natrialba and Halopiger, do not encode any chitinase-related genes. On the basis of their unique phenotypic properties and distinct phylogeny, we suggest that the obligate alkaliphilic AArcht isolates (group 1) with an identical phenotype are classified into a new genus and species Natrarchaeobius chitinivorans gen. nov., sp. nov., with strain AArcht4^T as the type strain (JCM 32476^T = UNIQEM U966^T), while the facultatively alkaliphilic strain AArcht-Sl^T (group 2) — as a new species Natrarchaeobius halalkaliphilus sp. nov. (JCM 32477^T = UNIQEM U969^T).     

Two novel species Enterococcus lemanii sp. nov. and Enterococcus eurekensis sp. nov., isolated from a swine-manure storage pit

A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular genetic methods was performed on six strains of unknown Gram-positive, nonspore-forming, facultative anaerobic coccus-shaped bacteria isolated from a swine-manure storage pit. On the basis of the 16S rRNA, RNA polymerase α-subunit (rpoA) and 60 kDa chaperonin (cpn60) gene sequence analyses, it was shown that all the isolates were enterococci but formed two separate lines of descent. Pairwise 16S rRNA gene sequence comparisons demonstrated that the two novel organisms were most closely related to each other (97.9 %) and to Enterococcus aquimarinus (97.8 %). Both organisms contained major amounts of C_16:0, C_16:1 ω7c, C_16:1 ω7c, and C_18:1 ω7c/12t/9t as the major cellular fatty acids. Based on biochemical, chemotaxonomic and phylogenetic evidence, the names Enterococcus lemanii sp. nov. (type strain PC32^T = CCUG 61260^T = NRRL B-59661^T) and Enterococcus eurekensis sp. nov. (type strain PC4B^T = CCUG 61259^T = NRRL B-59662^T) are proposed for these hitherto undescribed species.     

Desulfosporomusa polytropa gen. nov., sp. nov., a novel sulfate-reducing bacterium from sediments of an oligotrophic lake

Five strains of sulfate-reducing bacteria were isolated from the highest positive dilutions of a most probable number (MPN) series supplemented with lactate and inoculated with sediments from the oligotrophic Lake Stechlin. The isolates were endospore-forming and were motile by means of laterally inserted flagella. They stained Gram-negative and contained b-type cytochromes. CO difference spectra indicated the presence of P582 as a sulfite reductase. Phylogenetic analyses of the 16S rDNA sequences revealed that the isolates were very closely affiliated with the genus Sporomusa. However, sulfate and amorphous Fe(OH)₃, but not sulfite, elemental sulfur, MnO₂, or nitrate were used as terminal electron acceptors. Homoacetogenic growth was found with H₂/CO₂ gas mixture, formate, methanol, ethanol, and methoxylated aromatic compounds. The strains grew autotrophically with H₂ plus CO₂ in the presence or absence of sulfate. Formate, butyrate, several alcohols, organic acids, carbohydrates, some amino acids, choline, and betaine were also utilized as substrates. The growth yield with lactate and sulfate as substrate was 7.0 g dry mass/mol lactate and thus two times higher than in sulfate-free fermenting cultures. All isolates were able to grow in a temperature range of 4–37°C. Physiologically and by the presence of a Gram-negative cell wall, the new isolates resemble known Desulfosporosinus species. However, phylogenetically they are affiliated with the Gram-negative genus Sporomusa belonging to the Selenomonas subgroup of the Firmicutes. Therefore, the new isolates reveal a new phylogenetic lineage of sulfate-reducing bacteria. A new genus and species, Desulfosporomusa polytropa gen. nov., sp. nov. is proposed.Dedicated to Prof. H. G. Schlegel on the occasion of his 80th birthday.     

Gilliamella intestini sp. nov., Gilliamella bombicola sp. nov., Gilliamella bombi sp. nov. and Gilliamella mensalis sp. nov.: Four novel Gilliamella species isolated from the bumblebee gut

Spectra of five isolates (LMG 28358^T, LMG 29879^T, LMG 29880^T, LMG 28359^T and R-53705) obtained from gut samples of wild bumblebees of Bombus pascuorum, Bombus lapidarius and Bombus terrestris were grouped into four MALDI-TOF MS clusters. RAPD analysis revealed an identical DNA fingerprint for LMG 28359^T and R-53705 which also grouped in the same MALDI-TOF MS cluster, while different DNA fingerprints were obtained for the other isolates.Comparative 16S rRNA gene sequence analysis of the four different strains identified Gilliamella apicola NCIMB 14804^T as nearest neighbour species. Average nucleotide identity values of draft genome sequences of the four isolates and of G. apicola NCIMB 14804^T were below the 96% threshold value for species delineation and all four strains and G. apicola NCIMB 14804^T were phenotypically distinct. Together, the draft genome sequences and phylogenetic and phenotypic data indicate that the four strains represent four novel Gilliamella species for which we propose the names Gilliamella intestini sp. nov., with LMG 28358^T as the type strain, Gilliamella bombicola sp. nov., with LMG 28359^T as the type strain, Gilliamella bombi sp. nov., with LMG 29879^T as the type strain and Gilliamella mensalis sp. nov., with LMG 29880^T as the type strain.     

Spathaspora brasiliensis sp. nov., Spathaspora suhii sp. nov., Spathaspora roraimanensis sp. nov. and Spathaspora xylofermentans sp. nov., four novel d-xylose-fermenting yeast species from Brazilian Amazonian forest

Four new d-xylose fermenting yeast species of the clade Spathaspora were recovered from rotting-wood samples in a region of Amazonian forest, Northern Brazil. Three species produced unconjugated asci with a single elongated ascospore with curved ends. These species are described as Spathaspora brasiliensis, Spathaspora suhii and Spathaspora roraimanensis. Two isolates of an asexually reproducing species belonging to the Spathaspora clade were also obtained and they are described as Spathaspora xylofermentans. All these species are able to ferment d-xylose during aerobic batch growth in rich YP (1 % yeast extract, 2 % peptone and 2 % D-xylose) medium, albeit with differing efficiencies. The type strains are Spathaspora brasiliensis sp. nov UFMG-HMD19.3 (=CBMAI 1425=CBS 12679), Spathaspora suhii sp. nov. UFMG-XMD16.2 (=CBMAI 1426=CBS 12680), Spathaspora roraimanensis sp. nov. UFMG-XMD23.2 (CBMAI 1427=CBS 12681) and Spathaspora xylofermentans sp. nov. UFMG-HMD23.3 (=CBMAI 1428=CBS 12682).     

Anaerobic oxidation of fatty acids by Clostridium bryantii sp. nov., a sporeforming,obligately syntrophic bacterium

From marine and freshwater mud samples strictly anaerobic, Gram-positive, sporeforming bacteria were isolated which oxidized fatty acids in obligately syntrophic association with H₂-utilizing bacteria. Even-numbered fatty acids with up to 10 carbon atoms were degraded to acetate and H₂, odd-numbered fatty acids with up to 11 carbon atoms including 2-methylbutyrate were degraded to acetate, propionate and H₂. Neither fumarate, sulfate, thiosulfate, sullur, nor nitrate were reduced. A marine isolate, strain CuCal, is described as type strain of a new species, Clostridium bryantii sp. nov.     

Erratum to: Two novel species Enterococcus lemanii sp. nov. and Enterococcus eurekensis sp. nov., isolated from a swine-manure storage pit

A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular genetic methods was performed on six strains of an unknown Gram-positive, nonspore-forming, facultative anaerobic coccus-shaped bacterium isolated from a swine-manure storage pit. On the basis of 16S rRNA, RNA polymerase-subunit (rpoA), and the 60-kilodalton chaperonin (cpn60) gene sequence analyses, it was shown that all the isolates were enterococci but formed two separate lines of descent. Pairwise 16S rRNA sequence comparisons demonstrated that the two novel organisms were most closely related to each other (97.9 %) and to Enterococcus aquimarinus (97.8 %). Both organisms contained major amounts of C_16:0, C_16:1 ω7c, and C_18:1 ω7c/12t/9t as the major cellular fatty acids. Based on biochemical, chemotaxonomic, and phylogenetic evidence, the names Enterococcus lemanii sp. nov. (type strain PC32^T = CCUG 61260^T = NRRL B-59661^T) and Enterococcus eurekensis sp. nov. (type strain PC4B^T = CCUG 61259^T = NRRL B-59662^T) are proposed for the hitherto undescribed species.     

Phylogenetic classification of ten novel species belonging to the genus Bifidobacterium comprising B. phasiani sp. nov., B. pongonis sp. nov., B. saguinibicoloris sp. nov., B. colobi sp. nov., B. simiiventris sp. nov., B. santillanense sp. nov., B. miconis sp. nov., B. amazonense sp. nov., B. pluvialisilvae sp. nov., and B. miconisargentati sp. nov

Ten Bifidobacterium strains, i.e., 6T3, 64T4, 79T10, 80T4, 81T8, 82T1, 82T10, 82T18, 82T24, and 82T25, were isolated from mantled guereza (Colobus guereza), Sumatran orangutan (Pongo abeli), silvery marmoset (Mico argentatus), golden lion tamarin (Leontopithecus rosalia), pied tamarin (Saguinus bicolor), and common pheasant (Phaisanus colchinus). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic, and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on the core genome sequences revealed that isolated strains exhibit close phylogenetic relatedness with Bifidobacterium genus members belonging to the Bifidobacterium bifidum, Bifidobacterium longum, Bifidobacterium pullorum, and Bifidobacterium tissieri phylogenetic groups. Phenotypic characterization and genotyping based on the genome sequences clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, B. phasiani sp. nov. (6T3 = LMG 32224^T = DSM 112544^T), B. pongonis sp. nov. (64T4 = LMG 32281^T = DSM 112547^T), B. saguinibicoloris sp. nov. (79T10 = LMG 32232^T = DSM 112543^T), B. colobi sp. nov. (80T4 = LMG 32225^T = DSM 112552^T), B. simiiventris sp. nov. (81T8 = LMG 32226^T = DSM 112549^T), B. santillanense sp. nov. (82T1 = LMG 32284^T = DSM 112550^T), B. miconis sp. nov. (82T10 = LMG 32282^T = DSM 112551^T), B. amazonense sp. nov. (82T18 = LMG 32297^T = DSM 112548^T), pluvialisilvae sp. nov. (82T24 = LMG 32229^T = DSM 112545^T), and B. miconisargentati sp. nov. (82T25 = LMG 32283^T = DSM 112546^T) are proposed as novel Bifidobacterium species.     

Minimelanolocus bicolorata sp. nov., Paradendryphiopsis elegans sp. nov. and Corynesporella bannaense sp. nov. from southern China

Minimelanolocus bicolorata sp. nov., Paradendryphiopsis elegans sp. nov. and Corynesporella bannaense sp. nov., are described and illustrated. Minimelanolocus bicolorata is unique in possessing the schizolytic conidial secession and solitary, acropleurogenous, holoblastic conidia that are ellipsoidal, 3-euseptate, 30–35 × 7.5–9.5 μm, verruculose, pale brown, with an appendage at each end. Paradendryphiopsis elegans is characterized by monoblastic conidiogenous cells producing short chains of conidia that are 13–30.5 × 4–6.5 μm, 2–3-euseptate and fusiform to obclavate. Corynesporella bannaense is distinguished by terminal and integrated or discrete, monotretic conidiogenous cells that arise as lateral branches from the tip of the conidiophore and solitary conidia that are 12–16-distoseptate, smooth, obclavate, thick-walled, pale brown, and 100–140 × 10–14 μm. Keys to species of Minimelanolocus, Paradendryphiopsis and Corynesporella are provided.     

Description of five novel thermophilic species of the genus Thermus: Thermus hydrothermalis sp. nov., Thermus neutrinimicus sp. nov., Thermus thalpophilus sp. nov., Thermus albus sp. nov., and Thermus altitudinis sp. nov., isolated from hot spring sediments

Biological denitrification is a significant process in nitrogen biogeochemical cycle of terrestrial geothermal environments, and Thermus species have been shown to be crucial heterotrophic denitrifier in hydrothermal system. Five Gram-stain negative, aerobic and rod-shaped thermophilic bacterial strains were isolated from hot spring sediments in Tibet, China. Phylogenetic analysis based on 16S rRNA gene and whole genome sequences indicated that these isolates should be assigned to the genus Thermus and were most closely related to Thermus caldifontis YIM 73026^T, and Thermus brockianus YS38^T. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the five strains and the type strains of the genus Thermus were lower than the threshold values (95% and 70%, respectively) recommended for bacterial species, which clearly distinguished the five isolates from other species of the genus Thermus and indicated that they represent independent species. Colonies are circular, convex, non-transparent. Cell growth occurred at 37–80 °C (optimum, 60–65 °C), pH 6.0–8.0 (optimum, pH 7.0) and with 0–2.0% (w/v) NaCl (optimum, 0–0.5%). Denitrification genes (narG, nirK, nirS, and norB genes) detected in their genomes indicated their potential function in nitrogen metabolism. The obtained results combined with those of morphological, physiological, and chemotaxonomic characteristics, including the menaquinones, polar lipids, and cellular fatty acids showed that the isolates are proposed as representing five novel species of the genus Thermus, which are proposed as Thermus hydrothermalis sp. nov. SYSU G00291^T, Thermus neutrinimicus sp. nov. SYSU G00388^T, Thermus thalpophilus sp. nov. SYSU G00506^T, Thermus albus sp. nov. SYSU G00608^T, Thermus altitudinis sp. nov. SYSU G00630^T.