Two new species of anaerobic oxalate-fermenting bacteria,Oxalobacter vibrioformis sp. nov. and Clostridium oxalicum sp. nov., from sediment samples

Two types of new anaerobic bacteria were isolated from anoxic freshwater sediments. They grew in mineral medium with oxalate as sole energy source and with acetate as main carbon source. Oxalate as well as oxamate (after deamination) were decarboxylated to formate with growth yields of 1.2–1.4 g dry cell matter per mol oxalate degraded. No other organic or inorganic substrates were used, and no electron acceptors were reduced. Strain WoOx3 was a Gramnegative, non-sporeforming, motile vibrioid rod with a guanine-plus-cytosine content of the DNA of 51.6 mol%. It resembled the previously described genus Oxalobacter, and is described as a new species, O. vibrioformis. Strain AltOx1 was a Gram-positive, spore-forming, motile rod with a DNA base ratio of 36.3 mol% guanine-plus-cytosine. This isolate is described as a new species of the genus Clostridium, C. oxalicum.     

Four novel yeasts from decaying organic matter: Blastobotrys robertii sp. nov., Candida cretensis sp. nov., Candida scorzettiae sp. nov. and Candida vadensis sp. nov

Four novel yeast species are described, two from decaying mushrooms, viz. Candida cretensis and Candida vadensis, and two from rotten wood, viz. Blastobotrys robertii and Candida scorzettiae. Accession numbers for the CBS and ARS Culture Collections, and GenBank accession numbers for the D1/D2 domains of the large subunit of ribosomal DNA are: B. robertii CBS 10106^T, NRRL Y-27775, DQ839395; C. cretensis CBS 9453^T, NRRL Y-27777, AY4998861 and DQ839393; C. scorzettiae CBS 10107^T, NRRL Y-27665, DQ839394; C. vadensis CBS 9454^T, NRRL Y-27778, AY498863 and DQ839396. The GenBank accession number for the ITS region of C. cretensis is AY498862 and that for C. vadensis is AY498864. C. cretensis was the only species of the four that displayed fermentative activity. All four type strains grew on n-hexadecane. C. scorzettiae is the only one of the new species that assimilates some phenolic compounds, viz. 3-hydroxy derivatives of benzoic, phenylacetic and cinnamic acids, but not the corresponding 4-hydroxy acids. This is indicative of an operative gentisate pathway.     

Candida alocasiicola sp. nov., Candida hainanensis sp. nov., Candida heveicola sp. nov. and Candida musiphila sp. nov., novel anamorphic, ascomycetous yeast species isolated from plants

In a taxonomic study on the ascomycetous yeasts isolated from plant materials collected in tropical forests in Yunnan and Hainan Provinces, southern China, four strains isolated from tree sap (YJ2E(T)) and flowers (YF9E(T), YWZH3C(T) and YYF2A(T)) were revealed to represent four undescribed yeast species. Molecular phylogenetic analysis based on the large subunit (26S) rRNA gene D1/D2 domain sequences showed that strain YJ2E(T) was located in a clade together with Candida haemulonii and C. pseudohaemulonii. Strain YF9E(T) was most closely related to C. azyma and strain YWZH3C(T) to C. sorbophila and C. spandovensis. Strain YYF2A(T) was clustered in a clade containing small-spored Metschnikowia species and related anamorphic Candida species. The new strains differed from their closely related described species by more than 10% mismatches in the D1/D2 domain. No sexual states were observed for the four strains on various sporulation media. The new species are therefore assigned to the genus Candida and described as Candida alocasiicola sp. nov. (type strain, YF9E(T) = AS 2.3484(T) = CBS 10702(T)), Candida hainanensis sp. nov. (type strain, YYF2A(T) = AS 2.3478(T) = CBS 10696(T)), Candida heveicola sp. nov. (type strain, YJ2E(T) = AS 2.3483(T) = CBS 10701(T)) and Candida musiphila sp. nov. (type strain, YWZH3C(T) = AS 2.3479(T) = CBS 10697(T)).     

Classification of novel soil streptomycetes as Streptomyces aureus sp. nov., Streptomyces laceyi sp. nov. and Streptomyces sanglieri sp. nov

The taxonomic positions of soil isolates known as Streptomyces groups A, B and C were clarified. Comparative 16S rDNA sequence studies indicated that representatives of all three taxa formed distinct phyletic lines within the Streptomyces tree though the group A strains were shown to be related to Streptomyces griseus and associated validly described species. The taxonomic integrity of all three groups was highlighted by DNA:DNA relatedness and ribotype data though the group A strains encompassed a higher degree of genetic variation than the group B and C strains. In light of these and earlier phenotypic data it is proposed that Streptomyces groups A, B and C be given species status as Streptomyces sanglieri sp. nov., Streptomyces aureus sp. nov. and Streptomyces laceyi sp. nov., respectively. This revised version was published online in June 2006 with corrections to the Cover Date.     

Degradation of hydroxyhydroquinone by the strictly anaerobic fermenting bacterium Pelobacter massiliensis sp. nov.

A new rod-shaped, gram-negative, non-sporeforming, strictly anaerobic bacterium (strain HHQ7) was enriched and isolated from marine mud samples with hydroxyhydroquinone (1,2,4-trihydroxybenzene) as sole substrate. Strain HHQ7 fermented hydroxyhydroquinone, pyrogallol (1,2,3-trihydroxybenzene), phloroglucinol (1,3,5-trihydroxybenzene) and gallic acid (3,4,5-trihydroxybenzoate) to 3 mol acetate (plus 1 mol CO₂ in the case of gallic acid) per mol of substrate. Resorcinol accumulated intermediately during growth on hydroxy-hydroquinone. No other aliphatic or aromatic substrates were utilized. Sulfate, sulfite, sulfur, nitrate, and fumarate were not reduced with hydroxyhydroquinone as electron donor. The strain grew in sulfide-reduced mineral medium supplemented with 7 vitamins. The DNA base ratio was 59% G+C. Strain HHQ7 is classified as a new species of the genus Pelobacter, P. massiliensis. Experiments with dense cell suspensions of hydroxyhydroquinone-and pyrogallol-grown cells showed different kinetics of hydroxyhydroquinone and pyrogallol degradation, as well as different patterns of resorcinol accumulation, indicating that these substrates are metabolized by different transhydroxylation reactions.     

Tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes

Four anaerobic syntrophic acetate-oxidizing bacteria, the thermotolerant strains Re1^T, Re2, T1 and T2, were isolated from two different mesophilic methanogenic systems. The strains originate from sludge of a continuously stirred laboratory-scale reactor containing high levels of ammonium and from a high ammonium enrichment culture. Comparative 16S rRNA gene sequence analysis confirmed that the strains belong to the Firmicutes-Clostridia class. The most closely related species to strains Re1^T, Re2, T1 and T2 was Tepidanaerobacter syntrophicus, with a 16S rRNA gene sequence identity of 96%. The DNA-DNA relatedness of strains Re2, T1 and T2 to strain Re1^T was 92, 102, 81%, respectively. The gene encoding the acetogen key enzyme formyltetrahydrofolate synthetase (FTHFS) was detected and partly sequenced from the strains. In pure culture the bacteria used different organic compounds as carbon and energy source, such as organic acids, alcohols, sugars and amino acids. Furthermore, acetate-oxidizing ability was observed during co-cultivation with a hydrogen-consuming Methanoculleus sp. The bacteria were found to be spore-forming, rod-shaped and motile, and possessed Gram-positive cell walls. The four strains were thermotolerant and grew at temperatures between 25 and 55 °C. Strain Re1^T had a DNA G + C content of 38.4% and the major fatty acids were C_18:1 w7c, C_18:1 w9c, anteiso-C_17:0, C_16:1 w7c and C_18:0. The genetic and phenotypic properties of strains Re1^T, Re2, T1 and T2 suggest classification as representatives of a novel species of the genus Tepidanaerobacter; the name Tepidanaerobacter acetatoxydans sp. nov. is suggested. The type strain of T. acetatoxydans is Re1^T (=DSM 21804^T = JCM 16047^T).     

Actinomadura mexicana sp. nov. and Actinomadura meyerii sp. nov., two novel soil sporoactinomycetes

The taxonomic position of two soil isolates, strains A288(T) and A290(T) [provisionally assigned to the genus Actinomadura] was clarified in a polyphasic study. The organisms showed a combination of chemotaxonomic and morphological properties typical of actinomadurae. They also formed distinct phyletic lines in the 16S rRNA Actinomadura gene tree; strain A288(T) was associated with A. nitritigenes whereas strain A290(T) was closely related to a group that consisted of A. citrea, A. coerulea, A. glauciflava, A. luteofluorescens and A. verrucosospora. Strains A288(T) and A290(T) showed key phenotypic features which readily distinguish them from one another and from representatives of related validly described species of Actinomadura. It is proposed that the two organisms be classified as new species of the genus Actinomadura. The names proposed for the new taxa are Actinomadura mexicana (A290(T) = DSM 44485(T) = NRRL B-24203(T)), and Actinomadura meyerii (A288(T) = DSM 44485(T) = NRRL B-24203(T)).     

Bullera begoniae sp. nov. and Bullera setariae sp. nov., two new species of ballistoconidium-forming yeasts in the Bullera variabilis (Bulleribasidium) cluster isolated from plants in Taiwan

Two strains of xylose-containing and Q-10-having ballistoconidiogenous yeasts isolated from plant leaves collected in Taiwan were found to represent two new species of the genus Bullera. In the phylogenetic trees based on the sequence analysis of 18S rDNA and D1/D2 domain of 26S rDNA, these species are located in the Bullera variabilis (Bulleribasidum) cluster in Hymenomycetes. They are described as Bullera begoniae sp. nov. and Bullera setariae sp. nov., respectively.     

Halorubellus salinus gen. nov., sp. nov. and Halorubellus litoreus sp. nov., novel halophilic archaea isolated from a marine solar saltern

Two extremely halophilic archaeal strains GX3(T) and GX26(T) were isolated from the Gangxi marine solar saltern near the Weihai city of Shandong Province, China. Cells from the two strains were pleomorphic and stained Gram-negative, colonies were red-pigmented. Strains GX3(T) and GX26(T) were able to grow at 25-50 °C (optimum 37 °C), at 1.4-5.1M NaCl (optimum 3.1M), at pH 5.5-9.5 (optimum pH 7.0) and neither strain required Mg(2+) for growth. Cells lyse in distilled water and the minimal NaCl concentration to prevent cell-lysis was 8% (w/v). The major polar lipids of the two strains were PA (phosphatidic acid), PG (phosphatidylglycerol), PGP-Me (phosphatidylglycerol phosphate methyl ester) and three major glycolipids (GL1, GL2 & GL3) chromatographically identical to S-TGD-1 (sulfated galactosyl mannosy glucosyl diether), S-DGD-1 (sulfated mannosyl glucosyl diether), and DGD-1 (mannosyl glucosyl diether) respectively, an unidentified lipid (GL4) was also detected in strain GX26(T). Phylogenetic analysis based on 16S rRNA gene revealed that strain GX3(T) and strain GX26(T) formed a distinct clade with the closest relative, Haladaptatus paucihalophilus (89.9-92.4% and 90.4-92.7, respectively). The rpoB' gene similarities between strains GX3(T) and GX26(T), and between the two strains and the closest relative, Halorussus rarus TBN4(T) are 96.5%, 84.3% and 83.9%, respectively. The DNA G+C contents of strain GX3(T) and strain GX26(T) are 67.3 mol% and 67.2 mol%, respectively. The DNA-DNA hybridization value between strain GX3(T) and strain GX26(T) was 44%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain GX3(T) and strain GX26(T) represent two novel species in a new genus within the family Halobacteriaceae, Halorubellus salinus gen. nov., sp. nov. (type strain GX3(T)=CGMCC 1.10384(T)=JCM 17115(T)) and Halorubellus litoreus sp. nov. (type strain GX26(T)=CGMCC 1.10386(T)=JCM 17117(T)).     

Nonomuraea terrinata sp. nov., a novel soil actinomycete

The taxonomic position of a soil isolate, strain E626, was evaluated using the polyphasic approach. The organism was found to have chemical and morphological features consistent with its assignment to the genus Nonomuraea, a member of the family Streptosporangiaceae. Strain E626 consistently formed a distinct phyletic line within the Streptosporangiaceae 16S rDNA tree using four different algorithms. Furthermore, the taxonomic distinctness of the organism is underpinned by a range of phenotypic properties, notably morphological features. It is, therefore, proposed that the organism be classified in the genus Nonomuraea as Nonomuraea terrinata sp. nov. This revised version was published online in June 2006 with corrections to the Cover Date.     

<Emphasis Type="Italic">Aliihoeflea aestuarii</Emphasis> gen. nov., sp. nov., a novel bacterium isolated from tidal flat sediment

A novel Gram-negative and rod-shaped bacterium, designated N8^T, was isolated from tidal flat sediment. Phylogenetic analysis based on 16S rRNA gene sequences showed that N8^T strain is associated with the family Phyllobacteriaceae: two uncultured clones (98.4 and 99.8% 16S rRNA gene sequence similarity) and the genus Mesorhizobium (≤97.0%). The novel strain formed a separate clade with uncultured clones in the phylogenetic tree based on 16S rRNA gene sequences. Cellular fatty acid profiles predominately comprised C_18:1 ω7c and C_19:0 cyclo ω8c. The major isoprenoid quinone is ubiquinone-10 and genomic DNA G+C content is 53.4 mol%. The polyphasic taxonomic study indicates that the novel strain N8^T represents a novel species of the new genus in the family Phyllobacteriaceae, named Aliihoeflea aestuarii. The type strain is N8^T (= KCTC 22052^T= JCM 15118^T= DSM 19536^T).     

Clostridium halophilium sp. nov. and C. litorale sp. nov., an obligate halophilic and a marine species degrading betaine in the Stickland reaction

Two new mesophilic, sporeforming, gram-positive, strictly anaerobic, rod-shaped bacteria were isolated which utilized betaine in the Stickland reaction. Strain M1 was obtained from pasteurized hypersaline sediments. Cells were motile rods and formed spherical terminal spores. Betaine was used with hydrogen and several amino acids as electron donors. In addition, several carbohydrates served as substrates. Growth required 1.5% NaCl with an optimum at 6.0% NaCl. The guanine plus cytosine content of the DNA was 26.9%. This strain is described as a new species, Clostridium halophilum.Strain W6 was isolated from marine sediments. Cells were motile rods and formed ovoid, subterminal spores. Betaine was used with hydrogen and several amino acids as electron donors. Carbohydrates were not fermented. Growth optimum was at 1.0% NaCl. The guanine plus cytosine content of the DNA was 26.1%. This strain is described as a new species, Clostridium litorale.Non standard abbreviations DMG N,N-dimethylglycine - TMA trimethylamine - PY peptone-yeast extract - PYG peptone-yeast extract-glucose     

Succinate decarboxylation byPropionigenium maris sp. nov., a new anaerobic bacterium from an estuarine sediment

Enrichments on succinate plus yeast extract under anoxic conditions from intertidal mud-flat sediments yielded cultures dominated by oval to round-ended rod-shaped cells. Strain 10succ1, obtained in pure culture, was characterized in detail. The non-motile cells possessed a gram-negative cell wall and did not form spores. Carbohydrates were fermented to formate, acetate, ethanol, and lactate. Succinate was decarboxylated to propionate. Other organic and amino acids were variously fermented to formate, acetate, propionate, and butyrate. Sulfur, sulfate, thiosulfate, and nitrate were not used as electron acceptors. Growth required the presence of yeast extract and at least 5 g/l NaCl, and was possible only in the absence of oxygen. No cytochromes were detected. The DNA base ratio was 40 mol% G+C. Phylogenetically, strain 10succ1 is closely related to Propionigenium modestum, as revealed by 16S rDNA analysis, but is physiologically distinct. Accordingly, strain 10succ1 (DSM 9537) is described as the type strain of a new species of the genus Propionigenium, P. maris sp. nov. Received: 12 January 1995 / Accepted: 24 February 1995     

Streblocerus superserricaudatus sp. nov. from Venezuela

A new species of the genus Streblocerus is described from Venezuela and compared with European, Newfoundland and Australian specimens. The geographical distribution of the genus is discussed.     

Streptomyces daliensis sp. nov. from soil

A novel actinomycete strain YIM 31724^T was isolated from a soil sample collected from Dali, Yunnan Province, People’s Republic of China. The strain is characterized by white to yellow white aerial mycelia, spiral spore chains and smooth spore surface. The cell wall of strain YIM 31724^T contained LL-diaminopimelic acid (A₂pm) and traces of meso-A₂pm. Whole-cell hydrolysates contained mainly glucose and small amounts of galactose and xylose. The menaquinones were MK-9(H₆) (31%) and MK-9(H₈) (69%). Phosphatidylethanolamine was the diagnostic phospholipid. The DNA G+C content of strain YIM 31724^T was 67.2 mol%. Phylogenetic analysis indicated that the strain belongs to the genus Streptomyces, with highest similarity to Streptomyces rimosus subsp. rimosus JCM 4667^T (rRNA gene sequence similarity value of 98.9%) and Streptomyces erumpens DSM 40941^T (rRNA gene sequence similarity value of 98.7%). Based on its phenotypic and genotypic characteristics, including low DNA–DNA hybridization results, strain is proposed as the type strain of a novel species, Streptomyces daliensis sp. nov.     

Ponticoccus gilvus gen. nov., sp. nov., a novel member of the family Propionibacteriaceae from seawater

A novel actinobacterium, designated strain MSW-19^T, was isolated from a seawater sample in Republic of Korea. Cells were aerobic, Gram-positive, non-endospore-forming, and non-motile cocci. Colonies were circular, convex, opaque, and vivid yellow in colour. A phylogenetic tree based on 16S rRNA gene sequences exhibited that the organism formed a distinct clade within the radius encompassing representatives of the family Propionibacteriaceae. The phylogenetic neighbors were the type strains of the genera Friedmanniella, Microlunatus, Micropruina, Propionicicella, and Propionicimonas. Levels of 16S rRNA gene sequence similarity between the isolate and members of the family were less than 95.3%. The cell wall peptidoglycan of the organism contained LL-diaminopimelic acid as the diagnostic diamino acid. The isolate contained MK-9(H₄) as the predominant menaquinone, ai-C_15:0 as the major fatty acid and polar lipids including phosphatidylglycerol, phosphatidylethanolamine, and an unknown phospholipid. The G+C content of the DNA was 69.6 mol%. On the basis of the phenotypic and phylogenetic data presented here, the isolate is considered to represent a novel genus and species in the family Propionibacteriaceae, for which the name Ponticoccus gilvus gen. nov., sp. nov. is proposed. The type strain is strain MSW-19^T (= KCTC 19476^T= DSM 21351^T).     

Rhodococcus aetherivorans sp. nov., a new species that contains methyl t-butyl ether-degrading actinomycetes

The taxonomic positions of two actinomycetes, strains Bc663 and 10bc312T, provisionally assigned to the genus Rhodococcus were determined using a combination of genotypic and phenotypic properties. The organisms have phenotypic properties typical of members of the genus Rhodococcus and were assigned to the 16S rRNA subgroup which contains Rhodococcus rhodochrous and closely related species. The two strains, which have many phenotypic features in common, belong to the same genomic species albeit one readily separated from Rhodococcus ruber with which they form a distinct phyletic line. The organisms were also distinguished from all of the species classified in the R. rhodochrous subgroup, including R. ruber, using a combination of phenotypic properties. The genotypic and phenotypic data show that strains Bc663 and 10bc312T merit recognition as a new species of Rhodococcus. The name proposed for the new species is Rhodococcus aetherivorans (10bc312T = DSM 44752T = NCIMB 13964T).