- Volume 55, Issue 5, 2005
Volume 55, Issue 5, 2005
- Obituary
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- Validation List No. 105
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Validation of publication of new names and new combinations previously effectively published outside the IJSEM
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 55, part 3, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- New Taxa
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- Archaea
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Halobiforma lacisalsi sp. nov., isolated from a salt lake in China
More LessA Gram-negative, motile, neutrophilic and extremely halophilic strain, AJ5T, was isolated from a salt lake in Xinjiang, China, and subjected to polyphasic taxonomic study. The major polar lipids of the isolate were C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and glycolipid. The DNA G+C content was 64·9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain AJ5T clustered with members of the genus Halobiforma, exhibiting high sequence similarity to the 16S rRNA gene sequences of Halobiforma nitratireducens (96·3 %) and Halobiforma haloterrestris (99·0 %). Comparative analysis of phenotypic characteristics and DNA–DNA hybridization between strain AJ5T and Halobiforma species supported the conclusion that AJ5T represents a novel species within this genus, for which the name Halobiforma lacisalsi sp. nov. is proposed. The type strain is AJ5T (=CGMCC 1.3738T=JCM 12983T).
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- Other Bacteria
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Roseivirga echinicomitans sp. nov., a novel marine bacterium isolated from the sea urchin Strongylocentrotus intermedius, and emended description of the genus Roseivirga
A novel strictly aerobic, heterotrophic, pink-pigmented, non-motile, Gram-negative, oxidase-, catalase-, β-galactosidase- and alkaline phosphatase-positive marine bacterium, designated strain KMM 6058T, was isolated from the sea urchin Strongylocentrotus intermedius and studied using a polyphasic taxonomic approach. The G+C content of the DNA of the isolate was 41·3 mol%. The predominant fatty acids were i15 : 1, i15 : 0, a15 : 0 and i17 : 0 3-OH. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KMM 6058T formed a monophyletic clade with Roseivirga ehrenbergii, with 99 % similarity. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacterium should be assigned to the genus Roseivirga as Roseivirga echinicomitans sp. nov. The type strain is KMM 6058T (=KCTC 12370T=LMG 22587T).
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Prevotella multisaccharivorax sp. nov., isolated from human subgingival plaque
More LessSix bacterial strains isolated from the human oral cavity, PPPA16, PPPA20T, PPPA24, PPPA31, EPPA6 and EPPA7, were characterized by determining phenotypic and biochemical features, cellular fatty acid profiles, menaquinone profiles and phylogenetic position based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that the isolates represented the same species of the genus Prevotella. The strains were related to Prevotella dentalis with about 89 % similarity. In addition, the isolates were related to Prevotella sp. oral clone IDR-CEC-0032, which is a representative of the numerically dominant cluster VI in carious dentine lesions [ Nadkarni et al. (2004). J Clin Microbiol 42, 5238–5244 ], with about 99 % similarity. The strains were obligately anaerobic, non-pigmenting, non-spore-forming, non-motile, Gram-negative rods. The isolates could be differentiated from other Prevotella species by d-mannitol, d-melezitose, d-sorbitol and d-trehalose fermentation in API 20A tests. The cellular fatty acid composition of strains PPPA16, PPPA20T, PPPA24, PPPA31, EPPA6 and EPPA7 was significantly different from that of other Prevotella species. Compared with other Prevotella species, only these six strains contained dimethyl acetals. The major menaquinones of the clinical isolates were MK-12 and MK-13, whereas the major menaquinones of other Prevotella species were MK-10 and MK-11. On the basis of these data, a novel Prevotella species, Prevotella multisaccharivorax sp. nov., is proposed, with PPPA20T (=JCM 12954T=DSM 17128T) as the type strain.
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Gaetbulibacter saemankumensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat sediment in Korea
More LessThree Gram-negative, yellow-pigmented, rod-shaped bacterial strains, SMK-12T, SMK-36 and SMK-45, were isolated from a tidal flat sediment of the Yellow Sea in Korea, and their taxonomic positions were investigated by a polyphasic approach. The three strains grew optimally at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. They contained MK-6 as the predominant menaquinone. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1, anteiso-C15 : 0, iso-C15 : 0 3-OH and C16 : 1 ω7c and/or iso-C15 : 0 2-OH. The DNA G+C contents of the three strains were 34·7–34·9 mol%. The phylogenetic tree based on 16S rRNA gene sequences revealed that the three strains form one distinct evolutionary lineage supported by a bootstrap value of 100 % within the family Flavobacteriaceae. The three strains exhibited 16S rRNA gene sequence similarity levels of 93·8–94·9 % to the nearest phylogenetic neighbours, the genera Algibacter, Bizionia and Formosa. On the basis of differences in phenotypic characteristics and phylogenetic distinctiveness, strains SMK-12T, SMK-36 and SMK-45 were classified in a novel genus and species, for which the name Gaetbulibacter saemankumensis gen. nov., sp. nov. is proposed. The type strain for the novel species is SMK-12T (=KCTC 12379T=DSM 17032T).
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‘Candidatus Protochlamydia amoebophila’, an endosymbiont of Acanthamoeba spp.
The obligately intracellular coccoid bacterium UWE25, a symbiont of Acanthamoeba spp., was previously identified as being related to chlamydiae based upon the presence of a chlamydia-like developmental cycle and its 16S rRNA gene sequence. Analysis of its complete genome sequence demonstrated that UWE25 shows many characteristic features of chlamydiae, including dependency on host-derived metabolites, composition of the cell envelope and the ability to thrive as an energy parasite within the cells of its eukaryotic host. Phylogenetic analysis of 44 ribosomal proteins further confirmed the affiliation of UWE25 to the ‘Chlamydiae’. Within this phylum, UWE25 could be assigned to the family Parachlamydiaceae based on comparative analyses of the 16S rRNA, 23S rRNA and endoribonuclease P RNA genes. The distinct dissimilarities from its closest relative, Parachlamydia acanthamoebae Bn9 T (7·1, 9·7 and 28·8 %, respectively), observed in this analysis justify its classification in a new genus. Therefore, the name ‘Candidatus Protochlamydia amoebophila’ is proposed for the designation of the Acanthamoeba sp. symbiont UWE25 (=ATCC PRA-7).
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Chryseobacterium shigense sp. nov., a yellow-pigmented, aerobic bacterium isolated from a lactic acid beverage
More LessA yellow-pigmented bacterium designated strain GUM-KajiT was isolated from a lactic acid beverage. The strain had Gram-negative, non-motile, rod-shaped cells. It was strictly aerobic and chemo-organotrophic and grew at 5–30 °C and at pH 5–8. The major components of the non-polar and 3-hydroxy fatty acids were C15 : 0 iso and 3-OH-C17 : 0 iso, respectively. Menaquinone MK-6 was detected as the sole quinone. 16S rRNA gene sequence comparisons revealed that strain GUM-KajiT is affiliated to the genus Chryseobacterium, with Chryseobacterium joostei as its phylogenetic neighbour, but there were low levels of similarity (<96 %) to any established species of the genus. The G+C content of the genomic DNA was 36·6 mol%. The novel bacterium differed from any known species of Chryseobacterium in terms of a number of phenotypic properties. Thus, the name Chryseobacterium shigense sp. nov. is proposed for this novel bacterium. The type strain is strain GUM-KajiT (=BAMY 1001T=NCIMB 14047T=DSM 17126T).
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Maribacter dokdonensis sp. nov., isolated from sea water off a Korean island, Dokdo
More LessTwo Gram-negative, non-spore-forming, slightly halophilic gliding bacterial strains, DSW-8T and DSW-9, were isolated from sea water off a Korean island, Dokdo, of the East Sea, Korea, and their taxonomic position was investigated by a polyphasic study. The two strains grew optimally at 30 °C and in the presence of 2–3 % (w/v) NaCl. Strains DSW-8T and DSW-9 were characterized chemotaxonomically as containing MK-6 as the predominant menaquinone and iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 as the major fatty acids. Major polar lipids were phosphatidylethanolamine, two unidentified phospholipids, an unidentified glycolipid and an amino group-containing lipid that was ninhydrin-positive. Their DNA G+C contents were 36·1 and 35·9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains DSW-8T and DSW-9 fell within the genus Maribacter of the family Flavobacteriaceae. Strains DSW-8T and DSW-9 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 89 %. Strains DSW-8T and DSW-9 exhibited 16S rRNA gene sequence similarity levels of 96·9–98·0 % to the type strains of the four recognized Maribacter species, but their low level of DNA–DNA relatedness with these species demonstrated that they constitute a distinct Maribacter species. On the basis of phenotypic and phylogenetic data and genetic distinctiveness, strains DSW-8T (=KCTC 12393T=DSM 17201T) and DSW-9 were classified in the genus Maribacter as members of a novel species, for which the name Maribacter dokdonensis sp. nov. is proposed.
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Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces
More LessNine strains of Gram-negative, anaerobic rod were isolated from human faeces. Based on phylogenetic analysis and specific phenotypic characteristics, these strains were included within the Bacteroides cluster and were divided into two clusters. Strains from the two clusters showed 16S rRNA gene sequence similarities of 90·4 and 92·7 % to the nearest recognized species, Bacteroides vulgatus. The strains also formed two clusters exhibiting a 16S rRNA gene sequence divergence of approximately 6 %. DNA–DNA hybridization studies confirmed that the two novel strain clusters were distinct from each other. Based on the phenotypic and phylogenetic findings, two novel species, Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., are proposed, each representing one of the two strain clusters. The DNA G+C content of the type strains were 43·9 mol% for B. plebeius (M12T=JCM 12973T=DSM 17135T) and 42·4 mol% for B. coprocola (M16T=JCM 12979T=DSM 17136T).
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Chryseobacterium vrystaatense sp. nov., isolated from raw chicken in a chicken-processing plant
Yellow-pigmented, Gram-negative organisms isolated from raw chicken were investigated by means of a polyphasic taxonomic approach and were shown to represent a novel species in the genus Chryseobacterium, for which the name Chryseobacterium vrystaatense sp. nov. is proposed. Its nearest phylogenetic neighbours were Chryseobacterium joostei, Chryseobacterium indologenes and Chryseobacterium gleum, which showed 16S rRNA gene sequence similarity levels of 96·9, 97·1 and 96·1 %, respectively. Levels of DNA–DNA hybridization between strains of C. vrystaatense and Chryseobacterium reference species were below 46 %. Strain LMG 22846T (=CCUG 50970T) was chosen as the type strain and has a DNA G+C content of 37·1 mol%.
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Fluviicola taffensis gen. nov., sp. nov., a novel freshwater bacterium of the family Cryomorphaceae in the phylum ‘Bacteroidetes’
More LessA novel, strictly aerobic, Gram-negative, yellow–orange-pigmented, motile, catalase-positive, oxidase-negative bacterium, RW262T, was isolated from water of the River Taff, Cardiff, UK, during January 2000. Phylogenetic analysis of the 16S rRNA gene indicated that strain RW262T was a member of the family Cryomorphaceae within the phylum ‘Bacteroidetes’. The DNA G+C content of strain RW262T was 37·2 mol%. The predominant fatty acid was the branched-chain saturated fatty acid i15 : 0 (44·2 %). On the basis of polyphasic analysis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, it is proposed that this freshwater bacterium represents a novel genus and species within the family Cryomorphaceae, Fluviicola taffensis gen. nov., sp. nov. The type strain is RW262T (=NCIMB 13979T=DSM 16823T).
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- Proteobacteria
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Tetrathiobacter kashmirensis gen. nov., sp. nov., a novel mesophilic, neutrophilic, tetrathionate-oxidizing, facultatively chemolithotrophic betaproteobacterium isolated from soil from a temperate orchard in Jammu and Kashmir, India
More LessTwelve chemolithotrophic strains were isolated from temperate orchard soil on reduced sulfur compounds as energy and electron sources and characterized on the basis of their physiological properties and ability to oxidize various reduced sulfur compounds. The new isolates could oxidize tetrathionate as well as thiosulfate, and oxidation of the latter involved conversion of thiosulfate to tetrathionate followed by its accumulation and eventual oxidation to sulfate, manifested in the production of acid. The mesophilic, neutrophilic, Gram-negative and coccoid bacteria had a respiratory metabolism. Physiologically and biochemically, all the strains were more or less similar, differing only in their growth rates and ability to utilize a few carbon compounds as single heterotrophic substrates. 16S rRNA gene sequence analysis was performed with five representative strains, which revealed a high degree of similarity (⩾99 %) among them and placed the cluster in the ‘Betaproteobacteria’. The strains showed low levels (93·5–95·3 %) of 16S rRNA gene sequence similarity to Pigmentiphaga kullae, Achromobacter xylosoxidans, Pelistega europaea and species belonging to the genera Alcaligenes, Taylorella and Bordetella. The taxonomic coherence of the new isolates was confirmed by DNA–DNA hybridization. On the basis of their uniformly low 16S rRNA gene sequence similarities to species of all the closest genera, unique fatty acid profile, distinct G+C content (54–55·2 mol%) and phenotypic characteristics that include efficient chemolithotrophic utilization of tetrathionate, the organisms were classified in a new genus, Tetrathiobacter gen. nov. In the absence of any significant discriminatory phenotypic or genotypic characteristics, all the new isolates are considered to constitute a single species, for which the name Tetrathiobacter kashmirensis sp. nov. (type strain WT001T=LMG 22695T=MTCC 7002T) is proposed.
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Methylohalobius crimeensis gen. nov., sp. nov., a moderately halophilic, methanotrophic bacterium isolated from hypersaline lakes of Crimea
More LessA novel genus and species are proposed for two strains of methanotrophic bacteria isolated from hypersaline lakes in the Crimean Peninsula of Ukraine. Strains 10KiT and 4Kr are moderate halophiles that grow optimally at 1–1·5 M (5·8–8·7 %, w/v) NaCl and tolerate NaCl concentrations from 0·2 M up to 2·5 M (1·2–15 %). This optimum and upper limit are the highest for any methanotrophic bacterium known to date. The strains are Gram-negative, aerobic, non-pigmented, motile, coccoid to spindle-shaped bacteria that grow on methane or methanol only and utilize the ribulose monophosphate pathway for carbon assimilation. They are neutrophilic (growth occurs only in the range pH 6·5–7·5) and mesophilic (optimum growth occurs at 30 °C). On the basis of 16S rRNA gene sequence phylogeny, strains 10KiT and 4Kr represent a type I methanotroph within the ‘Gammaproteobacteria’. However, the 16S rRNA gene sequence displays <91·5 % identity to any public-domain sequence. The most closely related methanotrophic bacterium is the thermophilic strain HB. The DNA G+C content is 58·7 mol%. The major phospholipid fatty acids are 18 : 1ω7 (52–61 %), 16 : 0 (22–23 %) and 16 : 1ω7 (14–20 %). The dominance of 18 : 1 over 16 : 0 and 16 : 1 fatty acids is unique among known type I methanotrophs. The data suggest that strains 10KiT and 4Kr should be considered as belonging to a novel genus and species of type I methanotrophic bacteria, for which the name Methylohalobius crimeensis gen. nov., sp. nov. is proposed. Strain 10KiT (=DSM 16011T=ATCC BAA-967T) is the type strain.
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Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., isolated from various terrestrial environments
The bacterial strains IMB-1T and CC495T, which are capable of growth on methyl chloride (CH3Cl, chloromethane) and methyl bromide (CH3Br, bromomethane), were isolated from agricultural soil in California fumigated with CH3Br, and woodland soil in Northern Ireland, respectively. Two pesticide-/herbicide-degrading bacteria, strains ER2 and C147, were isolated from agricultural soil in Canada. Strain ER2 degrades N-methyl carbamate insecticides, and strain C147 degrades triazine herbicides widely used in agriculture. On the basis of their morphological, physiological and genotypic characteristics, these four strains are considered to represent two novel species of the genus Aminobacter, for which the names Aminobacter ciceronei sp. nov. (type strain IMB-1T=ATCC 202197T=CIP 108660T=CCUG 50580T; strains ER2 and C147) and Aminobacter lissarensis sp. nov. (type strain CC495T=NCIMB 13798T=CIP 108661T=CCUG 50579T) are proposed.
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Ferrimonas marina sp. nov.
More LessA novel Ferrimonas species is described on the basis of phenotypic, chemotaxonomic and phylogenetic studies. Four halophilic organisms were isolated from marine sand and marine macroalgae samples by using high-pH marine agar 2216. An analysis of the nearly complete 16S rRNA gene sequences of these new isolates indicated that they were phylogenetically close (16S rRNA gene sequence similarity >99·5 %, gyrB gene sequence similarity >97·8 %), and were most closely related to Ferrimonas balearica (16S rRNA gene sequence similarity 97·1–97·3 %, gyrB gene sequence similarity 84·4–85·0 %). Chemotaxonomic data (major menaquinone MK7; major fatty acids C16 : 0 and C18 : 1 ω9c) supported the affiliation of the new isolates to the genus Ferrimonas. The results of physiological and biochemical tests allowed phenotypic differentiation of the isolates from F. balearica. It is therefore proposed that the new isolates represent a novel species with the name Ferrimonas marina sp. nov. and type strain A4D-4T (=MBIC06480T=DSM 16917T).
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‘Candidatus Liberibacter americanus’, associated with citrus huanglongbing (greening disease) in São Paulo State, Brazil
Symptoms of huanglongbing (HLB) were reported in São Paulo State (SPS), Brazil, in March 2004. In Asia, HLB is caused by ‘Candidatus Liberibacter asiaticus' and in Africa by ‘Candidatus Liberibacter africanus’. Detection of the liberibacters is based on PCR amplification of their 16S rRNA gene with specific primers. Leaves with blotchy mottle symptoms characteristic of HLB were sampled in several farms of SPS and tested for the presence of liberibacters. ‘Ca. L. asiaticus' was detected in a small number of samples but most samples gave negative PCR results. Therefore, a new HLB pathogen was suspected. Evidence for an SPS-HLB bacterium in symptomatic leaves was obtained by PCR amplification with universal primers for prokaryotic 16S rRNA gene sequences. The amplified 16S rRNA gene was cloned and sequenced. Sequence analysis and phylogeny studies showed that the 16S rRNA gene possessed the oligonucleotide signatures and the secondary loop structure characteristic of the α-Proteobacteria, including the liberibacters. The 16S rRNA gene sequence phylogenetic tree showed that the SPS-HLB bacterium clustered within the α-Proteobacteria, the liberibacters being its closest relatives. For these reasons, the SPS-HLB bacterium is considered a member of the genus ‘Ca. Liberibacter’. However, while the 16S rRNA gene sequences of ‘Ca. L. asiaticus' and ‘Ca. L. africanus' had 98·4 % similarity, the 16S rRNA gene sequence of the SPS-HLB liberibacter had only 96·0 % similarity with the 16S rRNA gene sequences of ‘Ca. L. asiaticus' or ‘Ca. L. africanus’. This lower similarity was reflected in the phylogenetic tree, where the SPS-HLB liberibacter did not cluster within the ‘Ca. L asiaticus’/‘Ca. L. africanus group’, but as a separate branch. Within the genus ‘Candidatus Liberibacter’ and for a given species, the 16S/23S intergenic region does not vary greatly. The intergenic regions of three strains of ‘Ca. L. asiaticus’, from India, the People's Republic of China and Japan, were found to have identical or almost identical sequences. In contrast, the intergenic regions of the SPS-HLB liberibacter, ‘Ca. L. asiaticus' and ‘Ca. L. africanus' had quite different sequences, with similarity between 66·0 and 79·5 %. These results confirm that the SPS-HLB liberibacter is a novel species for which the name ‘Candidatus Liberibacter americanus' is proposed. Like the African and the Asian liberibacters, the ‘American’ liberibacter is restricted to the sieve tubes of the citrus host. The liberibacter could also be detected by PCR amplification of the 16S rRNA gene in Diaphorina citri, the psyllid vector of ‘Ca. L. asiaticus’, suggesting that this psyllid is also a vector of ‘Ca. L. americanus' in SPS. ‘Ca. L. americanus' was detected in 216 of 218 symptomatic leaf samples from 47 farms in 35 municipalities, while ‘Ca. L. asiaticus' was detected in only 4 of the 218 samples, indicating that ‘Ca. L. americanus' is the major cause of HLB in SPS.
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Methylothermus thermalis gen. nov., sp. nov., a novel moderately thermophilic obligate methanotroph from a hot spring in Japan
More LessA novel moderately thermophilic methanotroph, strain MYHTT, was isolated from a hot spring in Japan. The isolate grew on methane or methanol at 37–67 °C, and optimally at 57–59 °C. It was found to be a Gram-negative aerobe, with colourless colonies of non-motile coccoid cells, possessing type I intracytoplasmic membranes and regularly arranged surface layers of linear (p2) symmetry. Strain MYHTT expressed only the particulate methane monooxygenase and employed the ribulose monophosphate pathway for formaldehyde assimilation. It is a neutrophilic and halotolerant organism capable of growth at pH 6·5–7·5 (optimum pH 6·8) and in up to 3 % NaCl (optimum 0·5–1 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequence analysis indicated that strain MYHTT is most closely related to the thermophilic undescribed methanotroph ‘Methylothermus’ HB (91 % identity) and the novel halophilic methanotroph Methylohalobius crimeensis 10KiT (90 % identity). Comparative sequence analysis of particulate methane monooxygenase (pmoA) genes also confirmed the clustering of strain MYHTT with ‘Methylothermus’ HB and Methylohalobius crimeensis 10KiT (98 and 92 % derived amino acid sequence identity, respectively). The DNA G+C content was 62·5 mol%. The major cellular fatty acids were C16 : 0 (37·2 %) and C18 : 1 ω9c (35·2 %) and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The major ubiquinone was Q-8. On the basis of comparative phenotypic and genotypic characteristics, a new genus and species, Methylothermus thermalis gen. nov., sp. nov., is proposed, with MYHTT as the type strain (=VKM B-2345T=IPOD FERM P-19714T).
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Psychrobacter celer sp. nov., isolated from sea water of the South Sea in Korea
More LessA Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strain, SW-238T, was isolated from sea water collected from the South Sea in Korea, and subjected to a polyphasic taxonomic study. The organism grew optimally at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. Strain SW-238T was characterized chemotaxonomically as containing ubiquinone (Q-8) as the predominant respiratory lipoquinone and C18 : 1 ω9c as the major fatty acid. Its DNA G+C content was 47·6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SW-238T fell within the radiation of the cluster comprising Psychrobacter species. The 16S rRNA gene sequence of strain SW-238T had similarity levels of 94·8–97·9 % to sequences of the type strains of recognized Psychrobacter species. Levels of DNA–DNA relatedness between strain SW-238T and the type strains of 10 phylogenetically related Psychrobacter species were below 70 %. On the basis of phenotypic and phylogenetic data and genetic distinctiveness, strain SW-238T (=KCTC 12313T=JCM 12601T) was placed in the genus Psychrobacter as the type strain of a novel species, for which the name Psychrobacter celer sp. nov. is proposed.
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The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov.
More LessPhylogenetic analysis of the class ‘Alphaproteobacteria’, including physiologically diverse species, was conducted by using small-subunit rRNA gene sequences. The 16S rRNA gene sequences of 261 species in the class ‘Alphaproteobacteria’ were obtained from GenBank/EMBL/DDBJ for constructing a phylogenetic tree by using maximum-likelihood analysis. In the resulting tree, members of the class ‘Alphaproteobacteria’ were subdivided into five major clusters, which were compared with the taxonomic outline of Bergey's Manual of Systematic Biology and the arb tree. Based on this phylogenetic tree, three novel families are proposed: Hyphomonadaceae fam. nov. to accommodate the bacterial genera Hyphomonas, Hirschia, Maricaulis and Oceanicaulis, Xanthobacteraceae fam. nov. to include the genera Xanthobacter, Azorhizobium, Ancylobacter, Labrys and Starkeya, and Erythrobacteraceae fam. nov. to accommodate the genera Erythrobacter, Porphyrobacter and Erythromicrobium. The phylogenetic tree of 16S rRNA gene sequences established in this study may provide a sound basis for future taxonomic reconstruction of the class ‘Alphaproteobacteria’.
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Mitsuaria chitosanitabida gen. nov., sp. nov., an aerobic, chitosanase-producing member of the ‘Betaproteobacteria’
Four strains (3001T, 2, 12 and 13), which were isolated as chitosanase-producing bacteria from soil from Matsue city (Japan), were studied phenotypically, genotypically and phylogenetically. Based on sequence analysis of 16S rRNA genes, DNA G+C content (67·4–69·2 mol%), quinone type (UQ-8), major fatty acid composition (3-OH 10 : 0, 3-OH 14 : 0) and other phylogenetic studies, strains 3001T, 12 and 13 were found to occupy a separate position in the ‘Betaproteobacteria’. Roseateles depolymerans, Rubrivivax gelatinosus and Ideonella dechloratans were their closest neighbours (93–95 % 16S rRNA gene sequence similarity). The 16S rRNA gene sequence and other characteristics suggested that strain 2 belonged to the genus Flavobacterium. DNA–DNA hybridization experiments supported the conclusion that strains 3001T, 12 and 13 were of the same species (72–78 % DNA hybridization) and only distantly related to I. dechloratans and R. gelatinosus. It is proposed that strains 3001T, 12 and 13 represent a novel genus and species for which the name Mitsuaria chitosanitabida gen. nov., sp. nov. is proposed. The type strain of Mitsuaria chitosanitabida is 3001T (=IAM 14711T=ATCC BAA-476T).
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Thalassobacter stenotrophicus Macián et al. 2005 is a later synonym of Jannaschia cystaugens Adachi et al. 2004, with emended description of the genus Thalassobacter
More LessThe type strains of Jannaschia cystaugens (LMG 22015T) and Thalassobacter stenotrophicus (CECT 5294T) were analysed by means of genomic DNA–DNA hybridization, comparison of 16S rRNA gene sequences and phenotypic properties determined under the same methodological conditions. J. cystaugens LMG 22015T showed DNA–DNA relatedness levels of 72 % when hybridized with the genomic DNA of T. stenotrophicus CECT 5294T. Sequence comparisons revealed that the 16S rRNA genes of the two strains had a similarity of 99·8 %. The cellular fatty acid and polar lipid compositions of the two strains and their DNA mol% G+C contents were almost identical. Bacteriochlorophyll a (Bchl a) and polyhydroxybutyrate were produced by both strains under the same culture conditions. Their closest phylogenetic neighbours were Jannaschia helgolandensis and Jannaschia rubra; however, the low sequence similarity values (95·7–95·9 %) and several important differences in phenotypic traits (ionic requirements, Bchl a production and polar lipids) support the distinction between the genera Thalassobacter and Jannaschia. Thus, we propose the unification of J. cystaugens (LMG 22015T) and T. stenotrophicus (CECT 5294T) as Thalassobacter stenotrophicus (type strain, CECT 5294T=DSM 16310T). An emended description of the genus Thalassobacter is also presented.
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Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov.
Three strains of Sphingomonas paucimobilis, B90A, UT26 and Sp+, isolated from different geographical locations, were found to degrade hexachlorocyclohexane. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains do not fall in a clade that includes the type strain, Sphingomonas paucimobilis ATCC 29837T, but form a coherent cluster with [Sphingomonas] chungbukensis IMSNU 11152T followed by Sphingobium chlorophenolicum ATCC 33790T. The three strains showed low DNA–DNA relatedness values with Sphingomonas paucimobilis ATCC 29837T (8–25 %), [Sphingomonas] chungbukensis IMSNU 11152T (10–17 %), Sphingobium chlorophenolicum ATCC 33790T (23–54 %) and Sphingomonas xenophaga DSM 6383T (10–28 %), indicating that they do not belong to any of these species. Although the three strains were found to be closely related to each other based on 16S rRNA gene sequence similarity (99·1–99·4 %), DNA–DNA relatedness (19–59 %) and pulsed-field gel electrophoresis (PFGE) patterns indicated that they possibly represent three novel species of the genus Sphingobium. The three strains could also be readily distinguished by biochemical tests. The three strains showed similar polar lipid profiles and contained sphingoglycolipids. The strains differed from each other in fatty acid composition but contained the predominant fatty acids characteristic of other Sphingobium species. A phylogenetic study based on 16S rRNA gene sequences showed that [Sphingomonas] chungbukensis IMSNU 11152T formed a cluster with members of the genus Sphingobium. Based on these results, it is proposed that strains B90A, UT26 and Sp+, previously known as Sphingomonas paucimobilis, are the type strains of Sphingobium indicum sp. nov. (=MTCC 6364T=CCM 7286T), Sphingobium japonicum sp. nov. (=MTCC 6362T=CCM 7287T) and Sphingobium francense sp. nov. (=MTCC 6363T=CCM 7288T), respectively. It is also proposed that [Sphingomonas] chungbukensis be transferred to Sphingobium chungbukense comb. nov.
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Phyllobacterium trifolii sp. nov., nodulating Trifolium and Lupinus in Spanish soils
Bacterial strain PETP02T was isolated from nodules of Trifolium pratense growing in a Spanish soil. Phylogenetic analysis of the 16S rRNA gene sequence showed that this strain represents a member of the genus Phyllobacterium. However, divergence found with the 16S rRNA gene sequence of the single recognized species of this genus, Phyllobacterium myrsinacearum, indicated that strain PETP02T belongs to a different species. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain represents a novel species of the genus Phyllobacterium, for which the name Phyllobacterium trifolii sp. nov. is proposed. The type strain is PETP02T (=LMG 22712T=CECT 7015T). This strain was strictly aerobic and used several carbohydrates as carbon source. It was not able to reduce nitrate. Aesculin hydrolysis was negative. It did not produce urease, arginine dihydrolase, gelatinase or β-galactosidase. The DNA G+C content was 56·4 mol%. The nodD gene of this strain showed a sequence closely related to those of strains able to nodulate Lupinus. Infectivity tests showed that this strain is able to produce nodules in both Trifolium repens and Lupinus albus.
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Devosia limi sp. nov., isolated from a nitrifying inoculum
More LessA Gram-negative, rod-shaped, non-spore-forming bacteria was isolated from a nitrifying inoculum. On the basis of 16S rRNA gene sequence similarity, this strain, designated LMG 22951T, was shown to belong to the ‘Alphaproteobacteria’ and to be related to Devosia neptuniae (97·4 %) and Devosia riboflavina (97·0 %). The results of DNA–DNA hybridization, analysis of fatty acid composition, SDS-PAGE, physiological and biochemical tests allowed genotypic and phenotypic differentiation of LMG 22951T from the two recognized Devosia species. LMG 22951T therefore represents a novel species within this genus, for which the name Devosia limi is proposed. The type strain is LMG 22951T (=DSM 17137T).
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Phenylobacterium koreense sp. nov., isolated from South Korea
More LessA Gram-negative, aerobic, rod-shaped, non-spore-forming bacterium, Slu-01T, was isolated from activated sludge from a wastewater treatment plant in Daejeon, South Korea. After 3 days on R2A medium, strain Slu-01T developed colourless colonies (0·7–1·2 mm). The non-motile rods (0·7–1·0×1·0–2·0 μm) were slightly curved and occurred singly and in pairs. No filamentous cells were found. On the basis of 16S rRNA gene sequence similarity, strain Slu-01T was shown to belong to the family Caulobacteraceae and was most closely related to Phenylobacterium immobile (96·6 %) and Phenylobacterium lituiforme (96·5 %). The genomic DNA G+C content of strain Slu-01T was 68·1 mol%, within the range of 67·3–68·4 mol% for the genus Phenylobacterium. Chemotaxonomic data (major ubiquinone, Q-10; major fatty acids C18 : 1 ω7c, C16 : 0, C15 : 0 and C17 : 0) and 16S rRNA gene sequence analysis supported the affiliation of strain Slu-01T to the genus Phenylobacterium. However, DNA–DNA hybridization data and phenotypic properties showed that strain Slu-01T could be distinguished from the two other Phenylobacterium species with validly published names. Thus, it is suggested that strain Slu-01T represents a novel species of the genus Phenylobacterium, for which the name Phenylobacterium koreense is proposed. The type strain is Slu-01T (=KCTC 12206T=IAM 15119T).
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Halomonas almeriensis sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium from Cabo de Gata, Almería, south-east Spain
Halomonas almeriensis sp. nov. is a Gram-negative non-motile rod that was isolated from a saltern in the Cabo de Gata-Níjar wildlife reserve in Almería, south-east Spain. It is moderately halophilic, capable of growth at concentrations of 5–25 % w/v sea-salt mixture, the optimum being 7·5 % w/v. It is chemo-organotrophic and strictly aerobic, produces catalase but not oxidase, does not produce acid from any sugar and does not synthesize hydrolytic enzymes. The most notable difference between this micro-organism and other Halomonas species is that it is very fastidious in its use of a carbon source. It forms mucoid colonies due to the production of an exopolysaccharide. Its G+C content is 63·5 mol%. A comparison of 16S rRNA gene sequences confirmed its relationship to Halomonas species. The most closely related species is Halomonas halmophila with 95·8 % similarity between their 16S rRNA gene sequences. DNA–DNA hybridization with H. halmophila is 10·1 %. Its major fatty acids are 18 : 1ω7c, 16 : 0, 16 : 1ω7c/15 : 0 iso 2-OH, 12 : 0 3-OH, 12 : 0, 11-methyl 18 : 1ω7c and 10 : 0. The proposed name is Halomonas almeriensis sp. nov., with strain M8T (=CECT 7050T=LMG 22904T) as the type strain.
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Halomonas taeanensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea
A moderately halophilic, Gram-negative bacterium, strain BH539T, which was isolated from a solar saltern at Taean in Korea, was considered to be a member of the genus Halomonas. Strain BH539T grew at salinities of 1–25 % (w/v) and at temperatures of 10–45 °C. Cells were short rods that were motile by means of several flagella. Their major fatty acids were C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The genomic DNA G+C content was about 65 mol% and the predominant ubiquinone was Q-9. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate formed a branch of the species Cobetia marina. However, 23S and 16S rRNA gene sequence similarities revealed that strain BH539T was related more closely to the type strains of the genus Halomonas. Phylogenetic analyses based on 23S rRNA gene sequences also indicated that the strain formed a phyletic line within the genus Halomonas. Therefore, it was concluded that strain BH539T should be classified within the genus Halomonas, rather than Cobetia. On the basis of physiological and molecular properties, strain BH539T represents a novel species of the genus Halomonas, for which the name Halomonas taeanensis sp. nov. is proposed. The type strain is BH539T (=KCTC 12284T=DSM 16463T).
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Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the ‘Alphaproteobacteria’
More LessA marine bacterium, designated strain GW14-5T, capable of degrading high-molecular-mass polycyclic aromatic hydrocarbons was isolated from the sediments of Gwangyang Bay, Republic of Korea, after enrichment culture for 2 years with a mixture of benzo[a]pyrene and pyrene. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate forms a phyletic lineage that is distinct from the seven known orders within the ‘Alphaproteobacteria’. 16S rRNA gene sequence similarity of strain GW14-5T to all recognized bacterial species was not greater than 92 %. The dominant fatty acids of the isolate were i-17 : 1 (46·2 %), i-15 : 0 (15·1 %) and i-17 : 0 (12·6 %). The major respiratory quinone was MK-5, and the DNA G+C content was 39·3 mol%. Cells of strain GW14-5T were Gram-negative, motile, catalase-positive, oxidase-positive and weakly halophilic. Glucose, N-acetylglucosamine and maltose were utilized as sole carbon sources. The strain was positive for β-glucosidase activity. Optimal growth of strain GW14-5T was at pH 7·0 and 37–40 °C and required the presence of 2 % (w/v) NaCl. On the basis of this evidence, strain GW14-5T represents a novel genus and species in the ‘Alphaproteobacteria’ for which the name Kordiimonas gwangyangensis gen. nov., sp. nov. is proposed. The novel order Kordiimonadales is proposed for the distinct phyletic line represented by the genus Kordiimonas. The type strain is GW14-5T (=KCCM 42021T=JCM 12864T).
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Dechloromonas hortensis sp. nov. and strain ASK-1, two novel (per)chlorate-reducing bacteria, and taxonomic description of strain GR-1
Recent studies on the occurrence of (per)chlorate-reducing bacteria have resulted in the characterization of strains capable of dissimilatory (per)chlorate reduction. Phylogenetic analysis has shown that these bacteria are members of the Proteobacteria. Strains have been isolated from polluted and pristine sites, but only strains from polluted sites have been characterized in detail and deposited in culture collections. Herein we describe the isolation and characterization of perchlorate-reducing bacterium strain MA-1T and chlorate-reducing bacterium strain ASK-1, respectively isolated from a pristine and a chlorate-polluted site. Both isolates are members of the Proteobacteria. The 16S rRNA gene sequence similarity of MA-1T to Dechloromonas agitata DSM 13637T is 97·6 %, but the relatedness in DNA–DNA reassociation is only 37 %. Therefore, we propose to classify strain MA-1T (=DSM 15637T=ATCC BAA-776T) as the type strain of a novel species, Dechloromonas hortensis sp. nov. Strain ASK-1 and a previously described strain GR-1 show 100 and 99 % 16S rRNA gene sequence similarity to Pseudomonas chloritidismutans DSM 13592T and Dechlorosoma suillum DSM 13638T, respectively. DNA–DNA hybridization studies indicated that strains ASK-1 and GR-1 are related at the species level to P. chloritidismutans DSM 13592T (79 %) and Dechlorosoma suillum DSM 13638T (85 %), respectively. As suggested previously, Dechlorosoma suillum appears to be a later heterotypic synonym of Azospira oryzae. Although strain ASK-1 is identified as P. chloritidismutans, its morphology and growth requirements are different from those of the type strain.
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Defluvicoccus vanus gen. nov., sp. nov., a novel Gram-negative coccus/coccobacillus in the ‘Alphaproteobacteria’ from activated sludge
More LessA novel Gram-negative coccus/coccobacillus, strain Ben 114T, growing in tetrads, clusters or aggregates, was isolated from activated sludge by micromanipulation. 16S rRNA gene sequence analysis revealed that it belonged to the ‘Alphaproteobacteria’, with no close relatives among cultured bacterial isolates. On the basis of phylogenetic data, this organism is considered to belong to a new genus, Defluvicoccus, represented by the species Defluvicoccus vanus sp. nov., a name chosen because of the distinctive staining properties of this organism; only the cell wall stained strongly with a wide range of stains, giving the cell a hollow and empty appearance. No intracellular polyphosphate granules could be detected after staining, but poly-β-hydroxyalkanoate inclusions were detected using Nile blue A staining. Because of its taxonomic distance from its closest relatives among the ‘Alphaproteobacteria’, namely members of the genera Azospirillum, Phaeospirillum, Rhodospirillum, Rhodocista, Magnetospirillum and Rhodospira, D. vanus is considered to represent a new phylogenetic lineage within subgroup 1 of the ‘Alphaproteobacteria’, the D. vanus subgroup. The type strain is Ben 114T (=NCIMB 13612T=CIP 107350T).
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Dyadobacter hamtensis sp. nov., from Hamta glacier, located in the Himalayas, India
More LessStrain HHS 11T was isolated from a water sample collected from the snout of Hamta glacier located in the Himalayan mountain ranges of India. Phenotypic, chemotaxonomic and phylogenetic analyses established the affiliation of the isolate to the genus Dyadobacter. HHS 11T possessed 96 and 95 % 16S rRNA gene sequence similarity with respect to Dyadobacter crusticola and Dyadobacter fermentans, respectively. Furthermore, strain HHS 11T differs from D. crusticola and D. fermentans in a number of phenotypic characteristics. These data suggest that strain HHS 11T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter hamtensis sp. nov. is proposed. The type strain is HHS 11T (=JCM 12919T=MTCC 7023T).
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Serratia ureilytica sp. nov., a novel urea-utilizing species
More LessA Gram-negative, rod-shaped, urea-dissolving and non-spore-forming bacterium, designated strain NiVa 51T, was isolated from water of the River Torsa in Hasimara, Jalpaiguri district, West Bengal, India. On the basis of 16S rRNA gene sequence similarity, strain NiVa 51T was shown to belong to the γ-Proteobacteria and to be related to Serratia marcescens subsp. sakuensis (98·35 %) and S. marcescens subsp. marcescens (98·30 %); however, strain NiVa 51T exhibited only 43·7 % similarity to S. marcescens by DNA–DNA hybridization. The G+C content of the genomic DNA of the isolate was 60 mol%. Both biochemical characteristics and fatty acid analysis data supported the affiliation of strain NiVa 51T to the genus Serratia. Furthermore, strain NiVa 51T was found to utilize urea as nitrogen source. The results of DNA–DNA hybridization as well as physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain NiVa 51T from recognized Serratia species. Strain NiVa 51T therefore represents a novel species, for which the name Serratia ureilytica sp. nov. is proposed, with type strain NiVa 51T (=LMG 22860T=CCUG 50595T).
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Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean
One whitish and four pinkish strains of Gram-negative, non-motile, aerobic bacteria were isolated from sea-water and sediment samples collected in Chazhma Bay (Sea of Japan, Pacific Ocean). Analysis of 16S rRNA gene sequences revealed that these strains belonged to the ‘Alphaproteobacteria’, having highest sequence similarity of about 94–97 % with species of the genus Loktanella. None of the strains degraded gelatin, casein, chitin, agar, DNA or starch and they had limited ability to utilize carbon sources. The four pinkish strains, Fg36T, Fg1, Fg116 and Fg117, degraded Tween 80. Sea-water strain R10SW5T grew at 3–6 % NaCl and a temperature range of 8–35 °C, whilst strains Fg36T, Fg1, Fg116 and Fg117 grew at NaCl concentrations of 1–12 % and a temperature range of 4–35 °C. Phosphatidylglycerol (58/79 %), diphosphatidylglycerol (11/6 %) and phosphatidylcholine (28/22 %) were the major phospholipids. The predominant fatty acids were 16 : 0 (12·2/8·6 %) and 18 : 1ω7 (76·6/68·4 %). The DNA G+C content of strain R10SW5T was 59·1 mol% and those of the four pinkish strains ranged from 60·5 to 61·8 mol%. Based on the results of phenotypic, genotypic, chemotaxonomic and phylogenetic investigation, two novel species, Loktanella agnita sp. nov. and Loktanella rosea sp. nov., are proposed. The type strains are R10SW5T (=KMM 3788T=CIP 107883T) and Fg36T (=KMM 6003T=CIP 107851T=LMG 22534T), respectively.
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- Gram-Positive Bacteria
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Sanguibacter marinus sp. nov., isolated from coastal sediment
More LessA Gram-positive, coryneform bacterium, strain 1-19T, was isolated from coastal sediment from the Eastern China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that the organism formed a robust clade with the type species of the genus Sanguibacter and displayed less than 97 % gene sequence similarity. Phenotypic characteristics supported the assignment of this organism to the genus Sanguibacter. A range of biochemical features distinguished it from all other Sanguibacter species with validly published names. On the basis of a polyphasic taxonomical analysis, it is proposed that this bacterium is a novel species of Sanguibacter, for which the name Sanguibacter marinus sp. nov. is proposed. The type strain is 1-19T (=CGMCC 1.3457T=JCM 12547T).
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Salinispora arenicola gen. nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae
A taxonomic study was carried out to clarify the taxonomy of representatives of a group of marine actinomycetes previously designated MAR 1 and considered to belong to the family Micromonosporaceae. The organisms had phenotypic properties consistent with their assignment to this taxon. The strains formed a distinct taxon in the 16S rRNA Micromonosporaceae gene tree and shared a range of phenotypic properties that distinguished them from members of all of the genera with validly published names classified in this family. The name proposed for this novel taxon is Salinispora gen. nov. The genus contains two species recognized using a range of genotypic and phenotypic criteria, including comparative 16S–23S rRNA gene spacer region and DNA–DNA relatedness data. The names proposed for these taxa are Salinispora arenicola sp. nov., the type species, and Salinispora tropica sp. nov.; the type strains of these novel species have been deposited in service culture collections as strain CNH-643T (=ATCC BAA-917T=DSM 44819T) and strain CNB-440T (=ATCC BAA-916T=DSM 44818T), respectively.
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Quadrisphaera granulorum gen. nov., sp. nov., a Gram-positive polyphosphate-accumulating coccus in tetrads or aggregates isolated from aerobic granules
More LessA Gram-positive bacterium, designated strain AG019T, was isolated by micromanipulation from aerobic granules obtained from a laboratory-scale sequencing batch reactor. This isolate grew axenically as cocci clustered predominantly in tetrads, and was morphologically similar to the dominant organisms observed in the biomass. The morphology also resembled that of the tetrad-forming organisms commonly seen in activated sludge samples. Strain AG019T was found to be an oxidase-negative, catalase-positive, non-motile aerobe that does not reduce nitrate and grows at temperatures between 15 and 40 °C, with an optimum at 37 °C. The pH range for growth was 5·0–9·0, with an optimum at pH 7·5. Strain AG019T contained a peptidoglycan with directly cross-linked meso-diaminopimelic acid (type A1γ) and lacked mycolic acids. The G+C content of the DNA was 75 mol%. Menaquinone MK-8(H2) was the major isoprenoid quinone. The bacterium stained positively for intracellular polyphosphate granules but not for poly-β-hydroxyalkanoates. It produced capsular material and showed autoaggregation ability. Phenotypic and 16S rRNA gene analyses showed that the bacterium differed sufficiently from its closest phylogenetic relatives, namely members of the suborder Frankineae, which includes the genera Geodermatophilus, Blastococcus, Frankia, Sporichthya, Acidothermus and Microsphaera, that it is proposed that it be placed in a novel genus, Quadrisphaera, as Quadrisphaera granulorum gen. nov., sp. nov. The type strain is AG019T (=ATCC BAA-1104T=DSM 44889T).
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Thalassobacillus devorans gen. nov., sp. nov., a moderately halophilic, phenol-degrading, Gram-positive bacterium
More LessA novel moderately halophilic bacterium, strain G-19.1T, has been isolated from a phenol enrichment of samples collected in hypersaline habitats of southern Spain. This enrichment culture was a part of a screening programme to isolate halophilic bacteria able to degrade various aromatic compounds. Strain G-19.1T has been characterized as a potential phenol-degrader over a wide range of saline conditions. Strain G-19.1T was found to be an aerobic, Gram-positive, endospore-forming, non-pigmented, moderately halophilic rod that grew optimally in media containing 7·5–10 % NaCl at pH 7·0. The DNA G+C content was 42·4 mol%. Phylogenetic analysis based on comparison of 16S rRNA gene sequences indicated that the closest relatives were Halobacillus species (96·2–97·0 %), although this novel isolate constitutes a separate line of descent within the radiation of Gram-positive rods. The cell-wall peptidoglycan contained meso-diaminopimelic acid, indicating that this strain does not share the main characteristic that differentiates members of the genus Halobacillus (which contain Orn–d-Asp) from other related genera. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. On the basis of phenotypic, genotypic and phylogenetic analyses, this isolate should be classified in a novel genus and species, for which the name Thalassobacillus devorans gen. nov., sp. nov. is proposed. The type strain is strain G-19.1T (=DSM 16966T=CECT 7046T=CCM 7282T).
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Marinococcus halotolerans sp. nov., isolated from Qinghai, north-west China
An aerobic bacterium was isolated from saline soil located in Qinghai, north-west China. The bacterium, designated YIM 70157T, was investigated using a polyphasic taxonomic approach. The Gram reaction of the organism was positive. Comparative 16S rRNA gene sequence analysis demonstrated the isolate to be a member of the genus Marinococcus, the closest phylogenetic neighbour of the unknown bacterium being Marinococcus halophilus DSM 20408T with a similarity of 99·4 %. The peptidoglycan type of YIM 70157T was A1γ, with meso-diaminopimelic acid as diagnostic diamino acid. The major fatty acids were ai-C15 : 0, ai-C17 : 0 and i-C16 : 0. The menaquinones were MK-7 and MK-6. The phospholipids were diphosphatidylglycerol and phosphatidylinositol. The G+C content of total DNA was 48·5 mol%. On the basis of phylogenetic and phenotypic evidence and DNA–DNA hybridization data, this isolate should be classified as a novel species of Marinococcus, for which the name Marinococcus halotolerans sp. nov. is proposed. The type strain is YIM 70157T (=DSM 16375T=KCTC 19045T).
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Lentibacillus lacisalsi sp. nov., a moderately halophilic bacterium isolated from a saline lake in China
An aerobic, spore-forming, moderately halophilic bacterium, strain BH260T, was isolated from a salt lake in China. Cells of this strain were found to be motile rods with flagella. The organism grew optimally at 30–32 °C and pH 8·0 in the presence of 12–15 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a clade with the type strains of the genus Lentibacillus. The levels of 16S rRNA gene sequence similarity for strain BH260T with respect to Lentibacillus salsus KCTC 3911T, Lentibacillus juripiscarius JCM 12147T and Lentibacillus salicampi KCCM 41560T were 96·0, 95·5 and 95·3 %, respectively. Chemotaxonomic data (a DNA G+C content of 44 mol%; MK-7 as the major isoprenoid quinone; A1γ-meso-diaminopimelic acid as the cell-wall type; phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids; anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as the major fatty acids) also supported assignment of the isolate to the genus Lentibacillus. On the basis of physiological and molecular properties, the isolate represents a novel species within the genus Lentibacillus, for which the name Lentibacillus lacisalsi sp. nov. is proposed. The type strain is BH260T (=KCTC 3915T=DSM 16462T).
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Paenibacillus motobuensis sp. nov., isolated from a composting machine utilizing soil from Motobu-town, Okinawa, Japan
A novel bacterial strain, MC10T, was isolated from a compost sample produced in a composting machine utilizing soil from Motobu-town, Okinawa, Japan. The isolate was Gram-negative, but produced endospores. These conflicting characters prompted a taxonomic study of the isolate. The isolate was examined using a combination of phenotypic characterization, cellular fatty acid analysis, DNA base composition determination and 16S rRNA gene sequence analysis. Phylogenetic analysis, based on 16S rRNA gene sequence comparisons, placed strain MC10T within the genus Paenibacillus. As in other Paenibacillus species, the isolate contained anteiso-C15 : 0 as the major fatty acid and the DNA G+C content was 47·0 mol%. However, 16S rRNA gene sequence similarity values of less than 95·6 % were found between this isolate and all members of the genus Paenibacillus. Based upon these results, strain MC10T (=GTC 1835T=JCM 12774T=CCUG 50090T) should be designated as the type strain of a novel species within the genus Paenibacillus, Paenibacillus motobuensis sp. nov.
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Virgibacillus dokdonensis sp. nov., isolated from a Korean island, Dokdo, located at the edge of the East Sea in Korea
More LessA Gram-variable, motile, endospore-forming, slightly halophilic bacterial strain, DSW-10T, was isolated from Dokdo, an island located at the edge of the East Sea, Korea, and was characterized taxonomically by using a polyphasic approach. This isolate grew optimally at 37 °C and in the presence of 4–5 % NaCl. Strain DSW-10T had cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone, and anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipids. The DNA G+C content was 36·7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DSW-10T is phylogenetically affiliated to the genus Virgibacillus, and exhibited sequence similarity of 95·3–98·7 % to the type strains of Virgibacillus species. DNA–DNA relatedness levels between strain DSW-10T and the type strains of some phylogenetically related Virgibacillus species were in the range 8·4–17·5 %. On the basis of phenotypic properties and phylogenetic and genetic distinctiveness, strain DSW-10T (=KCTC 3933T=DSM 16826T) was classified as the type strain of a novel Virgibacillus species, for which the name Virgibacillus dokdonensis sp. nov. is proposed.
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Isoptericola halotolerans sp. nov., a novel actinobacterium isolated from saline soil from Qinghai Province, north-west China
A Gram-positive, non-motile actinobacterium, designated strain YIM 70177T, was isolated from a saline soil sample from Qinghai Province, north-west China. Phylogenetic analysis of this organism based on 16S rRNA gene sequences revealed 98·3 % similarity to Isoptericola variabilis DSM 10177T. Chemotaxonomic data determined for the isolate, such as the peptidoglycan type A4α, variation l-lys–d-Asp, supported the placement of strain YIM 70177T within the genus Isoptericola. Galactose was detected as cell wall sugar. Phospholipids identified were phosphatidylinositol, phosphatidylglycerol and diphosphatidylglycerol, and the predominant menaquinones were MK-9(H4) and MK-9(H2). The major fatty acids were ai-C15 : 0, C16 : 0, ai-C17 : 0 and i-C15 : 0. The DNA G+C content was 72·8 mol%. The low level of DNA–DNA relatedness (27·4 %) to I. variabilis DSM 10177T in combination with differentiating chemotaxonomic and physiological data demonstrated that the isolate YIM 70177T should be classified as representing a novel species of the genus Isoptericola. The name Isoptericola halotolerans sp. nov. is proposed, with strain YIM 70177T (=DSM 16376T=KCTC 19046T) as the type strain.
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Gordonia otitidis sp. nov., isolated from a patient with external otitis
The taxonomic positions of two clinically isolated actinomycetes were established using a polyphasic approach. The two strains, IFM 10032T, isolated from ear discharge of a 28-year-old Japanese female patient with external otitis, and IFM 10148, isolated from pleural fluid of a 60-year-old Japanese male patient with bronchitis, possessed meso-diaminopimelic acid as the diagnostic amino acid, MK-9(H2) as the predominant menaquinone and mycolic acids ranging from 58 to 64 carbons. The 16S rRNA gene sequences of the two strains were most closely related to those of Gordonia aichiensis, Gordonia sputi and ‘Gordonia jacobaea’. Differences in several phenotypic characteristics together with genotypic distinctiveness distinguish strains IFM 10032T and IFM 10148 from these three species. DNA–DNA hybridization results and the combination of genotypic and phenotypic data showed that the two strains belong to a single species, and merit recognition of a novel species within the genus Gordonia. The name proposed for this taxon is Gordonia otitidis sp. nov.; the type strain is IFM 10032T (=DSM 44809T=JCM 12355T=NBRC 100426T).
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Reclassification of Bacillus haloalkaliphilus Fritze 1996 as Alkalibacillus haloalkaliphilus gen. nov., comb. nov. and the description of Alkalibacillus salilacus sp. nov., a novel halophilic bacterium isolated from a salt lake in China
More LessA spore-forming, halophilic bacterium, designated strain BH163T, was isolated from a salt lake in China. Cells were motile, strictly aerobic rods that contained type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The isolate showed Gram- and catalase-positive reactions and formed a terminal endospore with a swollen sporangium. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The genomic DNA G+C content of the strain was 41·0 mol%. Comparative analysis of 16S rRNA gene sequences showed that strain BH163T formed a distinct line within the phyletic group classically defined as the genus Bacillus and was most closely related to the taxa [Bacillus] haloalkaliphilus DSM 5271T and Filobacillus milosensis DSM 13259T, with 16S rRNA gene sequence similarities of 95·9 and 94·5 %, respectively. On the basis of physiological and molecular properties, it is proposed that [Bacillus] haloalkaliphilus DSM 5271T is reclassified in the new genus Alkalibacillus as Alkalibacillus haloalkaliphilus gen. nov., comb. nov. Strain BH163T (=KCTC 3916T=DSM 16460T) was assigned as the type strain of the novel species Alkalibacillus salilacus.
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Agromyces subbeticus sp. nov., isolated from a cave in southern Spain
More LessAn actinomycete, strain Z33T, was isolated from a cyanobacterial biofilm in the Cave of Bats, near Zuheros (Cordoba, southern Spain). 16S rRNA gene sequence analysis showed that strain Z33T formed a distinct phyletic line within the genus Agromyces. This isolate could be readily distinguished from representatives of all recognized Agromyces species on the basis of a broad range of phenotypic characteristics and DNA–DNA relatedness data. Genotypic and phenotypic properties indicate that strain Z33T represents a novel species, for which the name Agromyces subbeticus sp. nov. is proposed. The type strain is Z33T (=HKI 0340T=DSM 16689T=NCIMB 14025T).
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Nocardia jiangxiensis sp. nov. and Nocardia miyunensis sp. nov., isolated from acidic soils
More LessThe taxonomic positions of two soil actinomycetes, strains 117T and 43401T, provisionally assigned to the genus Nocardia were determined in a polyphasic study. The organisms were found to have phenotypic properties typical of members of the genus Nocardia, and formed a distinct branch in the Nocardia 16S rRNA gene tree. It was evident from the phylogenetic data that the isolates were most closely, albeit loosely, associated with the type strains of Nocardia nova and Nocardia pseudobrasiliensis. However, all four of these organisms were readily distinguishable from one another using DNA–DNA relatedness and phenotypic data. It is evident from the genotypic and phenotypic data that the two isolates should be recognized as novel species of the genus Nocardia. It is proposed, therefore, that strains 117T (=CGMCC 4.1904T=JCM 12860T) and 43401T (=CGMCC 4.1905T=JCM 12861T) be classified in the genus Nocardia as the type strains of Nocardia miyunensis sp. nov. and Nocardia jiangxiensis sp. nov., respectively.
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Proposal of Yaniaceae fam. nov. and Yania flava sp. nov. and emended description of the genus Yania
A coccoid actinobacterium strain (designated YIM 70178T) was isolated from a soil sample collected in Qinghai Province, China. The isolate grew well with an optimum salt concentration of 10–15 % (KCl, w/v) but scarcely or not at all without salt. The cell-wall peptidoglycan type was A4α, l-lys–gly–l-Glu. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and an unknown glycolipid. The predominant menaquinones were MK-8 and MK-9. The major fatty acid was anteiso-C15 : 0. The DNA G+C content was 57·9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 70178T was most closely related to the type strain of Yania halotolerans. DNA–DNA hybridization and comparison of physiological and chemotaxonomic characteristics demonstrated that strain YIM 70178T was different from Yania halotolerans. The name Yania flava sp. nov. is proposed, with strain YIM 70178T (=DSM 16377T=KCTC 19047T) as the type strain. Based on the phenotypic characteristics and phylogenetic position, as determined by 16S rRNA gene analysis and 16S rRNA signature nucleotide data, the genus description of Yania is therefore emended and strains YIM 70085T and YIM 70178T represent a novel family of the suborder Micrococcineae, for which the name Yaniaceae fam. nov. is proposed.
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Streptomyces jietaisiensis sp. nov., isolated from soil in northern China
An actinomycete, strain FXJ46T, was isolated from cypress forest soil in northern China and shown to have chemotaxonomic and morphological properties consistent with streptomycetes. It developed greyish aerial mycelium and pinkish-brown substrate mycelium on oatmeal agar. Phylogenetic analyses based on an almost complete 16S rRNA gene sequence of the strain and on the 120 nucleotide variable γ-region of this molecule showed that it formed a distinct (but closely associated) line with Streptomyces griseoaurantiacus DSM 40430T in Streptomyces trees. However, the DNA–DNA relatedness between the two strains was only 48·8 %. A number of phenotypic properties also readily distinguished the isolate from S. griseoaurantiacus and related Streptomyces species with validly published names. It is proposed, therefore, that this organism be classified as a novel species of the genus Streptomyces, for which the name Streptomyces jietaisiensis sp. nov. is proposed. The type strain is FXJ46T (=AS 4.1859T=JCM 12279T).
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Volumes and issues
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Volume 74 (2024)
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