- Volume 69, Issue 5, 2019
Volume 69, Issue 5, 2019
- Obituary
-
- Validation List
-
- Notification List
-
- New Taxa
-
- Actinobacteria
-
-
Nocardioides ferulae sp. nov., isolated from root of an endangered medicinal plant Ferula songorica Pall. ex Spreng
A novel endophytic bacterium, designated strain SZ4R5S7T, was isolated from surface-sterilized root of an endangered medicinal plant (Ferula songorica Pall. ex Spreng) collected from Xinjiang, north-west China. The taxonomic position of the strain was investigated by using a polyphasic approach. The strain was found to be aerobic, Gram-stain-positive, oxidase-negative and catalase-positive, short rods and non-motile. Strain SZ4R5S7T grew at 4–37 °C (optimum, 28 °C), pH 5.0–9.0 (pH 6.0–8.0) and in the presence of 0–4 % (w/v) NaCl. The polar lipids detected for strain SZ4R5S7T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified lipids. The predominant menaquinone of strain SZ4R5S7T was MK-8(H4), and the major fatty acids were iso-C16 : 0 and anteiso-C14 : 0. The DNA G+C content was determined to be 72.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain SZ4R5S7T belongs to the genus Nocardioides and showed highest levels of 16S rRNA gene sequence similarity to members of the strain Nocardioides kribbensis KSL-2T (97.8 %). On the basis of phenotypic, genotypic and phylogenetic data, strain SZ4R5S7T represents a novel species in the genus Nocardioides, for which the name Nocardioides ferulae sp. nov. is proposed and the type strain is SZ4R5S7T (=CGMCC 4.7456T=KCTC 39994T).
-
-
-
Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov.
Five Bifidobacterium strains, i.e. 2020BT, 2028BT, 2033BT, 2034BT and 2036BT, were isolated from European beaver (Castor fiber), Goeldi's marmoset (Callimicogoeldii), black-capped squirrel monkey (Saimiriboliviensissubsp. peruviensis) and Patagonian mara (Dolichotispatagonum). All of these isolates were shown to be Gram-positive, facultative anaerobic, d-fructose 6-phosphate phosphoketolase-positive, non-motile and non-sporulating. Phylogenetic analyses based on 16S rRNA gene sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2020BT, 2028BT, 2033BT, 2034BT and 2036BT exhibit close phylogenetic relatedness to Bifidobacterium biavatii DSM 23969T, Bifidobacterium bifidum LMG 11041T, Bifidobacterium choerinum LMG 10510T, Bifidobacterium gallicum LMG 11596T, Bifidobacterium imperatoris LMG 30297T, Bifidobacterium italicum LMG 30187T and Bifidobacterium vansinderenii LMG 30126T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium castoris sp. nov. (2020BT=LMG 30937T=CCUG 72816T), Bifidobacterium callimiconis sp. nov. (2028BT=LMG 30938T=CCUG 72814T), Bifidobacterium samirii sp. nov. (2033BT=LMG 30940T=CCUG 72817T), Bifidobacterium goeldii sp. nov. (2034BT=LMG 30939T=CCUG 72815T) and Bifidobacterium dolichotidis sp. nov. (2036BT=LMG 30941T=CCUG 72818T) are proposed as novel Bifidobacterium species.
-
-
-
Saccharopolyspora rhizosphaerae sp. nov., an actinomycete isolated from rhizosphere soil in Thailand
A novel actinomycete, designated as strain H219T, was isolated from rhizosphere soil collected under an Elephant ear plant (Colocasiaesculenta) in Bangkok, Thailand. Strain H219T was characterised using a polyphasic approach. Phylogenetic analysis of the 16S rRNA gene sequences revealed that this isolate was most closely related to Saccharopolyspora tripterygii JCM 32123T (97.6 %), Saccharopolyspora dendranthemae NBRC 108675T (97.5 %) and Saccharopolyspora flava NBRC 16345T (97.5 %). However, DNA–DNA hybridization analyses showed a low relatedness in the range of 39–48 % between the novel isolate and the above closely related strains. The cell-wall peptidoglycan of strain H219T contained meso-diaminopimelic acid. The diagnostic whole-cell sugars consisted of arabinose and galactose. The cellular fatty acid profile mainly comprised iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0, and 10-methyl C17 : 0. The major menaquinone was MK-9(H4). The detected phospholipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylethanolamine-containing hydroxylated fatty acids and an unknown phospholipid. The DNA G+C content was 70.6 mol%. Strain H219T represented chemotaxonomic and morphological characteristics that were consistent with members of the genus Saccharopolyspora . However, strain H219T could be distinguished from closely related strains by several phenotypic properties. Based on the data from the polyphasic studies, we propose that strain H219T is a novel species within the genus Saccharopolyspora , Saccharopolyspora rhizosphaerae sp. nov. The type strain is H219T (=TBRC 8564T=NBRC 113388T).
-
-
-
Jiangella rhizosphaerae sp. nov., an actinomycete isolated from the rhizosphere soil of wheat (Triticum aestivum L.)
A novel actinomycete, designated strain NEAU-YY265T, was isolated from rhizosphere soil of wheat (Triticum aestivum L.) and characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain NEAU-YY265T belonged to the genus Jiangella and exhibited 16S rRNA gene sequence similarities of 99.1 and 99.1 % to Jiangella mangrovi 3SM4-07T and Jiangella alkaliphila D8-87T. The chemotaxonomic properties of strain NEAU-YY265T were consistent with those of the genus Jiangella : the cell-wall peptidoglycan type was based on ll -diaminopimelic acid; the whole-cell hydrolysates contained glucose, ribose and rhamnose; MK-9(H4) and MK-9(H2) were the predominant menaquinones. The novel strain produced branching mycelium which fragmented into short or elongated rods. The major fatty acids (>5 %) were anteiso-C15 : 0, anteiso-C17 : 0, C17 : 1ω8c, iso-C16 : 0, C17 : 0 and iso-C15 : 0. The DNA G+C content was 72.6 mol%. Strain NEAU-YY265T was phenotypically distinct from recognized Jiangella species and shown to belong to a separate genomic species based on DNA–DNA hybridization results. Thus, strain NEAU-YY265T is considered to represent a novel species of the genus Jiangella , for which the name Jiangella rhizosphaerae sp. nov. is proposed. The type strain is NEAU-YY265T (=JCM 32551T=CGMCC 4.7475T).
-
-
-
Micromonospora caldifontis sp. nov., isolated from hot spring soil
More LessA single spore forming actinomycete, designated strain HSS6-8T, was isolated from a sample of hot spring soil. The strain had the chemotaxonomic properties consistent with its classification in the genus Micromonospora . The strain was found to have meso-diaminopimelic acid in the cell-wall peptidoglycan. The acyl type of the cell-wall muramic acid was glycolyl. The reducing sugars in the cell hydrolysates were glucose, arabinose, xylose, ribose, mannose, galactose and rhamnose. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphoglycolipid. The major menaquinones were MK-10(H6) and MK-10(H4). The major cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0, C17 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 70.5 mol%. 16S rRNA gene sequence analysis revealed that strain HSS6-8T was closely related to Micromonospora nigra DSM 43818T (98.2 %), Micromonospora eburnea DSM 44814T (98.2 %) and Micromonospora spongicola S3-1T (98.1 %). The physiological and DNA–DNA hybridization data allowed the differentiation of strain HSS6-8T from its related species. Thus, the strain represents a novel species of the genus Micromonospora , for which the name Micromonospora caldifontis sp. nov. is proposed. The type strain is HSS6-8T (=TBRC 8927T=JCM 17126T).
-
-
-
Marmoricola mangrovicus sp. nov., an endophytic actinobacterium isolated from Kandelia candel
More LessA Gram-stain-positive, aerobic, motile, non-spore-forming and rod-shaped actinobacterium, designated strain 4Q3S-7T, was isolated from a piece of surface-sterilized bark of Kandelia candel collected at the Cotai Ecological Zone in Macao, China. Colonies were yellowish white, circular, smooth and convex. The 16S rRNA gene sequence of strain 4Q3S-7T exhibited highest similarities to Marmoricola ginsengisoli Gsoil 097T (97.6 %), Marmoricola solisilvae KIS18-7T (97.6 %) and Marmoricola pocheonensis Gsoil 818T (97.3 %). Phylogenetic analysis showed that strain 4Q3S-7T clustered with species of the genus Marmoricola and was clearly affiliated to the genus Marmoricola . Genomic analyses, including average nucleotide identity and DNA–DNA hybridization, clearly separated strain 4Q3S-7T from M. ginsengisoli Gsoil 097T, M. solisilvae KIS18-7T and M. pocheonensis Gsoil 818T with values below the thresholds for species delineation. Strain 4Q3S-7T had ll-2,6-diaminopimelic acid as the diagnostic diamino acid in the cell wall. The major fatty acids (>10 % of total fatty acids) were C18 : 0 10-methyl (TBSA), C18 : 1 ω9c, iso-C16 : 0 and iso-C16 : 0 2-OH. The predominant menaquinone was MK-8(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unidentified phospholipid. The DNA G+C content of strain 4Q3S-7T was 72.0 mol% (draft genome sequence). Based on its phylogenetic, phenotypic and chemotaxonomic features, strain 4Q3S-7T is considered to represent a novel species of the genus Marmoricola , for which the name Marmoricola mangrovicus sp. nov. is proposed. The type strain is 4Q3S-7T (=KCTC 39790T=CGMCC 4.7424T).
-
-
-
Streptomyces fodineus sp. nov., an actinobacterium with antifungal activity isolated from mine area soil
More LessA novel actinobacterial strain producing an antifungal substance was isolated from a sample of acidic mine area soil, and its taxonomic position was evaluated. The novel strain, designated TW1S1T, formed white-grey aerial mycelium and yellow substrate mycelium on oatmeal agar. Growth occurred at 10–45 °C (optimum, 30 °C), pH 4–9 (pH 6–7) and in the presence of up to 8 % (w/v) NaCl. Melanin was produced on peptone–yeast extract–iron agar. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that the novel strain should be assigned to the genus Streptomyces , and the closest species was Streptomyces puniciscabiei S77T with 99.1 % sequence similarity, which was followed by Streptomyces durhamensis NRRL B-3309T (99.0 %), Streptomyces filipinensis NBRC 12860T (98.9 %) and Streptomyces yaanensis Z4T (98.7 %). The chemotaxonomic properties were consistent with those of Streptomyces . ll-Diaminopimelic acid was the diagnostic diamino acid, and alanine, glutamic acid and glycine were present in the peptidoglycan. The cell-wall hydrolysate also contained galactose, glucose, mannose and ribose. The predominant isoprenoid quinones were MK-9(H4) and MK-9(H6), the major polar lipids were phosphatidylglycerol and an unidentified phospholipid, and the main fatty acids were iso-C16 : 0 and anteiso-C15 : 0. However, strain TW1S1T could be distinguished from its neighbouring species by its phenotypic properties. In addition, the genome-based comparison with the closest species indicated that strain TW1S1T should be recognized as a separate species. The phylogenetic, phenotypic and chemotaxonomic as well as genomic evidence supported that TW1S1T represents a novel species of Streptomyces , for which the name Streptomyces fodineus sp. nov. is proposed (type strain, TW1S1T = KCTC 49013T = JCM 32404T).
-
- Archaea
-
-
Halonotius aquaticus sp. nov., a new haloarchaeon isolated from a marine saltern
More LessA halophilic archaeon, strain F13-13T, was isolated from a marine saltern located in Isla Cristina, Huelva, on the south-west coast of Spain. It was a Gram-stain-negative, motile and aerobic haloarchaeon. It grew at 28–50 °C (optimum, 37 °C), pH 6.0–8.5 (pH 7.5) and in 15–30 % (w/v) total salts (25 %). Phylogenetic analyses based on the 16S rRNA gene sequences showed that strain F13-13T is a member of the genus Halonotius , the most closely related species being Halonotius pteroides 1.15.5T (96.7 % sequence similarity). The 16S rRNA gene sequence similarity to species of other genera is lower than 93.4 %. Strain F13-13T was also found to be closely related to Halonotius pteroides 1.15.5T (91.4 %) on the basis of rpoB′ gene sequence analysis. The Genome-to-Genome Distance Calculator relatedness result between strain F13-13T and Halonotius pteroides CECT 7525T was 35 %, a value lower than the 70 % threshold accepted for species delineation. The average nucleotide identity values based on OrthoANI, ANIb and ANIm of strain F13-13T and Halonotius pteroides CECT 7525T were 88.7, 87.8 and 89.4 %, respectively, these values are also lower than the threshold accepted for species delineation. The DNA G+C content of this isolate was 61.2 mol%. The major lipids of strain F13-13T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulphated diglycosyl diether. Based on the phylogenetic, phenotypic, genotypic and chemotaxonomic characterization, we propose the placement of strain F13-13T as a new species within the genus Halonotius , with the name Halonotius aquaticus sp. nov. The type strain is F13-13T (=CECT 9386T=IBRC-M 11204T).
-
-
-
Halococcoides cellulosivorans gen. nov., sp. nov., an extremely halophilic cellulose-utilizing haloarchaeon from hypersaline lakes
An extremely halophilic euryarchaeon, strain HArcel1T, was enriched and isolated in pure culture from the surface brines and sediments of hypersaline athalassic lakes in the Kulunda Steppe (Altai region, Russia) using amorphous cellulose as the growth substrate. The colonies of HArcel1T are pale-orange, and form large zones of cellulose hydrolysis around them. The cells are non-motile cocci of variable size with a thin monolayer cell wall. The isolate is an obligate aerobic heterotroph capable of growth with only three substrates: various forms of insoluble cellulose, xylan and cellobiose. Strain HArcel1T is an extremely halophilic neutrophile, growing within the salinity range from 2.5 to 5 M NaCl (optimum at 3.5–4 M). The core archaeal lipids are dominated by C20–C20 and C25–C20 dialkyl glycerol ethers, in approximately 6:1 proportion. The 16S rRNA and rpoB′ gene analysis indicated that HArcel1T forms a separate lineage within the family Haloarculaceae , order Halobacteriales , with the genera Halorhabdus and Halopricus as closest relatives. On the basis of the unique phenotypic properties and distinct phylogeny of the 16S rRNA and rpoB′ genes, it is suggested that strain HArcel1T is classified into a new genus and species Halococcoides cellulosivorans gen. nov., sp. nov. (JCM 31941T=UNIQEM U975T).
-
- Bacteroidetes
-
-
Tamlana carrageenivorans sp. nov., a carrageenan-degrading bacterium isolated from seawater
More LessA Gram-stain-negative, aerobic, non-motile, rod-shaped, agarolytic and carrageenolytic bacterial strain, designated UJ94T, was isolated from seawater of Uljin in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain UJ94T shared sequence similarities of 98.4, 96.1 and 95.4 % with Tamlana agarivorans JW-26T, Tamlana sedimentorum KMM 9545T and Tamlana crocina HST1-43T, respectively. Growth of strain UJ94T was observed at 4–37 °C and pH 6.5–8.0 in the presence of 2–9 % (w/v) NaCl. The major fatty acids of strain UJ94T were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and iso-C17 : 0 3-OH; MK-6 was the predominant menaquinone. Phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids were detected as major polar lipids. The whole circular genome comprised 4 116 543 bp and had a G+C content of 35.2 mol%. The ranges of average nucleotide identity and in silico DNA–DNA hybridization estimated by genome-to-genome distance were 90.6–74.2 % and 47.6–14.6 %, respectively, with the type strains of T. agarivorans and T. sedimentorum . The present polyphasic study, including phylogenetic, chemotaxonomic, biochemical and genomic data, suggested that strain UJ94T represents a novel species of the genus Tamlana , for which the name Tamlana carrageenivorans sp. nov. is proposed. The type strain is UJ94T (=KCTC 62451T=NBRC 113234T).
-
- Firmicutes and Related Organisms
-
-
Pradoshia eiseniae gen. nov., sp. nov., a spore-forming member of the family Bacillaceae capable of assimilating 3-nitropropionic acid, isolated from the anterior gut of the earthworm Eisenia fetida
A Gram-stain-positive, spore-forming bacterium, EAG3T, capable of growing on 3-nitropropionic acid as the sole source of carbon, nitrogen and energy, was isolated from the anterior gut of an earthworm (Eisenia fetida) reared at the Centre of Floriculture and Agribusiness Management of the University of North Bengal at Siliguri (26.7072° N, 88.3558° E), West Bengal, India. The DNA G+C content of strain EAG3T was 42.5 mol%. Strain EAG3T contained MK-7 and MK-8 as predominant menaquinones. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were 13-methyltetradecanoic acid, (9Z)−9-hexadecen-1-ol, 12-methyltetradecanoic acid and 14-methylpentadecanoic acid. The draft genome of strain EAG3T, distributed in 57 contigs, was found to be 3.8 Mb. A total of 3811 potential coding sequences or genes were predicted, including 3672 protein-coding and 108 RNA-coding ones together with 31 pseudogenes. One hundred and thirty-five genes encoded hypothetical proteins with no meaningful homologies with known proteins. The EAG3T genome encompassed two nitronate monooxygenase and one methylmalonate-semialdehyde dehydrogenase (CoA acylating) homologues. 16S rRNA gene sequence-based phylogeny revealed that the closest relative of strain EAG3T was Bacillus methanolicus NCIMB 13113T (95.7 % similarity). Phylogenetic, physiological and biochemical characteristics differentiated strain EAG3T from B. methanolicus, as well as from the other close taxonomic relatives Planococcus rifietoensis M8T, Bhargavaea cecembensis DSE10T, Planomicrobium flavidum ISL-41Tand Fermentibacillus polygoni IEB3T, with which strain EAG3T had 93.3–94.2 % 16S rRNA gene sequence similarities. The new isolate, therefore, was considered as representing a novel genus of family Bacillaceae , for which the name Pradoshia eiseniae gen. nov., sp. nov. is proposed, with EAG3T (=LMG 30312T=JCM 32460T) as the type strain.
-
-
-
Falsibacillus albus sp. nov., isolated from mangrove soil
A novel Gram-stain-positive, catalase- and oxidase-positive, endospore-forming bacterium, designated GY 10110T, was isolated from mangrove soil collected from Qinzhou, Guangxi province, China. Cells were aerobic, motile with peritrichous flagella and rod-shaped. The strain grew at 15–37 °C (optimum, 28 °C), at 0–3 %(w/v) NaCl (1 %) and at pH 6.0–9.0 (pH 7.0). The major fatty acids of strain GY 10110T were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. The predominant menaquinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphoglycolipid, glycolipid, two unidentified aminophospholipids and three unidentified phospholipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GY 10110T was closely related to Falsibacillus pallidus CCTCC AB 207188T (98.0 % sequence similarity) and Bacillus oceanisediminis CGMCC 1.10115T (96.9 %), respectively. The G+C content of strain GY 10110T based on the whole genome sequence was 42.3 mol%. The novel strain showed an average nucleotide identity (ANI) value of 77.8 % and a digital DNA–DNA hybridization (dDDH) value of 15.6 % with Falsibacillus pallidus CCTCC AB 207188T based on draft genome sequences, followed by Bacillus oceanisediminis CGMCC 1.10115T with ANI and dDDH values of 75.2 and 12.8 %, respectively. The results of the polyphasic taxonomic study, including phenotypic, chemotaxonomic and phylogenetic analysis, showed that strain GY 10110T represents a novel species of the genus Falsibacillus , for which the name Falsibacillus albus sp. nov. is proposed. The type strain is GY 10110T (=CGMCC 1.13648T=NBRC 113502T).
-
-
-
Paraliobacillus zengyii sp. nov., a slightly halophilic and extremely halotolerant bacterium isolated from Tibetan antelope faeces
Two rod-shaped, slightly halophilic and extremely halotolerant bacterial strains (X-1125T and X-1174), which were Gram-stain-positive, facultatively anaerobic and motile with peritrichous flagella, were isolated from the faeces of Tibetan antelopes. Their optimal temperature, NaCl concentration and pH for growth were 28 °C, 3 % (w/v) NaCl and pH 7.5, respectively. Based on the results of 16S rRNA gene sequences, and phylogenetic and phylogenomic analyses, their nearest phylogenetic neighbours were Paraliobacillussediminis KCTC 33762T (98.4 % similarity), Paraliobacillusquinghaiensis CGMCC 1.6333T (96.9 %) and Paraliobacillusryukyuensis NBRC 100001T (95.9 %) while the 16S rRNA genes of strains X-1125T and X-1174 were highly similar (99.7 %) to each other. The polar lipids comprised diphosphatidylglycerol, two unidentified phospholipids and four unidentified lipids. MK-7 was the sole menaquinone (100 %). The cell wall contained alanine, glycine, glutamic acid and meso-diaminopimelic acid. The major fatty acids (>9 %) were anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 1ω11c. The in silico DNA–DNA hybridization value between strains X-1125T and X-1174 was 97.8 % (well above the species threshold), but their values were lower than the 70 % threshold with the three closely related type strains. Strains X-1125T and X-1174 had DNA G+C contents (mol%) of 35.2 and 35.1 %, respectively. Based on the presented data, strains X-1125T and X-1174 hereby represent a novel species of the genus Paraliobacillus , for which the name Paraliobacillus zengyii sp. nov. is proposed. The type strain is X-1125T (=DSM 107811T=CGMCC 1.16464T).
-
-
-
Planomicrobium iranicum sp. nov., a novel slightly halophilic bacterium isolated from a hypersaline wetland
A novel strain, designated as MX6T was isolated from Meighan wetland, in the centre of Iran. The cells were Gram-stain-positive, motile, coccoid to rod-shaped, oxidase- and catalase-positive. The strain grew optimally at 35 °C, 3 % (w/v) NaCl and pH 7–7.5. A polyphasic taxonomic study was undertaken in order to characterize the strain in detail. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that MX6T represented a member of the phylum Firmicutes , family Planococcaceae , genus Planomicrobium , and showed the highest similarity with Planomicrobium flavidum ISL-41T (98.2 %) and Planomicrobium psychrophilum CMC 53orT (98.0 %). The main polar lipids of MX6T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and seven unidentified phospholipids and its DNA G+C content was 45.5 mol%. Major cellular fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol, iso-C14 : 0, iso-C15 : 0 and iso-C16 : 0 and the predominant respiratory quinone was Q-8 (62 %). Experimental DNA–DNA hybridization between MX6T and Planomicrobium flavidum IBRC-M 11047T was 20 %, supporting the differential taxonomic status of MX6T as representing a different taxon. All these data indicate that MX6T represents a novel species of the genus Planomicrobium , for which the name Planomicrobium iranicum sp. nov. is proposed. The type strain is MX6T (=IBRC M 10928T=LMG 28548T).
-
-
-
Filibacter tadaridae sp. nov., isolated from within a guano pile from a colony of Mexican free-tailed bats Tadarida brasiliensis
A Gram-stain-positive, aerobic bacterium, TB-66T, was isolated from a pile of bat guano in a cave of New Mexico, USA. On the basis of 16S rRNA gene sequence similarity comparisons, strain TB-66Tgrouped together with Filibacter limicola showing a 16S rRNA gene sequence similarity of 98.5 % to the type strain. The quinone system of strain TB-66T consisted predominantly of menaquinone MK-7. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylserine and three unidentified phospholipids. The peptidoglycan type was A4α l-Lys–d-Glu (A11.33). The major fatty acids were C15 : 0 anteiso, C16 : 0, and C16 : 1 ω7c. The G+C content of the genomic DNA was 37.6 (±1.8) mol%. On the basis of the genotypic and phenotypic properties it is clear that strain TB-66T represents a member of the genus Filibacter, but is distinct from the only other species in the genus, Filibacter limicola DSM 13886T. We propose a novel species with the name Filibacter tadaridae sp. nov. The type strain is TB-66T (= CIP 111629T= LMG 30660T= CCM 8866T).
-
-
-
Suicoccus acidiformans gen. nov., sp. nov., isolated from a sick pig
More LessA Gram-stain-positive, non-spore-forming, catalase-positive and facultatively anaerobic coccus, designated ZY16052T, was isolated from mesenteric lymph nodes of a sick piglet in Kunming, Yunnan Province, PR China and its taxonomic position was studied by following a polyphasic approach. Optimal growth was observed at 37 °C, pH 8.0 and 2 % NaCl (w/v) on Columbia agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZY16052T formed a separated evolutionary lineage from recognized genera of the family Aerococcaceae and shared low similarity to its closest related species Facklamia sourekii (93.8 %) and Ignavigranum ruoffiae (93.4 %). Phylogenetic analysis based on the housekeeping gene recA indicated that strain ZY16052T represented a deep and distinct evolutionary lineage, and was well separated from all genera in the family Aerococcaceae , with very low sequence similarity(≤73.2 %). Sequence analysis based on the housekeeping gene rpoA indicated that strain ZY16052T shared very low similarity ≤77.0 % to related genera. The genomic OrthoANI values between strain ZY16052T and type species of related genera in the family Aerococcaceae and species in the genus Facklamia were ≤67.77 and ≤68.11 %, respectively. The genomic G+C content was 42.3 mol%. The predominant fatty acids (>5 %) were C16 : 0, C18 : 1ω9c, C14 : 0 and summed feature 5 (C18 : 2ω6,9c and/or C18 : 0 ante). The major polar lipids were digalactosyldiacylglycerol, phosphatidylglycerol, diacylglycerols, triacylglycerol and phosphatidic acid. The peptidoglycan contained the amino acids lysine, glycine, alanine and glutamic acid, which is characteristic of peptidoglycan type A1a. Based on the phylogenetic and phenotypic evidence, we propose that the unknown bacterium be classified as Suicoccus acidiformans gen. nov., sp. nov. The type strain of Suicoccus acidiformans is ZY16052T (=CCTCC AB 2017017T=DSM 105755T).
-
-
-
Staphylospora marina gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae, isolated from a deep-sea hydrothermal vent in the Pacific Ocean
More LessA novel bacterium, designated SCSIO 07575T, was isolated from a deep-sea hydrothermal sediment sample collected from the western Pacific Ocean. Growth at 65 °C was observed, but not at 70 °C or below 37 °C. The optimum conditions for growth were at 55–65 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Strain SCSIO 07575T showed filamentous growth. Unstable formation of white aerial mycelia was observed, which disappeared after several times’ subculture. Abundant substrate mycelia were observed with grape-like spores. No soluble pigment was observed. Phylogenetic analysis of 16S rRNA gene sequences showed that SCSIO 07575T belonged to the family Thermoactinomycetaceae and formed a distinct clade in the phylogenetic tree. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Whole-cell hydrolysates contained ribose, xylose, glucose and galactose. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid and two unidentified phospholipids. The predominant menaquinone was MK-7. Major fatty acids were iso-C15 : 0, iso-C17 : 0 and iso-C16 : 0. Based on the whole genome sequence analysis, the genome size was 2 751 094 bp with a DNA G+C value of 57.2 mol%, including one circular chromosome and one plasmid. On the basis of polyphasic data, strain SCSIO 07575T represented a novel species of a new genus within the family Thermoactinomycetaceae , for which the name Staphylospora gen. nov. is proposed with the type species Staphylospora marina sp. nov. and the type strain SCSIO 07575T (=DSM 106793T=CGMCC 1.15879T).
-
-
-
Lactobacillus suantsaii sp. nov., isolated from suan-tsai, a traditional Taiwanese fermented mustard green
A Gram-stain-positive, rod-shaped, non-motile, catalase-negative and facultative anaerobic strain, L88T, was isolated from suan-tsai, a traditional Taiwanese fermented mustard green. Comparative analyses of 16S rRNA, pheS and rpoA gene sequences demonstrated that strain L88Twas a member of the genus Lactobacillus . On the basis of 16S rRNA gene sequence similarity, the type strains of Lactobacillus acidifarinae (98.2 % similarity), Lactobacillus namurensis (98.1 %), Lactobacillus zymae (98.1 %) and Lactobacillus spicheri (96.8 %) were the closest neighbours to this novel strain. The average nucleotide identity, digital DNA‒DNA hybridization and average amino acid identity values between L88T and its closest relatives were lower than 80, 30 and 90 %, respectively. Phenotypic and genotypic test results demonstrated that strain L88T represents a novel species of the genus Lactobacillus , for which the name Lactobacillus suantsaii sp. nov., is proposed. The type strain is L88T (=BCRC 12945T=NBRC 113535T).
-
- Proteobacteria
-
-
Proposal of Parashewanella gen. nov. to accommodate Parashewanella curva sp. nov. and Parashewanella spongiae comb. nov. in the Shewanellaceae
A Gram-stain-negative, non-spore-forming, motile, aerobic, curved rod shaped bacterium, designed strain C51T, was isolated from coral (genus Porites) sampled at Weizhou Island, China. The optimal growth occurred in 2-3 % NaCl (w/v), at 25 °C and pH 8. Phylogenetic analyses based on the 16S rRNA gene, the gyrB gene and the Up-to-date Bacterial Core Gene set (92 genes) indicated that strain C51T forms a stable cluster with Shewanella spongiae KCTC 22492T, and had 94 % 16S rRNA gene similarity to its closest type strain S. spongiae KCTC 22492T. The only detected respiratory quinone was Q-8 and it could not produce menaquinone. The genome DNA G+C content was 40.1 mol%. The major cellular fatty acids were iso-C11:0 3-OH, iso-C15:0, C16:0, C16:1ω7c/ω6c, C18:0 and iso-C13:0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified aminolipids and three unidentified polar lipids. Its low genome DNA G+C content, lack of an aminolipid and a difference in its substrate oxidation ability indicated that strain C51T should represent a new species. Furthermore, its distinct phylogeny, Shewanella-specific FISH probe SHEW227 mismatch, lower cellular G+C content and inability to produce menaquinones indicated that the C51T clade should represent a new genus in the Shewanellaceae , for which the name Parashewanella gen. nov. is proposed, the type species is Parashewanella spongiae comb. nov., and another species is Parashewanella curva sp. nov. The type strains of Parashewanella spongiae and Parashewanella curva are HJ039T (=KCTC 22492T=KCCM 42304T=JCM 13830T) and C51T (=MCCC 1K03463T=KCTC 62318T), respectively.
-
-
-
Paraburkholderia telluris sp. nov., isolated from subtropical forest soil
More LessStrain DHOC27T is a Gram-stain-negative, aerobic, non-motile, light yellow-pigmented and rod-shaped bacterium isolated from the forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. It grew at 4–37 °C (optimal 28–33 °C), pH 4.0–8.5 (optimal 4.5–6.0) and 0–1.5 (optimal 0–0.5) % (w/v) NaCl. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a clade with Paraburkholderia phenazinium LMG 2247T, Paraburkholderia. sartisoli LMG 24000T and Paraburkholderia. pallidirosea DHOK13T, with a sequence similarity of 98.5, 97.5 and 98.1 % to the above strains, respectively. The DNA G+C content of DHOC27T was 62.3 mol%. The digital DNA–DNA relatedness values and the average nucleotide identities between strain DHOC27T and P. phenazinium LMG 2247T and P. sartisoli LMG 24000T were 26.9 and 24.3 % and 82.3 and 79.9 %, respectively. C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c were the major fatty acids, and ubiquinone-8 was the major respiratory quinone detected, all of which supported the affiliation of DHOC27T to the genus Paraburkholderia . On the basis of the data presented above, strain DHOC27T represents a novel species of the genus Paraburkholderia and the name Paraburkholderia telluris sp. nov. is proposed. The type strain is DHOC27T (=LMG 30263T=GDMCC 1.1281T).
-
-
-
Frateuria defendens sp. nov., bacterium isolated from the yellows grapevine’s disease vector Hyalesthes obsoletus
A Dyella -like bacterium was previously isolated from the planthopper Hyalesthes obsoletus (Hemiptera). Based on its 16S rRNA gene sequence, strain DHoT was assigned to the family Rhodanobacteraceae with Dyella and Frateuria as its closest relatives. The closest 16S rRNA gene sequences were Frateuria aurantia DSM 6220T (98.2 %), Dyella thiooxydans ATSB10T (98 %), Dyella terrae JS14-6T (97.8 %) and Dyella marensis CS5-B2T (97.8 %). Strain DHoT is a Gram-negative, aerobic, motile, yellow-pigmented, rod-shaped bacterium. Strain DHoT cells grew well at 28–30 °C and at pH 6.5–7.5 on a nutrient agar plate. DNA–DNA hybridization showed that the relatedness between strain DHoT and D. jiangningensis strain SBZ3-12T, and F. aurantia DSM 6220T was 42.7 and 42.6 %, respectively. Ubiquinone Q-8 was the predominant respiratory quinone, and the major fatty acids (>10 %) were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. In silico analysis based on phylogenetics and sequence identity at the nucleotide and protein levels suggests that Frateuria is the closest known relative of strain DHoT. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain DHoT was designated as a novel species of the genus Frateuria , for which the name Frateuria defendens sp. nov. is proposed. The type strain is DHoT (=NCCB 100648T; =DLBT=DSM 106169T).
-
-
-
Vibrio zhugei sp. nov., a moderately halophilic bacterium isolated from pickling sauce
More LessStrain HBUAS61001T was isolated from the pickling sauce used to make a traditional fermented food product, datoucai, in China. The strain belonged to the genus Vibrio , but was placed in a clade separate from any known Vibrio species based on the 16S rRNA gene and MLSA results. The genome consisted of two chromosomes: chromosome I was 2 901 449 bp long with a G+C content of 45.4 mol%; and chromosome II was 1 107 930 bp long with a G+C content of 45.5 mol%. The most abundant fatty acids were C16 : 0 (28.1 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 29.4 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 10.1 %). The isoprenoid quinones detected were Q7 and Q8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Strain HBUAS61001T could grow in the presence of up to 17 % NaCl. The calculated average nucleotide identity and in silico DNA–DNA hybridization (GGDC) values of the strain against the closest related type strains were all lower than 95 and 70 %, respectively. Putative genes in the genome associated with survival under high salinity stress were identified. Based on whole genome sequence analysis and phenotypic characteristics, strain HBUAS61001T is a new species in the genus Vibrio , and the name Vibrio zhugei (=GDMCC 1.1416T=KCTC 62784T) is proposed.
-
-
-
Pseudomonas asiatica sp. nov., isolated from hospitalized patients in Japan and Myanmar
A novel Gram-negative, aerobic, rod-shaped, non-spore-forming bacterial strain, RYU5T, was isolated from a stool sample of an inpatient at a hospital in Okinawa, Japan. The optimal growth temperature of RYU5T was 30 °C. Phylogenetic analysis based on the sequences of housekeeping genes, including the 16S rRNA, rpoB, rpoD and gyrB genes, showed that RYU5T was a member of the Pseudomonas putida group and was located close to Pseudomonas monteilii and P. putida . Whole-genome comparisons, using average nucleotide identity and digital DNA–DNA hybridization, confirmed that strain RYU5T should be classified as a novel species of Pseudomonas . Phenotypic characterization tests showed that utilization of d-mannose, d-serine, l-arabinose and d-fructose could distinguish this strain from other related species of the genus Pseudomonas . Based on genetic and phenotypic evidence, strain RYU5T should be classified as a novel species, for which the name Pseudomonas asiatica sp. nov. is proposed. The type strain is RYU5T (=DSM 107182T, =JCM 32716T), with a DNA G+C content of 62.25 mol%.
-
-
-
Azospirillum ramasamyi sp. nov., a novel diazotrophic bacterium isolated from fermented bovine products
A Gram-stain-negative, rod-shaped, aerobic bacterium, designated M2T2B2T, was isolated from fermented bovine products in Suwon, Republic of Korea. The strain displayed growth at 15–45 °C (optimum, 28–30 °C), pH 6.0–10.0 (pH 7.0) and 0–2 % (w/v) NaCl (0 %). Colonies were light pink-coloured, round and convex. The cells were positive for oxidase and weakly positive for catalase. The major fatty acids in whole cells of strain M2T2B2T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), followed by summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 2 (C12 : 0 aldehyde/unidentified 10.928/C14 : 0 3-OH/iso-C16 : 1 I), C16 : 0, C18 : 1 2-OH, C16 : 0 3-OH and C17 : 1 ω6c. The polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, and three unidentified aminolipids. Ubiquinone 10 was the predominant ubiquinone. The DNA G+C content was 68.0 mol%. The strain could fix atmospheric nitrogen, which was evaluated by the acetylene reduction assay. Further, whole genome sequence analysis revealed the presence of a nif gene cluster. Strain M2T2B2T showed the highest 16S rRNA, rpoD and nifH gene sequence similarity to members of the genus Azospirillum , and showed 97.6 % 16S rRNA gene sequence similarity to Azospirillum oryzae COC8T. The phenotypic, phylogenetic and genomic analyses support the proposal of strain M2T2B2T as being a novel species of the genus Azospirillum , for which the name Azospirillum ramasamyi sp. nov. is proposed. The type strain is M2T2B2T (=KACC 14063T=NBRC 106460T).
-
-
-
Bosea psychrotolerans sp. nov., a psychrotrophic alphaproteobacterium isolated from Lake Michigan water
Three strains of a Gram-stain negative bacterium were isolated from Lake Michigan water. 16S rRNA gene sequence analysis revealed that strain 1131 had sequence similarities to Bosea vaviloviae LMG 28367T, Bosea lathyri LMG 26379T, Bosea lupini LMG 26383T, Bosea eneae CCUG 43111T, Bosea vestrisii CCUG 43114T and Bosea massiliensis CCUG 43117T of 99.8, 99.1, 98.4, 98.4, 98.4 and 98.2 %, respectively. The average nucleotide identity value between strain 1131T and Bosea vaviloviae Vaf-18T was 93.4 % and the DNA relatedness was 38 %. The primary cellular fatty acids of strain 1131T were C16 : 1ω7c and C18 : 1ω7c. The primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major compound in the quinone system was ubiquinone Q-10 and in the polyamine pattern sym-homospermidine was predominant. Additional phenotypic characteristics included growth at 5–35 °C, pH values of pH 5.5–8.0, a salt tolerance range of 0.0–1.2 % (w/v), and production of an unknown water soluble brown pigment. After phenotypic, chemotaxonomic and genomic analyses, this isolate was identified as a novel species for which the name Bosea psychrotolerans is proposed. The type strain is 1131T (NRRL B-65405=LMG 30034).
-
-
-
Roseicella frigidaeris gen. nov., sp. nov., isolated from an air-conditioning system
More LessA Gram-stain-negative, facultatively aerobic bacterial strain, designated DB1506T, of the family Acetobacteraceae , was isolated from an air-conditioning system in the Republic of Korea. Colonies were pink- to rosy-coloured and cells were non-motile cocci with catalase- and oxidase-positive activities. Growth of strain DB1506T was observed at 20–37 °C (optimum, 30 °C), pH 5.5–8.5 (pH 7.0) and in the presence of 0–0.5 % (w/v) NaCl (0 %). Strain DB1506T contained summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c) and C18 : 1 2-OH as major fatty acids and ubiquinone-10 as the sole isoprenoid quinone. Phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipids, unidentified aminolipids and unidentified polar lipids were detected as major polar lipids. The G+C content of the genomic DNA calculated from the whole genome sequence was 72.5 mol%. Strain DB1506T was most closely related to Paracraurococcus ruber NS89T, Dankookia rubra WS-10T and Siccirubricoccus deserti SYSU D8009T with 16S rRNA gene sequence similarities of 96.01, 95.88 and 95.44 %, respectively, but strain DB1506T formed a clearly distinct phylogenic lineage from them within the family Acetobacteraceae . On the basis of phenotypic, chemotaxonomic and molecular properties, strain DB1506T represents a novel species of a new genus within the family Acetobacteraceae , for which the name Roseicella frigidaeris gen. nov., sp. nov. is proposed. The type strain is DB1506T (=KACC 19791T=JCM 32945T).
-
-
-
Phenylobacterium soli sp. nov., isolated from arsenic and cadmium contaminated farmland soil
More LessA Gram-stain-negative, facultative anaerobic, non-motile and rod-shaped bacterial strain, designated LX32T, was isolated from arsenic and cadmium contaminated farmland soil. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain LX32T was closely related to Phenylobacterium hankyongense HKS-05T (97.7 % sequence similarity), Phenylobacterium kunshanense CCTCC AB 2013085T (97.4 %) and Phenylobacterium deserti CCTCC AB 2016297T (97.1 %). The average nucleotide identity values of the whole genome sequences of LX32T/P. hankyongense HKS-05T, LX32T/P. kunshanense CCTCC AB 2013085T and LX32T/P. deserti CCTCC AB 2016297T were 79.8, 77.9 and 77.5 %, respectively. Its genome size was 4.02 Mb, comprising 3998 predicted genes with a DNA G+C content of 70.1 mol%. The major fatty acids were C15 : 0, C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The polar lipid profiles consisted of phosphatidylglycerol, aminophospholipid, seven glycolipids and two unidentified polar lipids. The predominantly respiratory quinone was ubiquinone-10. Based on polyphasic analyses, the isolate is considered to represent a novel species of the genus Phenylobacterium , for which the name Phenylobacterium soli sp. nov. is proposed. The type strain is LX32T (=KCTC 62522=CCTCC AB 2018055).
-
-
-
Trinickia dinghuensis sp. nov. and Trinickia fusca sp. nov., isolated from forest soil
More LessTwo Gram-stain-negative, aerobic, non-spore forming and rod-shaped bacterial strains, designated DHOM06T and 7MK8-2T, were isolated from forest soil sampled at Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOM06T grew at 12–37 °C (optimum, 28–33 °C), pH 4.5–7.5 (pH 5.5) and in the presence of 0–0.5 % NaCl (w/v); while strain 7MK8-2T grew at 12–42 °C (28–33 °C), pH 4.0–8.5 (pH 4.5–5.5) and in the presence of 0–1.0 % NaCl (w/v). Strains DHOM06T and 7MK8-2T each has a 16S rRNA gene sequence similarity of 97.1–98.9 % as well as 97.4–97.9 % to Trinickia strains, respectively. In the 16S rRNA gene sequence phylogram, both strains and all five currently described Trinickia species formed a clade but they were all distinct from each other. The average nucleotide identity and digital DNA–DNA hybridization values for strains DHOM06T and 7MK8-2T and all Trinickia species were in the range of 77.4–82.6 % and 21.7–26.2 %, respectively. The DNA G+C content of DHOM06T and 7MK8-2T was 63.2 and 63.5 mol%, respectively, based on total genome calculations. These two strains contained ubiquinone 8 as the major respiratory quinone and C16 : 0, C17 : 0cyclo, C19 : 0cyclo ω8c, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) as the major cellular fatty acids. The major polar lipids of DHOM06T and 7MK8-2T were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of phenotypic, chemotaxonomic, phylogenetic and genomic analysis data, strains DHOM06T and 7MK8-2T represent two novel species of the genus Trinickia , for which the names Trinickia dinghuensis sp. nov. (type strain DHOM06T=GDMCC 1.1280T=LMG 30259T) and Trinickia fusca sp. nov. (type strain 7MK8-2T=GDMCC 1.1449T=KCTC 62469T) are proposed.
-
-
-
Stenotrophobium rhamnosiphilum gen. nov., sp. nov., isolated from a glacier, proposal of Steroidobacteraceae fam. nov. in Nevskiales and emended description of the family Nevskiaceae
More LessA Gram-stain-negative strain, designated GT1R17T, was isolated from an ervoconite sample collected from Gawalong glacier in the Tibet Autonomous Region, PR China. Strain GT1R17T was catalase- and oxidase-positive, and grew optimally at 20–25°C and pH 7.0. The highest level of 16S rRNA gene sequence similarities were found to members of the genera Nevskia (92.27–93.15 %) and Hydrocarboniphaga (91.92–92.96 %). Phylogenetic analyses based on 16S rRNA gene sequences and genomic data revealed that the strain GT1R17T belonged to the family Nevskiaceae , but could not be assigned to any known genera. The genomic DNA G+C content was 54.4 mol%. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1ω6c), C16 : 0, iso-C16 : 0 and summed feature 2 (C14 : 0 3OH and/or iso-C16 : 1 I). The polar lipids were phosphatidylglycerol, phosphatidylethanolamine and one unidentified lipid. The ubiquinone was Q-8. On the basis of the phenotypic, chemotaxonomic, genotypic and phylogenetic data, a novel species of a new genus,Stenotrophobiumrhamnosiphilum gen. nov., sp. nov. within the family Nevskiaceae , is proposed, with GT1R17T (=CGMCC 1.16137T=NBRC 113346T) as the type strain. In addition, phylogenetic analyses revealed that Steroidobacter and Povalibacter formed an independent clade in the order Nevskiales and were away from the families Nevskiaceae , Algiphilaceae and Salinisphaeraceae . Therefore, we propose to remove Steroidobacter and Povalibacter from the family Nevskiaceae and propose a new family Steroidobacteraceae in the order Nevskiales .
-
-
-
Brevundimonas lutea sp. nov., isolated from lake sediment
More LessA novel Gram-negative, aerobic, rod-shaped bacterium, designated NS26T, was isolated from a sediment sample collected from Taihu Lake in China. Colonies were orange, circular, smooth and neat-edged on Reasoner’s 2A agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NS26T belonged to the genus Brevundimonas and had the closest relationship with Brevundimonas halotolerans DSM 24448T (96.9 %). It grew at 20–37 °C (optimum, 28 °C), pH 5.5–10.5 (pH 7.0) and without NaCl. The major isoprenoid quinone was Q-10. The dominant cellular fatty acids were C18 : 1ω7c, C16 : 0 and C18 : 1ω7c 11-methyl. The polar lipid profile comprised 1,2-diacyl-3-O-(6-phosphatidyl-α-d-glucopyranosyl) glycerol, 1,2-di-O-acyl-3-O-α-d-glycopyranuronosyl glycerol, sulfoquinovosyl diacylglycerol, 1,2-di-O-acyl-3-O-[d-glycopyranosyl-(1→4)-α-d-glucopyranuronosyl] glycerol and phosphatidylglycerol. The G+C content of genomic DNA was 68.4 mol%. The average nucleotide identity value between strain NS26T and B. halotolerans DSM 24448T was 75.6 %. Based on the polyphasic taxonomic study, strain NS26T is suggested to be a novel species, for which the name Brevundimonas lutea sp. nov. is proposed. The type strain is NS26T (=CGMCC 1.13680T=NBRC 113554T).
-
-
-
Alteromonas indica Lin et al. 2018 is a later heterotypic synonym of Salinimonas sediminis Cao et al. 2018
More LessAlteromonas indica IO390401T was compared with Salinimonas sediminis N102T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of A. indica IO390401T shared high similarity (99.9 %) with that of S. sediminis N102T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Salinimonas . Whole genomic comparison between the two strains revealed an average nucleotide identity of 99.2 % and a digital DNA–DNA hybridization estimate of 92.6 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking difference in metabolic, physiological or chemotaxonomic features. Therefore, we propose Alteromonas indica as a later heterotypic synonym of Salinimonas sediminis .
-
-
-
Azoarcus pumilus sp. nov., isolated from seawater in Sanya, China
More LessA novel Gram-stain-negative, motile, rod-shaped (0.4–0.5×1.0–2.0 µm) strain with one polar flagellum, designated SY39T, was isolated from seawater in Sanya, China. Strain SY39T was able to grow at 15–40 °C (optimum, 35–37 °C), pH 6.5–8.5 (pH 8.0) and 0.5–6.0 % (w/v) NaCl (3.5 %). Chemotaxonomic analysis showed that the isoprenoid quinones were Q-8 (88.6 %) and Q-7 (11.4 %). The dominant fatty acids were C16 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). The polar lipids of strain SY39T consisted of diphosphatidyglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unknown phosphoglycolipid, one unknown glycolipid and two unknown aminophosphoglycolipids. The DNA G+C content of the genomic DNA was 66.5 mol%. The phylogenetic analysis of 16S rRNA gene sequences showed that strain SY39T belongs to the genus Azoarcus with similarity ranging from 92.3 to 95.2 %. Based on the phenotypic, chemotaxonomic and phylogenetic features, strain SY39T is concluded to represent a novel species of the genus Azoarcus , for which the name Azoarcus pumilus sp. nov. is proposed. The type strain is SY39T (=KCTC 62157T=MCCC 1K03430T).
-
-
-
Roseovarius faecimaris sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, obligate aerobic, non-motile and rod-shaped bacterium, designated MME-070T, was isolated from a tidal flat near Muui-do, Incheon, Republic of Korea. This bacterium belonged to the Roseobacter clade within the family Rhodobacteraceae . The isolate grew at 20–40 °C, pH 7.0–9.0 with 1–5 % (w/v) NaCl. Optimal growth required 2–3 % (w/v) NaCl at 25–30 °C and pH 8.0. The 16S rRNA gene sequence of strain MME-070T was most closely related to Roseovarius aestuarii SMK-122T (96.9 %). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain MME-070T clustered with the genus Roseovarius . The sole respiratory quinone was Q-10. Polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, unidentified aminolipid and some unidentified lipids. Major cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), 11-methyl C18 : 1 ω7c and C16 : 0. The genomic DNA G+C content of the type strain was 63.6 mol%. Based on polyphasic taxonomic analysis, strain MME-070T is proposed to represent a novel species of the genus Roseovarius , for which the name Roseovarius faecimaris sp. nov. is proposed. The type strain is MME-070T (=KCCM 43142T=JCM 30757T).
-
-
-
Paracoccus subflavus sp. nov., isolated from Pacific Ocean sediment
More LessA Gram-stain-negative, short rod-shaped, non-motile, catalase- and oxidase-positive, aerobic bacterium, designated GY0581T, was isolated from marine sediment sampled from the Western Pacific Ocean. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain GY0581T belonged to the genus Paracoccus and had the highest levels of sequence similarity to Paracoccus sediminis JCM 18467T (98.2 %). Levels of similarity between strain GY0581T and other Paracoccus species were lower than 97.0 %. The average nucleotide identity and the DNA–DNA hybridization values between strain GY0581T and P. sediminis JCM 18467T were 83.9 and 27 %, respectively, which are below the respective thresholds for species differentiation. The major cellular fatty acid was C18 : 1ω7c (79.5 %). The only isoprenoid quinone was Q-10. The polar lipid pattern indicated the presence of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, three unidentified phospholipids, three unidentified aminolipids, one unidentified glycolipid and two unidentified lipids. The DNA G+C content of strain GY0581T was 65.6 mol%. On the basis of polyphasic characterization, it is concluded that strain GY0581T represents a novel species of the genus Paracoccus , for which the name Paracoccus subflavus sp. nov. is proposed. The type strain is GY0581T (=KCTC 42710T=MCCC 1A10575T).
-
-
-
Photobacterium chitinilyticum sp. nov., a marine bacterium isolated from seawater at the bottom of the East China Sea
More LessA Gram-stain-negative, facultative aerobic, motile by a polar flagellum, rod-shaped strain, designated BEI247T, was isolated from seawater at the bottom of the East China Sea. Phylogenetic analysis of the 16S rRNA gene and whole genome data affiliated it with the genus Photobacterium . It was most closely related to Photobacterium alginatilyticum P03D4T (97.36 % 16S rRNA gene similarity). Multi-locus sequence analysis (MLSA) revealed a distinct lineage with P. alginatilyticum P03D4T as its closest relative. Strain BEI247T was found to have lower than 86.0 % similarities to the type strains of its most closely related species in MLSA, less than 82.3 % using genome average nucleotide identities, and less than 25.3 % in DNA–DNA relatedness studies. Growth occurred at 10–37 °C (optimum, 24 °C), pH 5.0–8.0 (pH 7.0) and in the presence of 1–5 % (w/v) NaCl (3 %). The dominant fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipids of strain BEI247T comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two phospholipids and one unknown lipid. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content of strain BEI247T was 46.45 mol%. On the basis of the polyphasic evidence, strain BEI247T is proposed as representing a novel species of the genus Photobacterium , for which the name Photobacterium chitinilyticum sp. nov. is proposed. The type strain is BEI247T (=JCM 32689T=MCCC 1K03517T=KCTC 62619T).
-
-
-
Marortus luteolus gen. nov., sp. nov., isolated from surface seawater of the East Sea in China
More LessA Gram-stain-negative, motile, aerobic, rod-shaped bacterium with flagella, designated ZX-21T, was isolated from surface seawater of the East Sea in Zhoushan, China. Growth of strain ZX-21T was observed at 10-–35 o°C (optimum, 30 °C), at pH 6.0–8.5 (pHoptimum 6.5–7.0) and in the presence of 0.5–8 % (w/v) NaCl (optimum 3–4 %). It was positive for oxidase and catalase activity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZX-21T constituted an independent lineage within the family Spongiibacteraceae and was most closely related to Zhongshania guokunii (96.83 %). Strain ZX-21T contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and summed feature 3 (C16 : 1ω77c and/or C16 : 1ω66c), summed feature 8 (C18 : 1ω77c and/or C18 : 1ω66c) and C16 : 0 as the major fatty acids. Phosphatidylglycerol (), phosphatidylethanolamine (), diphosphatidylglycerol () and an unidentified glycolipid were the major cellular polar lipids. The DNA G+C content was 49.1 mol%. Based on itsthe morphological, physiological and chemotaxonomic characteristics, strain ZX-21Tis described as a novel species in a novel genus for whichwith the name Marortus luteolus gen. nov., sp. nov. (type strain ZX-21T = MCCC 1K03431T=KCTC 62160T) is proposed.
-
-
-
Dyella dinghuensis sp. nov. and Dyella choica sp. nov., isolated from forest soil
More LessTwo aerobic, Gram-stain-negative, non-motile, rod-shaped bacterial strains, designated as DHOA06T and 4 M-K27T, were isolated from soil samples collected from the forest of Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31′ E 23° 10′ N). Strains DHOA06T and 4 M-K27T grew at pH 4.5–7.0 (optimum, pH 5.0–6.0) and pH 4.5–6.5 (pH 6.0), respectively. Both strains grew at 12–37 °C (optimum, 28 °C) and NaCl levels up to 1.0 % (optimum 0 %, w/v). Phylogenetic analysis based on both 16S rRNA gene sequences and the concatenated partial atpD, gyrB andlepA gene sequences showed that strains DHOA06T and 4 M-K27T formed two isolated clades with members of the genus Dyella, but they each occupied a distinctive position within the genus. Strains DHOA06T and 4 M-K27T showed the highest 16S rRNA gene sequence similarities to Dyellacaseinilytica DHOB09T (98.7 %) and Dyellaacidisoli 4M-Z03T (98.8 %), respectively. DNA–DNA hybridization values of strains DHOA06T/DHOB09T and 4 M-K27T/4M-Z03T were 27.4±2.4 % and 38.8±1.0 %, respectively. Ubiquinone-8 was the only respiratory quinone detected in both strains. Their major fatty acids consisted of iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1 ω9c, and strain DHOA06T had iso-C17 : 0 in addition. Their polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid, one unidentified phospholipid and two unidentified aminolipids, and strain DHOA06T had phosphatidylmethylethanolamine and one unidentified lipid in addition. The DNA G+C contents of strains DHOA06T and 4 M-K27T were 59.1 and 61.7 mol%, respectively. Based on the above results, we propose that strains DHOA06T and 4 M-K27T represent two novel species of the genus Dyella , namely Dyelladinghuensis sp. nov. (type strain DHOA06T = KCTC 52129T=NBRC 111978T) and Dyellachoica sp. nov. (type strain 4 M-K27T=GDMCC 1.1189T=LMG 30267T).
-
- Eukaryotic Micro-Organisms
-
-
Kurtzmaniella hittingeri f.a., sp. nov., isolated from rotting wood and fruits, and transfer of three Candida species to the genus Kurtzmaniella as new combinations
Twelve strains of a novel yeast species were isolated from rotting wood, mushrooms and fruit samples in Brazil and French Guiana. Analysis of the sequences of the internal transcribed spacer region and the D1/D2 domains of the large subunit rRNA gene showed that the novel species belongs to the Kurtzmaniella clade. The novel species differed from its closest relative, Candida natalensis, by 12 substitutions in the D1/D2 sequences. The novel species could be distinguished from C. natalensis by its inability to assimilate cellobiose and salicin, and growth at 50 % (w/w) glucose. The name Kurtzmaniella hittingeri f.a., sp. nov. is proposed for the novel species. The type strain of K. hittingeri sp. nov. is CBS 13469T (=UFMG CM-Y272T). The MycoBank number is 827183. We also propose the transfer of Candida fragi, Candida quercitrusa and Candida natalensis to the genus Kurtzmaniella as new combinations.
-
-
-
Wickerhamomyces menglaensis f.a., sp. nov., a yeast species isolated from rotten wood
More LessFive strains, NUNU 16637, NYNU 16645, NYNU 1673, NYNU 1680 and NYNU 1689, of a novel ascomycetous yeast were isolated from the Xishuangbanna tropical rainforest, Yunnan Province, PR China. The five strains shared identical sequences in both of the D1/D2 domains of the large subunit rRNA gene and the internal transcribed spacer (ITS) regions. Sequence analysis showed that they represent undescribed yeast species belonging to the genus Wickerhamomyces. They differed from their closest known species, Wickerhamomyces xylosivorus NBRC 111553T, by 3.4 % sequence divergence (14 substitutions and six gaps out of 584 bp) in the D1/D2 domains and by 9.6 % sequence divergence (28 substitutions and 24 gaps over 543 bp) in the ITS regions, respectively. The five strains of novel species reproduced asexually; no sexual reproduction could be found. In contrast to W. xylosivorus, the novel yeast species were able to assimilate l-arabinose, inulin, soluble starch, d-mannitol and citrate, and unable to assimilate trehalose, raffinose, 5-keto-d-gluconate, d-gluconate, ethanol, ethylamine and cadaverine. Growth was observed at 35 °C. The name Wickerhamomyces menglaensis f.a., sp. nov. is proposed to accommodate these strains, with NYNU 1673 as the holotype.
-
- ICSP Matters
-
-
-
Introducing the concept of the isonym into the International Code of Nomenclature of Prokaryotes
More LessThere are various ways in which the names of prokaryotes can be duplicated in the literature. An examination of the various ways that this may happen under the International Code of Nomenclature of Prokaryotes indicates that a concept is missing, namely the one that refers to the same name based on the same nomenclatural type published in the International Journal of Systematic Bacteriology/International Journal of Systematic and Evolutionary Microbiology, by the same or different authors in different manuscripts or in the Validation Lists. To cater for such instances it would be appropriate to introduce the concept of the isonym and to regulate how they are to be dealt with.
-
-
-
-
Proposed modifications to Rule 40d of the International Code of Nomenclature of Prokaryotes
More LessThe wording of Rule 40d was discussed at the XIIth International (IUMS) Congress of Bacteriology and Applied Microbiology, Istanbul in 2008 and some changes were made to clarify how the authorship of names covered by this rule were to be cited. However, a key topic that was raised and discussed was the issue of wording that either automatically creates a subspecies name or whether an automatic consequence of the rule was that a subspecies name based on the nomenclatural type of the corresponding species was required, but must be validly published in accordance with the Rules of the International Code of Nomenclature of Prokaryotes. The differences are subtle, but important.
-
-
-
International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of closed and open meetings, 3 September 2018, Berlin, Germany
More LessThe meeting of International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Bifidobacterium , Lactobacillus and related organisms was held within the frame of the FoodMicro 2018 Congress (FoodMicro 2018, 3–6 September 2018, Berlin, Germany). The meeting comprised an open session with a workshop entitled ‘Modern approaches of LAB identification and conservation’ and a closed session on issues related to ICSP Subcommittee activities.
-
-
-
Proposal to modify the Rules of the International Code of Nomenclature of Prokaryotes to abolish the taxonomic categories Subfamily, Subtribe and Kingdom
More LessAlthough the taxonomic categories covered by the International Code of Nomenclature of Prokaryotes include the ranks of Subtribe (Subtribus) and Subfamily (Subfamilia), no names of taxa belonging to these ranks have been validly published. To simplify the Rules of the Code I propose abolishing these ranks. The rank of Kingdom is mentioned once in the Code, in an example to Rule 8, but it is not further defined. Therefore, I propose modifying that example so that the rank of Kingdom is no longer mentioned in the Code.
-
-
-
Naming classes of prokaryotes based on the rules of Latin grammar
More LessRecently a proposal was published to unify Rules 7, 8 and 9 of the International Code of Nomenclature of Prokaryotes. Based on this proposal, all names of taxa above the rank of genus must be in the feminine gender, the plural number. For the rank of class, this proposal contravenes Principle 3 of the Code, which states that the scientific names of all taxa are treated as Latin. The –ia ending of most names of classes belongs to nominative plural nouns of the neuter gender.
-
- Corrigendum
-
Volumes and issues
-
Volume 74 (2024)
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)