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Volume 72,
Issue 7,
2022
Volume 72, Issue 7, 2022
- Validation Lists
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- Notification Lists
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- List of Changes in Taxonomic Opinion
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- Reviews
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Taxonomy of the anaerobic gut fungi (Neocallimastigomycota): a review of classification criteria and description of current taxa
Members of the anaerobic gut fungi (Neocallimastigomycota) reside in the rumen and alimentary tract of larger mammalian and some reptilian, marsupial and avian herbivores. The recent decade has witnessed a significant expansion in the number of described Neocallimastigomycota genera and species. However, the difficulties associated with the isolation and maintenance of Neocallimastigomycota strains has greatly complicated comparative studies to resolve inter- and intra-genus relationships. Here, we provide an updated outline of Neocallimastigomycota taxonomy. We critically evaluate various morphological, microscopic and phylogenetic traits previously and currently utilized in Neocallimastigomycota taxonomy, and provide an updated key for quick characterization of all genera. We then synthesize data from taxa description manuscripts, prior comparative efforts and molecular sequence data to present an updated list of Neocallimastigomycota genera and species, with an emphasis on resolving relationships and identifying synonymy between recent and historic strains. We supplement data from published manuscripts with information and illustrations from strains in the authors’ collections. Twenty genera and 36 species are recognized, but the status of 10 species in the genera Caecomyces, Piromyces, Anaeromyces and Cyllamyces remains uncertain due to the unavailability of culture and conferre (cf.) strains, lack of sequence data, and/or inadequacy of available microscopic and phenotypic data. Six cases of synonymy are identified in the genera Neocallimastix and Caecomyces, and two names in the genus Piromyces are rejected based on apparent misclassification.
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- New Taxa
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Whole genome-based taxonomy of Shewanella and Parashewanella
More LessThe family Shewanellaceae currently comprises three genera, Shewanella , Parashewanella and Psychrobium , the latter represented by a single species. From the second half of the 1990s, the number of novel species in the Shewanellaceae has steadily increased, suggesting that the true diversity of this family has only begun to emerge. In recent years, efforts to provide a genus-wide, whole genome-based taxonomy for Shewanella have been limited by the lack of numerous type strain genome sequences. To shed light on this question, we sequenced all Shewanella type strains that lacked a publicly available whole-genome sequence. Using state-of-the-art phylogenomic methods, here we provide a genus-wide taxonomy of Shewanella and Parashewanella that resulted in the identification of 48 novel species represented by 73 sequenced isolates, and we propose the correction of 43 misidentified non-type-strain isolates. Our work sets a reference for family-wide comparative genomic studies addressing genetic or ecophysiological aspects of Shewanellaceae , as well as subsequent species descriptions.
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- Actinobacteria
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Nocardioides nematodiphilus sp. nov., isolated from rhizosphere of Arabidopsis thaliana
An actinobacterial strain, designated R-N-C8T, was isolated from the rhizosphere soil of Arabidopsis thaliana collected in Yunnan Province, south-west China. Based on the results of 16S rRNA gene sequence analysis, strain R-N-C8T had highest similarity to Nocardioides terrae CGMCC 1.7056T (96.5%), Nocardioides opuntiae KCTC 19804T (96.3%) and Nocardioides currus IB-3T (96.1%), and lower than 96.0 % similarity to other members of the genus Nocardioides . Phylogenetic trees based on 16S rRNA gene sequences indicated that strain R-N-C8T formed an isolated branch with N. terrae CGMCC 1.7056T and N. opuntiae KCTC 19804T. The polar lipids contained phosphatidylglycerol, diphosphatidylglycerol, one unidentified phosphoglycolipid and four unidentified phospholipids in the cellular membrane. The major fatty acids were identified as iso-C16 : 0, anteiso-C17 : 0, iso-C17 : 0, summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl) and iso-C15 : 0. The predominant respiratory quinone was MK-8(H4) and ll-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The genomic DNA G+C content was 70.9 mol%. The orthologous average nucleotide identiy values between N. terrae CGMCC 1.7056T, N. currus IB-3T and strain R-N-C8T were 77.1 and 75.1 %, respectively. DNA–DNA hybridization values between N. terrae CGMCC 1.7056T, N. currus IB-3T and strain R-N-C8T were 20.7 and 19.9 % respectively. Data from phenotypic and genotypic analyses supported that strain R-N-C8T represents a new species of Nocardioides , for which the name Nocardioides nematodiphilus sp. nov. is proposed. The type strain is R-N-C8T (=CGMCC 1.18723T= KCTC 49528T).
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Actinomycetospora soli sp. nov., isolated from the rhizosphere soil of Averrhoa carambola L.
More LessA novel actinobacterium, designated strain SF1T, was isolated from the rhizosphere soil of a star fruit plant (Averrhoa carambola L.) collected from Bangkok, Thailand, and its taxonomic position was evaluated. The strain showed morphological, chemotaxonomic and phylogenetic characteristics consistent with its classification in the genus Actinomycetospora . Strain SF1T was an aerobic, Gram-stain-positive and non-motile actinobacterium. Growth occurred at 15–35 °C, at pH 4.0–12.0 and in the presence of 0–10 % (w/v) NaCl. The 16S rRNA gene sequence of strain SF1T showed the highest similarity to Actinomycetospora chiangmaiensis YIM 0006T (99.5 %), Actinomycetospora corticicola 014-5T (98.8 %) and Actinomycetospora endophytica A-T 8314T (98.8 %). The genome sequencing revealed a genome size of 6.52 Mbp and a DNA G+C content of 74.0 %. In addition, the average nucleotide identity values between strain SF1T and reference strains, A. chiangmaiensis DSM 45062T, A. corticicola DSM 45772T and A. endophytica TBRC 5722T, were found to be 86.1, 86.5 and 79.7 %, respectively, and the level of digital DNA–DNA hybridization between them were 32.4, 32.4 and 23.3 %, respectively. The whole-cell hydrolysates of strain SF1T contained meso-diaminopimelic acid as the diagnostic diamino acid, with arabinose, galactose, glucose and ribose as whole-cell sugars. The predominant menaquinone was MK-8(H4). Major cellular fatty acids were iso-C16 : 0 and a summed feature consisting of C16 : 1 ω6c/C16 : 1 ω7c. Characterization based on chemotaxonomic, phylogenetic, phenotypic and genomic evidence demonstrated that strain SF1T represents a novel species of the genus Actinomycetospora , for which the name Actinomycetospora soli sp. nov. is proposed. The type strain is strain SF1T (=TBRC 15166T= NBRC 115295T).
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Rhodococcus yananensis sp. nov., a novel denitrification actinobacterium isolated from microbial fermentation bed material from a pig farm
An opaque, pink-coloured, gram-positive, aerobic bacteria (designated as FBM22-1T), was isolated from microbial fermentation bed material from a pig farm in northwestern China. Optimal growth occurred at 30–37 °C, pH 7.0 and with 0.5 % NaCl (w/v). The strain had nitrification and denitrification functions. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate belonged to the genus Rhodococcus . Strain FBM22-1T was closely related to Rhodococcus zopfii NBRC 100606T and Rhodococcus rhodochrous NBRC 16069T, with 16S rRNA gene sequence similarities of 97.9 and 97.7 %, respectively. The predominant menaquinone in strain FBM22-1T was MK-8(H2). The cellular fatty acids consisted primarily of C16 : 1ω7c and/or C16 : 1 ω6c, C16 : 0 and 10-methyl C18 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and glycolipid. The G+C content of strain FBM22-1T was 68.64 mol%. Based on the phenotypic, phylogenetic and chemotaxonomic characterization results, in combination with low values of digital DNA–DNA hybridization between strain FBM22-1T and its closest neighbours, FBM22-1T represents a novel species of the genus Rhodococcus , for which the name Rhodococcus yananensis sp. nov. is proposed; the type strain is FBM22-1T (=KCTC 49502T=CCTCC AB2020275T).
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Humibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity isolated from activated sludge
More LessA novel Gram-stain-positive, thin rod-shaped, non-motile, aerobic and creamy-white pigmented bacterium (designated strain WJ7-1T) was isolated from activated sludge sampled in Suwon, Republic of Korea. 16S rRNA gene sequence analysis indicated that the isolate belongs to the genus Humibacter , family Microbacteriaceae , with a sequence similarity of 97.9 % to its nearest neighbour Humibacter albus KACC 20986T. Strain WJ7-1T contained menaquinone (MK)-10 (16.0 %), 11 (48.5 %) and 12 (35.5 %) as major respiratory quinones. The predominant cellular fatty acids (>15 %) were anteiso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. The peptidoglycan of strain WJ7-1T contained the diagnostic diamino acid ornithine and 2,4-diaminobutyric acid alanine. Alanine, glutamic acid and glycine were also present in the cell wall. The characteristic whole-cell sugars present were glucose, galactose, xylose and rhamnose. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and two unidentified phospholipids. Strain WJ7-1T possessed ginsenoside-converting (β-glucosidase) activity, which enabled it to transform ginsenoside protopanaxadiol-type Rb1 (one of the dominant active components of ginseng) to compound K. The genome size of strain WJ7-1T has 4.2 Mbp and the G+C content is 68.3 mol%. Average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values between strain WJ7-1T and the closely related strain were 79.8, 36.1 and 23.5 %, respectively, indicating that strain WJ7-1T represents a novel species of the genus Humibacter . Strain WJ7-1T could be distinguished from the other members of the genus Humibacter by a number of chemotaxonomic and phenotypic characteristics. Based on polyphasic taxonomic analysis, strain WJ7-1T (=KACC 19729T=LMG 30802T) represents a novel species within the genus Humibacter , for which the name Humibacter ginsenosidimutans sp. nov. is proposed.
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Actinomadura parmotrematis sp. nov., isolated from the foliose lichen, Parmotrema praesorediosum (Nyl.) Hale
A novel actinomycete strain PM05-2T was isolated from the lichen Parmotrema praesorediosum (Nyl.) Hale collected from Chaiyaphum Province, Thailand. The taxonomic position of the strain was studied using the polyphasic approach. Based on the morphology and chemotaxonomic properties, strain PM05-2T was identified as a member of the genus Actinomadura . The whole-cell hydrolysate contained meso-diaminopimelic acid, rhamnose, ribose, xylose, madurose, glucose and galactose. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phosphoglycolipid, four unidentified phospholipids and one unidentified lipid. The menaquinones were MK-9(H6), MK-9(H4), MK-9(H2), MK-9(H8) and MK-9(H0). The major cellular fatty acids were C16:0 and C18:1 ω9c. Strain PM05-2T showed the highest 16S rRNA gene similarity to Actinomadura hibisca NBRC 15177T (98.58%), Actinomadura kijaniata NBRC 14229T (98.29 %) and Actinomadura namibiensis DSM 44197T (98.14 %). The phylogenetic tree analysis revealed that strain PM05-2T was related to A. hibisca NBRC 15177T, A. kijaniata NBRC 14229T, A. namibiensis DSM 44197T and Actinomadura macrotermitis RB68T. The genomic analysis revealed that average nucleotide identity values based on both blast and MUMmer between strain PM05-2T and the relative type strains ranged from 77.6 to 86.4%. The digital DNA–DNA hybridization values among the strains were lower than the threshold for assigning to the same species. The taxonomic results suggested that strain PM05-2T represented a novel species of the genus Actinomadura for which the name Actinomadura parmotrematis is proposed. The type strain is PM05-2T (=TBRC 15492T=NBRC 115416T).
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- Bacteroidetes
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Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovénbreen, Arctic
A rod-shaped, Gram-stain-negative, non-motile and aerobic bacterium, designated Q8-18T, was isolated from soil of glacier foreland in Austre Lovénbreen, Arctic, and subjected to a polyphasic taxonomic study. Strain Q8-18T grew optimally at 20 °C, pH 5.0–8.0 and in the presence of 0–1.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Q8-18T belonged to the family Sphingobacteriaceae . Strain Q8-18T showed the highest sequence similarity to Pedobacter mendelii CCM 8685T (96.8%), Pedobacter lithocola CCM 8691T (96.8%), Pedobacter roseus CL-GP80T (96.7%), Pedobacter changchengzhani E01020T (96.7%), Pedobacter alluvionis DSM 19624T (96.6%), Pedobacter jejuensis THG-DR3T (96.3%), Pedobacter ginsengiterrae DCY49T (95.9%) and Pedobacter jamesrossensis CCM 8689T (95.9%). A whole genome-level comparison of strain Q8-18T with P. roseus CL-GP80T, P. changchengzhani E01020T, P. alluvionis DSM 19624T and Pedobacter heparinus LMG 10339T revealed average nucleotide identity values of 77.0, 76.0, 77.0 and 70.4%, respectively. The only respiratory isoprenoid quinone was menaquinone-7. The polar lipid profile of strain Q8-18T was found to contain one phosphatidylethanolamine, eight unidentified aminolipids, one aminophospholipids and five unidentified lipids. The G+C content of the genomic DNA was determined to be 35.4 mol%. The main fatty acids were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0 and anteiso-C15 : 0. On the basis of the evidence presented in this study, a novel species of the genus Pedobacter , Pedobacter mucosus sp. nov., is proposed, with the type strain Q8-18T (=CCTCC AB 2020009T=KCTC 82636T).
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Sinomicrobium kalidii sp. nov., an indole-3-acetic acid-producing endophyte from a shoot of halophyte Kalidium cuspidatum
More LessTo better understand the effects of endophytic bacteria on halophytes, a bacteria that produced indole-3-acetic acid and 1-aminocyclopropane-1-carboxylic acid deaminase, designated HD2P242T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. The cells of strain HD2P242T were Gram-stain-negative, strictly aerobic, motile by gliding, non-spore-forming and rod-shaped. Strain HD2P242T grew at pH 6.0–9.0 (optimum, pH 7.0) and 10–45 °C (optimum 37 °C), in the presence of 0–8 % (w/v) NaCl (optimum, 4 %). The strain was positive for oxidase and catalase. The phylogenetic trees based on the 16S rRNA gene sequences and the whole genome sequences both showed that strain HD2P242T clustered with Sinomicrobium pectinilyticum 5DNS001T and S. oceani SCSIO 03483T, and had 95.6, 94.3 and <94.3 % 16S rRNA gene similarities to S. pectinilyticum 5DNS001T, S. oceani SCSIO 03483T and all the other current type strains. Strain HD2P242T contained menaquinone 6 as its sole respiratory quinone. Its major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and an unidentified lipid. The major fatty acids were iso-C17 : 0, iso-C16 : 0 3-OH, anteiso-C17 : 0 and summed feature 6 (C19 : 1 ω9c and/or C19 : 1 ω11c). The genome consisted of a 5 364 211 bp circular chromosome, with a G+C content of 45.1 mol%, predicting 4391 coding sequence genes, 47 tRNA genes and two rRNA operons. The average nucleotide identity based on blast and the digital DNA–DNA hybridization values of strain HD2P242T with S. oceani SCSIO 03483T and S. pectinilyticum 5DNS001T were 73.8 and 77.0%, and 22.3 and 22.2%, respectively. The comparative genome analysis showed that the pan-genomes of strain HD2P242T and three Sinomicrobium type strains possessed 4236 clusters, whereas the core genome possessed 2162 clusters, which accounted for 52.3 % of all the clusters. The genomic analysis revealed that all four Sinomicrobium members could utilize d-glucose by the glycolysis–gluconeogenesis pathway or the pentose phosphate pathway. The tricarboxylic acid cycle was utilized as a metabolic centre. The phylogenetic, physiological and phenotypic characteristics allowed the discrimination of strain HD2P242T from its phylogenetic relatives. Therefore, Sinomicrobium kalidii sp. nov. is proposed, and the type strain is HD2P242T (=CGMCC 1.19025T=KCTC 92136T).
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Description of Abyssalbus ytuae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the sediment of the Mariana Trench
More LessIn this study, we describe a Gram-stain-negative, rod-shaped, non-motile and aerobic bacterium, named strain MT3330T, which was isolated from the deep-sea sediment of the Mariana Trench. Growth of MT3330T occurred at 15–40 °C (optimum, 25–30 °C), pH 5.0–10.0 (optimum, 7.0–8.0) and with 0–8.0 % (w/v) NaCl (optimum, 0–2.0 %). The results of phylogenetic analysis based on 16S rRNA gene sequence indicated that MT3330T represented a member of the family Flavobacteriaceae and was most closely related to Zhouia spongiae HN-Y44T (92.3 % sequence similarity). The results of genomic analysis indicated that MT3330T contains a circular chromosome of 4 365 036 bp with a DNA G+C content of 35.2 %. The predominant respiratory quinone of MT3330T was MK-6. The polar lipids of MT3330T included phosphatidylethanolamine, three unidentified amino lipids and four unidentified lipids. The major fatty acids of MT3330T included C15 : 0, iso-C15 : 1G, iso-C15 : 0 3-OH, and iso-C17 : 0 3-OH. On the basis of the results of the phylogenetic, physiological, biochemical and morphological analyses, it is suggested that strain MT3330T represents a novel genus and a novel species of the family Flavobacteriaceae , and the name Abyssalbus ytuae gen. nov., sp. nov. is proposed. The type strain is MT3330T (=MCCC 1K06012T=KCTC 82823T).
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- Firmicutes and Related Organisms
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Bacillus rhizoplanae sp. nov. from maize roots
A Gram-stain-positive, aerobic and endospore-forming bacterial strain, isolated from the root surface of maize (Zea mays) was taxonomically studied. It could be clearly shown that, based on 16S rRNA gene sequence similarity comparisons, strain JJ-63T is a member of the genus Bacillus , most closely related to the type strain of Bacillus pseudomycoides (98.61%), followed by Bacillus cereus (98.47 %). Detailed phylogenetic analysis based on the 16S rRNA gene and the 87 proteins conserved within the phylum Firmicutes placed the strain into the Cereus clade. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values against the type strain of B. pseudomycoides were 80.97, 81.45 and 26.30 %, respectively. The quinone system of strain JJ-63T consisted exclusively of menaquinone MK-7. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified glycolipid. Major fatty acids were iso- and anteiso-branched with the major compounds iso-C15 : 0 and iso-C17 : 0. Also, the characteristic compounds C13 : 0 iso and C16 : 1 cis10 were found. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-63T from the most closely related species. For this reason, JJ-63T represents a novel species of the genus Bacillus , for which the name Bacillus rhizoplanae sp. nov. is proposed, with JJ-63T (=LMG 32091T=CCM 9090T=DSM 111827T= CIP 111899T) as the type strain.
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Erysipelothrix anatis sp. nov., Erysipelothrix aquatica sp. nov. and Erysipelothrix urinaevulpis sp. nov., three novel species of the genus, and emended description of Erysipelothrix
Seven genotypically distinct strains assigned to the genus Erysipelothrix were isolated in different laboratories from several animal sources. Strain D17_0559-3-2-1T and three further strains were isolated from samples of duck, pig and goose. The strains had >99 % 16S rRNA gene sequence similarity to each other and to strain VA92-K48T and two further strains isolated from samples of medical leech and a turtle. The closest related type strains to the seven strains were those of Erysipelothrix inopinata (96.74 %) and Erysipelothrix rhusiopathiae (95.93 %). Average nucleotide identity, amino acid identity and in silico DNA–DNA hybridization results showed that the strains represented two separate novel species. One further phylogenetically distinct strain (165301687T) was isolated from fox urine. The strain had highest 16S rRNA gene sequence similarity to the type strains of Erysipelothrix tonsillarum (95.67 %), followed by Erysipelothrix piscisicarius (95.58 %) and Erysipelothrix larvae (94.22 %) and represented a further novel species. Chemotaxonomic and physiological data of the novel strains were assessed, but failed to unequivocally differentiate the novel species from existing members of the genus. MALDI-TOF MS data proved the discrimination of at least strain 165301687T from all currently described species. Based on the presented phylogenomic and physiological data, we propose three novel species, Erysipelothrix anatis sp. nov. with strain D17_0559-3-2-1T (=DSM 111258T= CIP 111884T=CCM 9044T) as type strain, Erysipelothrix aquatica sp. nov. with strain VA92-K48T (=DSM 106012T=LMG 30351T=CIP 111492T) as type strain and Erysipelothrix urinaevulpis sp. nov. with strain 165301687T (=DSM 106013T= LMG 30352T= CIP 111494T) as type strain.
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- Proteobacteria
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Bradyrhizobium cenepequi sp. nov., Bradyrhizobium semiaridum sp. nov., Bradyrhizobium hereditatis sp. nov. and Bradyrhizobium australafricanum sp. nov., symbionts of different leguminous plants of Western Australia and South Africa and definition of three novel symbiovars
More LessBradyrhizobium is a heterogeneous bacterial genus capable of establishing symbiotic associations with a broad range of legume hosts, including species of economic and environmental importance. This study was focused on the taxonomic and symbiovar definition of four strains – CNPSo 4026T, WSM 1704T, WSM 1738T and WSM 4400T – previously isolated from nodules of legumes in Western Australia and South Africa. The 16S rRNA gene phylogenetic tree allocated the strains to the Bradyrhizobium elkanii supergroup. The multilocus sequence analysis (MLSA) with partial sequences of six housekeeping genes – atpD, dnaK, glnII, gyrB, recA and rpoB – did not cluster the strains under study as conspecific to any described Bradyrhizobium species. Average nucleotide identity and digital DNA–DNA hybridization values were calculated for the four strains of this study and the closest species according to the MLSA phylogeny with the highest values being 95.46 and 62.20 %, respectively; therefore, both being lower than the species delineation cut-off values. The nodC and nifH phylogenies included strains WSM 1738T and WSM 4400T in the symbiovars retamae and vignae respectively, and also allowed the definition of three new symbiovars, sv. cenepequi, sv. glycinis, and sv. cajani. Analysis of morphophysiological characterization reinforced the identification of four novel proposed Bradyrhizobium species that are accordingly named as follows: Bradyrhizobium cenepequi sp. nov. (CNPSo 4026T=WSM 4798T=LMG 31653T), isolated from Vigna unguiculata; Bradyrhizobium semiaridum sp. nov. (WSM 1704T=CNPSo 4028T=LMG 31654T), isolated from Tephrosia gardneri; Bradyrhizobium hereditatis sp. nov. (WSM 1738T=CNPSo 4025T=LMG 31652T), isolated from Indigofera sp.; and Bradyrhizobium australafricanum sp. nov. (WSM 4400T=CNPSo 4015T=LMG 31648T) isolated from Glycine sp.
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Arsukibacterium indicum sp. nov., isolated from deep-sea sediment, and transfer of Rheinheimera tuosuensis and Rheinheimera perlucida to the genus Arsukibacterium as Arsukibacterium tuosuense comb. nov. and Arsukibacterium perlucidum comb. nov.
A Gram-stain-negative, aerobic, flagellated and rod-shaped bacterium, designated strain SM2107T, was isolated from a deep-sea sediment sample collected from the Southwest Indian Ocean. Strain SM2107T grew at 4–40 °C and with 0–10.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed casein, gelatin, chitin and DNA. The phylogenetic trees based on the 16S rRNA genes and single-copy orthologous clusters showed that strain SM2107T, together with Rheinheimera tuosuensis , Rheinheimera perlucida and Arsukibacterium ikkense , formed a separate clade, having the highest similarity to the type strain of Rheinheimera tuosuensis (98.3%). The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol and the major cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0, C17 : 1 ω8с and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The only respiratory quinone was Q-8. The genomic DNA G+C content of strain SM2107T was 48.8 %. The digital DNA–DNA hybridization values between strain SM2107T and type strains of Rheinheimera tuosuensis , Rheinheimera perlucida and Arsukibacterium ikkense were 41.16, 37.70 and 31.80 %, while the average amino acid identity values between them were 87.59, 86.76 and 83.64 %, respectively. Based on the polyphasic evidence presented in this study, strain SM2107T was considered to represent a novel species within the genus Arsukibacterium , for which the name Arsukibacterium indicum was proposed. The type strain is SM2107T (=MCCC M24986T=KCTC 82921T). Moreover, the transfer of Rheinheimera tuosuensis and Rheinheimera perlucida to the genus Arsukibacterium as Arsukibacterium tuosuense comb. nov. (type strain TS-T4T=CGMCC 1.12461T=JCM 19264T) and Arsukibacterium perlucidum comb. nov. (type strain BA131T=LMG 23581T=CIP 109200T) is also proposed.
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- Pseudomonadota
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Shewanella oncorhynchi sp. nov., a novel member of the genus Shewanella, isolated from Rainbow Trout (Oncorhynchus mykiss)
More LessA strain, S-1T was isolated from rainbow trout (Oncorhynchus mykiss) exhibiting clinical symptoms of lens atrophy, inappetence, visual impairment and growth retardation. The strain was identified as representing a member of the genus Shewanella on the basis of the results of 16S rRNA gene sequence analysis. The neighbor-joining phylogenetic tree based on 16S rRNA gene sequences indicated that S-1T clustered with Shewanella putrefaciens JCM 20190T, Shewanella profunda DSM 15900T, and Shewanella hafniensis P010T, sharing 99.3, 98.8 and 87.7% 16S rRNA gene similarities, respectively. A polyphasic taxonomic approach including phenotypic, chemotaxonomic, and genomic characterization was employed to ascertain the taxonomic position of S-1T within the genus Shewanella . The overall genome relatedness indices (OGRI) for S-1T compared with the most closely related type strains S. hafniensis ATCC BAA-1207T, Shewanella baltica NCTC 10735T, S. putrefaciens ATCC 8071T and S. profunda DSM 15900T were calculated as 40.8, 40.1, 28.5 and 27.3% for digital DNA–DNA hybridization (dDDH), and 91.6, 91.0, 86.3 and 85.1% for average nucleotide identity (ANI), respectively. OGRI values between S-1T and its close neighbours confirmed that the strain represents a novel species in the genus Shewanella .The DNA G+C content of the strain is 45.2%. Major fatty acids were C17 : 1ω8c, C15 : 0iso, and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The predominant polar lipids were phosphatidylethanolamine, phospholipid, amino-phospholipid and unidentified lipids. The major respiratory quinones were ubiquinone-8, ubiquinone-7 and menaquinone-7. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Shewanella oncorhynchi sp. nov. is proposed, with S-1T as the type strain (JCM 34183T= KCTC 82249T).
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- Proteobacteria
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Pseudomonas boanensis sp. nov., a bacterium isolated from river water used for household purposes in Boane District, Mozambique
A Gram-negative rod with a single polar flagellum was isolated from a freshwater reservoir used for household purposes in Boane District, near Maputo, Mozambique, and designated as strain DB1T. Growth was observed at 30–42 °C (optimum, 30–37 °C) and with 0.5–1.5 % NaCl. Whole-genome-, rpoD- and 16S rRNA-based phylogenies revealed this isolate to be distant from other Pseudomonas species with Pseudomonas resinovorans , Pseudomonas furukawaii and Pseudomonas lalkuanensis being the closest relatives. Phenotypic analyses of strain DB1T showed marked differences with respect to type strains P. resinovorans CCUG 2473T, P. lalkuanensis CCUG 73691T, P. furukawaii CCUG 75672T and Pseudomonas otiditis CCUG 55592T. Taken together, our results indicate that strain DB1T is a representative of a novel species within the genus Pseudomonas for which the name Pseudomonas boanensis is proposed. The type strain is DB1T (=CCUG 62977T=CECT 30359T).
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- Eukaryotic Micro-Organisms
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Moniliella aeria sp. nov., a novel yeast isolated from the air of a Wuliangye baijiu-making workshop
More LessDuring an investigation of the diversity of airborne yeasts in a famous Chinese baijiu fermentation workshop, two yeast strains were isolated from the air of the Wuliangye 501# baijiu-making workshop in Yibin, Sichuan Province, PR China and subjected to taxonomic analysis. The results of phylogenetic analysis of two regions of the rRNA gene cluster, the D1/D2 domains of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, indicated that these strains represented a novel species of the genus Moniliella distinct from closely related species. The similarity between the novel species and the most closely related known species, Moniliella dehoogii, was 94.1 % for the D1/D2 LSU rRNA gene (30 substitutions and 12 indels out of 556 bp) and 95.6 % for the ITS region (9 substitutions and 6 indels out of 475 bp). In contrast with M. dehoogii, this novel species was able to assimilate d-ribose, l-arabinose, d-arabinose, cellobiose, d-glucono-1,5-lactone, dl-lactate, citrate, 1,2-propanediol, 2,3-butanediol and ethanol but was unable to ferment raffinose or assimilate inulin. On the basis of the results of phylogenetic analysis and the physiological characteristics, these investigated strains represent a novel species of the genus Moniliella, for which the name Moniliella aeria sp. nov. is proposed. Its holotype is CGMCC 20235T, and the MycoBank number is MB840188.
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