- Volume 73, Issue 5, 2023
Volume 73, Issue 5, 2023
- New Taxa
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- Pseudomonadota
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Parathalassolituus penaei gen. nov., sp. nov., a novel member of the family Oceanospirillaceae isolated from a coastal shrimp pond in Guangxi, PR China
A Gram-stain-negative, strictly aerobic, rod-shaped and motile bacterium with bipolar flagella, designated G-43T, was isolated from a surface seawater sample collected from an aquaculture in Guangxi, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain G-43T was most closely related to the family Oceanospirillaceae and distantly to the most closely related genera Venatorbacter and Thalassolituus (95.52 % and 94.45–94.76 % 16S rRNA gene sequence similarity, respectively), while similarity values to other Oceanospirillaceae type strains were lower than 94.0 %. Strain G-43T was found to grow at 4–30 °C (optimum, 25–28 °C), pH 6–9.0 (optimum, pH 7.0) and with 0–4.0 % NaCl (w/v; optimum at 2 % NaCl). Chemotaxonomic analysis of strain G-43T indicated that the sole respiratory quinone was ubiquinone-8, the predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), and the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, aminolipid, diphosphatidylglycerol, phospholipids and an unidentified lipid. The G+C content of the genomic DNA was 55.4 mol%. The phylogenetic, genotypic, phenotypic and chemotaxonomic data demonstrate that strain G-43T represents a novel species in a novel genus within the family Oceanospirillaceae , for which the name Parathalassolituus penaei gen. nov., sp. nov. is proposed. Strain G-43T (=KCTC 72750T= CCTCC AB 2022321T) is the type and only strain of Parathalassolituus penaei.
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Photorhabdus aballayi sp. nov. and Photorhabdus luminescens subsp. venezuelensis subsp. nov., isolated from Heterorhabditis amazonensis entomopathogenic nematodes
Six Gram-negative, rod-shaped bacterial strains isolated from Heterorhabditis amazonensis entomopathogenic nematodes were characterized to determine their taxonomic position. 16S rRNA and gyrB gene sequences indicate that they belong to the class Gammaproteobacteria , family Morganellaceae and genus Photorhabdus , and that some of them are conspecifics. Two of them, APURET and JART, were selected for further molecular characterization using whole genome- and whole-proteome-based phylogenetic reconstructions and sequence comparisons. Phylogenetic reconstructions using whole genome and whole proteome sequences show that strains APURET and JART are closely related to Photorhabdus luminescens subsp. luminescens ATCC 29999T and to P. luminescens subsp. mexicana MEX47-22T. Moreover, digital DNA–DNA hybridization (dDDH) values between APURET and P. luminescens subsp. luminescens ATCC 29999T, APURET and P. luminescens subsp. mexicana MEX47-22T, and APURET and JART are 61.6, 61.2 and 64.1 %, respectively. These values are below the 70 % divergence threshold that delimits prokaryotic species. dDDH scores between JART and P. luminescens subsp. luminescens ATCC 29999T and between JART and P. luminescens subsp. mexicana MEX47-22T are 71.9 and 74.8 %, respectively. These values are within the 70 and 79 % divergence thresholds that delimit prokaryotic subspecies. Based on these genomic divergence values, APURET and JART represent two different taxa, for which we propose the names: Photorhabdus aballayi sp. nov. with APURET (=CCM 9236T =CCOS 2019T) as type strain and Photorhabdus luminescens subsp. venezuelensis subsp. nov. with JART (=CCM 9235T =CCOS 2021T) as type strain. Our study contributes to a better understanding of the biodiversity of an important bacterial group with enormous biotechnological and agricultural potential.
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Gymnodinialimonas phycosphaerae sp. nov., a phycosphere bacterium isolated from Karlodinium veneficum
A facultative anaerobic, Gram-negative, non-motile, rod-shaped bacterial strain, designated N5T, was obtained from the phycosphere microbiota of the marine planktonic dinoflagellate, Karlodinium veneficum. Strain N5T showed growth on marine agar at 25 °C, pH 7 and 1 % (w/v) NaCl and produced a yellow colour. According to a phylogenetic study based on 16S rRNA gene sequences, strain N5T has a lineage within the genus Gymnodinialimonas . The G+C content in the genome of strain N5T is 62.9 mol% with a total length of 4 324 088 bp. The NCBI Prokaryotic Genome Annotation Pipeline revealed that the N5T genome contained 4230 protein-coding genes and 48 RNA genes, including a 5S rRNA, 16S rRNA, 23S rRNA, 42 tRNA, and three ncRNAs. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus Gymnodinialimonas . The predominant fatty acids were C19 : 0 cyclo ω8c and feature 8 (comprising C18 : 1 ω6c and/or C18 : 1 ω7c). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The main respiratory quinone was Q-10. Based on its phenotypic, phylogenetic, genomic and chemotaxonomic features, strain N5T represents a novel species of the genus Gymnodinialimonas , for which the name Gymnodinialimonas phycosphaerae sp. nov. is proposed. The type strain is N5T (=KCTC 82362T=NBRC 114899T).
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Dyella humicola sp. nov., Dyella subtropica sp. nov., Dyella silvatica sp. nov. and Dyella silvae sp. nov., isolated from subtropical forest soil
More LessFour novel bacterial strains, designated RBB1W86T, RXD159T, RBB189T and RLT163T, were isolated from subtropical forest soil of the Nanling National Nature Reserve located in Guangdong Province, PR China. 16S rRNA gene phylogeny indicated their affiliation to the genus Dyella , among which strains RBB1W86T and RXD159T were closely related to Dyella halodurans CGMCC 1.15435T with 16S rRNA gene sequence similarities of 98.8 and 99.5 %, respectively, and strains RBB189T and RLT163T were closely related to Dyella tabacisoli CGMCC 1.16273T (98.8 %) and Dyella japonica JCM 21530T (99.4 %), respectively. Phylogenomic analysis based on 92 core genes showed consistent phylogeny with the 16S rRNA gene phylogeny for strains RBB1W86T, RBB189T and RLT163T, while strain RXD159T showed a closer relationship with D. tabacisoli CGMCC 1.16273T and strain RBB189T. The genome-derived average nucleotide identity (ANI) values between the newly isolated strains and their closely related species were 70.18‒90.20 %, and the corresponding digital DNA–DNA hybridization (dDDH) values were 20.80‒40.30 %. Meanwhile, the ANI and dDDH values between each pair of the newly isolated strains were 75.80‒79.77 % and 21.30‒23.30 %, respectively. They all took iso-C15 : 0 and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1 ω9c) as the major fatty acids. Moreover, C16 : 0, iso-C16 : 0, iso-C17 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) were also variously distributed as major components. They all took ubiquinone 8 as the only predominant respiratory quinone and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the major polar lipids. Phosphatidylmethylethanolamine was only present in strain RBB189T as another major component. Based on the results of phenotypic, genotypic and chemotaxonomic analyses, the newly isolated strains could be clearly distinguished from their closely related species and should represent four distinct novel species of the genus Dyella , for which the names Dyella humicola sp. nov. (type strain RBB1W86T=GDMCC 1.1901T=KACC 21988T), Dyella subtropica sp. nov. (type strain RXD159T=GDMCC 1.1902T=KACC 21989T), Dyella silvatica sp. nov. (type strain RBB189T=GDMCC 1.1900T=KACC 21990 T) and Dyella silvae sp. nov. (type strain RLT163T=GDMCC 1.1916T=KACC 21991T) are proposed.
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A novel strictly anaerobic sulfate-reducing diazotrophic bacterium Fundidesulfovibrio terrae sp. nov., isolated from paddy soil
More LessA strictly anaerobic sulfate-reducing strain, designated SG127T, was isolated from paddy soil. SG127T showed the highest 16S rRNA gene sequence similarity to the type strain of Fundidesulfovibrio magnetotacticus (98.2 %). A phylogenetic tree based on 16S rRNA gene sequences indicated that SG127T clustered with members of the genus Fundidesulfovibrio . Growth of SG127T was observed at 20–37 °C (optimum, 30 °C), pH 5.5–9.0 (optimum, 7.0–8.0) and with 0–0.2 % (w/v) NaCl (optimally without NaCl). SG127T contained MK-7 as the only menaquinone and anteiso-C15 : 0, anteiso-C17 : 1ω9c, C18 : 0, iso-C14 : 0, iso-C15 : 0, iso-C16:0, iso-C16 : 1H, iso-C18 : 1H and summed feature nine as the major fatty acids. The genomic DNA G+C content of SG127T was 64.6 %. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between SG127T and the closely related Fundidesulfovibrio magnetotacticus were 78.5% and 23.2 %, respectively, which were lower than the cut-off values (ANI 95–96% and dDDH 70 %) for prokaryotic species delineation. SG127T had desulfoviridin, possessed nitrogen fixation genes (nifHDK) and actively fixed nitrogen according to the acetylene reduction assay. On the basis of these results, strain SG127T represents a novel species of the genus Fundidesulfovibrio , for which the name Fundidesulfovibrio terrae sp. nov. is proposed. The type strain is SG127T (= GDMCC 1.3137T = JCM 35589T).
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Characterization of four novel bacterial species of the genus Sphingomonas, Sphingomonas anseongensis, Sphingomonas alba, Sphingomonas brevis and Sphingomonas hankyongi sp.nov., isolated from wet land
More LessFour novel bacterial strains, designated as RG327T, SE158T, RB56-2T and SE220T, were isolated from wet soil in the Republic of Korea. To determine their taxonomic positions, the strains were fully characterized. On the basis of genomic information (16S rRNA gene and draft genome sequences), all four isolates represent members of the genus Sphingomonas . The draft genomes of RG327T, SE158T, RB56-2T and SE220T consisted of circular chromosomes of 2 226 119, 2 507 338, 2 593 639 and 2 548 888 base pairs with DNA G+C contents of 64.6, 63.6, 63.0 and 63.1 %, respectively. All the isolates contained ubiquinone Q-10 as the predominant quinone compound and a fatty acid profile with C16 : 0, C17 : 1ω6c, C18 : 1 2-OH, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) as the major fatty acids, supporting the affiliation of strains RG327T, SE158T, RB56-2T and SE220T to the genus Sphingomonas . The major identified polar lipids in all four novel isolates were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Moreover, the physiological, biochemical results and low level of DNA–DNA relatedness and average nucleotide identity values allowed the phenotypic and genotypic differentiation of RG327T, SE158T, RB56-2T and SE220T from other species of the genus Sphingomonas with validly published names and indicated that they represented novel species of the genus Sphingomonas , for which the names Sphingomonas anseongensis sp. nov. (RG327T = KACC 22409T = LMG 32497T), Sphingomonas alba sp. nov. (SE158T = KACC 224408T = LMG 324498T), Sphingomonas brevis (RB56-2T = KACC 22410T = LMG 32496T) and Sphingomonas hankyongi sp. nov., (SE220T = KACC 22406T = LMG 32499T) are proposed.
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Arcobacter roscoffensis sp. nov., a marine bacterium isolated from coastal seawater
More LessA novel Gram-negative, aerobic, motile, rod-shaped, beige-pigmented bacterium, strain ARW1-2F2T, was isolated from a seawater sample collected from Roscoff, France. Strain ARW1-2F2T was catalase-negative and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA sequences revealed that strain ARW1-2F2T was closely related to Arcobacter lekithochrous LFT 1.7T and Arcobacter caeni RW17-10T(95.8 and 95.5 % gene sequence similarity, respectively). The genome of strain ARW1-2F2T was sequenced and had a G+C content of 28.7%. Two different measures of genome similarity, average nucleotide identity based on blast and digital DNA–DNA hybridization, indicated that strain ARW1-2F2T represents a new Arcobacter species. The predominant fatty acids were C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω7c/C18 : 1 ω6c. The results of a polyphasic analysis supported the description of strain ARW1-2F2T as representing a novel species of the genus Arcobacter , for which the name Arcobacter roscoffensis sp. nov. is proposed with the type strain ARW1-2F2T (DSM 29169T=KCTC 52423T).
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Novosphingobium mangrovi sp. nov., isolated from mangrove sediment
More LessA novel Gram-stain-negative, aerobic and rod-shaped bacterial strain, designated as HK4-1T, was isolated from mangrove sediments in Hong Kong, PR China. Based on 16S rRNA gene sequence data, strain HK4-1T was found to belong to the genus Novosphingobium , family Erythrobacteraceae , and showed high similarity to Novosphingobium chloroacetimidivorans BUT-14T (96.88 %) and Novosphingobium indicum H25T (96.88 %). The G+C content of the whole genome of strain HK4-1T was 64.05 mol%. The major fatty acids were C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and two unknown lipids. The predominant respiratory quinone was Q-10. Based on genomic, phylogenetic, phenotypic, physiological and chemotaxonomic data, strain HK4-1T should be classified as representing a novel species of the genus Novosphingobium , for which the name Novosphingobium mangrovi sp. nov. is proposed. The type strain of Novosphingobium mangrovi sp. nov. is HK4-1T (=MCCC 1K08252T=JCM 35764T).
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Physiological and genomic analyses of cobalamin (vitamin B12)-auxotrophy of Lysobacter auxotrophicus sp. nov., a methionine-auxotrophic chitinolytic bacterium isolated from chitin-treated soil
More LessA novel bacterium, designated 5-21aT, isolated from chitin-treated upland soil, exhibits methionine (Met) auxotrophy and chitinolytic activity. A physiological experiment revealed the cobalamin (synonym, vitamin B12)(Cbl)-auxotrophic property of strain 5-21aT. The newly determined complete genomic sequence indicated that strain 5-21aT possesses only the putative gene for Cbl-dependent Met synthase (MetH) and lacks that for the Cbl-independent one (MetE), which implies the requirement of Cbl for Met-synthesis in strain 5-21aT. The set of genes for the upstream (corrin ring synthesis) pathway of Cbl synthesis is absent in the genome of strain 5-21aT, which explains the Cbl-auxotrophy of 5-21aT. This strain was characterized via a polyphasic approach to determine its taxonomic position. The nucleotide sequences of two copies of the 16S rRNA gene of strain 5-21aT indicated the highest similarities to Lysobacter soli DCY21T(99.8 and 99.9 %) and Lysobacter panacisoli CJ29T(98.7 and 98.8 %, respectively), whose Cbl-auxotrophic properties were revealed in this study. The principal respiratory quinone was Q-8. The predominant cellular fatty acids were iso-C15:0, iso-C16:0 and iso-C17:1 ω9c. The complete genome sequence of strain 5-21aT revealed that the genome size was 4 155 451 bp long and the G+C content was 67.87 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain 5-21aT and its most closely phylogenetic relative L. soli DCY21T were 88.8 and 36.5%, respectively. Based on genomic, chemotaxonomic, phenotypic and phylogenetic data, strain 5-21aT represents a novel species in the genus Lysobacter , for which the name Lyobacter auxotrophicus sp. nov. is proposed. The type strain is 5-21aT (=NBRC 115507T=LMG 32660T).
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Rhizobium acaciae sp. nov., a new nitrogen-fixing symbiovar isolated from root nodules of Acacia saligna in Tunisia
Three bacterial strains, 1AS11T, 1AS12 and 1AS13, members of the new symbiovar salignae and isolated from root nodules of Acacia saligna grown in Tunisia, were characterized using a polyphasic approach. All three strains were assigned to the Rhizobium leguminosarum complex on the basis of rrs gene analysis. Phylogenetic analysis based on 1734 nucleotides of four concatenated housekeeping genes (recA, atpD, glnII and gyrB) showed that the three strains were distinct from known rhizobia species of the R. leguminosarum complex and clustered as a separate clade within this complex. Phylogenomic analysis of 92 up-to-date bacterial core genes confirmed the unique clade. The digital DNA–DNA hybridization and blast-based average nucleotide identity values for the three strains and phylogenetically related Rhizobium species ranged from 35.9 to 60.0% and 87.16 to 94.58 %, which were lower than the 70 and 96% species delineation thresholds, respectively. The G+C contents of the strains were 60.82–60.92 mol% and the major fatty acids (>4 %) were summed feature 8 (57.81 %; C18 : 1 ω7c) and C18 : 1 ω7c 11-methyl (13.24%). Strains 1AS11T, 1AS12 and 1AS13 could also be differentiated from their closest described species (Rhizobium indicum, Rhizobium laguerreae and Rhizobium changzhiense ) by phenotypic and physiological properties as well as fatty acid content. Based on the phylogenetic, genomic, physiological, genotypic and chemotaxonomic data presented in this study, strains 1AS11T, 1AS12 and 1AS13 represent a new species within the genus Rhizobium and we propose the name Rhizobium acaciae sp. nov. The type strain is 1AS11T (=DSM 113913T=ACCC 62388T).
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Stakelama marina sp. nov., isolated from seawater of the Tangyin hydrothermal field in the Okinawa Trough
More LessA Gram-stain-negative, strictly aerobic, rod-shaped and non-flagellated marine bacterium, designated strain LXI357T, was isolated from deep-sea water sampled at the Tangyin hydrothermal field in the Okinawa Trough. The growth temperature range was 20–45 °C (optimum, 28 °C). Strain LXI357T was also able to grow at pH 5.0–7.5 (optimum, pH 6.0–7.0) and in the presence of 0.5–11 % (optimum, 7%, w/v) NaCl. Strain LXI357T was oxidase-negative and catalase-positive. The predominant fatty acids were C18 : 1 ω7c and C16 : 0. The major polar lipids of strain LXI357T contained phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phospholipid, sphingoglycolipid, diphosphatidylglycero and an unidentified aminolipid. Based on the results of 16S rRNA gene sequence analysis, strain LXI357T belonged to the genus Stakelama and was most closely related to Stakelama flava CBK3Z-3T (96.28%, 16S rRNA gene sequence similarity), followed by Stakelama algicida Yeonmyeong 1-13T (95.67%), Stakelama pacifica JLT832T (95.46%) and Sphingosinicella vermicomposti YC7378T (95.43%). Genome relatedness between strain LXI357T and Stakelama flava CBK3Z-3T was computed using average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity, with values of 76.02, 20.9 and 71.1 %, respectively. The genomic DNA G+C content of strain LXI357T is 64.1 mol%. In addition, strain LXI357T has multiple genes related to sulphur metabolism, including genes encoding for the Sox system. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished strain LXI357T from its closest phylogenetic neighbours. According to the results of polyphasic analyses, strain LXI357T is considered to represent a novel species of the genus Stakelama , for which the name Stakelama marina sp. nov. is proposed. The type strain is LXI357T (=MCCC 1K06076T=KCTC 82726T).
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Opacimonas viscosa gen. nov., sp. nov., a novel bacterium isolated from phycosphere
More LessA novel strain of a member of the family Alteromonadaceae was isolated from the phycosphere of a diatom and designated as LMIT007T. LMIT007T could form milk-white, opaque, circular and smooth colonies on 2216E marine agar. LMIT007T cells were around 1.0–1.8 µm long, 0.8–1.8 µm wide, round or oval shaped and had polar flagella but were non-motile. Optimum conditions for growth were 25 °C, pH 7.0 and 6 % (w/v) NaCl. The results of 16S rRNA gene-based analysis indicated that LMIT007T had the highest similarity with the type strains Aestuaribacter halophilus JC2043T (95.95 %), Alteromonas lipolytica JW12T (95.60 %) and Alteromonas halophila KCTC 22164T (94.21 %). Furthermore, the results of phylogenetic analysis based on 16S rRNA gene sequences and of phylogenomic analysis indicated that LMIT007T could be clustered into the family Alteromonadaceae but formed a separate branch. The genome size of the strain was 2.95 Mbp and the DNA G+C content was 41.6 %. The average nucleotide identity (ANI) values of orthologous genes between LMIT007T and species of other closely related genera within the family Alteromonadaceae ranged from 66.9 to 69.2 %, and the average amino acid identity (AAI) values ranged from 60.0 to 65.7 %. The main respiratory quinone was ubiquinone-8. The major fatty acids were summed feature 3 (C16 : 1ω7c / C16 : 1ω6c) and C16 : 0. The polar lipid profile contain phosphatidylethanolamine, phosphatidylglycerol, aminolipid, two phospholipid and an unknown polar lipid. On the basis of the results of the polyphasic analysis, strain LMIT007T is suggested to represent a novel genus and species within the family Alteromonadaceae , for which the name Opacimonas viscosa gen. nov., sp. nov. is proposed. The type strain is LMIT007T (=MCCC 1K08161T=KCTC 92597T).
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Leeia speluncae sp. nov., isolated from Stegodon Sea Cave in Thailand
More LessA novel Gram-stain-negative, obligately aerobic, short rod-shaped and motile bacterium, designated strain BC00092T, was isolated from brackish ground water collected in Stegodon Sea Cave located at Satun UNESCO Global Geopark, Satun Province, Thailand. The phylogenetic analysis of BC00092T based on 16S rRNA gene sequences revealed that the strain represented a member of the genus Leeia and was closely related to Leeia oryzae DSM 17879T (96.68 %) and Leeia aquatica IMCC25680T (94.89 %). The average nucleotide identity and digital DNA–DNA hybridization values calculated from the whole-genome sequences between BC00092T and closely related type strains of species within the family Leeiaceae were lower than the species demarcation threshold values of 95 and 70 %, respectively. Moreover, five conserved signature indels of members of the family Leeiaceae were found in the protein sequences from the annotated assembled genome of BC00092T. According to the results of the polyphasic taxonomic study, strain BC00092T represents a novel species within the genus Leeia , for which the name Leeia speluncae sp. nov. is proposed. The type strain is BC00092T (TBRC 13508T = KCTC 92111T).
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Thermomonas mangrovi sp. nov., isolated from soil of a mangrove nature reserve
More LessA Gram-stain-negative, non-motile, aerobic and ovoid-rod-shaped bacterial strain, designated as 2C3345T, was isolated from soil of a mangrove nature reserve in Shenzhen, PR China and its taxonomic position was investigated. The 16S rRNA gene sequence of strain 2C3345T exhibited the highest similarity value to that of the type strains Thermomonas aquatica NBRC 113114T (98.4 %), Thermomonas carbonis KCTC 42013T (98.1 %), Thermomonas brevis DSM 15422T (98.0 %) and Thermomonas haemolytica DSM 13605T (97.9 %). Strain 2C3345T grew optimally at 28–30 °C, pH 7.0 and without NaCl. The predominant ubiquinone in 2C3345T was identified as Q-8. The major fatty acids of 2C3345T were iso-C15 : 0, iso-C16 : 0 and summed feature 9 (is0-C17:1ω9c and/or 10-methyl C16:0). The major polar lipids of 2C3345T were phosphatidylcholine (PC), phosphatidylglycerol (PG), diphosphatidglycerol (DPG), phosphatidylethanolamine (PE), an unidentified phospholipid, an unidentified aminolipid and two unidentified lipids. The DNA G+C content of strain 2C3345T was 69.9 %. The draft genome sequence of 2C3345T included 2 888 645 bp in total (N50 =310 730 bp) with a medium read coverage of 388.6×and 21 scaffolds. In silico DNA–DNA hybridisation with type strains of species of the genus Thermomonas showed 24.4, 22.4, 24.1 and 23.2% relatedness to T. aquatica NBRC 113114T, T. carbonis KCTC 42013T, T. brevis DSM 15422T and T. haemolytica DSM 13605T, respectively. And the average nucleotide identity by blast (ANIb) values between 2C3345T and these four reference strains were 81.9, 80.0, 81.2 and 80.6 %, respectively, lower than the 95–96% threshold value for dividing prokaryotic species. On the basis of its phenotypic, chemotaxonomic, phylogenetic and phylogenomic properties, strain 2C3345T is considered to represent a novel species within the genus Thermomonas , for which the name Thermomonas mangrovi sp. nov. is proposed. The type strain is 2C3345T (=KCTC 92730T =MCCC 1K08335T).
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Sphingomonas lycopersici sp. nov., isolated from tomato rhizosphere soil
More LessTwo aerobic, Gram-stain-negative, non-motile and non-spore-forming rods bacterial strains, designated MMSM20T and MMSM24, were isolated from tomato rhizosphere soil and could produce indole-3-acetic acid and siderophore. Phylogenetic analyses based on 16S rRNA gene sequences and 92 core genes showed that strains MMSM20T and MMSM24 belonged to the genus Sphingomonas and were most closely related to three validly published species Sphingomonas jeddahensis G39T, Sphingomonas mucosissima DSM 17494T and Sphingomonas dokdonensis DSM 21029T. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strains MMSM20T and MMSM24 were 97.6 and 81.0 %, respectively, demonstrating that they were conspecific. The ANI and dDDH values between the two strains and the three type strains above were below the threshold values for species delimitation. The genomic DNA G+C contents of strains MMSM20T and MMSM24 were 66.6 and 66.4 mol%, respectively. The major fatty acids of the two strains were identified as C14 : 0 2OH, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c); the predominant quinone was ubiquinone 10; the polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and unidentified lipids. Results of phenotypic and genotypic analyses supported that strains MMSM20T and MMSM24 represent a novel species of the genus Sphingomonas , for which the name Sphingomonas lycopersici sp. nov. is proposed. The type strain is MMSM20T (=GDMCC 1.3401T=JCM 35647T).
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- Eukaryotic Micro-Organisms
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Kodamaea samutsakhonensis f.a., sp. nov., a novel ascomycetous yeast species isolated from wild mushrooms in Thailand
Two strains of genus Kodamaea, representing a novel anamorphic yeast species, were isolated from two samples of Marasmiellus sp. collected in Thailand. Analysis of the sequences of the internal transcribed spacer (ITS) regions and the D1/D2 domains of the large subunit (LSU) rRNA gene showed that the two strains differed by 27–42 nucleotide substitutions in the D1/D2 domains of the LSU rRNA gene and 7–34 nucleotide substitutions in the ITS region of a group of related species, Kodamaea smagusa CBS 11430T, Kodamaea fungicola JCM 10142T, Kodamaea plutei ATCC MYA-4329T, Kodamaea lidongshanica SD5S01T and Kodamaea jinghongensis NYNU 167162T. Phylogenetic analysis based on the concatenated sequences of the ITS and the D1/D2 domains of the LSU rRNA gene showed that the two strains were placed in the Kodamaea clade and clearly separated from other recognized species of the genus. Therefore, the two strains were assigned as a novel species of the genus Kodamaea, for which we propose the name Kodamaea samutsakhonensis f.a., sp. nov. The holotype is TBRC 16043T (=DMKU-BP19T) and the isotype is PYCC 9354. The MycoBank number of the novel species is MB 846490.
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Cystofilobasidium josepaulonis sp. nov., a novel basidiomycetous yeast species
More LessA yeast strain belonging to the basidiomycetous yeast genus Cystofilobasidium was isolated from a marine sediment sample collected in an intertidal zone in Shandong province, PR China. The results of phylogenetic analyses based on sequences of the D1/D2 domain of the 26S ribosomal RNA gene and the internal transcribed spacer (ITS) region indicate that this strain, together with three other strains isolated from basal ice collected in Norway, the gut of an insect and an alga collected in Russia, represent a novel species of the genus, for which the name Cystofilobasidium josepaulonis sp. nov. (holotype strain CGMCC 2.6672T) is proposed. The novel species differs from the known species of the genus Cystofilobasidium by 1.7 %–4.1 and 11.3 %–17.1 % mismatches in the D1/D2 domain and the ITS region, respectively. This species forms teliospores on potato dextrose agar (PDA) and 10 % V8 juice agar, but teliospore germination with basidia was not observed.
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Testudinimyces gracilis gen. nov, sp. nov. and Astrotestudinimyces divisus gen. nov, sp. nov., two novel, deep-branching anaerobic gut fungal genera from tortoise faeces
More LessThe anaerobic gut fungi (AGF, Neocallimastigomycota) represent a basal zoosporic phylum within the kingdom Fungi. Twenty genera are currently described, all of which were isolated from the digestive tracts of mammalian herbivores. Here, we report on the isolation and characterization of novel AGF taxa from faecal samples of tortoises. Twenty-nine fungal isolates were obtained from seven different tortoise species. Phylogenetic analysis using the D1/D2 region of the LSU rRNA gene, ribosomal internal transcribed spacer 1, and RNA polymerase II large subunit grouped all isolates into two distinct, deep-branching clades (clades T and B), with a high level of sequence divergence to their closest cultured relative (Khoyollomyces ramosus). Average amino acid identity values calculated using predicted peptides from the isolates’ transcriptomes ranged between 60.80–66.21 % (clade T), and 61.24–64.83 % (clade B) when compared to all other AGF taxa; values that are significantly below recently recommended thresholds for genus (85%) and family (75%) delineation in the Neocallimastigomycota. Both clades displayed a broader temperature growth range (20–45 °C, optimal 30 °C for clade T, and 30–42 °C, optimal 39 °C for clade B) compared to all other AGF taxa. Microscopic analysis demonstrated that strains from both clades produced filamentous hyphae, polycentric rhizoidal growth patterns, and monoflagellated zoospores. Isolates in clade T were characterized by the production of unbranched, predominantly narrow hyphae, and small zoospores, while isolates in clade B were characterized by the production of multiple sporangiophores and sporangia originating from a single central swelling resulting in large multi-sporangiated structures. Based on the unique phylogenetic positions, AAI values, and phenotypic characteristics, we propose to accommodate these isolates into two novel genera (Testudinimyces and Astrotestudinimyces), and species (T. gracilis and A. divisus) within the order Neocallimastigales. The type species are strains T130AT (T. gracilis) and B1.1T (A. divisus).
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- Combined Taxa
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Proposal of Eoetvoesiella gen. nov., Paludihabitans gen. nov., Rivihabitans gen. nov. and Salella gen. nov. as replacement names for the illegitimate prokaryotic generic names Eoetvoesia, Paludicola, Rivicola and Sala, respectively
More LessThe prokaryotic generic names Eoetvoesia Felföldi et al. 2014, Paludicola Li et al. 2017, Rivicola Sheu et al. 2014 and Sala Song et al. 2023 are illegitimate because they are later homonyms of the genus names Eoetvoesia Schulzer et al. 1866 (Ascomycota), Paludicola Wagler 1830 (Amphibia) and Paludicola Hodgson 1837 (Aves), Rivicola Fitzinger 1833 (Mollusca) and Sala Walker 1867 (Hemiptera) and the subgenus name Sala Ross 1937 (Hymenoptera), respectively (Principle 2 and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic names Eoetvoesiella, Paludihabitans, Rivihabitans and Salella, with type species Eoetvoesiella caeni, Paludihabitans psychrotolerans, Rivihabitans pingtungensis and Sallella cibi, respectively.
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- Methods
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AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species
More LessTaxon-specific conserved signature indels (CSIs) in genes/proteins provide reliable molecular markers (synapomorphies) for unambiguous demarcation of taxa of different ranks in molecular terms and for genetic, biochemical and diagnostic studies. Because of their predictive abilities, the shared presence of known taxon-specific CSIs in genome sequences has proven useful for taxonomic purposes. However, the lack of a convenient method for identifying the presence of known CSIs in genome sequences has limited their utility for taxonomic and other studies. We describe here a web-based tool/server (AppIndels.com) that identifies the presence of known and validated CSIs in genome sequences and uses this information for predicting taxonomic affiliation. The utility of this server was tested by using a database of 585 validated CSIs, which included 350 CSIs specific for ≈45 Bacillales genera, with the remaining CSIs being specific for members of the orders Neisseriales , Legionellales and Chlorobiales , family Borreliaceae , and some Pseudomonadaceae species/genera. Using this server, genome sequences were analysed for 721 Bacillus strains of unknown taxonomic affiliation. Results obtained showed that 651 of these genomes contained significant numbers of CSIs specific for the following Bacillales genera/families: Alkalicoccus , ‘Alkalihalobacillaceae’, Alteribacter , Bacillus Cereus clade, Bacillus Subtilis clade, Caldalkalibacillus , Caldibacillus , Cytobacillus , Ferdinandcohnia, Gottfriedia , Heyndrickxia , Lederbergia , Litchfieldia , Margalitia , Mesobacillus , Metabacillus , Neobacillus , Niallia , Peribacillus , Priestia , Pseudalkalibacillus , Robertmurraya , Rossellomorea , Schinkia , Siminovitchia , Sporosarcina , Sutcliffiella , Weizmannia and Caryophanaceae . Validity of the taxon assignment made by the server was examined by reconstructing phylogenomic trees. In these trees, all Bacillus strains for which taxonomic predictions were made correctly branched with the indicated taxa. The unassigned strains likely correspond to taxa for which CSIs are lacking in our database. Results presented here show that the AppIndels server provides a useful new tool for predicting taxonomic affiliation based on shared presence of the taxon-specific CSIs. Some caveats in using this server are discussed.
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Volumes and issues
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Volume 74 (2024)
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