- Volume 70, Issue 12, 2020
Volume 70, Issue 12, 2020
- New taxa
-
- Proteobacteria
-
-
Arenibacterium halophilum gen. nov., sp. nov., a halotolerant bacterium in the family Rhodobacteraceae isolated from a coastal sand dune
More LessA Gram-stain-negative, non-pigmented, non-spore-forming, motile, strictly aerobic bacterial strain, designated CAU 1492T, was isolated from a coastal sand dune and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1492T grew optimally at 30 °C, pH 7.0 and in 3 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence of CAU 1492T showed that it formed a distinct lineage within the family Rhodobacteraceae as a separate deep branch, with 96.8 % or lower sequence similarity values to representatives of the genera Marivita , Donghicola , Sulfitobacter , Marinovum , Phaeobacter , Primorskyibacter , Roseovarius and Aestuariihabitans . Strain CAU 1492T was closely related to Marivita geojedonensis DPG-138T (96.8 %), Donghicola eburneus SW-277T (96.7 %), Sulfitobacter porphyrae SCM-1T (96.7 %), Marinovum algicola FF3T (96.6 %) and Aestuariihabitans beolgyonensis BB-MW15T (96.4 %) based on 16S rRNA gene sequences. The major cellular fatty acids of strain CAU 1492T were cyclo-C19 : 0 ω8c and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The polar lipid pattern was composed of phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified aminolipid. The strain contained Q-10 as the sole respiratory quinone. The draft genome of strain CAU 1492T was 4.63 Mb with a DNA G+C content of 63.1 mol%. The genome includes 4292 protein-coding genes and a five rRNA operons. On the basis of the phenotypic, chemotaxonomic and genomic data, strain CAU 1492T represents a novel genus in the family Rhodobacteraceae for which the name Arenibacterium halophilum gen. nov., sp. nov. is proposed. The type strain of Arenibacterium halophilum is CAU 1492T (=KCTC 62998T=NBRC 113696T).
-
-
-
Orrella amnicola sp. nov., isolated from a freshwater river, reclassification of Algicoccus marinus as Orrella marina comb. nov., and emended description of the genus Orrella
More LessA novel Gram-negative, aerobic, non-motile, ovoid to rod-shaped bacterium, designated NBD-18T, was isolated from a freshwater river in Taiwan. Optimal growth occurred at 30 °C, at pH 6 and in the absence of NaCl. The predominant fatty acids of strain NBD-18T were C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C17 : 0 cyclo and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyldimethylethanolamine. The major polyamine was putrescine. The major isoprenoid quinone was Q-8. The genomic DNA G+C content of strain NBD-18T was 50.9 %. Strain NBD-18T was most closely related to Orrella dioscoreae LMG 29303T and Algicoccus marinus HZ20T at a 16S rRNA gene sequence similarity of 97.7 %. 16S rRNA gene sequence similarity between O. dioscoreae LMG 29303T and A. marinus HZ20T was 97.7 %. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set indicated that strain NBD-18T, O. dioscoreae LMG 29303T and A. marinus HZ20T are affiliated with the same genus. Digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values among these three strains supported that they belong to the same genus and that strain NBD-18T represents a novel species. Thus, A. marinus HZ20T should be reclassified as Orrella marina comb. nov. based on the rules for priority of publication and validation. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain NBD-18T represents a novel species in the genus Orrella , for which the name Orrella amnicola sp. nov. is proposed. The type strain is NBD-18T (=BCRC 81197T=LMG 31338T).
-
-
-
Noviherbaspirillum aerium sp. nov., isolated from air
More LessA Gram-stain-negative, strictly aerobic, non-spore-forming, rod-shaped, motile with polar flagella and pale-orange bacterium, designated strain 122213-3T, was isolated from air, collected at the foot of the Xiangshan Mountain, located in Beijing, PR China. Optimal growth occurred at 28 °C, at pH 7 and in the presence of 0–1 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that 122213-3T clustered with species of the genus Noviherbaspirillum and formed a distinct sublineage, showing highest similarities to Noviherbaspirillum malthae CC-AFH3T (96.88 %), Noviherbaspirillum massiliense JC206T (95.78 %) and Noviherbaspirillum aurantiacum SUEMI08T (95.78 %). The predominant cellular fatty acids were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The predominant quinone was ubiquinone 8 (Q-8). The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid and two unidentified polar lipids. The polyamine pattern showed the presence of putrescine as the major polyamine, with minor amounts of 2-hydroxyputrescine. The DNA G+C content was 60.1 mol%. The phylogenetic analysis and physiological and biochemical data showed that strain 122213-3T should be classified as representing a novel species in the genus Noviherbaspirillum , for which the name Noviherbaspirillum aerium sp. nov. is proposed. The type strain of N. aerium is 122213-3T (=CFCC 14286T=LMG 30131T).
-
-
-
Alteromonas ponticola sp. nov., a gammaproteobacterium isolated from seawater
More LessA Gram-stain-negative, aerobic, non-spore-forming, non-motile and ovoid or rod-shaped bacterial strain, MYP5T, was isolated from seawater in Jeju island of South Korea. MYP5T grew optimally at 30–35 °C and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that MYP5T fell within the clade enclosed by the type strains of species of the genus Alteromonas , clustering with the type strains of Alteromonas confluentis and Alteromonas halophila . MYP5T exhibited the highest 16S rRNA gene sequence similarity value (98.0 %) to the type strain of A. confluentis and similarities of 95.1–97.9 % to the type strains of the other species of the genus Alteromonas . ANI and dDDH values of genomic sequences between MYP5T and the type strains of 22 species of the genus Alteromonas were 66.8–70.5 % and 18.6–27.5 %, respectively. The DNA G+C content of MYP5T, determined from the genome sequence, was 46.1 %. MYP5T contained Q-8 as the predominant ubiquinone and C18 : 1 ω7c, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and 10-methyl C17 : 0 as the major fatty acids. The major polar lipids of MYP5T were phosphatidylethanolamine and phosphatidylglycerol. Distinguishing phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that MYP5T is separated from species of the genus Alteromonas . On the basis of the data presented, MYP5T is considered to represent a novel species of the genus Alteromonas , for which the name Alteromonas ponticola sp. nov. is proposed. The type strain is MYP5T (=KCTC 82144T=NBRC 114354T).
-
-
-
Pseudopontixanthobacter vadosimaris gen. nov., sp. nov., isolated from shallow sea near Kueishan Island
More LessA Gram-stain-negative and aerobic bacterial strain, designated as JL3514T, was isolated from surface water of the hydrothermal system around Kueishan Island. The isolate formed red colonies and cells were non-flagellated, rod-shaped and contained methanol-soluble pigments. Growth was observed at 10–50 °C (optimum, 30 °C), at pH 5.0–9.0 (optimum, pH 7.0) and in the presence of 0–9 % (w/v) NaCl (optimum, 2 %). Strain JL3514T was positive for catalase and weakly positive for oxidase. Results of 16S rRNA gene sequence analyses showed highest similarities to species in the family Erythrobacteraceae , namely Croceibacterium atlanticum (96.1 %), Pelagerythrobacter marensis (96.0 %), Tsuneonella rigui (96.0 %) and Altericroceibacterium xinjiangense (96.0 %). Phylogenetic analysis based on core gene sequences revealed that the isolate formed a distinct branch with the related species and it had a lower average amino acid identity value than the suggested threshold for genera boundaries. The major fatty acids (>5 %) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, C17 : 1 ω6c, C14 : 0 2-OH and C12 : 0. The dominant polar lipids comprised diphosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, glycolipid, two unidentified lipids and one unidentified phospholipid. The main respiratory quinones were ubiquinone-10 (95.7 %) and ubiquinone-9 (4.3 %). The DNA G+C content from the genome was 63.0 mol%. Based on the presented data, we consider strain JL3514T to represent a novel genus of the family Erythrobacteraceae , with the name Pseudopontixanthobacter vadosimaris gen. nov., sp. nov. The type strain is JL3514T (=KCTC 62623T=MCCC 1K03561T).
-
-
-
Pseudomonas lalkuanensis sp. nov., isolated from a bacterial consortia of contaminated soil enriched for the remediation of e-waste
A novel e-waste-degrading strain, PE08T, was isolated from contaminated soil collected from a paper mill yard in Lalkuan, Uttarakhand, India. Strain PE08T was Gram-stain-negative, rod-shaped, aerobic, oxidase-positive and catalase-positive. Optimum growth was observed at 30 °C (range, 5–40 °C), with 1–2 % NaCl (range, 0–3 %) and at pH 7 (range 6–11). The phylogeny based on 16S rRNA gene sequences delineated strain PE08T to the genus Pseudomonas and showed highest sequence similarity to Pseudomonas furukawaii KF707T (98.70 %), followed by Pseudomonas aeruginosa DSM 50071T (98.62 %) and Pseudomonas resinovorans DSM 21078T (97.93 %). The genome of strain PE08T was sequenced and had one scaffold of 6056953 bp, 99.84 % completeness and 182× coverage were obtained. The G+C content in the genome was 64.24 mol%. The DNA–DNA hybridization and average nucleotide identity values between strain PE08T and its closely related type strain, P. resinovorans DSM 21078T were below 34.8 % and 87.96 %, respectively. The phylogenetic analysis based on whole-genome sequence and concatenated GyrB and RpoB proteins revealed that strain PE08T forms a district clade in the family Pseudomonadaceae . The predominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 :1 ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The phenotypic, chemotaxonomic and genetic analysis, including overall genome relatedness index values, indicated that strain PE08T represents a novel species of the genus Pseudomonas , for which the name Pseudomonas lalkuanensis sp. nov. is proposed. The type strain is PE08T (=MCC 3792=KCTC 72454=CCUG 73691).
-
- Eukaryotic Micro-organisms
-
-
Clavispora santaluciae f.a., sp. nov., a novel ascomycetous yeast species isolated from grapes
During a study of yeast diversity in Azorean vineyards, four strains were isolated which were found to represent a novel yeast species based on the sequences of the internal transcribed spacer (ITS) region (ITS1-5.8S–ITS2) and of the D1/D2 domain of the large subunit (LSU) rRNA gene, together with their physiological characteristics. An additional strain isolated from Drosophila suzukii in Italy had identical D1/D2 sequences and very similar ITS regions (five nucleotide substitutions) to the Azorean strains. Phylogenetic analysis using sequences of the ITS region and D1/D2 domain showed that the five strains are closely related to Clavispora lusitaniae, although with 56 nucleotide differences in the D2 domain. Intraspecies variation revealed between two and five nucleotide differences, considering the five strains of Clavispora santaluciae. Some phenotypic discrepancies support the separation of the new species from their closely related ones, such as the inability to grow at temperatures above 35 °C, to produce acetic acid and the capacity to assimilate starch. Neither conjugations nor ascospore formation were observed in any of the strains. The name Clavispora santaluciae f.a., sp. nov., is proposed to accommodate the above noted five strains (holotype, CBS 16465T; MycoBank no., MB 835794).
-
- Research article
-
-
-
Culicoidibacter larvae gen. nov., sp. nov., from the gastrointestinal tract of the biting midge (Culicoides sonorensis) larva, belongs to a novel lineage Culicoidibacteraceae fam. nov., Culicoidibacterales ord. nov. and Culicoidibacteria classis nov. of the phylum Firmicutes
More LessStrain CS-1T, a novel facultative anaerobic bacterium, was isolated from the larval gastrointestinal tract of the biting midge, Culicoides sonorensis, a vector of the epizootic haemorrhagic disease virus and the bluetongue virus. Cells were Gram-stain-positive, non-motile, non-spore-forming, pleomorphic rods. Optimal growth occurred at pH 7.5 and 37 °C. The G+C content of the genomic DNA was 38.3 mol%, estimated by using HPLC. The dominant cellular fatty acids were C14 : 0 (45.9 %) and C16 : 0 (26.6 %). The polar lipid profile comprised glycolipids, diphosphatidylglycerol, phospholipids and phosphoglycolipids. Respiratory quinones were not detected. Strain CS-1T had very low 16S rRNA gene similarity to members of the phylum Firmicutes : Macrococcus canis KM45013T (85 % similarity) and Turicibacter sanguinis MOL361T (88 % similarity). Phylogenetic analysis based on 16S rRNA, rpoB, gyrB genes, and conserved protein sequences of the whole genome revealed that strain CS-1T was related to members of the classes Bacilli and Erysipelotrichia within the phylum Firmicutes . Furthermore, average nucleotide identity and digital DNA–DNA hybridization analyses of the whole genome revealed very low sequence similarity to species of Bacilli and Erysipelotrichaceae ( Macrococcus canis KM45013T and Turicibacter sp. H121). These results indicate that strain CS-1T belongs to the phylum Firmicutes and represents a new species of a novel genus, family, order and class. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, we propose the novel taxon Culicoidibacter larvae gen. nov., sp. nov. with the type strain CS-1T (=CCUG 71726T=DSM 106607T) within the hereby new proposed novel family Culicoidibacteraceae fam. nov., new order Culicoidibacaterales ord. nov. and new class Culicoidibacteria classis nov. in the phylum Firmicutes .
-
-
- Evolution, Phylogeny and Biodiversity
-
-
-
Sequence analysis of 16S rDNA, gyrB and alkB genes of plant-associated Rhodococcus species from Tunisia
More LessThe genus Rhodococcus contains several species with agricultural, biotechnological and ecological importance. Within this genus, many phyllosphere, rhizosphere and endosphere strains are plant growth promoting bacteria, whereas strains designated as R. fascians are plant pathogens. In this study, we isolated 47 Rhodococcus strains from a range of herbaceous and woody plant species. Phylogenetic analysis based on 16S rDNA, gyrB and alkB genes was used to compare our strains with type strains of Rhodococcus . For most of our strains, sequence similarity of the 16S rDNA, gyrB and alkB regions to type strains ranged from 98–100 %. Results of the concatenated gene sequence comparisons identified 18 strains of R. fascians and three strains of R. kroppenstedtii . The remaining strains were unclassified, and may represent novel species of Rhodococcus . Phylogenetic analysis based on gyrB sequences provided a more precise classification of our strains to species level than 16S rDNA sequences, whereas analysis of alkB sequences was unable to identify strains with orange-coloured colonies to species level.
-
-
-
-
Diversity of the ‘Candidatus Phytoplasma asteris’ and ‘Candidatus Phytoplasma fraxini’ isolates that infect urban trees in Bogotá, Colombia
More LessPhytoplasmas have been associated with a disease that affects trees of at least 11 species from different botanic families in Bogotá, Colombia. ‘Candidatus Phytoplasma asteris’ and ‘Candidatus Phytoplasma fraxini’ are the major groups of phytoplasma in the area of Bogotá. In this study, the genetic diversity within ‘Ca. P. asteris’ and ‘Ca. P. fraxini’ was studied in five urban tree species: Croton species (Euphorbiaceae), Fraxinus uhdei (Oleaceae), Magnolia grandiflora (Magnoliaceae), Populus nigra (Salicaceae) and Quercus humboldtii (Fagaceae). Analyses of the 16S rRNA gene using nested PCR, RFLP and sequencing showed that phytoplasmas of ‘Ca. P. asteris’ could be assigned to: subgroup 16SrI-B; a new subgroup named 16SrI-AF, with a restriction pattern similar to that of 16SrI-B; and a new subgroup named 16SrI-AG, with a restriction pattern similar to that of 16SrI-K and 16SrI-AH with a restriction pattern similar to that of 16SrI-AC. ‘Ca. P. fraxini’ isolates belonged to a new subgroup named 16SrVII-G, with a restriction pattern similar to that of 16SrVII-A. To complement the identification of the phytoplasma strains, we amplified nonribosomal genes such as leuS and secA. Unexpectedly, it was observed that in 16 trees in which 16S rRNA gene analysis showed the presence of ‘Ca. P. fraxini’ only, the leuS or secA primers amplified sequences exclusively affiliated to ‘Ca. P. asteris. In those plants, sequences belonging to ‘Ca. P. fraxini’ leuS or secA genes were not amplified. The present work contributes to the identification of novel strains of both species in Colombia, and supports previous suggestions that phytoplasmas in South America are highly variable.
-
- Taxonomic Note
-
-
-
Reclassification of Geobacillus galactosidasius and Geobacillus yumthangensis as Parageobacillus galactosidasius comb. nov. and Parageobacillus yumthangensis comb. nov., respectively
More LessMembers of the genus Geobacillus within the phylum Firmicutes are Gram-stain-positive, aerobic, endospore-forming, obligate thermophiles. In 2016, the genus Geobacillus was subdivided into two genera based on whole-genome approaches. The new genus, Parageobacillus , comprises five genomospecies. In this study, we recommend the reclassification of two Geobacillus species, Geobacillus galactosidasius and Geobacillus yumthangensis , into the genus Parageobacillus . We have applied whole genome approaches to estimate the phylogenetic relatedness among the 18 Geobacillus and Parageobacillus type strains for which genome sequences are currently publicly available. The phylogenomic metrics AAI (average amino acid identity), ANI (average nucleotide identity) and dDDH (digital DNA–DNA hybridization) denoted that the type strains of G. galactosidasius and G. yumthangensis belong to the genus Parageobacillus . Furthermore, a phylogeny based on comparison of the 16S rRNA gene sequences, recN gene sequences and core genes identified from the whole-genome analyses designated that the type strains of G. galactosidasius and G. yumthangensis belong in the genus Parageobacillus . With these findings, we consequently propose that G. galactosidasius and G. yumthangensis should be reclassified as Parageobacillus galactosidasius comb. nov. and Parageobacillus yumthangensis comb. nov.
-
-
-
-
Phylogenetic analysis supporting the taxonomic revision of eight genera within the bacterial order Enterobacterales
More LessThe diverse members of the Enterobacterales are agriculturally and medically relevant species that have continued to undergo taxonomic revision. To assess the current taxonomy of 64 genera of the Enterobacterales , we carried out a phylogenetic analysis using 32 single-copy core proteins. The resulting phylogeny was robust, and shows that eight genera – Biostraticola , Enterobacillus , Gibbsiella , Limnobaculum , Izhakiella , ‘Nissabacter’, Rosenbergiella and Samsonia – are currently assigned to incorrect families. Taxonomic reassignment of these genera was also supported by average amino acid identity comparisons. We propose taxonomic revision of these genera to reflect their phylogenetic position within the Enterobacterales .
-
- Erratum
-
-
-
Erratum: Robust demarcation of seventeen distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for emended genus Bacillus limiting it only to the members of the subtilis and cereus clades of species
More Less
-
-
- 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)