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Volume 71,
Issue 1,
2020
Volume 71, Issue 1, 2020
- New Taxa
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- Proteobacteria
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Pseudomonas cremoris sp. nov., a novel proteolytic species isolated from cream
During a study investigating the microbiota of raw milk and its semi-finished products, strains WS 5106T and WS 5096 were isolated from cream and skimmed milk concentrate. They could be assigned to the genus Pseudomonas by their 16S rRNA sequences, but not to any validly named species. In this work, a polyphasic approach was used to characterize the novel strains and to investigate their taxonomic status. Examinations based on the topology of core genome phylogenomy as well as average nucleotide identity (ANIm) comparisons suggested a novel Pseudomonas species within the Pseudomonas fluorescens subgroup. With pairwise ANIm values of 90.1 and 89.8 %, WS 5106T was most closely related to Pseudomonas nabeulensis CECT 9765T and Pseudomonas kairouanensis CECT 9766T. The G+C content of strain WS 5106T was 60.1 mol%. Morphologic analyses revealed Gram-stain-negative, aerobic, catalase and oxidase positive, rod-shaped and motile cells. Proteolysis on skimmed milk agar as well as lipolysis on tributyrin agar occurred at both 28 and 6 °C. Tolerated growth conditions were temperatures between 4 and 34 °C, pH values between 6.0 and 8.0, and salt concentrations of up to 5 %. Fatty acid profiles showed a pattern typical for Pseudomonas , with C16 : 0 as the dominant component. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol and the dominating quinone was Q-9. Based on these results, it is proposed to classify the strains as a novel species, Pseudomonas cremoris sp. nov., with WS 5106T (=DSM 111143T=LMG 31863T) as type strain and WS 5096 (=DSM 111129=LMG 31864) as an additional strain.
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Pseudopuniceibacterium antarcticum sp. nov., isolated from an Antarctic marine sponge
A Gram-negative, aerobic, rod-shaped, non-motile bacterium, designated strain HQ09T, was isolated from a marine sponge off the coast of Fields Peninsula, West Antarctica. Strain HQ09T grew at 4–35 °C (optimum, 25 °C), pH 5–9 (optimum, pH 7.0), and with 1–10% NaCl (optimum, 2 %). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain HQ09T was affiliated with the genus Pseudopuniceibacterium in the family Rhodobacteraceae , sharing 99.64 % identity with the type strain of Pseudopuniceibacterium sediminis , the only known species in the genus. However, the low digital DNA–DNA hybridization (dDDH) (27.2 %) and average nucleotide identity (ANI) (83.63 %) values between strain HQ09T and the type strain of Pseudopuniceibacterium sediminis indicated that they did not belong to the same species. Strain HQ09T could also be differentiated from Pseudopuniceibacterium sediminis by many phenotypic characteristics. The major fatty acids (>5 %) of strain HQ09T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), 11-methyl C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The polar lipids included phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and one unidentified phospholipid. The predominant respiratory quinone was ubiquinone 10 (Q-10). The genomic DNA G+C content was 62.63 mol%. Four secondary metabolite biosynthetic gene clusters were detected in the genome, potentially producing ectoine and three types of unknown compounds. On the basis of the polyphasic evidences obtained in this study, strain HQ09T represents a novel species of the genus Pseudopuniceibacterium , for which the name Pseudopuniceibacterium antarcticum sp. nov. is proposed, with the type strain being HQ09T (=KCTC 52229T=CGMCC 1.15538T).
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Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas
Three bacterial strains, designated Red330T, Red736T and Red745T, were isolated from forest and paddy soils in Japan. Strains Red330T, Red736T and Red745T are flagella-harbouring and strictly anaerobic bacteria forming red colonies. A 16S rRNA gene sequence-based phylogenetic tree showed that all three strains were located in a cluster, including the type strains of Geomonas species, which were recently separated from the genus Geobacter within the family Geobacteraceae . Similarities of the 16S rRNA gene sequences among the three strains and Geomonas oryzae S43T, the type species of the genus Geomonas , were 96.3–98.5 %. The genome-related indexes, average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity, among the three strains and G. oryza e S43T were 74.7–86.8 %, 21.2–33.3 % and 70.4–89.8 %, respectively, which were lower than the species delineation thresholds. Regarding the phylogenetic relationships based on genome sequences, the three strains clustered with the type strains of Geomonas species, which were independent from the type strains of Geobacter species. The distinguishableness of the three isolated strains was supported by physiological and chemotaxonomic properties, with the profile of availability of electron donors and cellular fatty acids composition being particularly different among them. Based on genetic, phylogenetic and phenotypic properties, the three isolates represent three novel independent species in the genus Geomonas , for which the names Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov. are proposed. The type strains are Red330T (=NBRC 114028T=MCCC 1K03949T), Red736T (=NBRC 114029T=MCCC 1K03950T) and Red745T (=NBRC 114030T=MCCC 1K03951T), respectively.
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Parvularcula mediterranea sp. nov., isolated from marine plastic debris from Zakynthos Island, Greece
A Gram-negative, dark orange-pigmented, aerobic, non-spore-forming, coccoid-shaped bacterium designated as ZS-1/3T was isolated from a floating plastic litter (polypropylene straw) sample, collected from shallow seawater near the public beach of Laganas on Zakynthos island, Greece. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate is affiliated with the genus Parvularcula in the family Parvularculaceae . Its closest relatives are Parvularcula lutaonensis (98.09 %) and Parvularcula oceanus (95.89 %). The pH and temperature ranges for growth are pH 5–10 and 20–38 °C (optima, pH 7.0 and 28 °C). The predominant fatty acids are C18 : 1 ω7c (56.84 %), C16 : 0 (27.51 %), C18 : 0 (2.25 %) and C12 : 0 (1.42 %). The predominant respiratory quinone detected in strain ZS-1/3T is quinone-10 (Q10); the majority of detected polar lipids are glycolipid. The DNA G+C content is 62.5 mol%. Physiological and chemotaxonomic data further confirmed the distinctiveness of strain ZS-1/3T from other members of the genus Parvularcula . Thus, strain ZS-1/3T is considered to represent a novel species of the genus, for which the name Parvularcula mediterranea. sp. nov. is proposed. The type strain is ZS-1/3T (=NCAIM B 02654T=CCM 9032T).
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Photorhabdus heterorhabditis subsp. aluminescens subsp. nov., Photorhabdus heterorhabditis subsp. heterorhabditis subsp. nov., Photorhabdus australis subsp. thailandensis subsp. nov., Photorhabdus australis subsp. australis subsp. nov., and Photorhabdus aegyptia sp. nov. isolated from Heterorhabditis entomopathogenic nematodes
Three Gram-stain-negative, rod-shaped, non-spore-forming bacteria, BA1T, Q614T and PB68.1T, isolated from the digestive system of Heterorhabditis entomopathogenic nematodes, were biochemically and molecularly characterized to clarify their taxonomic affiliations. The 16S rRNA gene sequences of these strains suggest that they belong to the Gammaproteobacteria, to the family Morganellacea, and to the genus Photorhabdus . Deeper analyses using whole genome-based phylogenetic reconstructions suggest that BA1T is closely related to Photorhabdus akhursti, that Q614T is closely related to Photorhabdus heterorhabditis, and that PB68.1T is closely related to Photorhabdus australis. In silico genomic comparisons confirm these observations: BA1T and P. akhursti 15138T share 68.8 % digital DNA–DNA hybridization (dDDH), Q614T and P. heterorhabditis SF41T share 75.4 % dDDH, and PB68.1T and P. australis DSM 17609T share 76.6 % dDDH. Physiological and biochemical characterizations reveal that these three strains also differ from all validly described Photorhabdus species and from their more closely related taxa, contrary to what was previously suggested. We therefore propose to classify BA1T as a new species within the genus Photorhabdus , Q614T as a new subspecies within P. heterorhabditis, and PB68.1T as a new subspecies within P. australis . Hence, the following names are proposed for these strains: Photorhabdus aegyptia sp. nov. with the type strain BA1T(=DSM 111180T=CCOS 1943T=LMG 31957T), Photorhabdus heterorhabditis subsp. aluminescens subsp. nov. with the type strain Q614T (=DSM 111144T=CCOS 1944T=LMG 31959T) and Photorhabdus australis subsp. thailandensis subsp. nov. with the type strain PB68.1T (=DSM 111145T=CCOS 1942T). These propositions automatically create Photorhabdus heterorhabditis subsp. heterorhabditis subsp. nov. with SF41T as the type strain (currently classified as P. heterorhabditis ) and Photorhabdus australis subsp. australis subsp. nov. with DSM17609T as the type strain (currently classified as P. australis ).
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Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India
A moderately halophilic, Gram-stain-negative, aerobic bacterium, strain D1-1T, belonging to the genus Halomonas , was isolated from soil sampled at Pentha beach, Odisha, India. Phylogenetic trees reconstructed based on 16S rRNA genes and multilocus sequence analysis of gyrB and rpoD genes revealed that strain D1-1T belonged to the genus Halomonas and was most closely related to Halomonas alimentaria YKJ-16T (98.1 %) followed by Halomonas ventosae Al12T (97.5 %), Halomonas sediminicola CPS11T (97.5 %), Halomonas fontilapidosi 5CRT (97.4 %) and Halomonas halodenitrificans DSM 735T (97.2 %) on the basis of 16S rRNA gene sequence similarity. Sequence identities with other species within the genus were lower than 97.0 %. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values of 22.4–30 % and 79.5–85.4 % with close relatives of H. halodenitrificans DSM 735T, H . alimentaria YKJ-16T, H. ventosae Al12T and H. fontilapidosi 5CRT were lower than the threshold recommended for species delineation (70 % and 95–96 % for dDDH and ANI, respectively). Further, strain D1-1T formed yellow-coloured colonies; cells were rod-shaped, motile with optimum growth at 30 °C (range, 4–45 °C) and 2–8 % NaCl (w/v; grew up to 24 % NaCl). The major fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and C16 : 0 and the main respiratory quinone was ubiquinone Q-9 in line with description of the genus. Based on its chemotaxonomic and phylogenetic characteristics and genome uniqueness, strain D1-1T represents a novel species in the genus Halomonas , for which we propose the name Halomonas icarae sp. nov., within the family Halomonadaceae . The type strain is D1-1T (=JCM 33602T=KACC 21317T=NAIMCC-B-2254T).
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- Eukaryotic Micro-organisms
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Two new species of Euplotes with cirrotype-9, Euplotes foissneri sp. nov. and Euplotes warreni sp. nov. (Ciliophora, Spirotrichea, Euplotida), from the coasts of Patagonia: implications from their distant, early and late branching in the Euplotes phylogenetic tree
More LessTwo new Euplotes species have been isolated from cold shallow sandy sediments of the extreme Southern Chilean coasts: Euplotes foissneri sp. nov., from a low-salinity site at Puerto Natales on the Pacific coast, and Euplotes warreni sp. nov., from a marine site at Punta Arenas on the Atlantic coast. Euplotes foissneri has a medium body size (53×36 µm in vivo), a dorsal surface marked by six prominent ridges, a double dargyrome, six dorsal and two ventrolateral kineties, a buccal field extending to about 3/4 of the body length, an adoral zone composed of 28–32 membranelles, and nine fronto-ventral, five transverse and two or three caudal cirri. The bulky, hook-, horseshoe- or 3-shaped macronucleus is associated with one sub-spherical micronucleus. The central body region hosts taxonomically unidentified endosymbiotic eubacteria. Euplotes warreni has a small body size (39×27 µm in vivo), a smooth dorsal surface marked by three deep grooves, a double dargyrome, four dorsal and two ventrolateral kineties, a buccal field extending to about 2/3 of the body length, an adoral zone composed of 23–25 adoral membranelles, and nine fronto-ventral, five transverse and three caudal cirri. The macronucleus is hook- or C-shaped and associated with one spherical micronucleus. Endosymbiotic bacteria belonging to the genus Francisella reside preferentially in the anterior cell region. Both species lack the fronto-ventral cirrus numbered ‘V/2’, whereby their cirrotype-9 conforms to the so-called ‘pattern I’, which is the basic distinctive trait of the genus Euplotopsis Borror and Hill, 1995. Phylogenetic analyses of small subunit rRNA gene sequences, however, classify E. warreni into its own early branching clade and E. foissneri into a late branching clade. This indicates a polyphyletic nature and taxonomic inconsistency of the genus Euplotopsis, which was erected to include Euplotes species with cirrotype-9 pattern I.
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Remotididymella ageratinae sp. nov. and Remotididymella anemophila sp. nov., two novel species isolated from the invasive weed Ageratina adenophora in PR China
More LessTo determine if Ageratina adenophora can accumulate diverse pathogens from surrounding native plants, we intensively sampled fungal communities, including endophytes, leaf spot pathogens and canopy air fungi, associated with Ag. adenophora as well as native plants in its invasive range. In total, we collected 4542 foliar fungal strains from 10 geographic sites, including 1340 from healthy leaves of Ag. adenophora, 2051 from leaf spots of Ag. adenophora and 1151 from leaf spots of 56 species of native plants and crops. Taxonomically, the common fungal genera included Colletotrichum, Diaporthe, Alternaria, Nemania, Xylaria, Neofusicoccum, Nigrospora, Epicoccum, Gibberella, Pestalotiopsis, Irpex, Schizophyllum and Clonostachys. We also isolated the cultivable fungi from 12 air samples collected from six areas in Yunnan Province, PR China. Among the total of 1255 air fungal isolates, the most common genera were Cladosporium, Trichoderma and Epicoccum. Among them, two new Remotididymella species, Remotididymella ageratinae from leaf spot of Ag. adenophora and Remotididymella anemophila from canopy air of Ag. adenophora were found. The two species showed both asexual and sexual reproductive structures. The conidia of R. ageratinae and R. anemophila are larger than those of R. anthropophila and R. destructiva. The size of ascospores of R. ageratinae and R. anemophila also differ from R. bauhiniae. Phylogenetic analysis of the combined ITS, LSU rRNA, rpb2 and tub2 sequences showed that R. ageratinae and R. anemophila each formed a distinct clade, separated from all species previously described in Remotididymella and confirmed them as new species belonging to Remotididymella. Full descriptions of R. ageratinae and R. anemophila are provided in this study.
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- Research Article
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Alkalicaulis satelles gen. nov., sp. nov., a novel haloalkaliphile isolated from a laboratory culture cyanobacterium Geitlerinema species and proposals of Maricaulaceae fam. nov., Robiginitomaculaceae fam. nov., Maricaulales ord. nov. and Hyphomonadales ord. nov.
More LessA prosthecate bacterial strain, designated G-192T, was isolated from decaying biomass of a haloalkaliphilic cyanobacterium Geitlerinema sp. Z-T0701. The cells were aerobic, Gram-negative, non-endospore-forming and dimorphic, occurring either as sessile bacteria with a characteristic stalk or as motile flagellated cells. The strain utilized a limited range of substrates, mostly peptonaceous, but was able to degrade whole proteins. Growth occurred at 5–46 °C (optimum, 35–40 °C), pH 7.3–10.3 (optimum, pH 8.0–9.0), 0–14 % NaCl (v/w; optimum, 2.0–6.0 %, v/w). The G+C content of the genomic DNA of strain G-192T was 66.8%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain G-192T formed a distinct evolutionary lineage within the family Hyphomonadaceae . Strain G-192T showed the highest 16S rRNA sequence similarity to Glycocaulis profundi ZYF765T (95.2%), Oceanicaulis stylophorae GISW-4T (94.2%) and Marinicauda salina WD6-1T (95.5%). The major cellular fatty acids (>5% of the total) were C18:1 ω9c, C18:0 and 11-methyl-C18:1 ω7c. The major polar lipids were glycolipids and phospholipids. The only respiratory quinone was ubiquinone-10 (Q-10). Based on polyphasic results including phylogenomic data, the novel strain could be distinguished from other genera, which suggests that strain G-192T represents a novel species of a new genus, for which the name Alkalicaulis satelles gen. nov., sp. nov. is proposed. The type strain is G-192T (=VKM B-3306T=KCTC 72746T). The strain is the first representative of the stalked bacteria associated with a haloalkaliphilic cyanobacterium. Based on phylogenomic indices and phenotypic data, it is proposed to evolve two novel families Maricaulaceae fam. nov. and Robiginitomaculaceae fam. nov. out of the current family Hyphomonadaceae . In addition, it is proposed to place the first two families in the novel order Maricaulales ord. nov. and novel order Hyphomonadales ord. nov. is proposed to accommodate the family Hyphomonadaceae .
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- New Taxa
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- Actinomycetota
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Mycobacterium helveticum sp. nov., a novel slowly growing mycobacterial species associated with granulomatous lesions in adult swine
The occurrence of nontuberculous mycobacteria in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. Mycobacteriosis in pigs is usually associated with members of the Mycobacterium avium complex and, in particular, with ‘ Mycobacterium avium subsp. hominissuis ’. Here we describe a novel slow-growing mycobacterial species isolated from lymph nodes obtained from two sows housed in different Swiss farms. The animals presented chronic inappetence and mild diarrhoea. Gross pathology revealed focal caseous lymphadenopathy of the mesenteric lymph nodes. Complete genome sequencing of the two isolates from the two sows was performed. The genomes comprised 5.76 Mb and an average nucleotide identity score of 99.97 %. Whole genome sequence, mycolic acid and matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses revealed that the two isolates were not related to any previously described Mycobacterium species. The closest related species was Mycobacterium parmense , a slow-growing scotochromogenic mycobacterium first isolated from a cervical lymph node of a 3-year-old child. The name proposed for the new species is Mycobacterium helveticum sp. nov. and 16-83T (=DSM 109965T= LMG 2019-02457T) is the type strain.
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Volumes and issues
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Volume 75 (2025)
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Volume 72 (2022 - 2023)
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Volume 70 (2020)
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