Novel ultramicrobacterial isolates from a deep Greenland ice core represent a proposed new species, Chryseobacterium greenlandense sp. nov.

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

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“…The description is as given by Loveland-Curtze et al (2009) with the following restriction. The genomic G+C content of the type strain is 34.1%.…”

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of Bacteroidetes

et al. 2016

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“…Chryseobacterium spp. were also recovered from freshwater creeks [176] , lakes [177] , their sediments [178] , water cooling systems [179] , drinking water [180] , lactic acid beverages [181] , beer bottling plants [182] , bioreactor sludge [183] , polluted soil [184] , marine sediment [185] , and permafrost [186] . In contrast to Flavobacterium spp., multiple studies that examined the bacterial assemblages of glaciers and Antarctic ice have not detected Chryseobacterium spp.…”

Section: Introductionmentioning

confidence: 99%

Emerging flavobacterial infections in fish: A review

Loch

Faisal

2015

Journal of Advanced Research

228

152

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“…Today, the genus Chryseobacterium comprises over 60 different species isolated from various environments such as clinical sources (Kämpfer et al , 2009b), water reservoir (Kim et al , 2008) or soils (Benmalek et al , 2010; Weon et al , 2008; Zhou et al , 2007). Several isolates have been derived from polar habitats (Loveland-Curtze et al , 2010; Yi et al , 2005).…”

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confidence: 99%

Chryseobacterium frigidisoli sp. nov., a psychrotolerant species of the family Flavobacteriaceae isolated from sandy permafrost from a glacier forefield

Bajerski

Ganzert

Mangelsdorf

et al. 2013

International Journal of Systematic and Evolutionary Microbiology

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During diversity studies of the glacier forefields of the Larsemann Hills, East Antarctica, a novel psychrotolerant, non-motile Gram-negative, shiny yellow, rod-shaped, aerobic bacterium, designated strain PB4T was isolated from a soil sample. Strain PB4 T produces indole from tryptophan and hydrolyses casein. It grows between 0 and 25 6C with an optimum growth temperature of 20 6C. A wide range of substrates are used as sole carbon sources and acid is produced from numerous carbohydrates. The major menaquinone is MK-6. Identified polar lipids are ethanolamines and ornithine lipids. Major fatty acids (.10 %) are iso-C 15 : 0 (13.0 %) and iso-2OH-C 15 : 0 (51.2 %). G+C content is 33.7 mol%. The polyamine pattern is composed of symhomospermidine (25.1 mmol g "1 dry weight), minor amounts of cadaverine (0.2 mmol g "1 dry weight) and spermidine (0.4 mmol g "1 dry weight) and traces of putrescine and spermine (,0.1 mmol g "1 dry weight). Strain PB4 T had highest 16S rRNA gene similarities with the type strains of Chryseobacterium humi (97.0 %) and Chryseobacterium marinum (96.5 %). Considering phenotypic and genotypic characterization, strain PB4 T represents a novel species in the genus Chryseobacterium (family Flavobacteriaceae), for which the name Chryseobacterium frigidisoli sp. nov. is proposed. The type strain is PB4 T (5DSM 26000In , Vandamme et al. (1994 introduced new perspectives in the classification of the genus Flavobacterium. Six strains in the family Flavobacteriaceae were proposed as novel species in the genus Chryseobacterium with former Flavobacterium gleum (Holmes et al., 1984), renamed as Chryseobacterium gleum, as the type species. Today, the genus Chryseobacterium comprises over 60 different species isolated from various environments such as clinical sources (Kämpfer et al., 2009b), water reservoir or soils (Benmalek et al., 2010;Weon et al., 2008;Zhou et al., 2007). Several isolates have been derived from polar habitats (Loveland-Curtze et al., 2010;Yi et al., 2005).The isolation and characterization of micro organisms from extreme habitats has become more and more important in the past years, because representative isolates can help identify functions of micro organisms in these habitats. Members of the phylum Actinobacteria for example are known to use a wide range of substrates or degrade polymers at low temperatures as it was reported for Arthrobacter and Leifsonia species from Livingston Island in Antarctica (Ganzert et al., 2011a, b) In the context of microbial community analysis in extreme environments, several psychrotolerant bacteria were isolated from Antarctic soils. In this study, we report the isolation and identification of strain PB4 T which is considered to be a novel cold-adapted representative in the genus Chryseobacterium. Strain PB4T was isolated from sandy dry permafrost in 1-6 cm depth from a glacier forefield transect located in the Larsemann Hills region, East Antarctica (S 69 u 24, E 76 u 20). Soil material was suspended in a physiological salt solution (0.9 % NaCl, ...

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Novel ultramicrobacterial isolates from a deep Greenland ice core represent a proposed new species, Chryseobacterium greenlandense sp. nov.

Cited by 39 publications

References 37 publications

Genome-Based Taxonomic Classification of Bacteroidetes

Genome-Based Taxonomic Classification of Bacteroidetes

Emerging flavobacterial infections in fish: A review

Chryseobacterium frigidisoli sp. nov., a psychrotolerant species of the family Flavobacteriaceae isolated from sandy permafrost from a glacier forefield

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