Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria

Kulichevskaya, Irina S.; Suzina, N. E.; Liesack, Werner; Dedysh, Svetlana N.

doi:10.1099/ijs.0.013250-0

Cited by 138 publications

(85 citation statements)

References 25 publications

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“…2a). This cell morphology was profoundly different from that of B. aggregatus MPL3 T , which presents short (0.8-1.3 mm long) rods or coccoids assembled in aggregates (Kulichevskaya et al, 2010). On agar medium MM, strain P105 T formed colourless, circular colonies, 0.5-1 mm in diameter, after 2 weeks of incubation.…”

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“…1). At present, this subdivision includes only one member with a validly published name, the strictly aerobic chemo-organotroph Bryobacter aggregatus (Kulichevskaya et al, 2010). One additional, taxonomically uncharacterized representative of subdivision 3 with a determined genome sequence has been tentatively named 'Solibacter usitatus' and defined as an aerobic heterotroph (Ward et al, 2009 (91 %) (Fig.…”

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confidence: 99%

“…Since B. aggregatus was the closest taxonomically described relative of our novel isolate, the type strain of this species, MPL3 T (obtained in our earlier study; Kulichevskaya et al, 2010), was used as a reference organism in our study. It was grown in liquid medium MM and used in all comparative physiological tests.…”

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“…This probe hybridized to relatively large, rod-shaped cells that were present on some of the plates. Cell material from these plates was further restreaked on medium MM (Kulichevskaya et al, 2010) containing (g per litre distilled water) KH 2 PO 4 , 0.1; (NH 4 ) 2 SO 4 , 0.2; MgSO 4 . 7H 2 O, 0.1; CaCl 2 .…”

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Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria

Kulichevskaya

Suzina

Rijpstra

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria A facultatively anaerobic, non-pigmented, non-spore-forming bacterium was isolated from a littoral wetland of a boreal lake located on Valaam Island, northern Russia, and designated strain P105 T . Cells of this isolate were Gram-negative, non-motile rods coated by S-layers with p2 lattice symmetry. Sugars were the preferred growth substrates. Under anoxic conditions, strain P105 T was capable of fermentation and dissimilatory Fe(III) reduction. End products of fermentation were acetate, propionate and H 2 . Strain P105 T was a mildly acidophilic, mesophilic organism, capable of growth at pH 4.0-7.2 (optimum pH 5.5-6.0) and at 4-35 6C (optimum at 20-28 6C). The major fatty acids were iso-C 15 : 0 and C 16 : 1 v7c; the cells also contained significant amounts of 13,16-dimethyl octacosanedioic acid (isodiabolic acid). The major polar lipids were phosphocholine and phosphoethanolamine; the quinone was MK-8. The G+C content of the DNA was 60.5 mol%. 16S rRNA gene sequence analysis showed that strain P105 T belongs to subdivision 3 of the Acidobacteria and is only distantly related (90 % sequence similarity) to the only currently characterized member of this subdivision, Bryobacter aggregatus. The novel isolate differs from Bryobacter aggregatus in its cell morphology and ability to grow under anoxic conditions and in the presence of iron-and nitrate-reducing capabilities as well as quinone and polar lipid compositions. These differences suggest that strain P105 T represents a novel genus and species, for which the name Paludibaculum fermentans gen. nov., sp. nov., is proposed. The type strain of Paludibaculum fermentans is P105 T (5DSM 26340 T 5VKM B-2878 T ).Members of the phylum Acidobacteria represent one of the dominant bacterial groups in northern acidic wetlands (Dedysh et al., 2006;Dedysh, 2011;Pankratov et al., 2011;Lin et al., 2012;Serkebaeva et al., 2013). As revealed by molecular surveys, these bacteria inhabit both oxic and anoxic peat layers and mostly belong to subdivisions 1 and 3 of the Acidobacteria (Lin et al., 2012;Serkebaeva et al., 2013). The proportion of 16S rRNA gene sequences that can be assigned to taxonomically characterized members of the Acidobacteria is significantly higher in the surface layer than in the subsurface peat, indicating a major lack of knowledge about acidobacteria that thrive in anoxic peat (Serkebaeva et al., 2013). Indeed, with the exception of Telmatobacter bradus and Acidobacterium capsulatum (Pankratov et al., 2012), all currently characterized members of subdivisions 1 and 3 are strict aerobes. This study, therefore, aimed at isolation and characterization of those acidobacteria that inhabit anoxic peat layers of northern wetlands.Samples were collected from the anoxic peat layer (depth of 40-50 cm) of the littoral wetland of a boreal lake located on Valaam Island (61 u 229 N 30 u 569 E) in Lake Ladoga, Republic of Kare...

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Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria

Kulichevskaya

Suzina

Rijpstra

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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“…More than half of the currently characterised Acidobacteria belong to subdivision [1], and only 18/141 high-quality 16S rRNA gene sequences from bacterial isolates are classified as subdivision [3] (Ribosomal Database Project (RDP) II v10.4; http://rdp.msu.edu/). Members of Acidobacteria subdivision [1] (Dedysh et al, 2006;Kulichevskaya et al, 2010).…”

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Molecular detection on culture medium of Acidobacteria from Amazon soils

Navarrete¹,

Barreto²,

Arnaldo³

et al. 2013

Microbiol Discov

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Cultivation and molecular approaches were combined to recover and detect Acidobacteria from Amazon soils on culture medium. The strategy of the cultivation procedure included the following: the use of VL55 growth medium supplemented with 0.05% xylan as the carbon source and solidified with gellan gum; incubation under hypoxic conditions (2% O 2 [vol/vol], 2% CO 2 [vol/vol], and 96% N 2 [vol/vol]) for a relatively long period; inclusion of aluminium potassium sulphate in the growth medium; and soil dilution and plating. Of the 456 colonies recovered on the growth medium and subjected to PCR screening, three colonies belonging to Acidobacteria subdivision 1 and one colony belonging to Acidobacteria subdivision 3 were detected. The use of 16S rRNA gene based clone libraries comprising 437 clones confirmed that members of the phylum Acidobacteria grew primarily on plates on wich acidobacterial colonies were detected by PCR screening. The clones in the libraries consisted predominantly of Proteobacteria (orders Burkholderiales and Xanthomonadales). In summary, this work reports the recovery and molecular detection on VL55 growth medium of representatives of Acidobacteria subdivisions 1 and 3 concomitantly with to other bacterial groups inhabiting pasture and soybean cropland soils from the Amazon region.

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Acidobacteria

Dedysh¹,

Damsté

2018

Encyclopedia of Life Sciences

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Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria

Cited by 138 publications

References 25 publications

Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria

Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria

Molecular detection on culture medium of Acidobacteria from Amazon soils

Acidobacteria

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