Rhodoligotrophos appendicifer gen. nov., sp. nov., an appendaged bacterium isolated from a freshwater Antarctic lake

Fukuda, Wakao; Yamada, Kozo; Miyoshi, Yuki; Okuno, H.; Atomi, Haruyuki; Imanaka, Tadayuki

doi:10.1099/ijs.0.032953-0

Cited by 31 publications

(19 citation statements)

References 26 publications

(21 reference statements)

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“…Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MA2 T was affiliated with the order Rhizobiales in the class Alphaproteobacteria (). Closely related species with validly published names were Rhodobium orientis (Hiraishi et al , 1995) (93.0 % sequence similarity), Parvibaculum hydrocarboniclasticum (Rosario-Passapera et al , 2012) (92.4 % similarity) and Rhodoligotrophos appendicifer (Fukuda et al , 2012) (92.1 % similarity). Strain MA2 T was distantly related to other stalked bacteria such as Caulobacter crescentus , Maricaulis maris and Oceanicaulis alexandrii ().…”

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confidence: 99%

Tepidicaulis marinus gen. nov., sp. nov., a marine bacterium that reduces nitrate to nitrous oxide under strictly microaerobic conditions

Takeuchi

Yamagishi

Kamagata

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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Tepidicaulis marinus gen. nov., sp. nov., a marine bacterium that reduces nitrate to nitrous oxide under strictly microaerobic conditions T was most closely related to the genera Rhodobium, Parvibaculum, and Rhodoligotrophos (92-93 % similarity) within the class Alphaproteobacteria. Strain MA2 T was aGram-stain-negative and stalked dimorphic bacteria. The temperature range for growth was 16-48 6C (optimum growth at 42 6C). This strain required yeast extract and NaCl (.1 %, w/v) for growth, tolerated up to 11 % (w/v) NaCl, and was capable of utilizing various carbon sources. The major cellular fatty acid and major respiratory quinone were C 18 : 1 v7c and ubiquinone-10, respectively. The DNA G+C content was 60.7 mol%. Strain MA2 T performed denitrification and produced N 2 O from nitrate under strictly microaerobic conditions. Strain MA2 T possessed periplasmic nitrate reductase (Nap) genes but not membrane-bound nitrate reductase (Nar) genes. On the basis of this morphological, physiological, biochemical and genetic information a novel genus and species, Tepidicaulis marinus gen. nov., sp. nov., are proposed, with MA2 T

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confidence: 99%

Tepidicaulis marinus gen. nov., sp. nov., a marine bacterium that reduces nitrate to nitrous oxide under strictly microaerobic conditions

Takeuchi

Yamagishi

Kamagata

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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“…Strain 120-1 T grows between 5 and 35 • C, with an optimum temperature of 30 • C. The OD 660 reaches a maximum value of about 1.2 after incubation for about 120 h. Other features of strain 120-1 T were described in detail in our recent study. 52 S120-1 DNA was extracted by the following procedures. Strain 120-1 T was cultivated in 0.25 × Luria-Bertani medium (2.50 g/l of tryptone, 1.25 g/l of yeast extract, 5.0 g/l of NaCl, pH 7) at 30 • C for 5 days with gentle shaking.…”

Section: A Materialsmentioning

confidence: 99%

“…4,38,51 Here, we extended our investigation to a megabase-size genomic DNA (S120-1 DNA) that was successfully extracted from Rhodoligotrophos appendicifer (strain 120-1 T = JCM 16873 T = ATCC BAA 2115 T ). 52 Strain 120-1 T was isolated from a freshwater lake in Antarctica and is characterized by slow growth and low rates of metabolism associated with its oligotrophic environment. Both of these features may enable us to successfully isolate large genomic DNA fragments of near-megabase size.…”

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Critical behavior of megabase-size DNA toward the transition into a compact state

Yoshikawa

Suzuki

Yamada

et al. 2011

The Journal of Chemical Physics

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Naturally occurring branched-chain polyamines induce a crosslinked meshwork structure in a giant DNA The Journal of Chemical Physics 145, 235103 (2016) We studied the changes in the higher-order structure of a megabase-size DNA (S120-1 DNA) under different spermidine (SPD) concentrations through single-molecule observations using fluorescence microscopy (FM) and atomic force microscopy (AFM). We examined the difference between the folding transitions in S120-1 DNA and sub-megabase-size DNA, T4 DNA (166 kbp). From FM observations, it is found that S120-1 DNA exhibits intra-chain segregation as the intermediate state of transition, in contrast to the all-or-none nature of the transition on T4 DNA. Large S120-1 DNA exhibits a folding transition at lower concentrations of SPD than T4 DNA. AFM observations showed that DNA segments become aligned in parallel on a two-dimensional surface as the SPD concentration increases and that highly intense parallel alignment is achieved just before the compaction. S120-1 DNA requires one-tenth the SPD concentration as that required by T4 DNA to achieve the same degree of parallel ordering. We theoretically discuss the cause of the parallel ordering near the transition into a fully compact state on a two-dimensional surface, and argue that such parallel ordering disappears in bulk solution.

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“…The G+C content of the genomic DNA, respiratory quinone, fatty acids and polar lipids pattern were analysed by previously described methods with slight modification (Fukuda et al , 2012; Yamada, et al , 2011). The fatty acids composition was analysed by the Sherlock Microbial Identification System using version 6.0 of the TSBA6 library.…”

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Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from antarctic white rock

Fukuda

Chino

Araki

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, non-spore-forming, aerobic, oligotrophic bacterium (strain 262-7T) was isolated from a crack of white rock collected in the Skallen region of Antarctica. Strain 262-7T grew at temperatures between −4 and 30 °C, with optimal growth at 25 °C. The pH range for growth was between pH 6.0 and 9.0, with optimal growth at approximately pH 7.0. The NaCl concentration range allowing growth was between 0.0 and 1.0 %, with an optimum of 0.5 %. Strain 262-7T showed an unprecedented range of morphological diversity in response to growth conditions. Cells grown in liquid medium were circular or ovoid with smooth surfaces in the lag phase. In the exponential phase, ovoid cells with short projections were observed. Cells in the stationary phase possessed long tentacle-like projections intertwined intricately. By contrast, cells grown on agar plate medium or in liquid media containing organic compounds at low concentration exhibited short- and long-rod-shaped morphology. These projections and morphological variations clearly differ from those of previously described bacteria. Ubiquinone 10 was the major respiratory quinone. The major fatty acids were C17 : 1ω6c (28.2 %), C16 : 1ω7c (22.6 %), C18 : 1ω7c (12.9 %) and C15 : 0 2-OH (12.3 %). The G+C content of genomic DNA was 68.0 mol%. Carotenoids were detected from the cells. Comparative analyses of 16S rRNA gene sequences indicated that strain 262-7T belongs to the family Sphingomonadaceae , and that 262-7T should be distinguished from known genera in the family Sphingomonadaceae . According to the phylogenetic position, physiological characteristics and unique morphology variations, strain 262-7T should be classified as a representative of a novel genus of the family Sphingomonadaceae . Here, a novel genus and species with the name Polymorphobacter multimanifer gen. nov., sp. nov. is proposed (type strain 262-7T = JCM 18140T = ATCC BAA-2413T). The novel species was named after its morphological diversity and formation of unique projections.

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Rhodoligotrophos appendicifer gen. nov., sp. nov., an appendaged bacterium isolated from a freshwater Antarctic lake

Cited by 31 publications

References 26 publications

Tepidicaulis marinus gen. nov., sp. nov., a marine bacterium that reduces nitrate to nitrous oxide under strictly microaerobic conditions

Tepidicaulis marinus gen. nov., sp. nov., a marine bacterium that reduces nitrate to nitrous oxide under strictly microaerobic conditions

Critical behavior of megabase-size DNA toward the transition into a compact state

Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from antarctic white rock

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