Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm

Uchida, Hiromi; Hamana, Koei; Miyazaki, Masaru; Yoshida, Takao; Nogi, Yuichi

doi:10.1099/ijs.0.034033-0

Cited by 34 publications

(26 citation statements)

References 24 publications

(28 reference statements)

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“…This family comprises of four well-known PAH-degrading genera, namely; Sphingomonas (Busse et al, 2003;Chen et al, 2012Chen et al, , 2013Takeuchi et al, 2001;Yabuuchi et al, 2002Yabuuchi et al, , 1999, Sphingobium (Busse et al, 2003;Takeuchi et al, 2001), Novosphingobium (Busse et al, 2003;Takeuchi et al, 2001), Sphingopyxis (Busse et al, 2003;Takeuchi et al, 2001;Yoon et al, 2008, which make up the sphingomonads (Kosako et al, 2000). Currently, ten other genera have been established in this family, including Sphingosinicella Maruyama et al, 2006;Yasir et al, 2010), Sandarakinorhabdus (Gich and Overmann, 2006), Stakelama (Chen et al, 2010;Thawng et al, 2013), Sphingorhabdus , Zymomonas (Glaeser and K€ ampfer, 2014), Sandaracinobacter (Yurkov et al, 1997), Sphingomicrobium (K€ ampfer et al, 2012), Blastomonas (Hiraishi et al, 2000), Pacificamonas (Liu et al, 2014) and Parasphingopyxis (Uchida et al, 2012). This classification of the Sphingomonadaceae family is based on the sequence phylogeny of the 16S rDNA gene and the presence of 2'-hydroxymyristoyl dihydrosphingosine 1-glucuronic acid (SGL-1) as the major sphingoglycolipid in the cells (Busse et al, 1999;Kosako et al, 2000).…”

Section: Taxonomic Properties Of Sphingomonadsmentioning

confidence: 98%

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Waigi

Kang

Goikavi

et al. 2015

International Biodeterioration & Biodegradation

153

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Section: Taxonomic Properties Of Sphingomonadsmentioning

confidence: 98%

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Waigi

Kang

Goikavi

et al. 2015

International Biodeterioration & Biodegradation

153

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“…The sphingomonads represent a group of Alphaproteobacteria, which encompass in our days the genera Novosphingobium, Sphingobium, Sphingomonas, Sphingopyxis, Sphingosinicella, Sphingomicrobium, Sphingorhabdus and Parasphingopyxis. These genera share a number of phenotypic traits, such as the presence of sphingolipids in their outer membranes, the formation of usually yellowpigmented colonies and a specific pattern of polyamines (K€ ampfer et al, 2012;Uchida et al, 2012;Jogler et al, 2013). Sphingomonads have been intensively studied during the last years because of their pronounced ability to degrade recalcitrant natural and xenobiotic compounds, such as various polycyclic aromatic hydrocarbons (PAHs), nonylphenols, sulphonated naphthalenes, chlorinated dibenzofurans and dibenzodioxins, carbazole, polyethylene glycols and different herbicides and pesticides (Stolz, 2009).…”

Section: Introductionmentioning

confidence: 99%

Degradative plasmids from sphingomonads

Stolz

2013

FEMS Microbiol Lett

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Large plasmids ('megaplasmids') are commonly found in members of the Alphaproteobacterial family Sphingomonadaceae ('sphingomonads'). These plasmids contribute to the extraordinary catabolic flexibility of this group of organisms, which degrade a broad range of recalcitrant xenobiotic compounds. The genomes of several sphingomonads have been sequenced during the last years. In the course of these studies, also the sequences of several plasmids have been determined. The analysis of the published information and the sequences deposited in the public databases allowed a first classification of these plasmids into a restricted number of groups according to the proteins involved in the initiation of replication, plasmid partition and conjugation. The sequence comparisons demonstrated that the plasmids from sphingomonads encode for four main groups of replication initiation (Rep) proteins. These Rep proteins belong to the protein superfamilies RepA_C (Pfam 04796), Rep_3 (Pfam 01051), RPA (Pfam 10134) and HTH-36 (Pfam 13730). The 'degradative megaplasmids' pNL2, pCAR3, pSWIT02, pCHQ1, pISP0, and pISP1, which code for genes involved in the degradation of aromatic hydrocarbons, carbazole, dibenzo-p-dioxin and γ-hexachlorocyclohexane, carry Rep proteins which either belong to the RepA_C- (plasmids pNL2, pCAR3, pSWIT02), Rep-3- (plasmids pCHQ1, pISP0) or RPA-superfamily (pISP1). The classification of these 'degradative megaplasmids' into three groups is also supported by sequence comparisons of the proteins involved in plasmid partition (ParAB) and the organization of the three genes on the respective plasmids. All analysed 'degradative megaplasmids' carry genes, which might allow a conjugative transfer of the plasmids. Sequence comparisons of these genes suggest the presence of at least two types of transfer functions, which either are closer related to the tra- or vir-genes previously described for plasmids from other sources.

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“…T was obtained by direct sequencing of PCRamplified DNA as described previously (Uchida et al, 2012). The resulting 16S rRNA gene sequence (1404 nt) of strain JAMH 043…”

Section: Reduction Of Nitritementioning

confidence: 99%

Thalassobius abyssi sp. nov., a marine bacterium isolated from cold-seep sediment

Nogi

Mori

Makita

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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A novel marine bacterial strain, designated JAMH 043 T , was isolated from cold-seep sediment in Sagami Bay, Japan. Cells were Gram-stain-negative, rod-shaped, non-motile and aerobic chemo-organotrophs. The isolate grew optimally at 25 8C, at pH 7.0-7.5 and with 3 % (w/v) NaCl. The major respiratory quinone was ubiquinone-10 (Q-10). The predominant fatty acid was C 18 : 1 v7c. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated to members of the genus Thalassobius in the class Alphaproteobacteria, and 16S rRNA gene sequence similarity of the novel isolate with the type strain of its closest related species, Thalassobius aestuarii JC2049 T , was 98.4 %. The DNA G+C content of the novel strain was 58.0 mol%. The hybridization values for DNA-DNA relatedness between strain JAMH 043 T and reference strains belonging to the genus Thalassobius were less than 14.1¡2.2 %. Based on differences in taxonomic characteristics, the isolated strain represents a novel species of the genus Thalassobius, for which the name Thalassobius abyssi sp. nov. is proposed. The type strain is JAMH 043The genus Thalassobius, first proposed by Arahal et al. et al., 2012). In this taxonomic study, we used a polyphasic approach to investigate marine bacterial strain JAMH 043 T , which was found to represent a novel species belonging to the genus Thalassobius. Strain JAMH 043T was isolated from sediment of the deep-sea cold-seep area off Hatsushima, Sagami Bay, Japan (358 0099 N 1398 1369 E, depth: 1097 m) collected by means of a sterilized sediment sampler using the SHI-NKAI 6500 system operated by JAMSTEC (cruise YK07-05) in April 2007. The sediment was suspended with a small amount of sterilized artificial seawater (ASW; RohtoMarine, Rei-Sea), cooled with ice and allowed to stand for 10 min. The supernatant was spread on marine agar 2216 (MA; Difco) plates and incubated at 10 8C for 1 week upon isolation. A pure culture was obtained after at least three subcultivations on MA plates and the morphological, physiological and biochemical characteristics of strain JAMH 043 T were investigated by using routine incubation on MA plates or in marine broth 2216 (MB; Difco) at 25 8C. T. aestuarii JCM 14322 T , T. gelatinovorus IAM 12617 T , T. maritimus KCTC 23347 T , T. mediterraneus DSM 16398T and 'Thalassobius aquaeponti' NBRC 110378 were used as reference strains in the study for biochemical and antibiotic susceptibility tests, and analysis of cellular fatty acids.Growth conditions were investigated on Luria-Bertani (LB) medium supplemented with 3 % NaCl [1.0 % (w/v) tryptone (Difco), 0.5 % (w/v) yeast extract (Difco), 3.0 % (w/v) NaCl], trypticase soy broth agar (TSBA; Difco) supplemented with 3 % NaCl, nutrient agar (Difco) supplemented with 3 % NaCl and MA plates in triplicate at 25 8C for 1 week. Cell growth was not observed on TSBA or on nutrient agar, which do not contain yeast extract. The effects of temperature, NaCl concentrationThe GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of...

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Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm

Cited by 34 publications

References 24 publications

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Degradative plasmids from sphingomonads

Thalassobius abyssi sp. nov., a marine bacterium isolated from cold-seep sediment

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