Characterization of Rhizobium naphthalenivorans sp. nov. with special emphasis on aromatic compound degradation and multilocus sequence analysis of housekeeping genes

Abstract

IntroductionMicrobial transformation of polychlorinated dibenzop-dioxins/dibenzofurans (PCDD/Fs) has been well documented in connection with natural attenuation and engineered bioremediation of organohalogen pollution (Field and Sierra-Alvarez, 2008;Hiraishi, 2003Hiraishi, , 2008. Previously, we constructed laboratory-scale semi-anaerobic microcosms with sediment contaminated with high concentrations of PCDD/Fs in order to study microorganisms involved in the transformation J. Gen. Appl. Microbiol., 58, 211 224 (2012) Three strains of aerobic chemoorganotrophic naphthalene-degrading bacteria (designated TSY03b T , TSY04, and TSW01) isolated from sediment of a polychlorinated-dioxin-transforming microcosm were characterized. These strains had Gram-negative-stained, rod-shaped cells measuring 0.6 0.9 μm in width and 1.2 3.0 μm in length and were motile by means of peritrichous fl agella. Naphthalene was utilized as the sole carbon and energy source, and the transcription of a putative aromatic-ring hydroxylating gene was inducible by naphthalene. The major component of cellular fatty acids was summed feature 8 (C 18 1 ω7c and/or C 18 1 ω6c), and signifi cant proportions of C 18 0 and C 19 0 cyclo ω8cis were also found. The major respiratory quinone was ubiquinone-10. The G+C content of the DNA was 60.3 60.9 mol%. Phylogenetic analyses by studying sequence information on the housekeeping atpD, dnaK, glnII, gyrB, and recA genes as well as on 16S rRNA genes and the 16S-23S rDNA internal transcribed spacer region revealed that the strains grouped with members of the genus Rhizobium, with Rhizobium selenitireducens as their closest relative but formed a distinct lineage at the species level. This was confi rmed by genomic DNA-DNA hybridization studies. These phenotypic, genotypic, and phylogenetic data strongly suggest that our isolates should be classifi ed under a novel species of the genus Rhizobium. Thus, we propose the name Rhizobium naphthalenivorans sp. nov. to accommodate the novel isolates. The type strain is TSY03b T (= NBRC 107585 T = KCTC 23252 T ).

Hartmannibacter diazotrophicus gen. nov., sp. nov., a phosphate-solubilizing and nitrogen-fixing alphaproteobacterium isolated from the rhizosphere of a natural salt-meadow plant

“…Differential phenotypic characteristics that distinguish strain E19 T from related genera Taxa: 1, Hartmannibacter diazotrophicus gen. nov., sp. nov. E19 T (data from this study); 2, Rhizobium rhizoryzae J3-AN59 T (data from Zhang et al, 2014); 3, Rhizobium (Tighe et al, 2000;Kaiya et al, 2012;Xu et al, 2013;Zhang et al, 2014); 4, Stappia (Uchino et al,1998;Biebl et al, 2007;Lai et al, 2010;Kämpfer et al, 2013); 5, Labrenzia (Biebl et al, 2007;Bibi et al, 2014); 6, Mesorhizobium (Jarvis et al, 1997;Choma & Komaniecka, 2002;Zhou et al, 2010;Laranjo & Oliveira, 2011) and Hyphomicrobiaceae (Hwang & Cho, 2008). Related genera from the family Rhodobacteraceae present Q-10 as the dominant respiratory lipoquinone (Cho & Giovannoni, 2004;Biebl et al, 2007).…”

Aided Phytoremediation to Clean Up Dioxins/Furans-Aged Contaminated Soil: correlation between microbial communities and pollutant dissipation

“…The bioremediation of PCDD/F-contaminated soil requires diverse microbial degradation processes involving the activity of specialized microbial communities. It was suggested that PCDD/F degradation began by an initial dechlorination process to free several chlorine-substituted positions downstream for the hydroxylation and cleavage of aromatic rings [67]. Reductive dehalogenation and oxidative degradation, mediated by specific anaerobic and aerobic microbial populations, respectively, have been proposed as mechanisms involved in the transformation of PCDD/F [68].…”