Identification and genome analysis of Comamonas testosteroni strain JLU460ET, a novel steroid-degrading bacterium

Abstract A bacterial strain, Gram-stain negative, rod-shaped, aerobic and cellulose-degrading, designated NEAU-DD11T, was isolated from rhizosphere soil of rice collected from Northeast Agricultural University in Harbin, Heilongjiang province, North-east China. Base on 16S rRNA gene sequence analysis, strain NEAU-DD11T belongs to the genus Massilia and shared high sequence similarities with Massilia phosphatilytica 12-OD1T (98.46 %) and Massilia putida 6NM-7T (98.41 %). Phylogenetic analysis based on the 16S rRNA gene and whole genome sequences indicated that strain NEAU-DD11T formed a stable cluster with M. phosphatilytica 12-OD1T and M. putida 6NM-7T. The major fatty acids of the strain were C16:0, C17:0-cyclo and C16:1ω7c. The respiratory quinone was Q-8. The polar lipids profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified polar lipid and an unidentified phospholipid. In addition, the digital DNA-DNA hybridization values between strain NEAU-DD11T and M. phosphatilytica 12-OD1T and M. putida 6NM-7T were 45.4% and 35.6%, respectively, which are lower than the accepted threshold value of 70%. The DNA G + C content of strain NEAU-DD11T was 66.2 %. The whole genome analysis showed the strain contained carbohydrate enzymes such as glycoside hydrolase and polysaccharide lyase, which enabled the strain to had the function of degrading cellulose. On the basis of the phenotypic, genotypic and chemotaxonomic characteristics, strain NEAU-DD11T represents a novel species of the genus Massilia, for which the name Massilia cellulosiltytica sp. nov. is proposed. The type strain is NEAU-DD11T (= CCTCC AB 2019141T = DSM 109721T).

Download Full-text

Isolation, Identification and Genome Analysis of a Cellulose-Degrading Bacterium Bacillus aciditolerans YN-1T

Journal of Biobased Materials and Bioenergy ◽

10.1166/jbmb.2021.2079 ◽

2021 ◽

Vol 15 (4) ◽

pp. 491-496

Author(s):

Lijuan Chen ◽

Dawei Liu ◽

Mengjiao Ding ◽

Zifang Zhou ◽

Li Liu ◽

...

Keyword(s):

Genome Analysis ◽

Glycoside Hydrolase ◽

Yunnan Province ◽

Draft Genome ◽

Corn Straw ◽

Protein Coding ◽

Coding Sequences ◽

Degrading Bacterium ◽

Different Types ◽

Bacterium Bacillus

Bacillus aciditolerans YN-1T was isolated from Jietou town, Yunnan Province, China and exhibited various lignocellulolytic activities which had the ability to decompose straw. In this work, we found that strain YN-1T was capable of degrading different types of straw and showed the highest efficiency to the degrading of corn straw. We also draw the draft genome sequence of strain YN-1T , which composed of 4,633,983 bp chromosome. Results showed that Bacillus aciditolerans YN-1T contains 3455 protein coding sequences and 249 were associated with the carbohydrate metabolism. Meanwhile, CAZymes analysis also showed that strain YN-1T contains 60 coding genes of glycoside hydrolase (GH) family, implying that Bacillus aciditolerans YN-1T has broad applications in the degradation of straw.

Download Full-text

Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02812-0 ◽

2004 ◽

Vol 54 (3) ◽

pp. 851-855 ◽

Cited By ~ 52

Author(s):

Wan-Taek Im ◽

Hee-Sung Bae ◽

Akira Yokota ◽

Sung Taik Lee

Keyword(s):

16S Rdna ◽

Sequence Similarity ◽

Rdna Sequence ◽

The Novel ◽

Comamonas Testosteroni ◽

16S Rdna Sequence ◽

Rdna Sequences ◽

Degrading Bacterium ◽

16S Rdna Sequences ◽

Type Strains

A 4-chlorophenol-degrading bacterial strain, formerly designated as a strain of Comamonas testosteroni, was reclassified as a member of the genus Herbaspirillum based on its phenotypic and chemotaxonomic characteristics, as well as phylogenetic analysis using 16S rDNA sequences. Phylogenetic inference based on 16S rDNA sequences showed that strain CPW301T clusters in a phylogenetic branch that contains Herbaspirillum species. 16S rDNA sequence similarity of strain CPW301T to species of the genus Herbaspirillum with validly published names is in the range 98·7–98·9 %. Despite the considerably high 16S rDNA sequence similarity, strain CPW301T could be distinguished clearly from type strains of Herbaspirillum species with validly published names by DNA–DNA relatedness values, which were <15·7 %. The genomic DNA G+C content of strain CPW301T is 61·3 mol%. The predominant ubiquinone is Q-8 and the major cellular fatty acids are C16 : 0 and cyclo-C17 : 0. The strain does not fix nitrogen and is not plant-associated. It is an aerobic rod with one unipolar flagellum. On the basis of these characteristics, a novel Herbaspirillum species, Herbaspirillum chlorophenolicum sp. nov., is proposed. The type strain of the novel species is strain CPW301T (=KCTC 12096T=IAM 15024T).

Download Full-text

Rapid Assessment of the Physiological Status of the Polychlorinated Biphenyl Degrader Comamonas testosteroni TK102 by Flow Cytometry

Applied and Environmental Microbiology ◽

10.1128/aem.68.4.2031-2035.2002 ◽

2002 ◽

Vol 68 (4) ◽

pp. 2031-2035 ◽

Cited By ~ 36

Author(s):

Yoshinori Hiraoka ◽

Kazuhide Kimbara

Keyword(s):

Flow Cytometry ◽

Polychlorinated Biphenyl ◽

Rapid Assessment ◽

Live Cells ◽

Physiological Status ◽

Comamonas Testosteroni ◽

Double Staining ◽

Permeabilized Cells ◽

Degrading Bacterium ◽

Double Staining Method

ABSTRACT The viability of the polychlorinated biphenyl-degrading bacterium Comamonas testosteroni TK102 was assessed by flow cytometry (FCM) with the fluorogenic ester Calcein-AM (CAM) and the nucleic acid dye propidium iodide (PI). CAM stained live cells, whereas PI stained dead cells. When double staining with CAM and PI was performed, three physiological states, i.e., live (calcein positive, PI negative), dead (calcein negative, PI positive), and permeabilized (calcein positive, PI positive), were detected. To evaluate the reliability of this double-staining method, suspensions of live and dead cells were mixed in various proportions and analyzed by FCM. The proportion of dead cells measured by FCM directly correlated with the proportion of dead cells in the sample (y = 0.9872 x + 0.18; R 2 = 0.9971). In addition, the proportion of live cells measured by FCM inversely correlated with the proportion of dead cells in the sample (y = −0.9776 x + 98.36; R 2 = 0.9962). The proportion of permeabilized cells was consistently less than 2%. These results indicate that FCM in combination with CAM and PI staining is rapid (≤1 h) and distinguishes correctly among live, dead, and permeabilized cells.

Download Full-text

Flow Cytometry Analysis of Changes in the DNA Content of the Polychlorinated Biphenyl Degrader Comamonas testosteroni TK102: Effect of Metabolites on Cell-Cell Separation

Applied and Environmental Microbiology ◽

10.1128/aem.68.10.5104-5112.2002 ◽

2002 ◽

Vol 68 (10) ◽

pp. 5104-5112 ◽

Cited By ~ 22

Author(s):

Yoshinori Hiraoka ◽

Tohru Yamada ◽

Keiko Tone ◽

Yutaka Futaesaku ◽

Kazuhide Kimbara

Keyword(s):

Flow Cytometry ◽

Dna Content ◽

Cell Separation ◽

Polychlorinated Biphenyl ◽

Gene Replacement ◽

Comamonas Testosteroni ◽

Single Chromosome ◽

Degrading Bacterium ◽

Intermediate Metabolites ◽

Cell Cell

ABSTRACT Flow cytometry was used to monitor changes in the DNA content of the polychlorinated biphenyl (PCB)-degrading bacterium Comamonas testosteroni TK102 during growth in the presence or absence of PCBs. In culture medium without PCBs, the majority of stationary-phase cells contained a single chromosome. In the presence of PCBs, the percentage of cells containing two chromosomes increased from 12% to approximately 50%. In contrast, addition of PCBs did not change the DNA contents of three species that are unable to degrade PCBs. In addition, highly chlorinated PCBs that are not degraded by TK102 did not result in a change in the DNA content. These results suggest that PCBs did not affect the DNA content of the cells directly; rather, the intermediate metabolites resulting from the degradation of PCBs caused the increase in DNA content. To study the effect of intermediate metabolites on the DNA content of the cells, four bph genes, bphA1, bphB, bphC, and bphD, were disrupted by gene replacement. The resulting mutant strains accumulated intermediate metabolites when they were grown in the presence of PCBs or biphenyl (BP). When the bphB gene was disrupted, the percentage of cells containing two chromosomes increased in cultures grown with PCBs or BP. When grown with BP, cultures of this mutant accumulated two intermediate metabolites, 2-hydroxybiphenyl (2-OHBP) and 3-OHBP. Addition of 2- or 3-OHBP to a wild-type TK102 and non-PCB-degrading species culture also resulted in an increase in the percentage of cells containing two chromosomes. Electron microscopy revealed that cell-cell separation was inhibited in this culture. This is the first report that hydroxy-BPs can inhibit bacterial cell separation while allowing continued DNA replication.

Download Full-text

Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Comamonas testosteroni KF712 (NBRC 110673)

Genome Announcements ◽

10.1128/genomea.01214-15 ◽

2015 ◽

Vol 3 (5) ◽

Cited By ~ 4

Author(s):

Jun Hirose ◽

Atsushi Yamazoe ◽

Akira Hosoyama ◽

Nobutada Kimura ◽

Hikaru Suenaga ◽

...

Keyword(s):

Genome Sequence ◽

Aromatic Compounds ◽

Polychlorinated Biphenyl ◽

Draft Genome ◽

Gene Clusters ◽

Draft Genome Sequence ◽

Comamonas Testosteroni ◽

Degrading Bacterium

We present a 5.89-Mb draft genome sequence of Comamonas testosteroni KF712 (NBRC 110673), a polychlorinated biphenyl degrader. The genome sequence clarified that KF712 harbors the gene clusters coding for the catabolism of biphenyl and at least seven other aromatic compounds.

Download Full-text