Isolation and Characterization of Diverse Halobenzoate-Degrading Denitrifying Bacteria from Soils and Sediments

ABSTRACT Denitrifying bacteria capable of degrading halobenzoates were isolated from various geographical and ecological sites. The strains were isolated after initial enrichment on one of the monofluoro-, monochloro-, or monobromo-benzoate isomers with nitrate as an electron acceptor, yielding a total of 33 strains isolated from the different halobenzoate-utilizing enrichment cultures. Each isolate could grow on the selected halobenzoate with nitrate as the terminal electron acceptor. The isolates obtained on 2-fluorobenzoate could use 2-fluorobenzoate under both aerobic and denitrifying conditions, but did not degrade other halobenzoates. In contrast, the 4-fluorobenzoate isolates degraded 4-fluorobenzoate under denitrifying conditions only, but utilized 2-fluorobenzoate under both aerobic and denitrifying conditions. The strains isolated on either 3-chlorobenzoate or 3-bromobenzoate could use 3-chlorobenzoate, 3-bromobenzoate, and 2- and 4-fluorobenzoates under denitrifying conditions. The isolates were identified and classified on the basis of 16S rRNA gene sequence analysis and their cellular fatty acid profiles. They were placed in nine genera belonging to either the α-, β-, or γ-branch of theProteobacteria, namely, Acidovorax,Azoarcus, Bradyrhizobium,Ochrobactrum, Paracoccus,Pseudomonas, Mesorhizobium,Ensifer, and Thauera. These results indicate that the ability to utilize different halobenzoates under denitrifying conditions is ubiquitously distributed in theProteobacteria and that these bacteria are widely distributed in soils and sediments.

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Isolation and characterization of Reyranella massiliensis gen. nov., sp. nov. from freshwater samples by using an amoeba co-culture procedure

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.025775-0 ◽

2011 ◽

Vol 61 (9) ◽

pp. 2151-2154 ◽

Cited By ~ 26

Author(s):

Isabelle Pagnier ◽

Didier Raoult ◽

Bernard La Scola

Keyword(s):

Gene Sequence ◽

Novel Species ◽

Phenotypic Characterization ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Isolation And Characterization ◽

Novel Bacterium ◽

Gene Sequence Analysis ◽

Culture Procedure

The analysis of three water samples from two cooling towers and one river allowed us to isolate three strains of a novel species of the class Alphaproteobacteria which is phylogenetically related to uncultured alphaproteobacteria. Based upon 16S rRNA gene sequence analysis and phenotypic characterization, we propose to name this novel species Reyranella massiliensis gen. nov., sp. nov., type strain 521T ( = CSUR P115T = DSM 23428T). The most closely related cultivable micro-organism to this novel bacterium is a member of the genus Magnetospirillum.

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Construction of TnphoA gene fusions in Rhodobacter sphaeroides: isolation and characterization of a respiratory mutant unable to utilize dimethyl sulfoxide as a terminal electron acceptor during anaerobic growth in the dark on glucose.

Journal of Bacteriology ◽

10.1128/jb.171.8.4385-4394.1989 ◽

1989 ◽

Vol 171 (8) ◽

pp. 4385-4394 ◽

Cited By ~ 20

Author(s):

M D Moore ◽

S Kaplan

Keyword(s):

Dimethyl Sulfoxide ◽

Electron Acceptor ◽

Rhodobacter Sphaeroides ◽

Anaerobic Growth ◽

Gene Fusions ◽

Terminal Electron Acceptor ◽

Isolation And Characterization

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Magnetovibrio blakemorei gen. nov., sp. nov., a magnetotactic bacterium ( Alphaproteobacteria : Rhodospirillaceae ) isolated from a salt marsh

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.044453-0 ◽

2013 ◽

Vol 63 (Pt_5) ◽

pp. 1824-1833 ◽

Cited By ~ 52

Author(s):

Dennis A. Bazylinski ◽

Timothy J. Williams ◽

Christopher T. Lefèvre ◽

Denis Trubitsyn ◽

Jiasong Fang ◽

...

Keyword(s):

Salt Marsh ◽

Electron Acceptor ◽

Anaerobic Growth ◽

Rrna Gene ◽

Magnetotactic Bacterium ◽

Single Chain ◽

Circular Chromosome ◽

Terminal Electron Acceptor ◽

Content Type ◽

Link Type

A magnetotactic bacterium, designated strain MV-1T, was isolated from sulfide-rich sediments in a salt marsh near Boston, MA, USA. Cells of strain MV-1T were Gram-negative, and vibrioid to helicoid in morphology. Cells were motile by means of a single polar flagellum. The cells appeared to display a transitional state between axial and polar magnetotaxis: cells swam in both directions, but generally had longer excursions in one direction than the other. Cells possessed a single chain of magnetosomes containing truncated hexaoctahedral crystals of magnetite, positioned along the long axis of the cell. Strain MV-1T was a microaerophile that was also capable of anaerobic growth on some nitrogen oxides. Salinities greater than 10 % seawater were required for growth. Strain MV-1T exhibited chemolithoautotrophic growth on thiosulfate and sulfide with oxygen as the terminal electron acceptor (microaerobic growth) and on thiosulfate using nitrous oxide (N2O) as the terminal electron acceptor (anaerobic growth). Chemo-organoautotrophic and methylotrophic growth was supported by formate under microaerobic conditions. Autotrophic growth occurred via the Calvin–Benson–Bassham cycle. Chemo-organoheterotrophic growth was supported by various organic acids and amino acids, under microaerobic and anaerobic conditions. Optimal growth occurred at pH 7.0 and 26–28 °C. The genome of strain MV-1T consisted of a single, circular chromosome, about 3.7 Mb in size, with a G+C content of 52.9–53.5 mol%.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MV-1T belongs to the family Rhodospirillaceae within the Alphaproteobacteria , but is not closely related to the genus Magnetospirillum . The name Magnetovibrio blakemorei gen. nov., sp. nov. is proposed for strain MV-1T. The type strain of Magnetovibrio blakemorei is MV-1T ( = ATCC BAA-1436T = DSM 18854T).

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Taxonomic characterization of nine strains isolated from clinical and environmental specimens, and proposal of Corynebacterium tuberculostearicum sp. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02907-0 ◽

2004 ◽

Vol 54 (4) ◽

pp. 1055-1061 ◽

Cited By ~ 33

Author(s):

Carole Feurer ◽

Dominique Clermont ◽

François Bimet ◽

Adina Candréa ◽

Mary Jackson ◽

...

Keyword(s):

Gene Sequence ◽

Fatty Acid Content ◽

Food Samples ◽

Cell Protein ◽

Rrna Gene ◽

Biochemical Tests ◽

Taxonomic Analysis ◽

Gene Sequence Analysis ◽

Taxonomic Characterization

Nine unidentified Gram-positive, lipophilic corynebacteria were isolated from clinical and food samples and subjected to a polyphasic taxonomic analysis. The bacteria were distinguished from Corynebacterium species with validly published names by biochemical tests, fatty acid content and whole-cell protein analysis. Comparative 16S rRNA gene sequence analysis demonstrated unambiguously that the nine strains were related phylogenetically to the species ‘Corynebacterium tuberculostearicum’ and represented a distinct subline within the genus Corynebacterium. On the basis of both phenotypic and phylogenetic evidence, the formal description of Corynebacterium tuberculostearicum sp. nov. is proposed. The type strain of C. tuberculostearicum is Medalle XT (=LDC-20T=CIP 107291T=CCUG 45418T=ATCC 35529T).

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Isolation and characterization of the 5S rRNA gene of Leptospira interrogans.

Journal of Bacteriology ◽

10.1128/jb.172.6.3264-3268.1990 ◽

1990 ◽

Vol 172 (6) ◽

pp. 3264-3268 ◽

Cited By ~ 12

Author(s):

M Fukunaga ◽

I Horie ◽

I Mifuchi

Keyword(s):

5S Rrna ◽

Rrna Gene ◽

Leptospira Interrogans ◽

Isolation And Characterization ◽

5S Rrna Gene

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Isolation and characterization of the ethynylestradiol-biodegrading microorganism Fusarium proliferatum strain HNS-1

Water Science & Technology ◽

10.2166/wst.2002.0424 ◽

2002 ◽

Vol 45 (12) ◽

pp. 175-179 ◽

Cited By ~ 42

Author(s):

J.H. Shi ◽

Y. Suzuki ◽

B.-D. Lee ◽

S. Nakai ◽

M. Hosomi

Keyword(s):

Culture Medium ◽

Polar Compounds ◽

Sole Source ◽

Order Rate Constant ◽

Fusarium Proliferatum ◽

Rrna Gene ◽

28S Rrna ◽

Isolation And Characterization ◽

Phenolic Group

We cultivated hundreds of sediment, soil, and manure samples taken from rivers and farms in a medium containing ethynylestradiol (EE2) as the sole source of carbon, so that microorganisms in the samples would acclimatize to the presence of EE2. Finally, we isolated an EE2-degrading microorganism, designated as strain HNS-1, from a cowshed sample. Based on its partial nucleotide sequence (563 bp) of the 28S rRNA gene, strain HNS-1 was identified as Fusarium proliferatum. Over 15 days, F. proliferatum strain HNS-1 removed 97% of EE2 at an initial concentration of 25 mg.L−1, with a first-order rate constant of 0.6 d−1. Unknown products of EE2 degradation, which may be more polar compounds that have a phenolic group, remained in the culture medium.

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Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64778-0 ◽

2007 ◽

Vol 57 (5) ◽

pp. 941-946 ◽

Cited By ~ 81

Author(s):

Hidenori Hayashi ◽

Kensaku Shibata ◽

Mitsuo Sakamoto ◽

Shinichi Tomita ◽

Yoshimi Benno

Keyword(s):

Fatty Acid ◽

Sequence Similarity ◽

Cellular Fatty Acid ◽

Rrna Gene ◽

Fatty Acid Profiles ◽

Phenotypic Characteristics ◽

Human Faeces ◽

Gene Sequence Analysis ◽

Type Strains ◽

Fatty Acid Compositions

Six strains (CB7T, CB18, CB23, CB26, CB28 and CB35T) were isolated from human faeces. Based on phylogenetic analysis, phenotypic characteristics, cellular fatty acid profiles and menaquinone profiles, these strains could be included within the genus Prevotella and made up two clusters. 16S rRNA gene sequence analysis indicated that five strains were most closely related to Prevotella veroralis, sharing about 92 % sequence similarity; the remaining strain was most closely related to Prevotella shahii, sharing about 90 % sequence similarity. All six strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid compositions of the six strains differed significantly from those of other Prevotella species. Five strains (CB7T, CB18, CB23, CB26 and CB28) contained dimethyl acetals and the major menaquinones of these strains were MK-11, MK-12 and MK-13. The major menaquinones of CB35T were MK-12 and MK-13. Based on phenotypic and phylogenetic findings, two novel species, Prevotella copri sp. nov. and Prevotella stercorea sp. nov., are proposed, representing the two different strain clusters. The DNA G+C contents of strains CB7T and CB35T were 45.3 and 48.2 mol%, respectively. The type strains of P. copri and P. stercorea are CB7T (=JCM 13464T=DSM 18205T) and CB35T (=JCM 13469T=DSM 18206T), respectively.

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Isolation and Characterization of Levoglucosan Metabolizing Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.01868-21 ◽

2021 ◽

Author(s):

Ajay S. Arya ◽

Minh T. H. Hang ◽

Mark A. Eiteman

Keyword(s):

Recombinant Expression ◽

Bacterial Species ◽

Soluble Carbohydrate ◽

Rrna Gene ◽

Gene Products ◽

16S Rrna Gene Sequences ◽

E Coli ◽

Isolation And Characterization ◽

Charred Wood

Bacteria were isolated from wastewater and soil containing charred wood remnants based on their ability to use levoglucosan as a sole carbon source and on their levoglucosan dehydrogenase (LGDH) activity. On the basis of their 16S rRNA gene sequences, these bacteria represented diverse genera of Microbacterium, Paenibacillus , Shinella , and Klebsiella . Genomic sequencing of the isolates verified that two isolates represented novel species, Paenibacillus athensensis MEC069 T and Shinella sumterensis MEC087 T , while the remaining isolates were closely related to either Microbacterium lacusdiani or Klebsiella pneumoniae . The genetic sequence of LGDH, lgdA , was found in the genomes of these four isolates as well as Pseudarthrobacter phenanthrenivorans Sphe3. The identity of the P. phenanthrenivorans LGDH was experimentally verified following recombinant expression in E. coli . Comparison of the putative genes surrounding lgdA in the isolate genomes indicated that several other gene products facilitate the bacterial catabolism of levoglucosan, including a putative sugar isomerase and several transport proteins. Importance Levoglucosan is the most prevalent soluble carbohydrate remaining after high temperature pyrolysis of lignocellulosic biomass, but it is not fermented by typical production microbes such as Escherichia coli and Saccharomyces cerevisiae . A few fungi metabolize levoglucosan via the enzyme levoglucosan kinase, while several bacteria metabolize levoglucosan via levoglucosan dehydrogenase. This study describes the isolation and characterization of four bacterial species which degrade levoglucosan. Each isolate is shown to contain several genes within an operon involved in levoglucosan degradation, furthering our understanding of bacteria which metabolize levoglucosan.

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Halomonas daqiaonensis sp. nov., a moderately halophilic, denitrifying bacterium isolated from a littoral saltern

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.026344-0 ◽

2011 ◽

Vol 61 (7) ◽

pp. 1612-1616 ◽

Cited By ~ 12

Author(s):

Lingyun Qu ◽

Qiliang Lai ◽

Fengling Zhu ◽

Xuguang Hong ◽

Jinxing Zhang ◽

...

Keyword(s):

Gene Sequence ◽

East Coast ◽

Novel Species ◽

Cellular Fatty Acid ◽

Rrna Gene ◽

Fatty Acid Profiles ◽

Rrna Gene Sequence ◽

Bacterial Strains ◽

Cellular Fatty Acids ◽

Gene Sequence Analysis

Two novel Gram-negative, oxidase- and catalase-positive, rod-shaped bacterial strains, designated YCSA28T and YCSA39, were isolated from sediment of Daqiao saltern, Jimo, Qingdao, on the east coast of China. The two strains grew optimally at 28–30 °C, at pH 7.5 and in the presence of 7–8 % (w/v) NaCl. They were assigned to the genus Halomonas, class Gammaproteobacteria, based on 16S rRNA gene sequence analysis. The major cellular fatty acids of the two strains were C18 : 1ω7c (42.9 %), C16 : 0 (23.1 %) and C16 : 1ω7c/ω6c (18.0 %), and Q-9 was the major ubiquinone. The G+C content of the DNA of strains YCSA28T and YCSA39 was 63.7 and 63.9 mol%, respectively. The predominant respiratory lipoquinone, cellular fatty acid profiles and DNA G+C content of strains YCSA28T and YCSA39 were consistent with those of recognized species of the genus Halomonas. Levels of DNA–DNA relatedness between strains YCSA28T and YCSA39, between YCSA28T and Halomonas ventosae Al12T, and between YCSA39 and H. ventosae Al12T were 95, 45 and 50 %, respectively. Together, these data indicated that strains YCSA28T and YCSA39 represent a single novel species of the genus Halomonas, for which the name Halomonas daqiaonensis sp. nov. is proposed. The type strain is YCSA28T ( = CGMCC 1.9150T = NCCB 100305T = MCCC 1B00920T).

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