March 2015 – Wayne Nicholson Lab – Proposal to rename Carnobacterium inhibens to Carnobacterium inhibens subsp. inhibens and description of Carnobacterium inhibens subsp. gilichinskyi subsp. nov., a novel psychrotolerant bacterium isolated from Siberian permafrost

Published: May 26th, 2015

Category: Uncategorized

Abstract

A novel, psychrotolerant, facultative anaerobe, strain WN1359, was isolated from a permafrost borehole sample collected at the right bank of the Kolyma River in Siberia, Russia. Gram-positive staining, non-motile rod-shaped cells were observed with sizes of 1-2 μm long and 0.4-0.5 μm wide. Growth occurred in the pH range of 5.8-9.0 with optimum growth range at pH 7.8-8.6 (pH optimum 8.2). The novel isolate grew from 0-37˚C and optimal growth occurred at 25˚C. The novel isolate does not require NaCl; growth was observed between 0% and 8.8% (1.5 M) NaCl with optimum growth at 0.5%. The isolate was a catalase-negative, facultatively anaerobic, chemoorganoheterotroph that used as substrates sugars but not several single amino acids or dipeptides. The major metabolic end product was lactic acid in the ratio of 86% L-lactate :14% D-lactate. Strain WN1359 was sensitive to ampicillin, chloramphenicol, fusidic acid, lincomycin, monocycline, rifampicin, rifamycin SV, spectinomycin, streptomycin, troleandomycin, and vancomycin, and resistant to nalidixic acid and aztreonam. Fatty acid composition was predominantly unsaturated (70.9%), branched-chain unsaturated (11.7%) and saturated (12.5%). G+C content was 35.3 mol% by whole genome sequence analysis. 16S rRNA gene sequence analysis showed 98.7% sequence similarity between strain WN1359 and Carnobacterium inhibens. Genome relatedness was computed using both Genome-to-Genome Distance Analysis (GGDA) and Average Nucleotide Identity (ANI), which both strongly supported strain WN1359 belonging to the species C. inhibens. On the basis of these results, the permafrost isolate WN1359 represents a novel subspecies of C. inhibens, for which the name Carnobacterium inhibens subsp. gilichinskyi subsp. nov. is proposed The type strain is WN1359T (=ATCC BAA-2557T, =DSM27470T). The subspecies Carnobacterium inhibens subsp. inhibens subsp. nov. is automatically created. An emended description of C. inhibens is also provided.

 

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LEARN MORE ABOUT DR. WAYNE NICHOLSON!

ProfessorNicholson300

Department of Microbiology and Cell Science University of Florida

Florida Space Life Sciences Laboratory, Kennedy Spcae Center, FL
Ph.D. (1987) University of Wisconsin-Madison
Postdoctoral (1987-1990) University of Connecticut Health Center

Contact Information

321-261-3773
wln@ufl.edu

Description of Research

Mechanisms of bacterial spore resistance and longevity.

Bacterial endospores are the longest-lived cells known, and exhibit a high degree of resistance to extremes of temperature, desiccation, pressure, and radiation over extended time periods.  Spore DNA is a major target lethal and mutagenic damage, and research in our lab concentrates on mechanisms that protect spore DNA from damage and by which DNA damage is repaired during spore germination, using the model organism Bacillus subtilis. Understanding spore resistance has important applications in a variety of fields ranging from public health and bioterrorism to geomicrobiology and astrobiology.

Survival and proliferation of microorganisms in extreme extraterrestrial environments.

A portion of the spore resistance and longevity research in our lab is concentrated on placing physical constraints on lithopanspermia theory, which postulates the transfer of viable microorganisms between planets as the result of natural impact processes. Such research has important implications in the fields of astrobiology and in planetary protection research.

Microbial evolution in novel environments.

We have been conducting laboratory-scale evolution experiments of B. subtilis cells cultivated for thousands of generations in the presence or absence of strong selective pressure for sporulation. We have uncovered a number of interesting processes which occur during bacterial evolution.  We have isolated a number of spontaneous mutations in the RNA polymerase beta subunit that cause global changes in B. subtilis cell physiology and transcription. Our current plans are to extend these studies to microbial evolution in the space environment.

Publications in Pub Med

Selected Publications

Moeller R, Reitz G, Berger T, Okayasu R, Nicholson WL, Horneck G. Astrobiological aspects of the mutagenesis of cosmic radiation on bacterial spores. Astrobiology. 2010 Jun;10(5):509-21. PubMed PMID: 20624059.

Fajardo-Cavazos P, Schuerger AC, Nicholson WL. Exposure of DNA and Bacillus subtilis spores to simulated martian environments: use of quantitative PCR (qPCR) to measure inactivation rates of DNA to function as a template molecule. Astrobiology. 2010 May;10(4):403-11. PubMed PMID: 20528195.

R, Douki T, Rettberg P, Reitz G, Cadet J, Nicholson WL, Horneck G. Genomic bipyrimidine nucleotide frequency and microbial reactions to germicidal UV radiation. Arch Microbiol. 2010 Jul;192(7):521-9. Epub 2010 May 8. PubMed PMID: 20454780.

Hintze PE, Nicholson WL. Single-spore elemental analyses indicate that dipicolinic acid-deficient Bacillus subtilis spores fail to accumulate calcium. Arch Microbiol. 2010 Jun;192(6):493-7. Epub 2010 Apr 16. PubMed PMID: 20396869.

Rivas-Castillo AM, Yasbin RE, Robleto E, Nicholson WL, Pedraza-Reyes M. Role of the Y-family DNA polymerases YqjH and YqjW in protecting sporulating Bacillus subtilis cells from DNA damage. Curr Microbiol. 2010 Apr;60(4):263-7. Epub 2009 Nov 19. PubMed PMID: 19924481.

Fajardo-Cavazos P, Langenhorst F, Melosh HJ, Nicholson WL. Bacterial spores in granite survive hypervelocity launch by spallation: implications for lithopanspermia. Astrobiology. 2009 Sep;9(7):647-57. PubMed PMID: 19778276.

Nicholson WL, Schuerger AC, Race MS. Migrating microbes and planetary protection. Trends Microbiol. 2009 Sep;17(9):389-92. Epub 2009 Aug 31. PubMed PMID: 19726193.

Moeller R, Setlow P, Reitz G, Nicholson WL. Roles of small, acid-soluble spore proteins and core water content in survival of Bacillus subtilis spores exposed to environmental solar UV radiation. Appl Environ Microbiol. 2009 Aug;75(16):5202-8. Epub 2009 Jun 19. PubMed PMID: 19542328; PubMed Central PMCID: PMC2725452.

Nicholson WL. Ancient micronauts: interplanetary transport of microbes by cosmic impacts. Trends Microbiol. 2009 Jun;17(6):243-50. Epub 2009 May 21. Review. PubMed PMID: 19464895.

Nicholson WL, Fedenko J, Schuerger AC. Carbon-13 (13C) labeling of Bacillus subtilis vegetative cells and spores: suitability for DNA stable isotope probing (DNA-SIP) of spores in soils. Curr Microbiol. 2009 Jul;59(1):9-14. Epub 2009 Mar 11. PubMed PMID: 19280259.

Perkins AE, Schuerger AC, Nicholson WL. Isolation of rpoB mutations causing rifampicin resistance in Bacillus subtilis spores exposed to simulated Martian surface conditions. Astrobiology. 2008 Dec;8(6):1159-67. PubMed PMID: 19191541.

Maughan H, Birky CW Jr, Nicholson WL. Transcriptome divergence and the loss of plasticity in Bacillus subtilis after

6,000 generations of evolution under relaxed selection for sporulation. J Bacteriol. 2009 Jan;191(1):428-33. Epub 2008 Oct 24. PubMed PMID: 18952793; PubMed Central PMCID: PMC2612453.

Nicholson WL. The Bacillus subtilis ydjL (bdhA) gene encodes acetoin reductase/2,3-butanediol dehydrogenase. Appl Environ Microbiol. 2008 Nov;74(22):6832-8. Epub 2008 Sep 26. PubMed PMID: 18820069; PubMed Central PMCID: PMC2583490.

Fajardo-Cavazos P, Schuerger AC, Nicholson WL. Persistence of biomarker ATP and ATP-generating capability in bacterial cells and spores contaminating spacecraft materials under earth conditions and in a simulated martian environment. Appl Environ Microbiol. 2008 Aug;74(16):5159-67. Epub 2008 Jun 20. PubMed PMID: 18567687; PubMed Central PMCID: PMC2519281.

Moeller R, Setlow P, Horneck G, Berger T, Reitz G, Rettberg P, Doherty AJ, Okayasu R, Nicholson WL. Roles of the major, small, acid-soluble spore proteins and spore-specific and universal DNA repair mechanisms in resistance of Bacillus subtilis spores to ionizing radiation from X rays and high-energy charged-particle bombardment. J Bacteriol. 2008 Feb;190(3):1134-40. Epub 2007 Nov 30. PubMed PMID: 18055591; PubMed Central PMCID: PMC2223577.

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