The Exiguobacterium genus: Biodiversity and biogeography

Extremophiles

Volumn 13, Issue 3, 2009, Pages 541-555

  Vishnivetskaya, Tatiana A ^a,c   Kathariou, Sophia ^a   Tiedje, James M ^b  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Exiguobacterium; Macroarray; PFGE; Psychrophilic and thermophilic adaptations

Indexed keywords

BACTERIAL DNA; RNA 16S;

ARTICLE; BACTERIAL GENE; BIODIVERSITY; CLASSIFICATION; GENETICS; GEOGRAPHY; GRAM POSITIVE BACTERIUM; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; POLYMERASE CHAIN REACTION; PULSED FIELD GEL ELECTROPHORESIS;

BIODIVERSITY; DNA, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; GENES, BACTERIAL; GEOGRAPHY; GRAM-POSITIVE BACTERIA; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S;

BACTERIA (MICROORGANISMS); EXIGUOBACTERIUM; POSIBACTERIA;

EID: 67349173563     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-009-0243-5     Document Type: Article

References (58)

1. SF Altschul W Gish W Miller EW Myers DJ Lipman 1990 Basic local alignment search tool J Mol Biol 215 403 410 (Pubitemid 20364473)
2. CR Anderson GM Cook 2004 Isolation and characterization of arsenate-reducing bacteria from arsenic-contaminated sites in New Zealand Curr Microbiol 48 341 347 (Pubitemid 38507013)
3. ES Bogdanova IA Bass LS Minakhin MA Petrova SZ Mindlin AA Volodin ES Kalyaeva JM Tiedje JL Hobman NL Brown VG Nikiforov 1998 Horizontal spread of mer operons among Gram-positive bacteria in natural environments Microbiology 144 609 620 (Pubitemid 28127577)
4. E Bogdanova L Minakhin I Bass A Volodin JL Hobman V Nikiforov 2001 Class II broad-spectrum mercury resistance transposons in Gram-positive bacteria from natural environments Res Microbiol 152 503 514 (Pubitemid 32523928)
5. P Chaturvedi S Shivaji 2006 Exiguobacterium indicum sp nov., a psychrophilic bacterium from the Hamta glacier of the Himalayan mountain ranges of India Int J Syst Evol Microbiol 56 2765 2770
6. P Chaturvedi V Prabahar R Manorama PK Pindi B Bhadra Z Begum S Shivaji 2008 Exiguobacterium soli sp nov., a psychrophilic bacterium from the McMurdo Dry Valleys, Antarctica Int J Syst Evol Microbiol 58 2447 2453
7. MD Collins RM Kroppenstedt 1983 Lipid-composition as a guide to the classification of some coryneform bacteria-containing an A4-alpha type peptidoglycan Syst Appl Microbiol 4 95 104
8. MD Collins BM Lund JAE Farrow KH Schleifer 1983 Chemotaxonomic study of an alkaliphilic bacterium, Exiguobacterium aurantiacum gen nov., sp. nov J Gen Microbiol 129 2037 2042
9. JE Corkill R Graham CA Hart S Stubbs 2000 Pulsed-field gel electrophoresis of degradation-sensitive DNAs from Clostridium difficile PCR ribotype 1 strains J Clin Microbiol 38 2791 2792 (Pubitemid 30485177)
10. S Crapart ML Fardeau JL Cayol P Thomas C Sery B Ollivier Y Combet-Blanc 2007 Exiguobacterium profundum sp nov., a moderately thermophilic, lactic acid-producing bacterium isolated from a deep-sea hydrothermal vent Int J Syst Evol Microbiol 57 287 292 (Pubitemid 46306453)
11. JAE Farrow S Wallbanks MD Collins 1994 Phylogenetic interrelationships of round-spore-forming bacilli containing cell-walls based on lysine and the non-spore-forming genera Caryophanon, Exiguobacterium, Kurthia, and Planococcus Int J Syst Bacteriol 44 74 82 (Pubitemid 24023656)
12. A Fruhling P Schumann H Hippe B Straubler E Stackebrandt 2002 Exiguobacterium undae sp nov. and Exiguobacterium antarcticum sp. nov Int J Syst Evol Microbiol 52 1171 1176
13. JR Gibson K Sutherland RJ Owen 1994 Inhibition of DNase activity in PFGE analysis of DNA from Campylobacter jejuni Lett Appl Microbiol 19 357 358 (Pubitemid 24341743)
14. I Hara N Ichise K Kojima H Kondo S Ohgiya H Matsuyama I Yumoto 2007 Relationship between the size of the bottleneck 15 angstrom from iron in the main channel and the reactivity of catalase corresponding to the molecular size of substrates Biochemistry 46 11 22 (Pubitemid 46067733)
15. DG Higgins PM Sharp 1988 Clustal-a package for performing multiple sequence alignment on a microcomputer Gene 73 237 244 (Pubitemid 19033800)
16. BY Hwang JH Kim J Kim BG Kim 2005 Screening of Exigubacterium acetylicum from soil samples showing enantioselective and alkalitolerant esterase activity Biotechnol Bioprocess Eng 10 367 371 (Pubitemid 41245540)
17. K Ito 2005 Ribosome-based protein folding systems are structurally divergent but functionally universal across biological kingdoms Mol Microbiol 57 313 317 (Pubitemid 40979334)
18. CD Jeffries DF Holtman DG Guse 1957 Rapid method for determining the activity of microorganisms on nucleic acids J Bacteriol 73 590 591
19. RC Kasana SK Yadav 2007 Isolation of a psychrotrophic Exiguobacterium sp. SKPB5 (MTCC 7803) and characterization of its alkaline protease Curr Microbiol 54 224 229 (Pubitemid 46295116)
20. IG Kim MH Lee SY Jung JJ Song TK Oh JH Yoon 2005 Exiguobacterium aestuarii sp nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea Int J Syst Evol Microbiol 55 885 889 (Pubitemid 40485087)
21. King GM, Stetzenbach LD, Klima-Comba A (2005) Analysis of cultivable airborne bacteria from an altitude gradient on Kilauea and Mauna Loa Volcanoes (Hawaii). In: ASM general 105th meeting, ASM Press, Atlanta, GA, pp N-094
22. CHW Klaassen HA van Haren AM Horrevorts 2002 Molecular fingerprinting of Clostridium difficile isolates: Pulsed-field gel electrophoresis versus amplified fragment length polymorphism J Clin Microbiol 40 101 104 (Pubitemid 34027608)
23. Knudston KE, Haas EJ, Iwen PC, Ramaley WC, Ramaley RF (2001) Characterization of a Gram-positive, non-spore-forming Exiguobacterium-like organism isolated from a Western Colorado (USA) hot spring. In: ASM general 101th meeting, ASM Press, Orlando, FL, pp I-92
24. Kumar A, Singh V, Kumar R (2006) Characterization of an alkaliphile, Exiguobacterium sp. and it's application in bioremediation. In: International conference on extremophiles, Brest, France, p L89
25. SL Liu AB Schryvers KE Sanderson RN Johnston 1999 Bacterial phylogenetic clusters revealed by genome structure J Bacteriol 181 6747 6755 (Pubitemid 29517990)
26. L Lopez C Pozo B Rodelas C Calvo B Juarez MV Martinez-Toledo J Gonzalez-Lopez 2005 Identification of bacteria isolated from an oligotrophic lake with pesticide removal capacities Ecotoxicology 14 299 312 (Pubitemid 40576935)
27. A Lopez-Cortes P Schumann R Pukall E Stackebrandt 2006 Exiguobacterium mexicanum sp nov. and Exiguobacterium artemiae sp. nov., isolated from the brine shrimp Artemia franciscana Syst Appl Microbiol 29 183 190
28. BL Maidak JR Cole TG Lilburn CT Parker PR Saxman RJ Farris GM Garrity GJ Olsen TM Schmidt JM Tiedje 2001 The RDP-II (Ribosomal Database Project) Nucleic Acids Res 29 173 174 (Pubitemid 32054439)
29. VI Miteva PP Sheridan JE Brenchley 2004 Phylogenetic and physiological diversity of microorganisms isolated from a deep Greenland glacier ice core Appl Environ Microbiol 70 202 213 (Pubitemid 38090205)
30. E Newnham N Chang DE Taylor 1996 Expanded genomic map of Campylobacter jejuni UA580 and localization of 23S ribosomal rRNA genes by I-CeuI restriction endonuclease digestion FEMS Microbiol Lett 142 223 229 (Pubitemid 26279149)
31. Okeke BC, Laymon J, Oji C, Crenshaw S (2007) Rapid bioreduction of hexavalent chromium in water by Exiguobacterium sp. GS1. In: ASM general 107th meeting, ASM Press, Toronto, ON, Canada, pp Q-199
32. P Pattanapipitpaisal AN Mabbett JA Finlay AJ Beswick M Paterson-Beedle A Essa J Wright MR Tolley U Badar N Ahmed JL Hobman NL Brown LE Macaskie 2002 Reduction of Cr(VI) and bioaccumulation of chromium by Gram-positive and Gram-negative microorganisms not previously exposed to Cr-stress Environ Technol 23 731 745
33. MA Petrova SZ Mindlin ZM Gorlenko ES Kalyaeva VS Soina ES Bogdanova 2002 Mercury-resistant bacteria from permafrost sediments and prospects for their use in comparative studies of mercury resistance determinants Russ J Genet 38 1330 1334 (Pubitemid 135704537)
34. MA Ponder SJ Gilmour PW Bergholz CA Mindock R Hollingsworth MF Thomashow JM Tiedje 2005 Characterization of potential stress responses in ancient Siberian permafrost psychroactive bacteria FEMS Mcirobiol Ecol 53 103 115 (Pubitemid 40733513)
35. YH Qiu S Kathariou DM Lubman 2006 Proteomic analysis of cold adaptation in a Siberian permafrost bacterium-Exiguobacterium sibiricum 255-15 by two-dimensional liquid separation coupled with mass spectrometry Proteomics 6 5221 5233 (Pubitemid 44547162)
36. K Regha AK Satapathy MK Ray 2005 RecD plays an essential function during growth at low temperature in the Antarctic bacterium Pseudomonas syringae Lz4W Genetics 170 1473 1484 (Pubitemid 41362807)
37. B Reiter U Pfeifer H Schwab A Sessitsch 2002 Response of endophytic bacterial communities in potato plants to infection with Erwinia carotovora subsp. atroseptica Appl Environ Microbiol 68 2261 2268 (Pubitemid 34477820)
38. DF Rodrigues JM Tiedje 2007 Multi-locus real-time PCR for quantitation of bacteria in the environment reveals Exiguobacterium to be prevalent in permafrost FEMS Mcirobiol Ecol 59 489 499 (Pubitemid 46105886)
39. DF Rodrigues J Goris T Vishnivetskaya D Gilichinsky MF Thomashow JM Tiedje 2006 Characterization of Exiguobacterium isolates from the Siberian permafrost Description of Exiguobacterium sibiricum sp. nov Extremophiles 10 285 294 (Pubitemid 44325658)
40. DF Rodrigues N Ivanova Z He M Huebner J Zhou JM Tiedje 2008 Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach BMC Genomics 9 547
41. Rozen S, Skaletsky H (2000) Primer 3 on the WWW for general users and for biologist programmers. Bioinformatics methods and protocols: methods in molecular biology. In: Krawetz S, Misener S (eds). Humana Press, Totowa, NJ, pp 365-386
42. K Rutherford J Parkhill J Crook T Horsnell P Rice M Rajandream B Barrell 2000 Artemis: sequence visualization and annotation Bioinformatics 16 944 945
43. N Saitou M Nei 1987 The neighbor-joining method-a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425
44. S Suga N Koyama 2000 Purification and properties of a novel azide-sensitive ATPase of Exiguobacterium aurantiacum Arch Microbiol 173 200 205 (Pubitemid 30143578)
45. Y Suzuki M Haruki K Takano M Morikawa S Kanaya 2004 Possible involvement of an FKBP family member protein from a psychrotrophic bacterium Shewanella sp. SIB1 in cold-adaptation Eur J Biochem 271 1372 1381 (Pubitemid 38519614)
46. K Tamura M Nei S Kumar 2004 Prospects for inferring very large phylogenies by using the neighbor-joining method Proc Natl Acad Sci USA 101 11030 11035 (Pubitemid 38989579)
47. K Tamura J Dudley M Nei S Kumar 2007 MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 Mol Biol Evol 24 1596 1599 (Pubitemid 47236692)
48. S Uma RS Jadhav GS Kumar S Shivaji HK Ray 1999 A RNA polymerase with transcriptional activity at 0 degrees C from the Antarctic bacterium Pseudomonas syringae FEBS Lett 453 313 317 (Pubitemid 29326670)
49. Y Usuda H Kawasaki M Shimaoka T Utagawa 1998 Molecular characterization of guanosine kinase gene from a facultative alkaliphile, Exiguobacterium aurantiacum ATCC 35652 Biochim Biophys Acta-Gene Struct Expr 1442 373 379 (Pubitemid 28530830)
50. TA Vishnivetskaya S Kathariou 2005 Putative transposases conserved in Exiguobacterium isolates from ancient Siberian permafrost and from contemporary surface habitats Appl Environ Microbiol 71 6954 6962 (Pubitemid 43194185)
51. Vishnivetskaya TA, Ramaley R, Rodrigues DF, Tiedje JM, Kathariou S (2005) Exiguobacterium from frozen subsurface sediments (Siberian permafrost) and from other sources have growth temperature ranges reflective of the environmental thermocline of their origin. In: The joint international symposia for subsurface microbiology (ISSM 2005) and environmental biogeochemistry (ISEB XVII), Jackson Hole, WY, p 254
52. TA Vishnivetskaya MA Petrova J Urbance M Ponder CL Moyer DA Gilichinsky JM Tiedje 2006 Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods Astrobiology 6 400 414 (Pubitemid 44138337)
53. TA Vishnivetskaya R Siletzky N Jefferies JM Tiedje S Kathariou 2007 Effect of low temperature and culture media on the growth and freeze-thawing tolerance of Exiguobacterium strains Cryobiology 54 234 240 (Pubitemid 46528449)
54. Vishnivetskaya T, Podar M, Kathariou S, Tiedje JM (2008) Exiguobacterium: the psychrophilic vs the thermophilic lifestyle. In: The 3th international conference on polar and alpine microbiology, Banff, Canada, pp S4-S5
55. M Wada A Yoshizumi Y Furukawa H Kawabata M Ueda H Takagi S Nakamori 2004 Cloning and overexpression of the Exiguobacterium sp. F42 gene encoding a new short chain dehydrogenase, which catalyzes the stereoselective reduction of ethyl 3-oxo-3-(2-thienyl)propanoate to ethyl (S)-3-hydroxy-3-(2-thienyl) propanoate Biosci Biotechnol Biochem 68 1481 1488 (Pubitemid 40059210)
56. P Yarza M Richter J Peplies J Euzeby R Amann KH Schleifer W Ludwig FO Glockner R Rossello-Mora 2008 The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains Syst Appl Microbiol 31 241 250
57. I Yumoto M Hishinuma-Narisawa K Hirota T Shingyo F Takebe Y Nodasaka H Matsuyama I Hara 2004 Exiguobacterium oxidotolerans sp nov., a novel alkaliphile exhibiting high catalase activity Int J Syst Evol Microbiol 54 2013 2017 (Pubitemid 39585381)
58. SP Zheng MA Ponder JY Shih JM Tiedje MF Thomashow DM Lubman 2007 A proteomic analysis of Psychrobacter arcticus 273-4 adaptation to low temperature and salinity using a 2-D liquid mapping approach Electrophoresis 28 467 488 (Pubitemid 46243235)