Functional biogeography as evidence of gene transfer in hypersaline microbial communities

PLoS ONE

Volumn 5, Issue 9, 2010, Pages

  Jacob Parnell, J ^a   Rompato, Giovanni ^a   Latta IV, Leigh C ^a   Pfrender, Michael E ^a,d   van Nostrand, Joy D ^b   He, Zhili ^b   Zhou, Jizhong ^b   Andersen, Gary ^c   Champine, Patti ^a   Ganesan, Balasubramanian ^a   Weimer, Bart C ^a,e  

^a UTAH STATE UNIVERSITY   (United States)

^b UNIVERSITY OF OKLAHOMA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF NOTRE DAME   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; BACTERIAL DNA; SODIUM CHLORIDE;

ARTICLE; BIOGEOGRAPHY; DNA MICROARRAY; GENETIC SIMILARITY; HORIZONTAL GENE TRANSFER; MICROARRAY ANALYSIS; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; SALT LAKE; BACTERIUM; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; UNITED STATES;

BACTERIA (MICROORGANISMS);

BACTERIA; DNA, BACTERIAL; GENE TRANSFER, HORIZONTAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SODIUM CHLORIDE; UTAH; WATER MICROBIOLOGY;

EID: 77958609404     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012919     Document Type: Article

References (48)

1. Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6: 431-440.
2. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 103: 626-631.
3. Green JL, Bohannan BJM (2006) Spatial scaling of microbial biodiversity. Trends Ecol Evol 21: 510-517.
4. Green JL, Bohannan BJM, Whitaker RJW (2008) Microbial biogeography: from taxonomy to traits. Science 320: 1029-1043.
5. Horner-Devine MC, Lage M, Hughes JB, Bohannan BJM (2004) A taxa-area relationship for bacteria. Nature 432: 750-753.
6. Lozupone CA, Knight R (2007) Global patterns in bacterial diversity. Proc Natl Acad Sci U S A 104: 11436-11440.
7. Strom SL (2008) Microbial ecology of ocean biogeochemistry: a community perspective. Science 320: 1043-1045.
8. Slater FR, Bailey MJ, Tett AJ, Turner SL (2008) Progress towards understanding the fate of plasmids in bacterial communities. FEMS Microbiol Ecol 66: 3-13.
9. Zhou J, Kang S, Schadt CW, Garten CT (2008) Spatial scaling of functional gene diversity across various microbial taxa. Proc Natl Acad Sci U S A 105: 7768-7773.
10. Brown JR (2003) Ancient horizontal gene transfer. Nat Rev Genetics 4: 121-132.
11. Pal C, Papp B, Lercher MJ (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genetics 37: 1372-1375.
12. Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3: 711-721.
13. Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Bio Evol 19: 2226-2238.
14. Feil EJ, Holmes EC, Bessen DE, Chan MS, Day NP, et al. (2001) Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc Natl Acad Sci U S A 98: 182-187.
15. Lo I, Denef VJ, Verberkmoes NC, Shah MB, Goltsman D, et al. (2007) Strainresolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446: 537-541.
16. Xia X, Wei T, Xie Z, Danchin A (2002) Genomic changes in nucleotide and dinucleotide frequencies in Pasteurella multocida cultured under high temperature. Genetics 161: 1385-1394.
17. Klosterand M, Tang C (2008) SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation. Nucleic Acids Res 36: 3819-3827.
18. Puigbo P, Guzman E, Romeu A, Garcie-Vallve S (2007) OPTIMIZER: a web server for opotimizing the codon usage of DNA sequences. Nucleic Acids Res 35: W126-131.
19. Putoni C, Luo Y, Katili C, Chumakov S, Fox GE, et al. (2006) A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences. Mol Biol Evol 23: 1863-1868.
20. Azadand RK, Lawrence JG (2007) Detecting laterally transferred genes: use of entropic clustering methods and genome position. Nucleic Acids Res 35: 4629-4639.
21. Tsirigos A, Rigoutsos I (2005) A new computational method for the detection of horizontal gene transfer events. Nucleic Acids Res 33: 922-933.
22. Smets BF, Barkay T (2005) Horizontal gene transfer: perspectives at a crossroads of scientific disciplines. Nat Rev Microbiol 3: 675-678.
23. Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3: 711-721.
24. Dinsdale EA, Edwares RA, Hall D, Angly F, Briebart M, et al. (2008) Functional metagenomic profiling of nine biomes. Nature 452: 629-632.
25. Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3: 722-732.
26. Kassen R, Rainey PB (2004) The ecology and genetics of microbial diversity. Annu Rev Microbiol 58: 207-231.
27. Brandt KK, Vester F, Jensen AN, Ingvorsen K (2001) Sulfate reduction dynamics and enumeration of sulfate-reducing bacteria in hypersaline sediments of the Great Salt Lake (Utah, USA). Microb Ecol 41: 1-11.
28. Naftz D, Angeroth C, Kenney T, Waddell B, Darnall N, et al. (2008) Anthropogenic influences on the input and biogeochemical cycling of nutrients and mercury in Great Salt Lake, Utah, USA. Appl Geochem 23: 1731-1744.
29. Brodie EL, DeSantis TZ, Moeberg Parker JJ, Zubietta IX, Piceno YM, et al. (2007) Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci U S A 104: 299-304.
30. He Z, Gentry TJ, Schadt CW, Wu L, Leibich J, et al. (2007) GeoChip: A comprehensive microarray for investigating biogeochemical, ecological, and environmental processes. ISME J 1: 67-77.
31. Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66: 5488-5491.
32. Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316-322.
33. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.
34. Yergeau E, Kang S, He Z, Zhou J, Kowalchuk GA (2007) Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J 1: 163-179.
35. Raes J, O Korbel J, Lercher MJ, von Mering C, Bork P (2007) Prediction of effective genome size in metagenomic samples. Genome Biol 8: r10.
36. Bentley SD, Parkhill J (2004) Comparative genomic structure of prokaryotes. Annu Rev Genet 38: 771-792.
37. Tamames J, Moyá A (2008) Estimating the extent of horizontal gene transfer in metagenomic sequences. BMC Genomics 9: 136.
38. Wang F, Zhou H, Meng J, Peng Z, Jiang L, et al. (2009) GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc Natl Acad Sci U S A 109: 4840-4845.
39. Van Nostrand JD, Wu WM, Wu L, Deng Y, Carley J, et al. (2009) GeoChipbased analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. Environ Microbiol 11: 2611-2626.
40. Hardin G (1960) The competitive exclusion principle. Science 131: 1292-1297.
41. Parnell JJ, Crowl TA, Weimer BC, Pfrender ME (2009) Biodiversity in microbial communities: system scale patterns and mechanisms. Mol Ecol 18: 1455-1462.
42. Lefebure T, Stanhope MJ (2007) Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol 8: R71.
43. Sullivan MB, Lindell DL, Lee JA, Thompson L, Bielawski JP, et al. (2006) Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biology 4: e234.
44. Lonegran DJ, Jenter HL, Coates JD, Phillips EJP, Schmidt TM, et al. (1996) Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria. Appl Environ Microbiol 178: 2402-2408.
45. Branco R, Chung AP, Johnston T, Gurel V, Morais P, et al. (2008) The chromate-inducible chrBACF operon from the transposable element TnOtChr confers resistance to chromium(VI) and superoxide. J Bacteriol 190: 6996-7003.
46. Wu QL, Zwart G, Schauer M, Kamst-van Agterveld MP, Hahn MW (2006) Bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the Tibetan Plateua, China. Appl Environ Microbiol 72: 5478-5485.
47. Kurland CG, Canback B, Berg OG (2003) Horizontal gene transfer: A critical view. Proc Natl Acad Sci U S A 100: 9658-9662.
48. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.