[FeFe]-hydrogenase in Yellowstone National Park: Evidence for dispersal limitation and phylogenetic niche conservatism

ISME Journal

Volumn 4, Issue 12, 2010, Pages 1485-1495

  Boyd, Eric S ^a   Hamilton, Trinity L ^a   Spear, John R ^b   Lavin, Matthew ^a   Peters, John W ^a  

^a MONTANA STATE UNIVERSITY   (United States)

^b Department of Metallurgical and Materials Engineering   (United States)

Author keywords

FeFe hydrogenase; dispersal limitation; HydA; niche conservatism; pH; Yellowstone National Park

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; BACTERIOCHLOROPHYLL; HYDROGEN; HYDROGENASE; IRON HYDROGENASE; IRON SULFUR PROTEIN;

BACTERIUM; BIODEGRADATION; DISPERSAL; ENZYME ACTIVITY; FERMENTATION; GEOTHERMAL SYSTEM; HYDROGEN; MICROBIAL COMMUNITY; ORGANIC CARBON; PH; PHYLOGENETICS; PHYSICOCHEMICAL PROPERTY; SPECIES DIVERSITY;

ARTICLE; BACTERIUM; BIOLOGICAL MODEL; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; ECOSYSTEM; ENZYMOLOGY; GENETICS; METABOLISM; MICROBIOLOGY; PH; PHYLOGENY; THERMAL SPRING; UNITED STATES;

BACTERIA; BACTERIAL PROTEINS; BACTERIOCHLOROPHYLLS; DNA, BACTERIAL; ECOSYSTEM; HOT SPRINGS; HYDROGEN; HYDROGEN-ION CONCENTRATION; HYDROGENASE; IRON-SULFUR PROTEINS; MODELS, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA; WYOMING;

UNITED STATES; YELLOWSTONE NATIONAL PARK;

BACTERIA (MICROORGANISMS);

EID: 78649448514     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2010.76     Document Type: Article

References (56)

1. Abascal F, Zardoya R, Posada D. (2005). ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105.
2. Anderson KL, Tayne TA, Ward DM. (1987). Formation and fate of fermentation products in hot spring cyanobacterial mats. Appl Environ Microbiol 53:2343-2352.
3. Apps JA, van de Kamp PC. (1993). Energy gases of abiogenic origin in the Earth's crust. The future of energy gases. US Geol Survey 1570:81-132.
4. Boyd ES, Jackson RA, Encarnacion G, Zahn JA, Beard T, Leavitt WD. et al. (2007). Isolation, characterization, and ecology of sulfur-respiring Crenarchaea inhabiting acid-sulfate-chloride geothermal springs in Yellowstone National Park. Appl Environ Microbiol 73:6669-6677.
5. 2 uptake and fixation by a thermoacidophilic microbial community attached to precipitated sulfur in a geothermal spring. Appl Environ Microbiol 75:4289-4296.
6. Boyd ES, Spear JR, Peters JW. (2009b). [FeFe]-hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community. Appl Environ Microbiol 75:4620-4623.
7. Burke DH, Hearst JE, Sidow A. (1993). Early evolution of photosynthesis: clues from nitrogenase and chlorophyll iron proteins. Proc Natl Acad Sci USA 90:7134-7138.
8. Cardace D, Hoehler TM. (2009). Serpentinizing fluids craft microbial habitat. Northeastern Naturalist 16:272-284.
9. Chapelle FH, O'Neill K, Bradley PM, Methé BA, Ciufo SA, Knobel LL et al. (2002). A hydrogen-based subsurface microbial community dominated by methanogens. Nature 415:312-315.
10. Chivian D, Brodie EL, Alm EJ, Culley DE, Dehal PS, DeSantis TZ et al. (2008). Environmental genomics reveals a single-species ecosystem deep within Earth. Science 322:275-278.
11. Conrad R, Bonjour F, Aragno M. (1985). Aerobic and anaerobic microbial consumption of hydrogen in geothermal spring water. FEMS Microbiol Lett 29:201-205.
12. Cox AD, Shock EL. (2003). American Geophysical Union: San Francisco, abstract number 2003AGUFM. B41D0927C.
13. Dumbrell AJ, Nelson M, Helgason T, Dytham C, Fitter AH. (2010). Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J 4:337-345.
14. Fournier RO. (2005). Geochemistry and dynamics of the Yellowstone National Park Hydrothermal System. In: Inskeep WP, McDermott TR (eds). Geothermal Biology and Geochemistry in Yellowstone National Park. Montana State University: Bozeman, pp 143-162.
15. Frey M. (2002). Hydrogenases: hydrogen-activating enzymes. Chembiochem 3:153-160.
16. Gold T. (1992). The deep, hot biosphere. Proc Natl Acad Sci USA 89:6045-6049.
17. Goslee SC, Urban DL. (2007). The ecodist package for dissimilarity-based analysis of ecological data. J Stat Softw 22:1-19.
18. Harvey PH, Pagel MD. (1991). The Comparative Method in Evolutionary Biology. Oxford University Press: Oxford, UK.
19. Hoehler TM, Bebout BM, Des Marais DJ. (2001). The role of microbial mats in the production of reduced gases on the early Earth. Nature 412:324-327.
20. Hubbell SP. (2001). The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press: Princeton, NJ.
21. Huelsenbeck JP, Ronquist R. (2001). MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
22. Inskeep WP, McDermott TR. (2005). Geomicrobiology of acid-sulfate- chloride springs in Yellowstone National Park. In: Inskeep WP, McDermott TR (eds). Geothermal Biology and Geochemistry in Yellowstone National Park. Montana State University: Bozeman, pp 143-162.
23. Jannasch HW, Mottl MJ. (1985). Geomicrobiology of deepsea hydrothermal vents. Science 229:717-725.
24. Johnson JB, Omland KS. (2004). Model selection in ecology and evolution. Trends Ecol Evol 19:101-108.
25. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
26. Lauber CL, Hamady M, Knight R, Fierer N. (2009). Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111-5120.
27. Lehr CR, Frank SD, Norris TB, D'Imperio S, Kalinin AV, Toplin JA et al. (2007). Cyanidia (Cyanidiales) population diversity and dynamics in an acid-sulfatechloride spring in Yellowstone National Park. J Phycol 43:3-14.
28. 2, a potential energy source for the deep subsurface biosphere. Geochim Cosmochim Acta 69:893-903.
29. Lozupone CA, Knight R. (2007). Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104:11436-11440.
30. Martiny J B H, Bohannan B J M, Brown JH, Colwell RK, Fuhrman JA, Green JL et al. (2006). Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102-112.
31. McCann KS. (2000). The diversity-stability debate. Nature 405:228-233.
32. 2 the universal energy source for long-term survival? Microbiol Ecol 38:307-320.
33. Newton RJ, Jones SE, Helmus MR, McMahon KD. (2007). Phylogenetic ecology of the freshwater Actinobacteria acI lineage. Appl Environ Microbiol 73:7169-7176.
34. Nordstrom DK, Ball JW, McCleskey RB. (2005). Ground water to surface water: chemistry of thermal outflows in Yellowstone National Park. In: Inskeep WP, McDermott TR (eds). Geothermal Biology and Geochemistry in Yellowstone National Park. Montana State University: Bozeman, pp 143-162.
35. Oze C, Sharma M. (2005). Have olivine, will gas: serpentinization and the abiogenic production of methane on Mars. Geophys Res Lett 32:L10203.
36. 2 in planetary surfaces. Icarus 186:557-561.
37. Papke RT, Ramsing NB, Bateson MB, Ward DM. (2003). Geographical isolation in hot spring cyanobacteria. Environ Microbiol 5:650-659.
38. R Development Core Team (2010). R Foundation for Statistical Computing: Vienna, Austria. http://www.r-project.org/contributors.html.
39. Revsbech NP, Ward DM. (1984). Microelectrode studies of interstitial water chemistry and photosynthetic activity in a hot spring microbial mat. Appl Environ Microbiol 48:270-275.
40. Sanderson MJ. (2002). Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol 19:101-109.
41. Schink B. (1997). Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61:262-280.
42. Schloss PD, Handelsman J. (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501-1506.
43. Shock EL, Holland ME. (2007). Quantitative habitability. Astrobiology 7:839-851.
44. Spear JR, Walker JJ, McCollom TM, Pace NR. (2005). Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proc Natl Acad Sci USA 102:2555-2560.
45. Stevens TO, McKinley JP. (1995). Lithoautotrophic microbia, ecosystems in deep basalt aquifers. Science 270:450-454.
46. 2 production from basalt-water reactions and implications for aquifer biogeochemistry. Environ Sci Technol 34:826-831.
47. Takacs-Vesbach C, Mitchell K, Jackson-Weaver O, Reysenbach A-L. (2008). Volcanic calderas delineate biogeographic provinces among Yellowstone thermophiles. Environ Microbiol 10:1681-1689.
48. Tilman D, Knops J, Wedin D, Reich P, Ritchie M, Siemann E. (1997). The influence of functional diversity and composition on ecosystem processes. Science 277:1300-1302.
49. Vignais PM, Billoud B, Meyer J. (2001). Classification and phylogeny of hydrogenases. FEMS Microbiol Rev 25:455-501.
50. Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT et al. (2007). Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560-565.
51. Webb CO. (2000). Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am Naturalist 156:145-155.
52. Webb CO, Ackerly DD, Kembel SW. (2008). Phylocom: software for the analysis of phylogenetic community structure and character evolution. Bioinformatics 24:2098-2100.
53. Whitaker RJ, Grogan DW, Taylor JW. (2003). Geographic barriers isolate endemic populations of hyperthermophilic Archaea. Science 301:976-978.
54. Wiens JJ. (2004). Speciation and ecology revisited: phylogenetic niche conservatism and the origin of species. Evolution 58:193-197.
55. Wolin MJ. (1982) In: Bull AT, Slater JH (eds). Microbial Interactions and Communities, Vol. 1. Academic Press: London, England, pp 323-356.
56. 2-coproducing system, analyzed using the [Fe]-hydrogenase gene. Appl Environ Microbiol 74:1232-1239.