Hot spring siliceous stromatolites from Yellowstone National Park: Assessing growth rate and laminae formation

Geobiology

Volumn 9, Issue 5, 2011, Pages 411-424

  Berelson, W M ^a   Corsetti, F A ^a   Pepe Ranney, C ^b   Hammond, D E ^a   Beaumont, W ^a   Spear, J R ^b  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b Department of Geology and Geological Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CARBON; CESIUM; RADIUM; THORIUM;

BACTERIUM; CARBON DIOXIDE; CARBON FIXATION; CARBONATE; CEMENTATION; CYANOBACTERIUM; EXPERIMENTAL STUDY; FACIES; LAMINATION; LITHIFICATION; MICROBIAL COMMUNITY; MICROBIAL MAT; MOLECULAR ANALYSIS; MORPHOGENESIS; OBSIDIAN; PRESERVATION; RADIOMETRIC METHOD; SILICA; SILICEOUS DEPOSIT; SOLUBILITY; STROMATOLITE; THERMAL SPRING; TRACER;

ARTICLE; BACTERIUM; CHEMISTRY; CLASSIFICATION; COMPUTER ASSISTED DIAGNOSIS; CYANOBACTERIUM; DNA SEQUENCE; EVALUATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; LIMNOLOGY; METHODOLOGY; MICROBIOLOGY; PHYLOGENY; RADIOMETRIC DATING; SCANNING ELECTRON MICROSCOPY; SEDIMENT; THERMAL SPRING; UNITED STATES;

BACTERIA; CARBON RADIOISOTOPES; CESIUM; CYANOBACTERIA; DNA, BACTERIAL; FRESHWATER BIOLOGY; GEOLOGIC SEDIMENTS; HOT SPRINGS; IMAGE INTERPRETATION, COMPUTER-ASSISTED; MICROSCOPY, ELECTRON, SCANNING; PHYLOGENY; RADIOMETRIC DATING; RADIUM; SEQUENCE ANALYSIS, DNA; THORIUM; WYOMING;

UNITED STATES; YELLOWSTONE NATIONAL PARK;

BACTERIA (MICROORGANISMS); CYANOBACTERIA;

EID: 80051944667     PISSN: 14724677     EISSN: 14724669     Source Type: Journal    
DOI: 10.1111/j.1472-4669.2011.00288.x     Document Type: Article

References (64)

1. Allewalt JP, Bateson MM, Revsbech NP, Slack K, Ward DM (2006) Effect of temperature and light on growth of and photosynthesis by Synechococcus isolates typical of those predominating in the Octopus Spring microbial mat community of Yellowstone National Park. Applied and Environmental Microbiology, 72, 544-550.
2. Allwood AC, Walter MR, Kamber BS, Marshall CP, Burch IW (2006) Stromatolite reef from the Early Archaean era of Australia. Nature, 114, 714-718.
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
4. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews, 59, 143-169.
5. Awramik SM, Grey K (2005) Stromatolites: biogenicity, biosignatures, and bioconfusion. Proceedings of SPIE, 5906: 5906P-1-5906P-9.
6. Awramik SM, Riding RE (1988) Role of algal eukaryote in subtidal columnar stromatolite formation. Proceedings of the National Academy of Sciences (USA), 85, 1327-1329.
7. Awramik SM, Vanyo JP (1986) Heliotropism in modern stromatolites. Science, 231, 1279-1281.
8. Barghoorn ES, Tyler SA (1965) Microorganisms from the Gunflint Chert: these structurally preserved Precambrian fossils from Ontario are the most ancient organisms known. Science, 147, 563-575.
9. Benning LG, Phoenix VR, Mountain BW (2005) Biosilicification: the role of cyanobacteria in silica sinter deposition. In Micro-Organisms and Earth Systems: Advances in Geomicrobiology (eds Gadd MG, Semple TK, Lappin-Scott MH). Society for General Microbiology Symposium, Cambridge University Press, Cambridge, pp. 131-150.
10. Bhaya D, Grossman AR, Steunou A-S, Khuri N, Cohan FM, Hamamura N, Melendrez MC, Bateson MM, Ward DM, Heidelberg JF (2007) Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses. The ISME Journal, Multidisciplinary Journal of Microbial Ecology, 1, 703-713.
11. Blank CE, Cady SL, Pace NR (2002) Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone National Park. Applied and Environmental Microbiology, 68, 5123-5135.
12. Bosak T, Bush J, Flynn M, Liang B, Ono S, Petroff AP, Sim MS (2010) Formation and stability of oxygen-rich bubbles that shape photosynthetic mats. Geobiology, 8, 1-11.
13. Brantley SR, Lowenstern JB, Christiansen RL, Smith RB, Heasler H, Waite G, Wicksthermal C (2004) Tracking changes in Yellowstone's restless volcanic system. US Geological Survey Fact Sheet 100-03, 4.
14. Bryant DA, Costas AMG, Maresca JA, Chew AGM, Klatt CG, Bateson MM, Tallon LJ, Hostetler J, Nelson WC, Heidelberg JF, Ward DM (2007) Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic acidobacterium. Science, 317, 523-526.
15. Cady SL, Farmer JD (1996) Fossilization processes in siliceous thermal springs: trends in preservation along thermal gradients. In Evolution of Hydrothermal Ecosystems on Earth (and Mars?), Ciba Foundation Symposium 202. Wiley, Chichester, pp. 150-173.
16. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Gonzalez Peña A, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335-336.
17. Chivas AR, Torgersen T, Polach HA (1990) Growth rates and Holocene development of stromatolites from Shark Bay, Western Australia. Australian Journal of Earth Sciences, 37, 113-121.
18. Dill RF, Shinn EA, Jones AT, Kelly K, Steinen RP (1986) Giant subtidal stromatolites forming in normal salinity waters. Nature, 324, 55-58.
19. Doemel WN, Brock TD (1974) Bacterial stromatolites: origin of laminations. Science, 184, 1083-1085.
20. Dravis JJ (1983) Hardened subtidal stromatolites, Bahamas. Science, 219, 385-386.
21. Dupraz C, Patissina R, Verrecchia EP (2006) Simulation of stromatolite morphospace using 'DLA-CA' growth model': translation of energy in morphology. Sedimentary Geology, 185, 185-203.
22. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
23. Ferris MJ, Kuhl M, Wieland A, Ward DM (2003) Cyanobacterial ecotypes in different optical microenvironments of a 68 Degree C Hot Spring Mat Community revealed by 16S-23S rRNA internal transcribed spacer region variation. Applied and Environmental Microbiology, 69, 2893-2898.
24. Finsinger K, Scholz I, Serrano A, Morales S, Uribe-Lorio L, Mora M, Sittenfeld A, Weckesser J, Hess WR (2008) Characterization of true-branching cyanobacteria from geothermal sites and hot springs of Costa Rica. Environmental Microbiology, 10, 460-473.
25. Fukuda R, Ogawa H, Nagata T, Koike I (1998) Direct determination of carbon and nitrogen contents of natural bacterial assemblages in marine environments. Applied and Environmental Microbiology, 64, 3352-3358.
26. Grotzinger JP (1990) Geochemical model for Proterozoic stromatolite decline. American Journal of Science, 290-A, 80-103.
27. Grotzinger JP, Kasting JF (1993) New constraints on Precambrian ocean composition. Journal of Geology, 101, 235-243.
28. Grotzinger JP, Knoll AH (1999) Stromatolites in Precambrian carbonates; evolutionary mileposts or environmental dipsticks? Annual Review of Earth and Planetary Sciences, 27, 313-358.
29. Grotzinger JP, Rothman DH (1996) An abiotic model for stromatolite morphogenesis. Nature, 383, 423-425.
30. Guidry SA, Chafetz HS (2003) Depositional facies and diagenetic alteration in a relict siliceous hot-spring accumulation: examples from Yellowstone National Park, U.S.A. Journal of Sedimentary Research, 73, 806-823.
31. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature Methods, 5, 235-237.
32. Hinman NW, Lindstrom RF (1996) Seasonal changes in silica deposition in hot springs systems. Chemical Geology, 132, 237-246.
33. Hoffman P (1976) Stromatolite morphogenesis in Shark Bay, Western Australia. In Stromatolites (ed Walter MR). Elsevier Sci. Publ. Co., Amsterdam, Netherlands, pp. 261-271.
34. Hofmann HJ, Grey K, Hickman AH, Thorpe RI (1999) Origin of 3.45Ga coniform stromatolites in Warrawoona Group, Western Australia. Geological Society of America Bulletin, 111, 1256-1262.
35. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998) Novel division level bacterial diversity in a Yellowstone hot spring. Journal of Bacteriology 180, 366-376.
36. Hunter J (2007) Matplotlib: a 2D graphics environment. Computing in Science & Engineering, 9, 90-95.
37. Kempe S, Degens ET (1985) An early soda ocean. Chemical Geology, 53, 95-108.
38. Klatt CG, Bryant DA, Ward DM (2007) Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats. Environmental Microbiology, 9, 2067-2078.
39. Konhauser KO, Jones B, Reysenbach AL, Renaut RW (2003) Hot spring sinters: keys to understanding Earth's earliest life forms. Canadian Journal of Earth Sciences, 40, 1713-1724.
40. Konhauser K, Jones B, Phoenix V, Ferris G, Renaut R (2004) The microbial role in hot spring silicification. Ambio, 33, 552-558.
41. Lane D (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacteria Systematics (eds Stackebrandt E, Goodfellow M). Wiley and Sons, Chichester, UK, p. 329.
42. 2 level in mid-latitudes of the Northern Hemisphere (1959-2003). Radiocarbon, 46, 1261-1272.
43. Logan BW (1961) Cryptozoon and associate stromatolites from the Recent, Shark bay, Western Australia. Journal of Geology, 69, 517-533.
44. Lowe DR (1994) Abiological origin of described stromatolites older than 3.2Ga. Geology, 22, 387-390.
45. McLoughlin NA, Wilson LA, Brasier MD (2008) Growth of synthetic stromatolites and wrinkle structures in the absence of microbes; implications for the early fossil record. Geobiology, 6, 95-105.
46. van der Meer MTJ, Schouten S, Sinninghe-Damsté JS, Ward DM (2007) Impact of carbon metabolism on 13C signatures of cyanobacteria and green non-sulfur-like bacteria inhabiting a microbial mat from an alkaline siliceous hot spring in Yellowstone National Park (USA). Environmental Microbiology, 9, 482-491.
47. Pepe-Ranney C, Berelson WM, Corsetti FA, Treants M, Spear JR (2011) The geobiology of stromatolite construction by cyanobacteria in Yellowstone National Park. (Accepted: Environmental Microbiology and Env. Micro. Reports).
48. Petryshyn VA, Corsetti FA, Berelson WM, Lund SP, Beaumont W (2011) Stromatolite lamination frequency; Walker Lake, Nevada. Implications for stromatolites as biosignatures.
49. Reeder J, Knight R (2010) Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nature Methods 7, 668-669.
50. Reid RP, Visscher PT, Decho AW, Stolz JF, Bebout BM, Dupraz C, Macintyre IG, Paerl HW, Pinckney JL, Prufert-Bebout L, Steppe TF, Des Marais DJ (2000) The role of microbes in accretion, lamination and early lithification of modern marine stromatolites. Nature, 406, 989-992.
51. Riding RE (1990) Calcareous Algae and Stromatolites. Springer-Verlag, New York.
52. Riding RE, Awramik SM (2000) Microbial Sediments. Springer-Verlag, New York.
53. Schouten S, van der Meer MTJ, Hopmans EC, Rijpstra WIC, Reysenbach A-L, Ward DM, Sinninghe Damste JS (2007) Archaeal and bacterial glycerol dialkyl glycerol tetraether lipids in hot springs of Yellowstone National Park. Applied and Environmental Microbiology, 73, 6181-6191.
54. Shapiro RS (2000) A comment on the systematic confusion of thrombolites. Palaios, 15, 166-169.
55. Shock EL, Holland M, Meyer-Dombard DR, Amend JP (2005) Geochemical sources of energy for microbial metabolism in hydrothermal ecosystems: Obsidian Pool, Yellowstone National Park, USA. In Geothermal Biology and Geochemistry of Yellowstone National Park (eds Inskeep WP, McDermott TR). Montana State University Publications, Bozeman, Montana, pp. 95-112.
56. Spear JR, Walker JJ, McCollom TM, Pace NR (2005) Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proceedings of the National Academy of Sciences (USA), 102, 2555-2560.
57. Steunou A-S, Bhaya D, Bateson MM, Melendrez MC, Ward DM, Brecht E, Peters JW, Kühl M, Grossman AR (2006) In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats. Proceedings of the National Academy of Sciences (USA), 103, 2398-2403.
58. Steunou A-S, Jensen SI, Brecht E, Becraft ED, Bateson MM, Kilian O, Bhaya D, Ward DM, Peters JW, Grossman AR, Kuhl M (2008) Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat. The ISME Journal, Multidisciplinary Journal of Microbial Ecology, 2, 364-378.
59. Stuiver M, Polach HA (1977) Discussion: reporting of 14C data. Radiocarbon, 19, 355-363.
60. Visscher PT, Reid RP, Bebout BM (2000) Microscale observations of sulfate reduction: correlation of microbial activity with lithified micritic laminae in modern marine stromatolites. Geology 28, 919-922.
61. Walter MR (1976) Stromatolites. In Developments in Sedimentology 20 (ed. Walter MR). Elsevier, Amsterdam, pp. 790.
62. Walter MR, Bauld J, Brock TD (1972) Siliceous algal and bacterial stromatolites in hot spring and geyser effluents of Yellowstone National Park. Science, 178, 402-405.
63. Weed WH (1889) US Geological Survey Report 9 (1887-1888). 613.
64. Wilmotte A, Van der Auwera G, De Wachter R (1993) Structure of the 16 S ribosomal RNA of the thermophilic cyanobacterium Chlorogloeopsis HTF ('Mastigocladus laminosus HTF') strain PCC7518, and phylogenetic analysis. FEBS Letters, 317, 96-100.