Nitrospira-dominated biofilm within a thermal artesian spring: A case for nitrification-driven primary production in a geothermal setting

Geobiology

Volumn 10, Issue 5, 2012, Pages 457-466

  Marks, C R ^a   Stevenson, B S ^a   Rudd, S ^b   Lawson, P A ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b Hot Springs Diagnostic Associates   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA MONOOXYGENASE; ARCHAEAL DNA; ARCHAEAL RNA; BACTERIAL DNA; BACTERIAL RNA; OXIDOREDUCTASE; RIBOSOME DNA; RNA 16S;

ARTESIAN WELL; BACTERIUM; BIOFILM; DISSOLVED MATTER; DOMINANCE; GEOTHERMAL SYSTEM; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; MOLECULAR ANALYSIS; NITRIFICATION; PRIMARY PRODUCTION; SPECIES DIVERSITY; SPRING WATER; WATER CHEMISTRY;

ARCHAEON; ARTICLE; BACTERIUM; BIOFILM; BIOTA; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NITRIFICATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA GENE; SEQUENCE HOMOLOGY; THERMAL SPRING; UNITED STATES;

ARCHAEA; ARKANSAS; BACTERIA; BIOFILMS; BIOTA; CLUSTER ANALYSIS; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, RIBOSOMAL; GENES, RRNA; HOT SPRINGS; MOLECULAR SEQUENCE DATA; NITRIFICATION; OXIDOREDUCTASES; PHYLOGENY; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ARKANSAS; UNITED STATES;

ARCHAEA; BACTERIA (MICROORGANISMS); NITROSPIRA; NITROSPIRACEAE;

EID: 84865283609     PISSN: 14724677     EISSN: 14724669     Source Type: Journal    
DOI: 10.1111/j.1472-4669.2012.00335.x     Document Type: Article

References (31)

1. Amend JP, Shock EL (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiology Reviews, 25, 175-243.
2. Bedinger MS, Pearson FJ Jr, Reed JE, Sniegocki RT, Stone CG (1979) The Waters of Hot Springs National Park, Arkansas - Their Nature and Origin. Geological Survey Professional Paper, 1044-C.
3. Bell RW, Hays PD (2007) Influence of Locally Derived Recharge on the Water Quality and Temperature of Springs in Hot Springs National Park, Arkansas. U.S. Geological Survey Scientific Investigations Report 2007-5004.
4. 2 uptake and fixation by a thermoacidophilic microbial community attached to precipitated sulfur in a geothermal spring. Applied and Environmental Microbiology, 75, 4289-4296.
5. Costa KC, Navarro JB, Shock EL, Zhang CL, Soukup D, Hedlund BP (2009) Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin. Extremophiles, 13, 447-459.
6. Daims H, Lücker S, Paslier DL, Wagner M (2011) Diversity, environmental genomics, and ecophysiology of nitrite-oxidizing bacteria. In Nitrification (eds Ward BB, Arp DJ, Klotz MG). ASM Press, Washington, DC, pp. 295-322.
7. Dodsworth JA, Hungate B, de la Torre JR, Jiang H, Hedlund BP (2011) Measuring nitrification, denitrification, and related biomarkers in terrestrial geothermal ecosystems. In Methods in Enzymology, Vol. 486 (eds Abelson JN, Simon MI), Elsevier, San Diego, CA, pp. 171-203.
8. Dodsworth JA, Mcdonald AI, Hedlund BP (2012) Calculation of total free energy yield as an alternative approach for predicting the importance of potential chemolithotrophic reactions in geothermal springs. FEMS Microbiology Ecology, doi:10.1111/j.1574-6941.2012.01369.x.
9. Fournier RO (1989) Geochemistry and dynamics of the Yellowstone National Park hydrothermal system. Annu Review of Earth and Planetary Sciences 17, 13-53.
10. Francis CA, Beman JM, Kuypers MM (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME Journal, 1, 19-27.
11. Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proceedings of the National Academy of Sciences, 105, 2134-2139.
12. Huang Z, Hedlund BP, Wiegel J, Zhou J, Zhang CL (2007) Molecular phylogeny of uncultivated Crenarchaeota in great basin hot springs of moderately elevated temperature. Geomicrobiology Journal, 24, 535-542.
13. Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental Microbiology, 12, 1889-1898.
14. Inskeep WP, Ackerman GG, Taylor WP, Kozubal M, Korf S, Macur RE (2005) On the energetics of chemolithotrophy in nonequilibrium systems: case studies of geothermal springs in Yellowstone National Park. Geobiology, 3, 297-317.
15. Jackson BE, McInerney MJ (2002) Anaerobic microbial metabolism can proceed close to thermodynamic limits. Nature, 415, 454-456.
16. Kvist T, Mengewein A, Manzei S, Ahring BK, Westermann P (2005) Diversity of thermophilic and non-thermophilic crenarchaeota at 80°C. FEMS Microbiology Letters, 244, 61-68.
17. Lebedeva EV, Alawi M, Fiencke C, Namsaraev B, Bock E, Spieck E (2005) Moderately thermophilic nitrifying bacteria from a hot spring of the Baikal rift zone. FEMS Microbiology Ecology, 54, 297-306.
18. Lebedeva EV, Off S, Zumbragel S, Kruse M, Shagzhina A, Lucker S, Maixner F, Lipski A, Daims H, Spieck E (2011) Isolation and characterization of a moderately thermophilic nitrite-oxidizing bacterium from a geothermal spring. FEMS Microbiology Ecology, 75, 195-204.
19. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüßmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer K-H (2004) ARB: a software environment for sequence data. Nucleic Acids Research, 32, 1363-1371.
20. Martens-Habbena W, Berube PM, Urakawa H, Torre JRDL, Stahl DA (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature, 461, 976-981.
21. Meyer-Dombard DR, Shock EL, Amend JP (2005) Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA. Geobiology, 3, 211-227.
22. Pruesse E, Quast C, Knittel K, Fuchs B, Ludwig W, Peplies J, Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research, 35, 7188-7196.
23. Reigstad LJ, Richter A, Daims H, Urich T, Schwark L, Schleper C (2008) Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiology Ecology, 64, 167-174.
24. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75, 7537-7541.
25. Shock EL, Holland M, Meyer-Dombard DaR, Amend JP (2005) Geochemical sources of energy for microbial metabolism in hydrothermal ecosystems: Obsidian Pool, Yellowstone National Park. In Obsidian Black Literature In Review, (eds Inskeep WP, McDermott TR). Thermal Biology Institute, Montana State University, Bozeman, MT, pp. 95-110.
26. Spear JR, Walker JJ, Mccollom TM, Pace NR (2005) Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. PNAS, 102, 2555-2560.
27. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596-1599.
28. de La Torre JR, Walker CB, Ingalls AE, Könneke M, Stahl DA (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environmental Microbiology, 10, 810-818.
29. Tourna M, Stieglmeier M, Spang A, Könneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proceedings of the National Academy of Sciences, 108, 8420-8425.
30. Yeatts DS (2006) Characteristics of Thermal Springs and the Shallow Ground-Water System at Hot Springs National Park, Arkansas. U.S. Geological Survey Scientific Investigations Report 2006-5001.
31. Zhang CL, Ye Q, Huang Z, Li W, Chen J, Song Z, Zhao W, Bagwell C, Inskeep WP, Ross C, Gao L, Wiegel J, Romanek CS, Shock EL, Hedlund BP (2008) Global occurrence of Archaeal amoA genes in terrestrial hot springs. Applied and Environmental Microbiology, 74, 6417-6426.