Gene-centric approach to integrating environmental genomics and biogeochemical models

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 5, 2014, Pages 1879-1884

  Reed, Daniel C ^a   Algar, Christopher K ^b   Huber, Julie A ^b   Dick, Gregory J ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b MARINE BIOLOGICAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NITRITE; OXYGEN; SULFUR;

ARABIAN SEA; ARTICLE; BIOGEOCHEMISTRY; METABOLISM; METAGENOMICS; MICROBIAL COMMUNITY; NITROGEN CYCLING; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SEA; SULFUR CYCLE;

COMPUTER SIMULATION; GENES; HYDROGEN SULFIDE; METAGENOMICS; MODELS, BIOLOGICAL; NITRATES; NITROGEN CYCLE; OCEANS AND SEAS; OXIDATION-REDUCTION; OXYGEN;

EID: 84893483727     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1313713111     Document Type: Article

References (33)

1. Strous M, et al. (2006) Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440(7085):790-794.
2. Venter JC, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304(5667):66-74.
3. Canfield DE, et al. (2010) A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast. Science 330(6009):1375-1378.
4. Walsh DA, et al. (2009) Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 326(5952):578-582.
5. Lam P, Kuypers MM (2011) Microbial nitrogen cycling processes in oxygen minimum zones. Annu Rev Mar Sci 3:317-345.
6. Ulloa O, Canfield DE, DeLong EF, Letelier RM, Stewart FJ (2012) Microbial oceanography of anoxic oxygen minimum zones. Proc Natl Acad Sci USA 109(40):15996-16003.
7. Wright JJ, Konwar KM, Hallam SJ (2012) Microbial ecology of expanding oxygen minimum zones. Nat Rev Microbiol 10(6):381-394.
8. Larsen PE, Gibbons SM, Gilbert JA (2012) Modeling microbial community structure and functional diversity across time and space. FEMS Microbiol Lett 332(2):91-98.
9. Dick JM, Shock EL (2013) A metastable equilibrium model for the relative abundances of microbial phyla in a hot spring. PLoS ONE 8(9):e72395.
10. Houghton JL, Seyfried WE, Jr. (2010) An experimental and theoretical approach to determining linkages between geochemical variability and microbial biodiversity in seafloor hydrothermal chimneys. Geobiology 8(5):457-470.
11. Scheibe TD, et al. (2009) Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb Biotechnol 2(2): 274-286.
12. King EL, Tuncay K, Ortoleva P, Meile C (2009) In silico Geobacter sulfurreducens metabolism and its representation in reactive transport models. Appl Environ Microbiol 75(1):83-92.
13. Thullner M, van Cappellen P, Regnier P (2005) Modeling the impact of microbial activity on redox dynamics in porous media. Geochim Cosmochim Acta 69(21):5005-5019.
14. Thullner M, Regnier P, van Cappellen P (2007) Modeling microbially induced carbon degradation in redox-stratified subsurface environments: Concepts and open questions. Geomicrobiol J 24:139-155.
15. Jin Q, Bethke CM (2005) Predicting the rate of microbial respiration in geochemical environments. Geochim Cosmochim Acta 69(5):1133-1143.
16. Anantharaman K, Breier JA, Sheik CS, Dick GJ (2013) Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria. Proc Natl Acad Sci USA 110(1):330-335.
17. Roden EE, Jin Q (2011) Thermodynamics of microbial growth coupled to metabolism of glucose, ethanol, short-chain organic acids, and hydrogen. Appl Environ Microbiol 77(5):1907-1909.
18. Pitcher A, et al. (2011) Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone. ISME J 5(12):1896-1904.
19. Van Cappellen P, Wang Y (1996) Cycling of iron and manganese in surface sediments: A general theory for the coupled transport and reaction of carbon, oxygen, nitrogen, sulfur, iron and manganese. Am J Sci 296:197-243.
20. Kuypers MMM, et al. (2005) Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc Natl Acad Sci USA 102(18): 6478-6483.
21. Thamdrup B, et al. (2006) Anaerobic ammonium oxidation in the oxygen-deficient waters off northern Chile. Limnol Oceanogr 51(5):2145-2156.
22. Ward BB, et al. (2009) Denitrification as the dominant nitrogen loss process in the Arabian Sea. Nature 461(7260):78-81.
23. Bulow SE, Rich JJ, Naik HS, Pratihary AK, Ward BB (2010) Denitrification exceeds anammox as a nitrogen loss pathway in the Arabian Sea oxygen minimum zone. Deep Sea Res Part I Oceanogr Res Pap 57:384-393.
24. Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461(7266):976-979.
25. Newell SE, Babbin A, Jayakumar A, Ward BB (2010) Ammonia oxidation rates and nitrification in the Arabian Sea. Global Biogeochem Cycles 25:GB4016.
26. Lam P, et al. (2011) Origin and fate of the secondary nitrite maximum in the arabian sea. Biogeosciences 8:1565-1577.
27. Ward BB (2013) Oceans. How nitrogen is lost. Science 341(6144):352-353.
28. Serres MH, et al. (2001) A functional update of the escherichia coli K-12 genome. Genome Biol 2(9):0035.1-0035.7.
29. Handelsman J (2004) Metagenomics: Application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68(4):669-685.
30. Kujawinski EB (2011) The impact of microbial metabolism on marine dissolved organic matter. Annu Rev Mar Sci 3:567-599.
31. Litchman E, Klausmeier CA (2008) Trait-based community ecology of phytoplankton. Annu Rev Mar Sci 39:615-639.
32. Stocker R (2012) Marine microbes see a sea of gradients. Science 338(6107):628-633.
33. Moran MA, et al. (2013) Sizing up metatranscriptomics. ISME J 7(2):237-243.