Do we need to understand microbial communities to predict ecosystem function? A comparison of statistical models of nitrogen cycling processes

Soil Biology and Biochemistry

Volumn 68, Issue , 2014, Pages 279-282

  Graham, Emily B ^a   Wieder, William R ^a,b   Leff, Jonathan W ^a   Weintraub, Samantha R ^a   Townsend, Alan R ^a   Cleveland, Cory C ^c   Philippot, Laurent ^d   Nemergut, Diana R ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY CORPORATION FOR ATMOSPHERIC RESEARCH   (United States)

^c UNIVERSITY OF MONTANA   (United States)

^d UNIV BOURGOGNE FRANCHE COMTÉ   (France)

Author keywords

Biogeochemistry; Dissimilatory nitrate reduction to ammonium; Ecosystem processes; Functional genes; Modeling; N2O flux; Nitrification; QPCR; Structure function relationship

Indexed keywords

DISSIMILATORY NITRATE REDUCTION; ECOSYSTEM PROCESS; FUNCTIONAL GENES; QPCR; STRUCTURE-FUNCTION RELATIONSHIP;

BIOGEOCHEMISTRY; GENES; MICROORGANISMS; MODELS; NITRATES; NITRIFICATION; NITROGEN;

ECOSYSTEMS;

AMMONIUM; BIOGEOCHEMISTRY; COMPARATIVE STUDY; ECOSYSTEM FUNCTION; ECOSYSTEM MODELING; ENVIRONMENTAL FACTOR; FOREST SOIL; GENE EXPRESSION; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; NITROGEN CYCLE; NITROUS OXIDE; NUMERICAL MODEL; RAINFOREST; RELATIVE ABUNDANCE; STATISTICAL ANALYSIS;

EID: 84886792999     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2013.08.023     Document Type: Article

References (26)

1. Allison S.D. Atrait-based approach for modelling microbial litter decomposition. Ecol. Lett. 2012, 15:1058-1070.
2. Attard E., Recous S., Chabbi A., De Berranger C., Guillaumaud N., Labreuche J., Philippot L., Schmid B., Le Roux X. Soil environmental conditions rather than denitrifier abundance and diversity drive potential denitrification after changes in land uses. Glob. Change Biol. 2011, 17:1975-1989.
3. Burke C., Steinberg P., Rusch D., Kjelleberg S., Thomas T. Bacterial community assembly based on functional genes rather than species. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:14288-14293.
4. Carney K.M., Matson P.A. Plant communities, soil microorganisms, and soil carbon cycling: does altering the world belowground matter to ecosystem functioning?. Ecosystems 2005, 8:928-940.
5. Ehrenfeld J.G. Effects of exotic plant invasions on soil nutrient cycling processes. Ecosystems 2003, 6:503-523.
6. Ferrenberg S., O'Neill S.P., Knelman J.E., Todd B., Duggan S., Bradley D., Robinson T., Schmidt S.K., Townsend A.R., Williams M.W. Changes in assembly processes in soil bacterial communities following a wildfire disturbance. ISME J 2013, 7(6):1102-1111.
7. Fierer N., Morse J.L., Berthrong S.T., Bernhardt E.S., Jackson R.B. Environmental controls on the landscape-scale biogeography of stream bacterial communities. Ecology 2007, 88:2162-2173.
8. Follows M.J., Dutkiewicz S., Grant S., Chisholm S.W. Emergent biogeography of microbial communities in a model ocean. Science 2007, 315:1843-1846.
9. Fortuna A.M., Honeycutt C.W., Vandemark G., Griffin T.S., Larkin R.P., He Z.Q., Wienhold B.J., Sistani K.R., Albrecht S.L., Woodbury B.L., Torbert H.A., Powell J.M., Hubbard R.K., Eigenberg R.A., Wright R.J., Alldredge J.R., Harsh J.B. Links among nitrification, nitrifier communities, and edaphicproperties in contrasting soils receiving dairy slurry. J.Environ. Qual. 2012, 41:262-272.
10. Fukami T. Assembly history interacts with ecosystem size to influence species diversity. Ecology 2004, 85:3234-3242.
11. Hatzenpichler R. Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl. Environ. Microbiol. 2012, 78:7501-7510.
12. Jones S.E., Lennon J.T. Dormancy contributes to the maintenance of microbial diversity. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:5881-5886.
13. Leff J.W., Nemergut D.R., Grandy A.S., O'Neill S.P., Wickings K., Townsend A.R., Cleveland C.C. The effects of soil bacterial community structure on decomposition in a tropical rain forest. Ecosystems 2012, 15:284-298.
14. Legg T.M., Zheng Y., Simone B., Radloff K.A., Mladenov N., Gonzalez A., Knights D., Siu H.C., Rahman M.M., Ahmed K.M. Carbon, metals, and grain size correlate with bacterial community structure in sediments of a high arsenic aquifer. Front. Microbiol. 2012, 3.
15. Lennon J.T., Jones S.E. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat. Rev. Microbiol. 2011, 9:119-130.
16. Lozupone C.A., Hamady M., Kelley S.T., Knight R. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 2007, 73:1576-1585.
17. Nemergut D.R., Cleveland C.C., Wieder W.R., Washenberger C.L., Townsend A.R. Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest. Soil Biol. Biochem. 2010, 42:2153-2160.
18. Nemergut D.R., Schmidt S.K., Fukami T., O'Neill S.P., Legg T.M., Stanish L., Knelman J.E., Darcy J.L., Lynch R., Wickey P., Ferrenberg S. Microbial community assembly: patterns and processes. Microbiol. Mol. Biol. Rev. 2013, 77:342-356.
19. Petersen D.G., Blazewicz S.J., Firestone M., Herman D.J., Turetsky M., Waldrop M. Abundance of microbial genes associated with nitrogen cycling as indices of biogeochemical process rates across a vegetation gradient in Alaska. Environ. Microbiol. 2012, 14:993-1008.
20. Polz M.F., Hunt D.E., Preheim S.P., Weinreich D.M. Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2006, 361:2009-2021.
21. Schimel J.P. Global Biogeochemical Cycles in the Climate System 2001, 239-254. Academic, San Diego, CA. E.D. Schulze (Ed.).
22. Shade A., Read J.S., Youngblut N.D., Fierer N., Knight R., Kratz T.K., Lottig N.R., Roden E.E., Stanley E.H., Stombaugh J., Whitaker R.J., Wu C.H., McMahon K.D. Lake microbial communities are resilient after a whole-ecosystem disturbance. ISME J. 2012, 6:2153-2167.
23. Todd-Brown K.E.O., Hopkins F.M., Kivlin S.N., Talbot J.M., Allison S.D. Aframework for representing microbial decomposition in coupled climate models. Biogeochemistry 2012, 109:19-33.
24. van der Heijden M.G.A., Bardgett R.D., van Straalen N.M. The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol. Lett. 2008, 11:296-310.
25. Wieder W.R., Cleveland C.C., Townsend A.R. Throughfall exclusion and leaf litter addition drive higher rates of soil nitrous oxide emissions from a lowland wet tropical forest. Glob. Change Biol. 2011, 17:3195-3207.
26. Wieder W.R., Cleveland C.C., Taylor P.G., Nemergut D.R., Hinckley E.-L., Philippot L., Bru D., Weintraub S.R., Martin M., Townsend A.R. Experimental removal and addition of leaf litter inputs reduces nitrate production and loss in a lowland tropical forest. Biogeochemistry 2013, 113:629-642.