Effect of rainfall-induced soil geochemistry dynamics on grassland soil microbial communities

Applied and Environmental Microbiology

Volumn 78, Issue 21, 2012, Pages 7587-7595

  Cruz Martínez, Karelyn ^a,b   Rosling, Anna ^b,f   Zhang, Yang ^c   Song, Mingzhou ^c   Andersen, Gary L ^d   Banfield, Jillian F ^d,e  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^c New Mexico State University   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA; ACTINOBACTERIA; ARCHAEAL; BIOGEOCHEMICAL CYCLE; CALIFORNIA; COMMUNITY COMPOSITION; COMMUNITY STRUCTURES; ENVIRONMENTAL CONDITIONS; ENVIRONMENTAL PARAMETER; ENVIRONMENTAL VARIABLES; GRASSLAND ECOSYSTEMS; GRASSLAND SOILS; LOGICAL NETWORK; MICROBIAL COMMUNITIES; MICROBIAL COMMUNITY COMPOSITION; MICROBIAL COMMUNITY STRUCTURES; RAINFALL EVENT; RAINY SEASONS; RELATIVE ABUNDANCE; SHORT-TERM VARIATIONS; SOIL GEOCHEMISTRY; SOIL SAMPLE; TIME POINTS; TIME RESOLUTION; TRACK CHANGES; WETTING AND DRYING CYCLES;

CARBON; FORESTRY; MICROORGANISMS; PHENOLS; RAIN; RNA; SOCIAL SCIENCES; SOIL MOISTURE;

SOIL SURVEYS;

ARCHAEAL DNA; BACTERIAL DNA; RAIN; RNA 16S;

ABUNDANCE; BIOCHEMISTRY; COMMUNITY COMPOSITION; ENVIRONMENTAL CONDITIONS; GRASSLAND SOIL; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; PHENOLOGY; PROKARYOTE; RAINFALL; RELATIVE ABUNDANCE; SOIL CHEMISTRY; SOIL ECOSYSTEM; WETTING-DRYING CYCLE;

ARCHAEON; ARTICLE; BACTERIUM; CHEMISTRY; CLASSIFICATION; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; MICROBIAL CONSORTIUM; MICROBIOLOGY; POACEAE; SEASON; SOIL; TEMPERATURE; UNITED STATES;

ARCHAEA; BACTERIA; CALIFORNIA; DNA, ARCHAEAL; DNA, BACTERIAL; ECOSYSTEM; MICROBIAL CONSORTIA; POACEAE; RAIN; RNA, RIBOSOMAL, 16S; SEASONS; SOIL; SOIL MICROBIOLOGY; TEMPERATURE;

CALIFORNIA; UNITED STATES;

ACTINOBACTERIA; ANIMALIA; ARCHAEA; BACTERIA (MICROORGANISMS);

EID: 84868611858     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00203-12     Document Type: Article

References (59)

1. Allison VJ, Yermakov Z, Miller RM, Jastrow JD, Matamala R. 2007. Using landscape and depth gradients to decouple the impact of correlated environmental variables on soil microbial community composition. Soil Biol. Biochem. 39:505-516.
2. Balser TC, Firestone MK. 2005. Linking microbial community composition and soil processes in a California annual grassland and mixedconifer forest. Biogeochemistry 73:395-415.
3. Beck T, et al. 1997. An inter-laboratory comparison of ten different ways of measuring soil microbial biomass C. Soil Biol. Biochem. 29:1023-1032.
4. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B. Methodol. 57:289-300.
5. Berhe AA, Suttle KB, Burton SD, Banfield JF. 2012. Contingency in the direction and mechanics of soil organic matter responses to increased rainfall. Plant Soil doi:10.1007/s11104-012-1156-0.
6. Birch HF. 1958. The effect of soil drying on humus decomposition and nitrogen availability. Plant Soil 10:9-31.
7. Bottner P. 1985. Response of microbial biomass to alternate moist and dry conditions in a soil incubated with 14C- and 15N-labeled plant material. Soil Biol. Biochem. 17:329-337.
8. Brodie EL, et al. 2006. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl. Environ. Microbiol. 72:6288-6298.
9. Brooks PD, Stark JM, McInteer BB, Preston T. 1989. Diffusion method to prepare soil extracts for automated nitrogen-15 analysis. Soil Sci. Soc. Am. J. 53:1707-1711.
10. Chou W, Silver WL, Jackson RD, Thompson AW, Allen-Diaz B. 2008. The sensitivity of annual grassland carbon cycling to the quantity and timing of rainfall. Global Change Biol. 14:1382-1394.
11. Clarke KR. 1993. Non-parametric multivariate analyses of changes in community structure. Aust. J. Ecol. 18:117-143.
12. Craine JM, Morrow C, Fierer N. 2007. Microbial nitrogen limitation increases decomposition. Ecology 88:2105-2113.
13. Cruz-Martinez K, et al. 2009. Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J. 3:738-744.
14. DeAngelis KM, et al. 2008. Selective progressive response of soil microbial community to wild oat roots. ISME J. 3:168-178.
15. Denef K, Six J, Paustian K, Merckx R. 2001. Importance of macroaggregate dynamics in controlling soil carbon stabilization: short-term effects of physical disturbance induced by dry-wet cycles. Soil Biol.33:2145-2153.
16. DeSantis T, et al. 2007. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb. Ecol. 53:371-383.
17. Fierer N, Bradford MA, Jackson RB. 2007. Toward an ecological classification of soil bacteria. Ecology 88:1354-1364.
18. Fierer N, Schimel JP. 2002. Effects of drying-rewetting frequency on soil carbon and nitrogen transformations. Soil Biol. Biochem. 34:777-787.
19. Fierer N, Schimel JP, Holden PA. 2003. Variations in microbial community composition through two soil depth profiles. Soil Biol. Biochem. 35: 167-176.
20. Goodfellow M, Williams ST. 1983. Ecology of actinomycetes. Annu. Rev. Microbiol. 37:189-216.
21. Grogan P, Chapin FS. 2000. Nitrogen limitation of production in a Californian annual grassland: the contribution of arbuscularmycorrhizae.Biogeochemistry.49:37-51.
22. Halverson LJ, Jones TM, Firestone MK. 2000. Release of intracellular solutes by four soil bacteria exposed to dilution stress. Soil Sci. Soc. Am. J. 64:1630-1637.
23. Harper CW, Blair JM, Fay PA, Knapp AK, Carlisle JD. 2005. Increased rainfall variability and reduced rainfall amount decreases soil CO2 flux in a grassland ecosystem. Global Change Biol. 11:322-334.
24. Harpole W, et al. 2007. Ecosystem responses to water and nitrogen amendment in a California grassland. Global Change Biol. 13:2341-2348.
25. Hendershot WH, Lalande H. 1993. Ion exchange and exchangeable cations, p 167-176. In CarterMR(ed), Soil sampling and methods of analysis. Canadian Society of Soil Science/Lewis Publishers, Boca Raton, FL.
26. Hinsinger P, Plassard C, Jaillard B. 2006. Rhizosphere: a new frontier for soil biogeochemistry. J. Geochem. Explor. 88:210-213.
27. Hofer S. 2003. Determination of ammonia (salicylate) in 2 M KCl soil extracts by flow injection analysis. QuikChem method 12-107-06-2-A. Lachat Instruments, Loveland, CO.
28. Huxman TE, et al. 2004. Precipitation pulses and carbon fluxes in semiarid and arid ecosystems. Oecologia 141:254-268.
29. Jackson LE, Schimel JP, Firestone MK. 1989. Short-term partitioning of ammonium and nitrate between plants and microbes in an annual grassland. Soil Biol. Biochem. 21:409-415.
30. Kaye JP, Hart SC. 1997. Competition for nitrogen between plants and soil microorganisms. Trends Ecol. Evol. 12:139-143.
31. Kieft TL, Soroker E, Firestone MK. 1987. Microbial biomass response to a rapid increase in water potential when dry soil is wetted. Soil Biol. Biochem. 19:119-126.
32. Knapp AK, et al. 2002. Rainfall variability, carbon cycling, and plant species diversity in a mesic grassland. Science 298:2202-2205.
33. Knapp AK, Smith MD. 2001. Variation among biomes in temporal dynamics of aboveground primary production. Science 291:481-484.
34. Knepel K. 2003. Determination of nitrate in 2MKCl soil extracts by flow injection analysis. QuikChem method 12-107-04-1-B. Lachat Instruments,, Loveland, CO.
35. Kruskal JB, M Wish. 1978. Multidimensional scaling. Sage Publications, Beverly Hills, CA.
36. Lauber CL, Hamady M, Knight R, Fierer N. 2009. Pyrosequencingbased assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75:5111-5120.
37. Lozupone C, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235.
38. Lund V, Goksøyr J. 1980. Effects of water fluctuations on microbial mass and activity in soil. Microb. Ecol. 6:115-123.
39. Masuda N, Church GM. 2002. Escherichia coli gene expression responsive to levels of the response regulator EvgA. J. Bacteriol. 184:6225-6234.
40. Maynard DG, Kalra YP. 1993. Nitrate and exchangeable ammonium nitrogen, p 25-38. In Carter MR (ed), Soil sampling and methods of analysis. Lewis Publishers, Boca Raton, FL.
41. McCune B, Mefford MJ. 1999. PC-ORD: multivariate analysis of ecological data, 4.2 ed. MjM Software Design, Gleneden Beach, OR.
42. Mielke PW, Jr. 1984. Meteorological applications of permutation techniques based on distance functions, p 813-830. In Handbook of statistics. Elsevier Science Publishers, New York, NY.
43. Mielke PW, Jr, Berry KJ. 2001. Permutation methods: a distance function approach. Springer Series in Statistics. Springer, New York, NY.
44. Philippot L, et al. 2010. The ecological coherence of high bacterial taxonomic ranks. Nat. Rev. Microbiol. 8:523-529.
45. Philippot L, et al. 2009. Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree. Environ. Microbiol. 11:3096-3104.
46. Schimel JP, Jackson LE, Firestone MK. 1989. Spatial and temporal effects on plant-microbial competition for inorganic nitrogen in a California annual grassland. Soil Biol. Biochem. 21:1059-1066.
47. Schmidt SK, et al. 2007. Biogeochemical consequences of rapid microbial turnover and seasonal succession in soil. Ecology 88:1379-1385.
48. Schnurer J, Clarholm M, Bostrom S, Rosswall T. 1986. Effects of moisture on soil microorganisms and nematodes: a field experiment. Microb.12:217-230.
49. Song M, et al. 2009. Reconstructing generalized logical networks of transcriptional regulation in mouse brain from temporal gene expression data. EURASIP J. Bioinform. Systems Biol. 2009:13.
50. Suttle KB, Thomsen MA, Power ME. 2007. Species interactions reverse grassland responses to changing climate. Science 315:640-642.
51. Torsvik V, Ovreas L. 2002. Microbial diversity and function in soil: from genes to ecosystem. Curr. Opin. Microbiol. 5:240-245.
52. Torsvik V, Ovreas L, Thingstad TF. 2002. Prokaryotic diversity: magnitude, dynamics, and controlling factors. Science 296:1064-1066.
53. Uroz S, et al. 2007. Effect of the mycorrhizosphere on the genotypic and metabolic diversity of the bacterial communities involved in mineral weathering in a forest soil. Appl. Environ. Microbiol. 73:3019-3027.
54. U. S. Department of Agriculture Natural Resources Conservation Service. 2006. Land resource regions and major land resource areas of the United States, the Caribbean, and the Pacific Basin. U.S. Department of Agriculture Handbook 296. U.S. Department of Agriculture, Washington, DC.
55. Van Gestel M, Merckx VR, Vlassak K. 1993. Microbial biomass responses to soil drying and rewetting: the fate of fast- and slow-growing microorganisms in soils from different climates. Soil Biol. Biochem. 25:109-123.
56. Voroney RP, Winter JP. 1993. Soil microbial biomass C and N. In Carter MR (ed), Soil sampling and methods of analysis. Canadian Society of Soil Science/Lewis Publishers, Boca Raton, FL.
57. Waldrop MP, Firestone MK. 2006. Response of microbial community composition and function to soil climate change. Microb. Ecol. 52:716-724.
58. Waldrop MP, Firestone MK. 2006. Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils. Microb. Ecol. 52:470-479.
59. Wang H, Song M. 2011. Clustering in one dimension by dynamic programming. R J. 3:23-27.