Soil bacterial community succession during long-term ecosystem development

Molecular Ecology

Volumn 22, Issue 12, 2013, Pages 3415-3424

  Jangid, Kamlesh ^a   Whitman, William B ^b   Condron, Leo M ^c   Turner, Benjamin L ^d   Williams, Mark A ^e  

^a NATIONAL CENTRE FOR CELL SCIENCE   (India)

^b UNIVERSITY OF GEORGIA   (United States)

^c LINCOLN UNIVERSITY   (New Zealand)

^d SMITHSONIAN TROPICAL RESEARCH INSTITUTE   (Panama)

^e VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

16S rRNA pyrosequencing; bacterial diversity; Franz Josef chronosequence; soil development; soil nutrients; vegetative succession

Indexed keywords

BACTERIAL DNA; RNA 16S;

ANGIOSPERM; ARTICLE; BACTERIUM; ECOSYSTEM; GENETICS; MICROBIOLOGY; MICROFLORA; NEW ZEALAND;

ANGIOSPERMS; BACTERIA; DNA, BACTERIAL; ECOSYSTEM; MICROBIOTA; NEW ZEALAND; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 84879019064     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12325     Document Type: Article

References (57)

1. Allison VJ, Condron LM, Peltzer DA, Richardson SJ, Turner BL, (2007) Changes in enzyme activities and soil microbial community composition along carbon and nutrient gradients at the Franz Josef chronosequence, New Zealand. Soil Biology & Biochemistry, 39, 1770-1781.
2. Almond PC, Moar NT, Lian OB, (2001) Reinterpretation of the glacial chronology of South Westland, New Zealand. New Zealand Journal of Geology and Geophysics, 44, 1-15.
3. Bååth E, Anderson TH, (2003) Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biology & Biochemistry, 35, 955-963.
4. Banfield JF, Barker WW, Welch SA, Taunton A, (1999) Biological impact on mineral dissolution: application of the lichen model to understanding mineral weathering in the rhizosphere. Proceedings of the National Academy Sciences of the United States of America, 96, 3404-3411.
5. Bardgett RD, Wardle DA, (2010) Aboveground-Belowground Linkages. Biotic Interactions, Ecosystem Processes, and Global Change. Oxford University Press, New York.
6. Beauregard MS, Atul-Nayyar CH, St-Arnaud M, (2010) Long-term phosphorus fertilization impacts soil fungal and bacterial diversity but not AM fungal community in alfalfa. Microbial Ecology, 59, 379-389.
7. Bonanomi G, Giannino F, Mazzoleni S, (2005) Negative plant-soil feedback and species coexistence. Oikos, 111, 311-321.
8. Caporaso JG, Kuczynski J, Stombaugh J, et al,. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335-336.
9. Chaia E, Wall L, Huss-Danell K, (2010) Life in soil by the actinorhizal root nodule endophyte, A review. Symbiosis, 51, 201-226.
10. Crews TE, Kitayama K, Fownes JH, et al,. (1995) Changes in soil phosphorus fractions and ecosystem dynamics across a long chronosequence in Hawaii. Ecology, 76, 1407-1424.
11. De Vries FT, Manning P, Tallowin JRB, et al,. (2012) Abiotic drivers and plant traits explain landscape-scale patterns in soil microbial communities. Ecology Letters, 15, 1230-1239.
12. DeForest JL, Scott LG, (2010) Available organic soil phosphorus has an important influence on microbial community composition. Soil Science Society of America Journal, 74, 2059-2066.
13. Garcia SL, Jangid K, Whitman WB, Das KC, (2011) Transition of microbial communities during the adaptation to anaerobic digestion of carrot waste. Bioresource Technology, 102, 7149-7256.
14. Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS, (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Applied and Environmental Microbiology, 69, 1800-1809.
15. Griffiths RI, Thomson BC, James P, Bell T, Bailey M, Whiteley AS, (2011) The bacterial biogeography of British soils. Environmental Microbiology, 13, 1642-1654.
16. Högberg M, Högberg P, Myrold D, (2007) Is microbial community composition in boreal forest soils determined by pH, C-to-N ratio, the trees, or all three? Oecologia, 150, 590-601.
17. Jumpponen A, Trappe JM, Cazares E, (2002) Occurrence of ectomycorrhizal fungi on the forefront of retreating Lyman Glacier (Washington, USA) in relation to time since deglaciation. Mycorrhiza, 12, 43-49.
18. Kardol P, Bezemer TM, Van Der Putten WH, (2006) Temporal variation in plant-soil feedback controls succession. Ecology Letters, 9, 1080-1088.
19. Knelman JE, Legg TM, O'Neill SP, et al,. (2012) Bacterial community structure and function change in association with colonizer plants during early primary succession in a glacier forefield. Soil Biology & Biochemistry, 46, 172-180.
20. Kourtev PS, Ehrenfeld JG, Haggblom M, (2002) Exotic plant species alter the microbial community structure and function in the soil. Ecology, 83, 3152-3166.
21. Kourtev PS, Ehrenfeld JG, Haggblom M, (2003) Experimental analysis of the effect of exotic and native plant species on the structure and function of soil microbial communities. Soil Biology & Biochemistry, 35, 895-905.
22. Kulmatiski A, Beard KH, Stevens JR, Cobbold SM, (2008) Plant-soil feedbacks: a meta-analytical review. Ecology Letters, 11, 980-992.
23. Lambers H, Mougel C, Jaillard B, Hinsinger P, (2009) Plant-microbe-soil interactions in the rhizosphere: an evolutionary perspective. Plant and Soil, 321, 83-115.
24. Lauber CL, Hamady M, Knight R, Fierer N, (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environment Microbiology, 75, 5111-5120.
25. Leyval C, Berthelin J, (1990) Weathering of a mica by roots and rhizospheric microorganisms of pine. Soil Science Society of America Journal, 55, 1009-1016.
26. Lichter J, (1998) Rates of weathering and chemical depletion in soils across a chronosequence of Lake Michigan. Geoderma, 85, 255-282.
27. McCune B, Grace JB,. (2002) Analysis of Ecological Communities. MjM Software Design, Gleneden Beach, Oregon.
28. McIntosh RP, Odum EP, (1969) Ecological succession. Science, 166, 403-404.
29. Menge DNL, Hedin LO, (2009) Nitrogen fixation in different biogeochemical niches along as 120,000-year chronosequence in New Zealand. Ecology, 90, 2190-2201.
30. Menge DNL, Hedin LO, Pacala SW, (2012) Nitrogen and phosphorus limitation over long-term ecosystem development in terrestrial ecosystems. PLoS ONE, 7, e42045.
31. Michel HM, Williams MA, (2011) Soil habitat and horizon properties impact bacterial diversity and composition. Soil Science Society of America Journal, 75, 1440-1448.
32. Nemergut DR, Anderson SP, Cleveland CC, et al,. (2007) Microbial community succession in an unvegetated recently deglaciated soil. Microbial Ecology, 53, 110-122.
33. Nicol GW, Tscherko D, Embley TM, Prosser JI, (2005) Primary succession of soil Crenarchaeota across a receding glacier foreland. Environmental Microbiology, 7, 337-347.
34. Peltzer DA, Wardle DA, Allison VJ, et al,. (2010) Understanding ecosystem retrogression. Ecological Monographs, 80, 509-529.
35. Reeder J, Knight R, (2010) Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution. Nature Methods, 7, 668-669.
36. Richardson S, Peltzer D, Allen R, McGlone M, Parfitt R, (2004) Rapid development of phosphorus limitation in temperate rainforest along the Franz Josef soil chronosequence. Oecologia, 139, 267-276.
37. Rousk J, Baath E, Brookes PC, et al,. (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. The International Society of Microbial Ecology Journal, 4, 1340-1351.
38. Schloss PD, Westcott SL, Ryabin T, et al,. (2009) Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75, 7537-7541.
39. Schutte UME, Abdo Z, Bent SJ, et al,. (2009) Bacterial succession in a glacier foreland of the high arctic. The International Society of Microbial Ecology Journal, 3, 1258-1268.
40. Singh BK, Munro S, Potts JM, Millard P, (2007) Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils. Applied Soil Ecology, 36, 147-155.
41. Stevens PR, (1968) A chronosequence of soils near the Franz josef Glacier. Thesis, Lincoln College, University of Canterbury, New Zealand.
42. Tarlera S, Jangid K, Ivester AH, Whitman WB, Williams MA, (2008) Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development. FEMS Microbiology Ecology, 64, 129-140.
43. Tscherko D, Hammesfahr U, Marx MC, Kandeler E, (2004) Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence. Soil Biology & Biochemistry, 36, 1685-1698.
44. Turner BL, Condron LM, Richardson SJ, Peltzer DA, Allison VJ, (2007) Soil organic phosphorus transformations during pedogenesis. Ecosystems, 10, 1166-1181.
45. Turner BL, Condron LM, Wells A, Anderson KM, (2012) Soil nutrient dynamics during podzol development under lowland temperate rainforest in New Zealand. Catena, 97, 50-62.
46. van der Putten WH, Bardgett RD, De Ruiter PC, et al,. (2009) Empirical and theoretical challenges in aboveground-belowground ecology. Oecologia, 161, 1-14.
47. van der Putten WH, Van Dijk C, Peters BAM, (1993) Plant specific soil-borne diseases contribute to succession in foredune communities. Nature, 362, 53-56.
48. Van der Putten WH, Vet LEM, Harvey JA, Wäckers FL, (2001) Linking above- and belowground multitrophic interactions of plants, herbivores, pathogens, and their antagonists. Trends in Ecology and Evolution, 16, 547-554.
49. Vitousek PM, Farrington H, (1997) Nutrient limitation and soil development: experimental test of a biogeochemical theory. Biogeochemistry, 37, 63-75.
50. Wakelin S, Mander C, Gerard E, et al,. (2012) Response of soil microbial communities to contrasted histories of phosphorus fertilization in pastures. Applied Soil Ecology, 61, 40-48.
51. Walker TW, Syers JK, (1976) The fate of phosphorus during pedogenesis. Geoderma, 15, 1-19.
52. Walker LR, Wardle DA, Bardgett RD, Clarkson BD, (2010) The use of chronosequences in studies of ecological succession and soil development. Journal of Ecology, 98, 725-736.
53. Wardle DA, Walker LR, Bardgett RD, (2004) Ecosystem properties and forest decline in contrasting long-term chronosequences. Science, 305, 509-513.
54. Whittaker RH, (1972) Evolution and measurement of species diversity. Taxon, 21, 3-251.
55. Williams MA, Jangid K, Shanmugam SG, Whitman WB, (2013) Bacterial communities in soil mimic patterns of vegetative succession and ecosystem climax but are resilient to change between seasons. Soil Biology & Biochemistry, 57, 749-757.
56. Wu X, Zhang W, Liu G, et al,. (2012) Bacterial diversity in the foreland of the Tianshan no. 1 glacier, China. Environmental Research Letters, 7, 014038.
57. Zumsteg A, Luster J, Goransson H, et al,. (2012) Bacterial, archeal, and fungal succession in the forefield of a receding glacier. Microbial Ecology, 63, 552-564.