The influence of sampling strategies and spatial variation on the detected soil bacterial communities under three different land-use types

FEMS Microbiology Ecology

Volumn 78, Issue 1, 2011, Pages 70-79

  Osborne, Catherine A ^a,b   Zwart, Alexander B ^a   Broadhurst, Linda M ^a   Young, Andrew G ^a   Richardson, Alan E ^a  

^a CSIRO   (Australia)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

16S rRNA gene; Restoration; S rensen's pairwise dissimilarity; Soil pH; T RFLP

Indexed keywords

RNA 16S;

ASSESSMENT METHOD; BACTERIUM; ENVIRONMENTAL RESTORATION; EVERGREEN TREE; FRAGMENTATION; GENETIC ANALYSIS; LAND USE; LANDSCAPE; PASTURE; PH; POLYMORPHISM; REVEGETATION; SAMPLING; SOIL MICROORGANISM; SPATIAL VARIATION; WOODLAND;

ARTICLE; AUSTRALIA; BACTERIUM; BACTERIUM IDENTIFICATION; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; ECOSYSTEM; ENVIRONMENTAL MONITORING; GENETICS; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; MICROBIOLOGY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RHIZOSPHERE; SOIL;

AUSTRALIA; BACTERIA; BACTERIAL TYPING TECHNIQUES; BIODIVERSITY; ECOSYSTEM; ENVIRONMENTAL MONITORING; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RHIZOSPHERE; RNA, RIBOSOMAL, 16S; SOIL; SOIL MICROBIOLOGY;

AUSTRALIA;

BACTERIA (MICROORGANISMS);

EID: 79961173963     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2011.01105.x     Document Type: Article

References (31)

1. Allen DE, Mendham DS, Bhupinderpal-Singh, Cowie A, Wang W, Dalal RC & Raison RJ (2009) Nitrous oxide and methane emissions from soil are reduced following afforestation of pasture lands in three contrasting climatic zones. Aust J Soil Res47: 443-458.
2. Anderson MJ (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol26: 32-46.
3. Anderson MJ & Willis TJ (2003) Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology. Ecology 84: 511-525.
4. Baker KL, Langenheder S, Nicol GW, Ricketts D, Killham K, Campbell CD & Prosser JI (2009) Environmental and spatial characterisation of bacterial community composition in soil to inform sampling strategies. Soil Biol Biochem41: 2292-2298.
5. Beeton RJS, Buckley KI, Jones GJ, Morgan D, Reichelt RE & Trewin D (2006) Australia State of the Environment 2006. Independent Report to the Australian Government Minister for the Environment and Heritage. Department of the Environment and Heritage, Canberra.
6. Beisner B, Haydon D & Cuddington K (2003) Alternative stable states in ecology. Front Ecol Environ1: 376-382.
7. Bennett LT, Kasel S & Tibbits J (2009) Woodland trees modulate soil resources and conserve fungal diversity in fragmented landscapes. Soil Biol Biochem41: 2162-2169.
8. Berthrong ST, Schadt CW, Pineiro G & Jackson RB (2009) Afforestation alters the composition of functional genes in soil and biogeochemical processes in South American grasslands. Appl Environ Microb75: 6240-6248.
9. Bissett A, Richardson AE, Baker G, Wakelin S & Thrall PH (2010) Life history determines biogeographical patterns of bacterial communities over multiple scales. Mol Ecol19: 4315-4327.
10. Bossio DA, Girvan MS, Verchot L, Bullimore J, Borelli T, Albrecht A, Scow KM, Ball AS, Pretty JN & Osborn AM (2005) Soil microbial community response to land-use change in an agricultural landscape of western Kenya. Microb Ecol49: 50-62.
11. Buckley DH & Schmidt TM (2001) The structure of microbial communities in soil and the lasting impact of cultivation. Microb Ecol42: 11-21.
12. Colloff M, Pullen K & Cunningham S (2010) Restoration of an ecosystem function to revegetation communities: the role of invertebrate macropores in enhancing soil water infiltration. Restor Ecol 18: 65-72.
13. Delhaize E & Ryan PR (1995) Aluminum toxicity and tolerance in plants. Plant Physiol107: 315-321.
14. Dumas JB (1981) Sur les procédés de l'analyse organique. Annal ChimXLVII: 195-213.
15. Fierer N & Jackson RB (2006) The diversity and biogeography of soil bacterial communities. P Natl Acad Sci USA103: 626-631.
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?Oecologia150: 590-601.
17. Isbell RF (1996) The Australian Soil Classification System. CSIRO Publishing, Melbourne.
18. Jesus EC, Marsh TL, Tiedje JM & Moreira FMS (2009) Changes in land-use alter the structure of bacterial communities in Western Amazon soils. ISME J3: 1004-1011.
19. 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. Appl Environ Microb75: 5111-5120.
20. Legendre P & Legendre L (1998) Numerical Ecology, 2nd English edn. Elsevier, Amsterdam.
21. Lindenmayer DB, McCarthy MA, Parris KM & Pope ML (2000) Habitat fragmentation, landscape context, and mammalian assemblages in southeastern Australia. J Mammal81: 787-797.
22. Manter DK, Weir TL & Vivanco JM (2010) Negative effects of sample pooling on PCR-based estimates of soil microbial richness and community structure. Appl Environ Microb76: 2086-2090.
23. Mitchell RJ, Campbell CD, Chapman SJ & Cameron CM (2010) The ecological engineering impact of a single tree species on the soil microbial community. J Ecol98: 50-61.
24. Oksanen J, Blanchet FG, Kindt R, Legendre P, O'Hara RB, Simpson GL, Solymos P, Stevens MHH & Wagner H (2010) vegan: Community Ecology Package. R package version 1.17-3. Available at.
25. Olsen SR & Sommers LE (1982) Phosphorus. Methods of Soil Analysis. Part 2: Chemical and Microbiological Properties (Page AL, Miller RH & Keeney DR, eds), pp. 403-427. American Society of Agronomy, Madison, WI.
26. Osborne CA, Rees GN, Bernstein Y & Janssen PH (2006) New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex communities. Appl Environ Microb72: 1270-1278.
27. R Development Core Team (2010) R: A Language and Environment for Statistical Computing. ISBN 3-900051-07-0. R Foundation for Statistical Computing, Vienna, Austria. Available at.
28. Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Kight R & Fierer N (2010) Soil bacteria and fungal communities across a pH gradient in an arable soil. ISME J4: 1340-1351.
29. Rowell DL (1994) Soil Science: Methods and Applications. Longman Group Ltd, London, UK.
30. Thrall PH, Millsom DA, Jeavons AC, Waayers M, Harvey GR, Bagnall DJ & Brockwell J (2005) Seed inoculation with effective root-nodule bacteria enhances revegetation success. J Appl Ecol42: 740-751.
31. van der Heijden MGA, Bardgett RD & van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11: 296-310.