Crop monoculture rather than agriculture reduces the spatial turnover of soil bacterial communities at a regional scale

Environmental Microbiology

Volumn 17, Issue 3, 2015, Pages 678-688

  Figuerola, Eva L M ^a   Guerrero, Leandro D ^a   Türkowsky, Dominique ^a   Wall, Luis G ^b   Erijman, Leonardo ^a,c  

^a INSTITUTO DE INVESTIGACIONES EN INGENIERÍA GENÉTICA Y BIOLOGÍA MOLECULAR   (Argentina)

^b UNIVERSIDAD NACIONAL DE QUILMES   (Argentina)

^c UNIVERSIDAD DE BUENOS AIRES   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

ACIDOBACTERIA; BACTERIA (MICROORGANISMS); GLYCINE MAX; VERRUCOMICROBIA;

RNA 16S; SOIL;

ACIDOBACTERIA; AGRICULTURE; BIODIVERSITY; CLASSIFICATION; CROP; DNA SEQUENCE; ENVIRONMENT; GENETICS; MICROBIAL CONSORTIUM; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENY; SOIL; SOYBEAN; VERRUCOMICROBIA;

ACIDOBACTERIA; AGRICULTURE; BASE SEQUENCE; BIODIVERSITY; CROPS, AGRICULTURAL; ENVIRONMENT; MICROBIAL CONSORTIA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY; SOYBEANS; VERRUCOMICROBIA;

EID: 84925175358     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12497     Document Type: Article

References (62)

1. Allison, S.D., and Martiny, J.B.H. (2008) Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci USA 105: 11512-11519.
2. Anderson, M.J., and Willis, T.J. (2003) Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology. Ecology 84: 511-525.
3. Barberán, A., Bates, S.T., Casamayor, E.O., and Fierer, N. (2011) Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J 6: 343-351.
4. Bates, D.M. (2010). lme4: Mixed-effects modeling with R. Available from URL: http://lme4.r-forge.r-project.org/book.
5. Beauregard, M.S., Hamel, C., Atul-Nayyar, and St-Arnaud, M. (2010) Long-term phosphorus fertilization impacts soil fungal and bacterial diversity but not AM fungal community in alfalfa. Microb Ecol 59: 379-389.
6. Beketov, M.A., Kefford, B.J., Schäfer, R.B., and Liess, M. (2013) Pesticides reduce regional biodiversity of stream invertebrates. Proc Natl Acad Sci USA 110: 11039-11043.
7. Berthelet, M., Whyte, L.G., and Greer, C.W. (1996) Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns. FEMS Microbiol Lett 138: 17-22.
8. Bockus, W.W., and Shroyer, J.P. (1998) The impact of reduced tillage on soilborne plant pathogens. Annu Rev Phytopathol 36: 485-500.
9. Bray, J.R., and Curtis, J.T. (1957) An ordination of the upland forest communities of southern Wisconsin. Ecol Monogr 27: 325-349.
10. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., etal. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Meth 7: 335-336.
11. Castiglioni, M.G., Behrends Kraemer, F., and Morras, H.J.M. (2013) Efecto de la secuencia de cultivos bajo siembra directa sobre la calidad de algunos suelos de la región Pampeana. Cienc suelo 31: 93-105.
12. Ceja-Navarro, J.A., Rivera-Orduna, F.N., Patino-Zúñiga, L., Vila-Sanjurjo, A., Crossa, J., Govaerts, B., and Dendooven, L. (2010) Phylogenetic and multivariate analyses to determine the effects of different tillage and residue management practices on soil bacterial communities. Appl Environ Microbiol 76: 3685-3691.
13. Chase, J.M. (2003) Community assembly: when should history matter? Oecologia 136: 489-498.
14. Chase, J.M., and Myers, J.A. (2011) Disentangling the importance of ecological niches from stochastic processes across scales. Philos T Roy Soc B 366: 2351-2363.
15. Chaves, L.F. (2010) An entomologist guide to demystify pseudoreplication: data analysis of field studies with design constraints. J Med Entomol 47: 291-298.
16. Claesson, M.J., Wang, Q., O'Sullivan, O., Greene-Diniz, R., Cole, J.R., Ross, R.P., and O'Toole, P.W. (2010) Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res 38: e200-e200.
17. Derpsch, R., Friedrich, T., Kassam, A., and Li, H. (2010) Current status of adoption of no-till farming in the world and some of its main benefits. Intl J Agr Biol Eng 3: 1-25.
18. Díaz-Zorita, M., Duarte, G.A., and Grove, J.H. (2002) A review of no-till systems and soil management for sustainable crop production in the subhumid and semiarid Pampas of Argentina. Soil Till Res 65: 1-18.
19. Ding, G.-C., Piceno, Y.M., Heuer, H., Weinert, N., Dohrmann, A.B., Carrillo, A., etal. (2013) Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem. PLoS ONE 8: e59497.
20. Domínguez, A., Bedano, J.C., and Becker, A.R. (2010) Negative effects of no-till on soil macrofauna and litter decomposition in Argentina as compared with natural grasslands. Soil Till Res 110: 51-59.
21. Doxa, A., Paracchini, M.L., Pointereau, P., Devictor, V., and Jiguet, F. (2012) Preventing biotic homogenization of farmland bird communities: the role of high nature value farmland. Agr Ecosyst Environ 148: 83-88.
22. Ekroos, J., Heliölä, J., and Kuussaari, M. (2010) Homogenization of lepidopteran communities in intensively cultivated agricultural landscapes. J Appl Ecol 47: 459-467.
23. Fierer, N., Lauber, C.L., Ramirez, K.S., Zaneveld, J., Bradford, M.A., and Knight, R. (2011) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6: 1007-1017.
24. Figuerola, E.L.M., Guerrero, L.D., Rosa, S.M., Simonetti, L., Duval, M.A.E., Galantini, J.A., etal. (2012) Bacterial indicator of agricultural management for soil under no-till crop production. PLoS ONE 7: e51075.
25. Fukami, T. (2004) Community assembly along a species pool gradient: implications for multiple-scale patterns of species diversity. Popul Ecol 46: 137-147.
26. Girvan, M.S., Bullimore, J., Pretty, J.N., Osborn, A.M., and Ball, A.S. (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69: 800-1809.
27. González-Chávez, M.D.C.A., Aitkenhead-Peterson, J.A., Gentry, T.J., Zuberer, D., Hons, F., and Loeppert, R. (2010) Soil microbial community, C, N, and P responses to long-term tillage and crop rotation. Soil Till Res 106: 285-293.
28. Guo, L.B., and Gifford, R.M. (2002) Soil carbon stocks and land use change: a meta analysis. Glob Change Biol 8: 345-360.
29. Hammer, Ø., Harper, D.A.T., and Ryan, P.D. (2001) PAST: paleontological Statistics software package for education and data analysis palaeontol. Electronica 4: 1-9.
30. Hanson, C.A., Fuhrman, J.A., Horner-Devine, M.C., and Martiny, J.B.H. (2012) Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol 10: 497-506.
31. Heenan, D.P., Chan, K.Y., and Knight, P.G. (2004) Long-term impact of rotation, tillage and stubble management on the loss of soil organic carbon and nitrogen from a chromic luvisol. Soil Till Res 76: 59-68.
32. Jesus, E.D.C., Marsh, T.L., Tiedje, J.M., and de S Moreira, F.M. (2009) Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME J 3: 1004-1011.
33. Kallimanis, A.S., Mazaris, A.D., Tzanopoulos, J., Halley, J.M., Pantis, J.D., and Sgardelis, S.P. (2008) How does habitat diversity affect the species-area relationship? Global Ecol Biogeogr 17: 532-538.
34. Koleff, P., Gaston, K.J., and Lennon, J.J. (2003) Measuring beta diversity for presence - absence data. J Anim Ecol 72: 367-382.
35. Lauber, C.L., Ramirez, K.S., Aanderud, Z., Lennon, J., and Fierer, N. (2013) Temporal variability in soil microbial communities across land-use types. ISME J 7: 1641-1650.
36. Lindström, E.S., and Langenheder, S. (2012) Local and regional factors influencing bacterial community assembly. Environ Microbiol Rep 4: 1-9.
37. Lipson, D.A., and Schmidt, S.K. (2004) Seasonal changes in an alpine soil bacterial community in the Colorado rocky mountains. Appl Environ Microbiol 70: 2867-2879.
38. Loreau, M., Naeem, S., Inchausti, P., Bengtsson, J., Grime, J.P., Hector, A., etal. (2001) Biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294: 804-808.
39. Lozupone, C., Lladser, M.E., Knights, D., Stombaugh, J., and Knight, R. (2010) UniFrac: an effective distance metric for microbial community comparison. ISME J 5: 169-172.
40. Lundin, D., Severin, I., Logue, J.B., Östman, Ö., Andersson, A.F., and Lindström, E.S. (2012) Which sequencing depth is sufficient to describe patterns in bacterial and diversity? Environ Microbiol Rep 4: 367-372.
41. Marvier, M., Kareiva, P., and Neubert, M.G. (2004) Habitat destruction, fragmentation, and disturbance promote invasion by habitat generalists in a multispecies metapopulation. Risk Anal 24: 869-878.
42. Olden, J.D., LeRoy Poff, N., Douglas, M.R., Douglas, M.E., and Fausch, K.D. (2004) Ecological and evolutionary consequences of biotic homogenization. Trends Ecol Evol 19: 18-24.
43. Pasari, J.R., Levi, T., Zavaleta, E.S., and Tilman, D. (2013) Several scales of biodiversity affect ecosystem multifunctionality. Proc Natl Acad Sci USA 110: 10219-10222.
44. Philippot, L., Andersson, S.G.E., Battin, T.J., Prosser, J.I., Schimel, J.P., Whitman, W.B., and Hallin, S. (2010) The ecological coherence of high bacterial taxonomic ranks. Nat Rev Microbiol 8: 523-529.
45. Pinto, A.J., and Raskin, L. (2012) PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS ONE 7: e43093.
46. Rodrigues, J.L.M., Pellizari, V.H., Mueller, R., Baek, K., Jesus, E.D.C., Paula, F.S., etal. (2013) Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proc Natl Acad Sci USA 110: 988-993.
47. Rosa, S.M., Behrends Kraemer, F., Soria, M.A., Guerrero, L.D., Morrás, H.J.M., Figuerola, E.L.M., and Erijman, L. (2014) The influence of soil properties on denitrifying bacterial communities and denitrification potential in no-till production farms under contrasting management in the Argentinean Pampas. Appl Soil Ecol 75: 172-180.
48. Ross, D.J., Tate, K.R., Scott, N.A., and Feltham, C.W. (1999) Land-use change: effects on soil carbon, nitrogen and phosphorus pools and fluxes in three adjacent ecosystems. Soil Biol Biochem 31: 803-813.
49. Schloss, P.D., Gevers, D., and Westcott, S.L. (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6: e27310.
50. Schmalenberger, A., Schwieger, F., and Tebbe, C.C. (2001) Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl Environ Microbiol 67: 3557-3563.
51. Shaver, T.M., Peterson, G.A., Ahuja, L.R., Westfall, D.G., Sherrod, L.A., and Dunn, G. (2002) Surface soil physical properties after twelve years of dryland no-till management. Soil Sci Soc Am J 66: 1296-1303.
52. Smalla, K., Wieland, G., Buchner, A., Zock, A., Parzy, J., Kaiser, S., etal. (2001) Bulk and rhizosphere soil bacterial shifts studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal communities shift revealed. Appl Environ Microbiol 67: 4742-4751.
53. Soininen, J., McDonald, R., and Hillebrand, H. (2007) The distance decay of similarity in ecological communities. Ecography 30: 3-12.
54. Steenwerth, K.L., Jackson, L.E., Calderón, F.J., Stromberg, M.R., and Scow, K.M. (2002) Soil microbial community composition and land use history in cultivated and grassland ecosystems of coastal California. Soil Biol Biochem 34: 1599-1611.
55. Stevenson, F.J., and Cole, M.A. (1999) Cycles of Soil: Carbon, Nitrogen, Phosphorus, Sulfur, Micronutrients. New York, USA: Wiley.
56. Sul, W.J., Cole, J.R., Jesus, E.D.C., Wang, Q., Farris, R.J., Fish, J.A., and Tiedje, J.M. (2011) Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering. Proc Natl Acad Sci USA 108: 14637-14642.
57. Syers, J.K. (1997) Managing soils for long-term productivity. Phil Trans Roy Soc (London). Series B. Biological Sciences 352: 1011-1021.
58. Tscharntke, T., Sekercioglu, C.H., Dietsch, T.V., Sodhi, N.S., Hoehn, P., and Tylianakis, J.M. (2008) Landscape constraints on functional diversity of birds and insects in tropical agroecosystems. Ecology 89: 944-951.
59. Van Elsas, J.D., and Rutger, M. (2006) Soil microbial diversity and community composition. In Microbial Methods for Assessing Soil Quality. Bloem, J., Hopkins, D.H., and Benedetti, A. (eds). Cambridge, UK: CAB International Publishing, pp. 183-186.
60. Wall, L.G. (2011) The BIOSPAS Consortium: soil biology and agricultural production. In Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Bruijn, F.J.D. (ed.). Hoboken, NJ, USA: John Wiley & Sons, Inc., pp. 299-306.
61. Zhou, J., Wu, L., Deng, Y., Zhi, X., Jiang, Y.-H., Tu, Q., etal. (2011) Reproducibility and quantitation of amplicon sequencing-based detection. ISME J 5: 1303-1313.
62. Zhou, J., Jiang, Y.-H., Deng, Y., Shi, Z., Zhou, B.Y., Xue, K., etal. (2013) Random Sampling Process Leads to Overestimation of β-Diversity of Microbial Communities. mBio 4: e324-e313.