Agricultural intensification and the functional capacity of soil microbes on smallholder African farms

Journal of Applied Ecology

Volumn 52, Issue 3, 2015, Pages 744-752

  Wood, Stephen A ^a,b   Bradford, Mark A ^c   Gilbert, Jack A ^d   Mcguire, Krista L ^a,e   Palm, Cheryl A ^b   Tully, Katherine L ^b   Zhou, Jizhong ^f,g,h   Naeem, Shahid ^a  

^a Columbia University ^*  (United States)

^b Center for International Forestry Research   (United States)

^c Yale University   (United States)

^d ARGONNE NATIONAL LABORATORY   (United States)

^e Program on US Russia Relations at Columbia s Harriman Institute   (United States)

^f UNIVERSITY OF OKLAHOMA   (United States)

^g LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^h TSINGHUA UNIVERSITY   (China)

Author keywords

African Green Revolution; Agroforestry; Fertilization; Functional diversity; GeoChip; Microbial diversity; Smallholder agriculture

Indexed keywords

AGROFORESTRY; BACTERIUM; CROP YIELD; FUNCTIONAL CHANGE; GREEN REVOLUTION; INTENSIVE AGRICULTURE; MICROBIAL COMMUNITY; NUTRIENT CYCLING; SMALLHOLDER; SOIL FERTILITY; SOIL MICROORGANISM;

KENYA; SUB-SAHARAN AFRICA;

BACTERIA (MICROORGANISMS);

EID: 84929654856     PISSN: 00218901     EISSN: 13652664     Source Type: Journal    
DOI: 10.1111/1365-2664.12416     Document Type: Article

References (36)

1. Arrese-Igor, C., Gonza´lez, E.M., Gordon, A.J., Minchin, F.R., Ga´lvez, L., Royuela, M., Cabrerizo, P.M. & Aparicio-Tejo, P.M. (1999) Sucrose synthase and nodule nitrogen fixation under drought and other environmental stresses. Symbiosis, 27, 189-212.
2. Baayen, R.H., Davidson, D.J. & Bates, D.M. (2008) Mixed-effects modeling with crossed random effects for subjects and items. Journal of Memory and Language, 59, 390-412.
3. Barrios, E., Buresh, R.J. & Sprent, J.I. (1996) Organic matter in soil particle size and density fractions from maize and legume cropping systems. Soil Biology and Biochemistry, 28, 185-193.
4. Barron, A.R., Purves, D.W. & Hedin, L.O. (2011) Facultative nitrogen fixation by canopy legumes in a lowland tropical forest. Oecologia, 165, 511-520.
5. Bates, D., Maechler, M. & Bolker, B. (2012) lme4: Linear mixed-effects models using S4 classes. R package version 0.9.
6. Bell, T., Newman, J.A., Silverman, B.W., Turner, S.L. & Lilley, A.K. (2005) The contribution of species richness and composition to bacterial services. Nature, 436, 1157-1160.
7. Bobbink, R., Hicks, K., Galloway, J., Spranger, T., Alkemade, R., Ashmore, M. et al. (2010) Global assessment of nitrogen deposition effects on terrestrial plant diversity: a synthesis. Ecological Applications, 20, 30-59.
8. Bradford, M.A., Fierer, N. & Reynolds, J.F. (2008) Soil carbon stocks in experimental mesocosms are dependent on the rate of labile carbon, nitrogen and phosphorus inputs to soils. Functional Ecology, 22, 964-974.
9. Bradford, M.A., Wood, S.A., Bardgett, R.D., Black, H.I.J., Bonkowski, M., Eggers, T. et al. (2014a) Discontinuity in the response of ecosystem processes and multifunctionality to altered soil community composition. Proceedings of the National Academy of Sciences of the United States of America, 111, 14478-14483.
10. Bradford, M.A., Warren, R.J., Baldrian, P., Crowther, T.W., Maynard, D.S., Oldfield, E.E., Wieder, W.R., Wood, S.A. & King, J.R. (2014b) Climate fails to predict wood decomposition at regional scales. Nature Climate Change, 4, 625-630.
11. Brown, K.H., Bach, E., Drijber, R., Hofmockel, K., Jeske, E., Sawyer, J.E. & Castellano, M.J. (2014) A long-term nitrogen fertiliser gradient has little effect on soil organic matter in a high-intensity maize production system. Global Change Biology, 20, 1339-1350.
12. Byrnes, J.E., Gamfeldt, L., Isbell, F., Lefcheck, J.S., Griffin, J.N., Hector, A. et al. (2014) Investigating the relationship between biodiversity and ecosystem multifunctionality: challenges and solutions. Methods in Ecology and Evolution, 5, 111-124.
13. Conant, R.T., Ryan, M.G., A˚gren, G.I., Birge, H.E., Davidson, E.A., Eliasson, P.E. et al. (2011) Temperature and soil organic matter decomposition rates - synthesis of current knowledge and a way forward. Global Change Biology, 17, 3392-3404.
14. Degens, B.P. & Harris, J.A. (1997) Development of a physiological approach to measuring the catabolic diversity of soil microbial communities. Soil Biology and Biochemistry, 29, 1309-1320.
15. Drake, J., Darby, B., Giasson, M.-A., Kramer, M., Phillips, R. & Finzi, A. (2013) Stoichiometry constrains microbial response to root exudation-insights from a model and a field experiment in a temperate forest. Biogeosciences, 10, 821-838.
16. Fierer, N., Lauber, C.L., Ramirez, K.S., Zaneveld, J., Bradford, M.A. & Knight, R. (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME Journal, 6, 1007-1017.
17. 2-fixation of herbaceous, shrub and tree legumes in improved fallows. Soil Biology and Biochemistry, 34, 1059-1071.
18. Gilbert, J.A., Meyer, F., Jansson, J., Gordon, J., Pace, N., Tiedje, J. et al. (2010) The Earth Microbiome Project: meeting report of the "1st EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6th 2010. Standards in Genomic Sciences, 3, 249.
19. Glover, J.D., Reganold, J.P. & Cox, C.M. (2012) Plant perennials to save Africa's soils. Nature, 489, 359-361.
20. Hsiang, S.M. (2013) Visually-weighted regression. SSRN working paper.
21. Hurlbert, S.H. & Lombardi, C.M. (2009) Final collapse of the Neyman-Pearson decision theoretic framework and rise of the neoFisherian. Annales Zoologici Fennici, 46, 311-349.
22. Kuznetsova, A., Christensen, R. & Brockhoff, P. (2012) lmerTest: tests for random and fixed effects for linear mixed effect models (lmer objects of lme4 package). R package version, 1.0-2.
23. Lozupone, C., Lladser, M.E., Knights, D., Stombaugh, J. & Knight, R. (2011) UniFrac: an effective distance metric for microbial community comparison. ISME Journal, 5, 169-172.
24. Muggeo, V.M. (2003) Estimating regression models with unknown break-points. Statistics in medicine, 22, 3055-3071.
25. 2 from generalized linear mixed-effects models. Methods in Ecology and Evolution, 4, 133-142.
26. Ramirez, K.S., Craine, J.M. & Fierer, N. (2012) Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Global Change Biology, 18, 1918-1927.
27. Ramirez, K.S., Lauber, C.L., Knight, R., Bradford, M.A. & Fierer, N. (2010) Consistent effects of nitrogen fertilisation on soil bacterial communities in contrasting systems. Ecology, 91, 3463-3470.
28. Scheffer, M., Bascompte, J., Brock, W.A., Brovkin, V., Carpenter, S.R., Dakos, V. et al. (2009) Early-warning signals for critical transitions. Nature, 461, 53-59.
29. Schielzeth, H. (2010) Simple means to improve the interpretability of regression coefficients. Methods in Ecology and Evolution, 1, 103-113.
30. Schmidt, M.W.I., Torn, M.S., Abiven, S., Dittmar, T., Guggenberger, G., Janssens, I.A. et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49-56.
31. Vitousek, P.M., Naylor, R., Crews, T., David, M.B., Drinkwater, L.E., Holland, E. et al. (2009) Nutrient imbalances in agricultural development. Science, 324, 1519-1520.
32. West, A.W. & Sparling, G.P. (1986) Modifications to the substrate-induced respiration method to permit measurement of microbial biomass in soils of differing water contents. Jounal of Microbial Methods, 5, 177-189.
33. Wiggins, S., Kirsten, J. & Llambi, L. (2010) The future of small farms. World Development, 38, 1341-1348.
34. Wood, S.A., Almaraz, M., Bradford, M.A., McGuire, K.L., Naeem, S., Neill, C., Palm, C.A., Tully, K.L. & Zhou, J. (2015a) Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture. Frontiers Microbiology, 6, 90.
35. Wood, S.A., Bradford, M.A., Gilbert, J.A., McGuire, K.L., Palm, C.A., Tully, K.L., Zhou, J. & Naeem, S. (2015b) Data from: agricultural intensification and the functional capacity of soil microbes on smallholder African farms. Dryad Digital Repository, http://dx.doi.org/10.5061/dryad.7d5g4.
36. Yang, Y., Wu, L., Lin, Q., Yuan, M., Xu, D., Yu, H. et al. (2013) Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland. Global Change Biology, 19, 637-648.