Abstract
Soil fertility decline is increasingly leading to reduced food production worldwide. Over 70% of small holder farmers in the central highlands of Kenya are using crop manure, animal wastes and inorganic fertilizers to increase their farms’ fertility and subsequent productivity. The dilemma with these practices is that less is known on the impact of these resources on the below ground biodiversity particularly the microbial communities which play a key role in determining soil quality. A study was carried out on a 32 year old long-term trial in Kabete, Kenya. These soils were treated with organic (maize stover at 10 t ha−, farmyard manure at 10 t ha−) and inorganic fertilizers (120 kg N, 52.8 kg P plus farmyard manure at 10 t ha−1 (N2P2 + FYM), 120 kg N, 52.8 kg P plus maize stover at 10 t ha−1 (N2P2 + R), 120 kg N, 52.8 kg P (N2P2), and a control (Nil and fallow) for over 30 years. We examined 16S rRNA gene and 28S rRNA gene fingerprints of bacterial and fungal communities, respectively, by PCR amplification and denaturing gradient gel electrophoresis (PCR-DGGE) separation. Bacterial community structure and diversity were negatively affected by N2P2, as evidenced by changes in the PCR-DGGE banding patterns. Bacterial community structure in the N2P2-treated soil was more closely related to the bacterial structure in the untreated soil (fallow and Nil) than that in soils treated with a combination of inorganic and organic or inorganic fertilizers alone. For the fungal community the negative effect of N2P2 alone was not as adverse as for the bacterial community structure since the soils treated with N2P2 were closely related to those treated with N2P2 + FYM and N2P2 + maize stover. However, soils treated with organic inputs clustered away from soils amended with inorganic inputs. Organic inputs had a positive effect on both fungal and bacterial community structures with or without chemical fertilizers. Results from this study suggested that bacterial and fungal community structure was closely related to agro-ecosystem management practices conducted for over the past 30 years.
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References
Abbott LK, Murphy DV (2007) What is soil biological fertility? In: Abbott LK and Murphy DV (eds) Soil biological fertility-A key to sustainable land use in Agriculture. Spinger, Dordrecht, Netherlands, pp 1–15
Bouché MB (1977) Strategies lombriciennes. Ecol Bull 25:122–132
Brown GG (1995) How do earthworms affect microfloral and faunal community diversity. Plant Soil 170:209–231
Buckerfield JC, Kretzschmar A (1992) Earthworm population in dryland cropping soils under conservation tillage in South Australia. Soil Biol Biochem 24(12):1666–1672
Buckley DH, Schmidt TM (2001) Exploring the biodiversity of soil – a microbial rain forest. In: Staley JT, Reysenbach AL (eds) Biodiversity of microbial life: foundation of Earth’s biosphere. Wiley-Liss, Inc., New York, pp 183–208
Buckley DH, Schmidt TM (2003) Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environ Microbiol 5:441–452
Duineveld BM, Rosado AS, van Elsas JD, van Veen JA (1998) Analysis of the dynamic of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns. Appl Environ Microbiol 64:4950–4957
Egert M, Marhan S, Wagner B, Scheu S, Friedrich WM (2004) Molecular profoling of 16S rRNA genes reveals diet-related differences of microbial communities in soil, gut, and casts of Lumbricus terrestris L. (Oligochaeta: Lumbricidae). FEMS Microbiol Ecol 48:187–197
FAO (1990) FAO-UNESCO Soil Map of the World Revised Legend. Soil resources report 60. Food Agriculture Organization: Rome, Italy
Furlong MA, Singleton DC, Whitman WB (2002) Molecular and culture based analyses of prokaryotic communities from an agricultural soil and the burrows and casts of the earthworm Lumbricus rubellus. Appl Environ Microbiol 68:1265–1279
Hopkins DW, Shiel RS (1996) Size and activity of soil microbial communities in long-term experimental grassland plots treated with manure and inorganic fertilizers. Biol Fertil Soils 22:66–70
Horn MA, Schramm A, Drake HL (2003) The earthworm gut: an ideal habitat for ingested N2O- producing microorganisms. Appl Environ Microbiol 69:1662–1669
Jama BA, Niang IA, Amadalo B, De wolf J, Rao MR, Buresh RJ (1999) The potential of improved fallows to improve and conserve the fertility of nutrient depleted soils of western Kenya In: Proceedings of the 6th Biennial KARI Scientific Conference (KARI), Nairobi, Kenya, pp 133–144
Joy EKD, Reddy MV, Reddy SM (1992) Mycoflora associated with the body surface, gut and casting of earthworm (Lampito mauritii Kinberg) in relation to soil in semi-arid tropical grassland. Environ Ecol 10:914–918
Kapkiyai JJ, Karanja NK, Woomer P, Quersh JN (1998) Soil organic carbon fractions in a long-term experiment and the potential for their use as a diagnostic assay in highland farming systems of central Kenya. Afr Crop Sci J 6:15–20
Karsren GR, Drake HL (1995) Comparative assessment of the aerobic and anaerobic microfloras of earthworm guts and forest soils. Appl Environ Microbiol 61:1039–1044
Kazombo-Phiri SFM (2005) Main causes of declining soil productivity in Malawi: effects on agriculture and management technologies employed to alleviate the problems. In: Omanya GO, Pastern D (eds) Sustainable agriculture systems for the dry lands. Proceedings of the international symposium for sustainable dry land agriculture systems, Niamey, Niger, 2–5 Dec 2003, pp 59–66
Kibunja CN (2007) Impact of long-term application of organic and inorganic nutrient sources in a maize-bean rotation to soil nitrogen dynamics and soil microbial populations and activity. PhD thesis. University of Nairobi
Kibunja CN, Gikonyo EW, Wamaitha J, Thuranira EG, Nandwa S (2000) Sustainability of long term bean productivity using maize stover incorporation, residue fertilizers and manure. An Abstract of a paper presented during the 18th Conference and end of the Millennium Celebrations of the Soil Science Society of East Africa held on 4th–8th December, 2000, Mombasa Kenya. Oral paper 37
Kibunja CN, Mwaura FB, Mugendi DN (2010) Long-term land management effects on soil properties and microbial populations in a maize–bean rotation at Kabete, Kenya. Afr J Agric Res 5:108–113
Kimetu JM (2002) Nitrogen fertilizer equivalency values for organic materials of contrasting quality base on maize performance at Kabete, Kenya. Msc. Thesis, Kenyatta University, Kenya
Kristufek V, Ravasz K, Pizl V (1993) Actinomycete communities in earthworm guts and sorunding soil. Pedobiologia 37:379–384
Laryea KB, Anders MM, Pathak P (1995) Long-term experiments on alfisols and vertisols in the semi-arid tropics. In: Lal R, Stewart BA (eds) Soil management: experimental basis for sustainability and environmental quality. CRC Press, Boca Raton, pp 267–292
Lavelle P (1997) Faunal activities and soil processes: adaptive strategies that determine ecoisystem function. Adv Ecol Res 27:93–132
Lavelle P, Barois I, Brown GG, Blanchart E, Brussaard L, Decaëns T, Fragoso C, Jimenez J, Kajondo KK, Martinez M, Moreno A, Pashanasi B, Senapati B, Villenave C (2001) Earthworms as a resource in tropical agroecosystems. In: Subba Rao NS, Dommergues YR (eds) Microbial interactions in agriculture and forestry. Science Publishers, Enfield, pp 163–181. ISBN ISBN 1578081386
Lawes Agricultural Trust (2007) Genstat 7 release 1. VSN International, Wilkinson House, Jordan Hills Road, Oxford
Maiorana M, Convertini G, Di Bari V, Rizzo V (1992) Yield and quality of durum wheat (Triticum durum Desf.) under continuous cropping after 9 years of straw incorporation. Eur J Agronomy 1:11–19
Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G (2001) DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67:2354–2359
McLean MA (1997) Impacts of earthworm invasion on microbial activities and soil communities in a pine forest floor. PhD dissertation, University of Calgary
Øvreås L, Forney LJ, Daae FL, and Torsvik VL (1997) Distribution of acterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63:3367–3373
Parham JA, Deng SP, Raun WR, Johnson GV (2002) Long-term cattle manure application in soil. I. Effect on soil phosphorus levels, microbial biomass C, and dehydrogenase and phosphatase activities. Biol Fertil Soils 35:328–337
Parham JA, Deng SP, Da HN, Sun HY, Raun WR (2003) Long-term cattle manure application in soil. II. Effect on soil microbial populations and community structure. Biol Fertil Soils 38:209–215
Parthasarathi K, Ranganathan LS, Anandi V (1997) Predation of fungi by Lampito mauritii (Kinberg) reared on different substrates. Indian J Microbiol 37:41–42
Peacock AD, Mullen MD, Ringelberg DB, Tyler DD, Hedrick DB, Gale PM, White DC (2001) Soil microbial community responses to dairy manure or ammonium nitrate applications. Soil Biol Biochem 33:1011–1019
Qureshi JN (1987) The cumulative effects of N-P fertilizers, manure and crop residues on maize grain yields, leaf contents and some soil chemical properties at Kabete. pp. 12 in : National Maize Agronomy Workshop, Nairobi, 17–19th February 1987, KARI, Nairobi, Kenya
Ritz K, Wheatley RE, Griffiths BS (1997) Effects of animal manure application and crop plants upon size and activity of soil microbial biomass under organically grown spring barley. Biol Fertil Soils 24:372–377
Sanchez PA, Jama BA (2000) Soil fertility replenishment takes off in East and Southern Africa. ICRAF, Nairobi
Shannon C, Weaver W (1963) The mathematical theory of communication. University of Illinois Press, Urbana
Sigler V, William Ronald F, Turco (2002) The impact of chlorothalonil application on soil bacterial and fungal populations as assessed by denaturing gradient gel electrophoresis. Appl Soil Ecol 21:107–118
Smit E, Leeflang P, Gommans S, van den Broek J, van Mil S, Wernars K (2001) Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67:2284–2291
Swift MJ, Seward PD, Frost PGH, Qureshi JN, Muchena FN (1994) Long term experiments in Africa: developing a database for sustainable land use under global change. In: Leigh RA, Johnson AE (eds) Long term experiments in agriculture and ecological sciences, pp 229–251
Tandon HLS, Kanwar JS (1984) A review of fertilizer use research on Sorghum in India. International Crop Research Institute for the Semi-Arid Tropics. Research Bulleting No. 8. ICRISAT, Patancheru, 331 Andhara Pradesh, India
Trigo D, Barois MH, Gravin E, Huerta S, Irisson, Lavelle P (1999) Mutualism between earthworms and soil microflora. Pedobiologia 43:866–873
Waswa BS, Mugendi DN, Vanlauwe B, Kungu JB (2007) Changes in soil organic matter as influenced by organic residue management regimes in selected experiments in Kenya. In: Bationo A, Waswa B, Kihara J, Kimetu J (eds) Advances in integrated soil fertility management in Sub-Saharan Africa: Challenges and opportunities. Springer, Dordrecht, Netherlands, pp 457–469
Wolter C, Scheu S (1999) Changes in bacterial numbers and hyphal lengths during the gut passage through Lumbricus terrestris (Lumbricidae, Oligochaeta). Pedobiologia 43:891–900
Acknowledgement
This work was supported by the “Microbes” project coordinated by Dr. J.L. Chotte and funded by l’Agence Nationale de Recherche (France). The authors are very grateful to The African Network in Africa (AfNet CIAT-TSBF) which is financially supporting the maintaining cost of this long-term trial and to Dr Andre Bationo and colleagues for their patience and relevant discussions about the trial.
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Kamaa, M.M. et al. (2012). Effects of Organic and Inorganic Applications on Soil Bacterial and Fungal Microbial Communities Diversity and Impacts of Earthworms on Microbial Diversity in the Kabete Long-Term Trial, Kenya. In: Bationo, A., Waswa, B., Kihara, J., Adolwa, I., Vanlauwe, B., Saidou, K. (eds) Lessons learned from Long-term Soil Fertility Management Experiments in Africa. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-2938-4_7
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