African Journal of
Microbiology Research

  • Abbreviation: Afr. J. Microbiol. Res.
  • Language: English
  • ISSN: 1996-0808
  • DOI: 10.5897/AJMR
  • Start Year: 2007
  • Published Articles: 5233

Full Length Research Paper

Fungal diversity within organic and conventional farming systems in Central Highlands of Kenya

Edward Nderitu Karanja
  • Edward Nderitu Karanja
  • Department of Biological Sciences, School of Pure and Applied Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya.
  • Google Scholar
Andreas Fliessbach
  • Andreas Fliessbach
  • Research Institute of Organic Agriculture, Ackerstrasse 113, 5070 Frick, Switzerland.
  • Google Scholar
Noah Adamtey
  • Noah Adamtey
  • Research Institute of Organic Agriculture, Ackerstrasse 113, 5070 Frick, Switzerland.
  • Google Scholar
Anne Kelly Kambura
  • Anne Kelly Kambura
  • School of Agriculture, Earth and Environmental Sciences, Taita Taveta University, P. O. Box 635-80300, Voi, Kenya.
  • Google Scholar
Martha Musyoka
  • Martha Musyoka
  • International Centre for Insect Physiology and Ecology (icipe). P. O. Box 30772-00100, Nairobi, Kenya.
  • Google Scholar
Komi Fiaboe
  • Komi Fiaboe
  • International Centre for Insect Physiology and Ecology (icipe). P. O. Box 30772-00100, Nairobi, Kenya.
  • Google Scholar
Romano Mwirichia
  • Romano Mwirichia
  • Department of Biological Sciences, School of Pure and Applied Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya.
  • Google Scholar


  •  Received: 25 January 2020
  •  Accepted: 26 May 2020
  •  Published: 30 June 2020

References

Adamtey N, Musyoka MW, Zundel C, Cobo JG, Karanja E, Fiaboe KKM, Muriuki A, Mucheru-Muna M, Vanlauwe B, Berset E, Messmer MM, Gattinger A, Bhullar GC, Fliessbach A, Mäder P, Niggli U, Foster D (2016). Productivity, profitability and partial nutrient balance in maize-based conventional and organic farming systems in Kenya. Agriculture, Ecosystems and Environment 235:61-79.
Crossref

 

Anderson JM, Ingram JSI (1993). Tropical Soil Biology and Fertility: a Handbook of Methods. CAB International, Wallingford, UK.
Crossref

 
 

Bååth E, Anderson TH (2003). Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biology and Biochemistry 35:955-963.
Crossref

 
 

Balint M, Bahram M, Eren AM, Faust K, Fuhrman JA, Lindahl B, O'Hara RB, Opik M, Sogin ML, Unterseher M, Tedersoo L (2016). Millions of reads, thousands of taxa: Microbial community structure and associations analyzed via marker genes. FEMS Microbiology Reviews 40:686-700.
Crossref

 
 

Barea JM, Pozo MJ, Azcón R, Azcón-Aguilar C (2005). Microbial co-operation in the rhizosphere. Journal of Experimental Botany 56(417):1761-778.
Crossref

 
 

Bates D, Maechler M, Bolker B (2013). lme4: Linear mixed-effects models using S4 classes. R package version 0.999999-2. 

 
 

Berthrong ST, Buckley DH, Drinkwater LE (2013). Agricultural management and labile carbon additions affect soil microbial community structure and interact with carbon and nitrogen cycling. Microbial Ecology 66:158-170.
Crossref

 
 

Bloem J, Bolhuis PR, Veninga MR, Wieringa J (1995). Microscopic methods for counting bacteria and fungi in soil. In: Methods in Applied Soil Microbiology and Biochemistry. Alef K, Nannipieri P (Eds), pp. 162-173. Academic Press, London.

 
 

Bolyen E, Rideout JR, Dillon MR, Bokulich NA (2018). QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. Peer Journal Preprints 6:e27295v1.

 
 

Callahan BJ, McMurdie P, Rosen MJ, Han AW (2016). Dada2: High-resolution sample inference from illumina amplicon data. Nature Methods 13(7): 581.
Crossref

 
 

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushma FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7:335-336.
Crossref

 
 

Dighton J (2003). Fungi in Ecosystem Processes. Marcel Dekker, New York.
Crossref

 
 

Dixon J, Gulliver A, Gibbon D (2001). Farming systems and poverty: Improving farmers' livelihoods in a changing world. FAO, Rome.

 
 

Fierer N (2017). Embracing the unknown: Disentangling the complexities of the soil microbiome. Nature Reviews Microbiology 15:579-590.
Crossref

 
 

Fraç M, Hannula SE, BeÅ‚ka M, JÄ™dryczka M (2018). Fungal Biodiversity and Their Role in Soil Health. Frontiers in Microbiology 9:707.
Crossref

 
 

Gadd GM (2007). Geomycology: Biogeochemical transformations of rocks, minerals, metals and radionuclides by fungi, bio-weathering and bioremediation. Mycological Research 111(1):3-49.
Crossref

 
 

Gupta PK (1999). Soil, Plant, Water and Fertilizer Analysis. Agro Botanica Publishers, Bikaner, India, pp. 138-140.

 
 

Harman GE, Howell CR, Viterbo A, Chet, Lorito M (2004). Trichoderma species-Opportunistic, a virulent plant symbionts. Nature Reviews Microbiology 2:43-56.
Crossref

 
 

Hartmann M, Frey B, Mayer J, Mäder P, Widmer F (2015). Distinct soil microbial diversity under long-term organic and conventional farming. International Society for Microbial Ecology 9:1177-1194.
Crossref

 
 

Ihrmark K, Bo€deker ITM, Cruz-Martinez, Friberg H, Kubartova A, Schenck J, Lindahl BD (2012). New primers to amplify the fungal ITS2 region evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiology Ecology 82:666-677.
Crossref

 
 

IUSS Working Group WRB (2006). World reference base for soil resources 2006 (2nd Edition). World Soil Resources Reports No. 103. FAO, Rome.

 
 

Jaetzold R, Schmidt H, Hornetz B, Shisanya CA (2006a). Nairobi Farm Management Handbook of Kenya: Natural Conditions and Farm Management Information. Vol. II/C, East Kenya. Ministry of Agriculture, Nairobi, Kenya.

 
 

Jaetzold R, Schmidt H, Hornetz B, Shisanya CA (2006b). Nairobi Farm Management Handbook of Kenya: Natural Conditions and Farm Management Information. Vol. II/B, Central Kenya. Ministry of Agriculture, Nairobi, Kenya.

 
 

Johansson JF, Paul LR, Roger D (2004). Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture. FEMS Microbiology Ecology 48(1):1-13.
Crossref

 
 

Kazeeroni EA, Al-Sadi AM (2016). 454-Pyrosequencing reveals variable fungal diversity across farming systems. Frontiers in Plant Science 7:314.
Crossref

 
 

Kennedy JA, Powell HKJ (1986). Colorimetric determination of aluminium (III) with chrome azurol S and the reactivity of hydrolyzed aluminium species. Analytica Chimica Acta 184:329-333.
Crossref

 
 

Kojalg U, Larsson KH, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T, Sen R, Taylor AF, Tedersoo L, Vrålstad T, Ursing BM (2005). UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytologist 166:1063-1068.
Crossref

 
 

Koljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG,

 
 

Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiss M, Larsson KH (2013). Towards a unified paradigm for sequence-based identification of fungi. Molecular Ecology 22:5271-5277.
Crossref

 
 

Lahlali R, McGregor L, Song T, Gossen BD, Narisawa K, Peng G (2014). Heteroconium chaetospira induces resistance to clubroot via upregulation of host genes involved in jasmonic acid, ethylene, and auxin biosynthesis. PLoS ONE 9(4):e94144.
Crossref

 
 

Lahlali R, Hijri M (2010). Screening, identification and evaluation of potential biocontrol fungal endophytes against Rhizoctonia solani AG3 on potato plants. FEMS Microbiology Letters 311(2):152-159.
Crossref

 
 

Lentendu G, Wubet T, Chatzinotas A, Wilhelm C, Buscot F, Schlegel M (2014). Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: A multiple barcoding approach. Molecular Ecology 23(13):3341-3355.
Crossref

 
 

Lindahl BD, Ihrmark K, Boberg J, Trumbore SE, Högberg P, Stenlid J, Finlay RD (2007). Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. New Phytologist 173(3): 611-620.
Crossref

 
 

Lopes AR, Manaia CM, Nunes OC (2014). Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing. FEMS Microbiology Ecology 87(3):650-63.
Crossref

 
 

Madi L, Katan T, Katan J, Henis J (1997). Biological control of Sclerotium rolfsii and Verticillium dahliae by Talaromyces flavus is mediated by different mechanisms. Journal of phytopathology 87(10):1054-1060.
Crossref

 
 

McLaughlin DJ, Spatafora JW (2014). The Mycota. Systematics and Evolution Part A. Springer, Heidelberg.
Crossref

 
 

Mehlich A (1984). Mehlich-3 soil test extractant: A modification of Mehlich-2 extractant. Communications in Soil Science and Plant Analysis 15(12):1409-1416.
Crossref

 
 

Milner K (2014). Effects of Organic and Conventional Agricultural Practices on Soil Microbial Communities and Molecular Detection of Soil Borne Disease. Electronic Theses and Dissertations. 1213. 

View

 
 

Muriuki AW, Qureshi JN (2001). Fertilizer use manual. Kenya Agricultural Research Centre, Nairobi.

 
 

Musyoka MW, Adamtey N, Muriuki AW, Cadisch G (2017). Effects of organic and conventional farming systems on nitrogen uptake and use efficiencies of potato, maize and vegetables in the sub humid region of Central highlands of Kenya. European Journal of Agronomy 86:24-33.
Crossref

 
 

Okalebo JR, Gathua KW, Woomer PL (2002). Laboratory methods of soil and plant analysis: A working manual. TSBF: Nairobi, Kenya.

 
 

Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens HH, Szoecs E, Wagner H (2012). Vegan: Community Ecology Package, R Package version 2.0-3.

 
 

Persˇoh D (2015). Plant-associated fungal communities in the light of meta'omics. Fungal Diversity 75:1-25.
Crossref

 
 

Piepho HP (2004). An algorithm for a letter-based representation of all pairwise comparisons. Journal of Computational and Graphical Statistics 13:456-466.
Crossref

 
 

Purahong W, Wubet T, Lentendu G, Schloter M, Pecyna MJ, Kapturska D, Hofrichter M, Krüger D, Buscot F (2016). Life in leaf litter: Novel insights into community dynamics of bacteria and fungi during litter decomposition. Molecular Ecology 25:4059-4074.
Crossref

 
 

R Development Core Team (2012). A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.

 
 

R Development Core Team (2014). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

 
 

Rillig CM, Muller LAH, Lehmann A (2017). Soil aggregates as massively concurrent evolutionary incubators. International Society for Microbial Ecology 11:1943-1948.
Crossref

 
 

Sambrook KJ, Fritsch EF, Maniatis T (1989). Molecular Cloning: A Laboratory Manual. (2nd Eds.). New York, USA: Cold Spring Harbor Laboratory.

 
 

Schreiner RP, Bethlenfalvay GJ (1997). Mycorrhizae, biocides, and biocontrol 3. Effects of three different fungicides on developmental stages of three AM fungi. Biology and Fertility of Soils 24:18-26.
Crossref

 
 

Sharma-Poudyal D, Schlatter D, Yin C, Hulbert S, Paulitz T (2017). Long-term no-till: A major driver of fungal communities in dryland wheat cropping systems. PLoS ONE 12(9):e0184611.
Crossref

 
 

Singh M, Sarkar B, Biswas B, Bolan NS (2017b). Relationship between soil clay mineralogy and carbon protection capacity as influenced by temperature and moisture. Soil Biology and Biochemistry 109:95-106.
Crossref

 
 

Singh M, Sarkar B, Biswas B, Churchman J (2016). Adsorption-desorption behavior of dissolved organic carbon by soil clay fractions of varying mineralogy. Geoderma 280: 47-56.
Crossref

 
 

Six J, Elliott ET, Paustian K, Doran J (1998). Aggregation and Soil Organic Matter Accumulation in Cultivated and Native Grassland Soils. Soil Science Society of America Journal 62:1367-1377.
Crossref

 
 

Sommermann L, Geistlinger J, Wibberg D, Deubel A, Zwanzig J, Babin D, Schlüter A, Schellenberg I (2018). Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high throughput ITS-amplicon sequencing. PLoS One 13(4):e0195345.
Crossref

 
 

Tedersoo L, Sa'nchez-Ram'ırez S, Ko˜ljalg U, Bahram M, Do ring M, Schigel D, May T, Ryberg M, Abarenkov K (2018). High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal Diversity 90:135-159.
Crossref

 
 

Tedersoo L, Nilsson RH (2016). Molecular identification of fungi. In: Martin F (ed) Molecular mycorrhizal symbiosis. Wiley, Hobo-ken, pp 301-322.
Crossref

 
 

Tkacz A, Cheema J, Chandra G, Grant A, Poole PS (2015). Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. International Society for Microbial Ecology 9(11):2349-59.
Crossref

 
 

Wall DH, Bardgett RD, Behan-Pelletier V, Herrick JE, Jones TH, Ritz K, Six J, Strong DR, van der Putten WH (2012). Soil ecology and ecosystem services. 1st ed. Oxford University Press: USA.
Crossref

 
 

Wang H, Hyde KD, Soytong K, Lin F (2008). Fungal diversity on fallen leaves of Ficus in northern Thailand. Journal of Zhejiang University Science 9:835-841.
Crossref

 
 

Wang R, Zhang H, Sun L, Qi G, Chen S, Zhao X (2017). Microbial community composition is related to soil biological and chemical properties and bacterial wilt outbreak. Scientific Reports 7:343.
Crossref

 
 

White TJ, Bruns T, Lee S, Taylor JW (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide To Methods And Applications 18:315-322.
Crossref

 
 

Yu K, Zhang T (2012). Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge. PLoS ONE 7(5):e38183.
Crossref