The rhizosphere of Coffea arabica in its native highland forests of Ethiopia provides a niche for a distinguished diversity of Trichoderma

Diversity

Volumn 2, Issue 4, 2010, Pages 527-549

  Mulaw, Temesgen Belayneh ^a   Kubicek, Christian P ^a   Druzhinina, Irina S ^a  

^a VIENNA UNIVERSITY OF TECHNOLOGY   (Austria)

Author keywords

Biocontrol; Coffee; Diversity; DNA barcode; Ethiopia; Hypocrea; Molecular phylogeny; Rhizosphere

Indexed keywords

BIOCONTROL AGENT; COFFEE; DNA; ENDEMIC SPECIES; FOREST ECOSYSTEM; FUNGUS; NEW SPECIES; PHYLOGENY; RHIZOSPHERE; SPECIES DIVERSITY; UPLAND REGION;

ETHIOPIA;

COFFEA ARABICA; FUNGI; GIBBERELLA; GIBBERELLA XYLARIOIDES; HYPOCREA; TRICHODERMA;

EID: 79961093356     PISSN: None     EISSN: 14242818     Source Type: Journal    
DOI: 10.3390/d2040527     Document Type: Article

References (54)

1. Coffee; 2009. Available online: http://www.coffeeresearch.org/ (accessed on 5 May 2009).
2. Davids, K. Alternative Africas: Rwanda, Tanzania, Zimbabwe. Available online: http://www.coffeereview.com/ (accessed on 5 May 2009).
3. Fair Trade Farmers in Ethiopia; 2004. Available online: http://www.globalexchange.org/campaigns/fairtrade/coffee/EthiopiaFlyer.pdf (accessed on 5 May 2009).
4. Wellman, F.L. Coffee: Botany, Cultivation and Utilization. World Crop Series; Inter Science: New York, NY, USA, 1961.
5. Meyer, F. Notes on wild Coffea arabica from southwestern Ethiopia, with some historical considerations. Econ. Bot. 1965, 19, 136-151.
6. Friis, I. The wild populations of Coffea arabica L., and cultivated coffee. In Taxonomic Aspects of African Economic Botany, Proceedings of the IX plenary meeting of AETFAT, Las Palmas de Gran Canaria, 18-23 March, 1978; Kunkel, G., Ed.; Bentham-Moxon Trust: Les Palmas de Gran Canaria, Spain, 1979.
7. Adugna, G.; Hulluka, M.; Hindorf, H. Incidence of tracheomycosis, Gibberella xylarioides (Fusarium xylarioides), on Arabica coffee in Ethiopia. Ztschr. Pflanzenkrankh. Pflanzenschutz 2001, 108, 136-142.
8. Geiser, D.M.; Ivey, M.L.L.; Hakiza, G.; Juba, J.H.; Miller, S.A. Gibberella xylarioides (anamorph: Fusarium xylarioides), a causative agent of coffee wilt disease in Africa, is a previously unrecognized member of the G. fujikuroi species complex. Mycologia 2005, 97, 191-201.
9. Serani, S.; Taligoola, H.K.; Hakiza, G.J. An investigation into Fusarium spp. associated with coffee and banana plants as potential pathogens of robusta coffee. Afric. J. Ecol. 2007, 45, 91-95.
10. Silva, M.C.; Várzea, V.; Guerra-Guimarães, L.; Azinheira, H.G.; Fernandez, D.; Petitot, A.-S.; Bertrand Lashermes, B.P.; Nicole, M. Coffee resistance to the main diseases: Leaf rust and coffee berry disease. Braz. J. Plant Physiol. 2006, 18, 119-147.
11. Strange, R.N. Plant Disease Control: Towards Environmentally Acceptable Methods; Chapman and Hall: New York, NY, USA, 1993.
12. Van der Vossen, H.A.M. A critical analysis of the agronomic and economic sustainability of organic coffee production. Exper. Agricult. 2005, 41, 449-473.
13. Cook, R.J.; Bruckart, W.L.; Coulson, J.R.; Goettel, M.S.; Humber, R.A.; Lumsden, R.D.; Maddox, J.V.; McManus, M.L.; Moore, L.; Meyer, S.F.; Quimby, P.C.; Stack, J.P.; Vaughn, J.L. Safety of microorganisms intended for pest and plant disease control: A framework for scientific evaluation. Biol. Control 1996, 7, 333-351.
14. Harman, G.E.; Howell, C.R.; Viterbo, A.; Chet, I.; Lorito, M. Trichoderma species-opportunistic, avirulent plant symbionts. Nature Rev. Microbiol. 2004, 2, 43-56.
15. Jensen, D.F.; Wolffhechel, H. The use of fungi, particularly Trichoderma spp. and Gliocladium spp to control root rot and damping-off diseases. In Biological Control: Benefits and Risks. Hokkanen, H.M.T., Lynch, J.M., Eds.; Cambridge University Press: Cambridge, UK, 1993; pp. 177-189.
16. Bailey, B.A.; Lumsden, R.D. Direct effects of Trichoderma and Gliocladium on plant growth and resistance to pathogens In Trichoderma and Gliocladium Vol. 2; Harman, G.E., Kubicek, C.P., Eds.; Taylor and Francis: London, UK, 1998; pp. 185-204.
17. Whipps, J.M. Microbial interactions and biocontrol in the rhizosphere. J. Exp. Bot. 2001, 52, 487-511.
18. Bowen, G.D.; Rovira, A.D. Microbial colonization of plant roots. Annu. Rev. Phytopathol. 1976, 14, 121-144.
19. Weller, D.M. Biological control of soilborne plant pathogens in the rhizosphere with bacteria. Annu. Rev. Phytopathol. 1988, 26, 379-407.
20. Rubio-Pérez, E.; Molinero-Ruiz, M.L.; Melero-Vara, J.M.; Basallote-Ureba, M.J. Selection of potential antagonists against asparagus crown and root rot caused by Fusarium spp. Commun. Agric. Appl. Biol. Sci. 2008, 73, 203-206.
21. Gilardi, G.; Baudino, M.; Gullino, M.L.; Garibaldi, A. Attempts to control Fusarium root rot of bean by seed dressing. Commun. Agric. Appl. Biol. Sci. 2008, 73, 75-80.
22. Shanmugam, V.; Sharma, V.; Ananthapadmanaban, B. Genetic relatedness of Trichoderma isolates antagonistic against Fusarium oxysporum f.sp. dianthi inflicting carnation wilt. Folia. Microbiol. 2002, 53, 130-138.
23. Ojiambo, P.S.; Scherm, H. Biological and application-oriented factors influencing plant disease suppression by biological control: a meta-analytical review. Phytopathology 2006, 96, 1168-1174.
24. Druzhinina, I.S.; Kopchinskiy, A.G.; Komon, M.; Bissett, J.; Szakacs, G.; Kubicek, C.P. An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Genet. Biol. 2005, 42, 813-828.
25. Druzhinina, I.S.; Kubicek, C.P.; Komon-Zelazowska, M.; Mulaw, T.B.; Bissett, J. The Trichoderma harzianum demon: complex speciation history resulting in coexistence of hypothetical biological species, recent agamospecies and numerous relict lineages. BMC Evol. Biol. 2010, in press.
26. Nagy, V.; Seidl, V.; Szakacs, G.; Komon-Zelazowska, M.; Kubicek, C.P.; Druzhinina, I.S. Application of DNA BarCodes for screening of industrially important fungi: the haplotype of Trichoderma harzianum sensu stricto indicates superior chitinase formation. Appl. Environ. Microbiol. 2007, 73, 7048-7058.
27. Samuels, G.J.; Ismaiel, A.; Bon, M.-C.; De Respinis, S.; Petrini, O. Trichoderma asperellum sensu lato consists of two cryptic species. Mycologia 2009, DOI: 10.3852/09-243.
28. Dodd, S.L.; Lieckfeldt, E.; Samuels, G.J. Hypocrea atroviridis sp. nov., the teleomorph of Trichoderma atroviride. Mycologia 2003, 95, 27-40.
29. Druzhinina, I.S.; Komoń-Zelazowska, M.; Kredics, L.; Hatvani, L.; Antal, Z.; Belayneh, T.; Kubicek, C.P. Alternative reproductive strategies of Hypocrea orientalis and genetically close but clonal Trichoderma longibrachiatum, both capable to cause invasive mycoses of humans. Microbiology 2008, 154, 3447-3459.
30. Degenkolb, T.; Dieckmann, R.; Nielsen, K.F.; Grafenhan, T.; Theis, C.; Zafari, D.; Chaverri, P.; Ismaiel, A.; Bruckner, H.; Von Döhren, H.; Thrane, U.; Petrini, O.; Samuels, G.J. The Trichoderma brevicompactum clade: a separate lineage with new species, new peptaibiotics, and mycotoxins. Mycol. Prog. 2008, 7, 177-219.
31. Mittermeier, R.A.; Robles, G.P.; Hoffman, M.; Pilgrim, J.; Brooks, T.; Mittermeier, C.G.; Lamourex, J.; da Fonseca, G.A.B. Hotspots Revisited: Earth's Biologically Richest and Most Endangered Terrestrial Ecoregions; CEMEX: Mexico City, Mexico, 2004.
32. Migheli, Q.; Balmas, V.; Komoń-Zelazowska, M.; Scherm, B.; Caria, R.; Kopchinskiy, A.; Kubicek, C.P.; Druzhinina, I.S. Soils of a Mediterranean hotspot of biodiversity and endemism (Sardinia, Tyrrhenian Islands) are inhabited by pan-European and likely invasive species of Hypocrea/Trichoderma. Environ. Microbiol. 2009, 11, 35-46.
33. Zachow, C.; Berg, C.; Müller, H.; Meincke, R.; Komon-Zelazowska, M.; Druzhinina, I.S.; Kubicek, C.P.; Berg, G. Fungal biodiversity in the soils/rhizospheres of Tenerife (Canary Islands): relationship to vegetation zones and environmental factors. ISME J. 2009, 3, 79-92.
34. Hoyos-Carvajala, L.; Orduz, S.; Bissett, J. Genetic and metabolic biodiversity of Trichoderma from Colombia and adjacent neotropic regions. Fungal Genet. Biol. 2009, 46, 615-631.
35. Kullnig, C.; Szakacs, G.; Kubicek, C.P. Molecular identification of Trichoderma species from Russia, Siberia and the Himalaya. Mycol. Res. 2000, 104, 1117-1125.
36. Kubicek, C.P.; Bissett, J.; Kullnig-Gradinger, C.M.; Druzhinina, I.S.; Szakacs, G. Genetic and metabolic diversity of Trichoderma: a case study on South-East Asian isolates. Fungal Genet. Biol. 2003, 38, 310-317.
37. Zhang, C.L.; Druzhinina, I.S.; Kubicek, C.P.; Xu, T. Biodiversity of Trichoderma in China: evidence for a North to South difference of species distribution in East Asia. FEMS Microbiol. Letts. 2005, 251, 251-257.
38. Batjes, N.H. Total carbon and nitrogen in the soils of the world. Eur. J. Soil Sci. 1996, 47, 151.
39. Tondje, P.R.; Roberts, D.P.; Bon, M.C.; Widmer, T.; Samuels, G.J.; Ismaiel, A.; Begoude, A.; Tchana, T.; Nyemb-Tshomb, E.; Ndoumbe-Nkeng, M.; Bateman, R.; Fontem, D.; Hebbar, K.P. Isolation and identification of mycoparasitic isolates of Trichoderma asperellum with potential for suppression of black pod disease of cacao in Cameroon. Biol. Control 2007, 43, 202-212.
40. Jaklitsch, W.M.; Komon, M.; Kubicek, C.P.; Druzhinina, I.S. Hypocrea crystalligena sp. nov., a common European species with a white spored Trichoderma anamorph. Mycologia 2006, 98, 500-514.
41. Kopchinskiy, A.; Komon, M.; Kubicek, C.P.; Druzhinina, I.S. TRICHOBLAST: a mulilocus database for Trichoderma and Hypocrea identifications. Mycol. Res. 2005, 109, 658-660.
42. Thompson, J.D.; Gibson, T.J.; Plewniak, F.; Jeanmougin, F.; Higgins, D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acid. Res. 1997, 25, 4876-4882.
43. Nicholas, K.B.; Nicholas, H.B. Genedoc, a Tool for Editing and Annotating Multiple Sequence Alignments; 1996. Available online: http://www.cris.com/ketchup/genedoc.html (accessed on 1 January 2008).
44. Rannala, B.; Yang, Z. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 1996, 43, 304-311.
45. Yang, Z.; Rannala, B. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 1997, 14, 717-724.
46. Huelsenbeck, J.P.; Ronquist, F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17, 754-755.
47. Druzhinina, I.S.; Chaverri, P.; Fallah, P.; Kubicek, C.P.; Samuels, G.J. Hypocrea flaviconidia, a new species from Costa Rica with yellow conidia. Stud. Mycol. 2004, 50, 401-407.
48. Rita, N.; Tricita, H.Q. Soil mycoflora of black pepper rhizosphere in the Philippines and their In-vitro antagonism against phytophthora capsici L. Indo. J. Agric. Sci. 2004, 5, 1-10.
49. Shannon, C.E.; Weiner, W. The Mathematical Theory of Communication; University of Illionis Press: Urbana, IL, USA, 1963.
50. Simpson, E.H. Measurement of diversity. Nature 1949, 163, 688.
51. Giraud, T.; Refrégier, G.; de Vienne, D.; Le Gac, M. Speciation in fungi. Fungal Genet. Biol. 2008, 45, 791-802.
52. Aga, E.; Bryngelsson, T.; Bekele, E.; Salomon, B. Genetic diversity of forest arabica coffee (Coffea arabica L.) in Ethiopia as revealed by random amplified polymorphic DNA (RAPD) analysis. Hereditas 2003, 138, 36-46.
53. Masumbuko, L.I.; Bryngelsson, T.; Mneney, E.E.; Salomon, B. Genetic diversity in Tanzanian Arabica coffee using random amplified polymorphic DNA (RAPD) markers. Hereditas 2003, 139, 56-63.
54. Anthony, F.; Combes, C.; Astorga, C.; Bertrand, B.; Graziosi, G.; Lashermes, P. The origin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers. Theor. Appl. Genet. 2002, 104, 894-900.