Microbial Inputs in Coffee (Coffea arabica L.) Production Systems, Southwestern Ethiopia Implications for Promotion of Biofertilizers and Biocontrol Agents

Arabica coffee is the key cash crop and top mainstay of the Ethiopian economy and requires sustainable production methods. Southwestern natural forests, the site of this study, are believed to be the centre of origin and diversity for Coffea arabica and still harbour wild Arabica coffee that may serve as an important gene pool for future breeding. Cost reductions, sustainability and quality improvement are now the major priorities in coffee production systems and require organic growing of coffee. Current developments in sustainability involve rational exploitation of soil microbial activities that positively affect plant growth and this study examines this possibility. The composition of coffee shade tree species and density of arbuscular mycorrhizal fungi (AMF) spores and coffee-associated rhizobacteria in different coffee production systems in southwestern Ethiopia were investigated. The main objectives were to: 1) systematically identify the dominant coffee shade tree species; 2) quantify and characterize AMF populations with respect to spatial distribution; 3) screen for beneficial rhizobacteria (microbial biofertilizers and biocontrol agents), particularly in the rhizosphere of coffee plants; and 4) characterize rhizobacterial isolates of particular interest using molecular tools (polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis and 16S rDNA gene sequencing). Sampling and determination of microbial functional characteristics followed standard methods. Nineteen dominant shade tree species belonging to 14 plant families were identified, with the tree legume (Millettia ferruginea) dominating. All soil samples contained AMF spores and members of the Glomeromycota, Glomus spp. dominating. AMF spore density was affected by sampling point, site, depth, shade tree species and shade tree/coffee plant age. Coffee-associated rhizobacterial isolates showed multiple beneficial traits (phosphate solubilization, production of organic acids, siderophores, indoleacetic acid, hydrogen cyanide, lytic enzymes and degradation of an ethylene precursor). Many isolates also revealed a potent inhibitory effect against emerging fungal coffee pathogens such as Fusarium xylarioides, F. stilboides and F. oxysporum. According to in vitro studies Bacillus, Erwinia, Ochrobactrum, Pseudomonas, and Serratia spp. were the most important isolates to act as potential biofertilizers, biocontrol agents or both. Thus, these indigenous isolates deserve particular attention and further greenhouse and field trials could ascertain their future applicability for inoculum development.