Isolation, Screening and Biochemical Characterization of PhosphateSolubilizing Rhizobacteria Associated with Coffea arabica L

Abstract

This study focused on screening, identifying and characterizing P-solubilizing rhizobacteria associated with Coffea arabica L. growing in Southwestern Ethiopia. Samples were collected from Kaffa and Jimma zones in the Southwestern part of Ethiopia which are not only the major coffee growing areas of Ethiopia but also the origin of Coffea arabica L. Natural forest, agroforestry-based and monoculture plantations were included. A total of 110 Coffee roots with adhering soil samples were collected in sterile plastic bags. At each sampling site, plant roots with adhering soil (approximately 50 g) were collected from each corner of a randomly selected square meter (One from each of 4 quadrants) which lied around coffee plant at a depth of 10-20 cm and placed into a sterile plastic bag to give a composite sample. One composite sample was taken at each coffee plant. Care was taken to keep rhizosphere soil intact around the root. The shade trees at each sampling site were also registered. A total of 169 bacteria were isolated on nutrient agar from root washing solutions (61 isolates), surface sterilized roots (45 isolates) and soil (63 isolates). These bacteria isolates were subjected to GEN III Micro-plate tests of Biolog bacterial identification system kits and evaluated for their ability to solubilize phosphates on Pikovskaya's agar plates. Members of the isolated rhizobacteria were dominated by the genus Pseudomonas (44.1%) followed by Bacillus (11.6%), Enterobacter (10.5%) and Stenotrophomonas (10.5%). Over 32.5% of the Rhizobacteria (both Gram-negative and Gram-positive) associated with the coffee rhizosphere could solubilize mineral P on Pikovskaya's agar, indicating a high proportion of such species is associated with coffee plants.

Identification and characterization of Vietnamese coffee bacterial endophytes displaying in vitro antifungal and nematicidal activities

“…Regarding the distribution of the bacterial genera across the different samples, we highlighted that the Bacillus genus was present in all the samples, namely, C. canephora and C. liberica roots in Bao Loc as well as the C. canephora roots and seeds in Buon Ma Thuot. Moreover, it has already been demonstrated in various countries that members of this bacterial genus were able to colonize endophytically almost all coffee plant organs including cherries (Miguel et al, 2013;Oliveira et al, 2013), leaves (Bettiol et al, 2007;Shiomi et al, 2006;Silva et al, 2008;Vega et al, 2005), roots (Asyiah et al, 2018;Hoang et al, 2020;Mekete et al, 2009;Teshome et al, 2017;Vega et al, 2005), seeds (Vega et al, 2005) and stems (Nair et al, 2002;Shiomi et al, 2006). These findings indicate that the Bacillus genus members are competitive coffee colonizers able to adapt themselves to diverse environmental conditions.…”

“…'Ind', Indolic compounds production; 'Pho', Phosphate solubilization; 'Sid', Siderophores production; 'Hcn', Hydrogen cyanide production; 'Gel', Gelatinase production; 'Chi', Chitinase production; 'Lip', Lipase production; 'Est', Esterase production. roots (Asyiah et al, 2018;Hoang et al, 2020;Jimenez-Salgado et al, 1997;Nair et al, 2002;Nunes and de Melo, 2006;Sakiyama et al, 2001;Shiomi et al, 2006;Teshome et al, 2017;Vaughan et al, 2015;Vega et al, 2005). However, Miguel et al (2013) and Mekete et al (2009), isolated endophytes belonging to the phylum Bacterioidetes from coffee cherries and roots, but the relative abundance of this bacterial phylum was very low with Chryseobacterium as only genus.…”

“…Thus, endophytic genera associated with coffee cherries and seeds (Miguel et al, 2013;Oliveira et al, 2013;Vaughan et al, 2015) were recovered for the first time from the roots including members of Rhizobium, Staphylococcus, and Sphingomonas. Furthermore, members of the Mycobacterium genus already described as coffee root endophytes have never been isolated from the seeds (Teshome et al, 2017).…”

“…Several studies already highlighted their capacities to solubilize phosphate (Teshome et al, 2017), to fix the atmospheric nitrogen (Jimenez-Salgado et al, 1997) and to promote the growth of coffee seedlings (Silva et al, 2012). The in vitro nematicidal and antifungal activities of coffee associated endophytic bacteria were demonstrated against parasitic nematodes and plant pathogenic fungi (Hoang et al, 2020;Mekete et al, 2009;Shiomi et al, 2006;Silva et al, 2012).…”

Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review

“…In that case, some basic morphological identifications using staining and microscopy were frequently employed to identify mycorrhizal species (Caldeira et al, 1983;Bertolini et al, 2020) or filamentous fungi (Mislivec et al, 1983;Casas-Junco et al, 2018). The morphology was often combined with standard biochemical tests such as those analyzing carbon sources utilization and enzymatic assays to identify bacteria (Pederson and Breed, 1946;Teshome et al, 2017) and fungi including yeasts (Agate and Bhat, 1966;Ranjini and Raja, 2019). Some more complex biochemical tests were sometimes applied to confirm the microorganisms' identity such as the multilocus enzyme electrophoresis (MLEE) in the case of nitrogen-fixing (N-fixing) bacteria (Jimenez-Salgado et al, 1997;Fuentes-Ramírez et al, 2001), the fatty acid methyl esters gas chromatography (FAME-GC) for bacterial isolates (Vega et al, 2005;Silva et al, 2012;Miguel et al, 2013), and the matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) for several bacteria and yeasts (Martins et al, 2020).…”