Characterization and evaluation of plant growth promoting rhizobacteria from rice soils of Wayanad

Abstract

Plant growth promoting rhizobacteria (PGPR) are a group of bacteria that colonize the plant rhizosphere and enhance the growth and yield of plants. The present investigation entitled “Characterization and evaluation of plant growth promoting rhizobacteria from rice soils of Wayanad” was undertaken at the Department of Agricultural Microbiology” during the year 2018-2020, with the objective of isolation, characterization and evaluation of plant growth promoting rhizobacteria from rice soils of Wayanad and formulation of a consortium to improve the growth and yield of rice. Isolation of rhizobacteria with potential plant growth promoting (PGP) activities was attempted from rice rhizosphere soils collected from ten locations in Wayanad district of Kerala. Selective media were used for the isolation of PGPRs including nitrogen fixers, solubilizers of phosphate, K and Zn and fluorescent pseudomonads. A total of 149 isolates obtained on different media were subjected to preliminary screening for growth on selective media, which yielded 32 N-fixers, 16 phosphate solubilizers, four K solubilizers, six Zn solubilizers and two fluorescent pseudomonads. These isolates were evaluated in vitro for PGP activities (production of IAA, NH3, HCN and siderophore) and antagonistic activities against R. solani and X. oryzae. Twenty promising isolates were selected based on their functional efficiency for further characterization using cultural, morphological, biochemical and molecular methods. Four isolates were found to be Gram-positive rods and sixteen isolates were Gram-negative short rods. Eighteen isolates were identified based 16S rRNA gene sequencing and the sequences of all the eighteen isolates deposited in the GenBank of the NCBI. Phylogenetic analysis using MEGA 7 software showed two major clusters and several sub-clusters. A few of the native isolates stood out distinctly from the available accessions in the database, showing that they are genetically diverse. Based on the efficiency of N fixation, P, K and Zn solubilization and other PGP activities, isolates were ranked. Based on ranking, three N-fixers (Bacillus sp. AkNF3, Pseudomonas sp. PkNF4 and Pseudomonas putida KgNF1), three phosphate solubilizers (Bacillus megaterium PkPS1, Acinetobacter schindleri AkPS4 and Achromobacter sp. AvPS1), two K-solubilizers (Microbacterium sp. MvKS1 and Acinetobacter calcoaceticus MvKS3) and two zinc solubilizers (Achromobacter marplatensis ThZnS2 and Cytobacillus kochii PkZnS3) were selected for consortial formulation. Compatibility of ten promising isolates was tested by cross streaking and dual culture methods. Three PGPR based consortia (Consortium 1, 2 and 3) were formulated, each consisting of 5 native isolates (two N-fixers, one each of phosphate, K and Zn solubilizers). These consortia were evaluated in pot culture experiment, along with KAU commercial formulation (PGPR mix-1), at RARS, Ambalavayal, with rice (variety Valichoori) as the test crop. PGPR application was combined with two levels (50% and 75%) of recommended dosage of inorganic fertilizers (RDF). Population of total bacteria, N fixers, P, K and Zn solubilizers was higher in combined application of biofertilizer with inorganic fertilizers than uninoculated treatments and this was indicative of better colonization of native PGPRs in the rice rhizosphere. Growth and yield parameters indicated that application of PGPR consortium with 75% RDF was statistically on par with PoP (KAU) and 100% RDF. Results suggested that 25% inorganic N, P and K can be replaced by using native PGPR consortium without affecting plant growth, yield, plant nutrient content and soil nutrient content. Considering the above parameters, two best consortia (Consortium 2 and Consortium 3) were selected for further field evaluation. Field evaluation was carried out to assess the efficiency of two selected native PGPR consortia at RARS, Ambalavayal. Five treatments included were, consortium 2 + 75% RDF, consortium 3 + 75% RDF, reference biofertilizer PGPR mix-1 + 75% RDF, 100% RDF and farmer’s practice (farm yard manure 5t ha-1 ). Results suggested that root colonization of total bacteria, N fixers, P, K and Zn solubilizers was higher in all treatments of combined application of biofertilizers with 75% inorganic fertilizer than 100% RDF alone. Growth and yield parameters suggested that combined application of Consortium 2 with 75 % RDF was statistically on par with 100% RDF. Therefore, it can be concluded native PGPR strains in consortium 2 (Bacillus sp. strain AkNF3, Pseudomonas putida strain KgNF1, Bacillus megaterium strain PkPS1, Acinetobacter calcoaceticus strain MvKS3 and Cytobacillus kochii PkZnS3) successfully colonized the rice rhizosphere, increased nutrient availability to the plants and produced higher yield. The results also emphasized on the importance of exploiting native, location specific microorganisms as biofertilizer consortium, rather than a common consortium for the entire State. Native PGPR based consortia 2 reduced the 25% of inorganic fertilizer (N, P and K) without affecting the growth and yield of rice. This would be more cost effective and ecofriendly when compared with the use of chemical fertilizers alone. Further multi-locational field trials are required to validate the results before commercialization of this consortium, as a biofertilizer.