Analysis of Bacterial Diversity in the Rhizosphere of GM and Non- GM Maize Crops and Plant Growth-Promoting Characterization of the Isolated Strains

Abstract

The rhizosphere is a critical interface supporting the exchange of resources between plants and their associated soil environment. Rhizosphere microbial diversity is influenced by the physical and chemical properties of the rhizosphere, some of which are determined by the genetics of the host plant. However, within a plant species, the impact of genetic variation on the composition of the bacterial biota of GM and Non-GM maize rhizosphere is poorly understood. Here, we studied the bacterial diversity and population dynamics in the rhizosphere of one GM and two Non-GM maize varieties (IG and IW) grown under field conditions, by traditional cultivation techniques and 16S rRNA gene- based molecular analysis of DNA directly extracted from pre cultivated soil and rhizosphere samples. Rhizosphere and pre cultivated soil samples were taken at three different plant growth stages. The isolated bacterial strains were further screened for different functional characterization. Using pyrosequencing of bacterial 16S rRNA genes, around 160,000 sequences were obtained (20,000 reads per sample) representing 21 phyla's, 184 families, 469 genera and a small amount of unclassified bacteria. The predominant bacterial groups in the rhizosphere of GM and Non-GM maize as well as in bulk soil were Proteobacteria (39.455%), Actinobacteria (24.453%), Bacteroidetes (11.990%), Firmicutes (7.532%) and Planctomycetes (4.478%). Other groups that were consistently found, although at lower abundance were Fibrobacteres, Thermi, Euryarchaeota, Tenericutes, Synergistetes and Thermotogae. There was no indication of consistent bacterial variation in the rhizosphere of GM and Non-GM maize as well as in bulk soil sample. We observed no significant variation in bacterial richness, diversity, and relative abundances of taxa between different growth stages of GM and Non-GM maize rhizosphere. Bacterial diversity in the rhizosphere of GM and Non-GM maize as well as bulk soil sample was explored using a culture based approach at different growth stages. A total of 52 bacterial strains were isolated from the rhizosphere as well as from bulk soil samples (different growth stages) and subjected to further analysis. Based on the analysis of the xxvi16S rRNA gene sequences, all the bacterial isolates were classified into four major phyla's of the domain bacteria. The culturable component of the bacterial community revealed that the predominant groups were Firmicutes and Proteobacteria at Pre sowing stage). Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria (vegetative stage) and Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes (harvesting stage) were the pre dominant groups at different growth stages of GM and Non-GM maize rhizosphere. Zea mays, one of the most important cereals crop worldwide. The use of plant growth promoting (PGP) rhizobacteria may constitute a biological alternative to increase crop yield and plant resistance to diseases. In search for PGP rhizobacteria strains, all the cultured isolated bacterial strains (52) were in vitro screened for their PGP characteristics and biocontrol against plant pathogenic strains. Some of the bacterial isolates (different stages) were shown to produce indole acetic acid, phosphate solubilization, nitrate reduction and siderophore when tested in vitro for their plant growth promoting abilities. Their further application in a greenhouse experiment using Zea mays indicated that plant traits such as root and shoot elongation and biomass production, were influenced by the inoculation. Plant growth promoting traits of these strains indicated beneficial relationship between rhizobacteria and Zea mays plant. To understand the antagonistic potential, an in vitro antagonistic assay was performed to characterize and identify strains that were antagonistic to the plant pathogens Fusarium oxysporum, Aspergillus niger and Pseudomonas syringae, Xanthomonas axonopodis. Some of the strains (from different stages) exhibited in vitro inhibitory activity against the target plant pathogenic but none of the isolates were found to have antibacterial activity. Total 46 strains were screened (stages like pre sowing-14, vegetative-19 and harvesting-13) for enzymatic activities. Most of the isolates produced cell wall degrading enzymes. About isolates exhibited cellulase (43%), chitinase (43%), protease (54%), pectinase (63%) and lipase (70%). There was no significant variation in functional characterization of the isolates of GM maize rhizosphere as compared to their Non-GM counterpart.