Genetic and functional diversities of bacterial communities in the rhizosphere of Arachis hypogaea

Abstract

Bioinoculants are environmentally friendly, energy efficient and economically viable resources in sustainable agriculture. Knowledge of the structure and activities of microbial population in the rhizosphere of a plant is essential to formulate an effective bioinoculant. In this study, the bacterial community present in the rhizosphere of an important oilseed legume, Arachis hypogaea (L.) was described with respect to adjoining bulk soil as a baseline control using a 16S rDNA based metagenomic approach. Significantly higher abundance of Gamma-proteobacteria, a prevalence of Bacillus and the Cytophaga-Flavobacteria group of Bacteroidetes and absence of the Rhizobiaceae family of Alpha-proteobacteria were the major features observed in the matured Arachis-rhizosphere. The functional characterization of the rhizosphere-competent bacteria was performed using culture-dependent determination of phenotypes. Most bacterial isolates from the groundnut-rhizosphere exhibited multiple biochemical activities associated with plant growth and disease control. Validation of the beneficial traits in candidate bioinoculants in pot-cultures and field trials is necessary before their targeted application in the groundnut production system.

Application of targeted metagenomics to explore abundance and diversity of CO2-fixing bacterial community using cbbL gene from the rhizosphere of Arachis hypogaea

“…The bacterial diversity and abundance in rhizosphere of different plants and crops was studied using fingerprinting techniques and 16S rRNA gene as a target (Chauhan et al, 2011;Costa et al, 2005;Haldar et al, 2011;Sharma et al, 2005;Smalla et al, 2001). Previously, bacterial diversity was studied from groundnut rhizosphere using 16S rRNA restriction fragment length polymorphism (RFLP) under laboratory conditions by both culture dependent and independent methods (Haldar et al, 2011). Haldar et al (2011) reported Proteobacteria and Bacteroidetes as the dominant phyla while in the present study, Firmicutes was found abundant followed by Proteobacteria, Actinobacteria and Bacteroidetes (Supplementary Table S1).…”

“…This indicates a high diversity in groundnut rhizosphere, which was supported by both parametric and non-parametric diversity indices ( Table 2). The bacterial diversity and abundance in rhizosphere of different plants and crops was studied using fingerprinting techniques and 16S rRNA gene as a target (Chauhan et al, 2011;Costa et al, 2005;Haldar et al, 2011;Sharma et al, 2005;Smalla et al, 2001). Previously, bacterial diversity was studied from groundnut rhizosphere using 16S rRNA restriction fragment length polymorphism (RFLP) under laboratory conditions by both culture dependent and independent methods (Haldar et al, 2011).…”

“…There is a great scope for sustainable agriculture by using bioinoculants in the production system, and therefore to devise the efficient bioinoculants, understanding of the microbial structure and activity in the plant rhizosphere is important (Haldar et al, 2011). It can be considered that rhizospheric soil would have plenty of genes with PGPR-like functions.…”

“…The cbbL gene(s) attribute the presence of autotrophic microbial communities in rhizosphere and thus could be correlated with carbon cycling. Functional microbial community structure using cbbL gene as marker is not studied so far in rhizosphere of groundnut while 16S rRNA based study was limited to laboratory conditions only (Haldar et al, 2011). Previously, bacterial diversity from the rhizosphere of cereal crops like maize (Chauhan et al, 2011), and other economically important plants such as strawberry, oilseed rape, cotton and groundnut (Costa et al, 2005;Haldar et al, 2011;Zhang et al, 2011), was assessed using only phylogenetic 16S rRNA gene as molecular marker.…”

Microbial community analysis of a full-scale DEMON bioreactor

“…OTU 71090 had a 98 % similarity with GU245918.1 and a 97 % similarity with GU245920.1, which stand for Clostridium sp. [25] clones. Some Clostridium species are human pathogens related with tetanus or gas gangrene diseases, among others [26,27].…”