Genotypic diversity among rhizospheric bacteria of three legumes assessed by cultivation-dependent and cultivation-independent techniques

Abstract

The genotypic diversity of rhizospheric bacteria of 3 legumes including Vigna radiata, Arachis hypogaea and Acacia mangium was compared by using cultivation-dependent and cultivation-independent methods. For cultivation-dependent method, Random amplified polymorphic DNA (RAPD) profiles revealed that the bacterial genetic diversity of V. radiata and A. mangium rhizospheres was higher than that of A. hypogaea rhizosphere. For cultivation-independent method, Denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified 16S rRNA genes revealed the difference in bacterial community and diversity of rhizospheres collected from 3 legumes. The ribotype richness which indicates species diversity, was highest in V. radiata rhizosphere, followed by A. hypogaea and A. mangium rhizospheres, respectively. Three kinds of media were used to cultivate different target groups of bacteria. The result indicates that the communities of cultivable bacteria in 3 rhizospheres recovered from nutrient agar (NA) medium were mostly different from each other, while Bradyrhizobium selective medium (BJSM) and nitrogen-free medium shaped the communities of cultivable bacteria. Nine isolates grown on BJSM were identified by 16S rRNA gene sequence analysis. These isolates were very closely related (with 96% to 99% identities) to either one of the three groups including Cupriavidus-Ralstonia group, Bacillus group and Bradyrhizobium-Bosea-Afipia group. The rhizospheres were also examined for their enzymatic patterns. Of 19 enzymes tested, 3 rhizospheres were distinguishable by the presence or the absence of leucine acrylamidase and acid phosphatase. The selected cultivable bacteria recovered from NA varied in their abilities to produce indole-acetic acid and ammnonia. The resistance to 10 antibiotics was indistinguishable among bacteria isolated from different rhizospheres.

Water-Limiting Conditions Alter the Structure and Biofilm-Forming Ability of Bacterial Multispecies Communities in the Alfalfa Rhizosphere

“…These values are similar to or higher than counts obtained in previous studies of rhizospheric soils from legume and nonlegume plants [57,60,61]. In particular, our counts are consistent with those obtained for cultivable bacteria in rhizospheres of legumes such as Glycine max , Vigna radiata , Arachis hypogaea , and Acacia mangium [57,62,63]. …”

“…Aerial plant development reflects root development, which was considerably lower for DRS than for SRS or CRS. The observed differences in bacterial counts may be related to the differential composition of root exudates under each condition, in view of the role of the exudates in modulating plant-bacteria interaction through alterations of bacterial metabolism, gene expression, and bacterial community structure [62,64]. Nutrient and desiccation stress have been shown to produce significant changes in the quantity and composition of root exudates [65].…”

Biological activity and microbial genetic diversity of bare-fallow and grassland soils

“…It was useful to study the effects of temperature (Tourna et al 2008), soil pH (Stephen et al 1999), fertilization (Chu et al 2007;Yu et al 2010), vegetation types (Ceccherini et al 2008), and cropping effects (Yu et al 2010) on community structure of AOB. Molecular methods including DGGE assay are successfully used only to determine genetic microbial diversity in different soils (Asakawa & Kimura 2008;Pongsilp et al 2012) but not always agree with functional diversity obtained from Biolog® system (Saul-Tcherkas & Steinberger 2009). Eisenhauer et al (2012) claim that both genetic and functional diversity need to be maintained to protect microbial communities against biotic and abiotic stressors.…”

Analysis of the community composition and bacterial diversity of the rhizosphere microbiome across different plant taxa

“…Therefore, plants can also influence the structure and function of the bacterial communities in the rhizosphere soil around their roots. The studies on the microbial rhizosphere communities have shown the significant influence of plant species and cultivars in shaping microbial communities in the rhizosphere, including studies on different cultivars of potato (Inceoglu et al, 2011;Weinert et al, 2011), maize (Peiffer et al, 2013), Arabidopsis (Bulgarelli et al, 2012;Lundberg et al, 2012), rice (Edwards et al, 2015;Knief et al, 2011), and soybean (Mendes et al, 2014;Xu et al, 2009), or intraspecies comparison (Bouffaud, Poirier, Mulle, & Moënne-Loccoz, 2014;Bulgarelli et al, 2015;Ofek, Voronov-Goldman, Hadar, & Minz, 2014;Pongsilp, Nimnoi, & Lumyong, 2012;Schlaeppi et al, 2014;Turner, Ramakrishnan, et al, 2013;Wieland, Neumann, & Backhaus, 2001). Even different genotypes of the same plant species have also an effect on the bacterial community structure and composition of their rhizosphere microbiome (Marques et al, 2014;Rasch et al, 2006;Robin et al, 2006).…”