Bacterial Origin and Community Composition in the Barley Phytosphere as a Function of Habitat and Presowing Conditions

Abstract

An understanding of the factors influencing colonization of the rhizosphere is essential for improved establishment of biocontrol agents. The aim of this study was to determine the origin and composition of bacterial communities in the developing barley (Hordeum vulgare) phytosphere, using denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified from extracted DNA. Discrete community compositions were identified in the endorhizosphere, rhizoplane, and rhizosphere soil of plants grown in an agricultural soil for up to 36 days. Cluster analysis revealed that DGGE profiles of the rhizoplane more closely resembled those in the soil than the profiles found in the root tissue or on the seed, suggesting that rhizoplane bacteria primarily originated from the surrounding soil. No change in bacterial community composition was observed in relation to plant age. Pregermination of the seeds for up to 6 days improved the survival of seed-associated bacteria on roots grown in soil, but only in the upper, nongrowing part of the rhizoplane. The potential occurrence of skewed PCR amplification was examined, and only minor cases of PCR bias for mixtures of two different DNA samples were observed, even when one of the samples contained plant DNA. The results demonstrate the application of culture-independent, molecular techniques in assessment of rhizosphere bacterial populations and the importance of the indigenous soil population in colonization of the rhizosphere.The use of antagonistic bacteria for the protection of crops against soilborne pathogens provides a promising environment-friendly alternative to chemical pesticides. However, the root colonization efficiency of introduced biocontrol strains is often limited, potentially reducing the effectiveness of protection (8,25,32). The selection and use of biocontrol strains therefore depend heavily on our knowledge of survival of the inoculant and its potential activity in the rhizosphere ecosystem of a particular plant and soil. Consequently, successful biological control with inoculated strains requires an understanding of the dynamics and composition of the bacterial communities colonizing the rhizosphere.Previous studies, employing cultivation-based, laboratory methods or microscopy, have shown that different bacterial populations are present or active at different stages of root development and that rhizosphere communities are distinct from those found in bulk soil (1,14,17,19,21,27,30). However, recent molecular studies involving PCR amplification of 16S rRNA genes (rDNA), question some of these results. Duineveld et al. (9) reported that the bacterial communities of the Chrysanthemum rhizosphere, as measured by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA PCR products, changed very little with plant age and were similar to those of bulk soil. In contrast, different bacterial communities were identified in soil and in the root tissue of white clover and ryegrass by cluster analysis of a 16S rDNA clone library (16). Furthermore, DGG...

Indigenous Microbial Community of Barley Greatly Influences Grain Germination and Malt Quality

“…Lopez et al 34 and also Normander and Prosser 42 reported that universal bacterial primers can amplify plant chloroplast rDNA present in samples and therefore repress the PCR amplification of less dominant bacterial populations. It is obvious that amplification of non-target organisms can limit the detection of true bacterial or fungal species because the DNA from non-target organisms competes with the bacterial DNA for primers and deoxynucleoside triphosphates during PCR amplifications.…”

Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review

“…Soil is the main reservoir of the potential bacterial rhizosphere community (Normander and Prosser 2000;De Ridder-Duine et al 2005;Berg and Smalla 2009). Evidence is increasing that plants actively select specific elements of their bacterial rhizosphere microflora, establishing a habitat which is favorable for the plant (Latour et al 1996;Bais et al 2004;Garbeva et al 2004a;Robin et al 2007;Broeckling et al 2008;Houlden et al 2008;Rudrappa et al 2008).…”

Bacterial populations in juvenile maize rhizospheres originate from both seed and soil

“…While the origin of phyllosphere bacteria remains poorly defined (Bulgarelli et al 2013), the origins of both endophytic bacteria (Bulgarelli et al 2012;Edwards et al 2015;Long et al 2008;Lundberg et al 2012) and rhizosphere bacteria (Berg and Smalla 2009;Normander and Prosser 2000;Philippot et al 2013;Singh et al 2007) are traditionally thought to be from the soil. Contrary to a soil origin, there is evidence that bacterial endophytes in and/or on maize seeds contribute to the majority of the root endosphere bacterial population (Johnston-Monje et al 2014;JohnstonMonje and Raizada 2011a), and that at least some of these bacteria are able to travel within the plant, exit the roots and colonize the rhizosphere (Johnston-Monje and Raizada 2011a).…”