Influence of root exudates on soil microbial diversity and activity

Abstract

Interactions between plant roots and soil microorganisms in the rhizosphere are critical for plant growth. However, understanding of precisely how root exudates influence the diversity and activity of rhizosphere microorganisms is limited. The main objective of this study was to investigate the effect of radiata pine (Pinus radiata) root exudates on rhizosphere soil microbial communities, with an emphasis on the role of low molecular weight organic anions. The study involved the development and validation of new methods for investigating rhizosphere processes in a purpose-built facility. This included development of an in situ sampling technique using an anion exchange membrane strip to collect a range of organic anions exuded from radiata pine roots grown in large-scale rhizotrons. These included tartarate, quinate, formate, malate, malonate, shikimate, lactate, acetate, maleate, citrate, succinate and fumarate. Soil microbial activity and diversity were determined using dehydrogenase activity and denaturing gradient gel electrophoresis. Links between organic anions in root exudates and rhizosphere soil microbial community structures were investigated by comparing wild type and genetically modified radiata pine trees which were grown in rhizotrons for 10 months. As expected, there was considerable temporal and spatial variability in the amounts and composition of organic anions collected, and there were no consistent or significant differences determined between the two tree lines. Significant differences in rhizosphere microbial communities were detected between wild type and genetically modified pine trees; however, they were inconsistent throughout the experiment. The shifts in microbial communities could have been related to changes in exudate production and composition. Based on results from the main rhizotron experiment, a microcosm study was carried out to investigate the influence of selected pine root exudate sugars (glucose, sucrose and fructose) and organic anions (quinate, lactate and maleate) on soil microbial activity and diversity. Soil microbial activity increased up to 3-fold in all of the sugar and organic anion treatments compared to the control, except for a mixture of sugars and maleate where it decreased. The corresponding impacts on soil microbial diversity were assessed using denaturing gradient gel electrophoresis and 16S rRNA phylochips. Addition of the exudate compounds had a dramatic impact on the composition and diversity of the soil microbial community. A large number of bacterial taxa (88 to 1043) responded positively to the presence of exudate compounds, although some taxa (12 to 24) responded negatively. Organic anions had a greater impact on microbial communities than sugars, which indicated that they may have important roles in rhizosphere ecology of radiata pine. In addition, a diverse range of potentially beneficial bacterial taxa were detected in soil amended with organic anions, indicating specific regulation of rhizosphere microbial communities by root exudates. This project highlighted the considerable challenges and difficulties involved in detailed investigation of in situ rhizosphere processes. Nonetheless, the findings of this study represent a significant contribution to advancing understanding of relationships between root exudates and soil microbial diversity, which will be further enhanced by refinement and application of the specific methodologies and techniques developed.