SIP analysis of switchgrass rhizosphere microbes
Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass (Panicum virgatum L.) through root exudatesion
Identification of microbes that actively utilize root exudates is essential to understand plant-microbe interactions. To identify active root exudate-utilizing microorganisms associated with switchgrass – a potential bioenergy crop - plants were labeled in situ with 13CO2, and 16S and 18S rRNA genes in the 13C labeled rhizosphere DNA were pyrosequenced. Multi-pulse labeling for five days produced detectable 13C-DNA, which was well separated from unlabeled DNA.  The Burkholderiales Methylibium, Roseateles and two other unknown bacteria from the order Burkholderiales were the most heavily labeled bacteria. Pythium, Auricularia, Galerina and an unclassified Sironidae were the most heavily labeled eukaryotic microbes. All of these heavily labeled microorganisms were also among the most abundant species in the rhizosphere. Species belonging to Methylibium and Pythium were the most heavily labeled and the most abundant bacteria and eukaryotes in the rhizosphere of switchgrass. Our results revealed that nearly all of the dominant rhizosphere bacterial and eukaryotic microbes were able to utilize root exudates within the timeframe of this experiment. These results also show an enrichment of potential plant beneficial bacteria such as Methylibium and Burkholderiales in the rhizosphere of switchgrass.  The enrichment of microbial species in the rhizosphere is selective and mostly due to root exudation which functions as nutrition source, promoting the growth of these microbes.