Colonization of the rice rhizosphere by microbial communities involved in the syntrophic degradation of rhizodeposits to methane

Roots represent the primary site of direct interaction between rice plants and soil microorganisms. The influence of the plant on the soil microbial community includes the translocation of photosynthetically fixed carbon into the rhizosphere as rhizodeposition. This extends to the rhizosphere of rice plants, which is colonized by a syntrophic microbial community, which in turn is able to degrade root derived carbon to methane. Each plant species is thought to select a specific microbial community composition as root microbiome. A general understanding of microbial colonization of the rice rhizosphere and the consequential impact on the emission of methane originating from rhizodeposits is still uncertain, since the majority of the studies have so far focused exclusively on rice roots planted in rice paddy soils. Therefore, we used different initial soil microbial communities available for colonization of the rice roots. In order to do this, an inert sand-vermiculite matrix was inoculated with rice paddy soil and digested sludge, respectively, and was afterwards planted with rice. The microbial activity essential for the formation of methane from those soil-systems was tested in pre-experiments and the colonization of the rice rhizosphere was determined afterwards in plant-soil microcosms. Each of the microcosms possessed an individually structured microbial community, which served as a seed bank for the colonization of the rice roots. We analyzed the impact of the community composition on the emission of methane by combining 13CO2 pulse-labeling with illumina sequencing and quantitative PCR, targeting the 16S rRNA as phylogenetic-, as well as mcrA and pmoA as functional marker genes for methanogenic archaea and methane-oxidizing bacteria. The degradation of rhizodeposits to methane in the different microcosms was dependent on the bacterial and methanogenic community structure, but not on their absolute abundance in the rhizosphere. Like the colonization of the rhizosphere by bacteria and methanogenic archaea, the translocation of photosynthetically fixed carbon depended upon the initial microbial communities. Nevertheless, the rice rhizosphere was found to be a distinct habitat for bacteria and methanogenic archaea. We were able to identify a methanogenic community which was linked to the degradation of rhizodeposits to methane across the rhizosphere of all microcosms. Besides hydrogenotrophic Methanocella and Methanobacteriaceae, acetoclastic Methanosaeta could also be assigned to this community. Nevertheless, most methanogens which contribute to the emission of methane originating from root derived carbon were found to belong to those with a hydrogenotrophic pathway. Within the methanogenic community linked to the formation of methane from rhizodeposits, the root surface was mainly colonized by hydrogenotrophic methanogens, while those able to perform acetoclastic methanogenesis were highly abundant in the rhizospheric soil. This was true of the colonization of the rice rhizosphere by methanogenic archaea in general. Furthermore, we were able to identify methanogens which were ubiquitous in the rhizosphere of all microcosms. Those were considered as methanogenic community selected by the rice plant on its roots. Representatives of Methanobacteriaceae, Methanosaeta and Methanosarcina colonized the overall rhizosphere, while Methanocella were found to be present in the rhizospheric soil of all microcosms. In addition to this, all methanogenic archaea which were linked to the degradation of root derived carbon to methane also belonged to this root associated community. Hence, the methanogenic community selected on the rice root also contributed to the formation of methane from rhizodeposits. Besides methanogens, we were also able to identify certain bacterial groups, which are linked to the degradation of root derived carbon to methane. These includes representatives of Kineosporiaceae, Anaeromyxobacter, Bradyrhizobium, and Bacteroidales. A higher abundance of Kineosporiaceae also resulted in an increased conversion of root derived carbon compounds to acetate, CO2, and propionate. Therefore, at least the family of Kineosporiaceae was thought to be actively involved in the degradation of rhizodeposition to precursors for methanogenesis. Nevertheless, we were not able to determine bacteria which contributed to the emission of methane originating from root derived carbon and which were ubiquitous in the rhizosphere of all soil-systems. This resulted from the fact that the microbial community structure of the rhizosphere also depended on the initial pool of microorganisms available for root colonization