The plant microbiome helps plants acquire scarce resources and is an essential target for improving agricultural sustainability, particularly for biofuel feedstocks where reduction of anthropogenic inputs is desirable. However, the ability of modern crops to recruit and structure their microbiome may have been altered by domestication and breeding. Selection for high yields in environments with high nutrient inputs may have inadvertently led to changes in recruitment of the rhizosphere microbiome, such that mechanisms for nutrient acquisition and nutrient use efficiency may have been compromised. The first step to investigate this is to examine the structure and function of the microbiome as a function of plant genotype, with a specific focus on N cycling functional groups. The functional capacity of the rhizosphere microbiome and the benefit to the host plant, as well as ecosystem services such as nutrient cycling and greenhouse gas emissions, vary with the composition and abundance of microbial assemblages. We hypothesized that plant genotypes differ in their ability to recruit microbial functional groups. We used targeted functional metagenomic sequencing to survey the rhizosphere of diverse genotypes of bioenergy crops to compare their capability to recruit microbial nitrogen cycling functional groups, and examined rates of nitrogen transformations.
Results/Conclusions
Significantly different overall microbiomes (p<0.05) were observed as a function of crop genotype for miscanthus and maize, but not for sorghum. For all crops, variation in composition and abundance of specific N-cycling functional groups was observed among crop genotypes. In addition, differential abundance and composition of N cycling functional groups was associated with significant reduction in nitrification and denitrification in specific maize lineages.
Our observations suggest that limitations in the ability of modern crops to take advantage of sustainable nutrient management approaches may be a consequence of the differences in the recruitment of the microbiome, and may explain yield gaps observed in these systems. Our results link host-associated microbial communities to ecosystem function, and indicate that there is genetic capacity to optimize recruitment of N cycling functional groups in each crop and improve sustainability. Understanding the mechanistic underpinnings of this relationship will allow breeders and ecosystem scientists to select bioenergy crop cultivars that interact with the nitrogen cycle in ways that improve the efficiency and sustainability of agriculture, while protecting environmental quality.