Plant Diversity and Fertilizer Management Shape the Belowground Microbiome of Native Grass Bioenergy Feedstocks.

Daniel Revillini,Ryan Lancione,Gail W T Wilson,Nancy Collins Johnson,R Michael Miller

doi:10.3389/fpls.2019.01018

Abstract

Plants may actively cultivate microorganisms in their roots and rhizosphere that enhance their nutrition. To develop cropping strategies that substitute mineral fertilizers for beneficial root symbioses, we must first understand how microbial communities associated with plant roots differ among plant taxa and how they respond to fertilization. Arbuscular mycorrhizal (AM) fungi and rhizobacteria are of particular interest because they enhance nutrient availability to plants and perform a suite of nutrient cycling functions. The purpose of this experiment is to examine the root and soil microbiome in a long-term switchgrass (Panicum virgatum) biofuel feedstock experiment and determine how AM fungi and rhizobacteria respond to plant diversity and soil fertility. We hypothesize that intra- and interspecific plant diversity, nitrogen fertilization (+N), and their interaction will influence the biomass and community composition of AM fungi and rhizobacteria. We further hypothesize that +N will reduce the abundance of nitrogenase-encoding nifH genes on the rhizoplane. Roots and soils were sampled from three switchgrass cultivars (Cave-in-Rock, Kanlow, Southlow) grown in monoculture, intraspecific mixture, and interspecific planting mixtures with either Andropogon gerardii or diverse native tallgrass prairie species. Molecular sequencing was performed on root and soil samples, fatty acid extractions were assessed to determine microbial biomass, and quantitative polymerase chain reaction (qPCR) was performed on nifH genes from the rhizoplane. Sequence data determined core AM fungal and bacterial microbiomes and indicator taxa for plant diversity and +N treatments. We found that plant diversity and +N influenced AM fungal biomass and community structure. Across all plant diversity treatments, +N reduced the biomass of AM fungi and nifH gene abundance by more than 40%. The AM fungal genus Scutellospora was an indicator for +N, with relative abundance significantly greater under +N and in monoculture treatments. Community composition of rhizobacteria was influenced by plant diversity but not by +N. Verrucomicrobia and Proteobacteria were the dominant bacterial phyla in both roots and soils. Our findings provide evidence that soil fertility and plant diversity structure the root and soil microbiome. Optimization of soil communities for switchgrass production must take into account differences among cultivars and their unique responses to shifts in soil fertility.

Highlights

National initiatives to increase energy independence spurred interest in biofuel cropping systems and native feedstock options (Perlack et al, 2011)
The purpose of our study is to assess the effects of intra- and interspecific plant diversity and +N on the biomass and composition of communities of bacteria and arbuscular mycorrhizal (AM) fungi associated with both switchgrass roots and rhizosphere soils
Our results provide a baseline for switchgrass microbiome research

Summary

Introduction

National initiatives to increase energy independence spurred interest in biofuel cropping systems and native feedstock options (Perlack et al, 2011). An understanding of the belowground microbiome on roots and in soils is necessary to begin to understand how microbial symbioses can facilitate and maintain high plant yields in any cropping system (Johansson et al, 2004; Schlaeppi and Bulgarelli, 2015; Alori et al, 2017) This will be useful for native biofuel feedstocks, as they are promoted for cultivation on marginal lands no longer suitable for row cropping and where soil microbes will have likely been altered by conventional agricultural practices (Hart and Trevors, 2005; Verbruggen et al, 2015). Given the relatively recent breeding history of native grasses for biofuel production, it is important to begin to understand the roles of plant cultivar, plant diversity, and fertilization regime on the microbial communities that nutritionally support their productivity on marginal soils (Busby et al, 2017)

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