Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of "Hidden" Diversity.

David Bass,Sigrid Neuhauser,Sally Hilton,Gary D Bending,Christopher Van Der Gast,Serena Thomson

doi:10.3389/fmicb.2018.00168

Abstract

Microbial communities closely associated with the rhizosphere can have strong positive and negative impacts on plant health and growth. We used a group-specific amplicon approach to investigate local scale drivers in the diversity and distribution of plasmodiophorids in rhizosphere/root and bulk soil samples from oilseed rape (OSR) and wheat agri-systems. Plasmodiophorids are plant- and stramenopile-associated protists including well known plant pathogens as well as symptomless endobiotic species. We detected 28 plasmodiophorid lineages (OTUs), many of them novel, and showed that plasmodiophorid communities were highly dissimilar and significantly divergent between wheat and OSR rhizospheres and between rhizosphere and bulk soil samples. Bulk soil communities were not significantly different between OSR and wheat systems. Wheat and OSR rhizospheres selected for different plasmodiophorid lineages. An OTU corresponding to Spongospora nasturtii was positively selected in the OSR rhizosphere, as were two genetically distinct OTUs. Two novel lineages related to Sorosphaerula veronicae were significantly associated with wheat rhizosphere samples, indicating unknown plant-protist relationships. We show that group-targeted eDNA approaches to microbial symbiont-host ecology reveal significant novel diversity and enable inference of differential activity and potential interactions between sequence types, as well as their presence.

Highlights

Plant roots release considerable amounts of labile exudates and debris into the soil, which results in intense microbial activity in the rhizosphere soil which surrounds roots, and the selection of communities which are structurally and functionally distinct from the bulk soil (Morgan et al, 2005) The rhizosphere microbiome can have major impacts on plant growth and nutrition, which can be both positive and negative, through complex direct and indirect interactions
Our group-specific PCR approach coupled with high-throughput sequencing (HTS) showed that plasmodiophorids are common and diverse in both rhizosphere and bulk agricultural soils
Plasmodiophorid diversity was lower in the rhizosphere compared to bulk soil, illustrated by significantly lower Fisher’s alpha diversity indices, with respect to core OTUs in both wheat and oilseed rape (OSR) rhizospheres (Figure 3)

Summary

Introduction

Plant roots release considerable amounts of labile exudates and debris into the soil, which results in intense microbial activity in the rhizosphere soil which surrounds roots, and the selection of communities which are structurally and functionally distinct from the bulk soil (Morgan et al, 2005) The rhizosphere microbiome can have major impacts on plant growth and nutrition, which can be both positive and negative, through complex direct and indirect interactions. Protists are components of the rhizosphere microbiome (Mendes et al, 2013), and can have marked impacts on plant growth through direct and indirect pathways (Bonkowski, 2004). They are typically not considered in studies of rhizosphere microbiology, largely because culture independent techniques to profile complex protist communities remain limited (Adl et al, 2014), with the result that there is little understanding of the factors which shape protist communities in the rhizosphere. Polymyxa betae vectors Beet Necrotic Yellow Vein Virus, which causes sugar beet “rhizomania,” resulting in ca. 10% loss or the world production of sugar beet (Lemaire et al, 1988; Desoignies et al, 2014; Hassanzadeh Davarani et al, 2014; Biancardi and Lewellen, 2016)

Methods

Results

Conclusion