Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of “Hidden” Diversity

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.

Soil protist function varies with elevation in the Swiss Alps

“…the Janzen–Connell hypothesis applied to animals (Mahé et al ., 2017 ). The degree of specificity in parasites varies across clades, with Gregarinomorphea usually assumed to be specific (Smith and Cook, 2008 ; Rueckert et al ., 2019 ) while this is not as clear for Oomycota (Jiang and Tyler, 2012 ; Thines, 2018 ) and Phytomyxea (Neuhauser et al ., 2014 ; Bass et al ., 2018 ). While consumers dominated the regional pool of soil protists, we found large local variations: consumers represented between 17% and 89% of the sample read counts.…”

Quantitative proteomics provides an insight into germination‐related proteins in the obligate biotrophic plant pathogen Spongospora subterranea

“…Other plasmodiophorids include Spongospora subterranea f. sp. subterranea , Polymyxa graminis , Sorodiscus callitrichis and Polymyxa betae (Bass et al ., 2018). The production of long‐lived resting spores is a common feature of the plasmodiophorids.…”

Contrasting Responses of Rhizosphere Bacterial, Fungal, Protist, and Nematode Communities to Nitrogen Fertilization and Crop Genotype in Field Grown Oilseed Rape (Brassica napus)

“…The nematode and protist communities were profiled by extracting sequenes amplified using general microbial eukaryote primers. While this represents a low cost option relative to use of specific primers for these groups, such as those used by Hilton et al (2018) for nematodes, and by Bass et al (2018) for plant associated plasmodiophorid protists, it is possible that some loss of diversity within these groups occurred, resulting in dampening of the responses of these groups to both nitrogen and genotype.…”