Protists are an integral part of the Arabidopsis thaliana microbiome

Abstract

SummaryAlthough protists occupy a vast range of habitats and are known to interact with plants among other things via disease suppression, competition or growth stimulation, their contributions to the 'phytobiome' are not well described. To contribute to a more comprehensive picture of the plant holobiont, we examined cercozoan and oomycete taxa living in association with the model plant Arabidopsis thaliana grown in two different soils. Soil, roots, leaves and wooden toothpicks were analysed before and after surface sterilization. Cercozoa were identified using 18S rRNA gene metabarcoding, whereas the Internal Transcribed Spacer 1 was used to determine oomycetes. Subsequent analyses revealed strong spatial structuring of protist communities between compartments, although oomycetes appeared more specialized than Cercozoa. With regards to oomycetes, only members of the Peronosporales and taxa belonging to the genus Globisporangium were identified as shared members of the A. thaliana microbiome. This also applied to cercozoan taxa belonging to the Glissomonadida and Cercomonadida. We identified a strong influence by edaphic factors on the rhizosphere, but not for the phyllosphere. Distinct differences of Cercozoa found preferably in wood or fresh plant material imply specific niche adaptations. Our results highlight the importance of microeukaryotes for the plant holobiont.

Site‐specific distribution of oak rhizosphere‐associated oomycetes revealed by cytochrome c oxidase subunit II metabarcoding

“…For some rhizosphere samples, no PCR amplicons were obtained, including the samples from HYIII1, COIII3, HOI57, COIIIS3, COIIS4, and COIVS7 subsequently omitted from further analyses. Samples were prepared for sequencing as described previously (Sapp et al, ). Paired‐end sequencing was carried out by the BMFZ (Biologisch‐Medizinisches Forschungszentrum) of Heinrich Heine University Düsseldorf on an Illumina MiSeq machine using 5% PhiX.…”

“…Sequencing resulted in 1,232,979 merged cox2 reads (Table ). Sequence analyses were carried out as described previously (Sapp et al, ). Briefly, demultiplexed sequences were joined using fastq‐join (Aronesty, ) with minimum overlap of 50 bp.…”

“…Tree labels indicate species affiliation (H = holm oak, C = cork oak) and a health status class (I = healthy trees with 100%-95% foliation; II = trees of an intermediate health and a foliation of 94%-80%; III = diseased trees with crown foliation of 79%-50%, and IV = severely diseased or dead trees with 49%-0% foliation) (Satellite imagery © 2017 Google Earth) Initial tests for best performing annealing temperatures were carried out using Phytophthora infestans strain T30-4 (Haas et al, 2009 subsequently omitted from further analyses. Samples were prepared for sequencing as described previously (Sapp et al, 2018).…”

“…Metabarcoding of micro‐eukaryotic communities has received increased attention in the last few years. For oomycete communities, the ITS1 fragment is commonly used (Agler et al, ; Riit et al, ; Sapp, Ploch, Fiore‐Donno, Bonkowski, & Rose, ; Vettraino, Bonants, Tomassini, Bruni, & Vannini, ) but also fragments of the 18S rDNA have been applied (Singer et al, ). A positive aspect of using markers like ITS1 for this purpose is the broad coverage of diversity in reference databases (Robideau et al, ).…”

Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils

“…Among protists, the most prevalent core taxa were all cercozoans from the phyla Filosa-Sarcomonadae and Filosa-Granofilosea affiliated to Allapsidae -Group Te (77% of samples), Limonofila borokensis (70%) and Paracercomonas (63%). These three taxa have also been identified as extremely common and abundant in the rhizosphere of Arabidopsis thaliana [38] and Allapsidae -Group Te as a hub taxon in the maize rhizosphere [39]. Five Oomycetes were also categorized as core taxa with three of them affiliated to the Pythium genus and one to Phytophthora that are both described as potential plant pathogens.…”