Metabarcoding reveals rhizosphere microbiome shifts between healthy and declining Quercus robur trees

Oak dieback affecting Quercus robur L. (pedunculate oak) in Northern Europe, is driven by a complex interaction of abiotic and biotic factors, such as pests, diseases, and environmental stress, including drought. To better understand the role of the soil microbiome in oak dieback, we analysed the diversity and composition of the microbial communities in the rhizospheres of declining and visibly healthy trees. We used metabarcoding to describe the microbiome and baiting (i.e., the use of plant tissues to act as baits) to isolate species of Phytophthora, a protist genus known for its contribution to the decline of oak trees. Our findings revealed significant differences in bacterial alpha diversity and fungal beta diversity between the rhizospheres of healthy and declining trees. Viable isolates of several species of Phytophthora, such as Phytophthora plurivora, P. cactorum, and P. gonapodyides were obtained using the baiting technique. The results underscore the stand level diversity of rhizosphere soil microbiota and support our initial idea that microbial communities vary with tree health conditions.

This work was financially supported by the European Union's Horizon 2020 (H2020) Marie Skłodowska-Curie Actions Innovative Training Networks PROTECTA H2020-MSCA-ITN-2017 call, under grant agreement number 766048 (NLG, CBA, LGB). LGB is further supported by the Swedish Research Council, Vetenskapsrådet (grant number 2023-05529). CR received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement number 845419. We acknowledge and appreciate the kind contributions of Professor Stephen Woodward and Maja Brus-Szkalej, who provided valuable comments on an earlier version of this manuscript. Adam Flöhr and Jan-Eric Englund from Statistics@SLU provided statistical support and valuable comments. We are grateful for the thoughtful reviews of three anonymous reviewers and the editor-in-chief, which helped improve this article.

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