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<p>Over the last&#xa0;decades cork oak (<i>Quercus suber</i>) forests have been increasingly threatened by decline events, which are strongly associated with <i>Phytophthora</i> species. A 3-year survey was conducted to analyze the diversity of <i>Phytophthora</i> species in two different seasons (winter and summer) across six cork oak stands in Sardinia, Italy, in which the health status of the trees was visually assessed. The occurrence and diversity of <i>Phytophthora</i> species in the soil collected from cork oak trees were investigated through both soil baiting and molecular detection by metabarcoding. Overall, 354 rhizosphere soil samples from trees of <i>Quercus suber</i> (51), <i>Arbutus unedo</i> (5), <i>Erica arborea</i> (2) and <i>Pinus pinaster</i> (1), collected in summer and winter for 3&#xa0;years, were processed by baiting. The 59 samples collected in the summer of 2020 were also analyzed through metabarcoding. Overall, 35 of the 59 trees resulted positive to <i>Phytophthora</i> using both detection techniques. Six <i>Phytophthora</i> species were detected through soil baiting, and they were <i>P</i>. <i>cinnamomi</i>, <i>P</i>. <i>quercina</i>, <i>P</i>. <i>pseudocryptogea</i>, <i>P</i>. <i>tyrrhenica</i>, <i>P</i>. <i>psychrophila</i> and <i>P</i>. ×<i>cambivora</i>. All the species were detected in winter, while only <i>P</i>. <i>cinnamomi</i>, <i>P</i>. <i>tyrrhenica</i> and <i>P</i>. <i>pseudocryptogea</i> could be also isolated in summer. Metabarcoding enabled the detection of <i>P</i>. <i>cactorum</i>, <i>P</i>. <i>cinnamomi</i>, <i>P</i>. <i>quercina</i> and <i>P</i>. <i>tyrrhenica</i> as well as two unknown <i>Phytophthora</i> taxa closely related to <i>P. cactorum</i> and <i>P. quercina</i>. Overall baiting across six seasons resulted in more species than the single metabarcoding sample. However, a higher number of positive samples and taxa diversity was obtained with metabarcoding from the same sampling season. This study demonstrates the importance of integrating these two diagnostic techniques to achieve a more accurate assessment of <i>Phytophthora</i> diversity and distribution in forest ecosystems, which is crucial in phytosanitary surveys.</p>

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Detection and diversity of Phytophthora species from declining Quercus suber stands using both DNA metabarcoding and soil baiting techniques

  • 期刊论文

  • 发表日期：

    2025年2月22日

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  • Salvatore Seddaiu,
  • Carolyn Riddell,
  • Giovanni Piras,
  • Pino A. Ruiu,
  • Luca Sarais,
  • Antonietta Mello,
  • Peter J. A. Cock,
  • Andrea Brandano,
  • Sarah Green,
  • Bruno Scanu

摘要

Over the last decades cork oak (Quercus suber) forests have been increasingly threatened by decline events, which are strongly associated with Phytophthora species. A 3-year survey was conducted to analyze the diversity of Phytophthora species in two different seasons (winter and summer) across six cork oak stands in Sardinia, Italy, in which the health status of the trees was visually assessed. The occurrence and diversity of Phytophthora species in the soil collected from cork oak trees were investigated through both soil baiting and molecular detection by metabarcoding. Overall, 354 rhizosphere soil samples from trees of Quercus suber (51), Arbutus unedo (5), Erica arborea (2) and Pinus pinaster (1), collected in summer and winter for 3 years, were processed by baiting. The 59 samples collected in the summer of 2020 were also analyzed through metabarcoding. Overall, 35 of the 59 trees resulted positive to Phytophthora using both detection techniques. Six Phytophthora species were detected through soil baiting, and they were P. cinnamomi, P. quercina, P. pseudocryptogea, P. tyrrhenica, P. psychrophila and P. ×cambivora. All the species were detected in winter, while only P. cinnamomi, P. tyrrhenica and P. pseudocryptogea could be also isolated in summer. Metabarcoding enabled the detection of P. cactorum, P. cinnamomi, P. quercina and P. tyrrhenica as well as two unknown Phytophthora taxa closely related to P. cactorum and P. quercina. Overall baiting across six seasons resulted in more species than the single metabarcoding sample. However, a higher number of positive samples and taxa diversity was obtained with metabarcoding from the same sampling season. This study demonstrates the importance of integrating these two diagnostic techniques to achieve a more accurate assessment of Phytophthora diversity and distribution in forest ecosystems, which is crucial in phytosanitary surveys.