{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T13:24:17Z","timestamp":1788269057449,"version":"build-2803163510"},"reference-count":27,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"Tiakina Kauri"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Phytophthora<\/jats:italic>\n                      species are globally significant soilborne oomycetes responsible for widespread ecosystem decline. Standard soil sampling protocols, originally developed for qualitative baiting assays, typically require collecting substantial soil volumes to capture viable propagules. While effective for culture-based detection, these protocols are labor-intensive and can damage the shallow root systems of sensitive host species such as New Zealand kauri (\n                      <jats:italic toggle=\"yes\">Agathis australis<\/jats:italic>\n                      ).\n                      <jats:italic toggle=\"yes\">Phytophthora agathidicida<\/jats:italic>\n                      (PA), the causal agent of kauri dieback, is routinely surveyed using these methods. However, quantitative data describing the vertical distribution of PA in natural forest soils are lacking. Consequently, it remains unclear where in the soil profile PA is most concentrated and, therefore, the depth that should be sampled to ensure optimal detection. In this study, we applied a quantitative oospore DNA (oDNA) qPCR assay to characterize the fine-scale vertical distribution of PA at four soil depth increments (0\u20135, 6\u201310, 11\u201315, and 16\u201320 cm) from 12 kauri trees representing a range of disease stages. Results revealed distinct vertical stratification, with PA DNA concentrations peaking within the upper 0\u201310 cm of soil in non-symptomatic and possibly symptomatic trees. In symptomatic trees, the absolute peak occasionally reached 11\u201315 cm, while pathogen signals remained consistently detectable within the top 10 cm. Field validation from an additional eight trees confirmed that targeted 0\u201310 cm \u201cshallow\u201d sampling yielded higher PA concentrations than deeper sampling. Together, these findings provide a quantitative basis for refining soil sampling strategies, which will enable more sensitive molecular detection while minimizing disturbance and logistical effort in fragile ecosystems.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Phytophthora<\/jats:italic>\n                      species are among the most destructive soilborne pathogens globally, requiring robust diagnostic tools for both agricultural and conservation settings. Traditional sampling methods were designed around the biological requirements of baiting bioassays, which often necessitate collecting large soil volumes over broad depth profiles to maximize the likelihood of recovering viable propagules. However, this high-volume collection is labor-intensive and can cause significant soil and root disturbance in sensitive forest ecosystems. This study provides a quantitative assessment of how\n                      <jats:italic toggle=\"yes\">Phytophthora agathidicida<\/jats:italic>\n                      (PA) DNA is distributed vertically in the soil profile around kauri trees at different stages of disease severity. We demonstrated that while peak absolute abundance shifts within the 0\u201315 cm range as infection progresses, the pathogen signal remains consistently detectable within the top 10 cm. Our findings indicate that targeted, shallow sampling enhances sensitivity by reducing signal dilution, thereby offering a lower-impact pathway for kauri dieback surveillance.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01025-26","type":"journal-article","created":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T13:01:01Z","timestamp":1785330061000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Vertical distribution of\n                    <i>Phytophthora agathidicida<\/i>\n                    oospore DNA in kauri forest soils: implications for optimized sampling and disease monitoring"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-6779-7638","authenticated-orcid":false,"given":"Jade T. T.","family":"Palmer","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0040r6f76","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Biological Sciences, Victoria University of Wellington","place":["Wellington, New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-5798-5445","authenticated-orcid":false,"given":"Emily M. G.","family":"Hocking","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0040r6f76","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Biological Sciences, Victoria University of Wellington","place":["Wellington, New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7959-7852","authenticated-orcid":true,"given":"Monica L.","family":"Gerth","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0040r6f76","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Biological Sciences, Victoria University of Wellington","place":["Wellington, New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1111\/mpp.12190"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.3767\/persoonia.2018.40.08"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.envsci.2019.08.020"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/s43016-020-0075-0"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1111\/ppa.13312"},{"key":"e_1_3_3_7_2","unstructured":"Tiakina Kauri. 2023. Approved soil and root sampling method for Phytophthora agathidicida detection. Available from: https:\/\/www.kauriprotection.co.nz\/assets\/content-blocks\/downloads\/Tiakina-Kauri-1-SOP-for-Soil-and-root-Sampling-final-June-2023.pdf"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.11646\/phytotaxa.205.1.2"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1111\/ppa.13104"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2023.02.047"},{"key":"e_1_3_3_11_2","unstructured":"Tiakina Kauri. 2025. Best practice guide: kauri ora: hygiene principles Available from: https:\/\/www.kauriprotection.co.nz\/assets\/Documents-PDFs\/Best-Practice-Guides\/Kauri-Ora-Hygiene-Principles-guide.pdf"},{"key":"e_1_3_3_12_2","unstructured":"Bellgard SE Dick MA Horner IJ. 2011. Analysis of kauri dieback soil samples Phase 1 Final report. Prepared for the Ministry of Agriculture and Forestry. Contract RFQ12239. Available from: https:\/\/www.kauriprotection.co.nz\/assets\/Research-reports\/Surveillance-Detection-Diagnostics-and-Pathways\/Analysis-of-Kauri-Dieback-soil-and-tissue-samples\/ANALYS1.PDF"},{"key":"e_1_3_3_13_2","unstructured":"Tiakina Kauri. 2023. Approved soil baiting method for Phytophthora agathidicida. Ministry for Primary Industries. https:\/\/www.kauriprotection.co.nz\/assets\/content-blocks\/downloads\/MPI-Approved-Test-Soil-bioassay-baiting-protocol-FINAL-June-2023.pdf."},{"key":"e_1_3_3_14_2","unstructured":"BellgardSEW BevanS PennycookSRPaderesEBeever RE Than DJDJ HillL WilliamsSE. 2013. Specialist Phytophthora research: biology pathology ecology and detection of PTA: MPI contract 11927. Ministry for Primary Industries Wellington New Zealand7 Available from: https:\/\/www.kauriprotection.co.nz\/assets\/Research-reports\/Understanding-the-disease\/Specialist-Phytophthora-Research-Biology-Pathology-Ecology-and-Detection-of-PTA.pdf"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1094\/Phyto-86-1122"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.phyto.38.1.541"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1094\/PDIS-91-11-1419"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1007\/s42360-022-00553-1"},{"key":"e_1_3_3_19_2","first-page":"S39","article-title":"Distribution and recovery of Phytophthora cinnamomi in soils of mixed hardwood-pine forests of the south-eastern USA","volume":"41","author":"Meadows IM","year":"2011","unstructured":"Meadows IM, Jeffers SN. 2011. Distribution and recovery of Phytophthora cinnamomi in soils of mixed hardwood-pine forests of the south-eastern USA. 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Report 46320. https:\/\/www.kauriprotection.co.nz\/assets\/Research-reports\/Surveillance-Detection-Diagnostics-and-Pathways\/Preliminary-survey-for-Phytophthora.pdf."},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1094\/PHYTO-09-13-0263-R"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1002\/edn3.29"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11557-023-01892-7"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10658-024-02886-1"},{"key":"e_1_3_3_28_2","unstructured":"Horner IJ Hough E. 2015. Assay of stored soils for presence of Phytophthora agathidicida. A Plant and Food Research report prepared for The Ministry for Primary Industries Contract No. 32294. Available from: https:\/\/www.kauriprotection.co.nz\/assets\/Research-reports\/Understanding-the-disease\/Assay-of-stored-soils-for-presence-of-Phytophthora-agathidicida.pdf"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01025-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01025-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T13:12:03Z","timestamp":1788268323000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.01025-26"}},"subtitle":[],"editor":[{"given":"Lindsey Price","family":"Burbank","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,1]]},"references-count":27,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9,1]]}},"alternative-id":["10.1128\/spectrum.01025-26"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.01025-26","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,1]]},"assertion":[{"value":"2026-03-28","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-06-01","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-07-29","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01025-26"}}