King, ZoeBuckley, Hannah LLear, GavinSeale, BrentLee, Kevin CSchwendenmann, LuitgardLacap-Bugler, Donnabella C2026-04-072026-04-072026-04-01Environ Microbiol Rep, ISSN: 1758-2229 (Print); 1758-2229 (Online), Wiley, 18(2), e70324-. doi: 10.1111/1758-2229.703241758-22291758-2229http://hdl.handle.net/10292/20873Soil-borne pathogens can influence microbial communities and ecosystem function, making it important to understand their broader ecological impacts. We investigated interactions between Phytophthora agathidicida (the causal agent of kauri tree dieback) and soil microbial communities, while also comparing detection and community-profiling methods. Soils from 60 kauri trees across three sites in the Waitākere Ranges, New Zealand, were analysed using loop-mediated isothermal amplification (LAMP) for pathogen detection, and 16S rRNA gene/ITS gene amplicon sequencing alongside shotgun metagenomics for community characterisation. LAMP detected P. agathidicida in 39/60 samples, while shotgun sequencing detected Phytophthora-associated DNA at low abundance across all samples. Microbial community structure and functional potential showed weak association with pathogen presence, though differential abundance testing identified several genera enriched in pathogen-detected soils, including taxa previously linked to disease suppression. Amplicon and shotgun profiles indicated broadly comparable patterns at higher taxonomic and functional levels, while differences between approaches emerged primarily at finer taxonomic resolution. Importantly, functional predictions from PICRUSt2 closely matched shotgun-derived profiles at broader scales, indicating its suitability as a cost-effective tool for broad-scale monitoring. These findings suggest limited direct pathogen effects on microbial communities and highlight how integrating molecular approaches provides complementary insights into soil microbiome-pathogen interactions.© 2026 The Author(s). Environmental Microbiology Reports published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.Phytophthora agathidicidaLAMP detectionamplicon sequencingkauri diebackpathogen‐microbe interactionsshotgun metagenomicssoil microbiome0602 Ecology0603 Evolutionary Biology0605 MicrobiologyMicrobiology3103 Ecology3104 Evolutionary biology3107 MicrobiologyPhytophthoraSoil MicrobiologyNew ZealandRNA, Ribosomal, 16SMetagenomeForestsMicrobiotaPlant DiseasesMetagenomicsBacteriaNucleic Acid Amplification TechniquesPhylogenyJournal ArticleOpenAccess10.1111/1758-2229.70324