Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida
Date
Authors
King, Zoe
Buckley, Hannah L
Lear, Gavin
Seale, Brent
Lee, Kevin C
Schwendenmann, Luitgard
Lacap-Bugler, Donnabella C
Supervisor
Item type
Journal Article
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Journal Title
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Volume Title
Publisher
Wiley
Abstract
Soil-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.Description
Keywords
Phytophthora agathidicida, LAMP detection, amplicon sequencing, kauri dieback, pathogen‐microbe interactions, shotgun metagenomics, soil microbiome, 0602 Ecology, 0603 Evolutionary Biology, 0605 Microbiology, Microbiology, 3103 Ecology, 3104 Evolutionary biology, 3107 Microbiology
Source
Environ Microbiol Rep, ISSN: 1758-2229 (Print); 1758-2229 (Online), Wiley, 18(2), e70324-. doi: 10.1111/1758-2229.70324
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© 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.