ORCID Profile
0000-0002-5050-8553
Current Organisations
Murdoch University
,
Department of Primary Industries and Regional Development
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Publisher: Wiley
Date: 04-12-2018
DOI: 10.1111/ECOG.03904
Publisher: Scion
Date: 23-05-2014
Publisher: Wiley
Date: 23-12-2020
Publisher: Elsevier BV
Date: 11-2019
Publisher: Springer Science and Business Media LLC
Date: 08-04-2019
Publisher: Public Library of Science (PLoS)
Date: 10-12-2018
Publisher: Springer Science and Business Media LLC
Date: 28-11-2022
DOI: 10.1038/S41564-022-01266-X
Abstract: Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and h ers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a erse set of 880 microbial community s les collected for the Earth Microbiome Project. We include licon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore ersity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite ersity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for ex le, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from erse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.
Publisher: Naturalis Biodiversity Center
Date: 30-06-2009
Publisher: Wiley
Date: 06-11-0001
DOI: 10.1111/PPA.13104
Publisher: CABI
Date: 2013
Publisher: Springer Science and Business Media LLC
Date: 09-02-2019
Publisher: Wiley
Date: 19-04-2016
DOI: 10.1111/PPL.12442
Abstract: Phytophthora plant pathogens cause tremendous damage in planted and natural systems worldwide. Phosphite is one of the only effective chemicals to control broad-scale Phytophthora disease. Little work has been done on the phytotoxic effects of phosphite application on plant communities especially in combination with plant physiological impacts. Here, we tested the phytotoxic impact of phosphite applied as foliar spray at 0, 12, 24 and 48 kg a.i. ha(-1) . Eighteen-month-old saplings of 13 conifer and angiosperm species native to New Zealand, and two exotic coniferous species were treated and the development of necrotic tissue and chlorophyll-a-fluorescence parameters (optimal quantum yield, Fv /Fm effective quantum yield of photosystem II, ΦPSII ) were assessed. In addition, stomatal conductance (gs ) was measured on a subset of six species. Significant necrosis assessed by digital image analysis occurred in only three species: in the lauraceous canopy tree Beilschmiedia tawa (8-14%) and the understory shrub Dodonaea viscosa (5-7%) across phosphite concentrations and solely at the highest concentration in the myrtaceous pioneer shrub Leptospermum scoparium (66%). In non-necrotic tissue, Fv /Fm , ΦPSII and gs remained unaffected by the phosphite treatment. Overall, our findings suggest minor phytotoxic effects resulting from foliar phosphite application across erse taxa and regardless of concentration. This study supports the large-scale use of phosphite as a management tool to control plant diseases caused by Phytophthora pathogens in plantations and natural ecosystems. Long-term studies are required to ascertain potential ecological impacts of repeated phosphite applications.
Publisher: Springer Science and Business Media LLC
Date: 19-06-2014
Publisher: New Zealand Plant Protection Society
Date: 08-06-2018
DOI: 10.30843/NZPP.2018.71.127
Abstract: Phytophthora agathidicida is an aggressive soil-borne oomycete pathogen that kills New Zealand kauri trees (Agathis australis). When artificially inoculated, P. agathidicida causes lesions on leaves as well as roots, providing a non-invasive method for virulence screening. However, little is known about the extents to which the pathogen varies in virulence and kauri trees vary in disease susceptibility. Three isolates of P. agathidicida grown in culture were inoculated onto detached leaves from six kauri trees. Visible disease lesions were measured and the extent of asymptomatic leaf colonisation determined by culturing. All six trees were susceptible to P. agathidicida, but one showed higher susceptibility than the others. The pathogen also showed variability in virulence among isolates. Asymptomatic colonisation of leaf tissue was also found, suggesting a latent or biotrophic phase for the pathogen. Although further work is needed, the variability of both pathogen virulence and host susceptibility have important implications for management of kauri dieback. Furthermore, asymptomatic colonisation of kauri tissues suggests that P. agathidicida could be present outside of regions with visible disease symptoms.
Publisher: Springer Science and Business Media LLC
Date: 28-08-2020
Publisher: Springer Science and Business Media LLC
Date: 20-08-2013
Publisher: Wiley
Date: 14-02-2019
DOI: 10.1111/EFP.12502
Publisher: Wiley
Date: 19-12-2012
Publisher: Scientific Societies
Date: 07-2017
DOI: 10.1094/PDIS-12-16-1738-RE
Abstract: Phytophthora pluvialis is associated with early defoliation and shoot dieback in Douglas-fir in Oregon and New Zealand. In 2013, P. pluvialis was described from mixed tanoak-Douglas-fir forests in the Pacific Northwest and concurrently recognized as the main causal agent of red needle cast (RNC) in New Zealand radiata pine plantations. Little is known about its infection cycle and impact on host physiology. P. pluvialis studies in Douglas-fir are challenging due to the ubiquitous presence of the endophyte Phaeocryptopus gaeumannii, which produces similar symptoms and premature defoliation with persistent needle wetness, known as Swiss needle cast (SNC). Nonetheless, our study showed P. pluvialis infection in the presence of SNC. Exclusive expression of P. pluvialis is difficult to achieve as both diseases are promoted by high humidity. Here we established a ‘dry leaf’ strategy to suppress SNC when inoculating Douglas-fir needles for RNC studies. Sheltering plants along with drip irrigation to avoid needle wetness during the P. gaeumannii sporulation period suppressed its development in the new season flush. The diminished endophyte inoculum enabled bias-reduced studies of P. pluvialis impacts on Douglas-fir without the confounding effects of stomatal blockage and premature defoliation caused by P. gaeumannii.
Publisher: Elsevier BV
Date: 11-2018
DOI: 10.1016/J.MIMET.2018.10.006
Abstract: A high-throughput assay was developed to screen Phytophthora species for fungicide sensitivity using optical density measurements for unbiased, automated measurement of mycelial growth. The efficacy of the optical density assay (OD) to measure phosphite sensitivity in Phytophthora species was compared to two widely used methods, radial growth (RG) and dry weight (DW) assays. Three isolates of each of Phytophthora cinnamomi, P. multivora and P. pluvialis, with known phosphite exposure and three isolates of each species with no prior phosphite exposure, were screened for phosphite sensitivity using the three assays. Mycelial growth measurements were taken after culturing for 6, 14 and 15 days for the OD, DW and RG assays respectively. Mycelial growth inhibition at 15, 80, 200 and 500 μg/mL phosphite relative to growth on control media was used to determine effective concentration values for 50% growth reduction (EC50). The species varied in their tolerance to phosphite with P. cinnamomi being the least sensitive followed by P. multivora and P. pluvialis. No significant differences in tolerance were found between isolates within the same species using any method. The OD assay produced comparable EC50 values to the RG and DW assays. The growth of the three species was more sensitive to phosphite in the DW than the RG and OD assays, however limited s le throughput and greater variation in measuring small amounts of mycelia in the dry weight assessment increase variability and limits throughput. The OD assay offers a fast method to enable an inventory of chemical resistance and is particularly advantageous for slow growing species as it requires less time and offers greater throughput than existing RG and DW methods.
Publisher: Wiley
Date: 02-03-2021
DOI: 10.1111/EFP.12680
Abstract: New Zealand kauri ( Agathis australis ) trees are culturally, socially and ecologically significant within northern New Zealand's nutrient‐poor podocarp forest ecosystems. Phytophthora agathidicida is an aggressive oomycete pathogen, capable of killing A . australis across its ecological range, causing the disease known as kauri dieback. The pathogen, like many other forest Phytophthora species, commences as a fine root rot which progresses to collar rot and resinous cankers on the lower trunk. In this study, we investigated the eco‐physiological and fine root responses of kauri to infection by P . agathidicida and tested whether the foliar application of micronutrients (manganese and zinc combined, iron alone, or a trace element mix) affects dieback disease expression. Fortnightly assessments of chlorophyll‐ a ‐fluorescence were conducted over 12 weeks, and fine root length and tip numbers were recorded at the end of the experiment. None of the micronutrient treatments had a significant physiological effect regardless of pathogen infection. However, contrary to expectations, pathogen infection caused a significant upregulation in photosynthetic activity over time, as the electron transport rate of infected plants was approximately 26% higher than that of control plants at the end of the trial. These results indicate that an increase in the strength of the below‐ground carbon sink through pathogen consumption of labile carbohydrates (sugars), together with pathogen‐induced root damage, triggered upregulation of photosynthesis in the seedlings. Understanding how P . agathidicida infection affects the physiology and resource allocation in kauri is critical to determining the disease aetiology and management options.
Publisher: Cold Spring Harbor Laboratory
Date: 20-07-2023
DOI: 10.1101/2023.07.20.549584
Abstract: MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of ,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms’ role in ecology and human health.
Publisher: Springer Science and Business Media LLC
Date: 06-07-2013
Publisher: Springer Science and Business Media LLC
Date: 18-01-2012
Publisher: Springer Science and Business Media LLC
Date: 07-2015
Location: Australia
No related grants have been discovered for Peter Scott.