Opportunities and limitations for DNA metabarcoding in Australasian plant-pathogen biosecurity

Bulman, Simon; McDougal, Rebecca; Hill, Kelly; Lear, Gavin

doi:10.1007/s13313-018-0579-3

Cited by 26 publications

(18 citation statements)

References 72 publications

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“…NA values at the genus level were kept and included as part of the 'other' genus category. Species level assignment was not possible due to the short length of the targeted 16S rRNA region, which may be indistinguishable among species and / or strains (Bulman et al 2018;Osawa et al 2015).…”

Section: Laboratory Analysismentioning

confidence: 99%

“…Species level identification could not be achieved with the samples in this preliminary assessment due to the short length of the targeted 16S rRNA region, which may be indistinguishable among species and/or strains (a low level taxonomic rank used at the intraspecific level) (Bulman et al 2018;Osawa et al 2015). Future studies could overcome this limitation and improve taxonomic resolution by using more sensitive techniques, such as quantitative polymerase chain reaction (qPCR) with species-specific primers (Osawa et al 2015).…”

Section: Limitationsmentioning

confidence: 99%

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A preliminary assessment of bacteria in “ranched” ball pythons (Python regius), Togo, West Africa

D’Cruze¹,

Bates²,

Assou³

et al. 2020

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Captive reptiles are routinely identified as reservoirs of pathogenic bacteria and reports of reptile-associated infections relating to some species are well documented (e.g., salmonellosis). Currently, relatively little is known about the epidemiology and bacteria of ball pythons. We carried out a survey of ball python farms in Togo, West Africa to assess the presence of any potentially pathogenic bacterial taxa that have been identified in recent scientific literature relating to this species. The presence of bacteria belonging to the genera Acinetobacter, Bacteroides, Citrobacter, Enterobacter, Lysobacter, Proteus, Pseudomonas, Staphylococcus, and Tsukamurella in oral and cloacal samples taken from five individual ball pythons is of potential concern for horizontal transmission given that pathogenic species belonging to these genera have been previously documented. The presence of bacteria belonging to the genera Clostridium, Escherichia, Moraxella, and Stenotrophomonas in the oral and rectal samples taken from five mice used to feed ball pythons suggests that they represent a potential reservoir of infection for wild caught ball pythons and their progeny. Furthermore, possible sources of environmental contamination include other captive amphibians, birds, reptiles and mammals, as well as free ranging birds and small mammals. Additional surveillance of ball pythons in the wild and in captivity at python farms in West Africa will shed light on whether or not this type of commercial activity is increasing pathogen exposure and lowering barriers to transmission. Meanwhile, as a precautionary measure, it is recommended that python farms should immediately establish biosecurity and disease surveillance practices to minimize potential horizontal and vertical bacterial transfer.

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Section: Laboratory Analysismentioning

confidence: 99%

Section: Limitationsmentioning

confidence: 99%

A preliminary assessment of bacteria in “ranched” ball pythons (Python regius), Togo, West Africa

D’Cruze¹,

Bates²,

Assou³

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Despite the growing body of evidence for its usefulness in the early detection and surveillance of potentially invasive forest pathogens [27][28][29], and its high sensitivity and capacity to deal with large numbers of samples in less time compared to traditional methods [30], HTS is generally underutilized as a tool in plant biosecurity [31][32][33][34][35].…”

Section: Introductionmentioning

confidence: 99%

Cryptic Risks to Forest Biosecurity Associated with the Global Movement of Commercial Seed

Cleary

Oskay

Doğmuş

et al. 2019

Forests

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The import and export of tree seed carries with it risks of inadvertent introduction of pests and pathogens to hitherto unaffected regions. Although trade in seed of specified trees is regulated, phytosanitary requirements for most tree species are minimal, even those related to the most important forest tree species in a given region. A better understanding of the microbiome associated with seed intended for commercial production or ornamental use, and their potential risk with the transport from the source origin of distributors, will help regulatory agencies implement measures to safeguard seed health and avoid trade-related spread of potentially harmful pathogens. In this study we used high-throughput sequencing to show that highly diverse fungal communities were associated with seed of 14 different Pinus species obtained from seed banks (seed orchards) and retail sources (online distributors) in North America and Europe. Fungal diversity differed among the 23 seedlots tested. Community composition did not relate to the species of Pinus nor the country of origin. Assigned potential functions based on sequence identity using FUNGuild provided an overall understanding of the likely life strategies of fungal operational taxonomic units (OTUs). Of those sequences classified to a trophic level, 453 were plant pathogens, with the Dothideomycetes having the highest prevalence. The most common plant pathogens included Sydowia polyspora, Lasiodiplodia theobromae, Diplodia intermedia and Diplodia sapinea that were detected from the majority of Pinus species. The evidence presented here illustrates an urgent need for plant protection authorities, practitioners and the general public to recognize the potential risk of introducing harmful pathogens through innocent transport of seed.

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“…The advent of high throughput sequencing (HTS) opened a new era in fungal ecology [23] that allows for holistic insights into the immense taxonomic (relying on DNA metabarcoding) and functional (metatranscriptomics) diversity of fungi in different niches, with ever-increasing resolution [24][25][26]. Despite the growing body of evidence for its usefulness in the early detection and surveillance of potentially invasive forest pathogens [27][28][29], and its high sensitivity and capacity to deal with large numbers of samples in less time compared to traditional methods [30], HTS is generally underutilized as a tool in plant biosecurity [31][32][33][34][35].…”

Section: Introductionmentioning

confidence: 99%

Cryptic Risks to Forest Biosecurity Associated with the Global Movement of Commercial Seed

Cleary

Oskay

Doğmuş

et al. 2019

Preprint

View full text Add to dashboard Cite

The import and export of tree seed carries with it risks of inadvertent introduction of pests and pathogens to hitherto unaffected regions. Although trade in seed of specified trees is regulated, phytosanitary requirements for most tree species are minimal, even those related to the most important forest tree species in a given region. A better understanding of the microbiome associated with seed intended for commercial production or ornamental use, and their potential risk with the transport from the source origin of distributors, will help regulatory agencies implement measures to prevent new and emerging risks. In this study we used high throughput sequencing to show that highly diverse fungal communities were associated with seed of 14 different Pinus species obtained from seed banks (seed orchards) and retail sources (online distributors) in North America and Europe. Fungal diversity differed among the 23 seedlots tested. Community composition did not relate to the species of Pinus nor the country of origin. Assigned potential functions based on sequence identity using FUNGuild provided an overall understanding of the likely life strategies associated fungal OTUs. Of those sequences classified to a trophic level, 453 were plant pathogens, with the Dothideomycetes having the highest prevalence. The most common plant pathogens detected included Sydowia polyspora, Lasiodiplodia theobromae, Diplodia intermedia and Diplodia sapinea. The evidence presented here illustrates an urgent need for plant protection authorities, practitioners and the general public to recognize the potential risk of introducing harmful pathogens through innocent transport of seed.

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Opportunities and limitations for DNA metabarcoding in Australasian plant-pathogen biosecurity

Cited by 26 publications

References 72 publications

A preliminary assessment of bacteria in “ranched” ball pythons (Python regius), Togo, West Africa

A preliminary assessment of bacteria in “ranched” ball pythons (Python regius), Togo, West Africa

Cryptic Risks to Forest Biosecurity Associated with the Global Movement of Commercial Seed

Cryptic Risks to Forest Biosecurity Associated with the Global Movement of Commercial Seed

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