Pyrosequencing of environmental soil samples reveals biodiversity of the<i>Phytophthora</i>resident community in chestnut forests

Vannini, Andrea; Bruni, Natalia; Tomassini, A.; Franceschini, S.; Vettraino, Anna Maria

doi:10.1111/1574-6941.12132

Cited by 59 publications

(63 citation statements)

References 45 publications

(76 reference statements)

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“…Such results have proven challenging to obtain in studies targeting a broader array of microbes (Lemos et al 2011). In all comparative studies to date, number of species detected by high throughput sequencing (HTS) far exceeds those recovered using traditional isolation techniques (Vettraino et al 2012, Vannini et al 2013, Català et al 2015. In our current study, samples were collected from asymptomatic natural vegetation, and Phytophthora was detected from 64% of the sites sampled.…”

Section: Discussionmentioning

confidence: 89%

Predictors of Phytophthora diversity and community composition in natural areas across diverse Australian ecoregions

et al. 2018

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Comprehensive understanding of the patterns and drivers of microbial diversity at a landscape scale is in its infancy, despite the recent ease by which soil communities can be characterized using massively parallel amplicon sequencing. Here we report on a comprehensive analysis of the drivers of diversity distribution and composition of the ecologically and economically important Phytophthora genus from 414 soil samples collected across Australia. We assessed 22 environmental and seven categorical variables as potential predictors of Phytophthora species richness, α and β diversity, including both phylogenetically and non-phylogenically explicit methods. In addition, we classified each species as putatively native or introduced and examined the distribution with respect to putative origin. The two most widespread species, P. multivora and P. cinnamomi, are introduced, though five of the ten most widely distributed species are putatively native. Introduced taxa comprised over 54% of Australia's Phytophthora diversity and these species are known pathogens of annual and perennial crop habitats as well as urban landscapes and forestry. Patterns of composition were most strongly predicted by bioregion (R 2 = 0.29) and ecoregion (R 2 = 0.26) identity; mean precipitation of warmest quarter, mean temperature of the wettest quarter and latitude were also highly significant and described approximately 21, 14 and 13% of variation in NMDS composition, respectively. We also found statistically significant evidence for phylogenetic over-dispersion with respect to key climate variables.This study provides a strong baseline for understanding biogeographical patterns in this important genus as well the impact of key plant pathogens and invasive Phytophthora species in natural ecosystems.

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Section: Discussionmentioning

confidence: 89%

Predictors of Phytophthora diversity and community composition in natural areas across diverse Australian ecoregions

et al. 2018

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“…Previous studies have used oomycete-specific primers ITS6 and ITS7 to amplify the ITS1 region with highly variable success. For example, Vannini et al (2013) recovered only 23 oomycete OTUs from 10 forest soil samples, where oomycetes contributed to 79% of all reads. More recently, Coince et al (2013) recovered a total of 10 oomycete OTUs from 20 samples of forest soil that contributed to 15% of all reads.…”

Section: Discussionmentioning

confidence: 99%

Oomycete-specific ITS primers for identification and metabarcoding

Riit¹,

Tedersoo²,

Drenkhan³

et al. 2016

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Microbial metabarcoding studies using high throughput sequencing technologies generate unprecedented amounts of DNA sequence data and make it possible to determine not only the composition of the communities but also the underlying factors powering the evolution of these communities. Despite the potential of community level studies in helping to better understand the ecology of pathogens and to manage the losses caused by them, very few oomycete addressing metabarcoding studies have been carried out and with highly variable results. The aim of this study was to develop new oomycete-specific ITS region PCR primers with improved specificity for metabarcoding and identification of oomycetes. The modified ITS1oo and the newly developed ITS3oo primers show improved in silico specificity for oomycetes and when paired with the universal ITS4 successfully amplified the DNA from all eleven tested oomycete species from six genera. High throughput sequencing of 20 soil samples from forest nurseries and bordering areas, using the primer pair ITS1oo/ITS4, recovered more than 400 oomycete OTUs, which is a significant increase over previous studies, and indicates the ability of the new method to detect various oomycete groups from complex substrates. The average fraction of oomycete reads per soil samples was 32-36%, with a maximum of 69%. The recovered oomycete OTUs represented the groups Lagenidiales, Peronosporales, Pythiales and Saprolegniales, with Pythiales dominating in all samples. In addition, the new primers were successfully used in identifying pathogens directly from infected plant tissues with Sanger sequencing. The pathogen was identified to the species or genus level in four samples out of six. In conclusion, the developed oomycete-specific primers provide a reliable method for the identification and metabarcoding of oomycetes.Copyright Taavi RESEARCH ARTICLETaavi Riit et al. / MycoKeys 14: 17-30 (2016) 18

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“…The use of next-generation sequencing approaches to study community composition and diversity of soil-borne pathogens is becoming increasingly common, although very few studies so far have focused on oomycetes (e.g. Vannini et al, 2013). A promising recent advance has been the development of Phytophthora-specific primer sets (Scibetta et al, 2012).…”

Section: How Are Soil-borne Pathogens Spatially Distributed?mentioning

confidence: 99%

Phosphorus limitation, soil‐borne pathogens and the coexistence of plant species in hyperdiverse forests and shrublands

et al. 2014

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507I.507II.509III.510IV.510V.512VI.516VII.518518References518 Summary Hyperdiverse forests occur in the lowland tropics, whereas the most species‐rich shrublands are found in regions such as south‐western Australia (kwongan) and South Africa (fynbos). Despite large differences, these ecosystems share an important characteristic: their soils are strongly weathered and phosphorus (P) is a key growth‐limiting nutrient. Soil‐borne pathogens are increasingly being recognized as drivers of plant diversity in lowland tropical rainforests, but have received little attention in species‐rich shrublands. We suggest a trade‐off in which the species most proficient at acquiring P have ephemeral roots that are particularly susceptible to soil‐borne pathogens. This could equalize out the differences in competitive ability among co‐occurring species in these ecosystems, thus contributing to coexistence. Moreover, effective protection against soil‐borne pathogens by ectomycorrhizal (ECM) fungi might explain the occurrence of monodominant stands of ECM trees and shrubs amongst otherwise species‐rich communities. We identify gaps in our knowledge which need to be filled in order to evaluate a possible link between P limitation, fine root traits, soil‐borne pathogens and local plant species diversity. Such a link may help to explain how numerous plant species can coexist in hyperdiverse rainforests and shrublands, and, conversely, how monodominant stands can develop in these ecosystems.

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Pyrosequencing of environmental soil samples reveals biodiversity of thePhytophthoraresident community in chestnut forests

Cited by 59 publications

References 45 publications

Predictors of Phytophthora diversity and community composition in natural areas across diverse Australian ecoregions

Predictors of Phytophthora diversity and community composition in natural areas across diverse Australian ecoregions

Oomycete-specific ITS primers for identification and metabarcoding

Phosphorus limitation, soil‐borne pathogens and the coexistence of plant species in hyperdiverse forests and shrublands

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