scholarly journals Distribution and diversity of Phytophthora across Australia

2017 ◽  
Vol 23 (2) ◽  
pp. 150 ◽  
Author(s):  
Treena I. Burgess ◽  
Diane White ◽  
Keith M. McDougall ◽  
Jeff Garnas ◽  
William A. Dunstan ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Conservation Management ◽  
Phytophthora Cinnamomi ◽  
Environmental Dna ◽  
Phytophthora Species ◽  
Native Vegetation ◽  
New Techniques ◽  
Future Studies ◽  
Isolation Methods ◽  
Potential Impact

The introduction and subsequent impact of Phytophthora cinnamomi within native vegetation is one of the major conservation issues for biodiversity in Australia. Recently, many new Phytophthora species have been described from Australia’s native ecosystems; however, their distribution, origin, and potential impact remain unknown. Historical bias in Phytophthora detection has been towards sites showing symptoms of disease, and traditional isolation methods show variable effectiveness of detecting different Phytophthora species. However, we now have at our disposal new techniques based on the sampling of environmental DNA and metabarcoding through the use of high-throughput sequencing. Here, we report on the diversity and distribution of Phytophthora in Australia using metabarcoding of 640 soil samples and we compare the diversity detected using this technique with that available in curated databases. Phytophthora was detected in 65% of sites, and phylogenetic analysis revealed 68 distinct Phytophthora phylotypes. Of these, 21 were identified as potentially unique taxa and 25 were new detections in natural areas and/or new introductions to Australia. There are 66 Phytophthora taxa listed in Australian databases, 43 of which were also detected in this metabarcoding study. This study revealed high Phytophthora richness within native vegetation and the additional records provide a valuable baseline resource for future studies. Many of the Phytophthora species now uncovered in Australia’s native ecosystems are newly described and until more is known we need to be cautious with regard to the spread and conservation management of these new species in Australia’s unique ecosystems.

scholarly journals Flower visitation by honey possums (Tarsipes rostratus) in a coastal banksia heathland infested with the plant pathogen Phytophthora cinnamomi

2013 ◽  
Vol 35 (2) ◽  
pp. 166 ◽  
Author(s):  
Shannon J. Dundas ◽  
Patricia A. Fleming ◽  
Giles E. St J. Hardy
Keyword(s):  
Plant Pathogen ◽  
Conservation Management ◽  
Phytophthora Cinnamomi ◽  
Pollen Grains ◽  
Floristic Diversity ◽  
Vegetation Composition ◽  
Flower Visitation ◽  
South West ◽  
Potential Impact ◽  
A Site

The honey possum (Tarsipes rostratus) is a tiny (7–10 g) obligate nectarivore endemic to south-west Western Australia that relies on high floristic diversity for year-round nectar and pollen resources. We investigated flower visitation by honey possums at a site in the presence of the plant pathogen Phytophthora cinnamomi by sampling pollen on the head of captured and radio-tracked individuals. The aim of the study was to identify plant species that were visited and to compare these with known susceptibility to Phytophthora to assess the potential impact of further spread of the pathogen on honey possums. Nine plant taxa were regularly identified from pollen on honey possums, including four Banksia species. Six of the nine plant taxa identified (Banksia plumosa, Adenanthos cuneatus, Calothamnus gracilis, B. brunnea, B. nutans, B. tenuis) were most frequently visited by honey possums, each making up >20% of pollen grains for at least one season. Five of the nine plant taxa are known to be susceptible to Phytophthora, which substantially changes vegetation composition in its wake. The inevitable spread of Phytophthora is postulated to result in the localised loss of resources for honey possums and is a concern for on-going conservation management.

scholarly journals Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tatsuhiko Hoshino ◽  
Ryohei Nakao ◽  
Hideyuki Doi ◽  
Toshifumi Minamoto
Keyword(s):  
Fish Species ◽  
High Throughput Sequencing ◽  
Correlation Coefficients ◽  
Environmental Dna ◽  
Digital Pcr ◽  
Absolute Quantification ◽  
Taqman Probe ◽  
Individual Species ◽  
Natural Environments ◽  
Target Sequence

AbstractThe combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.

scholarly journals Phytophthora mediterranea sp. nov., a New Species Closely Related to Phytophthora cinnamomi from Nursery Plants of Myrtus communis in Italy

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 682
Author(s):  
Carlo Bregant ◽  
Antonio A. Mulas ◽  
Giovanni Rossetto ◽  
Antonio Deidda ◽  
Lucia Maddau ◽  
...  
Keyword(s):  
New Species ◽  
Root Rot ◽  
Phytophthora Cinnamomi ◽  
Colony Growth ◽  
Phytophthora Species ◽  
Maximum Temperature ◽  
Pathogenicity Test ◽  
Forest Nurseries ◽  
Collar And Root Rot ◽  
A New Species

Monitoring surveys of Phytophthora related diseases in four forest nurseries in Italy revealed the occurrence of fourteen Phytophthora species to be associated with collar and root rot on fourteen plants typical of Mediterranean and alpine regions. In addition, a multilocus phylogeny analysis based on nuclear ITS and ß-tubulin and mitochondrial cox1 sequences, as well as micromorphological features, supported the description of a new species belonging to the phylogenetic clade 7c, Phytophthora mediterranea sp. nov. Phytophthora mediterranea was shown to be associated with collar and root rot symptoms on myrtle seedlings. Phylogenetically, P. mediterranea is closely related to P. cinnamomi but the two species differ in 87 nucleotides in the three studied DNA regions. Morphologically P. mediterranea can be easily distinguished from P. cinnamomi on the basis of its smaller sporangia, colony growth pattern and higher optimum and maximum temperature values. Data from the pathogenicity test showed that P. mediterranea has the potential to threaten the native Mediterranean maquis vegetation. Finally, the discovery of P. cinnamomi in alpine nurseries, confirms the progressive expansion of this species towards cold environments, probably driven by climate change.

Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding

2021 ◽  
pp. 1-10
Author(s):  
Micheline Carvalho-Silva ◽  
Luiz Henrique Rosa ◽  
Otávio H.B. Pinto ◽  
Thamar Holanda Da Silva ◽  
Diego Knop Henriques ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Crater Lake ◽  
Environmental Dna ◽  
Food Sources ◽  
South Shetland Islands ◽  
Deception Island ◽  
Shetland Islands ◽  
Operational Taxonomic Units ◽  
First Time ◽  
Impacted Site

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

scholarly journals Antifungal Activity of Western Australian Soil Actinomycetes against Phytophthora and Pythium Species and a Mycorrhizal Fungus, Laccaria laccata

1983 ◽  
Vol 36 (2) ◽  
pp. 191 ◽  
Author(s):  
D Keast ◽  
C Tonkin
Keyword(s):  
Antifungal Activity ◽  
Phytophthora Cinnamomi ◽  
Mycorrhizal Fungus ◽  
Organic Matter Content ◽  
Phytophthora Species ◽  
Matter Content ◽  
Soil Organic Matter Content ◽  
Soil Actinomycetes ◽  
High Degree

Soil pH, soil moisture content and soil organic matter content did not appear to influence significantly the total numbers of actinomycetes isolated from sample sites in Western Australia. However, seasonal influences exist with summer conditions leading to higher spore isolation. Substantial but non-specific antifungal activity against Phytophthora cinnamomi, P. cryptogea, P. nicotiana, Pythium proli/erum and L. laccata was detected in vitro from many of the 2367 actinomycetes isolated. Antifungal activity mayor may not occur in members of the same actinomycete group, suggesting segregation of antifungal capacity within all groups. A limited number of actinomycete groups was isolated from the rhizosphere of plants and these exhibited similar properties to their counterparts in soil or litter. Actinomycetes isolated from the rhizosphere of Pinus radiata produced a high degree of in vitro antifungal activity against the Phytophthora species but, in general, actinomycetes isolated from root surfaces exhibited antibiosis against all the fungi tested. More actinomycetes showed antifungal activity from soils where P. cinnamomi was causing dieback of jarrah and other understorey species.

Temperature-Growth Relations and Genetic Diversity of A2 Mating-Type Isolates of Phytophthora cinnamomi in Australia

1974 ◽  
Vol 22 (2) ◽  
pp. 231 ◽  
Author(s):  
CJ Shepherd ◽  
BH Pratt
Keyword(s):  
Growth Rate ◽  
First Generation ◽  
Phytophthora Cinnamomi ◽  
Phytophthora Species ◽  
Temperature Growth ◽  
Field Isolates ◽  
Place Of Origin ◽  
Successive Generations ◽  
Cardinal Temperatures ◽  
Range Of Values

Determinations of cardinal temperatures for growth on various media of 50 Australian isolates of Phytophthova cinnamomi showed that growth did not occur outside the range 5-35°C. The range of temperatures at which growth optima occurred varied according to the isolate and medium used and encompassed the whole range of values reported by overseas authors. Growth rates of 361 isolates on corn meal agar at 25°C varied within the range 4.7-10.5 mm/day. There was no correlation between optimum temperature and whether isolates were slow- or fastgrowing or their place of origin. Fast-growing isolates (6-11 mm/day) were obtained from all States, but slower-growing isolates (<6 mm/day) were obtained only from southern and western regions of Australia. Populations from different regions of Australia exhibited different growth rate parameters. The variability of mycelial isolates in culture was studied by examining differences in growth rate among replicated parent, single-zoospore, single-zoosporangium and single terminal-hyphal isolates. Extensive variation was found among first generation single-zoospore progenies of field isolates, with lesser variation among progeny of single zoosporangia, terminal hyphal cultures and second and third generation zoospore derivatives. The origin of this variation is discussed and it is suggested that field isolates are heterokaryotic, since zoospores proved to be predominantly uninucleate. When various Phytophthora species were incubated at temperatures above those at which growth was possible and then returned to 25°C, their subsequent ability to resume growth depended on the particular time-temperature combination used. Considerable variation of response was found among a number of isolates of P. cinnamomi and, following the establishment of single zoospore isolates, the potential variability of field isolates was shown to persist through successive generations of zoospore propagation. It is suggested that a cytoplasmic mechanism of inheritance may be responsible for this variation.

scholarly journals High prevalence and diversity of beta-lactamase-encoding bacteria in cryosoils and ancient permafrost

2021 ◽  
Author(s):  
Sofia Rigou ◽  
Eugene Christo-Foroux ◽  
Sebastien Santini ◽  
Artemiy Goncharov ◽  
Jens Strauss ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Bacterial Genome ◽  
Environmental Dna ◽  
Single Copy ◽  
The Arctic ◽  
Human Society ◽  
Beta Lactamase ◽  
Extended Spectrum Beta Lactamase ◽  
Arctic Regions ◽  
Global Threat

Background: Antimicrobial resistance is one of the major challenges affecting public health. It is mostly due to the continuous emergence of extended-spectrum beta-lactamase from various environments followed by their rapid dissemination and selection in clinical settings. The warming of Earth' s climate is the other global threat facing human society, in particular with the Arctic regions experiencing a twice faster warming than the global average and permafrost affected by widespread thawing. A potentially dreadful combination of these two threats would be the release and dispersion of harmful microbes that have remained confined to largely uninhabited Arctic regions, or are stored dormant in permafrost. Methods: Environmental DNA was isolated from 12 soil samples from various Arctic and subarctic pristine regions in Siberia (Yakutia and Kamchatka), including 9 permafrost samples collected at various depths. The large datasets obtained from high throughput sequencing was assembled in contigs and their protein-gene contents predicted. We used exhaustive similarity searches to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. In addition, we specifically identified beta-lactamase genes and their prevalence per bacterial genome estimated through the detection of two universal single copy genes. Findings: A total of 9.217 1011 bp were exploited, leading to a total of 525,313 contigs at least 5kb in size. The DNA content of the various samples was found to be highly variable, not strictly correlated with the depth or radio-carbon-based deposit age, and most likely linked to the global density of microbes trapped in the corresponding permafrost layers. Bacteria account for more than 90% of the contigs in most samples, followed by Eukaryotes and Archaea (always lower than 10%). Viruses represented less than 2% of all contigs in all samples. The taxonomic profiles of surface cryosoils and deep permafrost samples exhibited a high diversity, including between permafrost samples originating from various depths in the same borehole. In all samples, bacterial contigs carrying different beta-lactamases from class A to D were identified. Interpretation: No clear common taxonomic feature could be found shared by surface cryosoils or ancient permafrost layers. However, most samples (9/12) exhibited a high frequency of beta-lactamase genes, with an estimated average close to 1 copy/bacterial genome. In addition to the well-documented reactivation of infectious ancient pathogens (bacteria, viruses, protozoa), we show now that global warming could contribute to the emergence of new antibiotic resistances through the mobilization by contemporary bacteria of ancient DNA released from thawing permafrost.

scholarly journals Pathogenicity of four Phytophthora species on kauri in vitro and glasshouse trials

2014 ◽  
Vol 67 ◽  
pp. 54-59 ◽  
Author(s):  
I.J. Horner ◽  
E.G. Hough
Keyword(s):  
Plant Growth ◽  
Forest Soils ◽  
Phytophthora Cinnamomi ◽  
Phytophthora Species ◽  
The Other ◽  
Root Damage ◽  
Soil Inoculation

In kauri forest soils surveys Phytophthora taxon Agathis (PTA) P cinnamomi P multivora and P cryptogea were detected frequently In vitro and glasshouse studies determined that all four Phytophthora species produced lesions on excised kauri leaves and stems Lesion advance was significantly slower with P cinnamomi P multivora and P cryptogea than with PTA When 2yearold kauri seedlings were trunkinoculated lesion spread was rapid with PTA trunks were girdled and all trees died within 46 weeks Phytophthora cinnamomi P multivora and P cryptogea produced substantially smaller lesions than PTA no trees died and plant growth was only slightly suppressed Following soil inoculation with PTA all kauri seedlings died within 10 weeks There were no deaths following soil inoculation with P cinnamomi P multivora or P cryptogea although feeder root damage was observed and the respective pathogens were reisolated Results suggest that PTA is an aggressive pathogen and the other three species are weaker pathogens of kauri

scholarly journals Re-evaluation of Phytophthora Species Isolated During 30 Years of Vegetation Health Surveys in Western Australia Using Molecular Techniques

Plant Disease ◽  
2009 ◽  
Vol 93 (3) ◽  
pp. 215-223 ◽  
Author(s):  
Treena I. Burgess ◽  
Janet L. Webster ◽  
Juanita A. Ciampini ◽  
Diane White ◽  
Giles E. StJ. Hardy ◽  
...  
Keyword(s):  
New Taxa ◽  
Western Australia ◽  
Dna Sequences ◽  
Phytophthora Cinnamomi ◽  
Sequence Data ◽  
Phytophthora Species ◽  
Molecular Techniques ◽  
Similar Species ◽  
Eucalyptus Marginata ◽  
Similar Morphology

For 30 years, large-scale aerial photography has been used to map the extent of Phytophthora dieback disease in native forests in the southwest of Western Australia, with validation of the observations involving routine testing of soil and root samples for the presence of Phytophthora cinnamomi. In addition to P. cinnamomi, six morpho-species have been identified using this technique: P. citricola, P. megasperma, P. cryptogea, P. drechsleri, P. nicotianae, and P. boehmeriae. In recent years, many new Phytophthora species have been described worldwide, often with similar morphology to existing species; thus, as many of the isolates collected in Western Australia have been difficult to identify based on morphology, molecular identification of the morpho-species is required. Based on amplification of the internal transcribed spacer (ITS) region of the rDNA gene, sequence data of more than 230 isolates were compared with those of existing species and undescribed taxa. P. inundata, P. asparagi, P. taxon PgChlamydo, P. taxon personii, and P. taxon niederhauserii were identified based on sequence data. Phylogenetic analysis revealed that nine potentially new and undescribed taxa can be distinguished. Several of the new taxa are morphologically indistinguishable from species such as P. citricola, P. drechsleri, and P. megasperma. In some cases, the new taxa are closely related to species with similar morphology (e.g., P.sp.4 and P. citricola). However, the DNA sequences of other new taxa such as P.sp.3 and P.sp.9 show that they are not closely related to morphologically similar species P. drechsleri and P. megasperma, respectively. Most of the new taxa have been associated with dying Banksia spp., while P.sp.2 and P.sp.4 have also been isolated from dying Eucalyptus marginata (jarrah). Some taxa (P.sp.3, 6, and 7) appear to have limited distribution, while others like P.sp.4 are widespread.

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