Kirramyces destructans in Australia: biosecurity threat or elusive native pathogen?

Kirramyces destructans was first described in 1996 from north Sumatra, Indonesia, where it caused severe leaf and shoot blight on Eucalyptus grandis in nurseries and young plantations. Since then it has been reported in nurseries and plantations in Vietnam, Thailand and China, with its host range extending to include E. camaldulensis and E. urophylla. K. destructans has also been reported from native E. urophylla in East Timor and was considered a significant biosecurity threat to Australia’s native eucalypt forests and plantations. A study on the population diversity of K. destructans isolates throughout south-east Asia in which 8 gene regions were sequenced (four nuclear genes, one mitochondrial gene and three microsatellite markers) detected very low nucleotide polymorphism. This genetic uniformity is indicative of an introduced population which has subsequently spread throughout Asia via human-mediated movement of germplasm. Surveys of sentinel plantings in northern Australia revealed a complex of Kirramyces spp. among which K. destructans was detected. The same gene regions and markers were sequenced as for the Asian study and diversity among the K. destructans isolates in Australia was found to be much greater than that in Asia. We believe that K. destructans is native to Australia where is resides symptomlessly within the native vegetation. The disease is only expressed when non-endemic eucalypts are planted. As such the pathogen is a major encumbrance to the establishment of commercial eucalypt plantations in Northern Australia. The disease has not been observed in native ecosystems, but the effect of inoculum build up within plantations on adjacent native eucalypt remnants is not known

A systemic parvo-like virus in the freshwater crayfish Cherax destructor

Systemic Cowdry Type A inclusions (CAs) were observed in a moribund Cherax destructor collected at an aquaculture farm in South Australia. Inclusions were most common in the gills and were associated with multifocal necrosis of the main gill axis and lamellae. The hepatopancreas was necrotic; however, only one CA was observed in the interstitial tissues. CAs were associated with necrosis in the abdominal and gut musculature. CAs were also observed in the spongy connective tissues and the epicardium. Empty capsids (17.5 +/- 0.5 nm) and microfilaments were most commonly observed within these inclusions by transmission electron microscopy. Complete icosahedral viral particles (20.8 +/- 1.2 nm) were difficult to distinguish within the viroplasm, but were visualised better in aggregates between the viroplasm and the inner nuclear membrane. The nucleolus was closely associated with the developing viroplasm, and was hypertrophied and segregated into its fibrillar and granular components. The virus was named Cherax destructor systemic parvo-like virus (CdSPV) on the basis of its histopathology, cytopathology and morphology. CdSPV is the first systemic virus described in a freshwater crayfish

Susceptibility of South African native conifers to the pitch canker pathogen, Fusarium circinatum

AbstractFusarium circinatum is an economically important pathogen of Pinus species, which also occurs on Douglas fir (Pseudotsuga menzeisii). It causes pitch canker of mature trees and root and collar rot of seedlings and cuttings. In 2007, pitch canker was observed on Pinus radiata in the Western Cape and this was the first outbreak of this disease in South Africa. The Cape flora in this area includes native coniferous species of Podocarpus and Widdringtonia. In this study, seedlings of P. latifolia, P. elongatus, P. henkelii, W. schwartzii, W. cederbergensis and W. nodiflora were inoculated with a virulent isolate of F. circinatum, to assess their susceptibility. Six weeks after inoculation, there was no lesion development in any of the species inoculated. Pinus patula seedlings used as a positive control were severely affected. Results of this study show that species of Podocarpus and Widdringtonia, native to the Western Cape, are not threatened by the pitch canker fungus

Robust microbial markers for non-invasive inflammatory bowel disease identification

Inflammatory Bowel Disease (IBD) is an umbrella term for a group of inflammatory diseases of the human gastrointestinal tract, including Crohn’s Disease (CD) and ulcerative colitis (UC). Changes to the intestinal microbiome, the community of micro-organisms that resides in the human gut, have been shown to contribute to the pathogenesis of IBD. IBD diagnosis is often delayed due its non-specific symptoms (e.g. abdominal pain) and an invasive colonoscopy is required for confirmation. Delayed diagnosis is linked to poor growth in children and worse treatment outcomes. Microbial communities are extremely complex and feature selection algorithms are often applied to identify key bacterial groups that drive disease. It has been shown that aggregating Ensemble Feature Selection (EFS) can be used to improve the robustness of feature selection algorithms. The robustness of a feature selector is defined as the variation of feature selector output caused by small changes to the dataset. Typical feature selection algorithms can be used to help build simpler, faster, and easier to understand models - but suffer from poor robustness. Having confidence in the output of a feature selector algorithm is key for enabling knowledge discovery from complex biological datasets. In this work we apply a two-step filter and an EFS process to generate robust feature subsets that can non-invasively predict IBD subtypes from high-resolution microbiome data. The predictive power of the robust feature subsets is the highest reported in literature to date. Furthermore, we identify five biologically plausible bacterial species that have not previously been implicated in IBD aetiology

A simple method for detection of mitochondrial DNA polymorphisms

Polymorphisms were identified in mtDNA of Heterobasidion annosum by digesting total genomic DNA with HaeIII, CfoI, or MspI, which recognize the restriction sites GGCC, GCGC, and CCGG, respectively. Most DNA was digested to fragments of less than 2 kb, while AT-rich fragments of 1.7 to 17 kb stood out as bands of uniform intensity after ethidium bromide staining. These fragments hybridized to mtDNA probes and were inherited in a uniparental fashion

Impact of indigenous storage systems and insect infestation on the contamination of maize with fumonisins

Four storage systems of maize commonly used by farmers in Benin, West Africa, were tested to determine their impact on infection of maize by Fusarium and subsequent contamination with fumonisins. The study showed that Fusarium incidence was significantly higher when maize was stored on a cemented floor in a house, a non ventilated facility (40.3 ± 17.4%), than in the other tested systems (p < 0.05). The lowest Fusarium incidence was recorded when maize was stored in a bamboo granary that is a ventilated facility (25.5 ± 13.5%) (p < 0.05). All maize samples from the tested storage systems were found to be fumonisin positive, with levels ranging from 0.6 to 2.4 mg/kg. Fumonisin level, overall, was found to decrease over the storage period, but not significantly in all the tested storage systems. Damage by lepidopterous pests was significantly and positively correlated with both infection of maize with Fusarium and contamination by fumonisin. In contrary, damage by coleopterous insects was significantly and negatively correlated with infection of maize with Fusarium and contamination by fumonisin. Avoiding the use of non-ventilated systems to store maize and reducing insect infestation in field and during storage are very important recommendations for farmers.Keywords: Maize, storage systems, Fusarium, fumonisins, insect infestatio

Identification of the causal agent of Botryosphaeria stem canker in Ethiopian Eucalyptus plantations

Plantations of exotic Eucalyptus make up more than 30% of Ethiopia's plantations, providing fuel and construction timber to the country. Species such as E. camaldulensis, E. saligna, E. grandis, E. citriodora and E. globulus are most commonly planted. During a survey of Eucalyptus diseases in 2000 and 2001, Botryosphaeria stem canker was observed in most plantations. The disease symptoms included tip die- back, coppice failure and stem cankers characterised by kino exudation. The aim of this study was to identify the species responsible for Botryosphaeria stem canker in Ethiopia. Culture and conidial morphology, as well as DNA-based identification involving Restriction Fragment Length Polymorphisms (RFLPs) and sequencing of the Internal Transcribed Spacer regions (ITS) of the ribosomal RNA gene and the elongation factor 1-alpha (EF1-α) gene, were used to identify isolates. Pathogenicity studies were conducted in the greenhouse and under field conditions. Results showed that Botryosphaeria parva is responsible for Botryosphaeria stem canker of Eucalyptus in Ethiopia. This is the first report of the fungus from this country. Greenhouse and field inoculation studies showed that the Ethiopian isolates are highly virulent. Careful site species selection and breeding trials are thus needed to reduce the impact of this disease in Ethiopia

Chromium sequencing: The doors open for genomics of obligate plant pathogens

It is challenging to sequence and assemble genomes of obligate plant pathogens and microorganisms because of limited amounts of DNA, comparatively large genomes and high numbers of repeat regions. We sequenced the 1.2 gigabase genome of an obligate rust fungus, Austropuccinia psidii, the cause of rust on Myrtaceae, with a Chromium 10X library. This technology has mostly been applied for single-cell sequencing in immunological studies of mammals. We compared scaffolds of a genome assembled from the Chromium library with one assembled from combined paired-end and mate-pair libraries, sequenced with Illumina HiSeq. Chromium 10X provided a superior assembly, in terms of number of scaffolds, N50 and number of genes recovered. It required less DNA than other methods and was sequenced and assembled at a lower cost. Chromium sequencing could provide a solution to sequence and assemble genomes of obligate plant pathogens where the amount of available DNA is a limiting factor. © 2018 Future Science. All rights reserved

Botanical gardens as key resources and hazards for biosecurity

Biodiversity and economic losses resulting from invasive plant pests and pathogens are increasing globally. For these impacts and threats to be managed effectively, appropriate methods of surveillance, detection and identification are required. Botanical gardens provide a unique opportunity for biosecurity as they accommodate diverse collections of exotic and native plant species. These gardens are also often located close to high-risk sites of accidental invasions such as ports and urban areas. This, coupled with routine activities such as the movement of plants and plant material, and visits by millions of people each year, place botanical gardens at risk to the arrival and establishment of pests and pathogens. Consequently, botanical gardens can pose substantial biosecurity risks to the environment, by acting as bridgeheads for pest and pathogen invasions. Here we review the role of botanical gardens in biosecurity on a global scale. The role of botanical gardens has changed over time. Initially, they were established as physic gardens (gardens with medicinal plants), and their links with academic institutions led to their crucial role in the accumulation and dissemination of botanical knowledge. During the second half of the 20th century, botanical gardens developed a strong focus on plant conservation, and in recent years there has been a growing acknowledgement of their value in biosecurity research as sentinel sites to identify pest and pathogen risks (novel pest-host associations); for early detection and eradication of pests and pathogens; and for host range studies. We identify eight specific biosecurity hazards associated with botanical gardens and note potential management interventions and the opportunities these provide for improving biosecurity. We highlight the value of botanical gardens for biosecurity and plant health research in general, and the need for strategic thinking, resources, and capacity development to make them models for best practices in plant health