Search

Tree decline is a global concern and the primary cause is often unknown. Complex interactions between fluctuations in nitrogen (N) and acidifying compounds have been proposed as factors causing nutrient imbalances and decreasing stress tolerance of oak trees. Microorganisms are crucial in regulating soil N available to plants, yet little is known about the relationships between soil N-cycling and tree health. Here, we combined high-throughput sequencing and qPCR analysis of key nitrification and denitrification genes with soil chemical analyses to characterise ammonia-oxidising bacteria (AOB), archaea (AOA) and denitrifying communities in soils associated with symptomatic (declining) and asymptomatic (apparently healthy) oak trees (Quercus robur and Q. petraea) in the United Kingdom. Asymptomatic trees were associated with a higher abundance of AOB that is driven positively by soil pH. No relationship was found between AOA abundance and tree health. However, AOA abundance was driven by lower concentrations of NH4+, further supporting the idea of AOA favouring lower soil NH4+ concentrations. Denitrifier abundance was influenced primarily by soil C:N ratio, and correlations with AOB regardless of tree health. These findings indicate that amelioration of soil acidification by balancing C:N may affect AOB abundance driving N transformations, reducing stress on declining oak trees.

Stem blight and dieback caused by species of the Botryosphaeriales are important diseases of blueberry worldwide. In recent years, stem blight and dieback symptoms have been increasingly observed affecting blueberry production in Australia. Thirty samples were collected from symptomatic plants in an orchard at Corindi NSW, a major blueberry growing region. In addition, samples from symptomatic blueberry plants were submitted by growers to the Plant Health Diagnostic Service, NSW Department of Primary Industries from eight orchards in New South Wales (NSW), and a single orchard in Western Australia (WA). Culture isolations, DNA sequencing and pathogenicity testing were undertaken to determine the species causing the disease. Fifty-two isolates were recovered in total, forty-eight from NSW, and four from WA. A multi-locus sequencing approach was used to assist species identification including the internal transcribed spacer region of rDNA including 5.8S (ITS), partial translation elongation factor 1-alpha (tef1-α), and DNA-directed RNA polymerase II second largest subunit (rpb2). Eight species from three genera were identified; the most common was Neofusicoccum parvum (n = 34), followed by N. kwambonambiense (n = 7), N. occulatum (n = 5), L. theobromae (n = 2), Botryosphaeria dothidea (n = 1), N. australe (n = 1), N. macroclavatum (n = 1) and Lasiodiplodia pseudotheobromae (n = 1). The pathogenicity testing showed all isolates produced lesions on blueberry stems. This study provides the first survey of Botryosphaeriales causing blueberry stem blight and dieback in Australia, and is a valuable resource for plant pathologists and growers trying to manage the disease.

The Botryosphaeriales, and in particular the Botryosphaeriaceae, are a well-studied group of fungi best known for the canker diseases they cause on woody hosts especially in stressed or damaged trees. Australian Plant Pathology herbaria contain many records for this group, but due to considerable taxonomic changes over the past decade, many of the species names have since been reclassified. In this article we used all published records with available sequence data of the Botryosphaeriaceae in Australia to examine the distribution and host range of these taxa. There are 24 genera encompassing 222 species in the Botryosphaeriaceae; 9 genera and 62 species have been recorded in Australia. Some genera such as Neoscytalidium are only found in warm, humid climates while Dothiorella species are more common in temperate climates. There were species, such as Lasiodiplodia theobromae, Neofusicoccum parvum and Botryosphaeria dothidea, which had a wide host range with many records. However, there were also several species found only in one location on a single host. While systematic data collection is still required, the information presented here provides a baseline of species present in Australia and will underpin future studies into this group of important pathogens.

International audience; Findings generated from data mining sometimes are not interesting to the domain users. The problem is that data miners and the domain users do not speak the same language, so human subjectivity towards the domain users' own knowledge fields affects the understanding of knowledge generated from data mining. This paper proposes a communication model based on the reference services model in the field of library science in order to bridge the communications between data miners and domain users. The creation of a data liaison specialist role in the data mining team aims at understanding the subjectivity as well as the thinking process of both parties in order to translate knowledge between the two fields and deliver findings to domain users. Through five steps—data interview, pre-mid evaluation, post-mid evaluation, knowledge delivery, and follow up—the data liaison specialist can achieve effective knowledge synthesis and delivery to the domain users.

A number of disinfection treatments are available to treat irrigation water to reduce the risk of plant disease. However, limited published studies had compared the efficacy of disinfection treatments on a range of plant pathogen species, on their various life stages and in different water qualities. In this study, propagules (spores, mycelium, cells) of eight plant pathogens including Clavibacter michiganensis subsp. michiganensis, Alternaria alternata, Chalara elegans, Colletotrichum gloeosporioides, Calonectria pauciramosa, Fusarium oxysporum, Phytophthora cinnamomi and Pythium aphanidermatum were exposed to chlorine (sodium hypochlorite), chlorine dioxide and ultraviolet radiation (UV) at a range of application rates and exposure times, in deionised water and dam water. The efficacy of treatments varied with exposure time, application rate, water type and the pathogen and propagule. Cl. michiganensis subsp. michiganensis, Ph. cinnamomi and Py. aphanidermatum propagules were most sensitive to all treatments, while propagules of Ch. elegans, Ca. pauciramosa and F. oxysporum required the highest rates and longest exposure times to chlorine, chlorine dioxide and UV to kill >99 % CFUs. Chlorine dioxide, applied as a “shock” treatment at a high rate for a limited time period, and UV radiation offered more effective biocidal activity than the chlorine levels tested in both water types. This study demonstrates that sensitivity to disinfection treatments and application rates varies between pathogens, and between propagules of the same pathogen.

The Gondwana Rainforests of Australia World Heritage Area (GRWHA) covers approximately 370,000 ha, extending along Australia’s east coast from southeast Queensland to central eastern New South Wales (NSW). The rainforests include cool temperate and subtropical ecosystems supporting a high biodiversity of plant and animal species. More than 200 plant species found in the GRWHA are rare or threatened, and invasion by pest species, including Phytophthora, is a significant concern. The current study used a sample design based on GIS layers representing conditions conducive to Phytophthora, including the presence of human disturbance, rainfall, temperature, elevation and slope, to determine the probability of Phytophthora occurring at a particular location and to identify sampling locations within the GRWHA. Sampling at these sites revealed eight Phytophthora species; P. cinnamomi, P. cryptogea, P. multivora, P. heveae, P. frigida, P. macrochlamydospora, two isolates referred to as Phytophthora gondwanense prov. nom. and one isolate referred to Phytophthora sp. (clade 4). Species were identified based on internal transcribed spacer (ITS) and cytochrome oxidase subunit II (cox II) data. The greatest diversity of Phytophthora species was found in the Oxley Wild Rivers National Park. This is the first report of P. frigida in Australia and is the first study to detect P. multivora within the GRWHA. Identification of these Phytophthora species within the GRWHA is concerning due to the unknown susceptibility of endemic native flora.

Fusarium oxysporum f. sp. cucumerinum is the fungal pathogen responsible for Fusarium vascular wilt of cucumber. In Australia, disease management in soilless greenhouse cucumbers is limited by the understanding of the disease cycle, in particular the risk associated with infection of pruning wounds by airborne propagules. Aerial dissemination of the pathogen in response to temperature and relative humidity was investigated using a specific and sensitive quantitative real-time PCR assay. Both macroconidia and microconidia were identified as airborne propagules and a potential relationship between fluctuation in relative humidity and spore release was found, however, it appears that crop disturbance may also influence conidia liberation. Experimental inoculation of stem wounds with conidia however, failed to establish infections. These results suggest that aerial inoculum propagates and disseminates the pathogen, however airborne spores are deposited on the substrate surface and infection occurs primarily through the root. We conclude that while airborne conidia are a risk to infection of cucumber plants in soilless greenhouse crops, resistant rootstocks are likely to provide good protection against this pathogen.

Decline-diseases are complex and becoming increasingly problematic to tree health globally. Acute Oak Decline (AOD) is characterized by necrotic stem lesions and galleries of the bark-boring beetle, Agrilus biguttatus, and represents a serious threat to oak. Although multiple novel bacterial species and Agrilus galleries are associated with AOD lesions, the causative agent(s) are unknown. The AOD pathosystem therefore provides an ideal model for a systems-based research approach to address our hypothesis that AOD lesions are caused by a polymicrobial complex. Here we show that three bacterial species, Brenneria goodwinii, Gibbsiella quercinecans and Rahnella victoriana, are consistently abundant in the lesion microbiome and possess virulence genes used by canonical phytopathogens that are expressed in AOD lesions. Individual and polyspecies inoculations on oak logs and trees demonstrated that B. goodwinii and G. quercinecans cause tissue necrosis and, in combination with A. biguttatus, produce the diagnostic symptoms of AOD. We have proved a polybacterial cause of AOD lesions, providing new insights into polymicrobial interactions and tree disease. This work presents a novel conceptual and methodological template for adapting Koch’s postulates to address the role of microbial communities in disease.

The options for managing Fusarium wilt in greenhouse cucumbers are limited by our poor understanding of the modes of survival and dissemination of the pathogen. This study uses a specific quantitative realtime PCR assay for Fusarium oxysporum f. sp. cucumerinum to investigate the significance of flying insects as aerial vectors of the pathogen in a commercial cucumber greenhouse. Shore flies were more frequently detected (35.5%) carrying F. oxysporum f. sp. cucumerinum than sciarids (25%), with both species carrying between 1 9 10 2 and 1 9 10 6 pathogen genome copies/individual. Sciarid and shore flies acquired F. oxysporum f. sp. cucumerinum following exposures to agar cultures of the pathogen of up to 94 h. Light microscopy revealed that spores were carried externally on the bodies of the adult flies. The ability of adult sciarid flies to vector the pathogen from peat-grown diseased cucumber plants and infect healthy cucumber plants was demonstrated in a caged glasshouse trial. An inoculum density trial showed that vascular wilt disease was initiated after inoculation of peat-grown seedlings with as few as 1000 conidia. We conclude that sciarid and shore flies play significant roles as vectors of F. oxysporum f. sp. cucumerinum in greenhouse cucumbers and need to be recognized in developing integrated crop management strategies.

The rapid and reliable identification and quantification of pathogens is essential for the management of economically important plant diseases. Fusarium oxysporum f. sp. cucumerinum is the soil borne fungus responsible for Fusarium vascular wilt of cucumber. In this study, we report the development of a specific and reliable real-time quantitative PCR assay and the development of an ultra-sensitive diagnostic pseudo-nested PCR assay. The capacity of the PCR assays to accurately identify and quantify Fusarium oxysporum f. sp. cucumerinum was experimentally tested by the development of standard curves from serial dilutions of copy numbers in a range of complex environmental DNA samples. The amplification efficiency, sensitivity and reproducibility of the qPCR assays were not significantly affected by the presence of any of the non-target background DNA tested. In quantitative real-time PCR, as few as 100 copies could be reliably quantified, and in simple and pseudo-nested PCR as little as 10 pg and 10 fg, respectively, could be detected. This rapid and sensitive qPCR method can be used to facilitate investigations into plant–pathogen interactions, epidemiology, and disease management practices.

A survey of a dieback-affected urban bushland reserve on the foreshore of Sydney Harbour found that deaths of native trees and increased weed density were associated with high levels of nutrients, particularly nitrogen, and Phytophthora cinnamomi. To test the interaction between P. cinnamomi and elevated soil nitrogen, a glasshouse trial was established to determine the susceptibility of the most common native trees of the Sydney Harbour foreshore; Angophora costata, Corymbia gummifera, Eucalyptus botryoides and Eucalyptus piperita to P. cinnamomi. Under low nitrogen conditions, inoculation with P. cinnamomi reduced the health of A. costata and C. gummifera, and reduced the root biomass of E. botryoides. Angophora costata and C. gummifera displayed signs of phytotoxicity with elevated levels of inorganic nitrogen. The presence of the pathogen, in combination with elevated nitrogen reduced the health of all species, but the symptoms were more severe in A. costata and E. piperita. The results suggest that the effect of elevated nitrogen application and susceptibility to P. cinnamomi is species specific. Mitigating soil nutrient loading in urban bushland areas by redirecting stormwater flow and surface runoff away from vulnerable bushland may assist in the management of dieback caused by P. cinnamomi.

Novel species of fungi described in the present study include the following from Australia: Neoseptorioides eucalypti gen. and sp. nov. from Eucalyptus radiata leaves, Phytophthora gondwanensis from soil, Diaporthe tulliensis from rotted stem ends of Theobroma cacao fruit, Diaporthe vawdreyi from fruit rot of Psidium guajava, Magnaporthiopsis agrostidis from rotted roots of Agrostis stolonifera and Semifissispora natalis from Eucalyptus leaf litter. Furthermore, Neopestalotiopsis egyptiaca is described from Mangifera indica leaves (Egypt), Roussoella mexicana from Coffea arabica leaves (Mexico), Calonectria monticola from soil (Thailand), Hygrocybe jackmanii from littoral sand dunes (Canada), Lindgomyces madisonensis from submerged decorticated wood (USA), Neofabraea brasiliensis from Malus domestica (Brazil), Geastrum diosiae from litter (Argentina), Ganoderma wiiroense on angiosperms (Ghana), Arthrinium gutiae from the gut of a grasshopper (India), Pyrenochaeta telephoni from the screen of a mobile phone (India) and Xenoleptographium phialoconidium gen. and sp. nov. on exposed xylem tissues of Gmelina arborea (Indonesia). Several novelties are introduced from Spain, namely Psathyrella complutensis on loamy soil, Chlorophyllum lusitanicum on nitrified grasslands (incl. Chlorophyllum arizonicum comb. nov.), Aspergillus citocrescens from cave sediment and Lotinia verna gen. and sp. nov. from muddy soil. Novel foliicolous taxa from South Africa include Phyllosticta carissicola from Carissa macrocarpa, Pseudopyricularia hagahagae from Cyperaceae and Zeloasperisporium searsiae from Searsia chirindensis. Furthermore, Neophaeococcomyces is introduced as a novel genus, with two new combinations, N. aloes and N. catenatus. Several foliicolous novelties are recorded from La Réunion, France, namely Ochroconis pandanicola from Pandanus utilis, Neosulcatispora agaves gen. and sp. nov. from Agave vera-cruz, Pilidium eucalyptorum from Eucalyptus robusta, Strelitziana syzygii from Syzygium jambos (incl. Strelitzianaceae fam. nov.) and Pseudobeltrania ocoteae from Ocotea obtusata (Beltraniaceae emend.). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.