Jen McComb

Tuber melanosporum was first harvested in Australia in 1999, and exports began in 2007. Australia is now the world's fourth-largest truffle producer. The main challenges Australian producers face are climate change, obtaining well-mycorrhized seedlings with no contaminants, and preventing entry of the contaminant species T. indicum and T. maculatum to Australia and T. brumale from east to Western Australia. There is also increasing competition from other southern hemisphere countries. Almost all truffle orchards in Australia are in regions with 600–1500 mm annual rainfall and a mean daily mid-summer temperature below 25 °C. As soils in agricultural lands of Australia are frequently acidic, lime is applied to achieve the alkaline pH required by truffles. New truffle orchards should be planned bearing in mind future climatic predictions. The incorporation of more T. borchii and T. aestivum in truffieres, and the possible use of T. magnatum will spread the harvest period, and thus exports. Oaks and hazel are currently used as major hosts, and new host species are being investigated, including Pinus. The cost of establishing a truffiere in Australia is high. However, Australia lacks many pests, diseases, and social problems associated with the European industry, and together with being an environmentally friendly industry, these factors make truffle production an attractive agricultural investment in Australia which will aid regional economies.

Truffles are possibly the only high-value cultivated organisms for which some aspects of the habit and life cycle have only recently been elucidated or remain unknown. Molecular techniques have helped explain the biological basis for some traditional empirical management techniques, such as inoculating soil with ascospores to improve yield, and have enhanced the detection of competitive or pathogenic soil microorganisms. Improved precision of assessment of the quality of inoculated seedlings is now possible. New knowledge of the genetic structure of populations has indicated that as trees age, the genotypes of mycorrhizae on inoculated trees change, and that there are large differences in the number of female and male genotypes participating in ascocarp formation. The plasticity of Tuber species has also been revealed, with maternal genotypes growing as an ectomycorrhiza in host tree roots and as surface mycelium or an endophyte in roots of adjacent non-mycorrhizal species. Refinement of management techniques has resulted from applying the new information, and the tools are now available to resolve the many outstanding gaps in our knowledge of Tuber biology.

The plant pathogen Phytophthora cinnamomi has significantly damaged the floristic diversity and community structure of the jarrah (Eucalyptus marginata) forest in Western Australia. Complete eradication of the pathogen from infested sites is not possible. This study assessed the feasibility of rehabilitating P. cinnamomi-infested forest sites with native resistant species using various methods of seed deployment. Precision burial of seeds at 5 mm was used as a control, mimicking optimum recruitment depths for many native species and compared against the use of extruded pellets (hereafter ‘pellets’) as an alternative method of precision seed placement. Eighteen rehabilitation plots were set up in three P. cinnamomi-infested reserves using six species. For Acacia acuminata, A. saligna, Calothamnus sanguineus and Melaleuca seriata, there were three treatments: precision buried (non-pelleted) seeds, pellets and pellets with an additive (i.e., a rhizobium bacterium for the Acacia spp. and ectomycorrhizal fungus spores for C. sanguineus and M. seriata). Banksia sessilis and Hakea laurina had only two treatments: precision buried (non-pelleted) seeds and pellets. Seedlings of all six species emerged successfully in P. cinnamomi-infested sites, and the numbers ranged between 23% and 88%. The survival of emerged seedlings after 9 months ranged between 16% and 84%, except M. seriata, which emerged at 59% but failed to survive. In most species, except A. acuminata, seedling emergence and survival from pellets were similar and within an acceptable seedling establishment range when compared to non-pelleted seeds. Pelletised seed with the addition of beneficial microbes did not improve seedling survival or shoot growth in the diseased areas of the jarrah forest. Overall, the results suggest that seedlings of resistant native species can successfully establish in P. cinnamomi-infested sites and pelletised seeds can be used as a viable method for precision planting.

Phytophthora root rot is a major problem for avocado growers around the world. This review summarises the current control measures and their impact on the soil microbiome. The fungicide phosphite is widely used in the avocado industry, and reports from several countries indicate that Phytophthora cinnamomi is developing resistance. For this reason, alternative control measures have been investigated. Applying organic mulches and soil dressings of calcium or silicon provides a level of control. Biological control through the application of suppressive microbes has been actively investigated over many years, but reports of successful field deployment are rare. This review examines the effects on the soil microbiome of these control measures and assesses the future directions for research.

For most Western Australian plant species, no information is available on the effect of Phytophthora cinnamomi on seedling emergence, early survival, and early plant growth. Such information is required when selecting species for rehabilitating Eucalyptus marginata (jarrah) forest areas affected by Phytophthora dieback. This study evaluates the response of several native species to P. cinnamomi to identify those resistant to the pathogen at the early stages of plant development. Firstly, the effect of P. cinnamomi on seedling emergence and early survival was evaluated for 50 native species. Then, 24 species were selected and tested for their resistance to P. cinnamomi when more mature. They were infested at 5–7 months old and disease impact assessed after two months. Of 38 species that emerged in sufficient numbers for statistical analysis, P. cinnamomi did not affect either emergence or survival of 9 species, emergence or survival was decreased in 14 species, and both emergence and survival were significantly decreased in 15 species. Of the species tested at 5–7 months old, two were resistant, six were moderately resistant, ten were susceptible, three were highly susceptible, and three were tolerant hosts of P. cinnamomi. These results indicate that field resistance recorded from mature plants may be due to asymptomatic infection or resistance may not be present in seedlings. Therefore, data from mature plants may not be appropriate when selecting species for seed-based restoration.

This review assesses possible reasons for the discrepancy between the high numbers of Phytophthora species and putative new species isolated from environmental samples using metabarcoding, compared with the low number cultured and identified through bating. Molecular protocols are unlikely to result in high numbers of false positives, except that variants in young hybrid species may be incorrectly identified as different species. Baiting conditions favour parasitic species that are fast to sporulate, able to infect a range of bait species, achieve infection with a low number of zoospores, and fast-growing on selective agar. Species may not be isolated because they are slow-growing saprophytes and slow to sporulate when baited. Changes to protocols that might result in the isolation of more species include changes in the timing of exposure of baits, inclusions of dead baits, reducing potential competition from fast-growing species by baiting only small volumes of soil, and isolation on media without antimicrobials. However, the species not isolated may have growth traits precluding easy isolation, such as host specificity or obligate biotroph lifestyle.

The ability of organic, microbial or mineral-based soil additives to suppress root rot caused by Phytophthora cinnamomi was compared with disease reduction resulting from the use of the fungicides phosphite or metalaxyl. The effect of glyphosate (commonly used for weed control) on plant health was also examined. Avocado plants were grown in a glasshouse in pots with soils collected under mature commercial avocado trees. To simulate ‘orchard soil’ conditions, chicken manure, wood mulch, and mulch from beneath 20-year-old trees in an avocado orchard were added to the pots. The effect of P. cinnamomi on plant growth and visible root damage was assessed using plants grown under these ‘orchard’ soil conditions, and treatments with further additives (two microbial soil conditioners, one organic and two mineral-based mulches). In two of three experiments, infestation of soil with P. cinnamomi resulted in no significant reduction on fine root dry weight for plants sprayed with phosphite, or treated with a silicate-based mulch. However, when a combination of these two treatments gave no additive effect. In one experiment, a microbial-based conditioner was also beneficial. Phosphite was preferable to metalaxyl as a chemical treatment, as the latter reduced shoot dry weight by 25% and fine root dry weight by 30% of that in non-inoculated plants. Glyphosate treatment of wheat seedlings growing in the pots with the avocados also reduced shoot dry weight (20%) and fine root dry weight (20%) of non-inoculated avocados. These observations need to be confirmed under field conditions.

Phytophthora species are detected from environmental samples through DNA metabar-coding than are isolated by baiting. We investigated whether bulking soil samples and baiting similar to 300 g samples in standard 1 L tubs resulted in the isolation of fewer Phytophthora and Phytophythium species compared with using 15 - 20 g samples of non-bulked soil in individual 200 ml tubs. At each of four sites with dying vegetation, 50 soil samples were collected and baited separately in small tubs, followed by plating of lesioned baits over 7 days. The number of Phytophthora species obtained was compared with those obtained from bulking the 50 samples and baiting subsamples in large tubs. Half of the asymptomatic baits were plated on day 7 and the remaining were assessed for the presence of Phytophthora using metabarcoding. Root samples with rhizosphere soil from the bulked soil in each site were also assessed using metabarcoding. A higher number of Phytophthora species was recovered from each site from baiting small volumes of non-bulked soil than large volumes of bulked soils. Metabarcoding of the asymptomatic baits revealed species not isolated from lesioned baits. More species were detected from the roots using metabarcoding than were isolated from baits. Metabarcoding did not reveal any species from the rhizosphere soil and roots that were not also detected from metabarcoding of the asymptomatic baits and/or plating. The numbers of Phytopythium species detected using the different methods followed the same trend as for Phytophthora. It was concluded that baiting small samples from across a site in separate small tubs results in the isolation of a higher number of Phytophthora species than the standard technique of baiting large samples of bulked soils, and that this, together with metabarcoding of asymptomatic baits, detects the highest total number of species.

Aim: Diversity-rich mediterranean-type sclerophyllous forests are home to 20% of described species on Earth. In the Eucalyptus marginata (jarrah) forest of southwest of Western Australia diversity is being reduced by extensive human use and the introduction of the plant pathogen Phytophthora cinnamomi. This study investigated the influence of P. cinnamomi infestation on the structure, taxonomic and functional diversity, and species composition of the forest.Location: Jarrah forest of southwestern Australia.Methods: Species abundance, understorey cover and canopy cover were assessed along 22, 30 m long transects which crossed infested and non-infested zones in five reserves in the jarrah forest. A trait database was assembled for 137 plants using 13 traits related to nutrient and carbon acquisition, disturbance tolerance and reproduction. The responses of canopy cover, understorey cover, species richness, Shannon diversity, evenness, abundance, and functional diversity for trait groups, and all groups combined were modelled against reserve and zone as fixed effects and transect and transect section as random effects. To assess the species composition, non-metric multidimensional scaling (NMDS) ordination based on Jaccard resemblance and indicator species analyses were used.Results: Significantly higher understorey cover, species richness, Shannon diversity and evenness were recorded in non-infested compared to infested zones, but there were no changes in the canopy cover and overall abundance. In non-infested zones, the functional diversity of nutrient acquisition and reproductive traits was higher, but the functional diversity of carbon acquisition traits was lower. No difference in functional diversity was recorded in disturbance tolerance and overall traits between the two zones. NMDS ordination and analysis of similarities (ANOSIM) revealed a significant difference in the species composition between the two zones, and 11 indicator species significantly associated with infested and non-infested zones were identified.Conclusion: Phytophthora cinnamomi has significantly affected the forest structure, taxonomic and functional diversity, and species composition. Contrasting responses of functional trait groups obscured overall trait responses to P. cinnamomi.