Endophytic Trichoderma spp. can protect strawberry and privet plants from infection by the fungus Armillaria mellea.

Armillaria mellea is an important fungal pathogen worldwide, affecting a large number of hosts in the horticulture and forestry industries. Controlling A. mellea infection is expensive, labour intensive and time-consuming, so a new, environmentally friendly management solution is required. To this effect, endophytic Trichoderma species were studied as a potential protective agent for Armillaria root rot (ARR) in strawberry and privet plants. A collection of forty endophytic Trichoderma isolates were inoculated into strawberry (Fragaria × ananassa) plants and plant growth was monitored for two months, during which time Trichoderma treatment had no apparent effect. Trichoderma-colonised strawberry plants were then inoculated with A. mellea and after three months plants were assessed for A. mellea infection. There was considerable variation in ARR disease levels between plants inoculated with different Trichoderma spp. isolates, but seven isolates reduced ARR below the level of positive controls. These isolates were further tested for protective potential in Trichoderma-colonized privet (Ligustrum vulgare) plants where five Trichoderma spp. isolates, including two highly effective Trichoderma atrobrunneum isolates, were able to significantly reduce levels of disease. This study highlights the potential of plants pre-colonised with T. atrobrunneum for effective protection against A. mellea in two hosts from different plant families.

Susceptibility of Garden Plants to Phytophthora Root Rot.

Phytophthora root rot (PRR) is a serious disease of horticultural, forest, and ornamental plant species caused by species of the oomycete genus Phytophthora. Their wide host range makes the choice of resistant plants in the management of the disease difficult. We used the Royal Horticultural Society diagnostic dataset of PRR records from U.K. gardens to compare the susceptibility of different host genera to the disease. The dataset was compared with existing reports of plants recorded as notably resistant or notably susceptible to PRR. An index-based approach was used to separate 177 genera of woody plants into three categories: 85 were low index (<0.10: rarely affected), 34 were medium index (0.10 to 0.20: sometimes affected) and 58 were high index (>0.20: frequently affected). Similarly, genera of nonwoody plants were separated into: 45 low index (<0.22), 16 medium index (0.22 to 0.44), and 18 high index (>0.44). Taxus was the genus with the highest index, while most genera in the Malvales and Ericales were in the high-index group. Most genera in the Myrtales, Fabales, and Monocotyledons were low index. While 30 Phytophthora species were recorded in our study, the wide host range spp., P. plurivora, P. cryptogea, and P. cinnamomi, represented 63% of identifications. P. plurivora was the most common species on woody plants and P. cryptogea on nonwoody plants. These results provide confidence in the use of host resistance as part of the integrated management of PRR.

Susceptibility of Garden Trees and Shrubs to Armillaria Root Rot.

Armillaria root rot (ARR) is a serious disease of woody plants caused by several species of Armillaria. Armillaria isolates from diagnostic samples received in 2017 were identified by genus- and species-specific PCR and compared with isolates from an earlier survey (2004 to 2007). The results were comparable and, therefore, were combined for further analysis. Three species were identified: Armillaria mellea (83%), A. gallica (15%), and A. ostoyae (2%). Their wide host range makes choice of resistant plants in management of the disease difficult. We used the Royal Horticultural Society diagnostic dataset of ARR records from U.K. gardens to compare the susceptibility of different host genera to the disease. The dataset was compared with an earlier experiment at the University of California. An index-based approach was used to separate genera into three categories: 77 low-index (<0.99), 37 medium-index (0.99 to 1.76), and 56 high-index (>1.76) genera were recorded. All three species were associated with both angiosperms and gymnosperms; moreover, A. ostoyae did not show the host preference for gymnosperms that has been reported elsewhere. A. gallica was particularly common on herbaceous perennials and showed a trend to occur on resistant hosts that may be under other stress, supporting its description as an opportunistic pathogen. Four monocotyledons grown as trees or shrubs in U.K. gardens had a very low ARR index according to indices associated with A. mellea and A. ostoyae. Genera in the order Myrtales were almost always low index, while those in the Saxifragales and Fagales were mostly high index. These results provide confidence in the use of host resistance as part of the integrated management of ARR.

Predicting Take-All Severity in Second-Year Wheat Using Soil DNA Concentrations of Gaeumannomyces graminis var. tritici Determined with qPCR.

The lack of accurate detection of Gaeumannomyces graminis var. tritici inoculum in soil has hampered efforts to predict the risk of severe take-all for wheat growers. The current study used a molecular method to quantify soil G. graminis var. tritici concentrations in commercial wheat fields in New Zealand and to compare them with the proportion of crops surpassing the thresholds for visible and moderate to severe take-all over three growing seasons. The study evaluated a soil G. graminis var. tritici DNA-based take-all prediction system developed in Australia, with four take-all risk categories. These categories were found to be useful for predicting disease severity in second wheat but did not clearly separate risk between fields in medium- and high-risk categories. A sigmoidal relationship was identified between inoculum concentration and the proportion of fields exceeding the two disease thresholds. A logistic response curve was used to further examine this relationship and evaluate the boundaries between take-all risk categories. G. graminis var. tritici boundaries between medium- and high-risk categories were clustered near or within the upper plateau of the relationship. Alternative G. graminis var. tritici boundaries for a three-category system were identified that provided better separation of take-all risk between categories. This information could improve prediction of the risk of severe take-all.

Characterisation of New Zealand Fusarium populations using a polyphasic approach differentiates the F. avenaceum/F. acuminatum/F. tricinctum species complex in cereal and grassland systems.

The purpose of this study was to determine the diversity and prevalence of Fusarium species in a survey of cereal and grassland systems from the South Island of New Zealand by applying morphological and molecular techniques. Isolates were collected from soil, roots, and stems from 21 cereal and grassland sites. Ten Fusarium species were identified using morphological characters, including F. acuminatum, F. avenaceum, F. crookwellense, F. culmorum, F. equiseti, F. oxysporum, F. poae, F. pseudograminearum, F. sambucinum, and F. tricinctum. In general, their distribution was found to be unrelated to biogeographical location, although agricultural practice increased the overall diversity of Fusarium. Phylogenetic analyses were successfully used to identify morphologically similar isolates belonging to the F. avenaceum/F. acuminatum/F. tricinctum species complex and to resolve previously undetermined relationships amongst these species. Fifty-eight isolates classified as either F. avenaceum, F. acuminatum, or other closely related species as well as several well-characterised isolates from international culture collections were examined using DNA sequence data for ß-tubulin (ßTUB), translation elongation factor 1α (EF1α), and mitochondrial small subunit ribosomal RNA (mtSSU). Analyses of DNA sequence data from both ßTUB and EF1α discriminated among isolates of F. avenaceum, F. acuminatum, and F. tricinctum and determined that these three distinct sequence groups formed a single clade. By contrast, mtSSU was unable to differentiate F. avenaceum from F. acuminatum and other closely related species believed to be F. tricinctum. Comparison of the EF1α sequences with the international FUSARIUM-ID database supported the identification of isolates in this study. As in other studies, F. avenaceum was found to be widespread in agricultural and native ecosystems. However, F. acuminatum in New Zealand was found only on non-wheat hosts. The reason for the absence of this wheat pathogen in cereal-based ecosystems in New Zealand remains unknown.

A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex.

We constructed a two-locus database, comprising partial translation elongation factor (EF-1alpha) gene sequences and nearly full-length sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA) for 850 isolates spanning the phylogenetic breadth of the Fusarium oxysporum species complex (FOSC). Of the 850 isolates typed, 101 EF-1alpha, 203 IGS rDNA, and 256 two-locus sequence types (STs) were differentiated. Analysis of the combined dataset suggests that two-thirds of the STs might be associated with a single host plant. This analysis also revealed that the 26 STs associated with human mycoses were genetically diverse, including several which appear to be nosocomial in origin. A congruence analysis, comparing partial EF-1alpha and IGS rDNA bootstrap consensus, identified a significant number of conflicting relationships dispersed throughout the bipartitions, suggesting that some of the IGS rDNA sequences may be non-orthologous. We also evaluated enniatin, fumonisin and moniliformin mycotoxin production in vitro within a phylogenetic framework.

Determination of the anastomosis grouping and virulence of Rhizoctonia spp. associated with potato tubers grown in Lincoln, New Zealand.

A total of 58 isolates of Rhizoctonia spp. (46 R. solani and 12 binucleate Rhizoctonia) were recovered from potato tubers showing black scurf disease symptom during the 2004 growing season in Lincoln, New Zealand. The isolates were assigned to 5 Anastomosis Groups (AG) ofR. solani AG-3 (54.34%), AG-5 (28.26%), AG-8 (8.69%), AG-4 (6.52%) and AG-2-2 IIIB (2.17%) and six anastomosis groups ofbinucleate Rhizoctonia, AG-K (25%), AG-Bi (25%), AG-Ba (8.33%), AG-C (8.33%), AG-D (8.33%) and AG-E (8.33%). Two isolates of BNR did not anastomose with any of the tester strains and remain unidentified. In pathogenicity tests that were carried out on radish, carrot, lettuce, onion, tomato and hemp, it was found that all the isolates of both R. solani and binucleate Rhizoctonia to be virulent at varying degrees to these 6 plants species from different families. In these tests, isolates of AG-3 and AG-8 from R. solani population caused the highest and lowest disease severity on all 6 plant species, respectively. In population of binucleate Rhizoctonia, on the other hand, the highest and lowest disease severities were caused by the isolates of AG-D and AG-Ba on all test plants, respectively. When the results of the pathogenicity tests were examined in terms of the susceptibility levels of the plants, the most resistant plant was tomato against different AGs of R. solani and BNR. On the other hand, radish was the most susceptible plant species tested in this study against both R. solani and BNR isolates.

Fusarium graminearum, F. cortaderiae and F. pseudograminearum in New Zealand: molecular phylogenetic analysis, mycotoxin chemotypes and co-existence of species.

Fusarium graminearum and F. pseudograminearum are important plant pathogens in New Zealand and around the world. Headblight and crown rot diseases of cereals caused by these species are responsible for large economic losses due to reduction in seed quality and contamination of grain with tricothecene mycotoxins. In the current study we have used two different molecular phylogenetic approaches, AFLPs and gene genealogies, to gain insight into the evolutionary relationships between F. graminearum, and F. pseudograminearum in New Zealand. The worldwide genetic diversity of F. graminearum clade is represented by at least eight biogeographically distinct species (previously designated as lineages of F. graminearum). Our analysis demonstrated that this clade is represented by F. graminearum (= F. graminearum Lineage 7) and F. cortaderiae (= F. graminearum Lineage 8) in New Zealand. Through our analysis we also confirm the presence of F. pseudograminearum in New Zealand as a first record for this organism. Information on species is necessary for preventing the inadvertent intercontinental introduction of genetically unique foreign pathogens associated with world trade. The ability to place species information into a worldwide context enabled postulation that the New Zealand representatives of F. graminearum clade originated from at least two regions, and probably on at least two hosts. Correlation of species descriptions with biogeographical and host information revealed evidence for co-localisation of F. graminearum clade species with potential for genetic outcrossing in the field. Mycotoxin analysis showed F. graminearum (= lineage 7) isolates produce either nivalenol (NIV) or deoxnivalenol (DON). In contrast, F. cortaderiae isolates produced only NIV. These findings support earlier observations that mycotoxin production in the F. graminearum clade is not species specific, but suggest maintenance of chemotype diversity through speciation may have been restricted to a subset of species.