Taxonomy and biodiversity of plant pathogenic fungi from Australia

TY - THES

T1 - Taxonomy and biodiversity of plant pathogenic fungi from Australia

AU - Tan, Yu Pei

PY - 2019/5/9

Y1 - 2019/5/9

N2 - Chapter one provides an insight into the multilayered Australian biosecurity system. One of the layers of biosecurity activity is the ability to successfully diagnose unwanted and threatening plant diseases. As such it relies heavily on knowing what pathogens are already present and established in Australia. Much of what is present in Australia has yet to be resolved in light of new molecular methods, particularly of important plant pathogenic fungal genera. The research presented in thesis examines the taxonomy and biodiversity of some important plant pathogenic fungi in the Queensland Plant Pathology Herbarium, which holds Australia’s largest collection of fungal cultures. In Chapter two of this thesis, six isolates identified as Diaporthe sp. (syn. Phomopsis sp.) from the Queensland Plant Pathology Herbarium and the Victorian Plant Pathology Herbarium were examined. The multilocus (ITS, tef1α and tub2) phylogenetic analysis revealed each of these six isolates represented a unique taxon. Diaporthe beilharziae, D. fraxini-angustifoliae and D. litchicola, were described on the basis of morphological and molecular characteristics. The other three species, D. nothofagi, D. pascoei, and D. salicicola, were sterile under the conditions that they were grown and did not produce any fruiting structures. Voucher specimens from the original collections displayed pycnidia and conidia that allowed the completion of morphological descriptions. Strong phylogenetic evidence based on multilocus sequence analyses supported the description and establishment of D. nothofagi as a unique taxon, despite the absence of morphological characteristics. In Chapter three of this thesis, 45 isolates representing 34 species of Bipolaris and Curvularia maintained in the Queensland Plant Pathology Herbarium and the Westerdijk Fungal Biodiversity Centre were examined. The multilocus (ITS, gapdh, LSU, and tef1α) phylogenetic analysis validated the generic placement of 12 Bipolaris species, namely B. chloridis, B. clavata, B. coffeana, B. crotonis, B. gossypina, B. heliconiae, B. luttrellii, B. panici-milacei, B. pluriseptata, B. salvinae, B. secalis and B. zeae. The phylogenetic analysis also showed B. eleusines sensu Alcorn and R.G. Shivas as a synonym of B. crotonis, and verified Dr. John L. Alcorn’s synonymy of B. melinidis and Drechslera curvispora with B. salviniae. Eight species of Curvularia were validated and supported by multilocus sequence analysis of ex-type cultures, namely C. akaiiensis, C. bannonii, C. bothriochloae, C. harveyi, C. heteropogonicola, C. papendorfii, C. richardiae and C. sorghina. Nine Bipolaris species were transferred to Curvularia, namely C. australis, C. crustacea, C. dactyloctenii, C. homomorpha, C. neergaardii, C. nicotiae, C. portulacae, C. ryleyi and C. tropicalis. To fix the application of the names, lectotypes were designated for B. secalis and C. richardiae, and an epitype was designated for C. crustacea. The phylogenetic tree showed that B. aberrans did not belong to either Bipolaris or Curvularia. Therefore, a monotypic genus Johnalcornia, was introduced to accommodate it. In Chapter four of this thesis, 13 unidentified Bipolaris isolates from the Queensland Plant Pathology Herbarium were examined. These isolates, which were recognised by Dr. Alcorn as taxonomically interesting and potentially distinct, were analysed against sequences of ex-type or reference cultures available from currently accepted Bipolaris species based on three loci, ITS, gapdh and tef1α. The phylogenetic analyses of the combined three locus dataset resolved the 13 BRIP isolates into eight novel Bipolaris species. The eight Bipolaris species were all associated with grasses as hosts. Four of the species, B. austrostipae, B. simmondsii, B. sivanesaniana and B. woodii, were described from native Australian grasses, while the other four, B. axonopicola, B. bamagaensis, B. shoemakeri and B. subramanianii, were described 161 from introduced grass hosts. The description of these species provides a foundation upon which additional sampling and accumulation of molecular data will improve knowledge of their host ranges and ecological roles. In Chapter five of this thesis, 17 unidentified Curvularia isolates from the Queensland Plant Pathology Herbarium were examined. These isolates were analysed against sequences of ex-type or reference cultures available from currently accepted Curvularia species based on three loci, ITS, gapdh and tef1α. The phylogenetic analyses of the combined three-locus-dataset resolved the 17 isolates into 13 novel Curvularia species. Eight species were described from grasses exotic to Australia, namely C. beasleyi on Chloris gayana, C. beerburrumensis on Eragrostis bahiensis, C. eragrosticola on E. pilosa, C. kenpeggii on Triticum aestivum, C. mebaldsii on Cynodon dactylon × transvaalensis, C. petersonii and C. warraberensis on Dactyloctenium aegyptium and C. platzii on Cenchrus clandestinus. Only two species were described from native Australian grasses, C. lamingtonensis on Microlaena stipoides and C. sporobolicola on Sporobolus australasicus. Two species were described from other hosts, C. coatesiae from Litchi chinensis (Sapindaceae) and C. colbranii from Crinum zeylanicum (Amaryllidaceae). One species, C. reesii, was described from an isolate obtained from an air sample. Furthermore, the phylogenetic analysis of the ex-type culture of Drechslera boeremae supported the transfer to Curvularia as a unique taxon, and rejects previous synonymy with B. indica based on morphology. In Chapter six of this thesis, 51 isolates identified as Botryosphaeriaceae preserved in the Queensland Plant Pathology Herbarium and the Victorian Plant Pathology Herbarium were examined. The 51 isolates were collected between 1971 and 2017, from 35 different host genera, with the dominant host genera being Mangifera (11 isolates), Acacia (10), and Persea (5). Multilocus sequence analyses re-identification 41 isolates into the genera Botryosphaeria (2 isolates), Diplodia (4), Dothiorella (1), Lasiodiplodia (19), and Neofusicoccum (15). Ten isolates that had been identified as Botryosphaeria, Diplodia and Fusicoccum were identified as not belonging to Botryosphaeriaceae, which illustrated the difficultures faced by plant pathologists and plant diagnosticians even at the generic level. Five species are reported for the first time in Australia, namely Botryosphaeria sinensis, Diplodia alatafructa, Lasiodiplodia gonubiensis, Neofusicoccum cryptoaustrale, and N. mangroviorum. New plant host associations are reported for 14 species, namely B. sinensis, D. africana, D. alatafructa, D. seriata, L. brasiliensis, L. gonubiensis, L. iraniensis, L. mahajangana, N. australe, N. cryptoaustrale, N. mangroviorum, N. occulatum, N. parvum and N. vitifusiforme. Furthermore, the multilocus phylogenetic tree revealed a distinct taxon in each of the genera Botryosphaeria, Dothiorella and Lasiodiplodia. These isolates remained undescribed as further DNA sequences were required to support their introduction as novel species. The results of this study provide fundamental information regarding the diversity of Botryosphaeriaceae species present in Australia.

AB - Chapter one provides an insight into the multilayered Australian biosecurity system. One of the layers of biosecurity activity is the ability to successfully diagnose unwanted and threatening plant diseases. As such it relies heavily on knowing what pathogens are already present and established in Australia. Much of what is present in Australia has yet to be resolved in light of new molecular methods, particularly of important plant pathogenic fungal genera. The research presented in thesis examines the taxonomy and biodiversity of some important plant pathogenic fungi in the Queensland Plant Pathology Herbarium, which holds Australia’s largest collection of fungal cultures. In Chapter two of this thesis, six isolates identified as Diaporthe sp. (syn. Phomopsis sp.) from the Queensland Plant Pathology Herbarium and the Victorian Plant Pathology Herbarium were examined. The multilocus (ITS, tef1α and tub2) phylogenetic analysis revealed each of these six isolates represented a unique taxon. Diaporthe beilharziae, D. fraxini-angustifoliae and D. litchicola, were described on the basis of morphological and molecular characteristics. The other three species, D. nothofagi, D. pascoei, and D. salicicola, were sterile under the conditions that they were grown and did not produce any fruiting structures. Voucher specimens from the original collections displayed pycnidia and conidia that allowed the completion of morphological descriptions. Strong phylogenetic evidence based on multilocus sequence analyses supported the description and establishment of D. nothofagi as a unique taxon, despite the absence of morphological characteristics. In Chapter three of this thesis, 45 isolates representing 34 species of Bipolaris and Curvularia maintained in the Queensland Plant Pathology Herbarium and the Westerdijk Fungal Biodiversity Centre were examined. The multilocus (ITS, gapdh, LSU, and tef1α) phylogenetic analysis validated the generic placement of 12 Bipolaris species, namely B. chloridis, B. clavata, B. coffeana, B. crotonis, B. gossypina, B. heliconiae, B. luttrellii, B. panici-milacei, B. pluriseptata, B. salvinae, B. secalis and B. zeae. The phylogenetic analysis also showed B. eleusines sensu Alcorn and R.G. Shivas as a synonym of B. crotonis, and verified Dr. John L. Alcorn’s synonymy of B. melinidis and Drechslera curvispora with B. salviniae. Eight species of Curvularia were validated and supported by multilocus sequence analysis of ex-type cultures, namely C. akaiiensis, C. bannonii, C. bothriochloae, C. harveyi, C. heteropogonicola, C. papendorfii, C. richardiae and C. sorghina. Nine Bipolaris species were transferred to Curvularia, namely C. australis, C. crustacea, C. dactyloctenii, C. homomorpha, C. neergaardii, C. nicotiae, C. portulacae, C. ryleyi and C. tropicalis. To fix the application of the names, lectotypes were designated for B. secalis and C. richardiae, and an epitype was designated for C. crustacea. The phylogenetic tree showed that B. aberrans did not belong to either Bipolaris or Curvularia. Therefore, a monotypic genus Johnalcornia, was introduced to accommodate it. In Chapter four of this thesis, 13 unidentified Bipolaris isolates from the Queensland Plant Pathology Herbarium were examined. These isolates, which were recognised by Dr. Alcorn as taxonomically interesting and potentially distinct, were analysed against sequences of ex-type or reference cultures available from currently accepted Bipolaris species based on three loci, ITS, gapdh and tef1α. The phylogenetic analyses of the combined three locus dataset resolved the 13 BRIP isolates into eight novel Bipolaris species. The eight Bipolaris species were all associated with grasses as hosts. Four of the species, B. austrostipae, B. simmondsii, B. sivanesaniana and B. woodii, were described from native Australian grasses, while the other four, B. axonopicola, B. bamagaensis, B. shoemakeri and B. subramanianii, were described 161 from introduced grass hosts. The description of these species provides a foundation upon which additional sampling and accumulation of molecular data will improve knowledge of their host ranges and ecological roles. In Chapter five of this thesis, 17 unidentified Curvularia isolates from the Queensland Plant Pathology Herbarium were examined. These isolates were analysed against sequences of ex-type or reference cultures available from currently accepted Curvularia species based on three loci, ITS, gapdh and tef1α. The phylogenetic analyses of the combined three-locus-dataset resolved the 17 isolates into 13 novel Curvularia species. Eight species were described from grasses exotic to Australia, namely C. beasleyi on Chloris gayana, C. beerburrumensis on Eragrostis bahiensis, C. eragrosticola on E. pilosa, C. kenpeggii on Triticum aestivum, C. mebaldsii on Cynodon dactylon × transvaalensis, C. petersonii and C. warraberensis on Dactyloctenium aegyptium and C. platzii on Cenchrus clandestinus. Only two species were described from native Australian grasses, C. lamingtonensis on Microlaena stipoides and C. sporobolicola on Sporobolus australasicus. Two species were described from other hosts, C. coatesiae from Litchi chinensis (Sapindaceae) and C. colbranii from Crinum zeylanicum (Amaryllidaceae). One species, C. reesii, was described from an isolate obtained from an air sample. Furthermore, the phylogenetic analysis of the ex-type culture of Drechslera boeremae supported the transfer to Curvularia as a unique taxon, and rejects previous synonymy with B. indica based on morphology. In Chapter six of this thesis, 51 isolates identified as Botryosphaeriaceae preserved in the Queensland Plant Pathology Herbarium and the Victorian Plant Pathology Herbarium were examined. The 51 isolates were collected between 1971 and 2017, from 35 different host genera, with the dominant host genera being Mangifera (11 isolates), Acacia (10), and Persea (5). Multilocus sequence analyses re-identification 41 isolates into the genera Botryosphaeria (2 isolates), Diplodia (4), Dothiorella (1), Lasiodiplodia (19), and Neofusicoccum (15). Ten isolates that had been identified as Botryosphaeria, Diplodia and Fusicoccum were identified as not belonging to Botryosphaeriaceae, which illustrated the difficultures faced by plant pathologists and plant diagnosticians even at the generic level. Five species are reported for the first time in Australia, namely Botryosphaeria sinensis, Diplodia alatafructa, Lasiodiplodia gonubiensis, Neofusicoccum cryptoaustrale, and N. mangroviorum. New plant host associations are reported for 14 species, namely B. sinensis, D. africana, D. alatafructa, D. seriata, L. brasiliensis, L. gonubiensis, L. iraniensis, L. mahajangana, N. australe, N. cryptoaustrale, N. mangroviorum, N. occulatum, N. parvum and N. vitifusiforme. Furthermore, the multilocus phylogenetic tree revealed a distinct taxon in each of the genera Botryosphaeria, Dothiorella and Lasiodiplodia. These isolates remained undescribed as further DNA sequences were required to support their introduction as novel species. The results of this study provide fundamental information regarding the diversity of Botryosphaeriaceae species present in Australia.

KW - biosecurity

KW - phylogenetics

KW - novel species

KW - diagnostics

M3 - PhD thesis

SN - 978-90-393-7126-8

ER -