Invasive Everywhere? Phylogeographic Analysis of the Globally Distributed Tree Pathogen Lasiodiplodia theobromae

Identity, Pathogenicity, and Genetic Diversity of Lasiodiplodia Species Associated with Stem-End Rot of Avocado in China

Stem-end rot (SER) causes brown necrotic lesions in the pulp near the base of the fruit pedicel and is one of the most devastating postharvest diseases of avocados in all avocado-growing regions of the world. China's avocado industry is growing very rapidly, and the planting area is expanding, but little is known about the pathogens and genetic diversity of avocado SER. To determine the causal agents of SER, avocado fruits were sampled from the main avocado-producing areas in China during 2020 and 2021. Fungal isolates were obtained from SER symptomatic avocado fruits and identified by morphology combined with phylogenetic analysis of internal transcribed spacer (ITS), translation elongation factor 1-α (EF1-α), and β-tubulin (TUB2) gene sequences. All 101 isolates belonged to Lasiodiplodia spp.; four Lasiodiplodia species were identified, namely, L. pseudotheobromae (59.41%), L. theobromae (24.75%), L. mahajangana (7.92%), and L. euphorbiaceicola (1.98%); and six others are classified as Lasiodiplodia sp. (5.94%). There were only slight morphological differences in colonies and conidia of these four species of Lasiodiplodia. The pathogenicity tests showed symptoms of SER, and 92.08% of the isolates exhibited a high level of virulence on avocado (disease index >70), related to the disease severity on avocado fruits. All tested isolates grew well under the temperature ranging from 23 to 33°C. There was a significant difference in mycelial growth between the four species of Lasiodiplodia after treatment with high or low temperatures. The growth of L. pseudotheobromae was the fastest at 13 to 18°C but was the lowest at 38°C (P < 0.05). The red pigment could be produced by all tested isolates after culturing for 7 days at 38°C. The mycelial growth rate was the fastest on PDA medium, and the slowest on the OMA medium but promoted spore formation (P < 0.05). In addition, the genetic diversity of pathogenic Lasiodiplodia species associated with SER collected from avocado, mango, guava, and soursop fruits was determined. A total of 74 isolates were clustered into four main ISSR groups by the unweighted pair-group method with arithmetic mean analysis, and the classification of this group was related to the host. Extensive diversity was detected in the Lasiodiplodia populations. The diverse geographical origins and host species significantly influenced the population differentiation, and most of the genetic variation occurred within populations (P < 0.001). This is the first study to identify the major pathogens of avocado SER in China, survey their occurrence and pathogenicity, and include a comparative analysis of genetic diversity with Lasiodiplodia spp. causing SER on other fruit hosts. Collectively, the Lasiodiplodia species complex affecting avocado showed high pathogenicity and diversity, while L. pseudotheobromae was the most frequently isolated species in China. The results of this study provide insights into the aspects of the epidemic of SER disease caused by Lasiodiplodia species, which will help in developing strategies for the management and control of SER in avocado.

Diversity of Lasiodiplodia Species Associated with Canker and Dieback in Fruit Trees in the Henan and Shandong Provinces of China

Lasiodiplodia is a widely distributed genus that is associated with a variety of diseases in many plant species, especially fruit trees. In this study, a disease survey of fruit trees growing in 12 orchards located in the Henan and Shandong provinces of China was conducted between 2020 and 2022. The symptoms observed included stem canker, branch dieback, and gummosis. Phylogenetic analyses of internal transcribed spacer, tub2, tef1, and rpb2 sequence data combined with morphological characteristics revealed that the 19 isolates collected during the survey belonged to five documented Lasiodiplodia species, namely, Lasiodiplodia citricola, L. chiangraiensis, L. huangyanensis, L. pseudotheobromae, and L. theobromae, and two previously undescribed species, L. xinyangensis and L. ziziphi. In addition, the survey identified three novel host-pathogen interactions: L. chiangraiensis on loquat, L. citricola on apple, and L. huangyanensis on grapevine. Furthermore, the detailed phylogenic analysis indicated that four previously described Lasiodiplodia species were genetically very closely related that they would be better classified as synonyms rather than distinct species, so L. paraphysoides and L. nanpingensis should be considered synonyms of L. citricola, L. fujianensis should be a synonym of L. iraniensis, and L. henanica should be a synonym of L. huangyanensis. Pathogenicity tests confirmed that representative isolates of the two novel species and three new host-pathogen interactions identified in the current study were pathogenic to their original hosts, thereby fulfilling Koch's postulates. Similarly, all of the isolates were found to be pathogenic on four alternative hosts, although a high degree of variation in virulence was observed.

MALDI mass spectrometry-based identification of antifungal molecules from endophytic Bacillus strains with biocontrol potential of Lasiodiplodia theobromae, a grapevine trunk pathogen in Peru

Lasiodiplodia theobromae, a grapevine trunk pathogen, is becoming a significant threat to vineyards worldwide. In Peru, it is responsible for Botryosphaeria dieback in many grapevine-growing areas and it has spread rapidly due to its high transmissibility; hence, control measures are urgent. It is known that some endophytic bacteria are strong inhibitors of phytopathogens because they produce a wide range of antimicrobial molecules. However, studies of antimicrobial features from endophytic bacteria are limited to traditional confrontation methods. In this study, a MALDI mass spectrometry-based approach was performed to identify and characterize the antifungal molecules from Bacillus velezensis M1 and Bacillus amyloliquefaciens M2 grapevine endophytic strains. Solid medium antagonism assays were performed confronting B. velezensis M1 - L. theobromae and B. amyloliquefaciens M2 - L. theobromae for antifungal lipopeptides identification. By a MALDI TOF MS it was possible identify mass spectra for fengycin, iturin and surfactin protoned isoforms. Masses spectrums for mycobacillin and mycosubtilin were also identified. Using MALDI Imaging MS we were able to visualize and relate lipopeptides mass spectra of fengycin (1463.9 m/z) and mycobacillin (1529.6 m/z) in the interaction zone during confrontations. The presence of lipopeptides-synthesis genes was confirmed by PCR. Liquid medium antagonism assays were performed for a proteomic analysis during the confrontation of B. velezensis M1 - L. theobromae. Different peptide sequences corresponding to many antifungal proteins and enzymes were identified by MALDI TOF MS/MS. Oxalate decarboxylase bacisubin and flagellin, reported as antifungal proteins, were identified at 99 % identity through peptide mapping. MALDI mass spectrometry-based identification of antifungal molecules would allow the early selection of endophytic bacteria with antifungal features. This omics tool could lead to measures for prevention of grapevine diseases and other economically important crops in Peru.

Lasiodiplodia iraniensis, a New Causal Agent of Tuber Rot on Yam (Dioscorea Species) Imported into the United States and Implications for Quarantine Decisions

One negative consequence of international trade of agricultural commodities is the inadvertent global spread of crop diseases. Yam (Dioscorea spp.) is a staple food crop in many countries and is traded globally. Most of the commercially traded yams in the United States are imported. In late 2020, samples of yam tubers from a commercial facility were submitted to the plant diagnostic clinic at the UF/IFAS Tropical Research and Education Center in Homestead, Florida. Samples showed rotten symptoms and were drawn from lots that were marked to be destroyed because the source of the rotting symptoms was unknown. Preliminary isolation showed that a fungus was consistently associated with the symptoms and was confirmed in the subsequent pathogenicity test as the causal agent. The fungus grew profusely on potato dextrose agar (PDA) with highly melanized hyphae. Matured conidia showed longitudinal striations. Based on its growth pattern and morphology, it was suspected that this fungus may be in the genus Lasiodiplodia. DNA-based identification using partial sequences of the internal transcribed spacer (ITS), β-tubulin (TUB2), 28S rDNA (LSU), and elongation factor alpha (EF1-α) genes confirmed the identity of the isolates as Lasiodiplodia iraniensis Abdollahz., Zare & A.J.L. Phillips (synonym: L. iranensis). This is the first report of L. iraniensis affecting yam and has implications for international trade. This finding will provide an important foundation for making quarantine decisions to prevent spread of this disease.

First Report of Lasiodiplodia theobromae Causing Dieback Symptoms on Plantain (Musa AAB subgroup) in Nigeria

Bananas (banana and plantains) rank sixth among staple food crops (FAO 2018), with production challenged by biotic factors, mainly fungal diseases that may cause a total loss in some orchards (Jones 2018). In April 2017, dieback symptoms (progressive blackening and necrotic aerial plant parts, leaves, fruits and peduncles) were observed on plantain (Musa AAB subgroup), in Onne, Rivers State, Nigeria (4°42'55.4012″N, 7°10'35.92128″E). Diseased plants (n=112) were either wilted with blackened necrotic areas, or dead (Fig. S1). Nearly 10% of the plants had blackened pseudostems and fruits with slate gray to black internal tissues when sliced (Fig. S1) and black, erumpent pycnidia were observed on diseased fruits. A fungal species was consistently isolated when surface disinfected pieces of diseased samples were cultured on PDA plates. Plates were incubated at 25±2°C for 4 to 15 d to observe conidia. Isolates had colonies and conidia consistent with members of the Botryosphaeriaceae family (Phillips et al. 2013). Immature conidia were single-celled, ellipsoidal and hyaline while mature conidia were two-celled, had a thick wall, a central septum, longitudinal striations, and a dark brown, cinnamon-like color. Size of mature conidia (n = 20) ranged 22.9 to 30.0 × 14.2 to 18.4 μm ( = 27.0 × 15.6 μm; Fig. S1). DNA templates of three isolates (23688-2_R16; 19144-18_R15 and PITA_22-1) were amplified using primers ITS1 and ITS4 for the ITS locus, EF1-688F and EF1-1251R for the translation elongation factor 1-α (TEF-1α) locus (Phillips et al. 2013) and sequenced (GenBank accession Nos. MZ413346, MZ413347, and MZ413348 for ITS; and MZ420177, MZ420178, and MZ420179 for TEF-1α). BLASTn query showed 100% identity with reference sequences of various isolates of Lasiodiplodia theobromae. Based on morphological characters and nucleotide homology, the isolates were identified as L. theobromae (Fig. S1 & S2). To fulfil Koch's postulates, 4-month-old plants of plantain hybrid PITA 24, and mature fruits from three genotypes (PITA 24, plantain cultivar Obino L'ewai) were inoculated with mycelial plugs from the margins of 5-d-old cultures of the three L. theobromae isolates. Pseudostems were drilled with a sterile 5 -mm cork borer, a mycelial plug placed down into the wound, covered with sterilized cotton, and sealed with parafilm. Sterile water was injected every third day to maintain moisture at the inoculated area. Toothpicks containing mycelia were used to inoculate fruits, placed in plastic Crisper boxes. Sterile PDA plugs or toothpicks were used for the controls. Inoculated plants and fruits were kept in a screenhouse at room temperature (~26°C) for 14 d. All inoculated materials developed symptoms similar to the diseased plants in the field. Control plants and fruits remained asymptomatic. L. theobromae was re-isolated from the artificially inoculated plant parts and its identity was confirmed. The fungus L. theobromae is distributed in tropical and subtropical regions and has a wide host range (Phillips et al. 2013; Mehl et al. 2017). This fungus was previously reported in grey literature as the causal agent of Musa spp. basal rot at Onne, Nigeria (Mwangi et al. 2005) but its molecular identification was not conducted; it was unknown whether the isolates were indeed L. theobromae or other cryptic species (L. pseudotheobromae or L. parva) (Alves et al. 2008). Over 15 years later, the present study confirms L. theobromae as the causal agent of basal rot of bananas based on nucleotide homology, and to our knowledge, this is the first report of L. theobromae causing dieback disease on plantain in Nigeria and in Africa. There is need to conduct a more comprehensive distribution surveys and develop appropriate control strategies in Nigeria.

Lasiodiplodia theobromae as a causal pathogen of leaf blight, stem canker, and pod rot of Theobroma cacao in Malaysia

Symptoms of leaf blight, stem canker, and pod rot were observed on T. cacao during a series of samplings conducted in several states of Malaysia from September 2018 to March 2019. The identity of the pathogen that was responsible for the diseases was determined using morphological characteristics, DNA sequences, and phylogenetic analyses of multiple genes, namely, internal transcribed spacer (ITS), elongation translation factor 1-alpha (tef1-α), β-tubulin (tub2), and RNA polymerase subunit II (rpb2). A total of 57 isolates recovered from diseased leaves of T. cacao (13 isolates), stems (20 isolates), and pods (24 isolates) showed morphological features that resembled Lasiodiplodia sp. The identity of the isolates was further determined up to the species level by comparing DNA sequences and phylogenetic analyses of multiple genes. The phylogenetic analysis of the combined dataset of ITS, tef1-α, tub2, and rpb2 elucidated that all of the isolates obtained were Lasiodiplodia theobromae as supported by 97% bootstrap value. The results of pathogenicity tests revealed L. theobromae as the causal pathogen of leaf blight, stem canker, and pod rot of T. cacao.

Diversity of Endophytes in the Botryosphaeriaceae Differs on Anacardiaceae in Disturbed and Undisturbed Ecosystems in South Africa

Botryosphaeriaceae represents a diverse family of fungi with a cosmopolitan distribution and a wide host range. We studied species diversity and overlap of Botryosphaeriaceae on selected tree species of Anacardiaceae in disturbed (farming or forestry) and undisturbed (isolated and/or protected) ecosystems in the Limpopo and Mpumalanga provinces, South Africa. The disturbed sites resided at Tshikundamalema and Tshipise in Limpopo and the undisturbed sites at Nwanedi and the Mapungubwe National Park in Limpopo and the Kruger National Park in Mpumalanga. Asymptomatic branches were collected from Mangifera indica, Sclerocarya birrea and Lannea schweinfurthii trees in 2017 and 2018. Eleven species were identified using a multi-gene sequencing approach, including Diplodia allocellula, Dothiorella brevicollis, Do. dulcispinae, Do. viticola, Lasiodiplodia crassispora, L. exigua, L. gonubiensis, L. mahajangana, Neofusicoccum parvum, Oblongocollomyces sp. 1 and Oblongocollomyces sp. 2. Ten of the 11 species were identified in undisturbed ecosystems (eight species being unique), while only three species were identified in disturbed ecosystems (one species being unique). Two species were generalists on trees in disturbed and undisturbed ecosystems. Lasiodiplodia mahajangana was the most dominant species as it occurred on the three tree species of Anacardiaceae. Isolates of N. parvum occurred on both S. birrea (a native species) and M. indica (a non-native species) that occurred adjacent to each other in disturbed ecosystems, confirming the ability of this invasive pathogen to cross-infect native and non-native hosts and its abundance in human-disturbed environments. The findings from this study confirm the lack of host specificity for most species of Botryosphaeriaceae. The results also indicate that disturbance through human activity, such as clear-cutting, selective cutting and land-use changes, negatively influences the diversity of the Botryosphaeriaceae.

Photodynamic inactivation of Lasiodiplodia theobromae: lighting the way towards an environmentally friendly phytosanitary treatment

The fungus Lasiodiplodia theobromae is one of the main causal agents of trunk canker and dieback of grapevine. The objective of this work was to evaluate the efficiency of photodynamic inactivation (PDI) of L. theobromae with synthetic and natural photosensitizers and irradiation with either sunlight or artificial photosynthetically active radiation. Although the growth of the mycelium could not be completely prevented with natural sunlight irradiation, phenothiazine dyes (methylene blue, MB; toluidine blue O, TBO), riboflavin and a cationic porphyrin (Tetra-Py⁺-Me) caused complete inhibition under continuous irradiation with artificial light. Free radicals were the main cytotoxic agents in the PDI with MB, indicating the predominance of the type I mechanism. PDI with MB or Tetra-Py⁺-Me may represent a promising approach for the sanitation of vine material in greenhouse nurseries, in order to reduce the risk of infection upon grafting.

What Do We Know about Botryosphaeriaceae? An Overview of a Worldwide Cured Dataset

Botryosphaeriaceae-related diseases occur worldwide in a wide variety of plant hosts. The number of studies targeting the distribution, diversity, ecology, and pathogenicity of Botryosphaeriaceae species are consistently increasing. However, with the lack of consistency in species delimitation, the name of hosts, and the locations of studies, it is almost impossible to quantify the presence of these species worldwide, or the number of different host–fungus interactions that occur. In this review, we collected and organized Botryosphaeriaceae occurrences in a single cured dataset, allowing us to obtain for the first time a complete perspective on species’ global diversity, dispersion, host association, ecological niches, pathogenicity, communication efficiency of new occurrences, and new host–fungus associations. This dataset is freely available through an interactive and online application. The current release (version 1.0) contains 14,405 cured isolates and 2989 literature references of 12,121 different host–fungus interactions with 1692 different plant species from 149 countries.

Tree health in South Africa: Retrospect and prospect

South Africa is a country with very limited natural forest cover. Consequently, the timber and fibre needs of the country cannot be provided for from indigenous forest. It is largely for this reason that South Africa initially developed a highly productive plantation forest industry, which today makes a substantial contribution to the local economy. These plantations are based on non-native species of Eucalyptus, Pinus and Australian Acacia. In the early years of establishment, South African plantations were relatively free of pest and pathogen problems. But, over time, an increasing number of insects, fungi and bacteria have emerged as serious threats to the sustainability of the forestry industry. Numerous native pests and pathogens, especially insects, have adapted to these introduced tree species to cause damage or disease. The problem is compounded by the accidental introduction of non-native pests and pathogens, and this has been at a rapidly increasing rate over the past three decades. Some of these introduced pests and pathogens also threaten the fitness and even the survival of many indigenous South African tree species. Fortunately, South Africa has developed an impressive knowledge base and range of integrated management options to deal with these problems. This development was first driven by government programmes, and in more recent years by public–private partnerships between industry, universities and government. It is clear from the pattern of emergence of pests and pathogens in recent years that South Africa will deal with an increasing number of these problems and a continuously changing tree health environment. This requires robust investment in both quarantine and mitigation mechanisms to protect the country’s biodiversity as well as to ensure the sustainability of its wood and fibre industries.

Variation in Botryosphaeriaceae from Eucalyptus plantations in YunNan Province in southwestern China across a climatic gradient

The Botryosphaeriaceae accommodates many important pathogens of woody plants, including Eucalyptus. Recently, Botryosphaeriaceae were isolated from diseased plant parts from surveys of Eucalyptus plantations in the YunNan Province, China. The aims of this study were to identify these Botryosphaeriaceae isolates and to evaluate their pathogenicity to Eucalyptus. A total of 166 isolates of Botryosphaeriaceae were obtained from six regions in the YunNan Province, of which 76 were from Eucalyptus urophylla × E. grandis hybrids, 49 from E. globulus trees, and 41 isolates were from other unknown Eucalyptus species or hybrids. Isolates were identified by comparing DNA sequences of the internal transcribed spacer ribosomal RNA locus (ITS), partial translation elongation factor 1-alpha (tef1), β-tubulin 2 (tub2) and DNA-directed RNA polymerase II subunit (rpb2) genes, and combined with their morphological characteristics. Eleven species were identified, including Botryosphaeria fusispora, B. wangensis, Lasiodiplodia pseudotheobromae, Neofusicoccum kwambonambiense, N. parvum, and six novel species described as B. puerensis, N. dianense, N. magniconidium, N. ningerense, N. parviconidium and N. yunnanense. The dominant species across the regions were N. yunnanense, N. parvum and B. wangensis, representing 31.3, 25.3 and 19.9% of the total isolates, respectively. Species diversity and composition changed across the different climatic zones, despite their relatively close geographic proximity and the fact that some of the species have a global distribution. All the Botryosphaeriaceae species were pathogenic to one-year-old plants of an E. urophylla × E. grandis clone and E. globulus seed-derived plants, but showed significant inter- and intra-species variation in aggressiveness amongst isolates. The study provides a foundation for monitoring and management of Botryosphaeriaceae through selection and breeding of Eucalyptus in the YunNan Province of southwestern China.

Secondary Metabolites of Lasiodiplodia theobromae: Distribution, Chemical Diversity, Bioactivity, and Implications of Their Occurrence

Lasiodiplodia theobromae is a plant pathogenic fungus from the family Botryosphaeriaceae that is commonly found in tropical and subtropical regions. It has been associated with many hosts, causing diverse diseases and being responsible for serious damages on economically important crops. A diverse array of bioactive low molecular weight compounds has been described as being produced by L. theobromae cultures. In this review, the existing literature on secondary metabolites of L. theobromae, their bioactivity, and the implications of their occurrence are compiled. Moreover, the effects of abiotic factors (e.g., temperature, nutrient availability) on secondary metabolites production are highlighted, and possible avenues for future research are presented. Currently, a total of 134 chemically defined compounds belonging to the classes of secondary metabolites and fatty acids have been reported from over 30 L. theobromae isolates. Compounds reported include cyclohexenes and cyclohexenones, indoles, jasmonates, lactones, melleins, phenols, and others. Most of the existing bioactivity studies of L. theobromae metabolites have assessed their potential phytotoxic, cytotoxic, and antimicrobial activities. In fact, its host adaptability and its ability to cause diseases in plants as well as in humans may be related to the capacity to produce bioactive compounds directly involved in host–fungus interactions.

Characterization and Pathogenicity of Botryosphaeriaceae Species Obtained from Avocado Trees with Branch Canker and Dieback and from Avocado Fruit with Stem End Rot in Chile

Several species of the Botryosphaeriaceae family have been associated with branch canker, dieback, and stem end rot in avocado (Persea americana Mill.). In Chile, the incidence of diseases affecting the avocado tree increased from 2011 to 2016, which coincided with a severe drought that affected avocado production. Moreover, distant countries importing avocados from Chile also reported an increase of stem end rot of ripe avocados. Therefore, the aims of this study were to identify the pathogen species associated with branch canker, dieback, and stem end rot of avocado in Chile and to study their pathogenicity. This study was conducted between 2015 and 2016 in 'Hass' avocado orchards located in the main avocado-producing regions in Chile. A diverse collection of fungal species was recovered from both necrotic woody tissue and necrotic tissue on harvested ripe fruit. On the basis of morphology and phylogenetic analyses of the internal transcribed spacer region (ITS1-5.8S-ITS2) and the translation elongation factor 1-α (TEF1-α) gene, eight species in the Botryosphaeriaceae family were identified: Diplodia mutila, D. pseudoseriata, D. seriata, Dothiorella iberica, Lasiodiplodia theobromae, Neofusicoccum australe, N. nonquaesitum, and N. parvum. For each of these species, pathogenicity studies were conducted on 1-year-old healthy Hass avocado plants. All isolates produced brown gum exudate and caused necrosis in the vascular system 3 weeks after inoculation. N. nonquaesitum, N. parvum, and D. pseudoseriata were the most virulent species. Necrotic lesions and cavities with white mycelia near the peduncle union were observed on Hass avocado fruit inoculated postharvest. L. theobromae, N. australe, and N. parvum were significantly more virulent than the other tested species in the Botryosphaeriaceae family. This study identified and characterized the pathogenicity of Botryosphaeriaceae species in Chile, which will prove useful to future research on these pathogens directed at establishing effective control strategies in avocado.

Ophiostoma quercus: An unusually diverse and globally widespread tree-infecting fungus

Ophiostoma quercus (Ascomycota, Ophiostomatales) is a globally widespread, insect-vectored fungus that colonizes a wide diversity of hardwood and conifer hosts. Although the fungus is considered to be non-pathogenic, it is closely related to the fungi that cause Dutch elm disease. We examined the global diversity of O. quercus based on a ribosomal RNA marker and three unlinked gene regions. The fungus exhibited substantial morphological diversity. In addition, O. quercus had high genetic diversity in every continent from which it was collected, although the fungus was most diverse in Eurasia. There was no evidence of geographical clustering of haplotypes based on phylogenetic and network analyses. In addition, the phylogenetic trees generated based on the different markers were non-congruent. These results suggest that O. quercus has been repeatedly moved around the globe, because of trade in wood products, and that the fungal species most likely outcrosses regularly. The high genetic diversity of the fungus, as well as its ability to utilize a wide variety of arthropod vectors and colonize a tremendous diversity of tree host species makes O. quercus truly unique among ophiostomatoid fungi.