Lasiodiplodia mitidjana sp. nov. and other Botryosphaeriaceae species causing branch canker and dieback of Citrus sinensis in Algeria

Discovery and characterization of a novel pathogen Erwinia pyri sp. nov. associated with pear dieback: taxonomic insights and genomic analysis

In 2022, a novel disease similar to pear fire blight was found in a pear orchard in Zhangye City, Gansu Province, China. The disease mainly damages the branches, leaves, and fruits of the plant. To identify the pathogen, tissue isolation and pathogenicity testing (inoculating the potential pathogen on healthy plant tissues) were conducted. Furthermore, a comprehensive analysis encompassing the pathogen's morphological, physiological, and biochemical characteristics and whole-genome sequencing was conducted. The results showed that among the eight isolates, the symptoms on the detached leaves and fruits inoculated with isolate DE2 were identical to those observed in the field. Verifying Koch's postulates confirmed that DE2 was the pathogenic bacterium that causes the disease. Based on a 16S rRNA phylogenetic tree, isolate DE2 belongs to the genus Erwinia. Biolog and API 20E results also indicated that isolate DE2 is an undescribed species of Erwinia. Isolate DE2 was negative for oxidase. Subsequently, the complete genome sequence of isolate DE2 was determined and compared to the complete genome sequences of 29 other Erwinia species based on digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses. The ANI and dDDH values between strain DE2 and Erwinia species were both below the species thresholds (ANI < 95-96%, dDDH<70%), suggesting that isolate DE2 is a new species of Erwinia. We will temporarily name strain DE2 as Erwinia pyri sp. nov. There were 548 predicted virulence factors in the genome of strain DE2, comprising 534 on the chromosome and 5 in the plasmids. The whole genome sequence of strain DE2 has been submitted to the NCBI database (ASM3075845v1) with accession number GCA_030758455.1. The strain DE2 has been preserved at the China Center for Type Culture Collection (CCTCC) under the deposit number CCTCC AB 2024080. This study represents the initial report of a potentially new bacterial species in the genus Erwinia that causes a novel pear dieback disease. The findings provide a valuable strain resource for the study of the genus Erwinia and establish a robust theoretical foundation for the prevention and control of emerging pear dieback diseases.

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.

Mitidjospirone, a new spirodioxynaphthalene and GC-MS screening of secondary metabolites produced by strains of Lasiodiplodia mitidjana associated to Citrus sinensis dieback

Mitidjospirone, a new spiridioxynaphthalene, was isolated from the mycelial extract of a strain of Lasiodiplodia mitidjana, a recently described species belonging to the family Botryosphaeriaceae. Its structure was elucidated by extensive spectroscopic analysis and the absolute configuration was determined by electronic circular dichroism (ECD) experiment. Furthermore, several known compounds were identified during the screening of secondary metabolites produced by four strains of L. mitidjana.

Diversity among Lasiodiplodia Species Causing Dieback, Root Rot and Leaf Spot on Fruit Trees in Egypt, and a Description of Lasiodiplodia newvalleyensis sp. nov

Lasiodiplodia (family Botryosphaeriaceae) is a widely distributed fungal genus that causes a variety of diseases in tropical and subtropical regions. During 2020−2021, a routine survey of fruit tree plants was conducted in five Egyptian Governorates, and fresh samples exhibiting dieback, decline, leaf spot and root rot symptoms were collected. Collection from eight different symptomatic leaves, twigs, branches and roots of fruit trees yielded 18 Lasiodiplodia-like isolates. The sequencing data from the internal transcribed spacer region (ITS), partial translation elongation factor 1-alpha (tef1-a) and β-tubulin (tub2) were used to infer phylogenetic relationships with known Lasiodiplodia species. Two isolates obtained from black necrotic lesions on Phoenix dactylifera leaves were identified as a putative novel species, L. newvalleyensis sp. nov., and were thus subjected to further morphological characterization. The results of isolation and molecular characterization revealed that L. theobromae (n = 9) was the most common species on Mangifera indica, Citrus reticulata, C. sinensis, Ficus carica, Prunus persica, Prunus armeniaca and Pyrus communis trees. Lasiodiplodia pseudotheobromae (n = 5) was isolated from M. indica, Prunus persica and C. sinensis. Lasiodiplodia laeliocattleyae (n = 2) was isolated from C. reticulata. Pathogenicity test results suggested that all Lasiodiplodia species were pathogenic to their hosts. The present study is considered the first to characterize and decipher the diversity of Lasiodiplodia species associated with fruit trees in Egypt, using the multi-locus ITS, tef1-a and tub2 sequence data, along with morphological and pathogenic trials. To our knowledge, this is the first report of L. newvalleyensis on Phoenix dactylifera and L. laeliocattleya on C. reticulata in Egypt and worldwide.

Pathogenicity Factors of Botryosphaeriaceae Associated with Grapevine Trunk Diseases: New Developments on Their Action on Grapevine Defense Responses

Botryosphaeriaceae are a family of fungi associated with the decay of a large number of woody plants with economic importance and causing particularly great losses in viticulture due to grapevine trunk diseases. In recent years, major advances in the knowledge of the pathogenicity factors of these pathogens have been made possible by the development of next-generation sequencing. This review highlights the knowledge gained on genes encoding small secreted proteins such as effectors, carbohydrate-associated enzymes, transporters and genes associated with secondary metabolism, their representativeness within the Botryosphaeriaceae family and their expression during grapevine infection. These pathogenicity factors are particularly expressed during host-pathogen interactions, facilitating fungal development and nutrition, wood colonization, as well as manipulating defense pathways and inducing impacts at the cellular level and phytotoxicity. This work highlights the need for further research to continue the effort to elucidate the pathogenicity mechanisms of this family of fungi infecting grapevine in order to improve the development of control methods and varietal resistance and to reduce the development and the effects of the disease on grapevine harvest quality and yield.

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.

Fungal canker agents in apple production hubs of Iran

To identify apple canker casual agents and evaluate their pathogenicity and virulence in apple production hubs including West Azarbaijan, Isfahan and Tehran provinces; samples were collected from symptomatic apple trees. Pathogenic isolates on the detached branches were identified as Cytospora cincta, Diplodia bulgarica, Neoscytalidium dimidiatum and Eutypa cf. lata. E. cf. lata was reported as a potential apple canker causal agent in Iran for the first time based on the pathogenicity test on the detached branches, whereas it caused no canker symptoms in apple trees until 6 months after inoculation. Currently, E. cf. lata seems to be adapted to a single city. C. cincta, D. bulgarica and N. dimidiatum caused canker symptoms in apple trees. “C. cincta” and also “C. cincta and N. dimidiatum” were the most widespread and aggressive apple canker species, respectively, associated with apple canker in Iran. Therefore, they are considered to be the main threat to apple production in Iran and should be carefully monitored. Disease progress curve, area under the disease progress curve and optimum temperatures were determined for mentioned species. It is concluded that the establishment of each species occurs in appropriate areas and times in terms of the optimum temperature for their growth.

https://botryosphaeriales.org/, an online platform for up-to-date classification and account of taxa of Botryosphaeriales

Fungi are eukaryotes that inhabit various ecosystems worldwide and have a decomposing effect that other organisms cannot replace. Fungi are divided into two main groups depending on how their sexual spores are formed, viz. Ascomycota and Basidiomycota. The members of Botryosphaeriales (Dothideomycetes, Ascomycota) are ubiquitous. They are pathogenic on a wide range of hosts, causing diverse diseases including dieback, canker, leaf spots and root rots and are also reported as saprobes and endophytes worldwide. As an important fungal group, of which most are plant pathogens, it is necessary to organize data and information on Botryosphaeriales so that scientific literature can be used effectively. For this purpose, a new website, https://botryosphaeriales.org is established to gather all published data together with updates on the present taxonomy of Botryosphaeriales. The website consists of an easy-to-operate searching system and provides an up-to-date classification together with accounts of Botryosphaeriales taxa, including colour illustrations, descriptions, notes and numbers of species in each genus, as well as their classification. Thus, readers will be able to obtain information on botryosphaerialean taxa through this platform. Database URL: https://botryosphaeriales.org/.

Occurrence and infective potential of Colletotrichum gloeosporioides isolates associated to Citrus limon var Eureka

•

37 fungi from damaged tissues of Italian lemon were obtained.

•

D1/D2, ITS1-5.8S-ITS2 and COX1 phylogenetic trees allow identify ten fungi genera.

•

Colletotrichum isolates were characterized by species-specific PCR, rep-PCR and multilocus analysis.

•

Colletotrichum isolates had leaves´s infection percentages between 17 to 67%.

•

This the first report of C. gloeosporioides on Italian lemon in Mexico.

A collection of 37 fungi associated to Italian lemon plants with disease symptoms, was obtained. Ten genera including Aspergillus, Alternaria, Nigrospora, Lasiodiplodia, Dothideomycetes, Pleurostoma, Setosphaeria, Penicillium, Fusarium and Colletotrichum were identified by using ITS1–5.8S–ITS2, D1/D2 26S and COX1 loci. The last three genera were abundant on the damaged fruits, being Colletotrichum the more abundant (32.4 %). CaInt2 and CgInt primers support the identity of these isolates as C. gloeosporioides. Variability, inferred by rep-PCR and multilocus sequence analysis shows genetic differences among the C. gloeosporioides isolates. Infective profile evaluated in Colletotrichum isolates shows different leave infection percentages (26 to 60 %). SEM analysis showed mycelium, spores and appressoria on the leaves of selected Colletotrichum isolates. Specifically, the AL-05 and AL-13 isolates showed a high chitin deacetylase activity (CDA) peaking at 1.2 U/mg protein in AL-13. This is the first report on C. gloeosporioides infecting Italian lemon leaves in Mexico.

Species of Botryosphaeriaceae associated with citrus branch diseases in China

Citrus is an important and widely cultivated fruit crop in South China. Although the species of fungal diseases of leaves and fruits have been extensively studied, the causal organisms of branch diseases remain poorly known in China. Species of Botryosphaeriaceae are known as important fungal pathogens causing branch diseases on citrus in the USA and Europe. To determine the diversity of Botryosphaeriaceae species associated with citrus branch diseases in China, surveys were conducted in the major citrus-producing areas from 2017 to 2020. Diseased tissues were collected from twigs, branches and trunks with a range of symptoms including cankers, cracking, dieback and gummosis. Based on morphological characteristics and phylogenetic comparison of the DNA sequences of the internal transcribed spacer region (ITS), the translation elongation factor 1-alpha gene (tef1), the β-tubulin gene (tub2) and the DNA-directed RNA polymerase II second largest subunit (rpb2), 111 isolates from nine provinces were identified as 18 species of Botryosphaeriaceae, including Botryosphaeria dothidea, B. fabicerciana, Diplodia seriata, Dothiorella alpina, Do. plurivora, Lasiodiplodia citricola, L. iraniensis, L. microconidia, L. pseudotheobromae, L. theobromae, Neodeightonia subglobosa, Neofusicoccum parvum, and six previously undescribed species, namely Do. citrimurcotticola, L. guilinensis, L. huangyanensis, L. linhaiensis, L. ponkanicola and Sphaeropsis linhaiensis spp. nov. Botryosphaeria dothidea (28.8 %) was the most abundant species, followed by L. pseudotheobromae (23.4 %), which was the most widely distributed species on citrus, occurring in six of the nine provinces sampled. Pathogenicity tests indicated that all 18 species of Botryosphaeriaceae obtained from diseased citrus tissues in this study were pathogenic to the tested Citrus reticulata shoots in vitro, while not all species are pathogenic to the tested Cocktail grapefruit (C. paradisi × C. reticulata) shoots in vivo. In addition, Lasiodiplodia was the most aggressive genus both in vitro and in vivo. This is the first study to identify Botryosphaeriaceae species related to citrus branch diseases in China and the results provide a theoretical basis for the implementation of prevention and control measures. Citation: Xiao XE, Wang W, Crous PW, et al. 2021. Species of Botryosphaeriaceae associated with citrus branch diseases in China. Persoonia 47: 106-135. https://doi.org/10.3767/persoonia.2021.47.03.

Increased Organic Fertilizer and Reduced Chemical Fertilizer Increased Fungal Diversity and the Abundance of Beneficial Fungi on the Grape Berry Surface in Arid Areas

Fertilizer practices can significantly impact the fruit quality and microbial diversity of the orchards. The fungi on the surface of fruits are essential for fruit storability and safety. However, it is not clear whether fertilization affects the fungal diversity and community structure on the surface of grape berries. Here, grape quality and the fungal diversity on the surface of grapes harvested from three fertilizer treatments were analyzed shortly after grape picking (T0) and following 8 days of storage (T1). The study involved three treatments: (1) common chemical fertilizer for 2 years (CH); (2) increased organic fertilizer and reduced chemical fertilizer for 1 year (A.O); and (3) increased organic fertilizer and reduced chemical fertilizer for 2 years (B.O). The application of increased organic fertilizer and reduced chemical fertilizer increased the soluble solids content (SSC) of the grape berries and decreased the pH of the grape juice. A total of 827,947 high-quality fungal sequences were recovered and assigned to 527 operational taxonomic units. Members of the Ascomycota phylum were dominant in all samples and accounted for 94.41% of the total number of detected sequences, followed by the Basidiomycota (5.05%), and unidentified fungi (0.54%). Alpha and beta diversity analyses revealed significantly different fungal populations in the three fertilizer treatments over the two time periods. The fungal diversity and richness on the grape berry surface in the B.O and A.O treatments were higher than those in the CH treatment. Among the detected fungi, the B.O treatments were mainly Pichia, Aureobasidium, and Candida genera, while the CH treatments were Botrytis, Aspergillus, and Penicillium. Moreover, significant differences were revealed between the two assessment times (T0 and T1). The samples from the T0 timepoint had higher fungal richness and diversity than the samples from T1 timepoint. Increasing organic fertilizer usage in grape management could improve grape quality and went on to increase the fungal diversity, as well as the relative abundance (RA) of beneficial fungi on grape berry surfaces. The correlation analysis suggested that the pH of the grape juice was significantly negatively correlated with fungal diversity parameters.

Genetic Diversity and Pathogenicity of Botryosphaeriaceae Species Associated with Symptomatic Citrus Plants in Europe

This study represents the first survey studying the occurrence, genetic diversity, and pathogenicity of Botryosphaeriaceae species associated with symptomatic citrus species in citrus-production areas in five European countries. Based on morphological features and phylogenetic analyses of internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA), translation elongation factor 1-alpha (TEF1) and β-tubulin (TUB2) genes, nine species were identified as belonging to the genera Diplodia, Dothiorella, Lasiodiplodia, and Neofusicoccum. Isolates of Neofusicoccum parvum and Diplodia pseudoseriata were the most frequently detected, while Dothiorella viticola had the widest distribution, occurring in four of the five countries sampled. Representative isolates of the nine Botryosphaeriaceae species used in the pathogenicity tests caused similar symptoms to those observed in nature. Isolates assayed were all re-isolated, thereby fulfilling Koch's postulates. Isolates of Diplodia pseudoseriata and Diplodia olivarum are recorded for the first time on citrus and all species found in our study, except N. parvum, are reported for the first time on citrus in Europe.