Isolation and molecular characterization of the fungal endophytic microbiome from conventionally and organically grown avocado trees in South Florida

Molecular Identification and Fungal Diversity Associated with Diseases in Hass Avocado Fruit Grown in Cauca, Colombia

Hass avocado fruit diseases are one of the main marketing constraints in Colombia. To identify and reveal the diversity of fungi associated with diseases in fruits and peduncles, symptomatic samples were collected from 67 farms in the 9 main Hass avocado-producing municipalities of the department of Cauca located in southwestern Colombia. A total of 237 monosporic isolates were obtained that were subjected to DNA extraction, amplification of the ITS region, sequencing and functional diversity analysis based on Hill numbers by municipality and altitude. The results indicated that the genera Pseudocercospora, Diaporthe, Colletotrichum, Neofusiococcum, Lasiodiplodia and Pestatoliopsis were associated with fruit diseases. The genus with the highest number of effective species was Colletotrichum. The ITS region revealed 100% identity of the species Pseudocercospora norchiensis, which was the first report of this pathogen in the crop. There was a greater richness and diversity of associated species in the three municipalities, revealing that the higher the altitude was, the lower the richness and diversity of fungi associated with fruit diseases. These results will provide a better understanding of the identification and diversity of pathogenic microorganisms present in avocado production systems in this region of Colombia.

Re-Evaluating Botryosphaeriales: Ancestral State Reconstructions of Selected Characters and Evolution of Nutritional Modes

Botryosphaeriales (Dothideomycetes, Ascomycota) occur in a wide range of habitats as endophytes, saprobes, and pathogens. The order Botryosphaeriales has not been subjected to evaluation since 2019 by Phillips and co-authors using phylogenetic and evolutionary analyses. Subsequently, many studies introduced novel taxa into the order and revised several families separately. In addition, no ancestral character studies have been conducted for this order. Therefore, in this study, we re-evaluated the character evolution and taxonomic placements of Botryosphaeriales species based on ancestral character evolution, divergence time estimation, and phylogenetic relationships, including all the novel taxa that have been introduced so far. Maximum likelihood, maximum parsimony, and Bayesian inference analyses were conducted on a combined LSU and ITS sequence alignment. Ancestral state reconstruction was carried out for conidial colour, septation, and nutritional mode. Divergence times estimates revealed that Botryosphaeriales originated around 109 Mya in the early epoch of the Cretaceous period. All six families in Botryosphaeriales evolved in the late epoch of the Cretaceous period (66-100 Mya), during which Angiosperms also appeared, rapidly diversified and became dominant on land. Families of Botryosphaeriales diversified during the Paleogene and Neogene periods in the Cenozoic era. The order comprises the families Aplosporellaceae, Botryosphaeriaceae, Melanopsaceae, Phyllostictaceae, Planistromellaceae and Saccharataceae. Furthermore, current study assessed two hypotheses; the first one being "All Botryosphaeriales species originated as endophytes and then switched into saprobes when their hosts died or into pathogens when their hosts were under stress"; the second hypothesis states that "There is a link between the conidial colour and nutritional mode in botryosphaerialean taxa". Ancestral state reconstruction and nutritional mode analyses revealed a pathogenic/saprobic nutritional mode as the ancestral character. However, we could not provide strong evidence for the first hypothesis mainly due to the significantly low number of studies reporting the endophytic botryosphaerialean taxa. Results also showed that hyaline and aseptate conidia were ancestral characters in Botryosphaeriales and supported the relationship between conidial pigmentation and the pathogenicity of Botryosphaeriales species.

Culturable endophytic fungal assemblages from Styrax sumatrana and Stryax benzoin and their potential as antifungal, antioxidant, and alpha-glucosidase inhibitory resources

Benzoin resin, produced by the native Indonesian trees Styrax sumatrana and Styrax benzoin, has been incorporated into medical practices to treat wounds, erythema, and many other conditions for centuries. Endophytic fungi that reside within medicinal plants have antimicrobial, antioxidant, and α-glucosidase inhibitory capacities, contributing to plant health and derivative products. In this study, we determined the antifungal, antioxidant, and α-glucosidase inhibitory capacities of endophytic fungal isolates from three different tissues (leaves, bark, and stems) of S. sumatrana and S. benzoin trees. The genera of fungal isolates were determined by phylogenetic analysis of internal transcribed spacer sequences. A total of 58 fungal isolates were classified into 15 different fungal genera from eight taxonomic orders—Hypocreales, Botryosphaeriales, Glomerellales, Diaphortales, Pleosporales, Eurotiales, Xylariales, and Mucorales—with a pattern of host species specificity. Among these isolates, Trichoderma sp. 6407 consistently exhibited high inhibition of the growth of plant pathogens Fusarium sp., Trichoderma viride, and Aspergillus niger. With respect to antioxidant activity, Phyllosticta sp. 6454 consistently showed 2,2-diphenyl-1-picrylhydrazyl inhibition (37.59 ± 0.05%), 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid)-based antioxidant activity (25.04 ± 0.27 mgTE/g), and α-glucosidase inhibitory activity (52.15 ± 10.08%). Neopestalotiopsis sp. 6431 was notably potent in 2,2-diphenyl-1-picrylhydrazyl inhibition (49.65 ± 0.80%), ferric reducing antioxidant power-based antioxidant activity (197.49 ± 8.65 mgTE/g), and α-glucosidase inhibitory activity (52.88 ± 4.93%). This study revealed that Trichoderma sp. 6407, Phyllosticta sp. 6454, and Neopestalotiopsis sp. 6431 exhibited antifungal, antioxidant, and α-glucosidase inhibitory activities.

Xylella fastidiosa Infection Reshapes Microbial Composition and Network Associations in the Xylem of Almond Trees

Xylella fastidiosa represents a major threat to important crops worldwide including almond, citrus, grapevine, and olives. Nowadays, there are no efficient control measures for X. fastidiosa, and the use of preventive measures and host resistance represent the most practical disease management strategies. Research on vessel-associated microorganisms is gaining special interest as an innate natural defense of plants to cope against infection by xylem-inhabiting pathogens. The objective of this research has been to characterize, by next-generation sequencing (NGS) analysis, the microbial communities residing in the xylem sap of almond trees affected by almond leaf scorch disease (ALSD) in a recent X. fastidiosa outbreak occurring in Alicante province, Spain. We also determined community composition changes and network associations occurring between xylem-inhabiting microbial communities and X. fastidiosa. For that, a total of 91 trees with or without ALSD symptoms were selected from a total of eight representative orchards located in five municipalities within the X. fastidiosa-demarcated area. X. fastidiosa infection in each tree was verified by quantitative polymerase chain reaction (qPCR) analysis, with 54% of the trees being tested X. fastidiosa-positive. Globally, Xylella (27.4%), Sphingomonas (13.9%), and Hymenobacter (12.7%) were the most abundant bacterial genera, whereas Diplodia (30.18%), a member of the family Didymellaceae (10.7%), and Aureobasidium (9.9%) were the most predominant fungal taxa. Furthermore, principal coordinate analysis (PCoA) of Bray–Curtis and weighted UniFrac distances differentiated almond xylem bacterial communities mainly according to X. fastidiosa infection, in contrast to fungal community structure that was not closely related to the presence of the pathogen. Similar results were obtained when X. fastidiosa reads were removed from the bacterial data set although the effect was less pronounced. Co-occurrence network analysis revealed negative associations among four amplicon sequence variants (ASVs) assigned to X. fastidiosa with different bacterial ASVs belonging to 1174-901-12, Abditibacterium, Sphingomonas, Methylobacterium–Methylorubrum, Modestobacter, Xylophilus, and a non-identified member of the family Solirubrobacteraceae. Determination of the close-fitting associations between xylem-inhabiting microorganisms and X. fastidiosa may help to reveal specific microbial players associated with the suppression of ALSD under high X. fastidiosa inoculum pressure. These identified microorganisms would be good candidates to be tested in planta, to produce almond plants more resilient to X. fastidiosa infection when inoculated by endotherapy, contributing to suppress ALSD.

Neopestalotiopsis siciliana sp. nov. and N. rosae Causing Stem Lesion and Dieback on Avocado Plants in Italy

Avocado (Persea americana) represents an important emerging tropical crop in Italy, especially in the southern regions. In this study, young plants of avocado showing symptoms of stem and wood lesion, and dieback, were investigated. Isolations from symptomatic tissues consistently yielded colonies of Neopestalotiopsis-like species. The characterization of representative isolates was based on the observation of morphological characters, the effect of temperature on mycelial growth rate, and on the sequencing of three different gene regions, specifically ITS, TEF1, and TUB2. Phylogenetic analyses were conducted based on maximum parsimony and maximum likelihood approaches. The results showed the presence of two species, viz. Neopestalotiopsis rosae and N. siciliana, the latter of which is here described as a new species. Pathogenicity tests were conducted using the mycelial plug technique on young potted avocado trees for both Neopestalotiopsis species. The results showed that both species were pathogenic to avocado. This study represents the first report of these two species affecting avocado and results in the description of a new species within the genus Neopestalotiopsis. Based on phylogeny, Pestalotiopsis coffeae-arabicae is combined in Neopestalotiopsis.

Two new species of Neopestalotiopsis from southern China

Background

Pestalotiopsis-like fungi are widely distributed in many plants and include endophytes, pathogens and saprobes. Five strains of Neopestalotiopsis were isolated from diseased leaves of Rhapisexcelsa (Principes, Palmae), Rhododendronsimsii and Rho.championiae (Ericales, Ericaceae) and Erythropalumscandens (Santalales, Olacaceae) in southern China.

New information

Based on morphology and multi-gene (ITS, tub2, tef1) phylogeny, our five strains of Neopestalotiopsis represent two new species and one extant species. Descriptions, illustrations and notes are also provided for the new species.

Fungal diversity within the phyllosphere of Pinus massoniana and the possible involvement of phyllospheric fungi in litter decomposition

Fungi play key roles in forest ecosystems and help to shape the forest's diverse functions. However, little is known about the diversity of phyllospheric fungi or their possible relationships with fungal communities residing in different micro-environments of Pinus massoniana forests. We investigated seven different sample types: mature needles (NM), dead needles (ND), needles falling as litter (L), fermenting needles (F), humus (H), top soil (0-20 cm) (TS), and secondary soil (20-40 cm) (SS). These seven fungal communities were examined and compared with ITS amplicons using a high-throughput sequencing technique. A total of 1213 fungal operational taxonomic units (OTUs) were obtained at a 97% sequence similarity level. Distinct fungal communities were associated with different sample types. A greater number of OTUs were present in both NM and F samples than those shared by both NM and TS samples, indicating that phyllospheric fungi may play crucial roles in litter decomposition. Sixty OTUs (the core microbiome) were found in all sample types, and they may probably play different ecological roles in different sample types. These findings extend our knowledge of the fungal diversity of the phyllosphere and its possible interactions with fungal communities found in distinct forest micro-habitats.