Development of a Polymerase Chain Reaction (PCR) assay for the specific detection of Biscogniauxia mediterranea living as an endophyte in oak tissues

Nanopore Hybrid Assembly of Biscogniauxia mediterranea Isolated from Quercus cerris Affected by Charcoal Disease in an Endangered Coastal Wood

Biscogniauxia mediterranea is the causal agent of charcoal disease, affecting oak decline under the trigger of various biotic and abiotic factors, including climate change. Here, we report the genome assembly of an Italian B. mediterranea strain obtained using hybrid sequencing technologies combining long and short reads.

Drought and Pathogen Effects on Survival, Leaf Physiology, Oxidative Damage, and Defense in Two Middle Eastern Oak Species

The charcoal disease agents, Biscogniauxia mediterranea and Obolarina persica are two latent, ascomycetous oak pathogens in the Middle Eastern Zagros forests, where they have devastating effects, particularly during drought. Under greenhouse conditions, we investigated the effects of the two charcoal disease agents individually and in combination with drought on survival, growth, foliar gas-exchange, pigment content, oxidative stress and the antioxidant response of Quercus infectoria and Q. libani, two of the dominant tree species in this region. Commonly, the strongest negative effects emerged in the drought–pathogen interaction treatments. Q. infectoria showed less severe lesions, higher survival, more growth, and less leaf loss than Q. libani under combined biotic and abiotic stress. In both oak species, the combination of pathogen infection and drought resulted in more than 50% reduction in foliar gas-exchange parameters with partial recovery over time in Q. infectoria suggesting a superior defense system. Indeed, enhanced foliar anthocyanin, total soluble protein and glutathione concentrations imply an upregulation of the antioxidant defense system in Q. infectoria under stress while none of these parameters showed a significant treatment response in Q. libani. Consequently, Q. infectoria foliage showed no significant increase in superoxide, lower lipoxygenase activity, and less electrolyte leakage compared to the highly elevated levels seen in Q. libani indicating oxidative damage. Our findings indicate greater drought tolerance and pathogen resilience in Q. infectoria compared to Q. libani. Under future climate scenarios, we therefore expect changes in forest community structure driven by a decline in Q. libani and closely associated organisms.

Differential physiological and biochemical responses of Quercus infectoria and Q. libani to drought and charcoal disease

The vast oak-dominated forests of the Zagros Mountains in southwestern Iran currently undergo large-scale dieback driven by a combination of drought and increasing incidence of charcoal disease caused by the fungal pathogens Biscogniauxia mediterranea and Obolarina persica. Here, we explore the interactive effects between drought and charcoal disease agents on the physiology and biochemistry of Quercus infectoria and Quercus libani seedlings. The combination of pathogen attack and water limitation hampered plant development, especially in Q. libani seedlings, negatively affecting growth, biomass production, photosynthetic efficiency, and leaf water potential. An increase in markers of oxidative damage together with the upregulation of the antioxidant defense revealed that drought stress and pathogen infection led to pro-oxidative conditions in both oak species, especially in Q. libani, where larger changes in malondialdehyde and hydrogen peroxide occurred. The upregulation of the antioxidant system was more prominent in Q. infectoria than in Q. libani, resulting in enhanced enzyme activity and accumulation of non-enzymatic antioxidants. Fungal infection stimulated the activity of chitinase, phenylalanine ammonia lyase and β-1,3-glucanase in Q. infectoria leaves and this response became more pronounced under water shortage. Our study highlights that drought stress greatly intensifies the effects of the charcoal disease. Moreover, our findings imply superior stress resistance of Q. infectoria conferred by a highly efficient antioxidant system, strong osmotic adjustment (through proline), and increases in resistance enzymes and secondary metabolites (phenols and flavonoids). Future investigations should focus on adult trees in their natural habitat including interactions with soil factors and other pathogens like nematodes, bacteria and other fungi. Because the present research was conducted on oak seedlings, the findings can be considered by forest nursery managers.

A molecular approach to explore the extent of the threatened fungus Hypocreopsis rhododendri within wood

Hypocreopsis rhododendri is a rare fungus that grows on woody stems in hyperoceanic climax scrub on the west coasts of Britain, Ireland, and France. Knowledge of the distribution and abundance of the fungus is based entirely on sporocarp records; it does not account for any occurrence as vegetative mycelia. To address this issue, a H. rhododendri-specific polymerase chain reaction (PCR) was developed and used to assay Corylus avellana (hazel) stems for the presence of H. rhododendri mycelia. The primers ITSHrF and ITSHrR were designed within the internal transcribed spacer 2 region, and their specificity to H. rhododendri was established by their failure to amplify DNA extracted from 14 other Hypocreaceae species. The sensitivity of the assay was demonstrated by amplifying DNA extracted from 4 mg C. avellana wood spiked with 0.0013 % H. rhododendri mycelium. Samples of wood and bark were then taken from around and directly underneath 11 H. rhododendri sporocarps and assayed for the presence of H. rhododendri. PCR products were obtained from a third of the surface bark samples, but only one faint product was obtained from 70 samples taken from beneath the outer bark. The results support the view that H. rhododendri does not form mycelia within stems. We suggest that H. rhododendri is not a saprotrophic fungus, but instead appears to be a parasitic on the wood decay fungus Hymenochaete corrugata, with which it always occurs. Evidence that tissue of H. corrugata is present within the sporocarps of H. rhododendri is discussed.

Host selectivity and genetic variation of Discula umbrinella isolates from two oak species: analyses of intergenic spacer region sequences of ribosomal DNA

Discula umbrinella, a fungal endophyte of oak species, colonizes and reproduces on leaves of Quercus alba and Q. rubra in forest ecosystems. Twenty-nine isolates collected from leaves of both oak species (16 from Q. alba and 13 from Q. rubra) were assayed for oak species preference and genetic variation based on primer-specific polymerase chain reactions for the intergenic spacer region (IGS) of ribosomal DNA. DNA sequencing of the polymerase chain reaction products revealed a 10-bp insertion (237-247 bp) at the 3' end of the IGS region present in nine isolates and absent in 20 of the isolates. Phylogenetic analysis of the IGS region using the neighbor-joining method identified IGS groups (groups I-V) based on single nucleotide sequence differences. Host selectivity and geographic origin of isolates were correlated in some instances with the IGS groups. Isolates within each IGS group were further analyzed for nucleotide polymorphisms to confirm genotype identity and genotype diversity. Ten different genotypes (Va-Vj) were identified among the isolates analyzed. Genotype diversity was greatest in IGS groups I, IV, and V. Seventy percent of the genotypes (Vc, Vd, Ve, Vf, Vg,Vi, and Vj) contained isolates with single tree species preferences.

Ambrosia fungi in the insect-fungi symbiosis in relation to cork oak decline

Ambrosia fungi live associated with beetles (Scolytidae and Platypodidae) in host trees and act as a food source for the insects. The symbiotic relation is important to the colonizing strategies of host trees by beetles. Ambrosia fungi are dimorphic: they grow as ambrosial form and as mycelium. The fungi are highly specialized, adapted to a specific beetle and to the biotope where they both live. In addition other fungi have been found such as tree pathogenic fungi that may play a role in insects host colonization success. Saprophytic fungi are also present in insects galleries. These may decompose cellulose and/or be antagonistic to other less beneficial fungi. This paper summarizes the importance of ambrosia fungi and the interaction with insects and hosts. The possibility of the transport of pathogenic fungi by Platypus cylindrus to cork oak thus contributing for its decline is discussed.

New PCR assay detects rare tooth fungi in wood where traditional approaches fail

Lu et al. (2002) described a method for identifying Hericium species by PCR, using the primers HT-U1 and HT-L1 which they specifically designed for this purpose. In our hands these primers do not appear to discriminate between tooth fungi and other wood decay species. Therefore PCR primers were designed that discriminated Creolophus cirrhatus from other species (HER2F/HER3R), and which discriminate Hericium alpestre, H. coralloides and H. erinaceus from other wood decay Ascomycota and Basidiomycota but not from each other (HER2F/HER2R). Using the HER2F/HER3R primers together with traditional isolation and direct incubation procedures, the location of C. cirrhatus in Turkey oak logs was mapped. The PCR approach often detected C. cirrhatus in locations where it was suspected to be, based on patterns of staining and decay, but where it was not revealed by isolation onto agar media, emphasising the value of adopting several approaches to unravel fungal community structure in wood.

Endophytism of Sclerotinia pseudotuberosa: PCR assay for specific detection in chestnut tissues

The endophytic behaviour of Sclerotinia pseudotuberosa, cause of black rot of fruits of Castanea sativa, was investigated in asymptomatic tissues of the host, including nuts, buds and bark. A nested polymerase chain reaction (PCR) assay was developed for the specific detection of S. pseudotuberosa. Two specific primers, RAC1 and RAC2 were designed within the ITS1-5.8S-ITS2 region of rDNA by comparison of sequences of 24 isolates of S. pseudotuberosa and related species. Specificity of primers was tested against isolates of related and unrelated genera and the total DNA of C. sativa. The assay proved to be highly sensitive and capable of detecting picograms of S. pseudotuberosa DNA. Our study showed that S. pseudotuberosa was present asymptomatically in all the chestnut tissues tested. It is discussed that latency of S. pseudotuberosa in chestnut tissues may represent a adaptive strategy of the pathogen for rapid and massive host colonization in favourable environmental conditions.

A protocol for direct sequencing of multiple gene specific PCR products from Discula umbrinella, a fungal endophyte, utilizing bufferless precast electrophoresis

A protocol for direct sequencing of polymerase chain reaction (PCR) products from mycelia of Discula umbrinella, a fungal endophyte, using bufferless electrophoresis is described. This improved method allows researchers to conduct high-capacity screening of multiple gene regions for fungal endophytes applicable to microbial ecology and population genetic studies.