A potential role for an extracellular methanol oxidase secreted by Moniliophthora perniciosa in Witches' broom disease in cacao

Pseudocercospora fijiensis Conidial Germination Is Dominated by Pathogenicity Factors and Effectors

Conidia play a vital role in the survival and rapid spread of fungi. Many biological processes of conidia, such as adhesion, signal transduction, the regulation of oxidative stress, and autophagy, have been well studied. In contrast, the contribution of pathogenicity factors during the development of conidia in fungal phytopathogens has been poorly investigated. To date, few reports have centered on the pathogenicity functions of fungal phytopathogen conidia. Pseudocercospora fijiensis is a hemibiotrophic fungus and the causal agent of the black Sigatoka disease in bananas and plantains. Here, a conidial transcriptome of P. fijiensis was characterized computationally. Carbohydrates, amino acids, and lipid metabolisms presented the highest number of annotations in Gene Ontology. Common conidial functions were found, but interestingly, pathogenicity factors and effectors were also identified. Upon analysis of the resulting proteins against the Pathogen-Host Interaction (PHI) database, 754 hits were identified. WideEffHunter and EffHunter effector predictors identified 618 effectors, 265 of them were shared with the PHI database. A total of 1107 conidial functions devoted to pathogenesis were found after our analysis. Regarding the conidial effectorome, it was found to comprise 40 canonical and 578 non-canonical effectors. Effectorome characterization revealed that RXLR, LysM, and Y/F/WxC are the largest effector families in the P. fijiensis conidial effectorome. Gene Ontology classification suggests that they are involved in many biological processes and metabolisms, expanding our current knowledge of fungal effectors.

Genomic and Pathogenicity Mechanisms of the Main Theobroma cacao L. Eukaryotic Pathogens: A Systematic Review

A set of diseases caused by fungi and oomycetes are responsible for large losses in annual world cocoa production. Managing the impact caused by these diseases is very complex because a common solution has yet to be found for different pathogens. In this context, the systematic knowledge of Theobroma cacao L. pathogens' molecular characteristics may help researchers understand the possibilities and limitations of cocoa disease management strategies. This work systematically organized and summarized the main findings of omics studies of T. cacao eukaryotic pathogens, focusing on the plant-pathogen interaction and production dynamics. Using the PRISMA protocol and a semiautomated process, we selected papers from the Scopus and Web of Science databases and collected data from the selected papers. From the initial 3169 studies, 149 were selected. The first author's affiliations were mostly from two countries, Brazil (55%) and the USA (22%). The most frequent genera were Moniliophthora (105 studies), Phytophthora (59 studies) and Ceratocystis (13 studies). The systematic review database includes papers reporting the whole-genome sequence from six cocoa pathogens and evidence of some necrosis-inducing-like proteins, which are common in T. cacao pathogen genomes. This review contributes to the knowledge about T. cacao diseases, providing an integrated discussion of T. cacao pathogens' molecular characteristics, common mechanisms of pathogenicity and how this knowledge is produced worldwide.

State of the Art of the Molecular Biology of the Interaction between Cocoa and Witches’ Broom Disease: A Systematic Review

Significant scientific advances to elucidate the Moniliophthora perniciosa pathosystem have been achieved in recent years, but the molecular biology of this pathogen-host interaction is still a field with many unanswered questions. In order to present insights at the molecular level, we present the first systematic review on the theme. All told, 1118 studies were extracted from public databases. Of these, 109 were eligible for the review, based on the inclusion and exclusion criteria. The results indicated that understanding the transition from the biotrophic-necrotrophic phase of the fungus is crucial for control of the disease. Proteins with strong biotechnological potential or that can be targets for pathosystem intervention were identified, but studies regarding possible applications are still limited. The studies identified revealed important genes in the M. perniciosa-host interaction and efficient molecular markers in the search for genetic variability and sources of resistance, with Theobroma cacao being the most common host. An arsenal of effectors already identified and not explored in the pathosystem were highlighted. This systematic review contributes to the understanding of the pathosystem at the molecular level, offering new insights and proposing different paths for the development of new strategies to control witches’ broom disease.

A broadly conserved fungal alcohol oxidase (AOX) facilitates fungal invasion of plants

Alcohol oxidases (AOXs) are ecologically important enzymes that facilitate a number of plant-fungal interactions. Within Ascomycota they are primarily associated with methylotrophy, as a peroxisomal AOX catalysing the conversion of methanol to formaldehyde in methylotrophic yeast. In this study we demonstrate that AOX orthologues are phylogenetically conserved proteins that are common in the genomes of nonmethylotrophic, plant-associating fungi. Additionally, AOX orthologues are highly expressed during infection in a range of diverse pathosystems. To study the role of AOX in plant colonization, AOX knockout mutants were generated in the broad host range pathogen Sclerotinia sclerotiorum. Disease assays in soybean showed that these mutants had a significant virulence defect as evidenced by markedly reduced stem lesions and mortality rates. Chemical genomics suggested that SsAOX may function as an aromatic AOX, and growth assays demonstrated that ΔSsAOX is incapable of properly utilizing plant extract as a nutrient source. Profiling of known aromatic alcohols pointed towards the monolignol coniferyl alcohol (CA) as a possible substrate for SsAOX. As CA and other monolignols are ubiquitous among land plants, the presence of highly conserved AOX orthologues throughout Ascomycota implies that this is a broadly conserved protein used by ascomycete fungi during plant colonization.

The Role of Fungi in the Cocoa Production Chain and the Challenge of Climate Change

Background: The role of fungi in cocoa crops is mainly associated with plant diseases and contamination of harvest with unwanted metabolites such as mycotoxins that can reach the final consumer. However, in recent years there has been interest in discovering other existing interactions in the environment that may be beneficial, such as antagonism, commensalism, and the production of specific enzymes, among others. Scope and approach: This review summarizes the different fungi species involved in cocoa production and the cocoa supply chain. In particular, it examines the presence of fungal species during cultivation, harvest, fermentation, drying, and storage, emphasizing the factors that possibly influence their prevalence in the different stages of production and the health risks associated with the production of mycotoxins in the light of recent literature. Key findings and conclusion: Fungi associated with the cocoa production chain have many different roles. They have evolved in a varied range of ecosystems in close association with plants and various habitats, affecting nearly all the cocoa chain steps. Reports of the isolation of 60 genera of fungi were found, of which only 19 were involved in several stages. Although endophytic fungi can help control some diseases caused by pathogenic fungi, climate change, with increased rain and temperatures, together with intensified exchanges, can favour most of these fungal infections, and the presence of highly aggressive new fungal genotypes increasing the concern of mycotoxin production. For this reason, mitigation strategies need to be determined to prevent the spread of disease-causing fungi and preserve beneficial ones.

Formaldehyde as a Chemical Defence Agent of Fruiting Bodies of Mycena rosea and its Role in the Generation of the Alkaloid Mycenarubin C

Mycenarubin C, a previously unknown red pyrroloquinoline alkaloid, was isolated from fruiting bodies of the mushroom Mycena rosea and its structure was elucidated mainly by NMR spectroscopy and mass spectrometry. Unlike mycenarubin A, the major pyrroloquinoline alkaloid in fruiting bodies of M. rosea, mycenarubin C, contains an eight-membered ring with an additional C1 unit that is hitherto unprecedented for pyrroloquinoline alkaloids known in nature. Incubation of mycenarubin A with an excess of formaldehyde revealed that mycenarubin C was generated nearly quantitatively from mycenarubin A. An investigation into the formaldehyde content of fresh fruiting bodies of M. rosea showed the presence of considerable amounts of formaldehyde, with values of 5 μg per gram of fresh weight in fresh fruiting bodies. Although mycenarubin C did not show bioactivity against selected bacteria and fungi, formaldehyde inhibits the growth of the mycoparasite Spinellus fusiger at concentrations present in fruiting bodies of M. rosea. Therefore, formaldehyde might play an ecological role in the chemical defence of M. rosea against S. fusiger. In turn, S. fusiger produces gallic acid-presumably to detoxify formaldehyde by reaction of this aldehyde with amino acids and gallic acid to Mannich adducts.

Potential of Yeasts as Biocontrol Agents of the Phytopathogen Causing Cacao Witches' Broom Disease: Is Microbial Warfare a Solution?

Plant diseases caused by fungal pathogens are responsible for major crop losses worldwide, with a significant socio-economic impact on the life of millions of people who depend on agriculture-exclusive economy. This is the case of the Witches’ Broom Disease (WBD) affecting cacao plant and fruit in South and Central America. The severity and extent of this disease is prospected to impact the growing global chocolate market in a few decades. WBD is caused by the basidiomycete fungus Moniliophthora perniciosa. The methods used to contain the fungus mainly rely on chemical fungicides, such as copper-based compounds or azoles. Not only are these highly ineffective, but also their utilization is increasingly restricted by the cacao industry, in part because it promotes fungal resistance, in part related to consumers’ health concerns and environmental awareness. Therefore, the disease is being currently tentatively controlled through phytosanitary pruning, although the full removal of infected plant material is impossible and the fungus maintains persistent inoculum in the soil, or using an endophytic fungal parasite of Moniliophthora perniciosa which production is not sustainable. The growth of Moniliophthora perniciosa was reported as being antagonized in vitro by some yeasts, which suggests that they could be used as biological control agents, suppressing the fungus multiplication and containing its spread. Concurrently, some yeast-based products are used in the protection of fruits from postharvest fungal spoilage, and the extension of diverse food products shelf-life. These successful applications suggest that yeasts can be regarded a serious alternative also in the pre-harvest management of WBD and other fungal plant diseases. Yeasts’ GRAS (Generally Recognized as Safe) nature adds to their appropriateness for field application, not raising major ecological concerns as do the present more aggressive approaches. Importantly, mitigating WBD, in a sustainable manner, would predictably have a high socioeconomic impact, contributing to diminish poverty in the cacao-producing rural communities severely affected by the disease. This review discusses the importance/advantages and the challenges that such a strategy would have for WBD containment, and presents the available information on the molecular and cellular mechanisms underlying fungi antagonism by yeasts.

The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases

BACKGROUND

The glucose-methanol-choline (GMC) superfamily is a large and functionally diverse family of oxidoreductases that share a common structural fold. Fungal members of this superfamily that are characterised and relevant for lignocellulose degradation include aryl-alcohol oxidoreductase, alcohol oxidase, cellobiose dehydrogenase, glucose oxidase, glucose dehydrogenase, pyranose dehydrogenase, and pyranose oxidase, which together form family AA3 of the auxiliary activities in the CAZy database of carbohydrate-active enzymes. Overall, little is known about the extant sequence space of these GMC oxidoreductases and their phylogenetic relations. Although some individual forms are well characterised, it is still unclear how they compare in respect of the complete enzyme class and, therefore, also how generalizable are their characteristics.

RESULTS

To improve the understanding of the GMC superfamily as a whole, we used sequence similarity networks to cluster large numbers of fungal GMC sequences and annotate them according to functionality. Subsequently, different members of the GMC superfamily were analysed in detail with regard to their sequences and phylogeny. This allowed us to define the currently characterised sequence space and show that complete clades of some enzymes have not been studied in any detail to date. Finally, we interpret our results from an evolutionary perspective, where we could show, for example, that pyranose dehydrogenase evolved from aryl-alcohol oxidoreductase after a change in substrate specificity and that the cytochrome domain of cellobiose dehydrogenase was regularly lost during evolution.

CONCLUSIONS

This study offers new insights into the sequence variation and phylogenetic relationships of fungal GMC/AA3 sequences. Certain clades of these GMC enzymes identified in our phylogenetic analyses are completely uncharacterised to date, and might include enzyme activities of varying specificities and/or activities that are hitherto unstudied.

Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass

Biomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.

Multiplicity of enzymatic functions in the CAZy AA3 family

The CAZy auxiliary activity family 3 (AA3) comprises enzymes from the glucose-methanol-choline (GMC) family of oxidoreductases, which assist the activity of other AA family enzymes via their reaction products or support the action of glycoside hydrolases in lignocellulose degradation. The AA3 family is further divided into four subfamilies, which include cellobiose dehydrogenase, glucose oxidoreductases, aryl-alcohol oxidase, alcohol (methanol) oxidase, and pyranose oxidoreductases. These different enzymes catalyze a wide variety of redox reactions with respect to substrates and co-substrates. The common feature of AA3 family members is the formation of key metabolites such as H2O2 or hydroquinones, which are required by other AA enzymes. The multiplicity of enzymatic functions in the AA3 family is reflected by the multigenicity of AA3 genes in fungi, which also depends on their lifestyle. We provide an overview of the phylogenetic, molecular, and catalytic properties of AA3 enzymes and discuss their interactions with other carbohydrate-active enzymes.

Saprotrophic proteomes of biotypes of the witches' broom pathogen Moniliophthora perniciosa

Nine geographically diverse Moniliophthora perniciosa (witches' broom disease pathogen) isolates were cultured in vitro. They included six C-biotypes differing in virulence on cacao (Theobroma cacao), two S-biotypes (solanaceous hosts), and an L-biotype (liana hosts). Mycelial growth rates and morphologies differed considerably, but no characters were observed to correlate with virulence or biotype. In plant inoculations using basidiospores, one C-biotype caused symptoms on tomato (an S-biotype host), adding to evidence of limited host adaptation in these biotypes. Mycelial proteomes were analysed by two-dimensional gel electrophoresis (2-DE), and 619 gel spots were indexed on all replicate gels of at least one strain. Multivariate analysis of gel spots discriminated the L-biotype, but not the S-biotypes, from the remaining strains. The proteomic similarity of the S- and C-biotypes is consistent with their reported lack of phylogenetic distinction. Sequences from tandem mass spectrometry of tryptic peptides from major 2-DE spots were matched with Moniliophthora genome and transcript sequences on NCBI and WBD Transcriptome Atlas databases. Protein-spot identifications indicated that M. perniciosa saprotrophic mycelial proteomes expressed functions potentially connected with a 'virulence life-style', including peroxiredoxin, heat-shock proteins, nitrilase, formate dehydrogenase, a prominent complement of aldo-keto reductases, mannitol-1-phosphate dehydrogenase, and central metabolism enzymes with proposed pathogenesis functions.

Exploring the potential of fungi for methane abatement: Performance evaluation of a fungal-bacterial biofilter

Despite several fungal strains have been retrieved from methane-containing environments, the actual capacity and role of fungi on methane abatement is still unclear. The batch biodegradation tests here performed demonstrated the capacity of Graphium sp. to co-metabolically biodegrade methane and methanol. Moreover, the performance and microbiology of a fungal-bacterial compost biofilter treating methane at concentrations of ∼2% was evaluated at empty bed residence times of 40 and 20 min under different irrigation rates. The daily addition of 200 mL of mineral medium resulted in elimination capacities of 36.6 ± 0.7 g m(-3) h(-1) and removal efficiencies of ≈90% at the lowest residence time. The indigenous fungal community of the compost was predominant in the final microbial population and outcompeted the inoculated Graphium sp. during biofilter operation.

High-resolution transcript profiling of the atypical biotrophic interaction between Theobroma cacao and the fungal pathogen Moniliophthora perniciosa

Witches' broom disease (WBD), caused by the hemibiotrophic fungus Moniliophthora perniciosa, is one of the most devastating diseases of Theobroma cacao, the chocolate tree. In contrast to other hemibiotrophic interactions, the WBD biotrophic stage lasts for months and is responsible for the most distinctive symptoms of the disease, which comprise drastic morphological changes in the infected shoots. Here, we used the dual RNA-seq approach to simultaneously assess the transcriptomes of cacao and M. perniciosa during their peculiar biotrophic interaction. Infection with M. perniciosa triggers massive metabolic reprogramming in the diseased tissues. Although apparently vigorous, the infected shoots are energetically expensive structures characterized by the induction of ineffective defense responses and by a clear carbon deprivation signature. Remarkably, the infection culminates in the establishment of a senescence process in the host, which signals the end of the WBD biotrophic stage. We analyzed the pathogen's transcriptome in unprecedented detail and thereby characterized the fungal nutritional and infection strategies during WBD and identified putative virulence effectors. Interestingly, M. perniciosa biotrophic mycelia develop as long-term parasites that orchestrate changes in plant metabolism to increase the availability of soluble nutrients before plant death. Collectively, our results provide unique insight into an intriguing tropical disease and advance our understanding of the development of (hemi)biotrophic plant-pathogen interactions.