Inhibition of growth and ochratoxin A production in Aspergillus species by fungi isolated from coffee beans

Application and antagonistic mechanisms of atoxigenic Aspergillus strains for the management of fungal plant diseases

This review covers, for the first time, all methods based on the use of Aspergillus strains as biocontrol agents for the management of plant diseases caused by fungi and oomycetes. Atoxigenic Aspergillus strains have been screened in a variety of hosts, such as peanuts, maize kernels, and legumes, during the preharvest and postharvest stages. These strains have been screened against a wide range of pathogens, such as Fusarium, Phytophthora, and Pythium species, suggesting a broad applicability spectrum. The highest efficacies were generally observed when using non-toxigenic Aspergillus strains for the management of mycotoxin-producing Aspergillus strains. The modes of action included the synthesis of antifungal metabolites, such as kojic acid and volatile organic compounds (VOCs), secretion of hydrolytic enzymes, competition for space and nutrients, and induction of disease resistance. Aspergillus strains degraded Sclerotinia sclerotiorum sclerotia, showing high control efficacy against this pathogen. Collectively, although two Aspergillus strains have been commercialized for aflatoxin degradation, a new application of Aspergillus strains is emerging and needs to be optimized.

Deciphering the antiochratoxigenic activity of plant extracts and Debaryomyces hansenii against Penicillium nordicum in a "chorizo"-based medium by proteomic analysis

Penicillium nordicum is the main ochratoxin A (OTA)-producing species on the surface of dry-fermented sausages, such as the "chorizo". New antifungal strategies are being developed using biocontrol agents (BCAs), such as plant extracts and native microorganisms. This work aimed to evaluate the antiochratoxigenic capacity and the causative modes of action of BCAs (rosemary essential oil (REO), acorn shell extract and the yeast Debaryomyces hansenii (Dh)) in a "chorizo"-based medium (Ch-DS). BCAs were inoculated on Ch-DS together with P. nordicum and incubated at 12 °C for 15 days to collect mycelia for OTA analyses and comparative proteomics. Both REO and Dh alone decreased OTA accumulation up to 99% and affected the abundance of P. nordicum proteins linked to cell wall organisation, synthesis of OTA-related metabolites and ergosterol synthesis. It is worth highlighting the increased abundance of an amidase by REO, matching with the decrease in OTA. The use of REO and Dh as BCAs could be an effective strategy to reduce the OTA hazard in the meat industry. Based on their not fully coincident modes of action, their combined application could be of interest in "chorizo" to maximise their potential against ochratoxigenic strains.

Reduction in Ochratoxin A Occurrence in Coffee: From Good Practices to Biocontrol Agents

Ochratoxin A (OTA) is a mycotoxin mainly produced by Aspergillus section Circumdati and section Nigri across the coffee chain. OTA is nephrotoxic and is a threat to human health. This review summarizes current knowledge on how to reduce OTA concentration in coffee from farm to cup. After a brief introduction to the OTA occurrence in coffee, current good management practices are introduced. The core of this review focuses on biocontrol and microbial decontamination by lactic acid bacteria, yeasts and fungi, and their associated enzymes currently reported in the literature. Special attention is given to publications closest to in vivo applications of biocontrol agents and microbial OTA adsorption or degradation agents. Finally, this review provides an opinion on which future techniques to promote within the coffee supply chain.

Comprehensive Review of Aflatoxin and Ochratoxin A Dynamics: Emergence, Toxicological Impact, and Advanced Control Strategies

Filamentous fungi exhibit remarkable adaptability to diverse substrates and can synthesize a plethora of secondary metabolites. These metabolites, produced in response to environmental stimuli, not only confer selective advantages but also encompass potentially deleterious mycotoxins. Mycotoxins, exemplified by those originating from Alternaria, Aspergillus, Penicillium, and Fusarium species, represent challenging hazards to both human and animal health, thus warranting stringent regulatory control. Despite regulatory frameworks, mycotoxin contamination remains a pressing global challenge, particularly within cereal-based matrices and their derived by-products, integral components of animal diets. Strategies aimed at mitigating mycotoxin contamination encompass multifaceted approaches, including biological control modalities, detoxification procedures, and innovative interventions like essential oils. However, hurdles persist, underscoring the imperative for innovative interventions. This review elucidated the prevalence, health ramifications, regulatory paradigms, and evolving preventive strategies about two prominent mycotoxins, aflatoxins and ochratoxin A. Furthermore, it explored the emergence of new fungal species, and biocontrol methods using lactic acid bacteria and essential mustard oil, emphasizing their efficacy in mitigating fungal spoilage and mycotoxin production. Through an integrative examination of these facets, this review endeavored to furnish a comprehensive understanding of the multifaceted challenges posed by mycotoxin contamination and the emergent strategies poised to ameliorate its impact on food and feed safety.

Rethinking Aspergillosis in the Era of Microbiota and Mycobiota

Aspergillosis encompasses a wide range of clinical conditions based on the interaction between Aspergillus and the host. It ranges from colonization to invasive aspergillosis. The human lung provides an entry door for Aspergillus. Aspergillus has virulence characteristics such as conidia, rapid growth at body temperature, and the production of specific proteins, carbohydrates, and secondary metabolites that allow A. fumigatus to infiltrate the lung's alveoli and cause invasive aspergillosis. Alveolar epithelial cells play an important role in both fungus clearance and immune cell recruitment via cytokine release. Although the innate immune system quickly clears conidia in immunocompetent hosts, A. fumigatus has evolved multiple virulence factors in order to escape immune response such as ROS detoxifying enzymes, the rodlet layer, DHN-melanin and toxins. Bacterial co-infections or interactions can alter the immune response, impact Aspergillus growth and virulence, enhance biofilm formation, confound diagnosis, and reduce treatment efficacy. The gut microbiome's makeup influences pulmonary immune responses generated by A. fumigatus infection and vice versa. The real-time PCR for Aspergillus DNA detection might be a particularly useful tool to diagnose pulmonary aspergillosis. Metagenomics analyses allow quick and easy detection and identification of a great variety of fungi in different clinical samples, although optimization is still required particularly for the use of NGS techniques. This review will analyze the current state of aspergillosis in light of recent discoveries in the microbiota and mycobiota.

Microbial Diversity of Anaerobic-Fermented Coffee and Potential for Inhibiting Ochratoxin-Produced Aspergillus niger

Coffee flavor considerably depends on the fermentation process, with contributing factors including fermentation temperature, oxygen concentration, and microbial diversity. Efficient controlling of the fermentation can improve the quality of coffee beverages. Therefore, several studies on coffee fermentation processes have been conducted in various regions. The objective of this study was to assess the microbial diversity of coffee beans undergoing anaerobic fermentation at various temperatures (4 °C or 37 °C) and fermentation durations (12 h or 36 h) using full-length 16S rRNA sequencing. This analysis aimed to evaluate the inhibitory effects of the fermented metabolites against ochratoxin-producing Aspergillus niger. From our results, Acetobacter was identified as the dominant microbial community at higher fermentation temperatures, whereas Leuconostoc and Gluconobacter were the dominant genera at lower temperatures. However, at lower temperatures, changes in microbial communities were relatively slow. This study expands our knowledge of the microbial diversity involved in the anaerobic fermentation of coffee beans in Taiwan. The findings of this study can be used in future research to cultivate microorganisms linked to the quality and improve the quality of coffee beverages through fermentation.

Discovery of a New Lichtheimia (Lichtheimiaceae, Mucorales) from Invertebrate Niche and Its Phylogenetic Status and Physiological Characteristics

Species of Lichtheimia are important opportunistic fungal pathogens in the order Mucorales that are isolated from various sources such as soil, indoor air, food products, feces, and decaying vegetables. In recent years, species of Lichtheimia have become an emerging causative agent of invasive mucormycosis. In Europe and USA, Lichtheimia are the second and third most common causal fungus of mucormycosis, respectively. Thus, the aim of this study was to survey the diversity of species of Lichtheimia hidden in poorly studied hosts, such as invertebrates, in Korea. Eight Lichtheimia strains were isolated from invertebrate samples. Based on morphology, physiology, and phylogenetic analyses of ITS and LSU rDNA sequence data, the strains were identified as L. hyalospora, L. ornata, L. ramosa, and a novel species, L. koreana sp. nov. Lichtheimia koreana is characterized by a variable columellae, sporangiophores arising solitarily or up to three at one place from stolons, and slow growth on MEA and PDA at all temperatures tested. The new species grows best at 30 and 35 °C and has a maximum growth temperature of 40 °C. Detailed descriptions, illustrations, and a phylogenetic tree are provided.

Research progress of ochratoxin a bio-detoxification

Ochratoxins (OTs) is an extremely toxic mycotoxin in which Ochratoxin A (OTA) is the most toxic and prevalent in the ochratoxin family. OTA is among the five most critical mycotoxins that are subject to legal regulations. Animals and humans may be exposed to OTA through dietary intake, inhalation, and dermal contact. OTA is considered nephrotoxic, genotoxic, cytotoxic, teratogenic, carcinogenic, mutagenic, immunotoxic, and myelotoxic. So, intake of OTA contaminated foods and feeds can impact the productivity of animals and health of people. According to this review, several studies have reported on the approaches that have been established for OTA removal. This review focused on the control approaches to mitigate OTA contamination, OTA bio-detoxification materials and their applicable techniques, recombinant strains for OTA bio-detoxification, and their detoxification effects, recombinant OTA-degrading enzymes and their sources, recombinant fusion enzymes for OTA, ZEN and AFB1 mycotoxins detoxification, as well as the current application and commercialized OTA bio-detoxification products. However, there is no single technique that has been approved to detoxify OTA by 100% to date. Some preferred current strategies for OTA bio-detoxification have been recombinant degrading enzymes and genetic engineering technology due to their efficiency and safety. Therefore, prospective studies should focus on standardizing pure enzymes from genetically engineered microbial strains that have great potential for OTA detoxification.

Efficient Biodegradation of Patulin by Aspergillus niger FS10 and Metabolic Response of Degrading Strain

Patulin, a mycotoxin commonly found in fruits and derived products, causes serious health problems for humans and animals worldwide. Several microbial strains have been observed to possess the ability to effectively remove patulin. However, these methods are presently associated with disadvantages such as low degradation efficiency and an unclear biodegradation mechanism. In the current study, the characteristics of patulin degradation via Aspergillus niger FS10 were evaluated, and the mechanisms involved were analyzed using metabolomics technologies. The results showed that the suspension of A. niger FS10 could degrade 94.72% of patulin within 36 h. The moment concentration pf patulin was 0.116 μg/mL, and the detection limit value was 0.01 μg/mL. In addition, the patulin content was reduced to levels below the detection limit within 48 h. A. niger FS10 mainly degrades patulin by producing intracellular enzymes, which can convert patulin into ascladiol. This degradation method can effectively reduce the damage caused by patulin to HepG2 cells. In addition, the patulin treatment significantly affects the pentose phosphate pathway and the glutathione pathway. These two metabolic pathways are speculated to be closely related to patulin degradation via A. niger FS10. The incubation of A. niger FS10 with patulin-contaminated apple pomace can not only eliminate patulin but also increase the utilization of apple pomace. Therefore, our research results provide a new method for addressing patulin contamination in the food and feed industries.

Single-Molecule Real-Time Sequencing to Explore the Mycobiome Diversity in Malt

This study determined the composition of fungal communities and characterized the enriched fungal species in raw and roasted malts via the third-generation PacBio-based full-length single-molecule real-time (SMRT) sequencing of the full-length amplicon of the internal transcribed spacer (ITS) region. In total, one kingdom, six phyla, 23 classes, 56 orders, 120 families, 188 genera, 333 species, and 780 operational taxonomic units (OTUs) were detected with satisfactory sequencing depth and sample size. Wickerhamomyces (56%), Cyberlindnera (15%), Dipodascus (12%), and Candida (6.1%) were characterized as the dominant genera in the raw malts, and Aspergillus (35%), Dipodascus (21%), Wickerhamomyces (11%), and Candida (3.5%) in the roasted malts. Aspergillus proliferans, Aspergillus penicillioides, and Wickerhamomyces anomalus represented the crucial biomarkers causing intergroup differences. Correlation analysis regarding environmental factors indicated that the water activity (a_w) of the samples affected the composition of the fungal communities in the malts. In practice, special attention should be paid to the mycotoxin-producing fungi, as well as other fungal genera that are inversely correlated with their growth, to ensure the safe use of malt and its end products.

IMPORTANCE Fungal contamination and secondary metabolite accumulation in agricultural products represent a global food safety challenge. Although high-throughput sequencing (HTS) is beneficial for explaining fungal communities, it presents disadvantages, such as short reads, species-level resolution, and uncertain identification. This work represents the first attempt to characterize the fungal community diversity, with a particular focus on mycotoxin-producing fungi, in malt via the third-generation PacBio-based full-length SMRT sequencing of the ITS region, aiming to explore and compare the differences between the fungal communities of raw and roasted malts. The research is beneficial for developing effective biological control and conservation measures, including improving the roasting conditions, monitoring the environmental humidity and a_w, and effectively eliminating and degrading fungi in the industry chain according to the diverse fungal communities determined, for the safe use of malts and their end products, such as beers. In addition, the third-generation SMRT sequencing technology allows highly efficient analysis of fungal community diversity in complex matrices, yielding fast, high-resolution long reads at the species level. It can be extended to different research fields, updating modern molecular methodology and bioinformatics databases.

Characterization of Ugandan Endemic Aspergillus Species and Identification of Non-Aflatoxigenic Isolates for Potential Biocontrol of Aflatoxins

Acute stunting in children, liver cancer, and death often occur due to human exposure to aflatoxins in food. The severity of aflatoxin contamination depends on the type of Aspergillus fungus infecting the crops. In this study, Aspergillus species were isolated from households’ staple foods and were characterized for different aflatoxin chemotypes. The non-aflatoxigenic chemotypes were evaluated for their ability to reduce aflatoxin levels produced by aflatoxigenic A. flavus strains on maize grains. Aspergillus flavus (63%), A. tamarii (14%), and A. niger (23%) were the main species present. The A. flavus species included isolates that predominantly produced aflatoxins B1 and B2, with most isolates producing a high amount (>20 ug/µL) of aflatoxin B1 (AFB1), and a marginal proportion of them also producing G aflatoxins with a higher level of aflatoxin G1 (AFG1) than AFB1. Some non-aflatoxigenic A. tamarii demonstrated a strong ability to reduce the level of AFB1 by more than 95% when co-inoculated with aflatoxigenic A. flavus. Therefore, field evaluation of both non-aflatoxigenic A. flavus and A. tamarii would be an important step toward developing biocontrol agents for mitigating field contamination of crops with aflatoxins in Uganda.

Comprehensive Review of Fungi on Coffee

Coffee is grown in more than 80 countries as a cash crop and consumed worldwide as a beverage and food additive. It is susceptible to fungal infection during growth, processing and storage. Fungal infections, in particular, can seriously affect the quality of coffee and threaten human health. The data for this comprehensive review were collected from the United States Department of Agriculture, Agricultural Research Service (USDA ARS) website and published papers. This review lists the fungal species reported on coffee based on taxonomy, life mode, host, affected plant part and region. Five major fungal diseases and mycotoxin-producing species (post-harvest diseases of coffee) are also discussed. Furthermore, we address why coffee yield and quality are affected by fungi and propose methods to control fungal infections to increase coffee yield and improve quality. Endophytic fungi and their potential as biological control agents of coffee disease are also discussed.

Assessment of ochratoxin A exposure risk from the consumption of coffee beans in Phnom Penh, Cambodia

This survey aimed to determine OTA contamination in roasted coffee samples commercialised in Phnom Penh, Cambodia and to assess the potential health risk from OTA exposure. Forty locally grown and imported coffee samples were collected and analysed. Analytical validation methods were fully performed. In 3 of 40 samples (7.5%), the results showed detectable levels of OTA, ranging from 0.19 to 1.12 µg kg^-1, with an overall average of 0.26 µg kg^-1 and an average over the LOQ (n = 3) at 0.81 µg kg^-1. OTA estimated daily intake (EDI) of both values were 0.05 (overall average) and 0.17 ng/kg bw/day (the worst-case scenario) with the calculated risk of OTA exposure expressed as a Hazard Quotient at 0.003 and 0.01, respectively. This result could imply a low health risk to Cambodian coffee consumers.

Interactive Inhibition of Aflatoxigenic Aspergillus flavus and Ochratoxigenic Aspergillus carbonarius by Aspergillus oryzae under Fluctuating Temperatures

This study aimed to evaluate the effectiveness of A. oryzae in inhibiting aflatoxin B1 (AFB1) and ochratoxin A (OTA) production by A. flavus and A. carbonarius, respectively, under shifting temperatures. A. oryzae was tested on different agar, namely coconut cream agar (CCA) and chili-based agar to figure out the variation in the effectiveness of A. oryzae on the most appropriate medium for A. flavus and A. carbonarius to produce mycotoxin and under natural condition where they are predominantly found. On CCA, the temperatures applied were 20, 30, 35, 40, 20/30, 20/35, and 20/40 °C, while on chili-based agar, the temperatures imposed were 20, 40, and 20/40 °C, at varied water activity of 0.92 and 0.97aw. The findings indicated that A. oryzae was much more effective in inhibiting the growth of A. flavus rather than A. carbonarius, yet it was able to inhibit higher OTA concentration than AFB1 at fluctuating temperatures on CCA as the most appropriate medium for A. flavus and A. carbonarius. A. oryzae effectively inhibited AFB1 and OTA at static temperature of 20 °C and water activity of 0.97aw on chili-based agar. Under fluctuating temperatures (20/40 °C), A. oryzae was also able to control mycotoxin, particularly OTA at high water activity (0.97aw).

Distribution, toxicity, interactive effects, and detection of ochratoxin and deoxynivalenol in food: A review

Mycotoxins are secondary metabolites of fungi that cause severe damage to agricultural products and food in the food supply chain. These detrimental pollutants have been directly linked with poor socioeconomic patterns and human health issues. Among the natural micropollutants, ochratoxin A (OTA) and deoxynivalenol (DON) are widely distributed in food materials. The primary occurrence of these mycotoxins is reported in almost all cereal grains and fresh agro-products. Both mycotoxins have shown harmful effects, such as nephrotoxic, hepatotoxic, and genotoxic effects, in humans due to their complex structural formation during the degradation/acetylation reaction. In addition, improper preharvest, harvest, and postharvest handling tend to lead to the formation of OTA and DON in various food commodities, which allows different harmful fungicides in practice. Therefore, this review provides more insight into the distribution and toxicity of OTA/DON in the food matrix and human health. Furthermore, the interactive effects of OTA/DON with co-contaminated organic and inorganic compounds are discussed. Finally, international regulation and mitigation strategies for detoxication are critically evaluated to meet food safety and good agriculture practices.

Prevalence of toxigenic fungi and mycotoxins in Arabic coffee (Coffea arabica): Protective role of traditional coffee roasting, brewing and bacterial volatiles

Fungal infection and synthesis of mycotoxins in coffee leads to significant economic losses. This study aimed to investigate the prevalence of toxigenic fungi, their metabolites, and the effect of traditional roasting and brewing on ochratoxin A (OTA) and aflatoxins (AFs) contents of naturally contaminated coffee samples. In addition, in vivo biocontrol assays were performed to explore the antagonistic activities of Bacillus simplex 350–3 (BS350-3) on the growth and mycotoxins synthesis of Aspergillus ochraceus and A. flavus. The relative density of A. niger, A. flavus, Penicillium verrucosum and A. carbonarius on green coffee bean was 60.82%, 7.21%, 3.09% and 1.03%, respectively. OTA contents were lowest in green coffee beans (2.15 μg/kg), followed by roasted (2.76 μg/kg) and soluble coffee (8.95 μg/kg). Likewise, AFs levels were highest in soluble coffee (90.58 μg/kg) followed by roasted (33.61 μg/kg) and green coffee (9.07 μg/kg). Roasting naturally contaminated coffee beans at three traditional methods; low, medium and high, followed by brewing resulted in reduction of 58.74% (3.50 μg/kg), 60.88% (3.72 μg/kg) and 64.70% (4.11 μg/kg) in OTA and 40.18% (34.65 μg/kg), 47.86% (41.17 μg/kg) and 62.38% (53.73 μg/kg) AFs contents, respectively. Significant inhibitions of AFs and OTA synthesis by A. flavus and A. carbonarius, respectively, on infected coffee beans were observed in presence of Bacillus simplex BS350-3 volatiles. Gas chromatography mass spectrochemistry (GC-MS/MS) analysis of head-space BS350-3 volatiles showed quinoline, benzenemethanamine and 1-Octadecene as bioactive antifungal molecules. These findings suggest that marketed coffee samples are generally contaminated with OTA and AFs, with a significant level of roasted and soluble coffee contaminated above EU permissible limits for OTA. Further, along with coffee roasting and brewing; microbial volatiles can be optimized to minimize the dietary exposure to mycotoxins.

Soil Microbiome Manipulation Gives New Insights in Plant Disease-Suppressive Soils from the Perspective of a Circular Economy: A Critical Review

This review pays attention to the newest insights on the soil microbiome in plant disease-suppressive soil (DSS) for sustainable plant health management from the perspective of a circular economy that provides beneficial microbiota by recycling agro-wastes into the soil. In order to increase suppression of soil-borne plant pathogens, the main goal of this paper is to critically discuss and compare the potential use of reshaped soil microbiomes by assembling different agricultural practices such as crop selection; land use and conservative agriculture; crop rotation, diversification, intercropping and cover cropping; compost and chitosan application; and soil pre-fumigation combined with organic amendments and bio-organic fertilizers. This review is seen mostly as a comprehensive understanding of the main findings regarding DSS, starting from the oldest concepts to the newest challenges, based on the assumption that sustainability for soil quality and plant health is increasingly viable and supported by microbiome-assisted strategies based on the next-generation sequencing (NGS) methods that characterize in depth the soil bacterial and fungal communities. This approach, together with the virtuous reuse of agro-wastes to produce in situ green composts and organic bio-fertilizers, is the best way to design new sustainable cropping systems in a circular economy system. The current knowledge on soil-borne pathogens and soil microbiota is summarized. How microbiota determine soil suppression and what NGS strategies are available to understand soil microbiomes in DSS are presented. Disturbance of soil microbiota based on combined agricultural practices is deeply considered. Sustainable soil microbiome management by recycling in situ agro-wastes is presented. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed.

Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review

Intensive coffee production is accompanied by several environmental issues, including soil degradation, biodiversity loss, and pollution due to the wide use of agrochemical inputs and wastes generated by processing. In addition, climate change is expected to decrease the suitability of cultivated areas while potentially increasing the distribution and impact of pests and diseases. In this context, the coffee microbiota has been increasingly studied over the past decades in order to improve the sustainability of the coffee production. Therefore, coffee associated microorganisms have been isolated and characterized in order to highlight their useful characteristics and study their potential use as sustainable alternatives to agrochemical inputs. Indeed, several microorganisms (including bacteria and fungi) are able to display plant growth-promoting capacities and/or biocontrol abilities toward coffee pests and diseases. Despite that numerous studies emphasized the potential of coffee-associated microorganisms under controlled environments, the present review highlights the lack of confirmation of such beneficial effects under field conditions. Nowadays, next-generation sequencing technologies allow to study coffee associated microorganisms with a metabarcoding/metagenomic approach. This strategy, which does not require cultivating microorganisms, now provides a deeper insight in the coffee-associated microbial communities and their implication not only in the coffee plant fitness but also in the quality of the final product. The present review aims at (i) providing an extensive description of coffee microbiota diversity both at the farming and processing levels, (ii) identifying the “coffee core microbiota,” (iii) making an overview of microbiota ability to promote coffee plant growth and to control its pests and diseases, and (iv) highlighting the microbiota potential to improve coffee quality and waste management sustainability.