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.

[1]  S. Lumyong,et al.  Taxonomic and phylogenic appraisal of a novel species and a new record of Stictidaceae from coffee in Yunnan Province, China , 2021, Phytotaxa.

[2]  Tharyn Reichel,et al.  Strategies for Coffee Leaf Rust Management in Organic Crop Systems , 2021, Agronomy.

[3]  O. Freitas-Silva,et al.  Brazilian Coffee Production and the Future Microbiome and Mycotoxin Profile Considering the Climate Change Scenario , 2021, Microorganisms.

[4]  P. R. Silveira,et al.  Elucidating the interactions between the rust Hemileia vastatrix and a Calonectria mycoparasite and the coffee plant , 2021, iScience.

[5]  R. Barreto,et al.  New species and records of Trichoderma isolated as mycoparasites and endophytes from cultivated and wild coffee in Africa , 2021, Scientific Reports.

[6]  K. Prasannath,et al.  Recent Advances in Molecular Diagnostics of Fungal Plant Pathogens: A Mini Review , 2021, Frontiers in Cellular and Infection Microbiology.

[7]  J. Maeght,et al.  Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review , 2020, Frontiers in Sustainable Food Systems.

[8]  C. Ogoshi,et al.  Epitypification of Cercospora coffeicola and its involvement with two different symptoms on coffee leaves in Brazil , 2020, European Journal of Plant Pathology.

[9]  Jie Ren,et al.  The potential of microbial endophytes to enhance the resistance to postharvest diseases of fruit and vegetables. , 2020, Journal of the science of food and agriculture.

[10]  W. Cardoso,et al.  Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil , 2020, Scientific Reports.

[11]  B. Gichimu,et al.  Quantitative trait loci (QTL) mapping of resistance to coffee berry disease (Colletotrichum kahawae Waller Bridge) in Coffea arabica L. variety Rume Sudan , 2020 .

[12]  D. Hopkins,et al.  Editorial: Role of Endophytes in Plant Health and Defense Against Pathogens , 2020, Frontiers in Plant Science.

[13]  M. Ryan,et al.  Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides , 2020, BMC Genomics.

[14]  R. Bates.  The International Coffee Organization: , 2020 .

[15]  C. Botero,et al.  Screening for phosphate-solubilizing fungi from colombian andisols cultivated with coffee (Coffea arabica L.) , 2020 .

[16]  K. Hyde,et al.  One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020) , 2020, Fungal Diversity.

[17]  S. M. Chalfoun,et al.  Fungi associated to beans infested with coffee berry borer and the risk of ochratoxin A , 2020 .

[18]  Ana Cláudia Alencar Lopes,et al.  Standardization of an analytical method to quantify ochratoxin A in green coffee beans by high performance liquid chromatography , 2020, Research, Society and Development.

[19]  N. Peres,et al.  Managing Colletotrichum on Fruit Crops: A "Complex" Challenge. , 2020, Plant disease.

[20]  Humberto E. Ortega,et al.  Patents on Endophytic Fungi Related to Secondary Metabolites and Biotransformation Applications , 2020, Journal of fungi.

[21]  P. Bayman,et al.  Pathogens Causing Anthracnose and Fruit Rots of Coffee Associated with the Coffee Berry Borer and the Entomopathogenic Fungus Beauveria bassiana in Puerto Rico. , 2020, Phytopathology.

[22]  M. A. Musumeci,et al.  Effectiveness of Trichoderma strains isolated from the rhizosphere of citrus tree to control Alternaria alternata, Colletotrichum gloeosporioides and Penicillium digitatum A21 resistant to pyrimethanil in post‐harvest oranges (Citrus sinensis L. (Osbeck)) , 2020, Journal of applied microbiology.

[23]  L. Ziska,et al.  Early growth phase and caffeine content response to recent and projected increases in atmospheric carbon dioxide in coffee (Coffea arabica and C. canephora) , 2020, Scientific Reports.

[24]  K. Hyde,et al.  Elucidation of the life cycle of the endophytic genus Muscodor and its transfer to Induratia in Induratiaceae fam. nov., based on a polyphasic taxonomic approach , 2020, Fungal Diversity.

[25]  S. Patil,et al.  Biological control of Fusarium wilt in crop plants using non-pathogenic isolates of Fusarium species , 2020, Indian Phytopathology.

[26]  T. Varzakas,et al.  Advances in Occurrence, Importance, and Mycotoxin Control Strategies: Prevention and Detoxification in Foods , 2020, Foods.

[27]  A. Ippolito,et al.  Nanomaterials as Alternative Control Means Against Postharvest Diseases in Fruit Crops , 2019, Nanomaterials.

[28]  L. De Vuyst,et al.  Influence of Various Processing Parameters on the Microbial Community Dynamics, Metabolomic Profiles, and Cup Quality During Wet Coffee Processing , 2019, Front. Microbiol..

[29]  A. Cinar,et al.  Mycotoxins: The Hidden Danger in Foods , 2019, Mycotoxins and Food Safety.

[30]  I. C. Pimentel,et al.  Inhibition of growth and ochratoxin A production in Aspergillus species by fungi isolated from coffee beans , 2019, Brazilian Journal of Microbiology.

[31]  Shahbaz Mushtaq,et al.  The impact of climate change and variability on coffee production: a systematic review , 2019, Climatic Change.

[32]  F. Mateo,et al.  Potential impact of engineered silver nanoparticles in the control of aflatoxins, ochratoxin A and the main aflatoxigenic and ochratoxigenic species affecting foods , 2019, Food Control.

[33]  F. Grognard,et al.  Modelling and controlling fungus Hemileia vastatrix, a coffee pest , 2019 .

[34]  M. Dosso,et al.  Prevention of Ochratoxin A (OTA) Production in Coffee Beans Using Natural Antifungal Derived from Solanum indicum L. Green Berries , 2019, Journal of Food Security.

[35]  A. Leitão,et al.  Occurrence of Ochratoxin A in Coffee: Threads and Solutions—A Mini-Review , 2019, Beverages.

[36]  E. Y. Hirooka,et al.  Effects of Subcutaneous Ochratoxin-A Exposure on Immune System of Broiler Chicks , 2019, Toxins.

[37]  Junling Shi,et al.  Beneficial effects of endophytic fungi colonization on plants , 2019, Applied Microbiology and Biotechnology.

[38]  E. Furlong,et al.  Efficiency of γ-oryzanol against the complex Fusarium graminearum growth and mycotoxins production , 2019, Food Science and Technology.

[39]  S. Lumyong,et al.  Use of endophytes as biocontrol agents , 2019, Fungal Biology Reviews.

[40]  Samy S. Abu-Naser,et al.  A Rule Based System for the Diagnosis of Coffee Diseases , 2019 .

[41]  S. M. Chalfoun,et al.  Evaluation of the effects of temperature on processed coffee beans in the presence of fungi and ochratoxin A , 2018, Journal of Food Safety.

[42]  M. Roopesh,et al.  Cold Plasma for Effective Fungal and Mycotoxin Control in Foods: Mechanisms, Inactivation Effects, and Applications. , 2018, Comprehensive reviews in food science and food safety.

[43]  S. F. Pascholati,et al.  SAPROBIC FUNGI AS BIOCONTROL AGENTS OF HALO BLIGHT (Pseudomonas syringae pv. garcae) IN COFFEE CLONES , 2018, Coffee Science.

[44]  P. Masi,et al.  Current methods for mycotoxins analysis and innovative strategies for their reduction in cereals: an overview. , 2018, Journal of the science of food and agriculture.

[45]  J. A. Ragazzo‐Sánchez,et al.  Determination of potentially mycotoxigenic fungi in coffee (Coffea arabica L.) from Nayarit , 2018, Food Science and Biotechnology.

[46]  V. P. Campos,et al.  Volatile compounds produced by Fusarium spp. isolated from Meloidogyne paranaensis egg masses and corticous root tissues from coffee crops are toxic to Meloidogyne incognita , 2018, Tropical Plant Pathology.

[47]  G. Strobel.  The Emergence of Endophytic Microbes and Their Biological Promise , 2018, Journal of fungi.

[48]  M. Busman,et al.  Evolution of structural diversity of trichothecenes, a family of toxins produced by plant pathogenic and entomopathogenic fungi , 2018, PLoS pathogens.

[49]  Ana Vieira,et al.  The coffee leaf rust pathogen Hemileia vastatrix: one and a half centuries around the tropics. , 2017, Molecular plant pathology.

[50]  J. Eloff,et al.  THE USE OF PLANTS TO PROTECT PLANTS AND FOOD AGAINST FUNGAL PATHOGENS: A REVIEW , 2017, African journal of traditional, complementary, and alternative medicines : AJTCAM.

[51]  K. Hyde,et al.  Life styles of Colletotrichum species and implications for plant biosecurity , 2017 .

[52]  A. Gomes,et al.  Fungal contamination in green coffee beans samples: A public health concern , 2017, Journal of toxicology and environmental health. Part A.

[53]  O. L. Pereira,et al.  Antimicrobial activity of endophytic fungi from coffee plants , 2017 .

[54]  P. Tixier,et al.  Primary and Secondary Yield Losses Caused by Pests and Diseases: Assessment and Modeling in Coffee , 2017, PloS one.

[55]  Birhanu Gizaw,et al.  Isolation, identification and characterization of yeast species from coffee waste collected from Sidama and Gedio zone , 2016 .

[56]  M. Takundwa.  Molecular identification of fungal species associated with leaf lesions of marama bean seedlings in Namibia , 2016 .

[57]  F. Perina,et al.  Alterations in antioxidant metabolism in coffee leaves infected by Cercospora coffeicola , 2016 .

[58]  J. Azevedo,et al.  Genetic diversity of endophytic fungi from Coffea arabica cv. IAPAR-59 in organic crops , 2016, Annals of Microbiology.

[59]  E. Pozza,et al.  Diagrammatic Scales for Assessing Brown Eye Spot (Cercospora coffeicola) in Red and Yellow Coffee Cherries , 2016 .

[60]  D. Alvindia,et al.  Survey of Philippine coffee beans for the presence of ochratoxigenic fungi , 2016, Mycotoxin Research.

[61]  R. Ramasamy,et al.  Current and Prospective Methods for Plant Disease Detection , 2015, Biosensors.

[62]  J. Papenbrock,et al.  Mycotoxins: Producing Fungi and Mechanisms of Phytotoxicity , 2015 .

[63]  F. Lemessa,et al.  Association of Mycoflora with Coffee (Coffea arabica L.) Beans at Limmu Coffee Plantation, Southwestern Ethiopia , 2015 .

[64]  J. Barcelo,et al.  Fungal and mycotoxin contamination of coffee beans in Benguet province, Philippines , 2015, Food additives & contaminants. Part A, Chemistry, analysis, control, exposure & risk assessment.

[65]  C. Vázquez,et al.  Evaluation of growth and ochratoxin A production by Aspergillus steynii and Aspergillus westerdijkiae in green-coffee based medium under different environmental conditions , 2014 .

[66]  Francisco J. Espinosa-García,et al.  Diversity and Communities of Foliar Endophytic Fungi from Different Agroecosystems of Coffea arabica L. in Two Regions of Veracruz, Mexico , 2014, PloS one.

[67]  Radhika Dave,et al.  Extreme vulnerability of smallholder farmers to agricultural risks and climate change in Madagascar , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[68]  M. A. Cirillo,et al.  Ochratoxigenic fungi associated with green coffee beans (Coffea arabica L.) in conventional and organic cultivation in Brazil , 2013, Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology].

[69]  D. Pot,et al.  Inheritance of resistance to coffee wilt disease (Fusarium xylarioides Steyaert) in Robusta coffee (Coffea canephora Pierre) and breeding perspectives , 2013, Tree Genetics & Genomes.

[70]  Aaron P. Davis,et al.  The Impact of Climate Change on Indigenous Arabica Coffee (Coffea arabica): Predicting Future Trends and Identifying Priorities , 2012, PloS one.

[71]  T. Alemu.  A review of coffee wilt disease, Gibberella xylarioides (Fusarium xylarioides) in Africa with special reference to Ethiopia , 2012 .

[72]  J. Vandermeer,et al.  Indirect biological control of the coffee leaf rust, Hemileia vastatrix, by the entomogenous fungus Lecanicillium lecanii in a complex coffee agroecosystem , 2012 .

[73]  M. Kenny,et al.  Germination and growth of Colletotrichum acutatum and Colletotrichum gloeosporioides isolates from coffee in Papua New Guinea and their pathogenicity to coffee berries , 2012, Australasian Plant Pathology.

[74]  C. Clément,et al.  Fungicide impacts on photosynthesis in crop plants , 2012, Photosynthesis Research.

[75]  T. Gianfagna,et al.  Aspergillus oryzae NRRL 35191 from coffee, a non-toxigenic endophyte with the ability to synthesize kojic acid , 2012, Mycological Progress.

[76]  G. Jard,et al.  Review of mycotoxin reduction in food and feed: from prevention in the field to detoxification by adsorption or transformation , 2011, Food additives & contaminants. Part A, Chemistry, analysis, control, exposure & risk assessment.

[77]  H. Hindorf,et al.  A review of three major fungal diseases of Coffea arabica L. in the rainforests of Ethiopia and progress in breeding for resistance in Kenya , 2011 .

[78]  S. Kocsubé,et al.  Chemical, Physical and Biological Approaches to Prevent Ochratoxin Induced Toxicoses in Humans and Animals , 2010, Toxins.

[79]  C. Costa-Neto,et al.  Biological activities of the fermentation extract of the endophytic fungus Alternaria alternata isolated from Coffea arabica L. , 2009 .

[80]  S. Kocsubé,et al.  An Overview of ochratoxin research , 2009 .

[81]  B. Goates,et al.  Effect of biofumigation with volatiles from Muscodor albus on the viability of Tilletia spp. teliospores. , 2009, Canadian journal of microbiology.

[82]  J. Frisvad,et al.  Isolation, identification and toxigenic potential of ochratoxin A-producing Aspergillus species from coffee beans grown in two regions of Thailand. , 2008, International journal of food microbiology.

[83]  M. C. Aime,et al.  Entomopathogenic fungal endophytes , 2008 .

[84]  S. Nelson.  Cercospora Leaf Spot and Berry Blight of Coffee , 2008 .

[85]  P. Zollo,et al.  Fungicidal Potential of Essential Oils and Fractions from Cymbopogon citratus, Ocimum gratissimum and Thymus vulgaris to Control Alternaria padwickii and Bipolaris oryzae, Two Seed-Borne Fungi of Rice (Oryza Sativa L.) , 2007 .

[86]  Naresh Magan,et al.  Post-harvest control strategies: minimizing mycotoxins in the food chain. , 2007, International journal of food microbiology.

[87]  J. Palumbo,et al.  Inhibition of ochratoxin A production and growth of Aspergillus species by phenolic antioxidant compounds , 2007, Mycopathologia.

[88]  B. Campbell,et al.  Suppression of ochratoxin biosynthesis by naturally occurring alkaloids , 2007, Food additives and contaminants.

[89]  S. McCook,et al.  Global rust belt: Hemileia vastatrix and the ecological integration of world coffee production since 1850 , 2006 .

[90]  M. Rutherford.  Current knowledge of coffee wilt disease, a major constraint to coffee production in Africa. , 2006, Phytopathology.

[91]  B. Bertrand,et al.  Coffee resistance to the main diseases: leaf rust and coffee berry disease , 2006 .

[92]  P. Bayman,et al.  Fungal Epiphytes and Endophytes of Coffee Leaves (Coffea arabica) , 2005, Microbial Ecology.

[93]  M. Wingfield,et al.  Identification of the Armillaria root rot pathogen in Ethiopian plantations , 2004 .

[94]  S. Schorr-Galindo,et al.  Study of ochratoxin A‐producing strains in coffee processing , 2004 .

[95]  A. Wheals,et al.  Toxigenic fungi associated with processed (green) coffee beans (Coffea arabica L.). , 2003, International journal of food microbiology.

[96]  A. Wheals,et al.  Microbial diversity during maturation and natural processing of coffee cherries of Coffea arabica in Brazil. , 2000, International journal of food microbiology.

[97]  M. Z. Basílico,et al.  Inhibitory effects of some spice essential oils on Aspergillus ochraceus NRRL 3174 growth and ochratoxin A production , 1999, Letters in applied microbiology.

[98]  J. Miller,et al.  Mycotoxin in grain , 1994 .

[99]  C. Levi,et al.  Mycotoxins in coffee. , 1980, Journal - Association of Official Analytical Chemists.

[100]  R. Maroun,et al.  Mycotoxins: Factors influencing production and control strategies , 2021, AIMS Agriculture and Food.

[101]  S. Dane,et al.  Isolation and Identification of Fungal Pathogens Contaminating Some Coffee Powder Marketed in the City of Abuja , 2020 .

[102]  Mark S. Calabon,et al.  Morphological approaches in studying fungi: collection, examination, isolation, sporulation and preservation , 2020 .

[103]  S. Ghosh,et al.  Endophytes: A Potential Bio-agent for the Plant Protection , 2020, Innovative Pest Management Approaches for the 21st Century.

[104]  A. Chakravarthy.  Innovative Pest Management Approaches for the 21st Century: Harnessing Automated Unmanned Technologies , 2020 .

[105]  B. Naik.  Biosynthesis of silver nanoparticles from endophytic fungi and their role in plant disease management , 2020, Microbial Endophytes.

[106]  A. Wassie.  Integrated Diseased Management on Coffee Wilt Disease Caused by Fusarium Xylarioides and its distribution in Ethiopian Review , 2019 .

[107]  M. Khan,et al.  Effect of Nanoparticles on Plant Pathogens , 2019, Advances in Phytonanotechnology.

[108]  G. Carrión,et al.  Fungal diversity and Fusarium oxysporum pathogenicity associated with coffee corky-root disease in Mexico , 2019 .

[109]  Zhaoxin Lu,et al.  Growth inhibition of Fusarium graminearum and reduction of deoxynivalenol production in wheat grain by bacillomycin D , 2018 .

[110]  S. Maharachchikumbura,et al.  Phaeosaccardinula coffeicola and Trichomerium chiangmaiensis, two new species of Chaetothyriales (Eurotiomycetes) from Thailand , 2018 .

[111]  D. Vaidya,et al.  Ochratoxin A in Food: An Overview , 2017 .

[112]  S. Indarti,et al.  Pathogenicity of Nematofagous Fungus for Control of Pratylenchus coffeae Nematodes on Coffee Plants , 2017 .

[113]  K. Hyde,et al.  Two new species of sooty moulds, Capnodium coffeicola and Conidiocarpus plumeriae in Capnodiaceae , 2015 .

[114]  A. Akarapisan,et al.  Isolation and identification of Aspergillus species producing Ochratoxin A in Arabica coffee beans. , 2015 .

[115]  Oliveira Rjv,et al.  Endophytic fungal diversity in coffee leaves (Coffea arabica) cultivated using organic and conventional crop management systems , 2014 .

[116]  J. Avelino,et al.  Impact of field pests and diseases on coffee quality , 2012 .

[117]  F. Rodrigues,et al.  Infection Process of Cercospora coffeicola on Coffee Leaf , 2011 .

[118]  K. Kouno,et al.  Evaluation of cellulolytic and hemicellulolytic abilities of fungi isolated from coffee residue and sawdust composts. , 2011, Microbes and environments.

[119]  Prihastuti.  Characterization of Colletotrichum species associated with coffee berries in northern Thailand , 2009 .

[120]  S. Arabia,et al.  Mycotoxins and Toxigenic Fungi in Arabic Coffee Beans in Saudi Arabia , 2007 .

[121]  M. Rutherford,et al.  Pests and Diseases of Coffee in Eastern Africa: A Technical and Advisory Manual , 2006 .

[122]  Jean Nicolas Wintgens,et al.  Coffee: growing, processing, sustainable production. A guidebook for growers, processors, traders, and researchers. , 2004 .

[123]  W. Otieno.  Armillaria root rot of tea in Kenya : characterization of the pathogen and approaches to disease management , 2002 .

[124]  Christina A. Cuomo,et al.  Source (or Part of the following Source): Type Article Title Comparative Genomics Reveals Mobile Pathogenicity Chromosomes in Fusarium Author(s) , 2022 .