Comprehensive Review of Fungi on Coffee
Abstract
:1. Introduction
2. Results
2.1. Records of Coffee Fungi
2.2. Endophyte Role in Coffee Plants
2.3. Pathogen Effect on Coffee and Coffee Disease
2.3.1. Detection and Identification of Diseases
2.3.2. Coffee Leaf Rust
- Hosts: C. arabica (arabica coffee) and C. canephora (robusta coffee), the two most important commercial coffee species [56].
- Symptoms and signs: Infection occurs on the leaves of coffee. The first observable symptoms are small, and light-yellow spots on the upper surface of leaves. As the diameter of these points gradually increases, a large number of orange urediniospores (=uredospores) appear under the leaf surface. The fungus forms spores through stomata instead of penetrating the epidermis like most rust-causing species, so it does not form many typical rust pustules. Powdery lesions under leaves appear orange-yellow to red-orange with a high degree of variance. Although disease spots can develop anywhere on the leaf, they tend to concentrate around the edges, where dew and raindrops gather. The center of the spot eventually dries out and turns brown, while edges of the lesions continue to expand and produce new spores. At the beginning of the season, the disease usually first appears on the lower branches, and infection progresses slowly up the tree. Infected leaves fall prematurely, leaving long branches without leaves [14,56,57,58,59].
- Pathogen biology: Hemileia vastatrix mainly exists in the form of dikaryotic, and nutrient-absorbing mycelium between cells in leaves of its coffee host. Short pedicels are clustered throughout stomata and below leaves, with dual-nucleated spores. Towards the end of the season, sometimes under cool, dry conditions, spores are produced from polyspores on older attached leaves. After nuclear division and meiosis, these sporozoites germinate to produce basidia, each of which forms four haploid sporozoites [14,56,57,58,59].
- Disease cycle: Urediniosporic life cycle as its most important source of inoculum, can cause infection and develop into lesions, producing more urediniospores. Spore adhesion to the host surface, germination of urediniospores, formation of an adhesion layer on stomata, penetration, and intercellular and intracellular colonization are various steps of the disease cycle. The disease cycle of Coffee Leaf Rust is discussed in Talhinhas et al. [22].
- Disease management:
- Cultural practices: Agroforestry practices of tree-crop mixing, timely pruning, handling and de-suckering, regular change of crop cycle [49].
- Biological practices: Pichia membranifaciens is a yeast strain isolated from soil that can reduce the Hemileia vastatrix spore viability [59].
- Resistant varieties: Such as HDT (Hıbrido de Timor), Catimor and Sarchimor populations [22].
2.3.3. Coffee Berry Disease
- Pathogen: Colletotrichum kahawae is a particularly devastating pathogen that affects developing berries, leading to berry rot and shedding before bean formation. Colletotrichum kahawae has not been reported outside Africa or in low altitudes. Coffee Berry Disease was first detected and identified by McDonald in Kenya in 1922 [14].
- Symptoms and signs: Characteristic symptoms are progressive anthracnose of young and expanding coffee berries. Symptoms present as small water-soaked lesions that rapidly become dark and sunken. These lesions expand, causing rot of the entire berry under humid conditions, and pink spore masses become visible on the lesion surface. Berries are often shed from branches at an early stage of the disease. Lesions may also occur on young berry stalks, causing them to shed before lesions are evident on berries. Pale, corky lesions (scab lesions) also appear on young and mature berries that are resistant to infection. They may completely heal or remain dormant until berries ripen. This disease also affects ripening berries, causing a ‘brown blight’ phase as typical dark, sunken anthracnose lesions that envelop the red berries. Colletotrichum kahawae may also infect flowers under wet conditions, causing brown lesions on petals [14,58,60].
- Pathogen biology: The fungus settles in the mature bark of coffee buds and infects flowers, mature fruits, and leaves. Under high humidity and high temperature, conidia germinate and form germ tubes and appendages when contacted with susceptible tissues [61].
- Disease cycle: The Coffee Berry Disease cycle begins each year at the first rain event and is subsequently maintained by rain-splash dispersal and secondary inoculation of conidia onto healthy berries in the rainy season. The disease cycle of Coffee Berry Disease is discussed in De Silva et al. [62].
- Disease management:
- Cultural practices: Shading with fruit trees and irrigation to induce early flowering to decrease the severity and all berries should be removed at the end of the planting season to prevent them from becoming a source of inoculation for new crops [60].
- Biological control: Many components in the microbiota (fungi and bacteria) on coffee trees show very high antagonistic levels and have a strong antagonistic effect on Colletotrichum kahawae. However, these agents have not been developed into commercial biocontrol agents [60].
2.3.4. Coffee Wilt Disease
- Symptoms and signs: First, leaves turn yellow before withering and developing brown necrotic lesions. Finally, leaves curl, dry, and fall. This process can start from any part of the plant, but eventually, symptoms spread to the rest of the plant. Symptoms first present on the coffee stem, where fungi colonize, and the host response blocks vascular bundles, resulting in blue-black stains [14,47,58,63].
- Pathogen biology: Conidia and ascospores are spread by wind, rain and through human activities (harvesting, pruning). Pathogens penetrate wounds, so any agent causing wounds aids the spread of the fungus. Krantz and Mogk in 1973 noted that most dying and dead trees had been wounded during weeding. Insects may also spread the disease from one tree to another tree [64].
- Disease cycle: Incubation period from first symptoms to death of tree varies, although most affected trees die 2–3 months after initial symptoms were observed. It usually quickly kills infected mature trees within just 6 months after the first external symptoms appear, resulting in a decline of total yield. Coffee quality may also be affected by premature berry ripening. The disease cycle of Coffee Wilt Disease is discussed in Alemu et al. [65].
- Disease management:
- Cultural practices: Frequent inspection, along with burning infected material and spraying soil surfaces with 2.5% copper (II) sulphate. Replanting should not be done until 6 months after uprooting infected trees to allow the viability of soil inoculum to decline. It is recommended to grow cover crops such as Desmodium sp. and haricot bean, which are very efficient in suppressing weeds (so reducing the need for slashing) and as legumes, promote the growth of coffee trees [63].
- Chemical control: Ridomil Gold (metalxyl 8% + Mancozeb 64%) 68% Wp 2.5 kg/ha, when disease on set, used at 7, 14, 21, 28 days. Pencase 80% WP (Mancozeb) at the rate of 2.5 kg/ha, when disease on set, used at 7, 14, 21 days [63].
- Biological control: The strain of Bacillus subtilis (AUBB20) is the most antagonistic to this disease. Tricoderma viride and Tricoderma harzianum have shown good potential in inhibiting the mycelial growth of Fusarium xylarioides, but no effective methods of biological control are currently available [63].
2.3.5. Brown Eye Spot or Cercospora Blotch
- Symptoms and signs: on the leaves, small, round to irregular spots, and brown to light brown lesions first appear. The number and size of lesions then increase before eventually the entire leaf is affected. The edge of the lesion may appear dark purple or black, and it may be encircled by a yellow halo. Severely infected leaves turn yellow and fall off; lesions on green berries are initially brown, sunken, longitudinal, irregular or oval with a gray center. Infection can occur at any stage of berry growth; on the red cherries, first, large, sunken, and blackened areas cover with silvery fungal spores. Penetration into the seeds may cause the pulp to stick to parchment paper during processing, and damage the product. Cercospora coffeicola reduces productivity and lowers the beverage quality of coffee [14,57,67].
- Pathogen biology: Wind, splashing water and human activities cause spores (conidia) to be deposited on leaves and petioles, beginning the disease cycle. Conidia germinate at moderate to warm (20–28 °C) temperatures [68].
- Disease cycle: In warm and humid periods, new infections and sporulation occur every 7 to 10 days. Pathogen easily spreads in fields via wind, rain, and irrigation water. It survives as a pathogen in weeds and infested crop fragments, where it is capable of re-infecting grown plants. The disease cycle of Cercospora Blotch is discussed in Souza et al. [69].
- Disease management:
- Biological control: No biological control measures have been developed [68].
- Cultural practices: Elimination of crop debris, weed hosts and provide 35–65% shade. In order to maintain adequate plant nutrition, nitrogen fertilizers are used. Plant only high-quality seeds, and destroy infected crops in time after the final harvest and before replanting. Select a reasonable planting density (10 ft × 10 ft for robusta while 8 ft × 8 ft for arabica). Avoid planting coffee transplants too deep in soils [68].
- Chemical control: Fungicide sprays are necessary for disease control in wet conditions, but proper fungicides, rates, and fungicide rotations such as Chlorothalonil and Chlorothalonil Mixtures, Strobilurins and Strobilurin Mixtures should be followed [68].
2.3.6. Armillaria Root Rot
- Pathogen biology: This fungus usually exists in soil, and when coffee trees grow in unfavorable conditions, it infects the tree. For example, drought, soil compaction, root injury, and nutrient deficiency may induce it to infect the coffee tree. The fungus produces filaments on the ground, and these filaments can invade healthy roots, move to the root collar, and spread throughout the trunk. The infection causes sapwood in the affected area to rot and eventually kill the tree [70].
- Disease cycle: Armillaria spreads in two ways. The first method of transmission is through airborne sexual spores, which can sometimes lead to the creation of new infection centers. The second method of spread is through the growth of pathogens from infected trees to neighboring trees via mycelial transfer at the location where the diseased roots come into contact with each other or via rhizomes that grow through the ground. Depending on the climate, stump size, and other factors, Armillaria can live up to 50 years or more. The disease cycle of Armillaria root rot is discussed in Jayawardena et al. [71].
- Disease management: The affected trees are incurable. However, if the disease is detected early enough, host trees can be preserved. It is important to prevent this disease by avoiding conditions that cause the tree’s vitality to decline. As Armillaria root rot can last for many years, avoid replanting where the diseased trees have been removed [14,58,70].
- Biological control: Use antagonistic fungi to preemptively settle or eliminate Armillaria species in coffee plants.
- Soil barrier: Creating a barrier in the soil to root and rhizomorph growth may be a practical way to limit the pathogen’s spread, and this is called trenching. This is done by digging a trench down to 1 m (about 3 ft), lining it with plastic, and backfilling.
- Chemical control: Usually after stump removal and before planting, fumigants such as chloropicrin, carbon disulphide, and methyl bromide are used in orchards to eradicate inocula from the soil.
2.4. Distribution of Pathogenic Fungi on Coffee Worldwide
2.5. Pathogenic and Toxigenic Fungi on Coffee
3. Discussion and Conclusions
4. Materials and Methods
4.1. Fungal Taxa Reported on Coffee
4.2. Tables of Coffee Fungi
4.3. Graphs of Coffee Fungi
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Lu, L.; Tibpromma, S.; Karunarathna, S.C.; Jayawardena, R.S.; Lumyong, S.; Xu, J.; Hyde, K.D. Comprehensive Review of Fungi on Coffee. Pathogens 2022, 11, 411. https://doi.org/10.3390/pathogens11040411
Lu L, Tibpromma S, Karunarathna SC, Jayawardena RS, Lumyong S, Xu J, Hyde KD. Comprehensive Review of Fungi on Coffee. Pathogens. 2022; 11(4):411. https://doi.org/10.3390/pathogens11040411
Chicago/Turabian StyleLu, Li, Saowaluck Tibpromma, Samantha C. Karunarathna, Ruvishika S. Jayawardena, Saisamorn Lumyong, Jianchu Xu, and Kevin D. Hyde. 2022. "Comprehensive Review of Fungi on Coffee" Pathogens 11, no. 4: 411. https://doi.org/10.3390/pathogens11040411