Untangling the coffee (root) knots in Africa

adminAnnual Report 2015, Making Crops Healthy0 Comments

A healthy, productive coffee plant.

A healthy, productive coffee plant.

If you are one of those whose day must be jump-started by coffee, then you are part of the millions that make coffee one of the world’s most important cash crops. Coffee is also the second most traded commodity, with an estimated total export value of US$19.1 billion in 2012/2013. More than 100 million people, mostly from developing tropical countries, depend on coffee-growing for their livelihoods. In Africa, it is a primary source of income for an estimated 10 million households across 25 countries and yet, production has been declining here by approximately 17% since the 1970s. Elsewhere, production has doubled over the last 50 years owing to skyrocketing increases in consumption.

This decline in production in Africa is primarily blamed on losses to pests and diseases and the associated costs in managing them. Pesticides, for example, account for over 30% of production costs. Among coffee pests, root-knot nematodes (Meloidogyne spp.) are a special threat, significant yet often overlooked. In South and Central America from where most of the information comes, root-knot nematodes are recognized as highly destructive pests that can wipe out entire coffee plantations and force a shift to other cash crops, such as sugarcane. In Brazil, for example, there is such emphasis on their importance that the Brazilian Agricultural Research Organization (EMBRAPA) has assembled a diagnostic kit specifically designed to rapidly detect the presence and assess the incidence of Meloidogyne spp. in coffee plantations.

Virtually no information exists on nematode pests affecting coffee in Africa, except for some early distribution and diagnostic studies. This is despite the obvious economic value of the crop in the continent. A key obstacle has been the lack of a robust and reliable diagnostic method. Identifying which species occur and the potential damage they pose provides valuable information towards making informed decisions on pest and disease management options. This is especially important for a perennial crop such as coffee.

IITA embarked on a quest to fill this gap together with experts and their students from the various partner academic and research institutions in the countries we work in, as well as from UC Davis (USA), EMBRAPA (Brazil), Ghent University (Belgium), and National Plant Protection Organization (The Netherlands). Over several years, hundreds of samples have been collected, cultured, processed, and disseminated to improve our knowledge of species diagnostics and their distribution.

These efforts are now beginning to achieve results, not only in building a wealth of knowledge about the pest in Africa but also in demonstrating how advanced technologies could help to clear the diagnostic confusion.

Traditionally, researchers have relied on morphometrics and female perineal patterns to identify Meloidogyne species—a burdensome, labor-intensive process dependent on scarce expertise that is now known to be greatly hampered by phenotypic plasticity and interspecific similarities. Despite its shortcomings, a biochemical-based diagnostic technique, reliant on isozyme profiles, has remained one of the most reliable and widely-used differentiation methods. Over time, molecular methods have been developed, in particular, species specific primers, but challenges and a lack of reproducibility persist for them. Even with rapidly declining costs, DNA barcoding has also continued to prove notoriously difficult, especially for the tropical root-knot nematodes. Mitochondrial genes, however, known for their uni-parental inheritance combined with high mutation rates, have increasingly become a focus as a useful diagnostic barcoding region. Using hundreds of populations from widespread geographical origins and variable crop hosts we screened a selection of quickly evolving mitochondrial coding genes. Our results indicated that mitochondrial haplotypes are strongly linked and consistent with traditional esterase isozyme patterns and confirmed that these barcodes can effectively distinguish closely-related species.

With this new tool in hand a rich abundance of species has recently been determined from just a handful of coffee samples from Kenya, Tanzania, and Uganda. At least six species of Meloidogyne have so far been identified, often demonstrating mixed species combinations from individual farms. The tropical species M. incognita and M. javanica were observed, as expected. The less commonly occurring and more temperate species, M.hapla, was also found, as was M. africana, a relatively unknown and little studied species. In addition M. paranaensis was collected from Uganda and M. izalcoensis from Tanzania, the first time either of these species had been found in Africa. At least two other populations represented new undescribed species, while a tentative identification of M.hispanica from Tanzania, if confirmed, would be the first known record of this species on coffee in Africa. Again, our vast lack of knowledge on pathogens in this region was underscored.

The recovery of M. africana from Tanzania creates interest from both taxonomic and pathological perspectives, as it is an early branching species of Meloidogyne that causes severe damage on coffee roots. From morphological measurements of our cultured populations, juveniles and females measured up perfectly with the description of M. africana by Whitehead (1959). Strangely though, the males perfectly matched the description of M. decalineata, which were also recorded by Whitehead (1968) from populations recovered from the same area as our M. africana from Lushoto, Tanzania. Sequencing of ribosomal (18S, ITS, 28S rDNA) and mitochondrial (Cox1) genes, however, confirmed that all specimens belonged to a single species. By carefully analyzing the typeslides, and with confirmation from the molecular analysis, it appears that the original descriptions of M. decalineata and M. africana may have been confused.

Left: Galling of roots by Meloidogyne africana. Right: Coffee tree root ball, showing extensive knotting and a galled clump of roots.

Left: Galling of roots by Meloidogyne africana.
Right: Coffee tree root ball, showing extensive knotting and a galled clump of roots.

To further complicate the situation, the other “African” coffee species, M. megadora, previously recovered and described from Angola and Uganda by Whitehead (1968) and M. oteifae recovered and described from the Congo by Elmiligy (1968), are morphologically very close to our current M. africana cultures. Using typeslides observation of M.oteifae, perineal patterns were found to be very similar to those of our M. africana population, which (another coincidence) also have the same sex-reversed dwarf males as described for M. megadora. Without cultures of these two species, it is not possible, yet, to clarify the link or dispel any further possible taxonomic confusion. It does, however, pose
the question about which species we really have infecting our coffee, and adds great weight to the value of establishing accurate diagnostic techniques to enable sound reliable information for use in crop and pest management decisions.

A further intriguing aspect is that M. africana is an early branching species within the genus. This basal position is of crucial importance in determining the ancestral characteristics of root-knot nematodes. Studying this nematode will allow us a glimpse into their origin, permitting us to have an insight into the evolution of their reproduction, virulence, and morphology. However, from another Tanzanian coffee field sample we recovered a population that is likely to represent a new, undescribed species, which appears to be an even earlier branching and more basal species than M. africana. So far, therefore, two African species from coffee, together with M. coffeicola (America) appear to be of a primitive nature, suggesting that coffee may have played a crucial role in the evolution of the pest. It is clear that M. africana substantially deforms and damages roots, and this is likely to lead to significant yield
losses. It is also clear that, although there appears quite a complex diversity of Meloidogyne species occurring on coffee, the situation may not be as complex as the existing literature may have us believe but we have very little knowledge about the true extent of the damage they are posing to the coffee sector.

And you thought having that aromatic “African” coffee was just as simple as brewing and pouring some into a cup!

This work has been made possible only through the interaction between a broad range of partners combining efforts and resources, which serves to demonstrate the impact that such a network can achieve. Support for this work has been received over an extended period of time from various separate projects, including those by USAID, Africa-Brazil Forum, BMZ/GIZ, VLIR, GGIAR CRP-RTB, CGIAR CRPHumidtropics.

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