Pest and Disease Threats to Coffee, Cocoa and Rice

Dr. Alan MacLeod & Dr. Julian Smith The Food and Environment Research Agency, UK

A brief introduction to crop pests, their impacts and the value of Pest Risk Analysis

Crop pests and types of consequence

Figures on the losses of crop production due to pests (FAO, 2002) are extremely hard to validate, however, it is suggested that total global potential losses are in the order of 34% for weeds, 18% for animals and 16% for pathogens (Oerke, 2006).  It has also been estimated that losses specifically in rice could be 30% annually due to weeds, 15% due to insect pests and 15% due to pathogens (Oerke et al 1994).  The same level of yield losses (15%) was estimated in coffee by both insect pests and diseases whilst weeds had a lower impact in the crop, causing 10% yield losses. 

When faced with a projected 34% increase in population to 9.3 billion by 2050 the justification to ‘produce more, and lose less’ (CABI) is compelling.  Add to this the recognised risk of increased pest introductions due to climate change, increased global trade and increased human mobility, and it is clear that any future must take seriously the threat presented by both current and new crop pests.  Yet losses due to crop pest are not only felt in terms of volume lost, and potentially the most significant impacts due to pests are not in the main felt around the scale of these norms, but in the extremes of unusual events.  Examples include impacts on food security when produce is scare, or on price when in excess, or when a pest outbreak triggers a quarantine and trade embargo on an exporting nation.

Indeed, a reasonable argument can be put forward that a pest, which exhibits a predictable behaviour and is amenable to control, provides for opportunity in a private sector commercial sense when a premium can be realised by the producer that is best able to effect control and maximise production and quality.  It could be ventured that this separates out the good commercial farmers.  The converse to this is with unpredictable pests, such as new pests or outbreak pests, which are not anticipated and, if only due to the unfamiliarity, hard to control, even by the best farmers.  A classic historic example is with coffee production in Sri Lanka where the introduction of coffee leaf rust, caused by the pathogen Hemileia vastatrix, was so devastating as to make cultivation uneconomic leading to eventually abandonment of the crop (Kushalappa and Eskes 1989).  Similarly, a quarantine situation that affects exports will not differentiate between good and bad farmers.  These pest events are levelling amongst farmers, with all being vulnerable.

Crop pest outbreaks on the rise

A recent study by Waage et al. (2009) mapped out a time sequence of pest introductions for Europe and Africa, and demonstrated the rise in new pest introduction events for Europe over recent deacades, but not Africa where, over the same period, records had decreased.  However, over the past 20 years East Africa alone has been beset by pest outbreaks that have reached epidemic status and yet were, hitherto, considered of minor, or of localised, impact (Smith et al, 2008a).  It was concluded that the disparity in trends for pest new pest records for Europe and Africa was attributable to European plant health systems being more effective than those in Africa; it was not to conclude that Africa was at less risk than Europe from new pests.

Box 1 gives example of some current and major crop pest outbreak events for East Africa that have occurred on staple crops that continue to have significant consequences for food security of the people in the region, especially for those of the most vulnerable households.

Box 1.

Cassava Mosaic Disease (CMD) and Cassava Brown Streak Disease (CBSD):  A new and highly virulent strain of the CMD virus appeared in Uganda in 1988, which subsequently spread to epidemic proportions between 1989 to 1999 over much of Africa.  In Uganda alone it was estimated that losses of 60,000ha of cassava were incurred, equivalent to over 600,000 metric tonnes (US$60 million) of fresh cassava roots.  All the local varieties were found to be highly susceptible and as a consequence there were massive food shortages, peaking in 1994 when an estimated 3,000 people died of starvation. 

Responding to CMD, plant breeders were successful in identifying good disease resistance to the CMD virus and during the 2000s through to the current day a vast and highly successful replacement of cassava cultivars has taken place with CMD tolerant cultivars.  However, associated with this transformation has been the rise of a second and equally destructive viral disease, Cassava Brown Streak Disease, which is seemingly virulent to all the new CMD varieties and the landraces.  Ironically, this succession of viruses may be as a consequence of the success of the CMD tolerant cultivars that, through their dissemination, may have spread the CBSD virus and, through their widespread adoption, created a genetically more uniforme cassava landscape that is more amenable to the spread of the CBSD virus.  It is also speculated that a new CBSD virus strain, which has now acquired species status, may be more aggressive within the regions hitherto not at risk to CBSD.  Probably all three factors are at work.  It is worth speculating to the extent that the rise of CBSD could have been anticipated as an outcome of the success of the CMD tolerant cultivar adoption by farmers and mitigated against.

Banana Xanthomonas Wilt (BXW):  This bacteroal pathogen appeared in Mukono district of Central Uganda in early 2000.  The casual bacterium, Xanthomonas campestris pv. musacearum, had previously only been reported in Ethiopia, as long ago as 1964, where it was considered of minor importance to banana and enset.  At the time of the first outbreak in Uganda, concern was raised by the Ugandan government and CAB International on the potential of the pest to spread in the more intensive, compared to Ethiopia, banana systems of Uganda and the Great Lakes region.  Over the coming years, and as a consequence of a slow response by the donor community to be associated with a ‘prevention’ rather than ‘cure’ campaign, BXW spread throughout Uganda’s banana areas and beyond, including Democratic Republic of Congo, Tanzania, Rwanda, Burundi and Kenya.  It was projected that the spread of BXW within Uganda had an economic cost borne by smallholders of US$4 billion by 2010, but an even greater loss can be expected when measured with respect to household subsistence values where mutoki (cooked banana) is seen as an essential part of any meal.  Although, BXW had been limited to Ethiopia for nearly 40 years, with the increased mobility of people and the known tendency of people to carry vegetative banana cuttings for planting, the introduction of the causal organism of BXW to the banana areas of the Great Lake region could have been foreseen and plans for mitigation thought through. 

Quarantine

With respect of impacts associated with trade and quarantine it is easiest to find example amongst developed countries.  By example, Australia has only recently allowed the importation of apple from New Zealand due to Fire blight, having imposed a ban in 1921 (Arcuri et al., 2010) and the European Union maintains conditions on the importation of wheat from the United States because of risks from Tilletia indica, the pathogen causing Karnal Bunt (Sansford et al., 2008). What is interesting about quarantine pests, as oppose to pests threatening food security, is that the prevalence of a pest in the exporting country does not have to be high to evoke the quarantine condition as the measure of impact is with the importing nation only (Waage et al., 2005).  The absence of physical loss is not to underestimate the consequence of a quarantine pest as these can be of a major economic scale, impacting on government revenue and all those related businesses and livelihoods that may be intrinsically linked to a high volume traded export.

Box 2 illustrates for coffee and cocoa some of the scales of cultivation and potential for harm associated with major cultivated commodities as may be incurred as an outcome of a new pest introduction to a country.

Box 2.

Coffee:  Coffee is the world’s most widely traded agricultural commodity, with an estimated export value of US$15.4 billion in 2009/10.  As an industry the sector may employ about 26 million people, with some 72 countries as coffee producers.  For some of these nations, particularly developing nations of Africa, the value associated with coffee accounts for a significant percentage of foreign exchange earnings.  In the period 2000-2010 the coffee export value exceeded 10% of the country total export value for Burundi (59%), Ethiopia (33%), Rwanda (27%), Honduras 920%), Uganda (18%), Nicaragua (17%) and Guatemala (12%).  Given the importance of coffee as a commodity crop a pest outbreak that threatens the stability of coffee production may have far reaching consequences. 

In illustrating how pests may shape production example is drawn on the rapid rise of Fusarium wilt (Gibberella xylariodes) in East Africa during the 1990 (Rutherford, 2006).  This fungal pathogen was first reported in Africa in 1927 and has had periodic outbreaks in different regions.  An outbreak in Democratic Republic of Congo in the 1970s, associated with abandonment of coffee plantings due to civil unrest, spread into Uganda in the 1990s.  In Uganda, smallholder income declined by up to 50% and losses in 2003 were estimated at US$9.6 million.  Prior to the occurrence of Fusarium wilt coffee production mainly involved two species, Coffea Arabica L.(Arabica coffee) and C. excelsa A. Chev.  However, due to the susceptibility of C. excelsa cultivation has moved towards C. canephora Pierre ex. A. (Robusta coffee) which has greater resistance.  Currently, Fusarium wilt distribution is limited to Africa, and the major growing regions of the rest of the world remain free of the pathogen. 

Cocoa:  The devastating impact of Moniliophthora perniciosa (=Crinipellis perniciosa), causal agent of Witches’ broom of cocao (Theobroma cocao L. ) production is well documented from its initial observation in the late 1780s in Amazonia and subsequent spread to Surinam (1895), Guyana (1906), Ecuador (1918), Trinidad (1928), Colombia (1929), Grenada (1948) and Brazil (1989).  In each case yield reduction of between 50-90% are cited.  For Brazil, the impact of Witches’ broom disease reduced production from some 347,000 tonnes in 1988-1990, with Brazil falling from a position of the world’s 3rd largest producing at about 15% of total world production to that of becoming a net importer at 141,000 tonnes in 1998-2000.  To date, even with the cultivation of cultivars that have some resistance to Witches’ broom disease, levels of production have not returned to their previous levels.  During these times the industry has been buffered by an increase in cultivation by West and South East Asia, that to date remain free of the pathogen.  It is with obvious concern that the chocolate industry eyes the potential for the pest to spread to these new regions (Meinhardt et al., 2008).

Three other major pests stand to impact on cocao production, namely Frosty pod rot (Moniliophthora roreri), Black pod (Phytophthora megakarya and P. palmivora) and Swollen Shoot virus.  All these pests have regional distribution that demonstrates the continued need for risk evaluation and vigilance within phytosanitary regimes over cacao cultivation and trade for entry, prevention, early detection of any introduction event and response.

International agendas and Pest Risk Analysis

Reflective of these types of shock and impact, various instruments are in place to limit plant pest spread.  An extreme is in listing plant pathogens as bioterrorism weapons (e.g. USDA), and crop pests have come under the consideration of the Biological and Toxins Weapons Convention and in reviews such as that by Suffert et al. (2009).  A specific study on the risk associated with deliberate release of banana pathogens was conducted by Ploetz (2009), which brought together various metrics of risk and impact in defining a priority to pests of banana in the context of entry.  However, rather than being spread maliciously, plant pests more commonly increase their global distribution as “hitchhikers” on plants or plant products through trade, human movement or by other means.  Recognising that the spread of pests of crops, including coffee, cocoa or rice, from one geographical area to another is an issue of worldwide concern, countries co-operate via several international agreements (MacLeod et al., 2010).

The principal agreement aimed at preventing the spread of plant pests is the International Plant Protection Convention (IPPC), a multilateral treaty for international cooperation in plant protection, whereby designated National Plant Protection Organisation (NPPO) become signatories.  Further international co-operation can be facilitated at a supra-national /regional level across the globe, through the networking of NPPOs at the regional level in forming Regional Plant Protection Organizations (RPPOs) that act as inter-governmental coordinating bodies in the area of plant health.  RPPOs play an important role with regard to coordination and participation in activities among their members in order to promote and achieve plant health objectives, for example promoting harmonized phytosanitary measures and gathering and disseminating information, in particular in relation to IPPC matters (Macleod et al., 2010).  However, unlike NPPOs, RPPOs do not regulate pests, rather they make recommendations about which pests to regulate.  Tables 1, 2 and 3 list the major pests of coffee, rice and cocoa that are recommended for regulation by RPPOs in order to inhibit their spread.

Under the Convention the level of a pest threat to an ‘endangered area’ is determined through the frame of Pest Risk Analysis (PRA) (see Box 3) upon which appropriate phytosanitary measures for pest control may be justified.  PRA is applied primarily with respect of trade and quarantine and in the main example of use centres with developed countries and homeland protection from imports from 3rd countries.  In a developing world context, especially amongst African nations and in looking at homeland food security, there is little history of structured pest risk analysis to be pointed to.  Yet, this situation is changing, for example through the development of a network of pest risk analysts coordinated through the Centre of Phytosanitary Excellence (COPE) coordinated by  the Kenya Plant Health Inspectorate Service (Flood, 2010).  In addition, regional PRAs, or PRA-like exercises, have been coordinated for recent major pests such as Banana Xathomonas Wilt (Smith et al., 2008b) and cassava planting material and Cassava Brown Streak Disease (Smith et al., 2010) for the Great Lakes region of East Africa (see Box 1).

Box 3.

Pest Risk Analysis:  Deciding which pests should be recommended for regulation should be determined through a formal process of Pest Risk Analysis (PRA), consisting of three stages:

  1. Initiation,
  2. Pest risk assessment, and
  3. Pest risk management.

The stage of initiation may be through identification of a pest or pest pathway (e.g. trade), or review of an existing phytosanitary policy that may be subject to change and recognises a geographic area at risk and that forms the area for evaluation, referred to as the endangered area.  Risk communication is an integral component that should occur throughout each step.  

PRA is a science-based process that provides the rationale for determining appropriate phytosanitary measures for a specified PRA area; it is a process that evaluates technical, scientific, social and economic evidence to determine the characteristics of a pest threat and options for control.  The assessment takes into account the likelihood of the pest entry, establishment and spread, and the magnitude of potential economic, social and environmental consequences (e.g. Baker & MacLeod, 2005; Soliman, et al., 2010).  If the pest risk is deemed unacceptable, the analysis goes on to identify and evaluate management options that will reduce the pest risk to an acceptable level.  These pest risk management options are likely to be used to establish phytosanitary regulations. 

In summary PRA can be regarded as a process to answer four questions:

  1. Is a particular organism a plant pest?
  2. What is the likelihood of the pest entering, establishing and spreading?
  3. How much damage could the pest cause? and,
  4. What can be done to mitigate unacceptable impacts? 

Conclusion

When risk analysis is considered in terms of pest prevention, in ‘getting ahead of an impending epidemic curve’, the value for Africa and developing nations to embrace and invest in risk analysis, not only for coffee, cocoa and rice, but for all crop and plant resources, is substantial.

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