Farmers are facing serious plant protection issues and phytosanitary risks, in particular in the tropics. Such issues are food insecurity, lower income in traditional low-input agroecosystems, adverse effects of pesticide use on human health and on the environment in intensive systems and export restrictions due to strict regulations on quarantine pests and limits on pesticide residues. To provide more and better food to populations in both the southern and northern hemispheres in a sustainable manner, there is a need for a drastic reduction in pesticide use while keeping crop pest and disease damage under control. This can be achieved by breaking with industrial agriculture and using an agroecological approach, whose main pillar is the conservation or introduction of plant diversity in agroecosystems. Earlier literature suggest that increasing vegetational biodiversity in agroecosystems can reduce the impact of pests and diseases by the following mechanisms: (1) resource dilution and stimulo-deterrent diversion, (2) disruption of the spatial cycle, (3) disruption of the temporal cycle, (4) allelopathy effects, (5) general and specific soil suppressiveness, (6) crop physiological resistance, (7) conservation of natural enemies and facilitation of their action against aerial pests and (8) direct and indirect architectural/physical effects. Here we review the reported examples of such effects on a broad range of pathogens and pests, e.g. insects, mites, myriapods, nematodes, parasitic weeds, fungi, bacteria and viruses across different cropping systems. Our review confirms that it is not necessarily true that vegetational diversification reduces the incidence of pests and diseases. The ability of some pests and pathogens to use a wide range of plants as alternative hosts/reservoirs is the main limitation to the suppressive role of this strategy, but all other pathways identified for the control of pests and disease based on plant species diversity (PSD) also have certain limitations. Improving our understanding of the mechanisms involved should enable us to explain how, where and when exceptions to the above principle are likely to occur, with a view to developing sustainable agroecosystems based on enhanced ecological processes of pest and disease control by optimized vegetational diversification.

Significance: Decades of research have fostered the now-prevalent assumption that noncrop habitat facilitates better pest suppression by providing shelter and food resources to the predators and parasitoids of crop pests. Based on our analysis of the largest pest-control database of its kind, noncrop habitat surrounding farm fields does affect multiple dimensions of pest control, but the actual responses of pests and enemies are highly variable across geographies and cropping systems. Because noncrop habitat often does not enhance biological control, more information about local farming contexts is needed before habitat conservation can be recommended as a viable pest-suppression strategy. Consequently, when pest control does not benefit from noncrop vegetation, farms will need to be carefully comanaged for competing conservation and production objectives.

Coffee rust is a leaf disease caused by the fungus, Hemileia vastatrix. Coffee rust epidemics, with intensities higher than previously observed, have affected a number of countries including: Colombia, from 2008 to 2011; Central America and Mexico, in 2012–13; and Peru and Ecuador in 2013. There are many contributing factors to the onset of these epidemics e.g. the state of the economy, crop management decisions and the prevailing weather, and many resulting impacts e.g. on production, on farmers’ and labourers’ income and livelihood, and on food security. Production has been considerably reduced in Colombia (by 31 % on average during the epidemic years compared with 2007) and Central America (by 16 % in 2013 compared with 2011–12 and by 10 % in 2013–14 compared with 2012–13). These reductions have had direct impacts on the livelihoods of thousands of smallholders and harvesters. For these populations, particularly in Central America, coffee is often the only source of income used to buy food and supplies for the cultivation of basic grains. As a result, the coffee rust epidemic has had indirect impacts on food security. The main drivers of these epidemics are economic and meteorological. All the intense epidemics experienced during the last 37 years in Central America and Colombia were concurrent with low coffee profitability periods due to coffee price declines, as was the case in the 2012–13 Central American epidemic, or due to increases in input costs, as in the 2008–11 Colombian epidemics. Low profitability led to suboptimal coffee management, which resulted in increased plant vulnerability to pests and diseases. A common factor in the recent Colombian and Central American epidemics was a reduction in the diurnal thermal amplitude, with higher minimum/lower maximum temperatures (+0.1 °C/-0.5 °C on average during 2008–2011 compared to a low coffee rust incidence period, 1991–1994, in Chinchiná, Colombia; +0.9 °C/-1.2 °C on average in 2012 compared with prevailing climate, in 1224 farms from Guatemala). This likely decreased the latency period of the disease. These epidemics should be considered as a warning for the future, as they were enhanced by weather conditions consistent with climate change. Appropriate actions need to be taken in the near future to address this issue including: the development and establishment of resistant coffee cultivars; the creation of early warning systems; the design of crop management systems adapted to climate change and to pest and disease threats; and socio-economic solutions such as training and organisational strengthening.

Despite the growing interest in Ecosystem-based Adaptation, there has been little discussion of how this approach could be used to help smallholder farmers adapt to climate change, while ensuring the continued provision of ecosystem services on which farming depends. Here we provide a framework for identifying which agricultural practices could be considered ‘Ecosystem-based Adaptation’ practices, and highlight the opportunities and constraints for using these practices to help smallholder farmers adapt to climate change. We argue that these practices are (a) based on the conservation, restoration or management of biodiversity, ecosystem processes or services, and (b) improve the ability of crops and livestock to maintain crop yields under climate change and/or by buffering biophysical impacts of extreme weather events or increased temperatures. To be appropriate for smallholder farmers, these practices must also help increase their food security, increase or diversify their sources of income generation, take advantage of local or traditional knowledge, be based on local inputs, and have low implementation and labor costs. To illustrate the application of this definition, we provide some examples from smallholders’ coffee management practices in Mesoamerica. We also highlight three key obstacles that currently constrain the use of Ecosystem-based Adaptation practices (i) the need for greater understanding of their effectiveness and the factors that drive their adoption, (ii) the development supportive and integrated agriculture and climate change policies that specifically promote them as part of a broader agricultural adaptation program; and (iii) the establishment and maintaining strong and innovative extension programs for smallholder farmers. Our framework is an important starting point for identifying which Ecosystem-based Adaptation practices are appropriate for smallholder farmers and merit attention in international and national adaptation efforts

The assessment of crop yield losses is needed for the improvement of production systems that contribute to the incomes of rural families and food security worldwide. However, efforts to quantify yield losses and identify their causes are still limited, especially for perennial crops. Our objectives were to quantify primary yield losses (incurred in the current year of production) and secondary yield losses (resulting from negative impacts of the previous year) of coffee due to pests and diseases, and to identify the most important predictors of coffee yields and yield losses. We established an experimental coffee parcel with full-sun exposure that consisted of six treatments, which were defined as different sequences of pesticide applications. The trial lasted three years (2013–2015) and yield components, dead productive branches, and foliar pests and diseases were assessed as predictors of yield. First, we calculated yield losses by comparing actual yields of specific treatments with the estimated attainable yield obtained in plots which always had chemical protection. Second, we used structural equation modeling to identify the most important predictors. Results showed that pests and diseases led to high primary yield losses (26%) and even higher secondary yield losses (38%). We identified the fruiting nodes and the dead productive branches as the most important and useful predictors of yields and yield losses. These predictors could be added in existing mechanistic models of coffee, or can be used to develop new linear mixed models to estimate yield losses. Estimated yield losses can then be related to production factors to identify corrective actions that farmers can implement to reduce losses. The experimental and modeling approaches of this study could also be applied in other perennial crops to assess yield losses.