7 Agroecology and Biodiversity Conservation

It might seem that all a seed needs to grow is fresh air, sunlight, fertile soil, and water—but a closer look reveals that there is a team of other organisms that support and protect the plant as it grows. Consider a hypothetical maize (Zea mays) crop. The essential nitrogen-containing nutrients it absorbs from the soil were deposited there by the nitrogen-fixing bacteria (Bradyrhizobium spp.) that lived in the leguminous soybean roots (Glycine max) that grew in the same field the previous season. The soil is rich in nutrients because it was fertilized with manure from cows (Bos taurus) and other livestock species. The maize plant’s ability to mine phosphorus and other nutrients from the soil is enhanced by the symbiosis between its roots and an arbuscular mycorrhizal fungus (Glomus fasciculatum). Molasses grass (Melinis minutiflora) intercropped with the maize both repels destructive stem borers (including Sesamia calamistis) and harbors a natural parasite of this pest (Cotesia sesamiae). This network of agriculture-associated organisms, together with the nonliving environment, is part of an agroecosystem. The study of agroecosystems in their environmental and socioeconomic contexts is known as agroecology.

Biodiversity

Earth is home to an amazing variety of life. Biological diversity, or biodiversity, is the term most commonly used to describe this variety. Living organisms, including plants, animals, and microbes, populate almost every environment on the planet. They interact and form complex associations in terrestrial environments like forests, grasslands, deserts, cities, and farmlands, as well as aquatic environments such as rivers, wetlands, estuaries, and oceans (Leemans & De Groot, 2003).

Biodiversity is complex. Scientists who study biodiversity seek to understand this complexity at multiple levels. Diversity ranges from the microscopic level, such as the genetics of individual organisms, to the landscape level, such as communities of different organisms (Gaston & Spicer, 2013). Scientists classify each unique organism into a species according to its genetic makeup, behavior, and ancestral history.

All species require energy, water, and nutrients to maintain life and reproduce. Each species accesses energy, water, and nutrients through unique means. Generally, species of terrestrial plants derive energy from the sun, and water and nutrients from the soil. Animals obtain energy and nutrients from consuming other organisms (“food”) and water from free-standing water bodies. Microorganisms, including bacteria, algae, protozoa, fungi, and viruses, are resourceful in obtaining nutrients through soil, water, other organisms, and the decomposition of organic materials (Gaston & Spicer, 2013; Leemans & De Groot, 2003).

Ecosystems and Ecosystem Services

In the physical environment, organisms interact to produce, transfer, and recycle energy, water, and nutrients. Organisms may interact through competition, herbivory, predation, parasitism, or mutualistic relationships. This network of organisms, the physical environment, and their interactions is known as an ecosystem. Within ecosystems, the processes that regulate the availability of energy, water, and nutrients are known as ecosystem functions (Leemans & De Groot, 2003).

Many ecosystem functions are essential for the survival of human beings. “Wait! Human beings?” you may ask. Yes! Humans make up an important part of ecosystems. Like all species, humans depend on ecosystems for water, energy, and food to survive. The ecosystem functions directly linked to human wellbeing are known as ecosystem services. Ecosystem services are wide-ranging. We encourage you to explore the Food and Agriculture Association’s website to learn more about ecosystem services and examples of services that are key to international agricultural development. Links are provided in the text box.

The examples available on the Food and Agriculture Association’s website all support this key point: human activity influences the health of ecosystems and the flow of ecosystem services. Human activity may enhance a particular service while simultaneously degrading another service. As ecosystem managers, humans are often chiefly concerned with the stability of a particular service and the resilience of ecosystems in the face of external shocks or disturbances (Galluzzi et al., 2011).

Let’s examine some principles and specific examples of how biodiversity in human-managed agroecosystems provisions critical ecosystem services that support plant, animal, and human health.

Biodiversity Within Agroecosystems

From an agroecological perspective, agriculture is an organized way in which humans manage natural processes and harness ecosystem services for producing food, fiber, fuel, medicines, and other goods for human consumption. The challenge of a well-managed agroecosystem is to harvest these goods according to human needs without compromising ecological functions. Agroecology, defined earlier in this chapter as the study of agroecosystems in their environmental and socioeconomic contexts, is an essential tool in optimizing this balance between extracting goods and preserving ecosystem services. As a science, agroecology applies ecological theory to the management of agricultural systems (Pretty et al., 2011). It emphasizes the interrelatedness of all agroecosystem components and the complex dynamics of ecological processes (Alteri, 2002).

Since modern agricultural practices often unsustainably exploit ecosystem services, there is a need for farmers, researchers, policy planners, and conservationists to reconsider the relationships between agricultural production and biodiversity conservation. Sustainable land management strategies must take into account how to balance economic pressures to maximize agricultural productivity with the reality that habitat loss and the exploitation of natural ecosystems are destructive to the earth’s environment, agricultural productivity, and human wellbeing (Galluzzi et al., 2011). For example, coffee producers may clear the land of trees to intensify and expand coffee production. However, this deforestation destroys habitats for pollinators and natural predators of coffee berry borers such as birds, often leading to the increased use of toxic chemical pesticides and in turn promoting pesticide resistance (Chain-Guadarrama et al., 2019). Thus, the long-term optimization of agricultural productivity requires consideration of the impacts of agricultural practices on the biodiversity of crop and non-crop species within agroecosystems.

The rest of this section considers several levels of biodiversity management and conservation within agroecosystems: genetic diversity within species, the integration of diverse agricultural species, and the significance of non-crop species in agroecosystems both above and below ground.

Genetic Diversity: A single species can include many breeds or varieties.

Traditionally, all varieties of agricultural species were landraces, local crops, or animal breeds adapted explicitly to a particular location. A crop that a group of people has cultivated for generations, bred using traditional methods, and incorporated into their cultural heritage is typically a landrace. Its characteristics are uniquely suited to its environment of origin. See Zeven (1998) for further discussion of landraces.

In the modern period of agricultural development, also known as the Green Revolution, more farmers have begun buying and growing newly developed and improved seeds representing a few crop species rather than the many traditional crops and varieties that they planted before. An improved breed is one that has been subjected to modern breeding programs to combine desirable qualities from various landraces. Similarly, a hybrid is a strategic cross between two inbred varieties made to exhibit superior traits. A key figure in advancing improved seed varieties is Norman Borlaug (1914–2009), who has been called the father of the Green Revolution. He won the Nobel Peace Prize in 1970 for his pioneering work in Mexico developing improved wheat varieties. The applications of such varieties have dramatically increased crop yields and improved food security status for populations around the world.

However, improved varieties are not readily available to everyone, especially in the Global South, due to a lack of applicable research, market access, knowledge, and/or monetary capital. Additionally, improved seeds are typically selected for highly fertile environments that use fertilizers, herbicides, and pesticides; they are not adapted to a wide range of environments. Thus, they may not be productive without costly agrochemical inputs that may be inaccessible or available only in limited quantities or at particular times in many locations around the world. Improved varieties must be specifically developed for the local environment to match the hardiest landraces in adverse conditions. Meanwhile, a drawback of hybrids is that they are not open-air-pollinated as landraces are, so farmers cannot own their seed lines. While all hybrids of the same type are uniform, many of their offspring revert to the less desirable characteristics of the original parent varieties, forcing a farmer to buy new hybrid seeds each year for the best results.

Excessive replacement of landraces with improved seeds or hybrids threatens to destroy cultural heritage and the genetic diversity that makes landraces well-suited to their environment. This phenomenon is called genetic erosion. For these reasons, landraces may be a better option for a farmer or farming community depending on environmental and financial circumstances. For a discussion of how improved seeds and chemical fertilizers are deployed in African agriculture, see Ariga et al. (2019). For a discussion of the preservation of landraces, see Dwivedi et al. (2016). The science and application of genetically modified organisms is covered in Chapter 10. See the vignette for a discussion of traditional cropping systems that favor indigenous crops and landraces over hybrids and their role in food security and climate change adaptation.

Crop Diversity: Species with complementary functions can support each other.

Conventional modern agricultural systems that have been developed during the Green Revolution typically intensify the production of a single crop using a package of practices, including improved seed, inorganic fertilizers, pesticides, and irrigation to create “ideal” conditions. This practice of cultivating a single crop in a field is termed monocropping, and the same crop grown in a field over successive years is described as a monoculture. However, in developing regions of the world, all the aspects of this package are often not readily available or financially accessible, rendering any implementation much less effective than it might otherwise be. Such a system may also be much less stable in the face of disturbances such as novel or resistant pests, droughts, and floods.

Many traditional cropping systems around the world incorporate more than one species per field in a complementary growth strategy termed intercropping or polyculture. Studies have shown higher total production per land unit when multiple crops are integrated rather than grown separately (Daryanto et al., 2020). Intentional mixtures can deter the growth of unwanted weed species and in some cases, the spread of pests and diseases (Malézieux et al., 2009). In agroforestry systems, tree species provide shade and/or other benefits for crops growing in the understory. The trees may or may not yield their own products, such as fruit or timber.

Crop diversity within an agroecosystem is significant not only spatially but also temporally. A primary example is crop rotation, where different crop species are planted in succession in each location from season to season. Over multiple years, the same field is planted with a diversity of crops, although the crops may be grown one at a time or in polyculture. Cover cropping, the practice of planting an additional crop between seasons or during fallow years, adds temporal diversity. Although they are not intended for harvesting, cover crops can add C to the soil by providing additional root biomass while also building soil structure and protecting against erosion. Living soil cover, which includes cover crops and perennials (i.e., plants that grow for multiple years, in contrast to annuals, which must be replanted each season), maintains live roots that support soil structure year-round. As discussed in the previous section, nonliving cover such as crop residues is another source of soil organic matter (SOM) that can improve nutrient and water retention and support microbial activity.

Crops strategically integrated into a diverse agricultural system have complementary functions, with one of the most important functions being nitrogen fixation. In a unique partnership, legumes such as groundnuts (peanuts) and beans form root nodules that house nitrogen-fixing bacteria and feed the bacteria carbohydrates while the bacteria convert nitrogen (N) gas into a mineral form that plants can use. Excess N not removed by harvesting adds to the soil nutrient pool that can be mineralized for uptake by future plant roots and other soil organisms. This service of replenishing soil N is so critical that the Conservation Farming Unit in Zambia defines crop diversification as planting 30% of the cultivated area with legumes. The organization promotes the practice as one of the three pillars of conservation agriculture (Conservation Farming Unit, 2017). See the vignette for examples of indigenous crops with benefits in cultivating marginal agroecosystems.

Agricultural biodiversity includes animals as well as plants. In addition to providing harvests that feed humans directly, crops leave residues commonly used as animal feed (although, as subsequently discussed, this presents a tradeoff with maintaining SOM). In many parts of the world, the production of plant products also benefits significantly from animal traction. Milk and meat products provide nutritious food and a source of farm income, while waste products such as animal manure can be added back to the soil to recycle nutrients and build SOM. An organic amendment, manure contributes to the soil’s functional capacity as a reservoir of plant nutrients, a buffer for acidity, and a water supplier. Managing biodiversity within an agroecosystem requires consideration of the full nutrient cycle, tracing nutrients that move from soil to plant to animal and facilitating their return to the soil.

Agroecosystems: Non-crop species can protect or threaten crop yields.

Not all forms of biodiversity in an agroecosystem are useful. Overgrown weeds can deplete the soil of plant-available nutrients; out-compete crop plants for sunlight, space, or water; and inhibit overall crop growth. Mechanical weed management can be time-consuming, especially in conservation agriculture systems where weeds are not uprooted by tillage. Organic weed management strategies include browsing by livestock and growing weed-suppressing cover crops. Where they are accessible, herbicides can be helpful, but their use requires caution to protect crop plants and limit the evolution and growth of resistant weeds.

Another threat to crop production is pests, including insects, arthropods, small mammals, and other animals that damage plants, seeds, or fruits. Dependence on purchased pesticides can be problematic and dangerous for resource-poor farmers. They may not be able to afford sufficient personal protective equipment and suffer adverse health impacts from pesticide application. Training on proper pesticide use might not be accessible, and the financial investment of buying pesticides upfront may not pay off every year. Similar to herbicides, pesticides must be used with caution to prevent the emergence of resistant pests.

Additionally, pesticides may harm beneficial insects or the natural predators of pests. Integrated pest management involves the strategic, limited use of pesticides alongside multiple other tactics to manage pests. One such tactic is biological control or the introduction or enhancement of natural enemy populations (predators or parasites). Other alternative strategies include intercropping with a non-host crop that will repel a pest and using an attractive plant to lure pests away from the crop. Combined, these two strategies are known as a “push–pull” pest management system. To learn more about the implementation of integrated pest management in sub-Saharan Africa, see Van Huis (2009).

Diseases caused by viruses, bacteria, and other microorganisms are another threat to agricultural yields. Some crop diseases can also harm the health of product consumers. For example, aflatoxin produced by fungi in the genus Aspergillus can cause stunted growth, cancer, and other illnesses in people and animals that consume contaminated maize and other cereals (Bandyopadhyay et al., 2007). Scientists are studying plant microbiomes to understand better how to maintain a healthy microbial community and even how to design microbial inoculants that can protect plants from pathogens (Vannier et al., 2019). In animal agriculture, antibiotics can be used to prevent and treat some diseases, but the emergence of antibiotic-resistant strains is an ever-increasing threat to both animal and human health (Manyi-Loh et al., 2018). Twenty-first-century advances in high-throughput molecular analysis technologies such as genetic sequencing and metabolomic analysis provide scientists with many tools to help farmers better understand and manage agricultural microbiomes.

Agroecosystems: Soil contains nutrient reservoirs that support microbe, plant, and animal life.

Soil is a dynamic ecosystem, with micro- and macro-organisms inhabiting a complex of water- and air-filled pores formed by a matrix of mineral and organic particles. Refer to Chapter 3 if you wish to review how soil supports agriculture by providing a medium for plant growth and supplying nutrients to roots. In this chapter, we explore the role of soil organisms in agricultural systems (Table 1).

At the microscopic level, soil microorganisms such as bacteria and fungi are key players in maintaining a healthy soil ecosystem for crop growth. Although soil microbes provide many services to support crop growth, three important ones are building soil structure, decomposing organic matter (OM), and aiding roots in nutrient acquisition. Fungal filaments and bacterial exudates build soil structure by binding together mineral particles to form a matrix of pores and aggregates (see image). OM decomposition occurs when soil microorganisms break down crop residues, manure, or other OM at the molecular level. Ultimately, this process allows the release of mineral nutrients in forms that plant roots can absorb. As for aiding root nutrient acquisition, some plants and microorganisms are symbiotic. For example, the mutually beneficial partnership between legume roots and N-fixing bacteria was described earlier in this chapter. While not all plants form a specific partnership with soil microorganisms in this way, they all can benefit from the nutrients released by microbial OM decomposition and a stable soil structure held together by microbial filaments and exudates.

Soil microorganisms are related to other soil life through the soil food web (see image). Moving up the food chain, protozoans graze on bacteria, which releases excess nutrients for uptake by plants and other organisms. Soil invertebrates, including earthworms and arthropods, incorporate OM from the surface deeper into the soil profile and shred it into smaller pieces, allowing microorganisms greater access to it. Some organisms are termed ecosystem engineers due to their burrowing activity that creates macropores in the soil, which in turn allow water and air to penetrate and reach plant roots easily. An example of termites as soil ecosystem engineers in agriculture is provided in this video of an experienced farmer combating deforestation in Burkina Faso.

Soil biodiversity can be positively or negatively impacted by management practices in agricultural systems, especially the application of amendments and the use of tillage. Soil amendments are materials added to the soil by farmers, such as fertilizers and composts. Organic, carbon-rich amendments can increase SOM content, providing energy and nutrients that fuel the soil food web (Masvaya et al., 2017). Manure as an agricultural amendment is further discussed in the following section. Inorganic mineral fertilizers can stimulate soil biological activity; however, without carbon inputs, SOM will ultimately be depleted, limiting soil organisms’ energy sources and harming soil physical quality. Intensive tillage can also deplete SOM because it quickly incorporates surface OM and oxygen into the soil, speeding up decomposition.

Tillage can also destroy soil structure by disrupting microbial filaments and killing soil invertebrates. In contrast, reduced or no tillage has the opposite effect: it preserves SOM content and structure. Additionally, retaining crop residues on the surface protects soil structure from destruction via rain and erosion and improves soil water retention. Compared with burning or removing residues, leaving residues in the field provides another source of SOM.

Let’s consider some examples of conservation agriculture (CA) practices in southern Africa that protect soil health and biodiversity. In Zambia, the Conservation Farming Unit (2017) defines minimum soil disturbance as planting in shallow basins or narrow rip lines on flat fields rather than in raised ridges completely tilled each year, and soil cover means leaving crop residues on the ground rather than burning them. (In addition to considering minimal soil disturbance and continuous soil cover, we have already discussed the third pillar of CA in this chapter: crop diversity.) A synthesis of several studies across Malawi, Zimbabwe, and Zambia reported that 80% of site-specific comparisons between conservation and conventional cropping systems showed higher maize yields under CA (Thierfelder et al., 2015). Some central mechanisms to which yield gains experienced under CA are attributed include improved soil health, mitigation of water-related risks, management of biodiversity, and earlier planting times. In on-station trials in Zambia, CA practices have been found to mitigate the loss in total soil carbon observed over time in conventional maize farming (Thierfelder et al., 2013). Similarly, the soil health measures of OM content and aggregate stability are higher under CA residue retention in research plots in Zambia (Thierfelder & Wall, 2010). These examples of reduced tillage and residue retention as two core pillars of CA illustrate CA’s benefits for SOM, the soil food web, and agricultural yields.