Climate Smart Agriculture Sourcebook

Genetic resources for Climate-Smart Agriculture Production

Production and Resources

Climate-smart management of micro-organisms and invertebrates

Micro-organisms (e.g. bacteria, fungi and yeasts) and invertebrates (e.g. insects, arachnids and earthworms) are invaluable contributors to terrestrial and aquatic ecosystems on which food production and agriculture depend. They pollinate plants including crops and cultured trees, recycle nutrients in soils, ferment bread and cheese, help animals digest otherwise indigestible forage and, with proper management, and can provide natural protection against plant pests in farmers’ fields. Micro-organisms and invertebrates also include pathogens and vectors, parasites and pests that attack plants and animals, and spread diseases. Agriculture and food production would not exist without this 'hidden' but critically important biodiversity (Beed et al., 2011).

B8 - 7.1 Impact of climate change on micro-organisms and invertebrates

It is very difficult to predict how climate change will affect micro-organisms and invertebrates, their interactions with the other components of the ecosystem, and their capacities to provide ecosystem services or act as pests. Only a few studies have attempted to investigate these issues. Nevertheless, there is a growing consensus that climate change could lead to an overall increase in the abundance and diversity of pests, as habitats become more favourable for their establishment and development; new ecological niches appear; stabilizing interactions are disrupted; and the distribution range of invasive species expands (e.g. Cannon, 1998; Patterson et al., 1999; Rosenzweig et al., 2001; Fuhrer, 2003; Luedeling et al., 2011; Grace et al., 2015). 

Soil biodiversity

The impacts of climate change on soil biodiversity and the services it provides are to a large extent mediated through plants. For example, shifting rainfall patterns and changes in temperature are expected to affect the nutritional composition of plant leaves and grazing patterns of animals, which will in turn have an impact on the diets of soil invertebrates. Modifications in diet will influence the capacity of these organisms to decompose plant litter, which could affect the turnover of soil organic matter and the rate at which nutrients are released and made available to plants (FAO, 2015b).

Both elevated temperatures and elevated carbon dioxide levels are known to affect the abundance and composition of soil communities (e.g. Jones et al., 1998; Briones et al., 2009). They also influence many of the processes that micro-organisms and invertebrates are involved in, including the retention and loss of soil nutrients, nitrogen mineralization and denitrification, litter decomposition and soil respiration. However, the impact of changes in these processes is expected to be stronger in soils in intensive farming systems, where a limited range of crops are grown, than in soils in natural ecosystems, where the diversity of the soil micro-organism community may allow for more rapid adaptation to change (Mocali et al., 2008).

Plant pathogens and biological control

As explained in chapter B1 - 1.2, climate change is expected to affect the distribution of crop species and varieties. Some pathogens will migrate with these crops and establish themselves in areas where they have not previously caused problems and where there may be no natural enemies to keep them under under control. The newly established crops will also be exposed to potentially harmful indigenous micro-organisms. 

Climate change is also likely to affect the behaviour, distribution, development, survival and reproduction of invertebrates. For instance, warmer temperatures could influence the ability of insects to act as disease vectors. Warmer temperatures are also expected to alter the hunting behaviour of predators and the feeding habits of herbivores. With a 2 °C rise in temperature, it is estimated that many insects will be able to complete one to five extra life cycles per season (Yamamura and Kiritani, 1998). Increasing humidity and temperatures may also boost the growth of food-spoiling micro-organisms on plants (e.g. moulds), which could in turn affect the dynamic equilibrium between these organisms and natural biological control agents. This disrupted equilibrium could necessitate increases in pesticide use. See also chapter B3-1.2 and Box B3.2 for the interactions between climate change and forest insect pests.

Climate change is expected to cause significant changes in the degree of synchrony between the life cycles of different species, which could substantially influence the efficacy of biological control agents on a local scale. Moreover, according to some climate change models, the level of ultraviolet-B radiation is set to increase due to depletion of the ozone layer. This could have a particularly significant impact on biological control by micro-organisms, as fungi and bacteria are generally more sensitive to damage by ultraviolet-B radiation than weeds and insects.


Aided in some cases by human activities, the majority of invertebrate pollinators and pests, along with their natural enemies, can be expected to move with their host plants, as the distribution ranges of crops and forages change (Cock et al., 2011). Many pollinators are able to move over long distances without assistance from humans. However, it is likely that climate change will increase demand for assisted movement of pollinators between countries.

Invertebrate species differ in their sensitivity to temperature and other climatic factors. As the climate changes, the species composition of invertebrate communities and the synchrony between the life cycles of individual pollinating species and those of flowering plants will also change. Not all species may be able follow their associated crop or livestock production systems. What the consequences of these changes will be are unknown (FAO, 2015b). Many pollinators are sensitive to high temperatures and drought. For example, increases in temperature may enhance the performance of insect species living at higher latitudes, as they have broader thermal tolerance and are living in climates cooler than their optimal thermal range. In contrast, warming could have negative impacts in tropical climate zones, where most pollinators already live close to their optimal range of temperature tolerance (Deutsch et al., 2008).

B8 - 7.2 Characterization, evaluation, inventory and monitoring of micro-organisms and invertebrates

While micro-organisms and invertebrates make up an immense and diverse population of living organisms, very little is known about their composition and dynamics. The 'invisible' nature of micro-organisms means that changes are particularly difficult to observe (FAO, 2015b). In most soil ecosystems, the resident micro-organism and invertebrate species have even not been counted, let alone identified and described. The intricate ecological relationships within soil communities, and between them and above-ground biodiversity, also remain very poorly understood (FAO, 2015b). 

Some predator species are considered 'specialists' because they may attack and reproduce on only a single pest species. Other species are 'generalists', attacking a range of pest species. Likewise, specialist bees forage for pollen that can only be found on a few or only just one plant species, while generalist bees often visit a wide range of flower types and species when seeking out pollen. To 'select' useful species from the diversity of micro-organisms and invertebrates that could be conserved and used for food and agricultural purposes, it is crucial to understand the specificity and functionality of these organisms, and the complex and dynamic relationships they have with other components of their environment (e.g. natural enemy-pest and plant-pollinator relationships). This requires extensive ecological research, taxonomical identification and related expertise (Waage, 2007; CBD, 2017). As reference collections, living ex situ culture collections are of enormous value in supporting research and taxonomy of micro-organisms. In the same way, collections of dead invertebrate material in natural history museums and botanical gardens help identify insects, spiders and mites that have the potential to be used in new biological control programmes. Culture collections will be important for gaining a better understanding of the identity of any new organisms discovered, and these organisms may then be added to these collections as future taxonomic resources (Waage, 2007). 

Generally speaking, taxonomy and genetic characterization of micro-organisms and invertebrates, including soil organisms, biological control agents and pollinators, found in agricultural ecosystems need to be improved. Systematic monitoring programmes that are able to identify trends in micro-organism and invertebrate genetic resources are also required. Some monitoring initiatives for soil organisms and pathogens have been established in technologically advanced countries, but similar programmes need to be set up in developing countries. Techniques for characterizing micro-organism and invertebrate species, communities and functions must also be improved, and studies are required on the effects of climate on micro-organisms and invertebrates and the services they provide. This will involve a combination of field and laboratory-based work. Techniques need to be standardized to allow a comparison of data from different locations (FAO, 2015b). 

B8 - 7.3 Sustainable use and development of micro-organisms and invertebrates for climate change adaptation

When it comes to responding to climate change, invertebrates and micro-organisms seem to have several advantages over other larger species. For example, their unparalleled rate of reproduction, which they achieve thanks to their short reproductive cycles, enables them to adapt extremely rapidly to changes in their environment or evolve in response to changing climatic conditions (FAO, 2015b). Micro-organisms also benefit from 'horizontal gene transfer', whereby DNA is able to move from one micro-organism cell to another. This means that micro-organisms do not have to wait for the next generation in order to change their genetic characteristics. 

Micro-organisms can play a key role in global efforts to adapt to the impacts of climate change. For example, plant-associated micro-organisms that contribute to plant traits, such as drought tolerance, may help crops to adapt to some of these impacts. However, much work needs to be done to better understand how micro-organisms can contribute to traits that increase adaptation to climate change in crops and the extent to which micro-organisms from one plant species may be adapted for use with other plant species (Beed et al., 2011).

Micro-organism communities in the soil can change the soil environment to make it less favourable or suppressive to fungal, bacterial or nematode pathogens. The potential of the soil micro-organism community to create these so-called suppressive soils represents a form of naturally occurring biological control that can reduce losses from plant disease (Beed et al., 2011). Management practices promoting the preservation and increase of micro-organism and invertebrate diversity, such as no-tillage farming in combination with a sound crop rotation-system and the retention of crop residue to keep the soil covered (conservation agriculture) also contribute to the effects of naturally occurring biological control (see chapter B1 - 2 on sustainable soil and land management). These practices can help keep the population of damaging pest and diseases at levels that do not cause economic losses. It is also possible that many other, currently unknown, roles of biological control micro-organisms exist, which will be able to be utilized in adapting to climate change (Beed et al., 2011). For example, research has shown that rice can cope with elevated carbon dioxide levels when combined with the right strains of mycorrhizal fungi (Tang et al., 2009). 

Most invertebrates are expected to change their geographical distribution in response to climate change, so that they remain in areas to which they are well adapted. Many of the challenges associated with the management of invertebrate genetic resources in agriculture in response to climate change adaptation will relate to climate-driven or human-assisted movement of these organisms. In this respect, it will be important to maintain predator and parasite species that could be deliberately introduced as biological control agents to assist crop production systems in adapting to new pest problems that arise because of climate change (Cock et al., 2011). 

B8 - 7.4 Sustainable use and development of micro-organisms and invertebrates for climate change mitigation

Micro-organisms and invertebrates can contribute to mitigation of climate change in agriculture and food production systems in multiple ways. Soil micro-organisms play an important role in the sequestration of carbon in soil organic matter and the release of carbon in the form of carbon dioxide when soil organic matter decomposes. Given the enormous amount of carbon stored in the world’s soils, micro-organisms are extremely significant in global efforts to mitigate climate change. Their contribution to carbon sequestration can be promoted by practices such as amending soil with organic fertilizers, proper management of crop residues, no-tillage agriculture, maintaining cover crops on the soil surface, avoiding flood irrigation and carefully managing the use of fertilizers. 

Many beneficial micro-organisms provide their services at a relatively low cost in terms of greenhouse gas emissions. For example, mycorrhizal fungi and rhizobia contribute to plant nutrition and increase plant productivity without the greenhouse gas emissions associated with production, transport and application of mineral fertilizers. The use of micro-organisms to increase shelf-life has potential to reduce the amount of energy expended on freezing or refrigerating food (Di Cagno et al., 2009). In ruminants, certain modifications to the composition of micro-organism populations in the rumen are believed to have a positive effect on methane emissions (methanogenesis). Current and future research on the role of these populations could provide a greater understanding of rumen function, feed conversion efficiency, methanogenesis and plant cell wall degradation, which would help find an optimal balance between food production and greenhouse gas emissions.

Sustainable use and domestication of edible insects may represent a climate-smart alternative to the production of food from other animals. Insects produce much smaller quantities of greenhouse gases per kilogram of product than conventional livestock species (Oonincx et al., 2010). See chapter B5 - 3 and Box B2.2 for more information on insect-based systems. 

By helping to maintain soil structure and retain water throughout the soil profile, earthworms can contribute to alleviating the effects of drought on crop production (e.g. Johnson et al., 2011). Studies have also revealed the remarkable ability of diverse soil invertebrate communities to restore the structure of degraded soils (e.g. Barros et al., 2004). Soil restoration or protection of soils against erosion can contribute both to retaining and increasing soil carbon stocks. 

Few if any deliberate attempts have been made to introduce soil invertebrates into new countries or ecosystems to enhance their beneficial roles. Given the potential for these species to become invasive, it is inadvisable to attempt any such introductions until soil ecology is much better understood. 

B8 - 7.5 Conservation of micro-organisms and invertebrates

Conservation of micro-organisms

Living ex situ microbial collections are of enormous value in the collection, authentication, maintenance and distribution of cultures of microorganisms and cultured cells. They also contribute to understanding the identity of newly discovered organisms, which may then be added to these collections as taxonomic references. Of the many existing microbial collections, several are of global significance, such as the Agriculture Research Service Culture Collection of the United States Department of Agriculture and the Centre for Agriculture and Bioscience International (CABI) Genetic Resources Collection, which provide microbial cultures freely to researchers. There are also important specialist collections, for example for species used in biological control, which are in effect an ex situ repository of microbial biological control agents (Waage, 2007).  

In situ conservation also has an important role to play. For example, the in situ conservation of wild crop relatives depends on the maintenance of the micro-organism communities to which they are associated under field conditions. This allows co-evolution among plants and micro-organisms to continue. Determining what micro-organism communities need to be maintained is challenging because of the limited knowledge of the dynamic interactions among the environment, plants and micro-organisms. Because micro-organisms are highly adaptive to new scenarios, such as those likely to be induced by climate change, ex situ collections of micro-organisms may become out-dated. Efforts are required to advance in situ conservation methods for micro-organisms. 

Developing a more complete understanding of many micro-organisms is important for determining how to prioritize micro-organism conservation. For example, micro-organisms that have the potential to support crop adaptation to new environments could be prioritized for conservation. 

Most of the foods currently eaten are partly the products of from different types of micro-organism processes that give food its specificity and unique taste. Ex situ conservation of cultures of food-borne micro-organisms is instrumental in maintaining specific food production systems and making them more adaptable to climate change. Conservation of food-borne micro-organisms also has a cultural function in that it helps maintain traditional food production systems.

Conservation of invertebrates

While micro-organisms are essentially conserved ex situ, the preferred approach for conserving invertebrates remains in situ conservation. The most important reservoirs for biological control agent species are agricultural ecosystems where management practices do not hinder their survival (e.g. those with little pesticide use). Most biological control agents are also likely to have reservoir populations in natural ecosystems (i.e. those not used for agriculture). Such habitats tend to harbour additional genetic diversity within known biological control agent species. They may also be home to unknown species with future potential to act as biological control agents. Conservation of both natural ecosystems and diversity-rich farming systems is essential to ensure that sufficient biological control agents remain available for the future. More research is needed before it will be possible to know which ecosystems are particularly important for maintaining biological control agents, and which biological control agents are particularly important to maintain.

Maintaining insect species that can provide pollination services for a wide range of crops is also vital to the future of agriculture. Pollinator populations not only need to be able to cope with changing climatic conditions, they must also be able to provide the pollination services needed to meet increasing demands for food and retain the capacity to adapt to potential changes in the types of crops grown. For this reason, the natural habitats of wild pollinator species need to be identified and preserved. As land use changes, it may be necessary to protect or develop corridors of suitable habitats that ensure food and nesting resources are available for pollinators.