Environment Conventions and agreements

Posted February 1998


Soil and Microbial Biodiversity

Introduction Crops Plants Animals Forests Fish Soil

This Special is an extract from "Human Nature: Agricultural Biodiversity and Farm-based Food Security" by Hope Shand, an independent study prepared by the Rural Advancement Foundation International (RAFI) for the Food and Agriculture Organization of the United Nations (December 1997). The full publication is available in Portable Document Format (PDF)
THOUGH SELDOM ACKNOWLEDGED in discussions of agricultural genetic resources, soils are "the critical life-support surface on which all terrestrial biodiversity depends" [1]. Soils are providers, storers and generators of biodiversity - but they are also one of the most undervalued and poorly researched habitats on earth [2]. At the very time soil ecologists are beginning to uncover the magnitude and importance of life in the soil, the resource itself is literally disappearing off the face of the earth. Human activities are the greatest threat to soil biodiversity:

The staggering diversity of soil biota may be orders of magnitude higher than above ground diversity of plants and animals, but no one has yet made an exhaustive census of even one natural habitat [7]. According to the Global Biodiversity Assessment, "a single gram of temperate forest soil could contain 10,000 million individual cells comprising 4,000-5,000 bacterial types, of which less than 10% have been isolated and are known to science;" more than 500 species of soil invertebrates (e.g. snails, earthworms, termites, mites, nematodes, etc.) have been recorded from a beech forest; over 2,500 species of fungi have been identified from a few hectares of land in southwest England [8]. Even moss tussock communities in the Antarctic Peninsula are home to over a hundred species of soil microorganisms and invertebrates [9]. Tropical soil biota, though perhaps richer than in temperate regions, is still relatively unknown and undocumented.

Microbial diversity encompasses a spectrum of microscopic organisms including bacteria, fungi, algae and protozoa. An estimated 50 percent of all living protoplasm on Earth is microbial [10]. There may be 1.5 million species of fungi yet only 5% are described; as many as one million species of bacteria may exist, but only about 5,000 have been described in the last century [11]. According to new estimates by the Center for Microbial Ecology at Michigan State University (USA) a gram of typical soil contains about 1 billion bacteria, but only 1 percent can be successfully grown (cultured) in the laboratory. Fewer than 5% of all microbial species have been discovered and named - and even less is known about the diversity within those species [12]. So little is known about most of the microbial world that no one has ever documented the extinction of a bacterium [13].

Life in the soil and life on Earth

Soil biodiversity influences a huge range of ecosystem processes that contribute to the sustainability of life on earth. For example, soil organisms maintain critical processes such as carbon storage, nutrient cycling and plant species diversity. Soil biodiversity plays a role in soil fertility, soil erosion, nutrient uptake by plants, formation of soil organic matter, nitrogen fixation, the biodegradation of dead plant and animal material, reducing hazardous waste, the production of organic acids that weather rocks, and control of plant and insect populations through natural biocontrol.

Through production of food, fibre and renewable forms of energy, soil-based plant productivity supports the livelihood of every person on earth. Soil biota enhance crop productivity because they recycle the basic nutrients required for all ecosystems, including nitrogen, phosphorous, potassium and calcium. Soil organisms enhance the productivity of the soil by increasing water infiltration, thereby reducing surface water runoff and decreasing soil erosion.

Termites, earthworms and other burrow-building soil organisms enhance soil productivity by churning and mixing the upper soil, which redistributes nutrients, aerates the soil and increases surface water infiltration [14]. Earthworms and other invertebrates can bring to the surface from 10 to 500 tonnes/per hectare/per year of soil, and thus play a critical role in the formation of topsoil. Cornell University entomologist David Pimentel estimates that the value of soil biota to soil formation on agricultural land worldwide is US$50,000 million per annum [15].

Nitrogen from natural and commercial sources is vital to plants and animals. It is the main nutrient required for growth in plants and for building proteins in animals. Biologically fixed nitrogen (primarily nitrogen-fixing microorganisms that live symbiotically on the roots of leguminous plants and trees) makes an enormous contribution to global agricultural productivity. In poor soils, where alternative sources of fertilizer are either unavailable or unaffordable, biological nitrogen-fixation is vital to crop production. Worldwide, an estimated 140 to 170 million tonnes of nitrogen, valued at approximately US$90,000 million are fixed by microorganisms in agricultural and natural systems each year [16].

Soil biota play a major role in stabilizing and regulating the earth's climate. Global warming is the result of increasing levels of carbon dioxide and other greenhouse gases in the Earth's atmosphere - primarily caused by the burning of fossil fuels by humans. The rate of exchange of carbon between the earth's surface, the oceans and the atmosphere, known as "the carbon cycle", is the primary mediating force with regard to climate change. Through the process of photosynthesis, green plants absorb carbon dioxide from the atmosphere. It is well known that trees and forests store the absorbed carbon in woody biomass. But it is actually soil organic matter that is the major global storage reservoir for carbon. The living microbes, fungi and invertebrates found in the soil are responsible for decomposing carbon and nitrogen and making them available for plant growth, while at the same time contributing to the rate of production and consumption of carbon dioxide, methane and nitrogen.

Despite the importance of soil biodiversity to life-sustaining ecosystem processes, soils are one of the most neglected habitats on earth [17]. In most cases, soil biologists simply don't know which organisms or groups of organisms play the most important roles in ecological processes, they don't know which soil taxa are being lost, or what impact these losses will have in the future.

There is general consensus that we are losing soil biodiversity. Many microbes live symbiotically with higher organisms. Every plant and animal that becomes extinct is likely to take several species of microorganism with it. According to soil ecologist Diana Freckman of Colorado State University, knowledge of soil species remains a "black box" in our understanding of how soil systems function [18]. A study published by the US National Research Council in 1993 noted that "Our lack of knowledge of microorganisms and invertebrates, which are estimated to make up as much as 88% of all species, seriously hampers our ability to understand and manage ecosystems" [19]

Soil ecologists believe that it is essential and urgent to establish the cause and effect relationships between the loss of soil biodiversity and the impact on terrestrial and global ecosystem processes. Only by knowing and understanding life in the soil can we begin to conserve and better utilize its life-sustaining services.

Industrial agriculture has contributed to the neglect of soil biodiversity because conventional soil science has generally relied on the use of purchased farm inputs to overcome constraints and modify the soil environment. (For example, if the soil is dry, irrigate; if soil fertility is low, buy synthetic fertilizer; if pests and weeds invade, spray chemicals). With growing awareness and need for low-input and sustainable agriculture, knowledge of soil biodiversity is increasingly important to future farming systems [20]. A better understanding of soil biota will enable farmers to depend less on modification of the natural environment and place greater emphasis on using biological processes to optimize nutrient cycling, minimize the use of purchased inputs, and maximize the efficiency of their use.

The value of microbial genetic resources

Microorganisms (or microbes) are tiny living things that are not visible except with a microscope. They include algae, bacteria, fungi (including yeasts), certain protists (one celled animals that are not bacteria) and viruses. Microbial biodiversity is a vast frontier and a potential goldmine for the biotechnology industry because it offers countless new genes and biochemical pathways to probe for enzymes, antibiotics and other useful molecules [21].

Worldwide, the economic value of microorganisms is estimated to be "at least many tens of billions of US dollars" [22] Pharmaceuticals of microbial origin account for sales of approximately $35-50 billion per annum in the North [23]. It is the invisible world of microbes that has given us more than 3,222 antibiotics, for example, many derived from soil samples. In 1993, five of the pharmaceutical industry's top-selling drugs were derived from microbes; accounting for more than $4,500 million in annual sales [24]. The commercial value of microbials extends beyond pharmaceuticals. The total world market for industrial enzymes, all produced by microorganisms, is $1,300 million. Enzymes are natural catalysts that can speed up a chemical reaction. Because the process is biological, they are biodegradable and can be used instead of synthetic chemicals. For example, industrial enzymes are used to enhance detergents, as biological pesticides, to clean up toxic wastes, to replace chemicals in paper and pulp processing, and for oil extraction.

With the use of modern biotechnnology, the potential applications of microorganisms is vast. Scientists are experimenting with genetically engineered bacteria that are capable of producing products such as biodegradable plastics, artificial skin, and fibres that are as strong as spider silk. Maize, rice, potato and cotton are among the crops that have been genetically engineered to produce insecticidal genes from a common soil bacterium, Bacillus thuringiensis (Bt). The Bt genes enable the crops to produce a toxic protein that kill insects which feed on the plant. Microbial diversity can play an important role in the decomposition of hazardous wastes. Molecular biologists are attempting to harness specific organisms, or groups of organisms, to clean-up toxic wastes in the environment, or reduce hazardous waste production in industrial processes.

Today, transnational microbe hunters are especially interested in exotic and hostile environments - including boiling hot springs, undersea hydrothermal vents, alkali lakes and the frozen tundra of Antarctica - as a source of unexplored microbial diversity. Bioprospecting for microbes goes, quite literally, to the ends of the earth. The following are just a few examples:

Microbial genetic resources in the international policy arena

Despite its growing economic importance, microbial genetic diversity has been under-valued and under-recognized in biodiversity debates. There is an obvious policy gap in the international arena, and it is poor farmers who will likely pay the greatest price for this oversight. The vast majority of microbial culture collections are located in the North, and there is a growing trend toward privatization and patenting of this material. Microbial genetic resources can no longer be disregarded as ubiquitous life forms outside of the mainstream of biodiversity policy debates. Today, the genetic resources of microorganisms are very much an issue in the international policy arena.

Microbial biodiversity - where's the political debate?

The Convention on Biological Diversity excludes from its scope all ex situ germplasm collected prior to the Convention coming into force at the end of 1993. This means that all microbial culture collections, the vast majority of which are located in the industrialized world, are the legal property of the depositor and not of the donor country, regardless of where the germplasm was collected. The U.S.-based American Type Culture Collection, the world's largest microbial culture collection, contains thousands of biological specimens from the South, dozens of which are the subject of patent claims by Northern pharmacueticals such as Bristol-Myers, Pfizer and Eli Lilly.

Patent culture depositories are regulated internationally by the Budapest Treaty on International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure administered by the World Intellectual Property Organization in Geneva. Currently, 32 countries are signatories to the Budapest Treaty. An estimated 86% of global microbial collections is held in industrialized nations [27].

A network of microbial resource centres for the developing world (MIRCENs) was established in the early 1970s by UNEP and UNESCO. Today, there are no policies in place to protect these microbial genetic resources from privatization or to insure equitable exchange of microbial genetic resources in culture collections worldwide. Normally, MIRCENs have a policy of free exchange of microbial materials within the network, but each MIRCEN may decide on a case-by-case basis.

The Uruguay Round of the General Agreement on Tariff and Trade (GATT) incorporates an element called Trade Related Aspects of Intellectual Property Rights (TRIPs) which specifies that microorganisms may not be excluded from patent protection (Section 5, Article 27.2). All countries that are signatories to the World Trade Agreement are now obligated to adopt and implement patent laws for microorganisms and for biotechnology processes applied to living organisms. What is the definition of a microorganism? When is a microorganism patentable? For the purposes of patent protection, there is considerable uncertainty and controversy regarding the answer to these questions. In many countries, the term microorganism extends to cell lines and plasmids - including human genetic material.

The patenting of human genetic material is no longer a theoretical concern, but a shocking reality. On March 14, 1995 the US Patent and Trademark Office granted a patent to the US National Institutes of Health (NIH) for an unmodified human cell line drawn from a 20-year old Hagahai man from Papua New Guinea. It is the first time that an indigenous person's cells have ever been patented. Not only plants, animals and microorganisms from gene-rich ecosystems of the South, but also the genes and cells of indigenous peoples have become targets of Northern scientists and industrial bioprospectors. Private ownership of human biological materials raises many profound moral, ethical, and political issues. There is no international protocol to protect human subjects from patent claims and unjust commercial exploitation. And there is no mechanism to compensate individuals or communities from whom DNA samples are taken.

Signatories to the World Trade Agreement must determine whether or not human genetic materials are included in its definition of microbial materials. At the Jakarta meeting of the Conference of Parties to the Convention on Biological Diversity held in November, 1995, delegates made it clear that they did not wish to regard human genetic materials as part of the Convention, despite the fact that the legally-binding Convention does not explicitly exclude human biodiversity from its mandate. The World Health Organization has yet to establish internationally-accepted medical ethics protocols covering the commericialization or patenting of human genetic material. There is a serious policy vacuum that some international body must fill.


1. Global Biodiversity Assessment, p. 526.
2. Global Biodiversity Assessment, p. 526.
3. Global Biodiversity Assessment, p. 406.
4. "Save Our Soil for Future Generations", New Scientist, 6 March 1996.
5. Pimentel, David et al., p. 3.
6. Pimentel, David et al., p. 3-5.
7. Holmes, Bob. "Life Unlimited", New Scientist, 10 February 1996.
8. Global Biodiversity Assessment, p. 406.
9. Global Biodiversity Assessment, p. 406.
10. "Priorities for Microbial Biodiversity Research", Report of a workshop organized by the Center for Microbial Ecology at Michigan State University, August, 1995, p. 3.
11. "Priorities for Microbial Biodiversity Research", p. 3.
12. Global Biodiversity Assessment, p. 433.
13. Miller, Susan K. "Save a Bug for Biotechnology," New Scientist, 1 August 1992, p. 7.
14. Global Biodiversity Assessment, p. 407.
15. Pimentel, David et al., "Environmental and Economic Benefits of Biodiversity", p. 5.
16. Cited in David Pimental et al., "Environmental and Economic Benefits of Biodiversity", p. 6.
17. Freckman, Diana W., ed., "Life in the Soil - Soil Biodiversity: Its Importance to Ecosystem Processes", Report of a Workshop Held at The Natural History Museum, London, England, August 30-September 1, 1994, p. 4.
18. "Life in the Soil - Soil Biodiversity: Its Importance to Ecosystem Processes", p. 12.
19. Cited in "Life in the Soil - Soil Biodiversity: Its Importance to Ecosystem Processes", p. 15.
20. Berg, Trygve , DRAFT.
21. Holmes, Bob, p. 26-29.
22. National Research Council Committee on Managing Global Genetic Resources, Agricultural Imperatives, Managing Global Genetic Resources, National Academy Press, Washington, 1993, p. 248-249.
23. "Priorities for Microbial Biodiversity Research", p. 5.
24. Robbins-Roth, Cynthis. "Xenova Ltd.: Growing New Technology", Bioventure View, May 1993.
25. Flitner, Michael. Sammler, Raeuber and Gelehrte: Die politischen Interessen anPflanzengenetischen Ressourcen, 1895-1995, Campus, Frankfurt/New York, 1995.
26. This example is cited in RAFI Communique, "Microbial Genetic Resources" Jan./Feb. 1995, p. 6.
27. RAFI, Conserving Indigenous Knowledge: Integrating Two Systems of Innovation, UNDP, New York, 1994, p. 22.

Introduction Crops Plants Animals Forests Fish Soil

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