Summary for

policy makers
2020

STATE of KNOWLEDGE
of SOIL BIODIVERSITY

Status, challenges and potentialities

Cover: ©FAO/ Matteo Sala
©FAO/Matteo Sala
 STATE of KNOWLEDGE
of SOIL BIODIVERSITY
Status, challenges and potentialities

Summary for
policy makers

Food and Agriculture Organization of the United Nations

Rome, 2020
Required citation
FAO, ITPS, GSBI, SCBD and EC. 2020. State of knowledge of soil biodiversity – Status, challenges and potentialities,
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Cover: ©FAO/Matteo Sala

Contents
Foreword VI

Introduction 1

Key messages2

1 Soil organisms drive processes that produce food, purify soil and water, and
preserve both human well-being and the health of the biosphere2

What is soil biodiversity?2

Contributions of soil biodiversity2

Soil biodiversity and agriculture 4

Soil biodiversity and climate change4

Soil biodiversity
and human health5

2 Our current understanding of the role of soil organisms in plant growth and
the transformation of pollutants has been harnessed to improve agricultural
production and reclaim degraded soils8

Agricultural sector 8

Environmental remediation12

Challenges to use of soil organisms12

3 Laboratory and analytical advances in the past decade allow us to move

beyond research on individual species to study whole communities of
organisms, and hence develop new approaches to address food security and
environmental protection14

Agricultural industry14

Food Industry14

Ecosystem restoration14

Pharmaceutical industry 16

4 The essential contributions of soil organisms are threatened by soil-

degrading practises. Policies that minimise soil degradation and protect soil
biodiversity should be a component of biodiversity protection at all levels 18

Invasive alien species23

Agricultural intensification23

Assessment of soil biodiversity 23

Policy development23

The way forward 25

III
Foreword
Our well-being and the livelihoods of human societies are highly dependent on biodiversity and the
ecosystem services it provides. It is essential that we understand these links and the consequences
of biodiversity loss for the various global challenges we currently face, including food insecurity and
malnutrition, climate change, poverty and diseases. The Agenda 2030 for Sustainable Development sets
out a transformative approach to achieve socio-economic development while conserving the environment.

There is increasing attention on the importance of biodiversity for food security and nutrition, especially
above-ground biodiversity such as plants and animals. However, less attention is being paid to the
biodiversity beneath our feet, soil biodiversity. Yet, the rich diversity of soil organisms drives many
processes that produce food or purify soil and water.

In 2002, the Conference of the Parties (COP) to the Convention on Biological Diversity (CBD) decided
at its 6th meeting to establish an International Initiative for the Conservation and Sustainable Use of Soil
Biodiversity and since then, the Food and Agriculture Organization of the United Nations (FAO) has been
facilitating this initiative. In 2012, FAO members established the Global Soil Partnership to promote
sustainable soil management and increase attention to this hidden resource. The Status of the World’s Soil
Resources (FAO, 2015) concluded that the loss of soil biodiversity is considered one of the main global
threats to soils in many regions of the world.
©Andy Murray
The 14th Conference of the Parties invited FAO, in collaboration with other organizations, to consider the
preparation of a report on the state of knowledge on soil biodiversity covering its current status, challenges
and potentialities. This report is the result of an inclusive process involving more than 300 scientists
from around the world under the auspices of the FAO’s Global Soil Partnership and its Intergovernmental
Technical Panel on Soils, the Convention on Biological Diversity, the Global Soil Biodiversity Initiative
and the European Commission. The report presents the state of knowledge on soil biodiversity, the
threats to it, the solutions that soil biodiversity can provide to problems in different fields, including
agriculture, environmental conservation, climate change adaptation and mitigation, nutrition, medicine
and pharmaceuticals, remediation of polluted sites, and many others.

The report will make a valuable contribution to raising awareness of the importance of soil biodiversity
and highlighting its role in finding solutions to today’s global threats; it is a cross-cutting topic at the
heart of the alignment of several international policy frameworks, including the Sustainable Development
Goals (SDGs) and multilateral environment agreements. Furthermore, soil biodiversity and the ecosystem
services it provides will be critical to the success of the recently declared UN Decade on Ecosystem
Restoration (2021-2030) and the upcoming Post-2020 Global Biodiversity Framework.

Soil biodiversity could constitute, if an enabling environment is built, a real nature-based solution to most
of the problems humanity is facing today, from the field to the global scale. Therefore efforts to conserve
and protect biodiversity should include the invisible array of microorganisms that make up more than 25%
of the total biodiversity of our planet.

FAO Director-General Executive Secretary of CBD

QU Dongyu Elizabeth Maruma Mrema

©Andy Murray
Introduction
A wealth of new scientific, technical and other
types of knowledge relevant to soil biodiversity
has been released since the establishment of the
International Initiative for the Conservation and
Sustainable Use of Soil Biodiversity in 2002,
the establishment of the Global Soil Biodiversity
Initiative in 2011, the Global Soil Partnership
in 2012, and the publication of the Global Soil
Biodiversity Atlas by the European Commission in
2016.

This new wave of research is a consequence of

improvement in the methods available for the study
of soil organisms by the scientific community.
This research has placed soil biodiversity at the
heart of international policy frameworks, including
the Sustainable Development Goals (SDGs).
Furthermore, soil biodiversity and ecosystem
services will be pivotal for the success of the
recently declared United Nations Decade on
Ecosystem Restoration (2021–2030).

This Summary for Policy Makers brings the key

messages from the report State of knowledge of soil
biodiversity: status, challenges and potentialities
prepared by the Food and Agriculture
Organization of the United Nations (FAO), the
Intergovernmental Technical Panel on Soils,
the Global Soil Partnership, the Convention on
Biological Diversity, the Global Soil Biodiversity
Initiative, and the European Commission. The
report is a result of the work of over 300 scientists
and experts on soil biodiversity from all regions
of the world, and it presents the best available
knowledge on soil biota and their ecosystem
functions and services.

1
Key messages These organisms are part of a vast food web that
ensures the cycling of energy and nutrients from
microscopic forms through the soil’s megafauna to
organisms that live on top of the soil.
1 Soil organisms drive
For the purpose of this summary the terms soil
processes that produce biological diversity, and below-ground biodiversity
have been used interchangeably, and they include
food, purify soil and water, soil microbes and soil fauna. Likewise, the terms
and preserve both human microbial diversity, soil microbes, soil microbiome
and soil microorganisms are used interchangeably
well-being and the health specifically to describe soil microbial diversity.

of the biosphere
Contributions of soil
biodiversity
What is soil biodiversity? The contributions of soil organisms can be
grouped into three broad categories (Figure 1).
We define soil biodiversity as the variety of life
First, soil microorganisms (i.e., bacteria, fungi)
belowground, from genes and species to the
and microfauna (i.e., protozoa and nematodes)
communities they form, as well as the ecological
transform organic and inorganic compounds
complexes to which they contribute and to
into accessible forms as part of their metabolism
which they belong, from soil micro-habitats to
through extraordinarily complex biochemical
landscapes. Soil biodiversity is essential for most
processes. These transformations are critical for
of the ecosystem services provided by soils, which
ecosystem services such as nutrient availability
benefit soil species and its multiple interactions
for the growth of plants and other organisms,
(biotic and abiotic) in the environment. Soil
soil organic matter and nutrient cycling, and the
biodiversity also supports most surface life forms
filtration, degradation and immobilization of
through the increasingly well understood links
contaminants in water and soil.
between above and belowground. For humans, the
services provided by soil biodiversity have strong Second, soil organisms are part of a vast food web
social, economical, health and environmental that cycles energy and nutrients from microscopic
implications. forms through the soil’s megafauna to organisms
that live on top of the soil. An important part of
Soils are one of the main global reservoirs of
the food web is represented by mesofauna such
biodiversity, more than 40% of living organisms
as springtails and mites, which accelerate litter
in terrestrial ecosystems are associated during
decomposition and enhance nutrient cycling and
their life-cycle directly with soils (Decaëns et
availability (especially nitrogen), and predate on
al., 2006). Soil organisms can be divided into
smaller soil organisms (Figure 1).
different groups: microbes, micro, meso, macro,
and megafauna. They include a wide range of Finally, soil macrofauna and megafauna such as
organisms, from unicellular and microscopic earthworms, ants, termites and some mammals act
forms, to invertebrates such as nematodes, as ecosystem engineers that modify soil porosity,
insect larvae and earthworms, arthropods and water and gas transport, and also bind together soil
their larval stages, to mammals, reptiles, and particles into stable aggregates that hold the soil in
amphibians that spend considerable parts of their place, reducing soil erosion (Figure 1).
lives below ground. In addition, there is a great
diversity of algae and fungi, as well as a wide
variety of symbiotic associations between soil
microorganisms and algae, fungi, mosses, lichens,
plant roots, and invertebrates.

2 State of knowledge of soil biodiversity

 Organization of the soil food web

Ea
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An

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ECOSYSTEM
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ENGINEERS
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Pr ma
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Sa icro

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es pod
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ha nd od
r
ha rop

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go od

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LITTER
us s

TRANSFORMERS
s
Ba

SOIL
Fu
cte

ng

ORGANIC
ria

MATTER
Fu art
ng hr
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Fu edi od
ot

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Pr ma
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at rop
or o
at de

y ds
or s
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MICRO-FOOD
WEB

Macrofauna Mesofauna Microfauna Microorganisms

Figure 1. Simplified model with the groups of soil organisms: microorganisms, micro, meso and macrofauna grouped into three
categories in the food web. First, the micro-food web (dotted lines) includes bacteria and fungi, which are at the base of the food
web and decompose soil organic matter, which represents the basic resource of the soil ecosystem, and their direct predators, pro-
tozoa and nematodes. Secondly, litter transformers include microarthropods that fragment litter, creating new surfaces for micro-
bial attack. Finally, ecosystem engineers, such as termites, earthworms and ants, modify soil structure by improving the circulation
of nutrients, energy, gases and water.

Summary for policy makers 3

Soil biodiversity Soil biodiversity
and agriculture and climate change
Soil organisms both serve as a source of nutrients The role of soil biodiversity in addressing global
for plant growth and drive the transformations of climate change cannot be understated: the soil
nutrients that make them available to plants. The community’s activities can contribute either to
collective carbon content of all soil bacterial cells the emission of greenhouse gases or to absorbing
is comparable to that of all plants on earth, and carbon into soils from the atmosphere. As part
their total nitrogen and phosphorous contents of the natural functions and ecosystem services
are far greater than that of all vegetation, making provided by soils, a healthy soil stores more carbon
these microorganisms the primary source of than that stored in the atmosphere and vegetation
indispensable nutrients for life. combined.

Plants fix carbon from the atmosphere, but Carbon is either fixed or released from soils,
they require macro and micronutrients that are depending the activity of the soil organisms and
absorbed from the soil to create biomass and driven by soil conditions. Carbon is fixed into soils
transfer nutrients and energy. Soil microbes through the transformation of plant and animal
and microfauna interact with abiotic factors – detritus, and also some bacteria and archaea can
temperature, pH, moisture content- and drive fix carbon by using atmospheric CO2 as their
these transformation processes. energy source. Beyond their direct role in the
carbon cycle, soil organisms are also critical for
Soil micro, meso and macrofauna play a key role in efforts to reduce overall greenhouse gas (GHG)
the physical breakdown of plant residues, allowing emissions from agriculture. Globally, agricultural
the soil microorganisms to liberate the nutrients ecosystems contribute 10 to 12 percent of all
and energy bound up in the plant material. direct anthropogenic GHG emissions each year,
with an estimated 38 percent resulting from soil
The role of soil organisms in agriculture has
nitrous oxide emissions and 11 percent from
many beneficial effects beyond plant nutrition.
methane in rice cultivation. Soil microorganisms
For example, soil microbiota such as arbuscular
are involved in every step of nitrogen and carbon
mycorrhizal fungi and nitrogen fixing bacteria
transformations that yield these greenhouse gases,
can minimise cost and dependence on synthetic
and managing the soil environment to minimise
nitrogen fertilizers in agriculture, and enhance
emissions is a key objective in sustainable soil
soil fertility and environmental sustainability,
management.
including reducing greenhouse gas emissions
from the energy-intensive manufacture of nitrogen
fertilizer.
©Andy Murray
Soil biodiversity Soil biodiversity and
and human health environmental protection
Soil biodiversity supports human health, both It is well established that preservation of soil
directly and indirectly, through disease regulation biodiversity is critical for the maintenance and
and food production. enhancement of above-ground biodiversity.
The complex food webs that transfer nutrients
Since early 1900, many drugs and vaccines have and energy from the organic materials in the
come from soil organisms, from well-known soil, through soil-dwelling organisms, to birds,
antibiotics like penicillin to bleomycin used mammals, reptiles and amphibians, are central to
for treating cancer and amphotericin for fungal life on earth.
infections. In a context of increasing illnesses due
to resistant microorganisms, soil biodiversity has Soil biodiversity can attenuate threats to
a huge potential to provide new drugs to combat ecosystem services, for instance by acting as a
them. powerful tool in bioremediation of contaminated
soils. Biostimulation and bioaugmentation are
Soil biodiversity and healthy soils help to mitigate environmentally sound strategies that contribute
the risk of foodborne illness by boosting plant to the filtration, degradation and immobilization
defenses against opportunistic infections. For of target contaminants (Figure 2). Furthermore,
example, the very harmful bacterium Listeria the integral use of organisms such as microbes
monocytogenes is found in low concentration (bioaugmentation), plants (phytoremediation) and
in many agricultural soils, but its pathogenicity worms (vermiremediation) as a bioremediation
depends on the richness and diversity of soil strategy in hydrocarbon-contaminated soils has
microbial communities, as well as soil type, pH and proven to be a viable alternative for increasing
other soil-related factors. hydrocarbon removal. On the other hand, soil
macrofauna, such as earthworms, termites, and
The relationship between plant roots and soil ants, play an important role in improving soil
biodiversity enables plants to manufacture structure and aggregation, which can improve
chemicals such as antioxidants that protect them resistance to soil erosion caused by wind and
from pests and other stressors. When we consume water.
these plants, these antioxidants benefit us by
stimulating our immune system and assist in
hormone regulation.

A series of studies and evidences suggests that

early exposure to a diverse collection of soil
microorganisms might help prevent chronic
inflammatory diseases, including allergy, asthma,
autoimmune diseases, inflammatory bowel disease
and depression.
 Bioremediation
Bioremediation
Biostimulation:
Changes in the
Bioaugmentation: environmental
Addition to the conditions to favor the
contaminated soil of growth of local
living cells able to microbial populations.
degrade the target
contaminant.

Trifolium pratense •Macronutrients

•Micronutrients

Bioremediation

Indigenous bacteria Exogenous bacteria

Contaminant agent Various forms of essential nutrients

Figure 2. Soil microorganisms as a tool in the management of contaminated soils.

6 State of knowledge of soil biodiversity

©FAO/Matteo Sala
 2 Our current Agricultural sector
understanding of the The commonly used organisms for stimulation
of nutrient cycling include mycorrhizal fungi and
role of soil organisms symbiotic nitrogen-fixing bacteria (Figure 3). In
Brazil and other countries in Latin America, the
in plant growth and inoculation of selected Bradyrhizobium bacterial
the transformation of strains in soybean is an example of a major success.
In 2018, soybean was cultivated in an area of about
pollutants has been 35 million ha in Brazil. Inoculation of selected
Bradyrhizobium strains in Brazilian soybean
harnessed to improve production totally replaced mineral nitrogen (N)
fertilizers, saving billions of dollars a year. Besides
agricultural production and its huge economic advantage, the biological fixation
of nitrogen from the atmosphere by Bradyrhizobium
reclaim degraded soils is a clean biotechnology that avoids the overuse of
synthetic fertilizers (Figure 4).

Soil organisms are also currently used in biocontrol

measures in agriculture. The basic concept of
biological control is to facilitate the natural
ecosystem to counteract the potential of pests and
generally to increase biodiversity and ecosystem
functioning.

Worldwide, the largest commercial success of a

biological control agent is without doubt Bacillus
thuringiensis (Bt), a common bacterium isolated
from soil. Bacillus thuringiensis is a biological
control agent with insecticidal activity against a
range of different insects, and different strains and
marketed products increases the specificity against
the target organisms (Figure 5).

Negative feedbacks between the use of soil

organisms and agricultural production also occur.
A significant proportion of antibiotics used in
crops and livestock ends up in the soil, affecting
soil biodiversity and creating antimicrobial
resistance in soil-dwelling organisms. 
©Andy Murray

8 State of knowledge of soil biodiversity

 The rhizosphere
The rhizosphere

Nodules

Symbiotic
relations

Arbuscules

Vesicle
Bacteria
zone
Hyphae

Rhizobium

Root
hair
Mycorrhizae

Figure 3.The rhizosphere is the narrow region of soil directly influenced by root secretions/exudates and associated microorgan-
isms’ interactions. Leguminous plants receive nitrogen –a limiting nutrient in many soils-, in the form of ammonia, thanks to rhi-
zobium, an N2-fixing bacteria that forms nodules in the plants’ roots. In return, Rhizobium receives nutrients and habitat from the
roots. Mycorrhizae (symbiont fungi in roots) play a key role in providing ecosystem services such as soil fertility, soil formation and
maintenance, nutrient cycling and improving plant root exploration of the soil.

Summary for policy makers 9

Clean biotechnology
Improvement ofinagricultural
agricultural production
production
Crop with microbial
inoculum, with higher
productivity and less
Conventional agricultural inputs
crop with

N
excessive use N2O
of fertilizers
N

N2O
N2O
N2O
N2O
N2O
N2O
N2O Emissions
N2O

Emissions
N2O
N2O

N2O

N2O

Leaching
+ Leaching

NO3-
Azospirillum Bradyrhizobium
Plant-growth N2- fixing
NO3-
NO3- promoting bacterial
NO3-
bacteria strains NO3-
NO3-
NO3- NO3 -
NO3-
NO3 -

Figure 4. The co-inoculation of N2-fixing efficient bacterial strains (Bradyrhizobium) with other plant-growth promoting bacteria
such as Azospirillum in cereals, could replace part of mineral N fertilizers reducing greenhouse gas emissions such as N2O, and
diminishing leaching of reactive forms of nitrogen (NO3-) that contaminate underground water and coastal ecosystems; besides
saving investments and capital input.

10 State of knowledge of soil biodiversity

Biological
Biological control
control

Corn crop with Corn crop produces Bt

caterpillar toxins in its tissues.
infestation Caterpillars that eat
these tissues die

Genetic engineering
to insert Bt genes
into plant tissues

Bacillus
thuringiensis (Bt)

Endospore
Ribosomes
Cell
DNA membrane
Bt Toxin
Crystal Cell wall

Figure 5. Bacillus thuringiensis (Bt), a bacterium species isolated from the soil, has been successfully used as a biological
control agent against insects. Bt produces an intracellular toxin that, when ingested by an insect, is released in the insect’s gut,
killing it. The genes that produce the Bt toxin are inserted into agricultural crops, particularly maize, giving the plant the ability
to avoid attack by certain pathogenic organisms.

Summary for policy makers 11

Environmental remediation Challenges to use of soil
Bioremediation technologies can lead to the organisms
degradation of a target contaminant to an
innocuous state or to levels below concentration Many microbial biofertilizers, biopesticides
limits established by regulatory authorities. Soil and other related products show great effects
organisms are also used directly to transform when tested under laboratory and greenhouse
toxic compounds into benign forms through conditions, but fail to provide reproducible results
bioremediation (Figure 2). Many soil bacteria can under field conditions. One reason is the difficulty
transform different contaminants such as saturated for certain organisms to survive in a highly
and aromatic hydrocarbons (for example, oil, competitive environment.
synthetic chemicals and pesticides). Soil bacteria In addition to their transient and environmentally
and fungi can reduce petroleum hydrocarbons dependent effect, the high cost of biological
after a spill by up to 85 percent. products also restrains their adoption by
farmers, and especially by smallholders with little
purchasing power and poor access to credit.

In response to these limitations, some farmers

with proper training attempt to reproduce native
consortia of soil microorganisms to assemble
biofertilizer, biocontrol and biostimulant farm
inputs. To this end, farmers rely on relatively
simple, rapid and affordable techniques. The use
of native consortia or native microbial species –as
opposed to allien species– as farm inputs may be
a valid strategy for increasing biotic resistance to
invasive alien pathogenic microorganisms.
©Andy Murray
©FAO/Matteo Sala
3 Laboratory and analytical are the determination of which mycorrhizal fungi
and nitrogen-fixing bacteria are present in the soil,
advances in the past decade and assistance to the field practitioner in assessing
the efficacy of these organisms.
allow us to move beyond
Soil microbiota have been found to influence
research on individual the quality and longevity of harvested crops
either positively (through beneficial microbial
species to study whole interactions) or negatively (through plant
pathogens). Thus, the application of screening
communities of organisms, methods for associated biota – such as by next
and hence develop new generation sequencing – and the subsequent
necessary interventions would prove valuable
approaches to address food in the post-harvest process. This may enhance
sustainability of the full agricultural value-chain.
security and environmental
protection
Food Industry
With the advent of novel methods, researchers Several soil bacteria and fungi are being used
are now able to move beyond a focus on individual traditionally in the production of soy sauce,
species. Scientists have started to discover how the cheese, wine and other fermented food and
hugely diverse soil microbiome is tied to pathogen beverages. Lactic acid bacteria that could
control, plant health, increased yield, and an potentially be used to produce heavy metal
increased ability to overcome abiotic stress. absorbing probiotic products. Soils provide
habitats for a variety of lactic acid bacteria
Especially in the last decade, method advances belonging to Lactobacillus, Lactococcus and
including molecular sequencing techniques and other genera, opening the possibility to probiotic
“big data” analytical tools have helped to identify bacteria useful in food fermentation or other
species living in soils and their communities. processes be isolated from soils.
Artificial intelligence has great potential in
the assembly of data and the aggregation of
information from multiple databases. Novel
metagenomics represents a promising approach Ecosystem restoration
for the simultaneous study of all DNA-based Field studies conducted at relevant scales for
information in soils, including all groups of soil ecosystem restoration (i.e. hectares) have
organisms and functional gene information. demonstrated that a whole-soil biota inoculation
method representing all soil biodiversity is a
powerful tool in the restoration of terrestrial
Agricultural industry ecosystems. However, the effectiveness of any soil
biodiversity restoration programme depends on
New molecular techniques using next generation the appropriate integration into its landscape and
molecular sequencing allow for improved the expected interactions within it. When soils
knowledge of what organisms are in the soil, and have been extremely degraded, the rehabilitation
what effects those organisms are likely to make of the physical and chemical properties of the
on associated cropping systems. This knowledge substrate is necessary. Under the influence of
provides predictive power to our understanding soil-forming factors, including soil biodiversity,
of how the soil systems will respond to changes in the development of new soils may occur (Figures 2
climatic factors, new cropping systems, and soil and 6).
management. Other applications for these tools

14 State of knowledge of soil biodiversity

Combination of soil rehabilitation strategies
Combination of soil rehabilitation strategies
Native
•Organic amendments plants
•Sewage sludge
•Mulches •Compost
•Gravel
•Woodchip

•Opencast mining
•Quarrying
•Mine spoil waste
•Engineering works
Under the influence of soil forming
factors, including biodiversity
management, technosols may again
provide ecosystem services

Soil rehabilitation

Mulching + organic
amendments
•Beneficial for restoring
degraded soils
• Stimulate the growth and
activity of soil fauna (i.e.,
microbes, neamtodes, mites,
springtails, earthworms, etc.).
•Increase soil fertility.

Figure 6. Mining activities have drastic negative effects on soils, especially in arid areas. An alternative to restore the biological
communities of the soils is the establishment of technosols. Essential actions in the recovery of soil functionality include the
addition of organic matter, which together with the action of pioneer plants, promotes the growth and activity of soil biota
populations, eventually influencing the improvement of the fertility of degraded soils.

Summary for policy makers 15

Pharmaceutical industry
Loss of soil biodiversity could limit our capacity
to develop new antibiotics and tackle infectious
diseases. While most biopharmaceutical research
is focused on identifying unique microbes that
can be developed into biotherapeutics, new
technologies that make it possible to study
the metagenome (or collective genome) in an
environmental sample have sparked an interest in
exploring how complex biological communities in
soil and other indoor and outdoor environments
influences human immune and nervous response
via the skin, gut and lungs.
©Andy Murray
4 The essential The important role of soil biodiversity in
ecosystem functioning and ecosystem service
contributions of soil delivery can be threatened by human activities as
well as by natural disasters, though the latter may
organisms are threatened also be influenced by human-induced changes.
These include deforestation, urbanization,
by soil-degrading practises. agricultural intensification, loss of soil organic
Policies that minimise soil matter/carbon, soil compaction, surface sealing,
soil acidification, nutrient imbalance, pollution,
degradation and protect salinization, sodification, desertification, wildfires,
erosion and landslides (Figure 7). These co-
soil biodiversity should be a occurring drivers of environmental change can
have synergistic effects and may thus pose a
component of biodiversity particular threat to soil organisms and ecosystem
functions. Deforestation and fires in particular
protection at all levels have very negative effects on soil biodiversity, and
policies designed to control and ideally reduce
their occurrence will have very beneficial impacts
on soil biodiversity.
©Andy Murray

18 State of knowledge of soil biodiversity

Major anthropogenic threats to soil biodiversity

Deforestation
drivers and effects • Land use change
• Loss of specialist species and
on soils • Loss of SOM and nutrients.
increase in generalist taxa.
• Changes in soil physical Impacts
on soil • Decrease in predator species.
properties. biodiversity
• Reduced soil and functional
• Disruption of suitable
diversity.
habitat.
• Recovery could take decades.
• Changes in pH.

Agricultural • Greater use of external inputs

• Decrease in soil biodiversity.
intensification (pesticides, fertilizers) and
more soil disturbance.
• Smaller and less complex
drivers and effects belowground food webs.
• Greater risk of soil erosion,
on soils • Recovery of soil
contamination, land Impacts
on soil communities may take
degradation, compaction biodiversity
years or decades.
and salinization.
• Less efficient and functional
• Alteration of hydrological and
soil food webs.
biogeochemical cycles.
• Loss of soil carbon and
• Disturbance of soil structure.
nutrients through leaching.
• Loss of SOM.

Cl Mg
P
Zn Na Cu

K
Mo S
Nutrient B Mn
imbalances Fe Si
drivers and Ca N
effects on soils • Reduces the growth capacity of
soil microorganisms.
• Change in the availability Impacts • Reduces nutrient flow through
of essential nutrients. on soil
biodiversity the soil food web.
• Excessive use of mineral
• Alteration of the nutritional
fertilizers.
content of primary producers
and litter inputs.

Summary for policy makers 19

 N

• Alteration of the environment

where soil organisms thrive.
• Inadequate fertilization.
• Hamper the activity of
• Pollutants.
organisms involved in
Acidification • Changes in plant
community composition.
Impacts
on soil
biodiversity
nitrogen cycling.
drivers and • Alteration of belowground
effects on soils • Changes in solubility of
food webs.
multiple elements in
• Changes in nutrient availability
soils.
and toxicity for
microorganisms.

Salinization
drivers and effects • Water absorption hampered by • Ion imbalance and
on soils changes in chemical and physical nutrient deficiency
soil properties. Impacts
on soil
decrease microbial
• Irrigation with brackish water. biodiversity functions and biomass.
• Salt water intrusion due • Shift in the composition of
to aquifer exhaustion. microbial, micro and
• Inadequate irrigation practices. mesofaunal communities.

Pollution
drivers and
effects on soils • Microplastics • Acute and chronic toxicity to soil
• Fertilizer application. Impacts
biota.
• Persistent organic on soil • Cascading effects from individual
biodiversity
pollutants. species to communities and
• Biocides and pesticides. ecosystem functions.
• Waste disposal. • Bioaccumulation in the food chain.

20 State of knowledge of soil biodiversity

Compaction
drivers and • Decreases macropore volume. • Loss of habitat and pore
effects on soils • Increases resistance to root spaces for soil biota.
penetration. Impacts
on soil • Affects faunal activity.
• Reduces water infiltration and biodiversity
• Decrease in faunal
increases runoff. biomass and population
• Affects oxygen, and CO2 fluxes density.
as well as redox potential.

Urbanization • Soil sealing, increasing water • Reduced habitat for soil biota,
drivers and effects runoff and reducing
Impacts
and increased spatial heterogeneity
on soils infiltration. on soil and fragmentation.
biodiversity
• Pollution. • Alteration in soil communities
• Topsoil removal or and food web dynamics.
replacement, and addition • Drastic alteration of the environment
of anthropogenic materials. where soil organisms live.

Surface sealing
drivers and effects • Increases water runoff and reduces
on soils water infiltration.
• Changes nutrient and carbon cycling. Impacts
• Affects climate and microclimate
on soil
biodiversity
• Loss of habitats for
regulation. soil organisms.
• Building of roads and other
permanent infrastructures.

Summary for policy makers 21

 Fire • Severe damage to soil biodiversity in the
drivers and topsoil.
effects on • Recolonization, with shift from
•Wildfires.
soils bacteria-driven towards fungi-driven
•Anthropogen burning Impacts
on soil community.
for land clearing. biodiversity
• Decrease in soil protist and invertebrate
•Removal of topsoil
abundance, biomass and diversity.
organic matter.
• Very slow recovery of macroinvertebrate
diversity and functional structure
(decades).

Erosion and
• Detachment, transport and • Inhabitants of upper soil layers
landslides deposition of soil particles by may be eliminated or
drivers and displaced.
water or wind.
effects on soils • Loss of habitat and decrese in
• Loss of organic matter and Impacts
on soil
changes in soil physical and biodiversity its quality for soil biota.
chemical properties. • Spread of pests and
• Creation of degraded and pathogens.
enriched depositional • Reduced soil biodiversity and
environments. functioning.

CO2 CO2
CO2
CO2
CO2 CO2
CO2 CO2 CO2
CO2 CO2

C C
Loss of C C C
C C C C
SOC/SOM C C
drivers and
effects on • Decrease in:
soils • Lower microbial biomass
• Formation and Impacts and diversity (especially in
stabilization of aggregates. on soil
biodiversity extreme environments).
• Cation exchange capacity.
• Decreased resources to
• Water infiltration and retention.
belowground food webs.
• Soil fertility and C sequestration.

Figure 7. Major anthropogenic threats to soil biodiversity.

22 State of knowledge of soil biodiversity

Invasive alien species to host specificity of many of the soil bacteria and
fungi and larger soil fauna they attract, facilitating
Most of our knowledge of invasive soil species the spread and expression of soil-borne diseases.
concerns agricultural pests, of which many
contribute to huge economic losses globally.
Invasive alien species threaten the integrity of
indigenous soil biodiversity. Non-native soil Assessment of soil
invertebrates can have dramatic negative impacts biodiversity
on native plants, microbial communities, and other
soil animals: terrestrial invasive species can arise Despite recent studies -using the latest technology
from any level of biological organization ranging and artificial intelligence- on the global
from viruses and microbes (bacteria and fungi) to distribution of some soil biota orders, the current
plants, invertebrates, and mammals. state of soil biodiversity and the distribution of
many soil biota remains poorly known in many
countries of the world.
Agricultural intensification Countries have assessed the status and trends of
soil biodiversity in a variety of ways, including the
Negative impacts due to agricultural intensification use of scientific knowledge, the latest technologies
have consequences for the specific functions and artificial intelligence, farmers’ innovations
soil animals perform, including soil structure and practices, indigenous and traditional
formation and ecosystem engineering, and knowledge, and mapping. Overall, there is an
population regulation by predation. Human urgent need to continue recent efforts using the
management of agricultural and other soils is latest technologies and artificial intelligence,
known to significantly alter soil biodiversity: and to coordinate and invest in soil biodiversity
Tillage: Tillage of the soil causes loss of larger soil assessment at the global level.
fauna and disruption of the soil food web.

Misuse of fertilizers: Synthetic fertilization

may have a negative impact on soil microbial Policy development
communities and fauna. Negative impacts of While above-ground biodiversity is familiar
synthetic N fertilization on microbial biomass, to most people, and its protection is managed
arbuscular mycorrhizal fungal (AMF) and faunal under national and global laws and regulations,
diversity have been observed. there are few comparable activities that focus on
Lime application for pH correction: Most the protection of soil biodiversity. Protecting
tropical rainforest soils are naturally acidic, and above-ground biodiversity is not always sufficient
often receive large quantities of lime following to protect soil biodiversity. Above-ground and
deforestation to neutralize pH, especially with below-ground biodiversity are shaped by different
the establishment of more intensive cropping environmental drivers, and are not necessarily
systems. Large shifts in pH impose stress on linked to one another. Above and below-ground
native microorganisms, affecting their growth and biodiversity requires tailored protection,
reducing ecosystem resilience to disturbance. conservation and restoration considerations
because they are connected but at the same
Misuse of pesticides: Pesticides may cause time very distinct.
resistance and bioaccumulation through the food
chains. The use of pesticides can have unintended To further promote the conservation and
effects on soil organisms, as different organism sustainable use of soil biodiversity, long-term
groups react differently to various chemical monitoring and standardized sampling and analysis
substances. protocols must be developed. With worldwide
collaboration, this should enable collation of large
Monocultures:  Monocultures limit the presence datasets, which are critical to amassing scientific
of beneficial bacteria, fungi and insects, and evidence for the quantitative and functional
contribute to ecosystem degradation. Large-scale significance of soil biodiversity.
monocultures also reduces soil biodiversity due
Summary for policy makers 23
While some countries have established indicators • There is a need to promote the necessary shift to
and monitoring tools for soil biodiversity, for the include biological indicators of soil health along
majority of countries there is a lack of knowledge, with physical and chemical.
capacity and resources to implement soil health
principles and adoption of best practices for soil • There is a need to standardize sampling and
biodiversity enhancement. analysis protocols worldwide to enable collation
of large comparable datasets.
Some of the major recommendations from the
report are as follows: • Increase inter-sectoral and inter-institutional
collaboration to explore synergies and avoid
• Soil biodiversity needs to be reflected in duplication or fragmentation, since soil polices
National Reports and National Biodiversity can be under the responsibility of different
Strategies and Action Plans (NBSAPs). Ministries.
• Strengthen education and capacity building in • Policies and urban planning need to integrate
the adoption of molecular tools to contribute to soil biodiversity into sustainable soil
human, plant and soil health. management and ecosystems restoration plans
to guarantee healthy soils to people by reducing
• Sustainable soil management practices should urban threats to/from soil biodiversity.
be adopted by farmers and land users to prevent
and minimize soil biodiversity loss.
• Soil remediation and ecosystem restoration
plans need to include soil health and soil
biodiversity considerations.
©Andy Murray
The way forward research centres, networks, universities, and
schools are starting to include soil biodiversity
in their programmes. Some of them are also
conducting research on technological innovations
Despite the clear importance of soil biodiversity as well as on traditional and agroecological
in the provision of essential ecosystem services approaches related to soil biodiversity (e.g.
(provision of food, fiber and fuel, filtering of research, practical application, assessment,
water, source of pharmaceuticals, carbon and indicators, and monitoring).
nutrient cycling, soil formation, GHG mitigation,
pest and disease control, decontamination and
remediation), its proper use and management We must take advantage of this momentum to:
is not up to scale. It is only just over a decade
ago that initiatives and research networks were • Advocate for mainstreaming soil biodiversity
established to contribute to the knowhow, into the sustainable development agenda, the
conservation, use, and sustainable management of Post-2020 biodiversity framework, the UN
soil biodiversity. These include the establishment decade on ecosystem restoration, and all areas
of the International Initiative for the Conservation where soil biodiversity can contribute;
and Sustainable Use of Soil Biodiversity in 2002,
the establishment of the Global Soil Biodiversity • Develop standard protocols and procedures for
Initiative in 2011 and the Global Soil Partnership assessing soil biodiversity at different scales;
in 2012, and the publication of the Global Soil • Promote the establishment of soil information
Biodiversity Atlas by the European Commission in and monitoring systems that include soil
2016. biodiversity as a key indicator of soil health;
Since then, soil biodiversity has started to emerge • Improve knowledge (including local or
as an alternative solution to global challenges traditional) of the soil microbiome;
and not only as an academic field emerged. Some
countries are starting to use soil biodiversity in • Strengthen the knowledge on the different soil
different areas such as agriculture, food safety, groups forming soil biodiversity (i.e., microbes,
bioremediation, climate change, pest and disease micro, meso, macro and megafauna);
control and human health. Some regions, like
the European Union, have set up action plans for • Establish a global capacity building programme
sustainable production, consumption, and growth for the use and management of soil biodiversity
to become the first climate-neutral continent in and the Global Soil Biodiversity Observatory.
the world by 2050; soils and soil biodiversity are
important components of the European Green
A summary for policy makers with a forward looking
Deal. In addition, some national institutions,
angle is presented in Table 1.

25
Table 1
Summary for policy makers

Theme Challenges/Gaps Specific actions *Cross-cutting actions *Cross-cutting scopes

• Better understanding of • Monitoring tools that • Advocate for the • Guarantee soil health
microbiome (or functional include: new analytical implementation of SSM for all ecosystem vitality &
groups/keystone species) approaches; advanced under the VGSSM at human well-being.
networks. computing power; next- national level. • Support agriculture for
• Better understanding generation sequencing • Implement the use/ sustainability, productivity,
of micro, meso and for the assessment of management and and resource use
macrofauna roles in soil microbial SB coupled with conservation of soil efficiency.
functions and nutrient traditional techniques; biodiversity as nature- • Support farmers to
cycling. increase predictive power based solutions. reduce vulnerability by
• More research is needed to changes in climatic • Promote ecosystem- diminishing production
to corroborate SB data in factors, new cropping based approaches that costs, increasing yields
different ecosystems and systems, and SSM; digital conserve, restore and and strengthening their
agroecosystems. soil mapping tools avoid soil degradation and capacity to design and
• Small and large-scale in combination with biodiversity loss. implement SSM practices.
SB studies in many biological information. • Develop partnerships • SB can significantly
ecoregions of the world, • Implement large- that support multi- contribute to tackle
especially in the southern scale (watershed and disciplinary approaches, environmental problems.
hemisphere. landscape) SB studies. foster synergies and • The knowledge that
• Targeted research • Include soil biodiversity
Understanding soil biodiversity, from cells to vertebrates

ensure a multi-stakeholder soil is alive expands the

about the long-term in the Guidelines of perspective regarding SSM possibilities for human-
impacts/risks of methods Soil Survey including and SB. soil relationships.
of biocontrol in the standard methods for • Implement the • SB must be considered a
environment. measurement. combined use of natural capital asset from
• Long-term continuous • Implement SB models traditional knowledge, which ecosystem services
monitoring programs based on big data novel technologies and are produced.
are needed in different generated from soil- innovation and ensure that
ecosystems, climate water-plant-atmosphere all relevant stakeholders
types and management information. have access to these tools
practices to address the • Obtaining or and associated policies.
temporal variability of increasing financial • Develop robust and
environmental changes. support to implement reliable biological
• It is necessary to develop novel technologies indicators, and
robust and reliable -metagenomic, monitoring/assessment
biological indicators and metabolomic, volatilomic- protocols for SB.
measurement methods. in developing countries. • Raise social awareness
• Establishment of a on SB loss and recovery;
Global Soil Biodiversity threats to SB including
Observatory. agricultural intensification
• Support the and best practices for
development of SB assessment; and
community-based management and
monitoring and monitoring for all land
information systems management activities.
(CBMIS).
• Simplify methodologies
and tools for soil
biodiversity assessment
that are directly accessible
in all regions of the world.
• Mobilize targeted
participatory research and
development, ensuring
gender equality, women’s
empowerment, youth,
gender-responsive
approaches and
the participation of
indigenous people and
local communities.
• Increase taxonomic *This content applies to all themes addressed in table 1
capacity and address
taxonomic assessment
needs in different regions. SB: soil biodiversity;
• Support training in N: nitrogen;
the identification and
description of SB at all SOC: soil organic carbon;
levels, and particularly for SSM: sustainable soil management.
lesser-known taxa.

26 State of knowledge of soil biodiversity

Theme Challenges/Gaps Specific actions *Cross-cutting actions *Cross-cutting scopes

• Economic valuations • Support projects focused • Advocate for the • Guarantee soil health
of SB functions and on the economic valuation implementation of SSM for all ecosystem vitality &
Contributions of soil biodiversity to ecosystem services and functions
ecosystem services on SB functions and under the VGSSM at human well-being.
provided are scarce. services. national level. • Support agriculture for
• More attention must • Measure SB contribution • Implement the use/ sustainability, productivity,
be paid to the regulation to different soil functions management and and resource use
services -such as carbon and services at different conservation of soil efficiency.
storage- that rely on SB. scales, and under different biodiversity as nature- • Support farmers to
• It is highly necessary conditions. based solutions. reduce vulnerability by
to develop methods to • Develop baseline data • Promote ecosystem- diminishing production
measure SB contribution on SB and make regular based approaches that costs, increasing yields
to all ecosystem services small and large-scale conserve, restore and and strengthening their
affected, and at different measurements over time. avoid soil degradation and capacity to design and
spatial and temporal • Better analyze the biodiversity loss. implement SSM practices.
scales. relationship between • Develop partnerships • SB can significantly
the structure of SB that support multi- contribute to tackle
communities and their disciplinary approaches, environmental problems.
role in the ecosystems foster synergies and • The knowledge that
and agroecosystems ensure a multi-stakeholder soil is alive expands the
functioning. perspective regarding SSM possibilities for human-
• Promote the adoption and SB. soil relationships.
and feasibility of Payment • Implement the • SB must be considered a
for Environmental combined use of natural capital asset from
Services based on SB, traditional knowledge, which ecosystem services
with appropriate policies novel technologies and are produced.
at various governmental innovation and ensure that
levels. all relevant stakeholders
have access to these tools
and associated policies.
• Develop robust and
reliable biological
indicators, and
monitoring/assessment
protocols for SB.
• Raise social awareness
on SB loss and recovery;
threats to SB including
agricultural intensification
and best practices for
SB assessment; and
management and
monitoring for all land
management activities.

*This content applies to all themes addressed in table 1 SB: soil biodiversity;
N: nitrogen;
SOC: soil organic carbon;
SSM: sustainable soil management.
©Andy Murray

Summary for policy makers 27

 Theme Challenges/Gaps Specific actions *Cross-cutting actions *Cross-cutting scopes

• It is crucial to envision • Consider SB and • Advocate for the • Guarantee soil health
land-use change and ecosystem services in land implementation of SSM for all ecosystem vitality &
management as a trigger use planning. under the VGSSM at human well-being.
for other threats to SB. • Foster activities to national level. • Support agriculture for
• There are knowledge promote the practical • Implement the use/ sustainability, productivity,
gaps in urban SB. application of SB, and management and and resource use
• Lack of knowledge integrate it into broader conservation of soil efficiency.
of contaminant policy agendas for food biodiversity as nature- • Support farmers to
concentrations in soils and security, ecosystem based solutions. reduce vulnerability by
exposure thresholds for SB. restoration, climate • Promote ecosystem- diminishing production
• Lack of understanding change adaptation based approaches that costs, increasing yields
on interactive effects and mitigation, and conserve, restore and and strengthening their
among multiple global sustainable development. avoid soil degradation and capacity to design and
change drivers on SB. • Promote sustainable biodiversity loss. implement SSM practices.
• Poor understanding of planning management of • Develop partnerships • SB can significantly
the role and impacts of urbanized environments that support multi- contribute to tackle
Threats to soil biodiversity

threats to SB in selected and urban soil disciplinary approaches, environmental problems.

ecoregions and global rehabilitation. foster synergies and • The knowledge that
region. • Assessment of ensure a multi-stakeholder soil is alive expands the
• Inability to adequately vulnerable species and perspective regarding SSM possibilities for human-
map the importance of landscapes to prioritize and SB. soil relationships.
threats to SB at the global their protection. • Implement the • SB must be considered a
level. • Minimise the drivers combined use of natural capital asset from
of SB loss and promote traditional knowledge, which ecosystem services
the improvement of soil novel technologies and are produced.
health. innovation and ensure that
• Inclusion of SB into the all relevant stakeholders
risk assessment of agro- have access to these tools
inputs. and associated policies.
• Regular assessment • Develop robust and
of soil contaminants and reliable biological
ecotoxicological test indicators, and
experiments with different monitoring/assessment
target species. protocols for SB.
• Perform detailed threat • Raise social awareness
assessments on SB at on SB loss and recovery;
various scales and/or for threats to SB including
various taxa. agricultural intensification
• Perform a regional and best practices for
and global synthesis of SB assessment; and
the threats to SB, using management and
georeferenced and monitoring for all land
spatially relevant data. management activities.
• Promote Red-listing of
endangered SB species at
the national and global
level.

*This content applies to all themes addressed in table 1 SB: soil biodiversity;
N: nitrogen;
SOC: soil organic carbon;
SSM: sustainable soil management.
©Andy Murray

28 State of knowledge of soil biodiversity

Theme Challenges/Gaps Specific actions *Cross-cutting actions *Cross-cutting scopes

• Increase research on the • Promote the prevention, • Advocate for the • Guarantee soil health
field-scale performance suppression and control implementation of SSM for all ecosystem vitality &
of microbial inoculants of pathogens and invasive under the VGSSM at human well-being.
and entomopathogenic species. national level. • Support agriculture for
nematodes as biological • Invest on targeted • Implement the use/ sustainability, productivity,
control of insect pests. research on soil-borne management and and resource use
• Insufficient knowledge diseases and promote conservation of soil efficiency.
of the role of direct and integrated pest biodiversity as nature- • Support farmers to
indirect management management. based solutions. reduce vulnerability by
of micro, meso and • Privilege the • Promote ecosystem- diminishing production
macrofauna in soil development of whole based approaches that costs, increasing yields
functioning and ecosystem community microbial conserve, restore and and strengthening their
service delivery. inoculants over single avoid soil degradation and capacity to design and
Management of soil biodiversity

• The portfolio of microbial isolates. biodiversity loss. implement SSM practices.

solutions to environmental • Implement nature- • Develop partnerships • SB can significantly
problems is currently based solutions towards that support multi- contribute to tackle
microbial-based; micro, the micro, meso and disciplinary approaches, environmental problems.
meso and macrofauna are macrofauna, not only in foster synergies and • The knowledge that
almost never included. microbes. ensure a multi-stakeholder soil is alive expands the
perspective regarding SSM possibilities for human-
and SB. soil relationships.
• Implement the • SB must be considered a
combined use of natural capital asset from
traditional knowledge, which ecosystem services
novel technologies and are produced.
innovation and ensure that
all relevant stakeholders
have access to these tools
and associated policies.
• Develop robust and
reliable biological
indicators, and
monitoring/assessment
protocols for SB.
• Raise social awareness
on SB loss and recovery;
threats to SB including
agricultural intensification
and best practices for
SB assessment; and
management and
monitoring for all land
management activities.

*This content applies to all themes addressed in table 1 SB: soil biodiversity;
N: nitrogen;
SOC: soil organic carbon;
SSM: sustainable soil management.

Summary for policy makers 29

©FAO/Matteo Sala
The Global Soil Partnership (GSP)
is a globally recognized mechanism
established in 2012. Our mission
is to position soils in the Global
Agenda through collective action.
Our key objectives are to promote
Sustainable Soil Management
(SSM) and improve soil governance
to guarantee healthy and
productive soils, and support the
provision of essential ecosystem
services towards food security and
improved nutrition, climate change
adaptation and mitigation, and
sustainable development.

Thanks to the financial support of

Ministry of Finance of the

Russian Federation

ISBN 978-92-5-133583-3

9 789251 335833
CB1929EN/1/11.20