SC Soil Biodiversity

CHAPTER II – DIVERSITY OF SOIL ORGANISMS
28 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

Introduction
Soil is one of the most diverse habitats on Earth. Nowhere in a b
nature are species so densely packed as in soil communities.
For example, a single gramme of soil may contain millions
of individuals and several thousand species of bacteria. The
complex physical and chemical nature of the soil, with a porous
structure, immense surface area and extremely variable supply
of organic materials, food, water and chemicals, provides a range
of habitats for a multitude of organisms. These range from
macro- to micro- levels depending on climate, vegetation and
physical and chemical characteristics of a given soil. The species
numbers, composition and diversity in a particular ecosystem
depend on many factors including temperature, moisture, acidity,
nutrient content and the nature of the organic substrates.
Soil biota includes archaea, bacteria, protists, tardigrades,

rotifers, nematodes, acari (mites), collembolans (springtails),
worms (enchytraeids and earthworms), macroarthropods
(e.g. ants, termites, centipedes, millipedes, woodlice, etc.) and
burrowing mammals. It also includes plant roots, fungi and
lichens. Root exudates attract a variety of organisms that either
feed directly on these secretions or graze on the microorganisms
concentrated near the roots, giving this busy environment the c d
name ‘rhizosphere’. There are also animals, such as beetle larvae,
flies and butterflies, that use the soil as a temporary habitat to
reproduce or to spend their early life stages feeding on different
live and dead plant materials until they reach their maturity.
Soil communities are so diverse in both size and numbers of
species, yet they are still extremely poorly understood and in dire
need of further assessment. Research has been limited by their
immense diversity, their small size and the technical challenge of
identifying them.
e f
Organisms can be classified in different ways. Taxonomy (from

Ancient Greek τάξις taxis, ‘arrangement’ and -νοµία -nomia,
‘method’) is the science of defining groups of biological
organisms on the basis of shared characteristics and giving
names to those groups. The rank-based method of classifying
living organisms we use today was originally popularised by g h
Swedish botanist Carl Linnaeus (1707-1778). In his landmark
publication ‘Systema Naturae’ (first edition published in 1735),
Linnaeus used seven taxonomic ranks to classify 10 000 species
of organisms: kingdom, phylum, class, order, family, genus and
species. Other ranks and sub-ranks have been added over the
years, with frequent discussions among taxonomists.
The greatest innovation of his system is the general use of

binomial nomenclature (i.e. the combination of a genus name and
a second term), which together uniquely identify each species of
organism within a kingdom. Both names use Latin grammatical
forms and they must be written in italics, or underlined when
handwritten. Furthermore, in modern usage, the first letter of
the first part of the name, i.e. the genus, is always capitalised
in writing, while the specific epithet is not. For example, the
human species is identified by the name Homo sapiens. When
the specific name cannot be identified, the abbreviation ‘sp.’ is
used to accompany the genus name (e.g. Lumbricus sp.). The
abbreviation ‘spp.’ (plural) indicates ‘several species’ in that
particular genus (e.g. Agaricus spp.). These abbreviations are not
italicised (or underlined).
CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 29

Introduction
When Linnaeus developed his classification system, there were
only two kingdoms, Vegetabilia (plants) and Animalia (animals). Linnaeus 1735 2 kingdoms Animalia Vegetabilia
The advances in microscopy and staining techniques led to the

identification of new organisms and a better understanding of cell
Haeckel 1866 3 kingdoms Animalia Plantae Protista
structure and functioning. Although a general consensus has not

Chatton 1925 2 empires Eukaryota Prokaryota
yet been reached on how many kingdoms there are, all proposed
classification schemes are based on three main criteria: cell
Copeland 1938 4 kingdoms Animalia Plantae Protista Monera
type (prokaryote without a membrane-bound nucleus – karyon
– or eukaryote with a nucleus and other organelles enclosed
Whittaker 1969 5 kingdoms Animalia Fungi Plantae Protista Monera
within membranes); the number of cells in the body (single cell
or multicellular); and the ability to obtain food (autotroph or
Woese et al. 1977 6 kingdoms Animalia Fungi Plantae Protista Archaebacteria Eubacteria
heterotroph).
From around the mid-1970s onwards, there was an increasing Woese et al. 1990 3 domains Eucarya Archaea Bacteria
emphasis on comparisons of genes on the molecular level
(initially ribosomal RNA genes – see box below) as the primary Cavalier-Smith 1993 8 kingdoms Animalia Fungi Plantae Chromista Protozoa Archezoa Archaebacteria Eubacteria
factor in classification (i.e. genetic similarities among organisms).

Accordingly, taxonomic ranks, including kingdoms, were to be
Cavalier-Smith 1998 6 kingdoms Animalia Fungi Plantae Chromista Protozoa Bacteria
groups of organisms with a common ancestor, and based on

Ruggiero et al. 2015 7 kingdoms Animalia Fungi Plantae Chromista Protozoa Archaea Bacteria
RNA studies the Linnaean categories have been updated to
include ‘Domain’ as the highest rank in the taxonomic hierarchy.
Therefore, although plants, fungi and animals may look different,
they are more closely related to each other than they are to either
the Bacteria or Archaea, which represent two different domains.
Prokaryotic cell Eukaryotic cell Unicellular Multicellular Autotroph Heterotroph
All the intracellular water-solu- The cytoplasm accommodates Also known as a single-celled Organisms that consist of “Self-feeding“ organism that produces Organism that cannot ﬁx
ble components (proteins, DNA membrane-bound organelles, organism, is an organism that more than one cell. complex organic compounds (such as carbon and uses complex
and metabolites) are located especially the nucleus, which consists of only one cell. carbohydrates, fats and proteins) from organic substances produced
together in the cytoplasm contains the genetic material, simple substances present in its by, or available in, other
enclosed by the cell membrane, and is enclosed by the nuclear surroundings, generally using energy organisms.
rather than in separate cellular envelope. from light (photosynthesis) or inorganic
compartments. chemical reactions (chemosynthesis).
DNA and RNA

• Deoxyribonucleic acid (DNA) is a molecule that encodes
the genetic instructions used in the development and
functioning of all known living organisms. Most DNA
molecules consist of two long polymer strands coiled
around each other to form a double helix.
• The two DNA strands are composed of simpler units called
nucleotides. Each nucleotide is composed of a nitrogen-
containing base known as guanine (G), adenine (A),
thymine (T), or cytosine (C) and a sugar called deoxyribose
and a phosphate group. According to fixed rules for pairing
the bases, A always goes with T and C with G.
• Like DNA, RNA (ribonucleic acid) is a chain of nucleotides,
but unlike DNA it is more often found in nature as a single-
strand. Furthermore, the nucleotide thymine is replaced by
uracile (U) in RNA. Organisms use RNA to convert genetic
information into specific proteins.
• Each of the three domains of life recognised by biologists
today contain portions of DNA (e.g. rDNA, ribosomal
DNA) which is unique to them, and this fact in itself
forms the basis of the three-domain system and allows
for the classification of organisms based on their DNA
(phylogenetic approach).

Main taxa For example:
Domain Eukaryota
Kingdom Animalia mm
ali
a
Supergroup (only for protists) Ma
lia
pti
Phylum Chordata
Re
ta
bia
br
Subphylum Vertebrata a
r te
phi
at
Diptera, H europtera
Ame
Rhiza
Ve
Am
d
St
Hymenop ptera,
ra,
ra
Class Mammalia
or
Alv
bozo
m
emipte
ria
Asc en
eo
tera,
Ch
om o
oleo
a, N
lat
Exc pile
a
B as yco
t a e P ro
Order Soricomorpha Pl a n
tha
Ectogna ta
idio av s
myc ta
Lepidopter
Isoptera, C
t is
or Insec
ata
Glom o ta
erom
ts
Family Talpidae ycota
H ex a p d a
Zygom
Fung
ycota
Genus Talpa Chytridiomyco
Collembola
ta
cea Entognatha
Eukaryota
Protura
Diplura
i
Blastocladiomycota
Species T. europea
a
Rotifer
op o d
tacea
al
ia
a
costra
C r us
A ni m
th r
Ne
da
Mala
Isopo
m
Ar
at
a
od
od
ia p
a
Pa iplop oda
eobacteria yarchaeota Mo
Sy ra da
Prot Eur
yr
llu
hyl a
D ilop
o
mp pod
s
M
ca
a
t a
Ch
A nne a da ra
lida Tardigr ce
u
eli
Ch
n o b a ct e ri a
Fir mic u t es
Ga ida
Bacteria Archaea str
opo
Ara
chn
ota
T h au m
da
ri
ha e
Cya
Clitella Aca eae nes

ta io
a rc
n
a rc
B a ct eria Ar ch aea Ara corp s

eo
en
ha
ta Cr udos pione
Ac ti e
Ps Scor
n o b a ct e ri a
Haplo
taxida
However, taxonomic classifications (i.e. using hierarchical ranks)

provide little understanding of their lifestyles and functional roles.
For this reason, this chapter explores the overwhelming diversity
of soil biota using another common approach to classify soil
organisms that involves using their body width to identify four
broad groupings: microfauna (less than 0.1 mm), mesofauna (0.1 microfauna mesofauna macrofauna megafauna
to 2 mm), macrofauna (2 to 20 mm) and megafauna (bigger than 1 000
20 mm). Body width appears to be a more consistent classifying
criterion than body length, which shows greater variability even Myriapoda Earthworms
among representatives of the same group. However, even these
ranges do not provide distinct limits and, on some occasions, 100 Diplura Formicidae
Pseudoscorpionida Termitidae
there is some confusion as to whether a particular organism Mole
should be considered macro, meso or micro.
Amphibian
Body length (millimetre)
Enchytraeidae
10 Reptiles
The size distribution of soil animals, together with some of their
anatomical features (such as the presence/absence of legs) Protura Gastropoda
Rotifera
and some behavioural responses (reactions to light and heat), Coleopteran larvae
Acari
determine the best collecting method for a particular group of Fungi Isopoda
1 Arachnida
organisms. For example, the soft bodies of the microfauna and
some of the mesofauna living in the water film surrounding
Dipteran larvae
soil particles can be extracted using a wet extraction method Nematoda
(Bearmann funnels; see pages 64-65) or by centrifugation. By 0.1
contrast, the legged microarthropods with hard exoskeletons Collembola
can be collected using dry extraction (Tullgren funnel; see pages Tardigrata
64-65) because these animals actively move away from light
and heat. Finally, hand-sorting and pitfall trapping are often 0.01 Protists
used to collect the macrofauna, while bait trapping has been
used to catch mammals such as moles. All of these organisms Archaea
are involved in creating and maintaining the soil structure and Bacteria
0.001
providing essential ecosystem services for humans (such as
regulating greenhouse gas emissions or preserving water quality).
Most of them cannot survive outside of soil, so it is necessary 1 2 4 8 16 32 64 128 256 512 1 024 2 4 8 16 32 64
to preserve healthy and diverse soil systems if we want to
preserve their beneficial influence. One of the main challenges micrometre millimetre
that soil conservation faces today is the lack of awareness of the Body width
ecological importance of soil biodiversity. So, open your eyes and
discover what lives under your feet!

Prokaryota – Archaea
Morphology Taxonomy a b
Archaea are unicellular microscopic organisms with a striking Archaea, the third domain of life (see page 31), were originally
variety of cell shapes (pleomorphism) and unique geometric forms split into two phyla, the Euryarchaeota and the Crenarchaeota.
[25]. Many are rod-like (referred to as bacilli – e.g. Methanocella The Crenarchaeota have now been divided to make a new phylum,
and Methanobrevibacter) or spherical (referred to as the Thaumarchaeota. There may be other phyla, such as the
cocci – e.g. Methanococcus) while the heat-loving (thermophiles) Korarchaeota, Nanoarchaeota and Aigarchaeota, but whether
Sulfolobus are highly irregular cocci. By contrast, Methanosaeta these represent true distinct phyla is disputed. The Euryarchaeota
and Methanospirillum have both a long rod shape (filamentous) are physiologically the most diverse, with a number of
with sheaths that surround adjoining cells. Additionally, some methane-producing orders (methanogens); the aerobic, salt-loving
archaea (e.g. Methanosarcina) form clusters, while the cells (halophilic) Halobacteriales; the thermophilic, Thermoplasmalates, c
of Haloterrigena form many irregular shapes. Some species sometimes lacking a cell wall; and several ‘orders’ with members
belonging to Halobacteriales can be square-shaped, triangles or that are not yet described. The Crenarchaeota are almost all
flat discs. extremophiles, living at high temperatures or extremes of pH (see
boxes below) and are primarily involved in sulphur or iron metabolism.
The Thaumarchaeota contain most of the isolated mesophilic
a b archaea, which are associated with aerobic ammonia oxidation
(nitrification). All three major phyla also contain many undescribed
groups and we know little about their ecology and physiology.
Microorganisms and the environment

• Some microorganisms, including the archaea, are able to modify
500 nm their shape or size in response to environmental conditions − this is
also known as pleomorphism.
• Organisms that exist only in moderate temperatures, typically
c d between 20°C and 45°C, are referred to as mesophiles. a b
• By contrast, extremophiles are organisms that thrive in extreme
environmental conditions. It is possible to have different classes of
extremophiles, depending on the evironmental factors:
- thermophile: an organism that loves high temperature;
- psychrophile: an organism that loves low temperature;
- alkaliphile: an organism that loves high pH values;
- acidophile: an organism that loves low pH values;
- halophile: an organism that loves high salt concentration.
e M Microhabitat
Euryarchaeota, in particular methanogens, dominate waterlogged
The versatile archaea soils. Six of the seven methanogen orders can be found in different
soil types, either free-living or associated with other organisms,
• The discovery of archaea altered our understanding of evolution, but such as ciliates and termites. Methanogens can also be found in
recent research suggests that eukaryotes evolved from archaea. So dry and aerated soils. Members of the Halobacteriales order are
humans may actually be derived from archaea. often found in high salinity soils, and many use light as an energy
f • Archaea live in the widest range of environmental conditions of any source. Archaea in soils under termperate climates are dominated
organisms, from pH 0 to pH 12, 0˚C to 120˚C, and up to 35 % by the Thaumarchaeota, a group that was previously linked to
salinity. the Crenarchaeota. Many Thaumarchaeota are able to convert
• Hyperthermophilic archaea survive at temperatures greater than ammonia to nitrite (amonia-oxidisers). In low pH soils, and under
90°C by having a thin membrane, made up of double-headed low ammonia and low oxygen conditions, these archaea are
lipids, that insulates the cell interior from the heat. In acid or salty more important than their bacterial counterparts. There are also
environments, this sort of membrane acts as a barrier to water non-ammonia oxidising Thaumarchaea, but it is not possible to
molecules and other ions. isolate these in the laboratory (see pages 64-65); therefore, they
• The halophilic archaeon, now called Haloquadratum walsbyi, was for remain uncharacterised. The extremophilic Crenarchaeota are
a long time known as ‘Walsby's square bacterium’ as it is box shaped primarily found in harsh soils, such as hot volcanic soils, rich in
and forms large fragile flat sheets in the environment. sulphur and iron compounds. A unique group was found to be
• Archaea do not have a nucleus. the dominant archaea in high acidic, deeply weathered, red soils
(Ferralsols – see pages 26-27) in China.
Diversity, abundance and biomass
Over 300 archaeal species have been described, primarily found

in extreme environments. However, many more species have been
detected in the environment but it is not possible to isolate and
describe them. Soils contain between 105 and 1010 microbial cells
in each gramme (0.04 ounces), and all contain archaea. Generally,
up to 10 % of microbial cells in temperate soils may be archaea
(mesophilic species), while in conditions of high temperature,
high salinity or at high or low pH, archaea (extremophilic species)
can be the dominant members of the microbial community.

Prokaryota – Bacteria
Morphology a b Microhabitats
Bacteria are one of the two domains, along with Archaea, Unlike eukaryotes, bacteria can be found in a wide range of
that include prokaryotic organisms [26]. The domain Bacteria environmental, chemical and physical conditions including
comprises microscopic organisms, single-celled or with the cells extremes of pH, temperature and salinity. Many soil bacteria are
forming simple associations. Most bacteria are 0.2 micrometres beneficial to human economic activities and are necessary for
(µm) in diameter and 2 - 8 µm in length. Bacteria have a variety environmental sustainability. Bacteria are part of chemical cycles
of shapes: round or spherical (commonly known as cocci), rod during which they release essential elements for recycling. They
shaped (bacilli) and spiral (spirilla). However, many bacteria can also decompose dead organic matter and are the only microbes
assume several shapes (pleomorphic). Depending on how the capable of biological nitrogen N2 fixation (see page 105). This is
newly formed cells adhere to each other, bacterial arrangements the ability to transform nitrogen (N2) from the atmosphere (about
c 80 % of the atmosphere is N2) into ammonium (NH4+) which is
include singles, pairs, chains and clusters. When bacteria are motile
(capable of moving) they have a specific structure (flagellum) assimilated by eukaryotes, plants in particular. Bacteria can exist
for locomotion. The flagellum is a whip-like structure that can either as independent (free-living) organisms or as symbionts
occur at one end, both ends, or all over the bacterial cell. Bacteria that depend on other organisms to live, subsisting either as
can live without oxygen (anaerobes) or depend on it to grow mutualists, parasites or commensalists (see box below).
(aerobes). They can also be adapted to live either in the presence
or absence of oxygen (facultative anaerobes). Some species of What is symbiosis?
bacteria contain endospores or exospores (see box next page). If
you break down the term endospore, ‘endo-’ means ‘inside’ and • Symbiosis is a close and often long-term interaction between two
‘-spore’ refers to the ‘dormant structure’, so the endospore is a different biological species.
structure of resistance formed inside the cell. By contrast, the • There are three main types of symbiosis:
exospores develop externally. Spores are a bacterial cell's way - mutualism is the way two organisms of different species exist in
of protecting itself against harsh changes in the environment or a relationship in which each individual benefits from the activity
nutrient depletion. A spore protects the bacterial genetic material of the other;
so that, when optimal conditions return, the bacterial cell can - commensalism is a class of relationship between two organisms
reform (germinate) and thrive again. where one organism benefits from the other without affecting it;
- parasitism is a relationship between species, where one species,
Taxonomy the parasite, benefits at the expense of the other, the host.
• Some symbiotic relationships are obligate, meaning that both
Currently, there are 30 known and recognised phyla of bacteria. symbionts entirely depend on each other for survival.
Highly diverse and abundant phyla in soil are Proteobacteria, • Other relationships are facultative, meaning that they are not
Firmicutes, Actinobacteria and Cyanobacteria (see pages 34-35). essential for the survival of either species. Individuals of each
However, some other phyla, such as Acidobacteria, can also be species engage in symbiosis when the other species is present.
found in soil.
Most microbial species (more than 90 % according to the current
estimates), including bacteria, still remain unculturable (i.e. they
cannot be grown in any culture medium in the laboratory). This
means that we do not yet know what they look like or what
functions they carry out. Advances in molecular techniques (see
pages 64-65) in the past 30 years have enabled us to understand
more about these species by sequencing parts of their DNA.
These advances have also allowed for the identification of new
culturable species. Today there are approximately 2 800 genera
comprising approximately 15 000 species of known bacteria.
Soil microbial biomass is made up of bacteria, fungi and other
microorganisms. This biomass represents 1 to 4 % of total soil
carbon (up to three tonnes of carbon per hectare). The ratio of
the size of bacterial to fungal biomass depends on soil properties
and other environmental factors (e.g. soil pH, temperature and
nutrient availability); for example, a 30-fold decrease in bacterial
biomass was found when comparing high to low pH soils.
a b
Bacterial phyla
• In contrast to eukaryotic nomenclature, there is no official
classification of prokaryotes because taxonomy remains a matter
of scientific judgment and general agreement.
• The List of Prokaryotic names with Standing in Nomenclature (LPSN)
is an online database that maintains and provides accurate names
(nomenclature) and related information of prokaryotes according to
the International Code of Nomenclature of Bacteria.
• The 30 phyla currently accepted by the LPSN are: Acidobacteria;
Actinobacteria; Aquificae; Armatimonadetes; Bacteroidetes;
Caldiserica; Chlamydiae; Chlorobi; Chloroflexi; Chrysiogenetes;
Cyanobacteria; Deferribacteres; Deinococcus-Thermus;
Dictyoglomi; Elusimicrobia; Fibrobacteres; Firmicutes; Fusobacteria;
Gemmatimonadetes; Lentisphaerae; Nitrospira; Planctomycetes;
Proteobacteria; Spirochaetes; Synergistetes; Tenericutes;
Thermodesulfobacteria; Thermomicrobia; Thermotogae. 1 µm
• Other existing phyla of bacteria, which cannot currently be cultured
in the laboratory (see pages 64-65), are called candidate phyla. If
these are included, the total number of phyla is 52.

Prokaryota – Bacteria
Proteobacteria Firmicutes Bacteria as workers
Proteobacteria is the largest and most diverse bacterial phylum The most representative genera in Firmicutes are Bacillus
• Many compounds are produced in large amounts by bacteria to
[26]. It contains about 30 % of the total number of bacterial species. and Clostridium, which are obligate and facultative anaerobic
be used for various purposes in industry and medicine. They can
Proteobacteria comes from the name of the Greek god Proteus, bacteria, respectively [26]. These genera include important be a part of silk, cotton and rubber manufacturing. Bacteria also
which could take various forms, thus reflecting the enormous species of human and animal pathogens that produce resistant synthesise certain antibiotics, such as bacitracin and polymyxin.
diversity of morphological and physiological characteristics cell structures called endospores. Spores tolerate different types
• Bacteria are able to degrade complex compounds. For example, they
observed in this bacterial phylum. Proteobacteria comprises the of stresses. For example, they are more resistant to heat than break down the woody and tough tissues of jute, coconut, hemp and
majority of Gram-negative (see box below) bacteria of medical normal cells by a factor greater or equal to 105. Furthermore, flax. They can also degrade hydrocarbons and clean up oil spills.
(e.g. Helicobacter), veterinary (e.g. Acinetobacter), industrial (e.g. they are 100 times or more resistant to ultraviolet radiation,
Campylobacter) and agricultural interest (e.g. Bradyrhizobium). It and more tolerant to drought, antibiotics and disinfectants. Most
also comprises bacteria involved in carbon, sulphur and nitrogen Bacillus species, such as B. cereus, which causes contamination
cycles (including N2 fixers – see pages 99, 105), phototrophic (i.e. of food, are soil inhabitants. Due to their pathogenicity on some
organisms that obtain energy from light) and non-phototrophic, soil insects, some Bacillus species, including B. popilliae, B.
aerobic and anaerobic bacteria. lentimorbus and B. thuringiensis, have been successfully used
in agriculture to control pests. Bacillus may also be dangerous:
Gram-positive and Gram-negative Bacillus anthracis is considered the most lethal biological weapon
for human beings because it is the origin of anthrax (see box
• Gram staining, also called Gram's method, is a method on page 108). Another Firmicute genus, Paenibacillus, includes
of differentiating bacterial species into two large groups: important soil-living nitrogen fixers (see page 99). Nitrogen-fixing
Gram-positive and Gram-negative, respectively. The name comes
bacteria are also present in both Bacillus and Clostridium genera.
from the Danish bacteriologist Hans Christian Gram, who developed
the technique. The technique is based on the use of a chemical
compound, the crystal violet. The name refers to its colour, similar a b
to that of the petals of a gentian flower. The Gram stain is almost
always the first step in the identification of bacterial organisms.
• Gram-positive bacteria are bacteria that give a positive result
in the Gram stain test. Gram-positive bacteria take up the
crystal violet stain used in the test, and then appear to be
purple-coloured when seen through a microscope. This is because
in the cell wall of the Gram-positive bacteria there is a layer that
retains the stain after it is washed away from the rest of the sample,
in the decolourisation stage of the test.
• Gram-negative bacteria are a group of bacteria that do not retain
the crystal violet stain. After staining with crystal violet, the excess
is washed off with alcohol, which decolourises the bacteria since the
layer in their cell wall is too thin to retain the stain. A counterstain is
then added, which coloures the bacteria red or pink.
c d
Endospores, what are they?

• Endospores can survive environmental assaults that would normally
kill the bacterium. These stresses include high temperatures, high
a
UV irradiation, desiccation and chemical damages. The extraordinary
resistance properties of endospores make them of particular importance
because they are not readily killed by many antimicrobial treatments.
• When favoured nutrients are exhausted, some Gram-positive
bacteria may develop an extreme survival strategy: the formation
of endospores.
• This complex development allows the bacterium to produce a highly
resistant cell to preserve the cell's genetic material in times of
extreme stress.
• The resilience of an endospore can be explained in part by its unique b
cellular structure. The outer coat surrounding the spore provides
much of the chemical resistance. Beneath the coat there is a very
thick layer called the cortex. Proper cortex formation is needed
for dehydration of the spore core, which aids in resistance to high
temperature. A germ cell wall is found under the cortex. This layer
will become the cell wall of the bacterium after the endospore
germinates. The inner membrane, under the germ cell wall, is a major
permeability barrier against several potentially damaging chemicals.
The centre of the endospore, the core, exists in a very dehydrated
state and houses the cell's DNA.
• The process of forming an endospore is complex and requires several
hours to complete.

Actinobacteria a b
Actinobacteria is a phylum of Gram-positive bacteria that have
a highly diverse morphology, ranging from micrococci (spherical)
and rods to branched filaments that resemble fungal hyphae
(see box on page 39) [26]. The bacterial filaments are narrow
(diameter from 0.5 to 2 µm) and can be short and rudimentary or
extensively branched. Throughout their life cycles, Actinobacteria
may combine these different forms. Their reproduction is by
fragmentation of hyphae or through the production of spores.
The spores may be of several types (e.g. arthrospores, very
primitive spore type, formed through the breaking up of hyphal
filaments in Streptomyces and zoospores, motile and flagellate
spores, in Spirillospora and Actinoplanes). Spores are produced
(from one to several in chains) on hyphae, in spore-producing
structures (sporangia) or vesicles. The ecological niche of most 10 µm
Actinobacteria is the aerobic zone in soil. A striking feature of 1 µm
Actinobacteria is the production of extracellular enzymes that
degrade complex macromolecules commonly found in soils (e.g.
c d
casein, starch, chitin, cellulose and lignocellulose). Furthermore,
they synthesise and excrete thousands of metabolites, such
as antibiotics. For example, Selman Waksman, one of the
most important soil microbiologists, won the Nobel Prize for
Medicine in 1952 for his discovery of streptomycin produced by
bacteria of the genus Streptomyces. In addition to streptomycin,
Streptomyces are capable of producing a wide variety of
antibiotics with numerous properties: antibacterial, antifungal,
antiviral, antitumor, antiparasitic, insecticide and weed controlling.
Actinobacteria also includes the nitrogen-fixing bacteria of the
genus Frankia, which form root symbioses with plants of eight
botanical families (e.g. Betulaceae – see page 43). Other species
belonging to the genera Streptomyces and Corynebacterium are
plant pathogens. Animal pathogens are found among the genera
Corynebacterium, Actinomyces, Nocardia, Thermoactinomyces
and Mycobacterium. Among them, the Mycobacterium
avium-intracellulare-scrofulaceum stands out as being lethal for
people who have contracted the human immunodeficiency virus
(HIV).
Why does the air smell of soil after rain?

• The earthy smell after it rains is linked to Actinobacteria.
• In particular, the molecule responsible for the aroma is known as geosmin.
• Geosmin is produced by the Gram-positive bacterium Streptomyces, a
genus of Actinobacteria, and released when these microorganisms die.
• The human nose is extremely sensitive to geosmin and is able to
detect it at very low concentrations.
• Geosmin is also responsible for the earthy taste of beetroots.
Cyanobacteria a What is photosynthesis?

Cyanobacteria is a group of bacteria that are able to obtain • Photosynthesis is a process used by plants, algae and cyanobacteria
their energy through photosynthesis. This is possible due to the to convert sunlight energy into chemical energy.
presence of chlorophyll, which is also found in other photosynthetic • This chemical energy is stored in carbohydrate molecules, such as
organisms, such as algae and plants. Being photosynthetic, they sugars, which are produced from carbon dioxide and water;
manufacture their own food. This has caused them to be dubbed • Oxygen is released as a waste product.
‘blue-green algae’, though they have no relationship to any of • Photosynthesis maintains atmospheric oxygen levels and supplies
the various eukaryotic algae. They are considered one of the most of the energy necessary for life on Earth.
most diverse groups of prokaryotes as they vary from unicellular
to complex filamentous or branched forms. In some cases they Sunlight
have highly differentiated cells that carry out different functions, Oxygen
(O2)
so they may be considered as truly multicellular organisms.
Cyanobacteria have the distinction of being the oldest known
fossils, more than 3.5 thousand million years old, in fact. The
cyanobacteria have been tremendously important in shaping the
b
course of evolution and ecological change throughout Earth's
history. Indeed, the atmospheric oxygen that we depend on was Sugar
generated by numerous cyanobacteria through photosynthesis.
Carbon dioxide
Furthermore, the photosynthetic structure of plant cells, the (CO2)
chloroplast, evolved from cyanobacterial ancestors. Cyanobacteria
also contribute to the health and growth of many plants in
another way: they have the ability to convert inert atmospheric
nitrogen into ammonia (nitrogen fixation) that plants can use (see
page 105). This process cannot occur in the presence of oxygen,
so nitrogen is fixed in specialised cells called heterocysts. These
Water
cells have an especially thickened wall that contains an anaerobic
environment. Cyanobacteria also form symbiotic relationships
with many fungi, forming complex symbiotic organisms known
as lichens (see page 42).

Protists
Protists are defined as unicellular eukaryotes (see page 30). Amoebozoa Alveolata
Many form filaments (such as some fungi), are colonial or
aggregate into larger clusters of cells. They are divided into
Morphology Morphology
the Archaeplastida (green algae, red algae and ancestors of
higher plants), the Amoebozoa (many amoeboid species), the The Amoebozoa is another group of unicellular organisms whose The Alveolata is a group of protists characterised by folded
Opisthokonta (collar cells, fungi and ancestors of animals), cells are covered by a very thin protein layer with or without membranes underneath their cell membranes (called alveoli)
Stramenopiles, Alveolata, Rhizaria and Excavata. Typically, they microscales. [29, 30] [31]. Ciliophora (the only soil-inhabiting Alveolata) have two
have one nucleus and soil species have a contractile vacuole for types of nuclei: a small inactive nucleus with condensed
regulating water and ion concentrations. Many species have a chromosomes, which becomes active only during reproduction,
Taxonomy
swimming dispersal stage with one or more cilia. Cysts form in and a large nucleus that is always active and holds many copies
sub-optimum living conditions or when prey are scarce. Although The Amoebozoa is a supergroup that contains bacterial-feeding of the chromosomes. Most species have rows of cilia that beat
many protists can be identified under the microscope to family or amoeboid species. Several lineages contain mostly aggregative in a coordinated manner, and a specialised funnel structure
genus level, species identification is made through DNA sequence species referred to as ‘social amoebae’, such as the Myxogastria for capturing and ingesting prey. They also often have specific
analysis (see pages 64-65). [27] and the Dictyostelia, but aggregative species occur in other defensive or aggressive structures, called ejectosomes. These are
protists as well. In Arcellinida the cell is inside a vase- or made of mucus that is ejected from the cell. A complex network
Rhizaria helmet-shaped structure made of protein, sometimes amended of vacuoles inside the cell regulates the digestion of food and the
with soil particles bound together by proteins. water balance.
Morphology
Social amoebae Taxonomy
Cells typically produce very thin hair-like extensions called
• Social amoebae occur among protists and not just in Amoebozoa. There are three main supergroups in the Alveolata (Apicomplexa,
filopodia that can branch and merge together again, forming
a complex network in some species. They tend to grow flat on • They are found in a wide variety of colours; more than 900 species of Dinoflagellata and Ciliophora), but only Ciliophora (ciliates) are
surfaces and their filopodia can extend into small crevices in the slime mould occur all over the world. found free-living in the soil. Most ciliates ingest bacteria, but some
soil searching for bacteria. When detached from surfaces, they • Some species may reach sizes of several square metres and masses ingest other protists or are specialised symbionts or parasites
swim with two cilia. They can also move by amoeboid locomotion of up to 30 grammes. (see box on page 33). Colpodellida prey on other protists and can
or gliding on surfaces. Soil species form resting cysts that enable • They live in any type of dead plant material and contribute to the reach higher numbers by feeding on soil invertebrate corpses. The
them to survive adverse environmental conditions. There are decomposition process. Colpodea includes most of the ciliates found in high abundance
many variations of this basic morphology as it is a diverse group. when soil samples are kept in the laboratory. Many genera
emerge from cysts when sufficient moisture and bacteria are
present and then reproduce. Colpodids are very diverse and can
Taxonomy be identified to the genus or family level (see page 29) through
This supergroup has one major soil lineage: the Cercozoa [28]. microscopy. The other genera that occur in some abundance in
The Cercozoa (common name cercomonads) consist of a diverse soils belong to the order Hypotrichea. These are also diverse but
variety of species of small bacterial-feeding unicells less than rarely dominant in terms of abundance. The Colpodid to Hypotrich
10 µm in size. One subgroup common in soils is the Silicofilosea ratio (also called the Colpodid to Stichotrich ratio) is used as an
that secrete silica scales on their surface. The Silicofilosea indicator of environmental quality.
also include the Euglyphida that form vase-shaped protective
layers (known as tests) outside the cell. Other Cercozoa include a b
Vampyrellida that feed on fungal hyphae (see box on page 39),
the Phytomyxea that are parasites of plants and Stramenopiles
(see page 37) and Ascetospora that are parasites on soil
invertebrates.
a b Microhabitat
Amoeboid species occur on moist surfaces and live in water
microfilms where they forage for palatable bacteria or other c d
prey. Some species prefer wet conditions, others occur in drier
conditions, some have depth and litter preferences, and some are
known colonisers and occur in disturbed soils where other species
are absent. Amoeba are very effective at scouring surfaces for
bacteria. A small number feed on fungal hyphae or prey on
protists or microinvertebrates.
10 µm 20 µm
Microhabitat
Rhizaria live on the surfaces of soil and organic matter particles Microhabitat
where they select bacteria to ingest. Species may have depth
As soil dries, the ciliates' habitat becomes restricted to water
preferences in the soil. Some prefer organic matter and litter on
films on surfaces. They detect prey by chemical-sensing and
the surface of the forest floor. Others, such as Vampyrellida, prefer
swim toward the signal, or away from toxic molecules. Their
to penetrate fungal hyphae or spores. Those species with cilia can
dispersal is by water infiltration through soil pores, or in the air if
explore their habitat by swimming. The filopodia can extend into
dry soil is disturbed.
very small crevices (< 1 µm) to search for bacterial prey.

More than 1 500 species of soil ciliates have been described, but
There are hundreds or even thousands of soil Cercozoa species
many more remain undescribed so far. One study from Namibia
that cannot be distinguished by microscopy and, therefore,
Diversity, abundance and biomass revealed 365 species, of which 128 were new species, from
many genera remain to be described. These are usually the
73 soil samples. Temperate soils typically hold 20 - 30 species
most common active protists in soils, and abundances vary with Although most genera have probably been described, and about per gramme of soil, but most are inactive. In moist soils with
moisture as well as with the abundance of bacteria or other prey. 3 000 species have been identified, many species still remain to plenty of bacteria or prey, there can be 10 000 active cells per
Densities may reach more than one million cells per gramme of be discovered. When active, there can be as many as 100 000 gramme declining to none in very dry soils. Although the biomass
soil but are usually 103 - 105 per gramme. cells per gramme of soil, but more typically numbers are 103 - 104, of ciliates per gramme of soil is very low, when active they can
depending on the ecosystem. ingest several hundred bacterial cells per minute.

Stramenopiles Excavata Other protists
Morphology Morphology Nuclearia, Ancyromonas and others

Stramenopiles are unicellular organisms with two cilia that beat The general body-type in this very diverse group is a small cell There are several genera that belong to the base of the
in different directions: a front one that includes tiny hairs (visible with a cilium directed backwards that generates locomotion and Opisthokonta, the group that includes animals and fungi.
on electron microscope images) that pulls the cell, and a trailing directs food (mostly bacteria) toward a feeding groove on the These genera are common in soil, though rarely abundant, and
one that pushes the cell. In some groups, however, the trailing ventral surface, as observed in Fornicata. Many groups have contribute to the ingestion of bacteria. These include Nuclearia,
cilium is missing. Other groups are usually filamentous and reduced mitochondrial function and prefer micro-aerophilic (low Fonticula, and the Rozella. Several genera found in soils cannot
only the dispersal cell is ciliated. Terrestrial species form resting oxygen) or anaerobic (no oxygen) environments. In contrast to yet be placed into our classification system. They are placed as
cysts in the soil, and in some sexual species dispersal spores are many Excavata groups, the Kinetoplastea (commonly called incertae sedis in the eukaryotes. These include Ancyromonas,
produced after sexual reproduction. [32, 33] kinetoplastids) have a characteristic mitochondrion with a large Breviata and Apusomonadida.
amount of DNA. Many kinetoplastid species rely on dissolved
Taxonomy nutrients for food (they are osmotrophic). In Parabasalia, the
single body-type is replicated hundreds of times to form large
This supergroup includes the brown algae and several groups multiciliated cells. Both Parabasalia and Preaxostyla have
previously thought to be fungi, such as Hyphochytriales and elaborate supporting cytoskeletal elements that provide shape
Peronosporomycetes, which are commonly found in soils. Some and assist in locomotion. The Heterolobosea are generally
species of true brown algae occur in alpine soils (for example, amoeboid species with two or four cilia that are used to move in
Vaucheria), but they are typically rare or absent. Most terrestrial search of food, but some have lost either the ciliated stage or the
species have lost the ability to photosynthesise (see box on page amoeboid stage. The Euglenids are typically spindle-shaped cells
35) and appear colourless. They absorb nutrients from the living covered by a flexible pellicle; and they can be photosynthetic or
or decomposing tissues into which they grow. not, with the non-photosynthetic species feeding on bacteria or
other protists. [34]
The Irish Potato Famine
a
• The Irish Potato Famine, a period of mass starvation, disease and
emigration in Ireland between 1845 and 1852, was caused by
Phytophthora infestans, a Peronosporomycetes.
• Originally from the Toluca Valley in Mexico, once introduced through
infected potatoes, it spread rapidly to much of northern and central Europe.
• Because prior to 1980 they were considered to be fungi, we still lack
an effective chemical compound to treat stramenopile parasites since
fungicides (aiming to disrupt fungi) do not work.
Microhabitat
Hyphochytriales are found in moist soil environments. They
absorb dissolved nutrients with a network of filaments that
extend from the cell. Terrestrial species of Peronosporomycetes
are decomposers of organic matter or live as plant parasites.
They feed by extending filaments into plant tissues. They are
economically important because they include species that cause b
some of the most damaging plant diseases, such as Pythium
(which causes the damping-off disease in greenhouses), downy
mildews and white blister rusts. Diatomea are typically aquatic
species that can be found in riparian or regularly flooded soils,
and sometimes inside rotting tree logs. Their role and presence
in soils is poorly documented. The motile stage is usually a small
swimming cell with two cilia, while sexual reproduction leads to
the growth of a thick walled spore for dispersal.
a b
a b
10 µm Taxonomy
c The Excavata is a supergroup, with genera that occur in soil

included in six phyla: Fornicata, Parabasalia, Preaxostyla, Discoba,
Heterolobosea and Euglenozoa.
Microhabitat
Heterolobosea are found in every ecosystem but are rarely the
dominant protists, except in some disturbed soils. The Euglenida,
both photosynthetic and heterotrophic genera, occur in soils that
are regularly moist or water-saturated (e.g. in wet soil and in
riparian areas). Among the Discoba, some free-living species
occur in the order Jakobida, such as those of the genus Andalucia.
Diversity, abundance and biomass Diversity, abundance and biomass

Only approximately 25 genera of Hyphochytriales are known to There are approximately 562 described species of Parabasalia
science, but many still remain to be described. Fewer than 700 and Preaxostyla, more than 80 species of Heterolobosea and
species of Peronosporomycetes are described, but there are likely more than 1 520 species of Euglenozoa.
to be 1 000 - 10 000 species.

Fungi – Macrofungi
Morphology Taxonomy Microhabitat
Within the fungus kingdom, macrofungi are a group that form Macrofungi, taxonomically belonging to the subkingdom Dikarya, Macrofungi are found in most terrestrial habitats, from woodlands
visible, often coloured, cup- or cap-like structures (scientifically are classified into two main phyla: Ascomycota and Basidiomycota. to grasslands, but they are probably most diverse in forests.
known as ‘fruiting bodies’ or ‘sporophores’) that emerge from the The Ascomycota, the largest group of macrofungi with more They need the right climatic conditions to form fruiting bodies; in
soil. These fruiting bodies are where the spores are formed. The than 64 000 described species, are usually characterised by a particular, moisture to allow their spores to develop. Depending
spores are small (1 - 100 µm), usually single-celled, reproductive cup-like or disc-like fruiting body (technically known as ascoma), on their functions, they can be defined as saprotrophic, parasitic
structures able to tolerate unfavourable growing conditions (e.g. where spores are formed within a typical structure, named the or mycorrhizal. The saprotrophic species play a key role in the
drought). Below the fruiting bodies, each fungus has a mass of ‘ascus’. The Basidiomycota (more than 31 000 described species) degradation of decaying organic matter (i.e. soil, leaf litter
hyphae, the typical branching thread-like filaments produced mostly have a fruiting body (called basidioma) with an umbrella- and dead wood). The parasitic (see box on page 33) fungi are
by most fungi. The mycelium is made up of the mass of these shaped cap (known as pileus) borne on a stalk (known as a stipe) responsible for several diseases in plants (see box, next page),
hyphae and is responsible for its growth. In the case of soil where the spores are produced. Other phyla that include soil animals (mostly invertebrates) and other fungi. The mycorrhizal
macrofungi, a large portion of the mycelium is hidden since it fungi are Glomeromycota, Zygomycota, Chytridiomycota and fungi form symbioses with plant roots, a mutualistic association
grows belowground. When environmental conditions become Blastocladiomycota (see pages 40-41). that is beneficial to both partners (see box, page 33).
favourable, the fungus develops the fruiting body and spores
that, once released, disperse through the air, or are carried by a b
insects or water. [35, 36]
c d
Fungi: edible, poisonous, bioluminescent and giant

• There are several edible Basidiomycota and Ascomycota. Mushrooms, such as Boletus
edulis and truffles (Tuber spp., see box on page 40), are consumed in many countries.
• Some Basidiomycota produce deadly toxins, such as amatoxin produced by Amanita
phalloides. Thirty grammes of this fungus may kill a person; others, such as Ganoderma
lucidum, are considered medicinal fungi.
• Some Basidiomycota (e.g. species belonging to the genus Mycena) are bioluminescent.
• In Hainan Island (southern China) a giant specimen of Fomitiporia ellipsoidea (belonging
to the group of bracket fungi, also included in Basidiomycota) was found to be 20 years
old with an estimated volume of 409 000 - 525 000 cm3 and a weight of 400 - 500 kg.
This represents the largest fungal fruiting body (both in volume and in weight) ever found.
d

Diversity, abundance and biomass How a fungus is made a
Fungi are extremely abundant. Millions of species have been
estimated, but only about 150 000 have been described.
Macrofungi have about 90 000 known species. Together with
bacteria, fungal hyphae constitute the largest portion of the
microbial biomass of soil. Generally, fungal biomass is found to
be greater than bacterial biomass in forest soils.
b c
b
• A hypha is a long, branching filamentous structure. In most fungi, hyphae
are the main mode of growth, and collectively form the mycelium.
• Hyphae grow at their tips. They can branch through the bifurcation
of a growing tip, or through the emergence of a new tip from an
established hypha.
• There are different types of hyphae:
- septate, which have cross walls (called septa) at fairly regular
intervals;
- aseptate or coenocytic, which do not have septa.
• Hyphae can fuse to one another. This process is known as anastomosis. d
• Yeasts are fungi that do not have hyphal structures. They are the
only unicellular fungi.
c d
e f
Soil-borne plant pathogenic fungi

• Soil-borne plant pathogenic fungi (SPPF) comprise organisms that are included in the Fungi
kingdom and in the group of fungal-like organisms currently assigned to the Stramenopiles (see a b
page 37). As pathogens, they are responsible for several plant diseases. [37]
• Among fungi, both Ascomycota and Basidiomycota are represented. The major species belong to
the genera Fusarium, Phoma, Sclerotinia and Verticillium within Ascomycota, and to Armillaria
and Rhizoctonia within Basidiomycota. g
• SPPF produce survival structures that may be as simple as cells, called chlamydospores, with
a thick wall, or may be more complex like the sclerotia, typical of some fungi (e.g. Sclerotium,
Sclerotinia and Botrytis).
• In addition to the survival function, aggregation of hyphae, called rhizomorphs since they
resemble plant roots, are typical of species belonging to the fungal genus Armillaria and may
c d
play a crucial role in fungal spread through the soil, host infection and disease transmission.
• Soil type, pH, water content and temperature of the soil are among the major factors affecting
the presence of the soil-borne plant pathogenic fungi.
• Fusarium species and Rhizoctonia solani, although commonly present in moist soils, tolerate
lower water content levels. They also prefer warmer soils (25 - 35 °C).
• SPPF are grouped into two functional categories: soil inhabitants and soil invaders. The first
category generally includes unspecialised microbes that infect seedlings and young roots, while
the second are disease agents that show a degree of host specificity. Seed decay, damping-off
and root rots of seedlings are the most common diseases caused by soil-borne fungi.
• Soil-borne plant pathogenic fungi are reported worldwide in agricultural and forests soils.
• The number of plant pathogenic fungal species on Earth has been estimated to be as high as
270 000; however, the number of SPPF is largely unknown.
• The abundance of SPPF is generally measured as ‘inoculum density’, which is expressed as the
mass, or the number, of spores per gramme of soil. Inoculum density has been reported as
ranging from 100 to 10 000 spores per gramme of soil, depending on the species.

Fungi – Mycorrhizal fungi
Morphology The significant mutual benefit of mycorrhizal symbioses is evident Ectomycorrhizas
from their tremendous abundance and diversity. Mycorrhizal fungi
Mycorrhizas are literally ‘fungus-roots’ created by symbiotic are found in all terrestrial biomes and in association with most Approximately 6 000 fungal species establish ectomycorrhizal
associations (see box, page 33) between plant roots and fungi. plant families. They are found with trees, shrubs, forbs, grasses associations with many species of trees and woody plants. At least
Mycorrhizal fungi help their host plants acquire mineral nutrients and agricultural crops. Arbuscular mycorrhizas are abundant in 20 families of Basidiomycota (e.g. Amanitaceae, Russulaceae,
from the soil in return for plant sugars. Mycorrhizal fungi form tropical forests, grasslands, savannahs, deserts and arable lands, Boletaceae) and seven families of Ascomycota (e.g. Pezizaceae,
structures outside and inside plant roots. All types form extensive and ectomycorrhizas dominate temperate and boreal forests. Tuberaceae) are known to establish ectomycorrhizas. The
networks of microscopic hyphae that extend outwards from plant Ericaceous mycorrhizas are common in boreal forests and biomass of ectomycorrhizal fungi mycelia has been estimated
roots into the surrounding soil or leaf litter. Arbuscular mycorrhizas heathlands. Orchid mycorrhizas are essential to the survival of to range from 700 to 900 kg per hectare, and 20 - 40 % of an
(AM), ericaceous mycorrhizas and orchid mycorrhizas are sometimes orchids throughout the world. ectomycorrhizal root weight is due to the fungus.
called ‘endomycorrhizas’ because the fungi form distinctive
structures between and inside the cortical cells of plant roots, but do
Glomeromycota a
not generally cause obvious changes in root morphology. By contrast,
ectomycorrhizas (EcM) often cause distinct changes to roots that Fungi in the phylum Glomeromycota form arbuscular mycorrhizal
can be observed without a microscope. Reproductive structures symbioses with the majority of plant species, by colonising the
also differ among mycorrhizal types. Arbuscular mycorrhizal fungi root cortex (see box, page 43) and forming an extensive mycelium,
reproduce with microscopic spores produced in the soil or within vesicles and arbuscules. This phylum contains 17 genera and
plant roots, whereas many ectomycorrhizal fungi reproduce with 240 species distributed in nine families and four orders. Common
mushrooms or underground truffles. [38] genera include Glomus, Rhizopaghus, Sclerocystis, Gigaspora,
Scutellospora, Cetraspora and Acaulospora. Glomeromycota
a produce abundant hyphae and spores in soils. In grasslands and
agricultural lands, these fungi comprise an estimated 20 - 30 %
of soil microbial biomass, making arbuscular mycorrhizal fungi
among the most abundant organisms in many soils.
b
a
100 µm
b
b
100 µm
c
Ericaceous and orchid mycorrhizas
Most plant species belonging to Ericaceae, including the genera
Rhododendron, Calluna and Vaccinium, form ericoid mycorrhizas.
These plants form delicate roots lacking root hairs and their
c outermost radical cells become heavily colonised by Ascomycota
from the genera Rhizoscyphus and Hymenoschyphus. Orchid
mycorrhizas are established between plant species of the family
Orchidaceae (20 000 to 35 000 species) and several groups of fungi
in the phylum Basidiomycota, as well as some rare Ascomycota.
Microhabitat
Diamonds of cuisine
• Mycorrhizas are among the most widespread symbionts in the world.
The They are found in more than 80 % of all plant species and 92evident
% of
fromall their tremendous abundance and diversity. Mycorrhizal
plant families.
fungi are foundcan
• Mycorrhizas in be
allmanaged
terrestrial biomes andasinthey
as biofertilisers association with
increase plant
Microhabitat
nutrient uptake (see pages 98-99).
• Many species of ectomycorrhizal
fungi are important culinary
mushrooms and truffles.

Fungi – Other fungi
Zygomycota a The hat thrower
A unique feature of the Zygomycota is the zygospore, which
• A unique spore dispersal strategy for the Zygomycota of the order
is formed within a structure called the zygosporangium after
Mucorales is exhibited by the dung fungus of the genus Pilobolus.
the fusion of specialised hyphae called gametangia during
sexual reproduction [35, 36]. The mature zygospore is often • Its name literally means ‘the hat thrower’. When spores are ready,
the turgor pressure within the vesicle beyond the sporangium
thick-walled and undergoes a dormant period before germination.
(spore-producing structure) builds to a sufficient level that allows
Nevertheless, asexual reproduction occurs much more frequently
the sporangium to be launched. The entire black sporangium is
than sexual reproduction in the zygomycetes. During asexual explosively shot off up to distances of several metres.
reproduction, hyphae grow over the surface of the material on
• For an organism less than 1 cm tall, this involves acceleration from
which the fungus feeds and produce clumps of erect stalks, b 0 to 20 km/h in only 2 µs, equivalent to a human being launched at
called sporangiophores. The tips of the sporangiophores form 100 times the speed of sound (more than 120 000 km/h).
spore-producing structures, the sporangia. Thin-walled spores
are produced within the sporangia and are thus shed above the
substrate, in a position where they may be dispersed by wind or
water, allowing the fungus to spread and colonise new substrates
quickly and efficiently. The Zygomycota include two main classes:
Zygomycetes (that comprise Mucorales, the most studied order)
and Trichomycetes. More than 1 000 species have been described
so far. Zygomycetes are commonly decomposers, symbionts or
parasites (see box, page 33) in terrestrial habitats. For example,
members of the Mucorales are easily isolated from soil, humus
and dung. Furthermore, some Mucorales are used to ferment
foods and produce important industrial products, such as lactic
acid and rennin (used to make cheese). Conversely, some species
have a negative economic impact by causing storage rot in fruits.
Trichomycetes are obligate associates of arthropods, including c d
insects and millipedes. The host may be an adult or larva, in
terrestrial or aquatic habitats. The fungi are usually found
attached to the gut lining of the host. The precise relationship is
difficult to determine in most cases; however, they often seem
to be commensals, doing little or no harm to their hosts, with
the fungus gaining nutrients from the gut of the host. Some
zygomycota can also be pathogens of animals, plants, amoebae
and, especially, other fungi. Of the more than 1 000 species of
described Zygomycota, the majority are found in soil, with some
genera (Mucor, Mortierella and Rhizopus) that are extremely
common and reported in almost all surveys of soil fungi.
Chytridiomycota Blastocladiomycota
a
Chytridiomycota (chytrids) are characterised by their asexual The Blastocladiomycota (blastoclads) are one of the currently
state, a motile (capable of moving) zoospore with a single recognised phyla within the Fungi kingdom. Blastoclads
whiplash flagellum oriented and located posteriorly [35, 36]. were originally the order Blastocladiales within the phylum
Zoospores are released through an opening in the wall, and Chytridiomycota, until molecular and zoospore structural
their release usually indicates the death of the ‘body’ of fungus, characters were used to demonstrate that it was a group separated
called thallus. They are the only fungi that form flagellate spores. from chytrids. Similar to Chytridiomycota, Blastocladiomycota
Chytridiomycota are typically unicellular, with limited hyphal produce zoospores to colonise new substrates. Furthermore,
growth in some cases. Chytrids require a water film in which members of Blastocladiomycota are capable of decomposing
zoospores can swim until a desirable substrate is found. For this complex materials, such as cellulose and chitin. Of economic
reason, chytrids are usually regarded as aquatic fungi, although importance is Physoderma maydis, a parasite of maize and
those that thrive in the capillary network around soil particles the causal agent of brown spot disease. There is a blastoclad,
are typically considered terrestrial. Approximately 700 species of Sorochytrium milnesiophthora, that is a tardigrade parasite (see
chytrids have been described, including species living in temperate page 44). However, the best known species, belonging to the genus
forest and rainforest soils. Soil chytrids include plant pathogens Catenaria, are nematode parasites. As they are mainly known to
and vectors of plant viruses such as Synchytrium endobioticum, be aquatic fungi, a reliable evaluation of their abundance in soil
which causes the potato wart disease (black scab) and serious is not available.
commercial damage. Some chytrids are nematode (see pages
46-47) and algae parasites. As Chytridiomycota often feed on a
decaying organisms, they are also important decomposers. These b
organisms are responsible for the decomposition of resistent
materials, such as pollen and cellulose. This colonisation of pollen
usually occurs during the spring when bodies of water accumulate
pollen falling from trees and plants. Estimates of the number of
chytrid species occurring in soil are currently unavailable.

Photosynthesisers – Lichens
Morphology Taxonomy a
Lichens originate from symbiosis, involving a fungus ‘mycobiont’ Lichens are derived from the fusion of two unrelated groups of
(the dominant partner) and one or several photosynthetic organisms, where the taxonomy of the resulting hybrid organism
‘photobionts’ (the energy producers), either unicellular green algae, is based on the fungus. Ninety-eight percent of lichenised
cyanobacteria (see page 35) or both. The symbiosis is mutualistic fungi are Ascomycota in 18 of the 45 recognised orders (only
since the fungus benefits from the food (carbohydrates) produced five contain exclusively lichenised taxa), and two percent are
by algae or cyanobacteria, and the algae or cyanobacteria benefit Basidiomycota (see pages 38-39). The lichenised green algae are
by being protected from the environment by the fungus. This placed in Trebouxiophyceae (Chlorophyta), while cyanobacteria
symbiosis is also cyclical as the two partners must activate the comprise several orders.
association with every new generation. Also, specific bacterial
communities are obligate lichen symbionts and, therefore, Microhabitat
considered to be an integral part of lichen structure. The thallus is
the vegetative and assimilative body that relies on the interactions Lichens growing on the ground are ‘terricolous’ or ‘epigeous’
among the symbionts. The thalli (growth forms) can vary from and colonise a wide range of soils. The habitats include: mineral
discrete granules of 0.5 - 50 mm to pendent lichens of 2 m in or organic soils, thin layers of strongly weathered rocks, rock
length, and have an extraordinary range of growth types, each of crevices, sand dunes, grasslands, bryophytes (i.e. mosses,
which show particular adaptations to different environments. [39] hornworts and liverworts), damp trunks or rocks, peatlands and
rotting wood. In tundras, cushions of ‘reindeer lichens’, mostly
Cladonia species, are basic food for these herbivores. Continental
steppes harbour specialised types of erratic vagrant thalli that
allow them to disperse easily. Lichens are a major component of
b
biological soil crusts (see page 73) in desert and dryland regions,
growing in patches that increase soil stability and permeability,
as well as resist erosion.

There are about 28 000 species living in all types of habitats.
Only 5 - 12 species thrive in tundra or desert soils, while in
tropical areas, rocks and bark surfaces may support more than
50 species in less than 0.5 m2.
Uniqueness of lichens
• Lichens are complex and unique entities with characteristics not
found in either the original fungi or algae. These include slow growth, c
long life, ability to revive from severe desiccation, high habitat
specificity, tolerance to extreme temperatures and the ability to
survive on all types of substrata and habitats.
• Some rock-inhabiting species are among the oldest living organisms
on Earth.
• Lichens are extremely vulnerable to habitat alteration and are
effective ‘early warning indicators’ of environmental changes.
a b c
a b c
f
a b c d

Photosynthesisers – Plants
Morphology Microhabitat
Plants are organisms that have a visible part aboveground Plants are found everywhere, from tundra to desert. The
(the shoot system) and a hidden part belowground (the root aboveground parts of plants are responsible for the photosynthesis
system). The extreme variety in the shapes of the visible portion (see box on page 35) that provides energy for the plants and
of the plants is also present in the roots below the surface of replenishes oxygen in the atmosphere. By contrast, the root
the soil. The two main types of root systems are fibrous and system has three main functions: 1) absorption of nutrients and
taproot. Fibrous roots are the traditional structures formed by water; 2) anchorage to soil; 3) storage of nutrients. Plant roots
primary and secondary roots branching in all directions in the generally grow anywhere with suitable environmental conditions
soil. By contrast, taproots are characterised by a single firm root and readily explore soil macropores (see page 72). The part of the
growing straight down, with minor roots developing either side soil that is directly influenced by roots is called the rhizosphere,
of it. Other specialised roots do exist; for example, the tuberous and is very rich in soil microorganisms (e.g. in bacteria and fungi).
roots of sweet potato are modified for the storage of nutrients
and water, while the stilt roots of mangroves allow the plant to Diversity, abundance and biomass
be stable in wet and muddy soils by cropping up from the trunk
and growing downwards. Roots are usually covered by root hairs The number of known plant species has been estimated to be
that are invisible to the naked eye and form a large surface area around 400 000. The majority (i.e. 260 000 - 290 000 species)
allowing plants to take up water and mineral nutrients from the belong to seed plants with around 1 000 Gymnosperms. Nearly
soil. [40, 41] all the others are classified as flowering plants (Angiosperms).
It is difficult to estimate plant root biomass because: 1) the fine
a roots are difficult to sample and 2) the separation of living from
dead roots is very tedious. Nevertheless, as a general rule, plants
allocate relatively more biomass to roots if the limiting factor for
growth is belowground (e.g. water), while they allocate relatively
more biomass to shoots if the limiting factor is aboveground
(e.g. light). For this reason, a low root biomass is usually typical
of plants living in forests and woodlands, while a higher root
biomass can be found in desert plants.
Incredible numbers of plant roots

• The maximum rooting depth, 68 metres, was found in a plant in the
Kalahari Desert.
• A single winter rye plant (Secale cereale) can grow roots measuring
620 kilometres in only 0.5 cubic metres of soil.
• A grove of over 40 000 clonal quaking aspens (Populus tremuloides),
located in south-central Utah (USA), has the largest root system in
the world. It is estimated to weigh 6 600 tonnes.
a b c
Root structure
Observing a cross section of a plant root, the main visible structures are:
• root hair: they have fundamental importance in absorbing water Xylem Epidermis
and nutrients and in attaching the plant to the soil or other growing
surface. They are lateral extensions of a single cell; Phloem Cortex
• epidermis: a single-layer group of cells that forms a boundary

between the plant and the external environment. Its functions are:
protection against water loss, regulation of gas exchanges, and
absorption of water and mineral nutrients;
Taxonomy • cortex: formed by unspecialised cells lying between the epidermis and
the vascular, or conducting, tissues (xylem and phloem). These cells can
Green plants (Viridiplantae), are a kingdom of organisms including be colonised by symbiotic fungi (see page 40). In some plants, such as
from 300 000 to 315 000 different species. The majority, carrots, the cortex becomes a storage organ;
260 000 to 290 000 species, produce seeds. The two main groups • phloem: conducts products of photosynthesis (i.e. sugars – see box
of seed plants are the flowering plants (Angiosperms) and the on page 35) from leaves to roots;
naked-seed plants (Gymnosperms). Angiosperms produce fruits • xylem: conducts water and minerals from the roots up through the
containing seeds and include the most common vegetables plant.
and fruits used as food by humans. Angiosperms comprise • Typical roots contain meristematic, elongation, and differentiation
monocotyledons (e.g. grasses, such as maize or wheat) that have zones. In the meristematic zone, cells undergo rapid division, creating 100 µm
fibrous root systems, and dicotyledons (e.g. carrots and apples) new cells for root growth. These cells begin to elongate (elongation
that have taproot systems. Gymnosperms include the conifers, zone), giving the root added length. The zone of differentiation Root hair
which are woody plants with cones and root structures similar to contains mature, specialised cells, such as phloem, xylem, and root
those of dicotyledons. hairs.

Microfauna – Tardigrada
Tardigrades are microscopic animals (0.1 - 1.7 mm) that are Their scientific name Tardigrada was suggested by the Italian Tardigrades are common in both marine and freshwater systems
strongly dependent on the availability of water to permit gas biologist Lazzaro Spallanzani in 1776 meaning ‘slow walker’. A but also in the water films surrounding soil particles. They are
exchange and avoid desiccation. This led to their original name number of morphological and molecular studies have tried to also found in mosses, which are the plants that have the most
‘little water bears’, which was given to them by the German resolve their systematic status, and recent analyses indicate developed capacity to absorb and retain water, thus giving them
pastor J.A.E. Goeze, who first described them in 1773. Their that they are probably basal arthropods. The phylum Tardigrada their second common name ‘moss piglets’.
bodies are short, slightly segmented and equipped with eight includes three classes and over 110 genera, and is continuously
poorly articulated legs ending in four to eight claws. They move updated with newly discovered species. For example, a new genus, Diversity, abundance and biomass
very slowly, in a manner similar to that of a bear. All tardigrades Pilatobius, was proposed in 2014. The class Mesotardigrada
possess an eversible buccal tube and two stylets to pierce animal includes only one species: Thermozodium esakii. This species Approximately 1 150 species of tardigrades have been described
or plant cells, and a pumping pharynx to suck out their internal was recorded in 1937 from a hot spring near Nagasaki, Japan. and can be found in almost every type of habitat around the
fluids, although some species are carnivorous and consume Unfortunately, this place was destroyed by an earthquake and world, from above 6 000 m in the Himalayas to the deep sea
rotifers and nematodes (see pages 45-47). The morphology subsequent searches for specimens have been unsuccessful. (below 4 000 m) and from the polar regions to the Equator.
of the claws, cuticle (outer covering) and the buccal apparatus Many of these environments experience dramatic environmental
(mouth) is used to identify the different species. [43, 44] changes throughout the year, and tardigrades survive thanks
a to their extraordinary ability to enter into ‘cryptobiosis’, a
Tardigrades in space! suspended animation (deathlike) state in which their metabolism
drops to 0.01 % of normal (or is entirely undetectable) and the
• Their resistance to cosmic radiation and vacuum has led tardigrades water content of the body decreases to less than 1 %. In this
to be part of several space expeditions: the TARDIS project in 2007, cryptobiotic state, known as a ‘tun’, they can live for a long time
as part of the Russian FOTON-M3 mission, which was sponsored by (up to 200 years!) and can survive extremes of temperature,
the European Space Agency (ESA), and the Tardkiss experiment in toxicity, dehydration, salinity and oxygen tension. Revival typically
2011, which included the BIOKIS Project, sponsored by the Italian takes a few hours but depends on how long the tardigrade has
Space Agency. been in the cryobiotic state. Although their ecological role has not
• The revelation that these tiny animals survived exposure to yet been fully evaluated, recent studies suggest they could have
the harsh space environment has given further support to the a regulatory function for plant-parasitic nematode populations
‘panspermia theory’. This old idea holds that ‘seeds of life’ could when predatory nematodes have disappeared, due to predation
have spread between planets and, for some, represents a possible
pressure and/or unfavourable environmental conditions.
origin of life on Earth. So could these eight-legged creatures have
travelled through space to eventually colonise other planets, such
as our Blue Planet? a
• They are the toughest animals on the planet, able to withstand a
dose of 5 000 grays of gamma radiation (a human withstands 4 - 10
grays), temperatures ranging from 151 °C to near absolute zero 100 µm
−273 °C, and can live for 200 years.
• Recent studies have shown that only 82.5 % of the tardigrade's DNA
is pure (see box on page 30), the remainder originating in plants,
b
bacteria and fungi. These fragments of foreign DNA are incorporated
during repairing processes of DNA damaged during exposure to
hostile environments.
b 100 µm
100 µm c

Microfauna – Rotifera
Rotifers are minute multicellular organisms (0.05 to 3 mm Rotifers (phylum Rotifera) are related to other worm-like Like many other minute organisms, rotifers have an absolute
long). Their mostly transparent body is subdivided into a head, organisms belonging to Gnathostomulida and Micrognathozoa. requirement for a water matrix during their active phase. They
trunk, and a foot. They have three easily visible unique features: Recent studies in DNA evolution (molecular phylogeny) have inhabit the capillary water retained between soil particles, litter
1) their anterior ciliary organ called the corona (or crown); 2) a revealed that the parasitic worms of the phylum Acanthocephala or mosses, where they feed on bacteria or small algal cells. They
specialised food processing apparatus made of strong muscles are their closest relatives, if not themselves a group of specialised are filter-feeders (i.e. feed by filtering food particles from water)
and a set of hard jaws (the mastax with trophi); 3) a unique rotifers. Scientists recognise three groups of Rotifera, but only or browse the bacterium film for particles. A few are predators of
and well developed cuticle (the lorica), giving the animals a one, the Bdelloidea, is an important soil inhabitant. ciliates or of other rotifers, or suck out the content of cells after
pseudo-segmented appearance, that can be exquisitely piercing the cell wall using specialised trophi. Although they need
ornamented. The head and foot can be retracted inside the trunk a water to live actively, the bdelloids, which are the most successful
if the animal is disturbed or if the environment dries out. [45, 46] soil rotifers, have an extraordinary ability to survive prolonged
periods of desiccation through a process called anhydrobiosis (a
type of cryptobiosis – see page 44). In this state (known as a
a b ‘tun’), they not only survive adverse conditions but can also be
easily transported to other habitats. Because of this and their
reproductive features (see box, below) they are very effective
at colonising and recolonising areas. Most rotifers, in particular
bdelloids, can only be identified while alive. This has hampered
their study significantly, to the extent that little is known of their
role in the functioning of soil systems.
Bdelloid rotifers, a female affair

• Rotifers are usually dioecious (have distinct male and female
organisms) and sexually dimorphic (have distinct male and female
forms), with the females always being larger than the males. They
reproduce sexually or parthenogenetically.
• Among rotifers, there is a particular group, the bdelloid rotifers, that
originated around 80 million years ago, and there are now about
460 morphologically distinct species.
c d • Bdelloid rotifers have evolved entirely without sexual reproduction
and are assumed to have reproduced without sex for many
millions of years. Males are absent and females reproduce only by
parthenogenesis.
• No male sex organs have ever been observed in these microscopic
animals. Asexual reproduction is generally thought to be an
evolutionary dead end as it leads to reduced diversity and the build-
up of deleterious mutations.
• The ability to acquire new functions (i.e. of evolving) has been
achieved by incorporating DNA fragments of other organisms, such
as bacteria, algae and fungi into their genome. This process is known
as horizontal gene transfer.
• These findings overturn current thinking that reproduction without sex
is less likely to endure evolutionary changes than sexual reproduction.
e
b There are about 2 030 described species. They can be extremely

abundant in moist soils and mosses but can occur in dry soils as
well. They live in virtually every terrestrial habitat, from the Poles
to the Equator, mostly near the soil surface.
f g

Microfauna – Nematoda
Morphology Taxonomy a
Nematodes are aquatic transparent roundworms (0.1 - 5 mm The phylum Nematoda contains multicellular animals that
in length in soil species) and are dependent on water films are related to other moulting animals (the Ecdysozoa) such
surrounding soil particles for their activity and gas exchange. as Nematophora. Terrestrial nematodes predominate in the
The ability of nematodes to have many food sources and to large orders of Panagrolaimida, Rhabditida, Mononchida and
live in numerous habitats (marine and freshwater sediments, as Dorylaimida.
parasites of plants, invertebrates and vertebrates) is due largely
to their morphological adaptations and survival strategies. Microhabitat
Nematodes survive the harshest conditions (desiccation, heat,
freezing, osmotic and oxygen stress), by shutting down their Global studies of the distribution of soil nematode species show
metabolism, altering their biochemical pathways and body that most are endemic to a site or region, and only a small fraction
shape and entering a dormancy state (cryptobiosis – see pages are cosmopolitan. Climate, vegetation, as well as soil physical
44 and 86), which is reversible when favourable environmental and chemical characteristics all contribute to determining the
conditions return. While in cryptobiosis, they can be dispersed habitat suitability of each community of nematode species.
by wind. Nematodes generally have an elongated body shape Nematodes are a key group for regulating biogeochemical
tapering at both ends, but they also can be spherical or pear cycling and ecosystem processes. These processes include
shaped. They have a non-segmented flexible cuticle and their mineralisation and decomposition in the soil system. Nematodes
body organs (excretory, nervous, digestive and reproductive are also indicators of environmental quality. For these studies,
systems) are in a fluid-filled cavity, called coelom, and present nematodes can be differentiated into feeding groups based on
in many other animals (e.g. earthworms – see page 58). Their their morphology and, in particular, the shape and size of their
movement is undulatory, contracting certain muscles against mouthparts. There are five main feeding types: bacterivores,
internal pressure. Most soil nematodes have separate sexes fungivores, omnivores, plant parasites and predators. Ecological
but some can be parthenogenic or hermaphroditic. Nematodes characteristics or life history traits of nematodes can also be
generally lay eggs that develop through four moulting juvenile indicators of environmental quality. For example, species that
stages to adults. [47, 48] reproduce quickly in response to a nutrient-rich addition to the
b
soil, are ‘colonisers’, while species with long life cycles and low
a reproduction rates are ‘persisters’. Soil nematodes carry bacteria
on their cuticle and can excrete viable bacteria, thus serving as a
vehicle for translocation of bacteria throughout the soil, and as a
potential food source.

Nematodes are among the most diverse and abundant animals
on Earth: one in five animals on Earth is estimated to be a
nematode. Terrestrial nematodes make up a substantial portion of
the more than 25 000 described species of the group. Nematodes
are found in soils, marine and freshwater sediments, and as
parasites of plants and animals, such as insects, humans and
birds. Many nematode infections cause serious human diseases
in the developing world (e.g. Guinea worm and elephantiasis).
b
Nematodes, everywhere!
• Soil nematodes feeding on bacteria occur more than 3.6 km below c
the surface of the Earth – deeper than any known animal, and at a
temperature of 48 °C.
• The smallest nematode, belonging to the genus Micronema, is
0.3 mm in size and lives between sediment particles.
• Nematodes were the first animal genome ever sequenced, and are
thought to be the most genetically diverse of all animals.
• Based on DNA sequences, two nematode species can be as different
as a tiger and a mouse.
• Nematodes can survive in space and are known to have survived the
U.S. Columbia Space Shuttle crash.
• A nematode released to control the invasive species of Sirex
woodwasp (Sirex noctilio) has saved the Australian forest industry an
estimated US$80 M (approx. €75 M) per year.
• In 2013, groundsmen at Scotland's national rubgy stadium sprayed
a solution of garlic on to the field in a bid to cure a nematode
infestation that was destroying the playing surface.
Plant-feeding nematodes
Nematodes puncture the cell walls of plant roots with large hollow
needle-like spears in their mouths and suck out plant nutrients.
Their spears are called stylets and vary in shape. Enzymes, (e.g.
cellulase and chitinase) are injected through the stylets of some
plant parasitic species to help break down cell walls. Other species, Omnivorous nematodes
such as Xiphenema spp., can carry plant viruses in their stylets
These are large free-living soil nematodes (up to 5 mm in length),
and vector the viruses from plant to plant. Plant-feeding nematode
and are omnivorous, using a variety of food sources. They have a
species can be migratory or sedentary, feeding either inside the host
hollow tooth that can pierce other organisms and suck out nutrients.
plant root (endoparasites) or outside the plant root (ectoparasites)
Depending on environmental conditions and food availability, they
and can cause serious economic damage to agricultural crops,
can feed on algal filaments, protists, other nematodes and then,
including citrus, rice, maize, soybean and numerous vegetable crops.
when their primary food sources are unavailable, switch to feeding
The plant parasitic nematodes Meloidogyne and Pratylenchus spp.
on fungal hyphae and bacteria. They often have low reproduction
infect wide ranges of host plants, while Globodera and Heterodera
rates and generally occur in stable habitats, rather than in newly
spp. have more restricted plant host ranges. Crop rotations help
established or disturbed habitats.
avoid damage by the latter two nematode species.

Predaceous nematodes
Predaceous nematodes have one or more large teeth or a pointed
spear that are used to attack and ingest nematodes and other
small animals, such as enchytraeids, tardigrades, rotifers and
protists (see pages 36-37, 44-45, 48). Predatory nematodes
make up approximately 5 % of the overall soil nematode
community, and decline in abundance when soils are disturbed.
Mononchoides spp. can also feed on bacterial cells and can be
cultured in the laboratory as biocontrol agents against plant
parasitic and other nematodes.
Bacterial-feeding nematodes Fungal-feeding nematodes

Bactivorous nematodes have tubular mouths and graze on bacteria Fungal-feeding nematodes have small, fine stylets optimally
by swallowing them or scraping them from soil substrates using adapted for feeding on fungal hyphae (see box, page 39).
structures on top of their head. Grazing of bacteria increases Fungivorous nematodes can affect plant growth indirectly via
the rate of decomposition of the chemical compounds in organic the destruction of arbuscular mycorrhizal fungi (see page 40) or
matter (carbon and nitrogen mineralisation) in soil. There is also other beneficial fungi, leading to reduced nutrient availability for
evidence that grazing on bacteria can positively affect the plant the plant. Other species are beneficial for pest control through
root growth. These animals have germination times ranging from the destruction of plant fungal pathogens (see box, page 39).
a few days to a week, which is advantageous for colonising new Fungal-feeding nematodes are generally less abundant in
habitats. highly disturbed soils (e.g. agriculture) than bacterial-feeding
nematodes.

Mesofauna – Enchytraeidae
Morphology Microhabitat Nothing amazing, apparently...
Enchytraeidae are also known as ‘potworms’ and owe their Enchytraeids are concentrated in the uppermost soil layers
• The most amazing fact about enchytraeids is that there is nothing
name to first being discovered in flower pots (from the Greek (0 - 5 cm), where organic matter accumulates. Most studies
amazing about them. However, it seems that cold, wet and organic
enchytraeon meaning ‘in the pot’). Each body segment bears regard them as microbial-feeders, frequently grazing on bacteria rich ecosystems cannot function without them.
four bundles of bristles (setae), two located on the ventral side and fungal mycelia (see box, page 39), although they are also
• The largest species (Mesenchytraeus antaeus) can be up to 6 cm
and two occupying lateral or dorsolateral positions. Numbers of saprovores, consuming dead organic matter.
long with more than 100 segments; the smallest species (Marionina
setae per bundle vary between 1 and 16. However, two, three or eleonorae) is only 1 mm long and has no more than 15 segments.
four are most common, although in some species they are totally Diversity, abundance and biomass • Enchytraeids have a variety of ways to reproduce: by ordinary cross-
absent. Setae are resistent structures, made of chitin, that allow
breeding, with both partners exchanging sperm and laying eggs; by
the animal to anchor itself to substrate. Like earthworms (see About 700 valid species of enchytraeids have been described. self-fertilisation; by parthenogenesis (i.e. without fertilisation); and
page 58) and leeches, they are hermaphrodites, as they have Although they are distributed globally, they are more abundant also completely asexually by breaking up of a worm into several
reproductive organs normally associated with both male and in non-wooded habitats. In particular, cold and wet organic-rich pieces and regeneration of full-grown worms out of each piece.
female sexes. They develop a ‘clitellum’, a glandular modification environments, such as moorlands, contain high numbers (ranging
of the epidermis (the sheet of cells that covers the body of all from 12 000 to 311 000 individuals per m2), and here enchytraeids
animals) which secretes a cocoon where the eggs are deposited; are the dominant soil fauna (in terms of live biomass). Seasonal
however, some species can reproduce through parthenogenesis climatic fluctuations have a strong influence on their population 100 µm
or asexually by fragmentation (see the box on the right). [49, 50] dynamics, and extreme weather conditions, such as summer
droughts and severely cold winters, can lead to high mortality
rates. Although some species can migrate to deeper soil layers to
avoid these adverse environmental conditions, this seems to be a
short-term survival strategy due to a lack of food in these more
humified horizons. Feeding and burrowing activities influence soil
structure and turnover of soil organic matter, thus making them
‘ecosystem engineers’, like termites, ants and earthworms (see
pages 54-55, 58).
Pharyngeal glands
Brain
200 µm
Taxonomy
The Enchytraeidae are a family of Annelida (class Oligochaeta),
resembling small white earthworms (1 - 30 mm in length) that
include both terrestrial and aquatic species. Enchytraeids are
identified when alive, since the taxonomy uses external and 100 µm
internal structures, which can be clearly seen only through the
living transparent body. A single sample generally contains about
1 - 15 (rarely more) species. New species are often found; most
subtropical and tropical species are still undescribed.
20 µm
100 µm

Mesofauna – Acari
Morphology An exceptional persistence in nature a
Soil mites are relatively small (from 60 µm to 2 - 5 mm), have
• Mites can withstand doses of radioactivity 100 times higher than
rounded or elongated bodies and, like other Arthropoda, are covered
those that would kill a human being.
in a rigid structure, called exoskeleton or cuticle. Adult mites and
• In heavily disturbed ecosystems, such as cities or industrial areas,
nymphs have usually four pairs of legs, while larval stages have
soil mites can be the last indicator of primary habitats (i.e. habitats
three pairs. They lack jaws and use the chelicerae and pedipalps
present before the development of cities/factories).
(cephalic appendages) to grab their food. Chelicerae are diverse
• This means that it is still possible to reconstruct the vegetation type
in form, which reflects mites' varied feeding habits. Most are
and landscape conditions based on the mite communities remaining
ground-dwelling (i.e. subterranean) and some have one or two
in the degraded areas.
pairs of simple eyes (ocelli) in their outer covering. Being blind,
• Oribatid mites (belonging to the superorder Acariformes) have hard
they generally rely on physical and chemical sensing during
exoskeletons that often fossilise.
navigation through the small soil pores. [51, 52]
• That is why fossil mite assemblages, together with pollen analyses,
are used by scientists as an additional tool for palaeogeographic (the
Taxonomy study of past geography) reconstructions.
Mites (Acari) are an ancient lineage that have been known since
the Devonian period, at least. Traditionally, they belong to the
class Arachnida, together with spiders. There are roughly 40 000
described soil-living species and more than half of them live
on or in the ground. Representatives of both mite superorders
(Acariformes and Parasitiformes) are found in soils. Moreover,
they comprise up to 40 % of all soil microarthropod species. b
Microhabitat
Soil mites occupy practically all natural soil substrates and
have a world-wide distribution. They spread across all soil
horizons starting from the surface of the litter down to 2 - 3 m in
mineral soil. Their normal abundance in undisturbed ecosystems 100 µm
varies from a few hundred individuals in the arctic and tropical
deserts up to one million per square metre in temperate mixed
forests. Mites are among the first animals to colonise emerging
mineral and organic substrates. They disperse in various ways,
allowing them to cover large distances. These methods include:
transport on mammals, birds and insects (phoresy), as well as
passive distribution by wind or flowing water. Most mite species 250 µm
are characterised by clearly defined feeding habits, and their
contribution to the cycles of carbon and nitrogen (see pages
104-105) in soil is fairly well quantified. Acariform mites have c
a variety of feeding preferences, from microbes (microbivory)
and the remains of plants and animals (detritophagy) through
omnivory to predation. Parasitiform mites are predominantly
predaceous as they survive by preying on other organisms.
Distribution, abundance and biomass

In undisturbed systems, hundreds of mite species can be found in
one square metre of soil. However, little is still known about general
distribution patterns of mite species globally. Despite numerous
reviews at both regional and global geographic coverage levels,
the drivers of most general trends in mite species richness are
not completely understood. However, they seem to be related
to climate, availability and quality of organic matter, intensity
of disturbance and the geological history of individual regions.
Latitudinal climatic gradients are expected to be the major factor
explaining regional oribatid family and species richness across
large areas.
a b

Mesofauna – Collembola
Morphology Microhabitat Diversity, abundance and biomass
Collembola are small (0.12 - 17 mm) wingless hexapods (with six Collembola vary in their habitat preferences. Entomobryomorpha There are around 8 500 described species, which are found in a
legs – see page 31) commonly known as ‘springtails’. The scientific and Symphypleona are mainly epiedaphic, living in surface litter great variety of habitats, from Antarctica and the Subantarctic
name, Collembola, derives from the Greek words kolla (meaning and emergent vegetation, and are fast movers and good jumpers, Islands to rainforests, warm beaches and deserts. As well as being
‘glue’) and embolon (meaning ‘piston’) and was initially proposed in whereas the slow-moving Poduromorpha and Neelipleona are widespread, they are the most abundant hexapods in the world,
reference to the ventral tube (collophore), which plays an important mainly within-soil dwellers (euedaphic). Most Collembola feed and an average square metre of soil in a temperate grassland or
role in their fluid and electrolyte balance and may also serve as on fungal hyphae and spores (see box, page 39), bacteria (see a woodland can yield as many as 40 000 individuals.
a ‘glue piston’ for adhering to smooth surfaces or for grooming. pages 33-35) and decaying plant material. However, ssome
Another characteristic, albeit not always present, gives them their species are predators, feeding on nematodes (see pages 46- Generally, habitats may support anything from two to 30
common name: the forked springing organ or ‘furca’. This is held 47) or on other Collembola and their eggs. Ecologically, they are different collembolan species. However, in the tropics, up to 150
by a special catch mechanism on the ventral side of their abdomen not as important as earthworms in decomposition processes, species can be found, if species present in epiphytes (plants living
which, when released, acts as a spring that can propel them, within but are still responsible for up to 30 % of total soil invertebrate in trees) are taken into account.
seconds, several times the length of their body. [53, 54] respiration, depending on the habitat.
a b
1 mm
c d
200 µm
a b
Taxonomy 100 µm
Collembola belong to the phylum Arthropoda. They are part of

the class Entognatha that, together with the class Insecta, form c d
the subphylum Hexapoda (see page 31). They are classified into
four orders: the Entomobryomorpha and Poduromorpha, with
a more or less elongated body shape, and Symphypleona and
Neelipleona, which are spherical in shape.
The frozen and colourful collembola

• Collembola can withstand freezing conditions by using anti-freeze
compounds in their body tissues.
• Cryptopygus antarcticus, native to Antarctica and Australia, is the
only Collembola species to have appeared on a postage stamp.
• Collembola can have multi-coloured stripes: Paralobella orousetii
from the Philippines has a yellow head and first two thoracic
segments, the third thorax segment and the first three abdominal 50 µm
segments are red and the remaining abdominal segments are white.

Mesofauna – Protura
Proturans are small soil-inhabiting primitive hexapods (ranging The class Protura (phylum Arthropoda, subphylum Hexapoda) Protura are found in moist soils, leaf litter, humus, moss and
in size from 0.5 and 2.5 mm – see page 31) with no antennae includes three orders: Acerentomata (families Hesperentomidae, decaying wood in woodland, grassland and agricultural soils.
and no eyes. The forelegs are used as sensory organs; they have Protentomidae and Acerentomidae), Sinentomata (families They do not thrive in very acid soils (e.g. coniferous woodlands).
many sensory organs (‘sensilla’) covering their posterior segments Fujientomide and Sinentomidae) and Eosentomata (families Usually, they are part of the decomposer community and
(tarsi). On the dorsal side of the head there are a pair of other Eosentomidae and Antelientomidae). help break down organic matter in soil and litter. In particular,
important sensory organs (pseudoculi) whose functions are not proturans feed mainly on fungal hyphae (see box, page 39), but
well understood. Their bodies are cylindrical, pointed at both The ‘young’ proturans they are also important prey for small predators, such as spiders,
ends and generally unpigmented, pale or yellowish. Similar to the mites (see page 49) and pseudoscorpions (see page 53).
Collembola, they are wingless arthropods and their mouthparts • Among hexapods (see page 31), Protura was the last class to be
are entognathous, meaning that they are retracted within the described. The first description of these minute soil arthropods was Diversity, abundance and biomass
head capsule: the mandibles and maxillae are slender and their given in 1907.
maxillary palps (mouthparts) are long, with setae and sensilla. • Filippo Silvestri and Antonio Berlese, two Italian entomologists, Proturans are found all over the world, with the exception of the
They are born with nine abdominal segments and grow by discovered proturans independently. polar regions. There are more than 700 described species. Their
successive moultings during which they add new distal segments. • The first species to be described was Acerentomon doderoi, found in density is variable in relation to the characteristics of the soil and
The adult has 12 abdominal segments. They have small pairs soil near Syracuse, New York, USA. the content of organic matter. In disturbed and degraded soils
of lateral-ventral appendages on the first three abdominal • When disturbed, proturans seem to raise the end of the abdomen in they can be completely absent, while in undisturbed habitats,
segments. They lack cerci, the paired appendages on the a defensive posture similar to that adopted by scorpions. such as natural grasslands, there can be as many as 85 000
rear-most segment of the body present in many other hexapods. individuals per square metre.
Reproduction occurs with indirect fertilisation: the males deposit
packets of sperm (spermatophores) and the females collect the a
spermatophores. [55, 56]
a
20 µm

Mesofauna – Diplura
Morphology Diplurans are not earwigs
Diplura are small wingless hexapods (see page 31), with body
• Some diplurans in the Japygidae family may be occasionally confused with earwigs. This
lengths ranging from 0.3 to 1 cm, although the largest species
confusion is due to the presence in both groups of pincer-like abdominal appendages, a
can be longer than 2 cm. Diplurans have a narrow and elongated scientifically known as cerci.
body, and are generally white or colourless. The head has a pair
• Diplurans are not insects. Earwigs are insects of the order Dermaptera and live in
of long and moniliform (a string formed of bead-like segments)
similar habitats: moist places beneath stones, boards, sidewalks, debris or in the soil.
antennae and no eyes. The abdomen ends with a pair of cerci, i.e.
• The forcep-like appendages, i.e. cerci, of some diplurans are designed to break off
prominent abdominal appendages, which can contain silk glands.
near the base if they are mishandled. This behaviour is probably an anti-predatory
The cerci can have either a pair of pincers (Japygoidea) or can
adaptation. It is known as autotomy and is typical also of reptiles, such as lizards, and
be filamentous (Campodeoidea). Some species of japygid Diplura amphibians, such as salamanders. Diplurans are among the few terrestrial arthropods
are robust and darker in colour, and are often confused with known to be able to regenerate lost body parts (legs, antennae and cerci) over the
earwigs (Dermaptera – see box to the right). However, Diplura course of several moults.
have neither eyes nor wings. Fertilisation is similar to that found
in proturans and collembolans (see pages 50-51): the males b
produce and deposit a large number of spermatophores, capsules
containing spermatozoa, on the substrate that are then picked up
by a female. The females lay eggs in clumps in the soil cavities
or decomposing vegetation. Some species check the eggs and
the larvae. Diplura are known to be able to regenerate lost body
parts, such as legs, antennae and cerci. [57, 58]
Taxonomy
The class Diplura (phylum Arthropoda, superclass Hexapoda)
comprises nine extant families, the main ones being Japygidae
and Campodeidae (each with more than 400 species).
Microhabitat
Diplura live in wood, leaf litter, under stones, rocks or logs, on
the surface of, or in deeper layers of soil, in mosses or in termite
and ant nests. Many species are herbivores and detritivores
(feed on decomposing plant and animal parts) and feed on a
wide range of plant material. However, some species have well-
developed mandibles and eat nematodes (see pages 46-47),
b
small arthropods, enchytraeids (see page 48), etc. They can also
consume fungal mycelia (see box on page 39) and plant detritus.
They are often part of the decomposer community, helping
recycle dead plant material.
There are approximately 1 000 described species that are

common inhabitants of most natural and human modified soils.
They are distributed worldwide, from the tropics to temperate
zones. They do not have specific habitat preferences and,
generally, their population densities are not high (< 50 individuals
per square metre).
Maternal care of diplura

• Male diplurans produce large numbers of spermatophores (up to
200 per week), probably because sperm only remain viable in the
spermatophore for about two days.
• The eggs of campodeid and japygid diplurans are normally laid in
a mass of up to 40, in clumps or on small stalks in little cracks or
cavities in the ground.
• Female campodeid diplurans abandon their eggs, but japygid species
are known to remain in the brood chamber with the egg cluster,
protecting the eggs and the newborn larvae.

Mesofauna – Pseudoscorpionida
Morphology
Pseudoscorpions are tiny arachnids known as ‘false scorpions’
because they look similar to scorpions but do not have an
elongated postabdomen with a venomous sting at the end. Usually
less that 5 mm in length, they are brownish arachnids with large
pincer-like chela (pedipalps). The body is divided in two regions:
the cephalothorax (or prosoma, a fused head and thorax) and the
abdomen (or opisthosoma) clearly divided into 11 - 12 segments.
The cephalothorax is covered dorsally by a shield (carapace) and
bears the appendages. One to two pairs of simple eyes (ocelli)
are sometimes present on the head, but many species are
blind. The first pair of cephalic appendages, the chelicerae, are
two-segmented, chelate (clawed) and used for feeding. Chelicerae
have silk glands. Behind the chelicerae are the pedipalps, which
are used to capture prey and for defence. Pseudoscorpions, like
all arachnids, have four pairs of thoracic legs. The abdomen
has no appendages. These animals have a long lifecycle (the
course of developmental changes through which an organism
passes from its birth to the mature state in which it may give
birth to another organism), depending on the environment and
the temperature. The males produce a spermatophore, and pull
the female over it. The female carries a silken egg bag of about
12 - 40 eggs in a brood sac that is attached to the ventral surface
of the opisthosma. She can produce several broods each year. The
young pseudoscorpions moult, passing from several larval instars
(protonymph, deutonymph and tritonymph) before becoming
adults that can live three to four years. [59]
Taxonomy Microhabitat
The Pseudoscorpionida or Pseudoscorpiones is a large group Pseudoscorpions live under bark and stones, in leaf litter, in caves,
comprising 27 different families. They are found everywhere, but under rocks on the ground and in soil. They are also often found
their highest diversity is found in the tropics. in moss and lichens, in ant and bee nests and in the burrows of
ground-dwelling mammals. The cosmopolitan species Chelifer
cancroides is often found in houses.
A beetle for a house
• The dispersion of the tropical American pseudoscorpion
Cordylochernes scorpioides from one tree to another is mediated
Approximately 3 400 species of Pseudoscorpions have been
by the Harlequin beetle Acrocinus longimanus. The males show
described. Their density, in general, is not high (< 300 individuals
territorial behaviour on the back of the beetles and even mate with
females there. per square metre). In some cases they are considered beneficial
to humans as they prey on various pest species; for example,
• Nesticus birsteini (today Carpathonesticus birsteini) distributed in
carpet beetle larvae, ants, mites and booklice. Occasionally
Russia and Georgia, is the only pseudoscorpion to have appeared
on a postage stamp. Pseudoscorpiones may disperse attached to flying insects, birds
and mammals (phoresy).
a b
c d

Macrofauna – Formicidae
Morphology a b
Ants are social insects, among the most abundant in the world.
Many ants have a sting but some groups have lost theirs and
instead spray formic acid. They are distinguished from other
closely related groups by the petiole (a constriction between the
abdomen and thorax with either one- or two-nodes or scales) and
their elbowed antennae. Ants live in large complex colonies with
a division of labour, involving reproductive and non-reproductive
individuals, cooperative care of the young and overlapping
generations. This defines them as eusocial insects. This division
of labour leads to different castes (groups of individuals with
the same function). The reproductive caste is the queen,
while the sterile caste are workers (and in a few species also
soldiers). Reproductively active males are produced only during
c d
the breeding season and die soon after mating. The workers
perform all the other functions of the colony, including protection,
foraging, cleaning, building nests and care of the larvae. [60, 61]
Taxonomy
Ants have been around for over 120 million years. They belong
to the family Formicidae of the order Hymenoptera (the group
containing also bees and wasps).
a
e f
g h
Microhabitat Many ants are predators or herbivores, but others are omnivorous
(with a diet consisting of a variety of food sources) or specialist
Ant colonies form nests in which the colony lives. In most cases the predators (e.g. on termites). Leaf-cutting ants use leaves as a
colony centre is fixed, but some army ants have no fixed colony substrate for their symbiotic fungus (fungus-growers), which
centre. Ants can have nests that are arboreal (in tree canopies), they use as food source. Ants interact closely with many
epigeic (on the soil surface) or hypogeic (underground). Ants that other organisms and are fundamental for some functions of
nest underground dig tunnels that are interconnected by larger ecosystems; for example, protection of certain plant species (‘ant
chambers, some of which give access to the outside world. The plants’) from herbivory and facilitation of seed germination in
chambers can have specific functions, such as nurseries, larders appropriate locations by carrying them to their nests. Ants also
and rubbish dumps. Among the ants that nest in the ground some play an important role in the maintenance and functioning of
of the most impressive are the leaf-cutter ants, especially in the soils, as they dig tunnels and chambers, thus promoting nutrient
genus Atta, that build very large nests up to 300 m2 in surface cycling through soil bioturbation (the reworking of soil) and water
c area, and excavate a great deal of soil. Atta laevigata nests may infiltration. They produce soil organic debris, thus enabling the
be up to 7 m deep and contain over 7 800 chambers. processes of decomposition performed by fungi (see pages
38-41) and bacteria (see pages 33-35) and increasing the
heterogeneity of the soil resource.
‘Ant cow’ aphids
• Certain aphid (small sap-sucking insects) species have a symbiotic
relationship (see box on page 33) with various species of ants, which The family Formicidae is subdivided into 22 extant subfamilies,
resembles that of domestic cattle to humans; hence the name ‘ant cow’. 300 genera and 14 000 described species. The diversity of
• The ants tend to the aphids, transporting them to their food plants at species varies among world regions, with peaks in South America,
the appropriate stages of the aphids' life cycle and sheltering their Central and South Africa and Australia. They are dominant
eggs in their nests during the winter. invertebrates in many ecosystems, particularly tropical ones, and
• The aphids, in turn, provide sugary secretions (honeydew) for the occur on all continents except Antarctica. The biomass of ants in
ants to feed on. tropical rainforests is often thought to be greater than that of all
vertebrates in the rainforest combined.

Macrofauna – Termites
Morphology Diversity, abundance and biomass a
Termites are medium to small sized fully social insects (2 mm There are about 2 700 described species. They are found in
to 20 mm long). They are soft bodied and of colours ranging very large numbers throughout the warmer parts of the world,
from very pale white to deep brown or black. They live inside particularly in tropical rain forests, tropical savannahs and hot arid
colonies with two reproductive individuals (i.e. the king and the areas; they are not found, however, in many temperate regions
queen) and a very large number of sterile castes (i.e. workers and and never in polar ones. They have their highest densities and
soldiers). The soldiers and workers look very different from the diversities in tropical rain forests in Africa where they can reach
reproductive castes. The workers do most of the various tasks up to 10 000 individuals per square metre (m2) and biomasses of
required by the colony (e.g. rearing young, foraging for food, nest up to 100 grammes per m2.
building), while the soldiers defend the colony and have no other
roles. [62] Extraordinary architects b
Taxonomy • Termites move around in tunnels in the soil or live entirely in tunnels
in dead wood.
Termites are hexapods (see page 31) that form the order • They are nature's most accomplished non-human architects and
Isoptera, including 12 families. Termites are a special kind of build nests and mounds of extraordinary complexity, such as those
social cockroach and, despite some similarities in shape and size, in savannahs in Africa, South America and Australia.
they are not closely related to ants. However, similar to ants, they • Some termite mounds may have been continuously occupied for
are fully eusocial insects. 50 000 years.
Microhabitat
They feed on dead plant material at different stages of decay; for
c
example, dead wood, dry grass, leaf litter and soil. Some form a
mutualistic relationship with a fungus called Termitomyces that
breaks down dead plant material for the termites, who then eat
parts of the fungus. Because of these food preferences, a few
are serious timber and crop pests. However, most termites have
a generally positive effect on ecosystems, living and feeding in
the soil where they transform its structure, decompose plant
residues, and help stabilise soils. They perform many of the
same functions as earthworms, but the two groups are generally
not found in large numbers together. They are often known as
ecosystem engineers (see box on page 95) as they profoundly
affect the structure of habitats for other organisms, both inside
and outside their nests.
a b
c d

Macrofauna – Isopoda
Morphology Diversity, abundance and biomass a
Most species of isopods belong to the soil macrofauna, and adult The Mediterranean region is a hotspot of isopod diversity, and
sizes range from 5 to 15 mm, with some species reaching only 1 Europe is the most studied region. Relatively little is known
to 2 mm. Terrestrial isopods, commonly known as woodlice or pill about terrestrial isopods in many tropical countries. Regional
bugs, have bodies divided into a cephalon (head), pereion (thorax) species richness increases from the cold-temperate to the
and pleon (abdomen). The cephalon bears the compound eyes, warm-temperate and the tropical zones. Local abundances are
two pairs of antennae (one pair is vestigial, meaning functionless) quite variable and are particularly high in temperate forests and
and four pairs of mouthparts for food processing. The pereion has grasslands, reaching about 100 to 600 individuals per square
seven pairs of walking legs (pereiopods). The abdomen comprises metre.
five pairs of modified appendages (pleopods). The pleopods have
become modified and adapted for respiration through the course Isopod manipulators
of isopod evolution. In males, the first two pleopods are modified
to participate in sperm transfer. The sperm is transferred to • Bacterial symbionts, such as Wolbachia, can induce sex changes and
the female through the modified second pleopod which, after force males to develop into functional females.
receiving the sperm from the penis, is then inserted into a female • Parasitic acanthocephalan worms can manipulate the pigmentation
gonopore (genital pore). After successful copulation, the female and behaviour of the infected individuals.
moults and produces a structure on the ventral side of her
thorax that resembles a pouch and is called marsupium. Inside b
the marsupium the eggs stay protected while they develop into
young independent isopods. [63]
Taxonomy
Isopoda is an order of crustaceans (see page 31). The
semi-terrestrial and ‘truly’ terrestrial isopods form a monophyletic
(developed from a single common ancestral form) group (the
suborder Oniscidea), with 3 637 described species.
Microhabitat
Numerous morphological, anatomical and physiological
adaptations to the soil environment make isopods the most
successful land inhabitants. Terrestrial isopods occupy essentially
all terrestrial habitats, ranging from the supralittoral (shore of a
lake, sea, or ocean) to the high alpine regions, from the tropics c
to the cold-temperate zones, from wetlands to deserts. They
are crepuscular or nocturnal animals and spend the day mostly
hidden underneath stones, coarse woody or loose bark, or in
crevices, where they can easily be captured. In deserts, species
of the genus Hemilepistus form monogamous (having a single
partner during their lives) relationships and live inside self-
dug burrows essential for their survival. As macro-detritivores,
terrestrial isopods significantly contribute to decomposition
processes through feeding on and digesting leaf litter, dispersing
microbial spores and mediating microbial activity and nutrient
cycles (see pages 102-106). Digestion is supported by microbes
that are ingested together with food. In their gut, isopods can
also develop symbiotic relationships with bacteria, but at least
some part of the cellulose digestion seems to be facilitated by
endogenous enzymes (cellulases). Gut bacterial symbionts live d
protected inside the digestive glands, which enables them to
survive on nutrient-poor diets that are difficult to digest.

Macrofauna – Myriapoda
Morphology a b
Myriapods (centipedes, millipedes, pauropods and symphylans)
are small- to large-sized arthropods (0.5 - 385 mm) with
elongated segmented bodies and many legs (from eight pairs
up to 750 pairs). Myriapods' bodies have a head and a more or
less uniformly segmented trunk. Millipedes have fused pairs of
segments (diplosegments) and, consequently, they have two pairs
of legs per segment. Centipedes have forcipules, the first pair of
modified walking legs on their trunk segment that contain venom
glands to catch and immobilise prey. Pauropoda are very small
and have branched antennae with segmented stalks. By contrast,
Symphyla have a pair of conical cerci with spinning glands on the
posterior part of their body. [64, 65]
Taxonomy
Myriapods (phylum Arthropoda, subphylum Myriapoda) are c d
categorised into four classes: Diplopoda (millipedes, 16 orders,
approximately 12 000 species), Chilopoda (centipedes, five orders,
approximately 3 000 species), Pauropoda (two orders, approximately
800 species) and Symphyla (one order, approximately 200
species). The most diverse orders are: Polydesmida (flat-backed
millipedes, 3 500 species) and Geophilomorpha (soil centipedes,
1 300 species).
Microhabitat
Generally, myriapods are soil dwellers. Larger species burrow,
while smaller and thinner species use crevices and spaces in the
soil. They can be found in both deep and shallow soil layers. They
all thrive at high humidity, stable temperatures and low ultraviolet
radiation levels; therefore, they are typically found under stones,
logs and barks, and in litter, in tree hollows, stumps and caves.
Some species of millipedes and centipedes can climb trees.

Myriapods are found in almost all terrestrial habitats from deep
soil layers and caves to above the timberline in mountains.
a
Antarctica is the only continent with no myriapods. Myriapods are
not exceptionally abundant in any habitats, with the exception of
some millipede species. In temperate regions, the abundance of
millipedes can reach up to tens to several hundred individuals per
square metre (m2). In some temperate forest soils, millipedes can
reach densities of over 1 000 m2 . Symphylans and pauropods are
distributed more unevenly, and in lower abundance since they are
very responsive to changes in soil properties (chemical as well as
physical) and food availability. Different myriapod groups have
different feeding preferences. Centipedes are generally predators
and often regulate populations of smaller animals, although some
feed on decaying plant matter. Symphylans are root-feeders, or
saprophagous. Pauropods are fungal-feeders, although some
species prey on small animals or suck liquids from rotting plant
material. Millipedes are important decomposers of leaf litter.
They are estimated to break down 10 - 15 % of the annual leaf
fall, and their significance for litter processing is higher than that
of earthworms in boreal forests.
Poisonous, luminous and singers

b
• Although centipedes are venomous and sting frequently, the
United States National Center for Health Statistics reports only five
‘possible’ deaths attributable centipede stings in the US between
1991 and 2001.
• Almost all millipedes have defensive poisonous liquid secretion or
produce prussic acid (hydrogen cyanide) gas.
• Some species of millipedes are bioluminescent, allowing them to
be avoided by nocturnal predators. This luminescence may be the
equivalent of colours used in other animal species to warn off
potential predators (aposematic colours).
• A defense mechanism of some millipedes is to roll into a ball. Consequently,
a male may find it hard to persuade a female to copulate.
• Although millipedes are deaf, males of the order Sphaerotheriida
‘sing’ to potential mates using vibrations in order to uncoil them.
• Some centipedes inhabit tidal zones, probably in search of food.
In Brazil, there is a documented record of a sea anemone species
feeding on a centipede belonging to the family Scolopendridae.
• The largest millipedes in the world are the African giant black
millipedes (Archispirostreptus gigas) which may reach 30 cm. They
have approximately 256 legs and a life expectancy of five to seven
years.

Macrofauna – Earthworms
Morphology a b
Earthworms are segmented animals with coelom (coelomates).
The body is divided into two parts: an anterior part with segments
containing cephalic ganglions, reproductive organs, foregut,
calciferous glands and hearts, and a posterior part with a series
of similar segments which contains the intestine. Earthworms
range from a few cm to 2 - 3 m long, with most species falling
into the range of 5 to 15 cm. Size varies considerably within
single species populations, and the largest adults may be more
than 100 times those of newly hatched individuals. [66, 67]
Taxonomy
Earthworms belong to the phylum Annelida (class Clitellata,
subclass Oligochaeta). The Oligochaeta contain 10 400 - 11 200
species in approximately 800 genera, and 38 families comprised c d
of approximately 7 000 true earthworms.
Microhabitat
Earthworms have been classified into three main functional
groups, each with a preferred habitat:
a. epigeics, which live in the litter layer, a relatively harsh and
exposed environment. They are small and uniformly coloured
worms, pigmented green, blue or reddish depending on
whether they inhabit grassland or forest. They counterbalance
a high mortality rate with high quality food (leaf litter), which
allows them to grow and reproduce rapidly
b. anecics feed on surface litter that they mix with soil. They
live in vertical subterranean tunnels created within the soil.
They are large worms with a dark pigmentation and strong
anterior digging muscles. They are long lived, with low growth e f
and mortality rates
c. endogeics are unpigmented soil-feeding worms that live
entirely within the soil, which is a more buffered and predictable
environment than the leaf litter, but where the quality of
the food is much lower. They have also developed different
ways of exploiting it. They include small filiform earthworms
that selectively ingest fine organic rich soil (polyhumics),
medium-sized ones that ingest soil with no selection
(mesohumics) and the very large ones that live down to a
30 - 60 cm depth where the extremely low quality of their
food is compensated for by steady environmental conditions
(oligohumics)

Although 7 000 ‘true’ earthworms (in 20 families) have been g h
described to date, the total is probably around 30 000 species
globally. They live everywhere except in dry and cold deserts. They
are, however, mostly found in soil and leaf litter, although they
occasionally climb trees and can live in suspended soils of epiphytic
plants (that grow on other plants). Local species richness is often
as low as 10 or fewer, although it may reach 15 species in well
conserved soils of temperate regions and a maximum of 40 - 50 in
some tropical regions. Density is often in the range of 100 to 500
individuals per square metre and may reach 2 000 in temperate
pastures of New Zealand or irrigated orchards in Australia. Live
biomass commonly ranges between 30 and 100 grammes (g) per
square metre, with maximum values of 200 g to 400 g.
Rescuers, hermaphrodites and carnivores

i j
• Earthworms are able to produce plant growth hormones and
to modify the expression of plant genes. They may, for example,
render a plant tolerant to plant parasitic nematodes (see pages
45-46) by inhibiting the gene responsible for the repair of damaged
roots, preventing plant death after all leaves have wilted.
• While several cosmopolitan species are parthenogenetic (virgin
births), the majority are hermaphrodites as they can produce progeny
after the mating of two sexually mature specimens. Sperm stored
in specific structures (spermathecae) fertilise eggs produced by the
same individual when the female reproductive system matures.
• Earthworms may ingest up to 20 - 30 times their own weight of soil
every day, and more than 1 000 tonnes of dry soil a year.
• In West Africa, the genus Agastrodrilus has been shown to be
carnivorous, feeding on smaller worms.
• The title for the largest earthworm in the world, with a length of
2.9 m, is claimed by Amynthas mekongianus, about the same as
large Megascolides australis, the ‘Giant Gippsland Earthworm’.

Macrofauna – Coleoptera
Morphology Diversity, abundance and biomass The caring gravediggers
The defining feature of beetles (Coleoptera) is the hardened There are more than 370 000 described species of
• Burying beetles bury carcasses of small vertebrates, such as birds
forewings (elytra) that cover their body. The largest known Coleoptera – it is the largest and most diverse order of organisms and rodents, as a food source for their larvae.
beetles are more than 160 mm long (e.g. Dynastes hercules), but on the planet, making up about 40 % of all described insect
• They are unusual among insects in that both the male and female
most beetles are less than 5 mm long. Their colours are variable, species, and about 30 % of all described animal species. The
parents take care of the brood.
although most soil-dwelling beetle species are brown or black. abundance and biomass of beetles on ephemeral and nutrient-
• Although parental responsibilities are usually carried out by a couple
Their body shape is also variable: some have long horns or sharp rich resources, such as carrion and dung, are very high. Beetles
of beetles, a male or a female may also care for the brood alone,
tusks, some can curl up like myriapods (see page 57), some are significantly contribute to decomposition processes. Besides being
when the other partner is lost or the carcass is small.
flat and some are slim. A number of soil beetles, such as the abundant and varied, soil beetles are able to exploit the wide
• Sometimes more than two unrelated individuals can raise a brood
genus Carabus, are wingless. [68, 69] diversity of food sources that are available in their habitat. Many
together, when the carcass is large or many potential competitors
species are predators of small soil animals such as earthworms,
are present.
Taxonomy collembolans and nematodes (see pages 46-47, 50, 58). Others
feed on fungi or dead wood.
Beetles are hexapods belonging to the order Coleoptera. This
includes four suborders: Archostemata, Adephaga, Myxophaga
and Polyphaga. Of these, Adephaga and Polyphaga have more
species than other suborders, including most soil species.
Microhabitat
In terrestrial environments, many beetles can be found in soil,
humus and leaf litter, under logs or in decomposing wood,
under stones, in dung, carrion and in the fruiting bodies of many
types of fungi (see pages 38-41). Numerous beetles (families
Carabidae, Leiodidae, Staphylinidae and Scarabaeidae) are well
adapted to the soil environment. Some carrion beetles (family
Silphidae) and some dung beetles (family Scarabaeidae) build
nests in the soil, in which they take care of their brood. Some
species, such as some members of the family Staphylinidae, live
solely in caves while others are myrmecophiles (ant lovers) or
termitophiles (termite lovers) as they strikingly resemble ants or
termites (see pages 54-55) and live in their hives.
a b c
d e f
g h i

Macrofauna – Soil insect larvae
The vast majority of insects, up to 95 % in fact, are linked to the Diptera larvae Coleoptera larvae
soil during their life cycle. Some lay eggs in the soil or use it as a
substrate for overwintering. Due to very specific features of the Diptera larvae in general look like small worms as they are all Coleoptera larvae are represented by hundreds of families
soil as a habitat, insect larvae have made numerous adaptations legless. However, their ecological functions are very diverse. Some with different feeding habits. Some longhorn beetle larvae
to live in this particular environment. According to their life cycle, of them mine taproots (see page 43) and feed on the internal (Cerambycidae) bore into roots or rhizomes. Click beetles and
insects can be classified as holometabolous, hemimetabolous cortex. Others live in litter or dung, which they decompose. scarabaeid larvae chew fine roots or decaying plants. Some
or ametabolous, depending on whether they undergo complete, scarabaeid larvae are parasitised by Hymenoptera. Tiger beetle
incomplete or no metamorphosis, respectively (see box below).
a larvae (Cicindelidae) live in cylindrical burrows, and wait for their
Larvae of hemimetabolous insects do not undergo substantial prey to pass by on the soil surface.
changes in their body form; they are often called nymphs and
look very similar to adult insects lacking well developed wings and a
the ability to reproduce. The holometabolous larvae differ greatly
from the adult and often occupy different ecological niches. The
change to adulthood occurs during pupation. Morphologically,
holometabolous insects are very diverse and cover a wide range
of trophic levels, from detritivores to herbivores and predators.
Among different species, they may vary from less than 1 mm to
12 cm. [70, 71]
Hemiptera larvae b b
Cicada nymphs (Hemiptera) may be among the most well-known,
most likely due to their long life in the soil and huge biomass.
They feed by sucking sap from roots and can live in the soil for up
to 17 years. Emergence of over 300 nymphs of periodical cicadas
per square metre represents the highest recorded biomass (up to
4 000 kilos per hectare) for any terrestrial animal.
Lepidoptera larvae One works, the others feast
Lepidoptera larvae show diverse feeding strategies. The majority • Some parasitic species undergo hypermetamorphosis, which refers
to a class of variants of holometabolism. In hypermetamorphosis
feed on green plants. Ghost-moth larvae in Tibet dig soil and
some larval instars (usually the first one) are functionally and
feed on live roots. They are often infected by a caterpillar fungus
morphologically distinct from each other.
(Ophiocordyceps sinensis, Ascomycota) valued in herbal medicine.
• In the beetle family Meloidae, the first instar is called triungulin (as
Some others live in ant colonies, and are fed mouth-to-mouth by
it has three claws on each foot) and actively seeks out prey on which
ants, or feed on residuals of ant food.
subsequent instars feed.
• Triungulin is elongated and flattened and in this form it does not feed.
a When it finds its prey it moults, transforming into a scarabaeiform or
vermiform larva that does not hunt, but feeds.
Metamorphosis
Neuroptera larvae
• The word ‘metamorphosis’ derives from Greek meta (change) and
morphe (form). Most Neuroptera larvae are predators, with elongated mandibles.
• Metamorphosis refers to a major change in form or structure, By using the mandibles, they catch and pierce prey, and inject
usually associated with the development of the wings. One of the digestive juices. Ant lions (family Myrmeleontidae) create pitfall
most dramatic forms of metamorphosis is the change from the traps, and eat small arthropods that fall in.
immature insect into the adult form.
• Metamorphosis is sometimes accompanied by a change of habitat a
or behaviour.
• In insects there are different types of metamorphosis. The principle
is that metamorphosis is closely linked to wing development;
therefore:
- ametabolous are wingless insects (apterygota), so they do not
develop wings (no metamorphosis); b
- hemimetabolous insects have wings that develop gradually
(incomplete metamorphosis);
- holometabolous insects have wings that develop during the
pupation period (inactive) where the insect undergoes dramatic
physiological and morphological changes to acquire the wings
and to feed on different things (complete metamorphosis).
b
• In hemimetabolous insects, immature stages are called nymphs.
Development proceeds in repeated stages of growth and moult
(ecdysis); these stages are called instars. The juvenile forms closely
resemble adults but are smaller and lack adult features, such
as well developed wings and genitals. The differences between
nymphs in different instars are small, often just differences in body
proportions. Examples of the hemimetabolous insects are: aphids,
cicadas and leafhoppers.
• In holometabolous insects, immature stages are called larvae, and
differ markedly from adults. Insects that undergo holometabolism
pass through a larval stage, then enter an inactive state called
pupa, or chrysalis, and finally emerge as adults. Examples of the
holometabolous insects are: beetles, flies, ants and bees.

Macrofauna – Ground- and litter-dwelling macrofauna
Introduction Arachnida Gastropoda
The soil surface and leaf litter are important components of The class Arachnida are arthropods. Their eight legs that distinguish Snails and slugs are the two most relevant groups of gastropods
soil and may represent a perfect habitat. In particular, leaf litter, them from insects, which have six legs. The most well-known related to soil. Taxonomically, they are both included in the order
made up of dead plant material, such as leaves, bark, needles groups of arachnids are spiders (order Araneae) and scorpions Pulmonata. The clear difference between them is the presence
and twigs, that has fallen to the ground, is very rich in nutrients (order Scorpiones). Spiders come in a large range of sizes, from less of a conspicuous shell in snails, which is very reduced, totally
and keeps the soil moist. It also offers the perfect conditions in than 1 mm up to 30 cm, such as the Goliath birdeater (Theraphosa absent or internal in slugs. A snail's shell is made of calcium
which to build nests: hiding places and protected spots. Many of blondi), a spider belonging to the tarantula family. Scorpions range carbonate and has the typical spiral shape. Both snails and
the organisms inhabiting the ground and the litter fall within the in size from 9 mm up to specimens such as the Mexican cave- slugs range greatly in size; the largest species can reach 30 cm.
group of soil macrofauna (animals that are at least one centimetre dwelling Typhlochactas mitchelli that can reach up to 20 cm. Around 25 000 snail species are present worldwide, whereas
long). Macrofauna include myriapods, beetles, insect larvae, slugs, Spiders' bodies consist of two sections (tagmata): the cephalothorax only approximately 5 000 slug species exist. Terrestrial snails are
snails, spiders and scorpions (see pages 57, 59-60). Some of these or prosoma at the front, and the abdomen or opisthosoma at the usually herbivorous; however, some species are carnivores. Most
organisms spend their entire lives on the soil surface and in leaf back. Spiders have a pair of cephalic appendages in front of the slugs feed on a broad spectrum of organic materials, including
litter, while others are found only there at certain points in their mouth (chelicerae), which they use to inject venom into prey from leaves from living plants, lichens (see page 42), fungi (see pages
lives. These organisms may have a high ecological importance venom glands. Scorpions' bodies are also divided into two regions: 38-41) and even carrion. Some slugs are predators and eat other
(e.g. as decomposers of litter). In these pages, we focus on the the head (cephalothorax), the abdomen (opisthosoma), which is slugs and snails or earthworms (see page 58). Some snail and
Arachnida (e.g. spiders and scorpions), Gastropoda (e.g. snails and subdivided into mesosoma (seven segments) and the metasoma or slug species can cause damage to agricultural crops and garden
slugs) and some Hymenoptera (e.g. mining bees). [72, 73] tail (five segments plus a sixth, the telson, bearing the sting). The plants and are, therefore, often considered as pests.
sting consists of the vesicle, which holds a pair of venom glands, and
a the aculeus, the venom-injecting barb. Spiders make up a very large a
group of organisms comprising more than 40 000 species. About
1 700 species of scorpion have been recordered to date. Spiders and
scorpions are found on all major land masses, except Antarctica.
Both groups are predators. They mostly prey on insects, although a
few large species can also take lizards, birds and small mammals.
An exception is represented by the herbivorous spider species
Bagheera kiplingi. Soil is often used as their hunting ground, in
which they use different methods of capturing prey. One of the most
clever strategies is adopted by the ambush ‘trapdoor spiders’ (family
Ctenizidae); they burrow holes into the soil, often closed by trapdoors
and surrounded by networks of silk threads that alert these spiders
to the presence of prey. Scorpions are nocturnal hunters, remaining
in underground holes or under rocks during the day. Scorpions can
b
survive long periods of food deprivation thanks to a specific food-
storage organ and slow digestion process; some are able to survive
b 6-12 months of starvation.
Burrowing or mining bees

• Not all bees (Arthropoda, Ectognatha, Hymenoptera) live in hives like
honey bees do and, in fact, five of the seven recognised families of
bees are ground-nesting bees (approximately 70 % of the 20 000
c known bee species). Their burrows can reach 60 cm in depth and
the entrance is often marked by a small mound of excavated soil.
Depending on the species, the female fills the brood cells at the end
b of the branched burrow with pollen, honey or a mixture of nectar and
pollen and, once the clump reaches the right size (sometimes after
a good number of trips to flowers), she lays an egg on each one. The
larva hatches within a few days, grows quickly and pupates within a
few weeks. The adults emerge the following spring after hibernation.
• Unlike social bees and wasps, ground-nesting bees do not live
in colonies, although some species could nest in large groups
(‘gregarious nesters’) and become so visible, especially in lawns
and paths, that gardeners consider them as pests. However, in
reasonable numbers they will not harm your garden. They are not
aggressive insects even though the females do have stings.
• These solitary bees (specifically Colletes and Andrena, two common
widespread genera) are good pollinators of economically important
d plants. They are often ‘oligolectic’, meaning that they collect pollen
from only a select few plant species, and if that plant becomes rare
c or extinct, so does its pollinator.

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CHAPTER II – DIVERSITY OF SOIL ORGANISMS

28 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

Soil biota includes archaea, bacteria, protists, tardigrades,

Organisms can be classified in different ways. Taxonomy (from

The greatest innovation of his system is the general use of

CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 29

The advances in microscopy and staining techniques led to the

structure and functioning. Although a general consensus has not

factor in classification (i.e. genetic similarities among organisms).

groups of organisms with a common ancestor, and based on

Prokaryotic cell Eukaryotic cell Unicellular Multicellular Autotroph Heterotroph

DNA and RNA

30 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

Supergroup (only for protists) Ma

Clitella Aca eae nes

B a ct eria Ar ch aea Ara corp s

However, taxonomic classifications (i.e. using hierarchical ranks)

CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 31

Microorganisms and the environment

Diversity, abundance and biomass

Over 300 archaeal species have been described, primarily found

32 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 33

Endospores, what are they?

34 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

Why does the air smell of soil after rain?

Cyanobacteria a What is photosynthesis?

CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 35

Diversity, abundance and biomass

36 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

Morphology Morphology Nuclearia, Ancyromonas and others

c The Excavata is a supergroup, with genera that occur in soil

Diversity, abundance and biomass Diversity, abundance and biomass

CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 37

Fungi: edible, poisonous, bioluminescent and giant

38 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

Soil-borne plant pathogenic fungi

CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 39

40 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 41

Diversity, abundance and biomass

42 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

Incredible numbers of plant roots

• epidermis: a single-layer group of cells that forms a boundary

CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 43

44 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

Bdelloid rotifers, a female affair

b There are about 2 030 described species. They can be extremely

CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 45

Diversity, abundance and biomass

46 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

Bacterial-feeding nematodes Fungal-feeding nematodes

CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 47

48 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

Distribution, abundance and biomass

CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 49

Collembola belong to the phylum Arthropoda. They are part of

The frozen and colourful collembola

50 Global Soil Biodiversity Atlas | CHAPTER II – DIVERSITY OF SOIL ORGANISMS

CHAPTER II – DIVERSITY OF SOIL ORGANISMS | Global Soil Biodiversity Atlas 51