improve plant growth to meet the global challenge of feeding
billions of people in a changing environment and to do so
must better integrate the constraints and benefits of
plant–microbe interactions. In the field of agronomy, this
concerns in particular the principles of crop breeding
schemes, cultivation techniques, and the development of ecological engineering approaches in cropping systems.
11.4 Interactions Between Microorganisms
and Animals
11.4.1 Introduction
Man and animals, whether vertebrate or invertebrate, live in
environments (air, water, soil) constantly populated by
microorganisms consisting mainly of bacteria, fungi,
protozoa, and viruses. Such cohabitation usually leads to
more or less intimate associations between microorganisms
and animals. Spatial proximity, contact time, and the degree
of dependence between the interacting partners influence the
type and evolution of these associations. Microorganisms use
animals as habitats in which they live and from which they
retrieved nutrients necessary for their multiplication. They
colonize the outlying areas, such as the surface of the skin
or mucous membranes, and can penetrate the tissues and
organs of host animals. Some microorganisms can colonize
the cytoplasm of germ cells, oocytes, and sperm and are thus
subject to possible vertical transmission (from parents to
offsprings), which can allow a greater ability to spread
among host population. The presence and activities of
microorganisms will affect development, reproduction, and
survival of host animals. The nature of the effects caused by
microorganisms and the animal responses to these infections
are very diverse and are part of a continuum from parasitism
to mutualism (Buchner 1965). Whatever the outcome of the
interaction (neutral, beneficial, or deleterious), animals
respond to infection by implementing defense systems, either
by inducing immune responses or setting up physical barriers
to prevent or limit the spread of microorganisms considered as
potentially infectious agents. In parallel, microorganisms
develop strategies to circumvent the defenses of animals by
manipulation host traits or molecular mimicry. It is the tradeoff between cost and benefits, that is to say, the balance of the
association in terms of adaptive value, which defines the type
of interaction (Moran 2007). Knowledge and understanding
of the interactions between microorganisms and animals represent major challenges in various areas of biology. In the
fundamental domain, microorganisms and their animal hosts
entail a great diversity of species potentially giving rise to a
variety of interactions. These interactions are of great interest
in cell biology, molecular biology, evolutionary biology, and
ecology. In human and animal health, the interactions
between microorganisms and their vertebrate or invertebrate
hosts are important because they are the cause of many
diseases involving emerging human and animal pathogens.
11.4.2 Diversity, Distribution, and Abundance
of Microorganisms Associated
with Animals
Since the first microscopic observations of microbes by
Dutchman Antonie van Leeuwenhoek, followed by successful
cultivation of some of them by Louis Pasteur and other
scientists, and, more recently, the development of molecular
methods for the detection and identification without prior
culturing (culture-independent methods), the list of microbes
documented in animals is increasing. It remains that, for most
microbes, animals are hostile habitats due to the physicochemical conditions for growth and survival. One can mention, in healthy individuals, the often constant temperature
inside the body but variable at the surface exposed to environmental stress (radiation), the pH that can be either neutral
or acidic in the stomach, the osmotic pressure (variation of ion
concentration), the partial pressure of oxygen (aerobic and
anaerobic), the presence of various microbial inhibitors, and
limited energy resources both in quality and quantity.
Compared to the great diversity of microbial phyla
(DeLong and Pace 2001) present in areas where animals
live, only certain groups or certain strains or variants of a
group have the capacity for colonization (adhesion, secretion
systems, lytic enzymes, metabolism) and are able to adapt
and associate transiently or permanently with animals.
11.4.2.1 Microbial Diversity
Bacteria are the group most frequently encountered both
at the surface and in the internal parts of animal bodies
(cf. Sect. 8.1.5). Bacteria associated with humans belong to
the mesophiles and have their growth optimum around 37
C.
The culturable bacteria from the skin mostly belong to two
groups (Noble 1993). One is the Gram-positive cocci family
Micrococcaceae, with a dominance of staphylococci, and the
other consists of corynebacteria, in particular, bacteria belonging to genus Corynebacterium, which are found on all parts of
the human body surface. Bacteria belonging to genera Propionibacterium and Brevibacillus occupy more limited areas with
high production of lipids such as the sebaceous glands, the face,
and the scalp. Microbial flora of the skin of pets (cats, dogs) and
farm animals (pigs, cows) is also dominated by staphylococci
and some fungi (Nagase et al. 2002).
Review of various studies on the microbiota (cultivable
or unculturable microbes associated to an individual) of
human or other vertebrate species confirmed previous dominance of bacteria, but it has also expanded the repertoire of
microbial taxa (fungi, protozoa, viruses) residing in external
11 Microorganisms and Biotic Interactions
421
billions of people in a changing environment and to do so
must better integrate the constraints and benefits of
plant–microbe interactions. In the field of agronomy, this
concerns in particular the principles of crop breeding
schemes, cultivation techniques, and the development of ecological engineering approaches in cropping systems.
11.4 Interactions Between Microorganisms
and Animals
11.4.1 Introduction
Man and animals, whether vertebrate or invertebrate, live in
environments (air, water, soil) constantly populated by
microorganisms consisting mainly of bacteria, fungi,
protozoa, and viruses. Such cohabitation usually leads to
more or less intimate associations between microorganisms
and animals. Spatial proximity, contact time, and the degree
of dependence between the interacting partners influence the
type and evolution of these associations. Microorganisms use
animals as habitats in which they live and from which they
retrieved nutrients necessary for their multiplication. They
colonize the outlying areas, such as the surface of the skin
or mucous membranes, and can penetrate the tissues and
organs of host animals. Some microorganisms can colonize
the cytoplasm of germ cells, oocytes, and sperm and are thus
subject to possible vertical transmission (from parents to
offsprings), which can allow a greater ability to spread
among host population. The presence and activities of
microorganisms will affect development, reproduction, and
survival of host animals. The nature of the effects caused by
microorganisms and the animal responses to these infections
are very diverse and are part of a continuum from parasitism
to mutualism (Buchner 1965). Whatever the outcome of the
interaction (neutral, beneficial, or deleterious), animals
respond to infection by implementing defense systems, either
by inducing immune responses or setting up physical barriers
to prevent or limit the spread of microorganisms considered as
potentially infectious agents. In parallel, microorganisms
develop strategies to circumvent the defenses of animals by
manipulation host traits or molecular mimicry. It is the tradeoff between cost and benefits, that is to say, the balance of the
association in terms of adaptive value, which defines the type
of interaction (Moran 2007). Knowledge and understanding
of the interactions between microorganisms and animals represent major challenges in various areas of biology. In the
fundamental domain, microorganisms and their animal hosts
entail a great diversity of species potentially giving rise to a
variety of interactions. These interactions are of great interest
in cell biology, molecular biology, evolutionary biology, and
ecology. In human and animal health, the interactions
between microorganisms and their vertebrate or invertebrate
hosts are important because they are the cause of many
diseases involving emerging human and animal pathogens.
11.4.2 Diversity, Distribution, and Abundance
of Microorganisms Associated
with Animals
Since the first microscopic observations of microbes by
Dutchman Antonie van Leeuwenhoek, followed by successful
cultivation of some of them by Louis Pasteur and other
scientists, and, more recently, the development of molecular
methods for the detection and identification without prior
culturing (culture-independent methods), the list of microbes
documented in animals is increasing. It remains that, for most
microbes, animals are hostile habitats due to the physicochemical conditions for growth and survival. One can mention, in healthy individuals, the often constant temperature
inside the body but variable at the surface exposed to environmental stress (radiation), the pH that can be either neutral
or acidic in the stomach, the osmotic pressure (variation of ion
concentration), the partial pressure of oxygen (aerobic and
anaerobic), the presence of various microbial inhibitors, and
limited energy resources both in quality and quantity.
Compared to the great diversity of microbial phyla
(DeLong and Pace 2001) present in areas where animals
live, only certain groups or certain strains or variants of a
group have the capacity for colonization (adhesion, secretion
systems, lytic enzymes, metabolism) and are able to adapt
and associate transiently or permanently with animals.
11.4.2.1 Microbial Diversity
Bacteria are the group most frequently encountered both
at the surface and in the internal parts of animal bodies
(cf. Sect. 8.1.5). Bacteria associated with humans belong to
the mesophiles and have their growth optimum around 37
C.
The culturable bacteria from the skin mostly belong to two
groups (Noble 1993). One is the Gram-positive cocci family
Micrococcaceae, with a dominance of staphylococci, and the
other consists of corynebacteria, in particular, bacteria belonging to genus Corynebacterium, which are found on all parts of
the human body surface. Bacteria belonging to genera Propionibacterium and Brevibacillus occupy more limited areas with
high production of lipids such as the sebaceous glands, the face,
and the scalp. Microbial flora of the skin of pets (cats, dogs) and
farm animals (pigs, cows) is also dominated by staphylococci
and some fungi (Nagase et al. 2002).
Review of various studies on the microbiota (cultivable
or unculturable microbes associated to an individual) of
human or other vertebrate species confirmed previous dominance of bacteria, but it has also expanded the repertoire of
microbial taxa (fungi, protozoa, viruses) residing in external
11 Microorganisms and Biotic Interactions
421