Keywords
Endosymbiosis Hierarchical classification History of systematics Life domains
Microbial classification Microbial systematics Nomenclature codes Phylogeny
Tree of life
5.1
History and Development
of Systematics
5.1.1 Interest of Systematics in Microbial
Ecology
Each group of organisms should have a solid taxonomy to be
studied in a structured way. It is of course possible to study
the physiology and genetics of an organism without further
justification beyond that it contributes to improving
community’s health and bioprocesses without a solid identification, but it will be impossible to replace the conclusions
drawn in an evolutionary perspective, which is a crucial
input in biology. If the concepts of taxonomy and phylogeny
are necessary for the study of the ecology of multicellular
eukaryotes (plants and animals in the traditional sense),
these disciplines are even more essential in microbial ecology, since these organisms have few morphological
characters to provide a reliable identification.
Microbial ecology aims at understanding the interactions
of microorganisms with each other and with their environment, in particular the role of microorganisms in biogeochemical cycles. If such study must be analytical and predictive, it
must be made in relation to specific taxa, and so a solid
taxonomic framework should be proposed. This is the reason
why microbial ecologists are the most interested in taxonomy
and microbial evolution among microbiologists.
One of the important concepts regarding the microbial
world is the enormous diversity of organisms on Earth. The
diversity of metabolic activities is a characteristic and originality of the microbial world (cf. Chaps. 3 and 14). This
enormous diversity needs to be structured and organized to
be better understood. Man has always sought to understand
and name the components of the world around him. If this
attempt proved relatively easy with multicellular eukaryotes,
it was much more difficult, if not artificial, with
microorganisms, because of the change of scale and the
need to extend our organs of perception with the instruments
adapted such as techniques of microscopy, metabolic analysis, and tools of molecular biology. Thus, as and when there
are changes in methods, our approach to design and organize
the microbial world has changed. As a result, taxonomy and
systematics are constantly changing since the beginning of
the history of microbiology. They will continue to evolve
and even be upset with the gradual addition of new
techniques, becoming more sophisticated and powerful,
such as genomics and proteomics. Such changes will not
occur as rapidly in multicellular eukaryotes.
Thus, the systematics of microorganisms, which underlies
all the studies directed towards the knowledge of their biodiversity, is an interesting central area for biotechnologists and
epidemiologists as well as ecologists. They first try to isolate
and study new microorganisms for large biotechnological or
epidemiological potential. In parallel, microbial ecologists
and biogeochemists study the role of microorganisms in
ecosystems and their biodiversity in the history of life considering the environmental changes that result.
5.1.2 From the Discovery of the Microbial
World to a Taxonomic Scheme
of Its Diversity
Even before Pasteur, the cloth merchant Antonie van
Leeuwenhoek in 1672 with his famous microscope could
discern shapes in microorganisms. However, the number of
categories that he could identify was limited, ranging from
cocci (spherical shapes), bacilli (rod-shaped forms), spirilla
(curved or spiral shapes), and filaments, and was much
smaller than those that can be distinguished with presentday microscopes. The work of Pasteur (second half of the
nineteenth century) and his students raised awareness that
microorganisms were conducting more or less complex and
diverse biochemical changes according to the types of
microorganisms, including prokaryotes (cf. Sect. 2.3). Thus
was born an attempt at bacterial classification based not only
on their shape but also on their ability to perform specific
biochemical transformations.
The microbial world concerns all microorganisms
(visible under the microscope and usually unicellular), as
single cells or groups of cells (colonies, filaments), whether
their structure is prokaryotic (Bacteria and Archaea)
or eukaryotic (which were named microalgae, protozoa,
microscopic fungi that are polyphyletic groups; cf.
Sects. 5.5.1, 5.5.2, and 5.5.3). Viruses require living prokaryotic (bacteriophages) or eukaryotic cells to multiply and
108
C.-F. Boudouresque et al.
Endosymbiosis Hierarchical classification History of systematics Life domains
Microbial classification Microbial systematics Nomenclature codes Phylogeny
Tree of life
5.1
History and Development
of Systematics
5.1.1 Interest of Systematics in Microbial
Ecology
Each group of organisms should have a solid taxonomy to be
studied in a structured way. It is of course possible to study
the physiology and genetics of an organism without further
justification beyond that it contributes to improving
community’s health and bioprocesses without a solid identification, but it will be impossible to replace the conclusions
drawn in an evolutionary perspective, which is a crucial
input in biology. If the concepts of taxonomy and phylogeny
are necessary for the study of the ecology of multicellular
eukaryotes (plants and animals in the traditional sense),
these disciplines are even more essential in microbial ecology, since these organisms have few morphological
characters to provide a reliable identification.
Microbial ecology aims at understanding the interactions
of microorganisms with each other and with their environment, in particular the role of microorganisms in biogeochemical cycles. If such study must be analytical and predictive, it
must be made in relation to specific taxa, and so a solid
taxonomic framework should be proposed. This is the reason
why microbial ecologists are the most interested in taxonomy
and microbial evolution among microbiologists.
One of the important concepts regarding the microbial
world is the enormous diversity of organisms on Earth. The
diversity of metabolic activities is a characteristic and originality of the microbial world (cf. Chaps. 3 and 14). This
enormous diversity needs to be structured and organized to
be better understood. Man has always sought to understand
and name the components of the world around him. If this
attempt proved relatively easy with multicellular eukaryotes,
it was much more difficult, if not artificial, with
microorganisms, because of the change of scale and the
need to extend our organs of perception with the instruments
adapted such as techniques of microscopy, metabolic analysis, and tools of molecular biology. Thus, as and when there
are changes in methods, our approach to design and organize
the microbial world has changed. As a result, taxonomy and
systematics are constantly changing since the beginning of
the history of microbiology. They will continue to evolve
and even be upset with the gradual addition of new
techniques, becoming more sophisticated and powerful,
such as genomics and proteomics. Such changes will not
occur as rapidly in multicellular eukaryotes.
Thus, the systematics of microorganisms, which underlies
all the studies directed towards the knowledge of their biodiversity, is an interesting central area for biotechnologists and
epidemiologists as well as ecologists. They first try to isolate
and study new microorganisms for large biotechnological or
epidemiological potential. In parallel, microbial ecologists
and biogeochemists study the role of microorganisms in
ecosystems and their biodiversity in the history of life considering the environmental changes that result.
5.1.2 From the Discovery of the Microbial
World to a Taxonomic Scheme
of Its Diversity
Even before Pasteur, the cloth merchant Antonie van
Leeuwenhoek in 1672 with his famous microscope could
discern shapes in microorganisms. However, the number of
categories that he could identify was limited, ranging from
cocci (spherical shapes), bacilli (rod-shaped forms), spirilla
(curved or spiral shapes), and filaments, and was much
smaller than those that can be distinguished with presentday microscopes. The work of Pasteur (second half of the
nineteenth century) and his students raised awareness that
microorganisms were conducting more or less complex and
diverse biochemical changes according to the types of
microorganisms, including prokaryotes (cf. Sect. 2.3). Thus
was born an attempt at bacterial classification based not only
on their shape but also on their ability to perform specific
biochemical transformations.
The microbial world concerns all microorganisms
(visible under the microscope and usually unicellular), as
single cells or groups of cells (colonies, filaments), whether
their structure is prokaryotic (Bacteria and Archaea)
or eukaryotic (which were named microalgae, protozoa,
microscopic fungi that are polyphyletic groups; cf.
Sects. 5.5.1, 5.5.2, and 5.5.3). Viruses require living prokaryotic (bacteriophages) or eukaryotic cells to multiply and
108
C.-F. Boudouresque et al.