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My name is Raphaël Lami, I am an associate
professor working at Sorbonne University
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at the marine station of Banyuls-sur-mer.
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I was recruited in 2010 after a PhD
in environmental microbiology.
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I have been working since my
PhD on environmental biofilms.
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In my research, I am interested in looking
at the diversity and functions of bacteria
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colonising biofilms. I am also interested in
looking at the fundamental mechanisms
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which drive the growth of biofilms, and I
am also working on innovative applications
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to develop environmentally-friendly and
sustainable anti-fouling solutions.
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One of the most famous models
in Life Sciences is undoubtedly
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the proteobacteria Escherichia coli.
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This enteric bacteria was discovered in 1885
by Theodor Escherich and has served as a
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universal living model to characterise
many fundamental mechanisms of life.
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Some of the results and observations
obtained with this model were so important
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that they led to several Nobel Prizes, such
as the one awarded to Jacob, Monod,
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and Lwoff in 1965.
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Significant discoveries resulting
from research on E. coli include
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the elucidation of the genetic code, the
description of DNA replication mechanisms,
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and the understanding of the bacterial genome
organisation in operons, among many others.
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Firstly, the cell structure and mechanisms
appear to be less complicated compared
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to eukaryotes. This means that the
characterization of biological processes
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is usually expected to require fewer steps
than other famous biological models,
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such as the mouse or the zebrafish.
Secondly, E. coli is easily grown,
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maintained, and preserved in a laboratory
setting. It presents a short generation time
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of 20 minutes in optimal conditions, and
more than 10^9 cells per mL can be
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obtained in a few hours. E. coli I also grows
easily in basic media and can be preserved
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at -80°C for decades, and is thus an
inexpensive model organism to work
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with in laboratories. Finally, most E. coli
strains are non-pathogenic and therefore
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are not hazardous for scientists. However,
perhaps the most critical feature that
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makes E. coli an excellent model in Life
Sciences is that genetic manipulation protocols
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were established very early on, as soon as
researchers began to study this organism.
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Since then, the genetic engineering of
E. coli has become so straightforward that
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it is used as a host in synthetic biology.
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Other bacteria are also well-known models
in biology, even if they are less commonly
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used in research laboratories, and less
well-known to the general public compared
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to E. coli. One such example is Bacillus
subtilis, a firmacute that lives in soils
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and is widely used in food
and biotechnology industries.
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This non-pathogenic bacterium attracts
researchers who want to study the mechanisms
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of pathogenesis, as it presents some
features that are shared with pathogenic cells
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including biofilm formation and sporulation.
After considering E. coli and B. subtilis,
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the list of common model bacteria is not
so long. Researchers working on skin
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microbiota and antibiotic resistance would
probably include Staphylococcus strains
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in such a list. Others working on gut
microbiota might add the gut coloniser
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Bifidobacterium and those working on
Pseudomonas aeruginosa or florescens
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would argue that these commonly grown
microorganisms serve as models in the
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medical fields or even in environmental
sciences. Whatever the final list of
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standard bacterial models, there is a
consensus among microbiologists that it
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should be expanded. Indeed, the diversity
of mechanisms to study in Life Sciences
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requires considerable efforts to develop and
promote many more types of bacterial models.
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This is exactly what we are going to see
in this course! The marine environment
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may potentially be a very important reservoir
of prokaryotic models that could be used
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to explore many types of biological
mechanisms, either to investigate their
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diversity, or to access some of the
particular features linked to their
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adaptation to marine life.
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In this online course, will emphasise
the diversity of biological questions
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that can be addressed using marine models
and for which the current traditional models
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cannot provide enough answers. Indeed
many major questions in biology and
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evolutionary studies cannot be fully
addressed using the famous models like
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Escherichia coli or Bacillus subtilis.
Many of them are connected to
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environmental issues and include, for
example, those related to molecular
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adaptations to environmental changes,
including in ecotoxicology, or to the
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identification of organisms suited to
develop innovative "green" or "blue"
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biotechnological applications.
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We will illustrate this interest with the
long-established model Vibrio fischeri,
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also known as Allivibrio fischeri,
but the historic name Vibrio fischeri
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is still widely used. Indeed, this prokaryote
is a widely-known bacterial model isolated
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from the marine environment. We will see
that this bacterium serves as a model for
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the study of bioluminescence mechanisms,
cell-to-cell communication systems, and
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host-symbiont relationships. If you are
interested in this subject, I highly
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recommend that you also read
the associated book chapter.