8 Marine Biotechnology
293
2003), functional screens were combined with genome data mining. In some cases,
the initial research step was an in silico analysis and searches for specific targets
were followed, when successful, by biochemical characterization. The characterization of Pyrococcus abyssi thermostable nitrilase is a good example of this procedure
applied to enzyme discovery (Mueller et al. 2006).
The recent oil crisis emphasized the need for the development of alternatives to
fossil fuels. A recent review of “bioenergy genomes” (Rubin 2008) listed the species
already known as biomass degraders or fuel producers whose genomes have been
completely sequenced or for which projects are under way. This list highlights the
small contribution of marine genomes to this huge project. This does not mean that
marine species are inappropriate in this context, we have already underlined the
presence of thermostable amylases, cellulases, xylanases, etc. in hyperthermophilic
archaea (Table 8.2), but it is likely that a strong bias toward terrestrial species
underlies these choices (see also below).
8.3.2 The Growing Contribution of Metagenomes
The title of a review published in the Biotechnological Journal and entitled
“Metagenomics: an inexhaustible access to nature’s diversity” summarizes a common opinion about the potential contribution of metagenomes to biotechnology
(Langer et al. 2006). Marine metagenomics is mostly based on techniques and methods developed from the study of soil metagenomics. It emerged as the combination
of extraction and digestion of bacterial DNA from soil (Torsvik 1980), the generation of gene libraries from environmental DNA (Pace et al. 1986), the conception
and generation of marine plankton environmental DNA libraries (Schmidt et al.
1991). The term metagenome was proposed by Handelsman to describe the entire
set of sequences of organisms living in a defined habitat (Handelsman et al. 1998).
The biotechnological potential of this novel approach was soon recognised (Short
et al. 1997). The initial goal of marine metagenomics was the inventory of microbial
diversity in the oceans, with the aim of providing access to the functions of previously hidden key players and their role in the main geochemical cycles. However, it
was only at the beginning of the twenty-first century, following the introduction of
large sequencing facilities, that this approach was used on a large scale by C. Venter
and his team during the Sargasso Sea metagenome investigation (Venter et al. 2004)
and the Sorcerer II/GOS expedition (Rusch et al. 2007).
The principal advantage of metagenomics is that it allows the current limits of culture-dependent methods to be bypassed. This is especially interesting
when microbial samples are recovered from highly complex communities and
from “metaorganisms” (usually one eukaryote and its associated microbiome), like
sponges where the vast majority of the microbial community remains uncultured.
Marine environments are extremely diverse on Earth and their exploration
and exploitation offer untapped gene resources for biotechnology. Metagenomic
approaches, combined with heterologous expression, appropriate high throughput
293
2003), functional screens were combined with genome data mining. In some cases,
the initial research step was an in silico analysis and searches for specific targets
were followed, when successful, by biochemical characterization. The characterization of Pyrococcus abyssi thermostable nitrilase is a good example of this procedure
applied to enzyme discovery (Mueller et al. 2006).
The recent oil crisis emphasized the need for the development of alternatives to
fossil fuels. A recent review of “bioenergy genomes” (Rubin 2008) listed the species
already known as biomass degraders or fuel producers whose genomes have been
completely sequenced or for which projects are under way. This list highlights the
small contribution of marine genomes to this huge project. This does not mean that
marine species are inappropriate in this context, we have already underlined the
presence of thermostable amylases, cellulases, xylanases, etc. in hyperthermophilic
archaea (Table 8.2), but it is likely that a strong bias toward terrestrial species
underlies these choices (see also below).
8.3.2 The Growing Contribution of Metagenomes
The title of a review published in the Biotechnological Journal and entitled
“Metagenomics: an inexhaustible access to nature’s diversity” summarizes a common opinion about the potential contribution of metagenomes to biotechnology
(Langer et al. 2006). Marine metagenomics is mostly based on techniques and methods developed from the study of soil metagenomics. It emerged as the combination
of extraction and digestion of bacterial DNA from soil (Torsvik 1980), the generation of gene libraries from environmental DNA (Pace et al. 1986), the conception
and generation of marine plankton environmental DNA libraries (Schmidt et al.
1991). The term metagenome was proposed by Handelsman to describe the entire
set of sequences of organisms living in a defined habitat (Handelsman et al. 1998).
The biotechnological potential of this novel approach was soon recognised (Short
et al. 1997). The initial goal of marine metagenomics was the inventory of microbial
diversity in the oceans, with the aim of providing access to the functions of previously hidden key players and their role in the main geochemical cycles. However, it
was only at the beginning of the twenty-first century, following the introduction of
large sequencing facilities, that this approach was used on a large scale by C. Venter
and his team during the Sargasso Sea metagenome investigation (Venter et al. 2004)
and the Sorcerer II/GOS expedition (Rusch et al. 2007).
The principal advantage of metagenomics is that it allows the current limits of culture-dependent methods to be bypassed. This is especially interesting
when microbial samples are recovered from highly complex communities and
from “metaorganisms” (usually one eukaryote and its associated microbiome), like
sponges where the vast majority of the microbial community remains uncultured.
Marine environments are extremely diverse on Earth and their exploration
and exploitation offer untapped gene resources for biotechnology. Metagenomic
approaches, combined with heterologous expression, appropriate high throughput