290
J. Querellou et al.
could also be a reason to not look for an activity or, if the activity is vital, a reason
to look for alternative enzymes with similar activities.
8.3 Expanding Gene Resources Through Microbial-Community
Genomic Projects, Complete Genomes of Isolated Organisms
and Data Mining
Gene resources for biotechnology have been increasing exponentially during the last
decade owing to improved sequencing technology and the resulting increase in the
number of genome projects. However, the databases are filled with human-centric
genomic information with model species, (including human, rat, mouse, rice) as
well as their associated pathogens (both human and agricultural) constituting the
bulk of genome projects. Nevertheless, several marine species and marine communities have directly benefited from the genomic revolution either because their
position in the tree of life is strategic or for their potential in biotechnology.
The first genome-scale information was obtained directly from isolated and cultured species of interest, already available in microbial culture collections. However,
the vast majority of archaeal and bacterial taxa remain uncultivated (Amann et al.
1995, Rappé and Giovannoni 2003). In addition, analyses of marine viromes have
demonstrated that most marine virus genes are unrelated to those in the current
databases (Breitbart et al. 2002, Angly et al. 2006) and of course, they are massively unexploited. Gaining access to the almost unlimited microbial gene resources
from various marine environments is an exciting task. It relies mainly on two complementary approaches: metagenomics and single-cell genomics. A third approach
aiming at developing high throughput protocols for isolation and culture of previously uncultured (the vast majority) microorganisms has largely been ignored during
the last ten years, despite its obvious interest and some pioneering work in this area
(Giovannoni and Stingl 2007).
Many metagenomic projects are based on the sequencing of large DNA libraries
constructed from environmental DNA as exemplified by the Sargasso Sea project
(Venter et al. 2004). In order to obtain a more complete picture beyond random
examples, the exploration of microbial diversity needs to be carried out in a rational manner. The development of appropriate methods and strategies to estimate
the sampling effort necessary for a particular marine environment is in progress
(Quince et al. 2008). Despite the obvious limits of metagenomics, this approach has
aroused a considerable interest and it has been suggested that it might be possible
in the future to gain access to most of the gene resources of the biosphere, including those of rare species, by applying high-throughput sequencing methodology.
A single metagenomic project, the Sorcerer II Global Ocean Survey, nearly doubled the number of known proteins in the databases (Rusch et al. 2007). One major
consequence of metagenome projects is the radical change in our understanding of
microbial diversity in samples of marine environments like sediments and deep-sea
vents (Sogin et al. 2006, Huber et al. 2007, Quince et al. 2008). Strategies to fully
J. Querellou et al.
could also be a reason to not look for an activity or, if the activity is vital, a reason
to look for alternative enzymes with similar activities.
8.3 Expanding Gene Resources Through Microbial-Community
Genomic Projects, Complete Genomes of Isolated Organisms
and Data Mining
Gene resources for biotechnology have been increasing exponentially during the last
decade owing to improved sequencing technology and the resulting increase in the
number of genome projects. However, the databases are filled with human-centric
genomic information with model species, (including human, rat, mouse, rice) as
well as their associated pathogens (both human and agricultural) constituting the
bulk of genome projects. Nevertheless, several marine species and marine communities have directly benefited from the genomic revolution either because their
position in the tree of life is strategic or for their potential in biotechnology.
The first genome-scale information was obtained directly from isolated and cultured species of interest, already available in microbial culture collections. However,
the vast majority of archaeal and bacterial taxa remain uncultivated (Amann et al.
1995, Rappé and Giovannoni 2003). In addition, analyses of marine viromes have
demonstrated that most marine virus genes are unrelated to those in the current
databases (Breitbart et al. 2002, Angly et al. 2006) and of course, they are massively unexploited. Gaining access to the almost unlimited microbial gene resources
from various marine environments is an exciting task. It relies mainly on two complementary approaches: metagenomics and single-cell genomics. A third approach
aiming at developing high throughput protocols for isolation and culture of previously uncultured (the vast majority) microorganisms has largely been ignored during
the last ten years, despite its obvious interest and some pioneering work in this area
(Giovannoni and Stingl 2007).
Many metagenomic projects are based on the sequencing of large DNA libraries
constructed from environmental DNA as exemplified by the Sargasso Sea project
(Venter et al. 2004). In order to obtain a more complete picture beyond random
examples, the exploration of microbial diversity needs to be carried out in a rational manner. The development of appropriate methods and strategies to estimate
the sampling effort necessary for a particular marine environment is in progress
(Quince et al. 2008). Despite the obvious limits of metagenomics, this approach has
aroused a considerable interest and it has been suggested that it might be possible
in the future to gain access to most of the gene resources of the biosphere, including those of rare species, by applying high-throughput sequencing methodology.
A single metagenomic project, the Sorcerer II Global Ocean Survey, nearly doubled the number of known proteins in the databases (Rusch et al. 2007). One major
consequence of metagenome projects is the radical change in our understanding of
microbial diversity in samples of marine environments like sediments and deep-sea
vents (Sogin et al. 2006, Huber et al. 2007, Quince et al. 2008). Strategies to fully