1 Genomics in the Discovery and Monitoring
15
In addition to the phylotype system employed to identify microbes, the past few
years has witnessed the establishment of a DNA barcoding system of species identification for larger metazoans (Hebert et al. 2003). One drawback that arises when
attempting to apply a barcoding framework to micro- and meiofaunal organisms is
that in order to extract DNA from the organisms for PCR purposes, the whole animal is usually sacrificed, destroying the voucher specimen. An attractive solution
to this problem lies in video capture and editing (VCE) microscopy (DeLey et al.
2005), which consists of recording a taxonomically relevant multifocal series of “3D like” microscopy images as digital videoclips, that can act as “electronic voucher
specimens”. Images can then be deposited in appropriate publicly available repositories (e.g. NemAToL – http://nematol.unh.edu /) to be interrogated by the research
community.
Commonly though, biodiversity questions revolve around communities of meiofaunal organisms, rather than single individuals. An alternative to the barcoding
framework, analogous to methods employed in the study of prokaryotes, is to
sequence a large number of individuals derived from environmental samples and
recent research has highlighted the efficacy of an 18S rDNA molecular operational
taxonomic unit (MOTU) scheme for environmental samples (Floyd et al. 2002,
Blaxter and Floyd 2003, Bhadury et al. 2006). The MOTUs do not have any formal
relationship with published species descriptions, but identifications can be achieved
with existing databases, or future classifications in an approach that has been termed
“reverse taxonomy” (Markmann and Tautz 2005). MOTU-based studies to date have
investigated diversity via chain-termination sequencing of individual organisms, or
cloning and sequencing a few hundred PCR products derived from environmental
samples (Floyd et al. 2002, Blaxter et al. 2005). These data are highly informative,
but molecular diversity accumulation curves typically do not reach an asymptote,
suggesting that much larger sampling efforts are required to yield representative sets
of organisms present in the meiobenthos (Markmann and Tautz 2005). As with many
metagenetic (meta analyses of homologous gene regions) and metagenomic (meta
analyses of multiple, fractionated genomes) endeavours, ultrasequencing and downstream microarray-based technologies are likely to offer significant opportunities to
directly and simultaneously qualitatively assess molecular diversity (Creer 2008),
akin to species richness measures. Moreover, a significant advantage of the use of
VCE, is that functional diversity can be retrospectively assigned to environmental
community representatives, by referring to the trophic mode, body size and life history strategy of the voucher specimens (Moens and Vincx 1997, Schratzberger et al.
2007).
1.2.4 DNA Barcoding and Fisheries
To illustrate certain principles of DNA barcoding and its role in the management
of global marine resources, we consider briefly the application of the approach
to marine fishes. In May 2004, an international consortium of organisations – the
15
In addition to the phylotype system employed to identify microbes, the past few
years has witnessed the establishment of a DNA barcoding system of species identification for larger metazoans (Hebert et al. 2003). One drawback that arises when
attempting to apply a barcoding framework to micro- and meiofaunal organisms is
that in order to extract DNA from the organisms for PCR purposes, the whole animal is usually sacrificed, destroying the voucher specimen. An attractive solution
to this problem lies in video capture and editing (VCE) microscopy (DeLey et al.
2005), which consists of recording a taxonomically relevant multifocal series of “3D like” microscopy images as digital videoclips, that can act as “electronic voucher
specimens”. Images can then be deposited in appropriate publicly available repositories (e.g. NemAToL – http://nematol.unh.edu /) to be interrogated by the research
community.
Commonly though, biodiversity questions revolve around communities of meiofaunal organisms, rather than single individuals. An alternative to the barcoding
framework, analogous to methods employed in the study of prokaryotes, is to
sequence a large number of individuals derived from environmental samples and
recent research has highlighted the efficacy of an 18S rDNA molecular operational
taxonomic unit (MOTU) scheme for environmental samples (Floyd et al. 2002,
Blaxter and Floyd 2003, Bhadury et al. 2006). The MOTUs do not have any formal
relationship with published species descriptions, but identifications can be achieved
with existing databases, or future classifications in an approach that has been termed
“reverse taxonomy” (Markmann and Tautz 2005). MOTU-based studies to date have
investigated diversity via chain-termination sequencing of individual organisms, or
cloning and sequencing a few hundred PCR products derived from environmental
samples (Floyd et al. 2002, Blaxter et al. 2005). These data are highly informative,
but molecular diversity accumulation curves typically do not reach an asymptote,
suggesting that much larger sampling efforts are required to yield representative sets
of organisms present in the meiobenthos (Markmann and Tautz 2005). As with many
metagenetic (meta analyses of homologous gene regions) and metagenomic (meta
analyses of multiple, fractionated genomes) endeavours, ultrasequencing and downstream microarray-based technologies are likely to offer significant opportunities to
directly and simultaneously qualitatively assess molecular diversity (Creer 2008),
akin to species richness measures. Moreover, a significant advantage of the use of
VCE, is that functional diversity can be retrospectively assigned to environmental
community representatives, by referring to the trophic mode, body size and life history strategy of the voucher specimens (Moens and Vincx 1997, Schratzberger et al.
2007).
1.2.4 DNA Barcoding and Fisheries
To illustrate certain principles of DNA barcoding and its role in the management
of global marine resources, we consider briefly the application of the approach
to marine fishes. In May 2004, an international consortium of organisations – the