8
G.R. Carvalho et al.
surge of activity in the analysis of microbial communities by isolating and sequencing large fragments of DNA directly from the environment, an approach known
as “metagenomics” (see Chapter 2). Such work has led to the discovery of novel
biochemical pathways (e.g. Peers and Price 2006) and novel organisms (Massana
et al. 2006). For example, the application of “whole-genome shotgun sequencing”
to microbial populations collected from the Sargasso Sea identified at least 1,800
genomic species based on sequence relatedness, including 148 previously unknown
bacterial phylotypes (Venter et al. 2004). The Sargasso Sea study additionally identified over 1.2 million previously unknown genes, including more than 782 new
rhodopsin-like photoreceptors, revealing unprecedented levels of phyletic and functional oceanic microbial diversity. Such approaches increase further the ability to
analyze directly samples from the wild, and promise to revolutionize our ability
to characterize gene function in relation to organismal and ecosystem processes.
Finally, the enhanced awareness that biodiversity underpins ecosystem resilience
and recovery from perturbations (reviewed in Palumbi et al. 2008a), has shifted
interest and focus of environmental management from individuals, populations and
species, to communities and ecosystems, with particular attention on functional
relationships between biotic diversity and ecosystem processes. Such a focus on
relationships is ideally suited for genomic applications because it is the linkages
between gene structure, function and phenotypic diversity at the cellular, metabolic
and ecological processes that characterize variability in patterns of productivity,
nutrient and energy flow.
Having provided a brief overview of key developments in marine genomics in
relation to marine biodiversity, we now examine some molecular approaches for
identifying marine species and classifying functional capacity of marine assemblages.
1.2 Molecular Identification of Marine Biodiversity
With the increasing focus on the relationship between biodiversity and ecosystem
functioning on such processes as elemental cycling, production and trophic transfer
(Chapin et al. 1997, Duffy and Stachowicz 2006), it is crucial to obtain realistic
estimates of species diversity and quantification of functional capability. Particular
challenges in the assessment of biodiversity in the marine environment arise from
limited access to certain habitats, communities and the patchy distribution of species
in pelagic environments. Accordingly, new genomic approaches have recently been
developed that provide the means to access previously undetected biodiversity.
Species identification is the critical starting point of any research in marine biology. Conventional identification approaches based on phenotypic characters may be
apparently straightforward. However there are various situations in which they may
fail or have limited efficiency, such as cryptic species, inherently difficult taxonomic
groups, or taxonomically ambiguous eggs and larvae (Kochzius et al. 2008). The
discovery of new marine habitats and associated new species, increased threats to
G.R. Carvalho et al.
surge of activity in the analysis of microbial communities by isolating and sequencing large fragments of DNA directly from the environment, an approach known
as “metagenomics” (see Chapter 2). Such work has led to the discovery of novel
biochemical pathways (e.g. Peers and Price 2006) and novel organisms (Massana
et al. 2006). For example, the application of “whole-genome shotgun sequencing”
to microbial populations collected from the Sargasso Sea identified at least 1,800
genomic species based on sequence relatedness, including 148 previously unknown
bacterial phylotypes (Venter et al. 2004). The Sargasso Sea study additionally identified over 1.2 million previously unknown genes, including more than 782 new
rhodopsin-like photoreceptors, revealing unprecedented levels of phyletic and functional oceanic microbial diversity. Such approaches increase further the ability to
analyze directly samples from the wild, and promise to revolutionize our ability
to characterize gene function in relation to organismal and ecosystem processes.
Finally, the enhanced awareness that biodiversity underpins ecosystem resilience
and recovery from perturbations (reviewed in Palumbi et al. 2008a), has shifted
interest and focus of environmental management from individuals, populations and
species, to communities and ecosystems, with particular attention on functional
relationships between biotic diversity and ecosystem processes. Such a focus on
relationships is ideally suited for genomic applications because it is the linkages
between gene structure, function and phenotypic diversity at the cellular, metabolic
and ecological processes that characterize variability in patterns of productivity,
nutrient and energy flow.
Having provided a brief overview of key developments in marine genomics in
relation to marine biodiversity, we now examine some molecular approaches for
identifying marine species and classifying functional capacity of marine assemblages.
1.2 Molecular Identification of Marine Biodiversity
With the increasing focus on the relationship between biodiversity and ecosystem
functioning on such processes as elemental cycling, production and trophic transfer
(Chapin et al. 1997, Duffy and Stachowicz 2006), it is crucial to obtain realistic
estimates of species diversity and quantification of functional capability. Particular
challenges in the assessment of biodiversity in the marine environment arise from
limited access to certain habitats, communities and the patchy distribution of species
in pelagic environments. Accordingly, new genomic approaches have recently been
developed that provide the means to access previously undetected biodiversity.
Species identification is the critical starting point of any research in marine biology. Conventional identification approaches based on phenotypic characters may be
apparently straightforward. However there are various situations in which they may
fail or have limited efficiency, such as cryptic species, inherently difficult taxonomic
groups, or taxonomically ambiguous eggs and larvae (Kochzius et al. 2008). The
discovery of new marine habitats and associated new species, increased threats to