6 Genomics of Marine Algae
191
tides”, which can contain up to several million cells per litre of seawater (Guiry
and Guiry 2008), can have a huge impact on the environment through the bioaccumulation of their toxins in the food chain, affecting fish, birds and mammals. High
toxin concentrations in fish and filter-feeding molluscs consumed by humans may
cause gastrointestinal disorders, permanent neurological damage or even result in
death (Faust and Gulledge 2002). Alexandrium tamarense and A. catenella produce
saxitoxins leading to paralytic shellfish poisoning (PSP), while the brevetoxin of
Karenia brevis is responsible for neurolytic shellfish poisoning (NSP) (Faust and
Gulledge 2002). The fish mortality associated with blooms of Heterocapsa triquetra, on the other hand, appears to be due to oxygen depletion of the water when cells
decompose, rather than toxin production (Guiry and Guiry 2008). The cytotoxins
of Amphidinium gibbosum have been studied for their potent antitumor activities
(Bauer et al. 1995). Additional toxin-producing groups include the heterokonts and
the haptophytes. Some species of the diatom Pseudo-nitzschia (e.g. P. pseudodelicatissima), for example, produce domoic acid, a neurotoxin that may cause amnesic
shellfish poisoning (AMS) in humans when consuming contaminated molluscs.
The pelagophyte Aureococcus anophagefferens is thought to secrete a toxin into
its extracellular polysaccharide sheath. The haptophyte Prymnesium parvum produces prymnesin toxins, which are highly toxic to fish (La Claire 2006). Genomic
approaches such as EST sequencing are being used to study the organisms that cause
toxic algal blooms, with a major aim being to understand how and why toxins are
produced (http://genome.imb-jena.de/ESTTAL/cgi-bin/Index.pl).
6.4.5 Organism-Based Approaches for Exploring the Biology
of Planktonic Algae
The approaches discussed above are providing increasingly detailed information
about the organisms that are present in the plankton. By describing the ensemble
of genes present in the ecosystem (the metagenome), high-throughput sequencing
is also providing insights into the metabolic and cellular process that are going on
in these ecosystems. However, to really understand how these communities work it
is also necessary to have detailed information about the biology of the individual
species that they are composed of. Classical biological techniques, in particular isolation and study of individual strains of phytoplankton in culture, have, and still are,
making extremely important contributions to understanding phytoplankton biology
(Vaulot et al. 2008). In recent years, however, these techniques have been complemented by powerful new genomic approaches based on whole genome sequencing
and the establishment of model organisms.
Initially, genome sequencing was only applied to a very limited number of algae.
These were selected primarily based on their small genome sizes, although additional factors such as ecological relevance, phylogenetic position and availability of
axenic cultures and other biological characteristics, were also taken into account.
However, as sequencing technologies have improved, the number of algal genome
191
tides”, which can contain up to several million cells per litre of seawater (Guiry
and Guiry 2008), can have a huge impact on the environment through the bioaccumulation of their toxins in the food chain, affecting fish, birds and mammals. High
toxin concentrations in fish and filter-feeding molluscs consumed by humans may
cause gastrointestinal disorders, permanent neurological damage or even result in
death (Faust and Gulledge 2002). Alexandrium tamarense and A. catenella produce
saxitoxins leading to paralytic shellfish poisoning (PSP), while the brevetoxin of
Karenia brevis is responsible for neurolytic shellfish poisoning (NSP) (Faust and
Gulledge 2002). The fish mortality associated with blooms of Heterocapsa triquetra, on the other hand, appears to be due to oxygen depletion of the water when cells
decompose, rather than toxin production (Guiry and Guiry 2008). The cytotoxins
of Amphidinium gibbosum have been studied for their potent antitumor activities
(Bauer et al. 1995). Additional toxin-producing groups include the heterokonts and
the haptophytes. Some species of the diatom Pseudo-nitzschia (e.g. P. pseudodelicatissima), for example, produce domoic acid, a neurotoxin that may cause amnesic
shellfish poisoning (AMS) in humans when consuming contaminated molluscs.
The pelagophyte Aureococcus anophagefferens is thought to secrete a toxin into
its extracellular polysaccharide sheath. The haptophyte Prymnesium parvum produces prymnesin toxins, which are highly toxic to fish (La Claire 2006). Genomic
approaches such as EST sequencing are being used to study the organisms that cause
toxic algal blooms, with a major aim being to understand how and why toxins are
produced (http://genome.imb-jena.de/ESTTAL/cgi-bin/Index.pl).
6.4.5 Organism-Based Approaches for Exploring the Biology
of Planktonic Algae
The approaches discussed above are providing increasingly detailed information
about the organisms that are present in the plankton. By describing the ensemble
of genes present in the ecosystem (the metagenome), high-throughput sequencing
is also providing insights into the metabolic and cellular process that are going on
in these ecosystems. However, to really understand how these communities work it
is also necessary to have detailed information about the biology of the individual
species that they are composed of. Classical biological techniques, in particular isolation and study of individual strains of phytoplankton in culture, have, and still are,
making extremely important contributions to understanding phytoplankton biology
(Vaulot et al. 2008). In recent years, however, these techniques have been complemented by powerful new genomic approaches based on whole genome sequencing
and the establishment of model organisms.
Initially, genome sequencing was only applied to a very limited number of algae.
These were selected primarily based on their small genome sizes, although additional factors such as ecological relevance, phylogenetic position and availability of
axenic cultures and other biological characteristics, were also taken into account.
However, as sequencing technologies have improved, the number of algal genome