12
G.R. Carvalho et al.
Not all functional biodiversity studies require huge sequencing efforts. For example, a novel approach has seen a virus isolate-specific microarray used to probe for
the presence of genes in other natural virus isolates from the same family (Allen
et al. 2007). The application of this genome wide approach can actually provide
important information on the functional potential of an organism by identifying
regions or single genes that are diverse enough to avoid hybridization or conserved
enough to allow hybridization to occur. Providing sufficient information is available
about the genes under study, a brief overview can be gleaned on the potential of an
organism to perform specific metabolic functions and pathways.
1.2.2 Between the Microbes and Metazoans: Eukaryotic Protists
The functioning of marine ecosystems is based on organisms that belong to the
pico-, nano-, and micro- plankton. These three size fractions comprise bacteria and
eukaryotic protists, such as phytoplankton or heterotrophic protozoa. In contrast
to the important ecological role of microbes in the marine environment, in many
respects knowledge about their biodiversity is limited. Biodiversity assessment in
this group of species is challenged by various factors. First, the size of organisms,
particularly in the picoplankton fraction, renders microscopic observation and identification very difficult or even impossible. Eukaryotic marine picoplankton are a
group of species with limited information on biodiversity or ecology, but extremely
high ecological relevance. In open oceanic oligotrophic waters, picoplankton contribute up to 80% of the biomass and constitute an important prey for heterotrophic
nanoflagellates (Ishizaka et al. 1997, Caron et al. 1999). Diatoms are another example of ecologically important eukaryotic microbes with limited information on their
biodiversity and ecology. They account for at least 20% of the annual global carbon fixation by photosynthesis (Mann 1999). However, in this case species size
is not the limiting factor for biodiversity assessment, but rather an uncertainty of
the significance of small morphological variation among closely related species.
The identification of diatoms is challenged by limited morphological differentiation among closely related species and cryptic speciation is widespread among
cosmopolitan species (Evans et al. 2007, Medlin 2007). The consequence of cryptic
species is an underestimation of species numbers. However, species dimorphisms
can in turn lead to an overestimation of biodiversity. Dimorphic species occur in
different morphological appearances usually in different stages of a haplo-diploint
life cycle and have been misleadingly identified as different species. This phenomenon has been observed, for example, in the microalgal classes Cryptophyceae
(Hoef-Emden and Melkonian 2003) and Prymnesiophyceae (see review in Billard
1994).
1.2.2.1 Ribosomal Probes
The continually growing number of available algal 18S rDNA-sequences, as for
example, in the Ribosomal Database Project (RDP, Maidak et al. 2001), and in
G.R. Carvalho et al.
Not all functional biodiversity studies require huge sequencing efforts. For example, a novel approach has seen a virus isolate-specific microarray used to probe for
the presence of genes in other natural virus isolates from the same family (Allen
et al. 2007). The application of this genome wide approach can actually provide
important information on the functional potential of an organism by identifying
regions or single genes that are diverse enough to avoid hybridization or conserved
enough to allow hybridization to occur. Providing sufficient information is available
about the genes under study, a brief overview can be gleaned on the potential of an
organism to perform specific metabolic functions and pathways.
1.2.2 Between the Microbes and Metazoans: Eukaryotic Protists
The functioning of marine ecosystems is based on organisms that belong to the
pico-, nano-, and micro- plankton. These three size fractions comprise bacteria and
eukaryotic protists, such as phytoplankton or heterotrophic protozoa. In contrast
to the important ecological role of microbes in the marine environment, in many
respects knowledge about their biodiversity is limited. Biodiversity assessment in
this group of species is challenged by various factors. First, the size of organisms,
particularly in the picoplankton fraction, renders microscopic observation and identification very difficult or even impossible. Eukaryotic marine picoplankton are a
group of species with limited information on biodiversity or ecology, but extremely
high ecological relevance. In open oceanic oligotrophic waters, picoplankton contribute up to 80% of the biomass and constitute an important prey for heterotrophic
nanoflagellates (Ishizaka et al. 1997, Caron et al. 1999). Diatoms are another example of ecologically important eukaryotic microbes with limited information on their
biodiversity and ecology. They account for at least 20% of the annual global carbon fixation by photosynthesis (Mann 1999). However, in this case species size
is not the limiting factor for biodiversity assessment, but rather an uncertainty of
the significance of small morphological variation among closely related species.
The identification of diatoms is challenged by limited morphological differentiation among closely related species and cryptic speciation is widespread among
cosmopolitan species (Evans et al. 2007, Medlin 2007). The consequence of cryptic
species is an underestimation of species numbers. However, species dimorphisms
can in turn lead to an overestimation of biodiversity. Dimorphic species occur in
different morphological appearances usually in different stages of a haplo-diploint
life cycle and have been misleadingly identified as different species. This phenomenon has been observed, for example, in the microalgal classes Cryptophyceae
(Hoef-Emden and Melkonian 2003) and Prymnesiophyceae (see review in Billard
1994).
1.2.2.1 Ribosomal Probes
The continually growing number of available algal 18S rDNA-sequences, as for
example, in the Ribosomal Database Project (RDP, Maidak et al. 2001), and in