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microorganisms teem in most marine waters, and the genomes of even the simplest
among them encode for thousands of active biomolecules. The coalescent behavior
of these numerous variables is often limited to outward observations, measurements, and qualitative classifications: cell size, growth rate, fluorometry, and elemental contents. However, the complex, dynamic, and interacting molecular and
genetic parameters that give rise to emergent biological functions must be explicitly
considered in order to reach sufficient or predictive answers to many fundamental
questions. For example, certain species dominate others, depending on environmental factors. The cyanobacteria thrive in nutrient-limited pelagic waters (Zwirglmaier
et al. 2008), while the large eukaryotic phytoplankton tend to dominate in areas
abundant in macronutrients (de Vargas et al. 2015). But why is this? What combinations gene functions have critically coevolved into these divergently optimized
systems- level properties? Which emergent properties of their molecular systems
produce their respective advantages? What are the constraints and boundaries on
their niches and adaptabilities? What are the minimum molecular and genetic differences (among many) required to explain and account for the outward differences
between species? How have proliferative, competing, or cooperating species
coevolved or co-opted advantages to become successful in each other’s niches
through evolution, gene transfer, and symbiosis? What are the possibilities and
opportunities for this to continue and change in new and future environments?
The consideration of complex molecular, genetic, ecological, and environmental
data and models becomes necessary in order to accurately and scientifically answer
questions like these. The advent of efficient large-scale comprehensive molecular
data collection (genomics, transcriptomics, proteomics, metabolomics, etc.) now
offers broad and explicit information that can help to explicitly link genotype to
phenotype, phenotype to environment, species to ecosystems, and intra- and interspecies evolution to adaptation. The amount of new data available is immense and
is superseded in importance and opportunity only by a careful focus on biological
questions, well-conceived hypotheses, and measurements and experiments designed
to address them.
10.3 Marine Microalgal Genomics
The first comprehensive molecular data rapidly, efficiently, and completely collected for living systems were arguably the first microbial genomes (Fleischmann
et al. 1995; Fraser et al. 1995, 1997, 1998; Bult et al. 1996). The rapid, systematic
sequencing of genomes provided the first precise molecular descriptions of complete biological systems. Every functional biomolecule in the organism is encoded
or imprinted in its genome, as well as the hardcoded portion of the biological program that controls its physiology, metabolism, life cycle, responses to change,
potential for interactions with the extracellular environment, evolutionary history
and relationships, and heritable capacity to genetically evolve new functions, adaptations, and emergent properties. The whole genome of an organism is necessary
J. Ashworth
microorganisms teem in most marine waters, and the genomes of even the simplest
among them encode for thousands of active biomolecules. The coalescent behavior
of these numerous variables is often limited to outward observations, measurements, and qualitative classifications: cell size, growth rate, fluorometry, and elemental contents. However, the complex, dynamic, and interacting molecular and
genetic parameters that give rise to emergent biological functions must be explicitly
considered in order to reach sufficient or predictive answers to many fundamental
questions. For example, certain species dominate others, depending on environmental factors. The cyanobacteria thrive in nutrient-limited pelagic waters (Zwirglmaier
et al. 2008), while the large eukaryotic phytoplankton tend to dominate in areas
abundant in macronutrients (de Vargas et al. 2015). But why is this? What combinations gene functions have critically coevolved into these divergently optimized
systems- level properties? Which emergent properties of their molecular systems
produce their respective advantages? What are the constraints and boundaries on
their niches and adaptabilities? What are the minimum molecular and genetic differences (among many) required to explain and account for the outward differences
between species? How have proliferative, competing, or cooperating species
coevolved or co-opted advantages to become successful in each other’s niches
through evolution, gene transfer, and symbiosis? What are the possibilities and
opportunities for this to continue and change in new and future environments?
The consideration of complex molecular, genetic, ecological, and environmental
data and models becomes necessary in order to accurately and scientifically answer
questions like these. The advent of efficient large-scale comprehensive molecular
data collection (genomics, transcriptomics, proteomics, metabolomics, etc.) now
offers broad and explicit information that can help to explicitly link genotype to
phenotype, phenotype to environment, species to ecosystems, and intra- and interspecies evolution to adaptation. The amount of new data available is immense and
is superseded in importance and opportunity only by a careful focus on biological
questions, well-conceived hypotheses, and measurements and experiments designed
to address them.
10.3 Marine Microalgal Genomics
The first comprehensive molecular data rapidly, efficiently, and completely collected for living systems were arguably the first microbial genomes (Fleischmann
et al. 1995; Fraser et al. 1995, 1997, 1998; Bult et al. 1996). The rapid, systematic
sequencing of genomes provided the first precise molecular descriptions of complete biological systems. Every functional biomolecule in the organism is encoded
or imprinted in its genome, as well as the hardcoded portion of the biological program that controls its physiology, metabolism, life cycle, responses to change,
potential for interactions with the extracellular environment, evolutionary history
and relationships, and heritable capacity to genetically evolve new functions, adaptations, and emergent properties. The whole genome of an organism is necessary
J. Ashworth