214
marine microeukaryotes (Keeling et al. 2014), resulting in an atlas of transcribed
and functional coding sequences of unprecedented comparative breadth and depth
against which to integrate and contextualize individual new studies conducted in the
laboratory and in the field.
Metatranscriptomic mRNA sequencing studies, or those conducted on samples
collected in natural marine systems, are beginning to produce a deep and unprecedented richness of functional eukaryotic coding sequences operating in wild environments. The transcriptomic complexity and response of a wild phytoplankton
community during iron supplementation experiments at sea revealed a rapid and
iron-specific response encoded in native organisms that are evolutionarily and adaptively primed to cope with and take advantage of fluctuating iron levels in the North
Pacific Ocean (Marchetti et al. 2012), confirming and expanding upon observations
from related laboratory experiments. Environmentally responsive biological programs can be identified within these large data sets that help to explain acclimation
and evolved survival mechanisms in unpredecented precision and detail (Marchetti
et al. 2017). Meanwhile, in the Atlantic Ocean, transcriptomics are being used to
more deeply observe and understand the intracellular behaviors and responses of
phytoplankton with respect to nutrient conditions (Alexander et al. 2015). The ability to track detailed and specific intracellular programs in the natural environment
provides an opportunity to deeply understand what native cellular communities are
really doing as they occupy and experience different marine environments, and this
may soon be broadly automated to study and predict the dynamics of communities
in situ (Ottesen et al. 2013, 2014; Aylward et al. 2015).
10.5 Proteomics and Metabolomics
The majority of unique functional biomolecules in marine systems are proteins, and
the majority of the remainder are metabolites and the products of enzymes. It would
be deeply informative to know the identity and quantity of all proteins, metabolites,
and biomaterials present in a cell or sample from the ecosystem—this could be used
to model and predict metabolic flux—and would be more closely representative of
true physiology and activity than transcript levels, from which the levels and functions of posttranscriptional, posttranslational, and metabolic products may importantly diverge.
Proteins are more complex polymers than nucleic acids, are complicated to
uniquely separate and identify, and cannot be amplified; unfortunately, unlike for
DNA and RNA, there is no simple way to simply sequence or quantify complex
pools of proteins. Proteomic technologies based on peptide generation, automated
multidimensional separation, and mass spectrometry are now able to finely sample
and detect thousands of different peptides at high resolution, resulting in successful,
albeit noncomprehensive proteomic analyses of microalgae in response to changing
conditions (Nunn et al. 2009; Dyhrman et al. 2012; Nunn et al. 2013).
J. Ashworth
marine microeukaryotes (Keeling et al. 2014), resulting in an atlas of transcribed
and functional coding sequences of unprecedented comparative breadth and depth
against which to integrate and contextualize individual new studies conducted in the
laboratory and in the field.
Metatranscriptomic mRNA sequencing studies, or those conducted on samples
collected in natural marine systems, are beginning to produce a deep and unprecedented richness of functional eukaryotic coding sequences operating in wild environments. The transcriptomic complexity and response of a wild phytoplankton
community during iron supplementation experiments at sea revealed a rapid and
iron-specific response encoded in native organisms that are evolutionarily and adaptively primed to cope with and take advantage of fluctuating iron levels in the North
Pacific Ocean (Marchetti et al. 2012), confirming and expanding upon observations
from related laboratory experiments. Environmentally responsive biological programs can be identified within these large data sets that help to explain acclimation
and evolved survival mechanisms in unpredecented precision and detail (Marchetti
et al. 2017). Meanwhile, in the Atlantic Ocean, transcriptomics are being used to
more deeply observe and understand the intracellular behaviors and responses of
phytoplankton with respect to nutrient conditions (Alexander et al. 2015). The ability to track detailed and specific intracellular programs in the natural environment
provides an opportunity to deeply understand what native cellular communities are
really doing as they occupy and experience different marine environments, and this
may soon be broadly automated to study and predict the dynamics of communities
in situ (Ottesen et al. 2013, 2014; Aylward et al. 2015).
10.5 Proteomics and Metabolomics
The majority of unique functional biomolecules in marine systems are proteins, and
the majority of the remainder are metabolites and the products of enzymes. It would
be deeply informative to know the identity and quantity of all proteins, metabolites,
and biomaterials present in a cell or sample from the ecosystem—this could be used
to model and predict metabolic flux—and would be more closely representative of
true physiology and activity than transcript levels, from which the levels and functions of posttranscriptional, posttranslational, and metabolic products may importantly diverge.
Proteins are more complex polymers than nucleic acids, are complicated to
uniquely separate and identify, and cannot be amplified; unfortunately, unlike for
DNA and RNA, there is no simple way to simply sequence or quantify complex
pools of proteins. Proteomic technologies based on peptide generation, automated
multidimensional separation, and mass spectrometry are now able to finely sample
and detect thousands of different peptides at high resolution, resulting in successful,
albeit noncomprehensive proteomic analyses of microalgae in response to changing
conditions (Nunn et al. 2009; Dyhrman et al. 2012; Nunn et al. 2013).
J. Ashworth