231
flavobacteria (Polaribacter and Formosa) and gammaproteobacteria (SAR92)
which had expression profiles different to their predecessors. Thus in this study,
metaproteomics allowed the investigation of the protein expression profiles to
explain why different bacterioplankton taxa dominate across the progression of a
phytoplankton bloom.
The study by Saito et al. (2014) demonstrated a different approach using proteomics, that is, targeted quantification of specific proteins of interest that were
first identified using metaproteomics. This study explored how the cyanobacterium,
Prochlorococcus, deals with multiple nutrient limitations to dominate nutrient-poor
open ocean environments. Expression of targets identified from metaproteomes and
culture-based studies, namely, flavodoxin (IdiA), global nitrogen response regulator
(NtcA), nitrogen regulatory protein (P-II) and a urea transporter, was measured with
high taxonomic resolution. The change in expression of these targets at stations in
the Pacific Ocean was correlated with shifts in nutrient availability and involved
increased expression of IdiA in regions of reduced iron availability and high expression of P-II in low-nitrogen regions. Thus using both targeted and non-targeted proteomic approaches, the influence of nutrient availability on specific taxa and the
strategy adopted to tolerate nutrient limitations were explored.
11.5 Conclusion
Cultivation-independent ‘omic’ approaches have increased our understanding of the
planet’s most abundant organisms and their roles in the ocean. The application of
genomic, transcriptomic and proteomic approaches to natural communities and
microbial isolates have revealed previously undescribed microorganisms, new
genes, and novel metabolic pathways. We now know that microscopic marine
microbes are the most evolutionarily diverse organisms in the biosphere, are responsible for ~50% of global primary production (Field et al. 1998) and influence the
Earth’s climate by driving global biogeochemical cycles (Falkowski et al. 2008).
These studies illustrate the immense potential that ‘omic approaches have in understanding microbial communities beyond just the presence of species and their functional potential. By studying organisms at the gene expression level, we can begin
to decipher how taxa adjust their molecular and physiological machinery to take
advantage of changing environmental conditions and in turn shape microbial community structure, which ultimately determines ecosystem function. However, there
is still much to learn about the responses of microbes to oceanographic processes,
including the relative impact of physico-chemical changes in growth conditions versus biological interactions.
Acknowledgements We thank Justin Seymour, University of Technology Sydney and Martin
Ostrowski, Macquarie University, for useful discussions and feedback, which greatly improved the
content. This work was supported by the Climate Change Cluster, University of Technology
Sydney and the Australian Research Council Discovery Scheme (DP14010134) to MD.
11 Application of ‘Omics’ Approaches to Microbial Oceanography
flavobacteria (Polaribacter and Formosa) and gammaproteobacteria (SAR92)
which had expression profiles different to their predecessors. Thus in this study,
metaproteomics allowed the investigation of the protein expression profiles to
explain why different bacterioplankton taxa dominate across the progression of a
phytoplankton bloom.
The study by Saito et al. (2014) demonstrated a different approach using proteomics, that is, targeted quantification of specific proteins of interest that were
first identified using metaproteomics. This study explored how the cyanobacterium,
Prochlorococcus, deals with multiple nutrient limitations to dominate nutrient-poor
open ocean environments. Expression of targets identified from metaproteomes and
culture-based studies, namely, flavodoxin (IdiA), global nitrogen response regulator
(NtcA), nitrogen regulatory protein (P-II) and a urea transporter, was measured with
high taxonomic resolution. The change in expression of these targets at stations in
the Pacific Ocean was correlated with shifts in nutrient availability and involved
increased expression of IdiA in regions of reduced iron availability and high expression of P-II in low-nitrogen regions. Thus using both targeted and non-targeted proteomic approaches, the influence of nutrient availability on specific taxa and the
strategy adopted to tolerate nutrient limitations were explored.
11.5 Conclusion
Cultivation-independent ‘omic’ approaches have increased our understanding of the
planet’s most abundant organisms and their roles in the ocean. The application of
genomic, transcriptomic and proteomic approaches to natural communities and
microbial isolates have revealed previously undescribed microorganisms, new
genes, and novel metabolic pathways. We now know that microscopic marine
microbes are the most evolutionarily diverse organisms in the biosphere, are responsible for ~50% of global primary production (Field et al. 1998) and influence the
Earth’s climate by driving global biogeochemical cycles (Falkowski et al. 2008).
These studies illustrate the immense potential that ‘omic approaches have in understanding microbial communities beyond just the presence of species and their functional potential. By studying organisms at the gene expression level, we can begin
to decipher how taxa adjust their molecular and physiological machinery to take
advantage of changing environmental conditions and in turn shape microbial community structure, which ultimately determines ecosystem function. However, there
is still much to learn about the responses of microbes to oceanographic processes,
including the relative impact of physico-chemical changes in growth conditions versus biological interactions.
Acknowledgements We thank Justin Seymour, University of Technology Sydney and Martin
Ostrowski, Macquarie University, for useful discussions and feedback, which greatly improved the
content. This work was supported by the Climate Change Cluster, University of Technology
Sydney and the Australian Research Council Discovery Scheme (DP14010134) to MD.
11 Application of ‘Omics’ Approaches to Microbial Oceanography