223
© Springer International Publishing AG 2017
M. Kumar, P. Ralph (eds.), Systems Biology of Marine Ecosystems,
DOI 10.1007/978-3-319-62094-7_11
Chapter 11
Application of ‘Omics’ Approaches
to Microbial Oceanography
Deepa R. Varkey and Martina A. Doblin
Abstract Viruses, bacteria, archaea and single celled eukaryotes, collectively
known as microbes, dominate the biomass and metabolism of ocean ecosystems.
Marine microbes are highly abundant and critical to human survival, but the vast
majority of taxa have not yet been cultured. The use of environmental nucleic acid
sequencing as a cultivation-independent approach to microbial oceanography has
therefore significantly expanded our understanding of the diversity, evolution, biogeography and important biogeochemical roles of marine microorganisms. Here we
provide illustrative examples of how genomic, transcriptomic and proteomic
approaches have been applied to marine microbes to advance our understanding of
their ecology. A remaining challenge is the need to link phenotypes to their environment, requiring a better understanding of genomic features that influence transcription (e.g. promoters and methylation) as well as post-translational modifications,
and how such regulatory processes are impacted by extracellular abiotic and biotic
processes. In addition, the expansion of available protein and taxonomic databases
will greatly increase our capacity to link microbial function to specific taxa.
Keywords Marine microbes • Microbial function • Genomics • Proteomics •
Transcriptomics
D.R. Varkey • M.A. Doblin (*)
Climate Change Cluster, University of Technology Sydney,
PO Box 123 Broadway, Sydney, NSW 2007, Australia
e-mail: martina.doblin@uts.edu.au
Contents
11.1 Introduction .................................................................................................................... 224
11.2 Influence of Oceanographic Processes on Microbial Distribution and Diversity .......... 224
11.3 Influence of Oceanographic Processes on Microbial Gene Expression ......................... 227
11.4 Influence of Oceanographic Processes on Microbial Protein Expression ..................... 229
11.5 Conclusion ..................................................................................................................... 231
References ................................................................................................................................. 232
© Springer International Publishing AG 2017
M. Kumar, P. Ralph (eds.), Systems Biology of Marine Ecosystems,
DOI 10.1007/978-3-319-62094-7_11
Chapter 11
Application of ‘Omics’ Approaches
to Microbial Oceanography
Deepa R. Varkey and Martina A. Doblin
Abstract Viruses, bacteria, archaea and single celled eukaryotes, collectively
known as microbes, dominate the biomass and metabolism of ocean ecosystems.
Marine microbes are highly abundant and critical to human survival, but the vast
majority of taxa have not yet been cultured. The use of environmental nucleic acid
sequencing as a cultivation-independent approach to microbial oceanography has
therefore significantly expanded our understanding of the diversity, evolution, biogeography and important biogeochemical roles of marine microorganisms. Here we
provide illustrative examples of how genomic, transcriptomic and proteomic
approaches have been applied to marine microbes to advance our understanding of
their ecology. A remaining challenge is the need to link phenotypes to their environment, requiring a better understanding of genomic features that influence transcription (e.g. promoters and methylation) as well as post-translational modifications,
and how such regulatory processes are impacted by extracellular abiotic and biotic
processes. In addition, the expansion of available protein and taxonomic databases
will greatly increase our capacity to link microbial function to specific taxa.
Keywords Marine microbes • Microbial function • Genomics • Proteomics •
Transcriptomics
D.R. Varkey • M.A. Doblin (*)
Climate Change Cluster, University of Technology Sydney,
PO Box 123 Broadway, Sydney, NSW 2007, Australia
e-mail: martina.doblin@uts.edu.au
Contents
11.1 Introduction .................................................................................................................... 224
11.2 Influence of Oceanographic Processes on Microbial Distribution and Diversity .......... 224
11.3 Influence of Oceanographic Processes on Microbial Gene Expression ......................... 227
11.4 Influence of Oceanographic Processes on Microbial Protein Expression ..................... 229
11.5 Conclusion ..................................................................................................................... 231
References ................................................................................................................................. 232