233
Moon-van der Staay SY, van der Staay GW, Guillou L et al (2000) Abundance and diversity of
prymnesiophytes in the picoplankton community from the equatorial Pacific Ocean inferred
from 18S rDNA sequences. Limnol Oceanogr 45:98–109
Morris RM, Nunn BL, Frazar C et al (2010) Comparative metaproteomics reveals ocean-scale
shifts in microbial nutrient utilization and energy transduction. ISME J 4:673–685
Pace NR, Olsen GJ, Woese CR (1986) Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell 45:325–326
Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol
57:369–394
Saito MA, McIlvin MR, Moran DM et al (2014) Multiple nutrient stresses at intersecting Pacific
Ocean biomes detected by protein biomarkers. Science 345:1173–1177
Santoferrara LF, Grattepanche JD, Katz LA et al (2014) Pyrosequencing for assessing diversity
of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with
traditional methods. Environ Microbiol 16:2752–2763
Sharpton TJ (2014) An introduction to the analysis of shotgun metagenomic data. Front Plant Sci
5:209
Shi Y, Tyson GW, Eppley JM et al (2011) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J 5:999–1013
Sowell SM, Abraham PE, Shah M et al (2011) Environmental proteomics of microbial plankton in
a highly productive coastal upwelling system. ISME J 5:856–865
Sowell SM, Wilhelm LJ, Norbeck AD et al (2009) Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J 3:93–105
Teeling H, Fuchs BM, Becher D et al (2012) Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336:608–611
Thomas T, Gilbert J, Meyer F (2012) Metagenomics—a guide from sampling to data analysis.
Microb Inform Exp 2:3
Treusch AH, Vergin KL, Finlay LA et al (2009) Seasonality and vertical structure of microbial
communities in an ocean gyre. ISME J 3:1148–1163
Villar E, Farrant GK, Follows M et al (2015) Environmental characteristics of Agulhas rings affect
interocean plankton transport. Science 348:1261447
Wang D-Z, Xie Z-X, Zhang S-F (2014) Marine metaproteomics: current status and future directions. J Proteome 97:27–35
Williams TJ, Cavicchioli R (2014) Marine metaproteomics: deciphering the microbial metabolic
food web. Trends Microbiol 22:248–260
Zehr J, Turner P (2001) Nitrogen fixation: nitrogenase genes and gene expression. Method
Microbiol 30:271–286
Zielinski BL, Allen AE, Carpenter EJ et al (2016) Patterns of transcript abundance of eukaryotic
biogeochemically-relevant genes in the amazon river plume. PLoS One 11:e0160929
Zinger L, Gobet A, Pommier T (2012) Two decades of describing the unseen majority of aquatic
microbial diversity. Mol Ecol 21:1878–1896
11 Application of ‘Omics’ Approaches to Microbial Oceanography
Moon-van der Staay SY, van der Staay GW, Guillou L et al (2000) Abundance and diversity of
prymnesiophytes in the picoplankton community from the equatorial Pacific Ocean inferred
from 18S rDNA sequences. Limnol Oceanogr 45:98–109
Morris RM, Nunn BL, Frazar C et al (2010) Comparative metaproteomics reveals ocean-scale
shifts in microbial nutrient utilization and energy transduction. ISME J 4:673–685
Pace NR, Olsen GJ, Woese CR (1986) Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell 45:325–326
Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol
57:369–394
Saito MA, McIlvin MR, Moran DM et al (2014) Multiple nutrient stresses at intersecting Pacific
Ocean biomes detected by protein biomarkers. Science 345:1173–1177
Santoferrara LF, Grattepanche JD, Katz LA et al (2014) Pyrosequencing for assessing diversity
of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with
traditional methods. Environ Microbiol 16:2752–2763
Sharpton TJ (2014) An introduction to the analysis of shotgun metagenomic data. Front Plant Sci
5:209
Shi Y, Tyson GW, Eppley JM et al (2011) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J 5:999–1013
Sowell SM, Abraham PE, Shah M et al (2011) Environmental proteomics of microbial plankton in
a highly productive coastal upwelling system. ISME J 5:856–865
Sowell SM, Wilhelm LJ, Norbeck AD et al (2009) Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J 3:93–105
Teeling H, Fuchs BM, Becher D et al (2012) Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336:608–611
Thomas T, Gilbert J, Meyer F (2012) Metagenomics—a guide from sampling to data analysis.
Microb Inform Exp 2:3
Treusch AH, Vergin KL, Finlay LA et al (2009) Seasonality and vertical structure of microbial
communities in an ocean gyre. ISME J 3:1148–1163
Villar E, Farrant GK, Follows M et al (2015) Environmental characteristics of Agulhas rings affect
interocean plankton transport. Science 348:1261447
Wang D-Z, Xie Z-X, Zhang S-F (2014) Marine metaproteomics: current status and future directions. J Proteome 97:27–35
Williams TJ, Cavicchioli R (2014) Marine metaproteomics: deciphering the microbial metabolic
food web. Trends Microbiol 22:248–260
Zehr J, Turner P (2001) Nitrogen fixation: nitrogenase genes and gene expression. Method
Microbiol 30:271–286
Zielinski BL, Allen AE, Carpenter EJ et al (2016) Patterns of transcript abundance of eukaryotic
biogeochemically-relevant genes in the amazon river plume. PLoS One 11:e0160929
Zinger L, Gobet A, Pommier T (2012) Two decades of describing the unseen majority of aquatic
microbial diversity. Mol Ecol 21:1878–1896
11 Application of ‘Omics’ Approaches to Microbial Oceanography