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underpinning community dynamics and structure. Below we provide some illustrative examples of how these approaches have been used to characterise the responses
of marine microbial communities to different oceanographic processes. Given that
many oceanographic phenomena cause local and regional changes in resources for
growth, many of these transcriptomic studies have explored responses to different
nutrient conditions.
In a laboratory study, Mock et al. (2008) grew the widely distributed marine
eukaryote Thalassiosira pseudonana axenically (clone CCMP 1335 for which the
whole-genome sequence is available) to examine its transcriptome in response to
different growth environments. Whole-genome expression profiling of this species
revealed a set of 75 genes specifically upregulated during silicon limitation but not
under low concentrations of nitrogen or iron, alkaline pH, or low temperatures
(Mock et al. 2008). This study also found unexpectedly tight coupling of pathways
initiated by iron (Fe) and silicon (Si) bioavailability (84 common genes upregulated
by both Fe and Si limitation but no other treatments), suggesting that the in situ iron/
silicon nutritional status of diatoms could be detected using molecular indicators,
thereby enhancing our understanding of these important nutritional controls on diatom productivity.
Shi et al. (2011) compared the diversity and metabolic activity of a bacterioplankton community at discrete depths in a stratified water column using a metatranscriptomic approach. Comparison of the DNA and cDNA libraries suggested
differential relative transcriptional activities per cell and revealed a transcriptionally
active but less abundant Prochlorococcus population in the bottom of the photic
zone. The metatranscriptomic dataset sheds light on the genes that were required to
maintain function at different depths such as the high expression of oxidative stressassociated genes at the surface, carbon fixation and photosynthetic genes at DCM
and ammonium assimilation genes at mesopelagic region (500 m depth). Functional
information was used to associate individual taxa to biogeochemical processes
including the role of Roseobacter in aerobic anoxygenic phototrophy (expression of
proteorhodopsin) and Crenarchaeota in ammonia oxidation (expression of ammonium transporters and ammonium monooxygenase subunits). The study also highlighted the adjustment of gene expression based on nutrient availability and
requirement, i.e. distinct profiles of transporters such as ABC-transporters, Na+/
solute symporters and tripartite ATP-independent periplasmic transporters expressed
by Pelagibacter populations at different depths (Shi et al. 2011).
To explore the role of iron in a natural phytoplankton community, Marchetti
et al. (2012) undertook a microcosm experiment investigating the differential gene
expression under conditions of iron limitation versus iron enrichment. Iron enrichment resulted in a community shift from small picophytoplankton to larger eukaryotic phytoplankton, mainly diatoms, haptophytes and chlorophytes, but there was
also a distinct difference in expression within the three dominant phytoplankton
groups. Under iron amendment, diatoms increased expression of genes involved in
photosynthesis, N assimilation and carbohydrate storage, whilst haptophytes
upregulated iron-containing proteins for light harvesting and photosynthesis with
no change in nitrate assimilation genes. Notably, under iron-replete conditions,
D.R. Varkey and M.A. Doblin
underpinning community dynamics and structure. Below we provide some illustrative examples of how these approaches have been used to characterise the responses
of marine microbial communities to different oceanographic processes. Given that
many oceanographic phenomena cause local and regional changes in resources for
growth, many of these transcriptomic studies have explored responses to different
nutrient conditions.
In a laboratory study, Mock et al. (2008) grew the widely distributed marine
eukaryote Thalassiosira pseudonana axenically (clone CCMP 1335 for which the
whole-genome sequence is available) to examine its transcriptome in response to
different growth environments. Whole-genome expression profiling of this species
revealed a set of 75 genes specifically upregulated during silicon limitation but not
under low concentrations of nitrogen or iron, alkaline pH, or low temperatures
(Mock et al. 2008). This study also found unexpectedly tight coupling of pathways
initiated by iron (Fe) and silicon (Si) bioavailability (84 common genes upregulated
by both Fe and Si limitation but no other treatments), suggesting that the in situ iron/
silicon nutritional status of diatoms could be detected using molecular indicators,
thereby enhancing our understanding of these important nutritional controls on diatom productivity.
Shi et al. (2011) compared the diversity and metabolic activity of a bacterioplankton community at discrete depths in a stratified water column using a metatranscriptomic approach. Comparison of the DNA and cDNA libraries suggested
differential relative transcriptional activities per cell and revealed a transcriptionally
active but less abundant Prochlorococcus population in the bottom of the photic
zone. The metatranscriptomic dataset sheds light on the genes that were required to
maintain function at different depths such as the high expression of oxidative stressassociated genes at the surface, carbon fixation and photosynthetic genes at DCM
and ammonium assimilation genes at mesopelagic region (500 m depth). Functional
information was used to associate individual taxa to biogeochemical processes
including the role of Roseobacter in aerobic anoxygenic phototrophy (expression of
proteorhodopsin) and Crenarchaeota in ammonia oxidation (expression of ammonium transporters and ammonium monooxygenase subunits). The study also highlighted the adjustment of gene expression based on nutrient availability and
requirement, i.e. distinct profiles of transporters such as ABC-transporters, Na+/
solute symporters and tripartite ATP-independent periplasmic transporters expressed
by Pelagibacter populations at different depths (Shi et al. 2011).
To explore the role of iron in a natural phytoplankton community, Marchetti
et al. (2012) undertook a microcosm experiment investigating the differential gene
expression under conditions of iron limitation versus iron enrichment. Iron enrichment resulted in a community shift from small picophytoplankton to larger eukaryotic phytoplankton, mainly diatoms, haptophytes and chlorophytes, but there was
also a distinct difference in expression within the three dominant phytoplankton
groups. Under iron amendment, diatoms increased expression of genes involved in
photosynthesis, N assimilation and carbohydrate storage, whilst haptophytes
upregulated iron-containing proteins for light harvesting and photosynthesis with
no change in nitrate assimilation genes. Notably, under iron-replete conditions,
D.R. Varkey and M.A. Doblin