Response of Emiliania huxleyi to a high CO2 world: assessing the extent of genetic diversity in the pattern of gene expression

Lead Research Organisation: University of Essex
Department Name: Biological Sciences


Emiliania huxleyi is a fast growing 'coccolithophorid' phytoplankton species that forms calcium carbonate (CaCO3) plates on the outside of its cells. In the modern ocean, E. huxleyi is one of the most abundant 'bloom forming' phytoplankton species and consequently plays a major role in removal (export) of both carbon and alkalinity from surface waters. Substantial laboratory research has previously examined how environmental factors, such as light, temperature and nutrients, interact to affect the growth and calcification of E. huxleyi. However, the major factor that is critical to the balance between growth and calcification for E. huxleyi is the pH of seawater. With this in mind, global attention has focused upon how E. huxleyi will respond to the decrease in ocean pH (ocean acidification) that has been predicted as a result of elevated atmospheric CO2 concentrations. Recent research has demonstrated that an increase in atmospheric CO2 directly reduces calcification by E. huxleyi; in turn, the efficiency with which this organism can export material from the surface ocean will likely decrease. Despite such progress, the last report of the Intergovernmental Panel on Climate Change highlighted that 'the impact of ocean acidification on marine biota especially for organisms achieving bio-calcification remains a key uncertainty'. Of major concern is that the species of E. huxleyi is comprised of an 'untold number' of genetic variants and independent experiments (including CO2 perturbations) do not always examine environmentally-driven characteristics for the same variant. Results from our laboratory support this statement: two variants exhibited very different modes of acclimation to perturbations of light and CO2 conditions for growth. Changes in gene expression are the bases by which these organisms appear to respond to environmental change, a fact that has led to suggestions that genomics and transcriptomics should be applied to increase our knowledge of ocean biogeochemistry. However, a huge conceptual gap still exists between molecular genetics and biogeochemistry: geochemists need generalisations that can be applied to the entire ocean over long time periods; biologists focus on what makes an organism unique. Key to bridging the current gap between molecular biology and biogeochemistry is to examine the extent with which variability in gene expression is due to genetic differences amongst isolates versus general responses to environmental forcing. This study builds immediately upon previous NERC grants held by the investigators by addressing how gene expression responds to changes of ocean pH for genetic variants of E. huxleyi. We propose a programme of collaborative research involving the University of Essex and Marine Biological Association of the UK under the SOFI call 'Coccolithophore gene expression profiles in chemostat culture and microarray analysis' (WP 2.8, 2.9) within priority topic area marine biogeochemical cycles. 'pH-stat' technology developed in our laboratory will be used to grow four E. huxleyi genetic variants at two pH conditions (present day versus that predicted beyond the year 2100). Microarray-based molecular signals in response to the different pH conditions within and between variants will be compared but also analysed alongside physiological signals (photosynthesis and calcificiation). Work proposed here will establish a core link between two research centers with an excellent track record investigating E. huxleyi biology, the University of Essex and the UK's Marine Biological Association, which is an Ocean 2025 Centre.


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Description In addressing our overall goal "to identify common molecular (and physiological) responses of Emiliania huxleyi to elevated CO2 conditions" we have produced substantial achievements and outcomes far beyond our originally proposed expectation:
1. Using state of the art pH-stat technology, 3 genetic strains of E. huxleyi (Ch25, CCMP1516, and NZEH) were grown under present day and (at least one) future CO2/pH condition. One strain (CCMP1516) was also additionally grown under simultaneous CO2 and nitrate manipulations. Under elevated CO2, Strain Ch25 and CCMP1516 exhibit a calcification (decreased) but not a growth response whereas NZEH exhibited a growth (increased) but not a calcification response under elevated CO2. We employed specialized techniques (e.g. active fluorescence and membrane inlet mass spectrometry) to identify underlying physiological mechanisms and in part explain these strain-specific productivity and growth responses to elevated CO2. Opportunistic trace gas measurements (DMS-DMSP) also identified strain-specific differences to altered CO2. We finally collected a set of samples from strain NZEH for future proteomic expression analyses to compliment this genomic work by identifying operation of more complex physiological processes.
2. Two-colour tiling arrays (TA) from two of the strains (Ch25 and CCMP1516) from across the cell growth cycle(s) has thus far enabled us to identify ca. 20000 transcribed regions; after mapping to the E. huxleyi genome, these correspond to ca. 15000 genes expressed with identification of new sequences not previously annotated. Our list of genes and active regions are currently being analysed against the EST data set provided by collaborators JGI/Betsy Reid
3. A cutting edge Solexa tag-based approach (454-pyrosequencing) run in parallel with TA for a set of CCMP1516 samples yielded expression of only 3 459 genes (98.6% of those were also found using TA indicating that while both techniques correlate well); therefore, we fundamentally identified, via this additional proof of concept study, that TA was more applicable for E. huxleyi transcriptome studies than the potentially more novel Solexa approach.
Exploitation Route We have made substantial advances in understanding the nature and extent with which genetic variants of a single key species (Emiliania huxleyi) respond to predicted "ocean acidification" (OA, lowered ocean pH) conditions; such data is proving fundamental for trait-based (population) approaches to examine biogeochemical responses to environmental change. Successful growth of these strains has encouraged other researchers interested in OA to adopt the same practice (and be extremely mindful of the 'choice' of strain used for experimentation). Of particular benefit is our development and optimization of molecular approaches for E. huxleyi, which will be central to the growing number of systems-based studies focusing on this species. Such advances are extremely timely given significant recent directed funding by NERC, NSF and the EU into OA. Funded projects within these calls have a continued focus on phytoplankton including E. huxleyi. Research here and elsewhere (e.g. NE/G003688/1) is examining wider 'omic' responses, including proetomics and metabolomics, to environmental regulation of growth and productivity (including resource allocation) of E. huxleyi as a model organism. We therefore have no doubt that our outputs are currently, and will continue to be, of benefit to the wider international research community. Such immediate benefits are in fact already underway as a result of funding to the PI (Suggett) and project partners (Schroeder and Brownlee) though the NERC funded consortium "Ocean Acidification Impacts on Sea-Surface Biology, Biogeochemistry and Climate" (NE/H017062/1), that specifically examine strain specific selection (and associated impacts) BY OA within coccolithophore (E. huxleyi) populations. Thus new funding streams combined with continuing analysis of the molecular data sets generated here ensure significant longer-term impact of this research.
Sectors Environment

Description We have met our objectives (as well as capitalized on additional opportunities to collect novel data, e.g. trace gas production and proteomic expression from the E. huxleyi cultures); importantly, the extremely large molecular data sets, required to address our remaining objectives, are still being analysed enabling us to further deliver additional objectives in the longer term. Our novel outcomes have so far been reported via academic conference presentations (8), and currently in preparation for peer review journal publication (3); also, as magazine articles (1), live television interviews (1) and public science talks (2).
First Year Of Impact 2009
Sector Environment
Impact Types Societal