IAP-24-068

Telling the time in turbulent oceans: How do phytoplankton use clocks and carbon to survive deep mixing?

Phytoplankton are the main primary producers underpinning ocean ecosystems and contribute as much to global carbon fixation as terrestrial plants. Some of this carbon becomes locked away in the ocean’s interior and deep-sea sediments, helping mitigate climate change. Although photosynthetic, the most important ocean phytoplankton are not related to higher plants and green algae but belong to a diverse range of taxonomic groups across the Eukaryotic tree of life, including the diatoms, dinoflagellates, haptophytes and cryptophytes. These understudied groups have unique cellular and physiological adaptations, and fascinating evolutionary histories that we are only just beginning to understand.

Photosynthetic organisms often use an internal biological timer called a circadian clock to anticipate changes in the light environment and optimise their metabolism. For example, higher plants grown in conditions where their internal clock wrongly anticipates the external light environment, they display reduced fitness, largely due to mis-regulation of carbon reserve use at night.

Phytoplankton are subject to the same day-night cycles as terrestrial plants, but in in addition may be plunged into very low light or darkness for periods of hours, days, or even weeks when they are mixed into deeper ocean waters. Some diatoms, dinoflagellates and haptophytes have been shown to survive for many days or weeks in the dark in vegetative states, using carbohydrates, lipid stores and perhaps phagotrophy to survive, rapidly regaining photosynthetic capacity on re-illumination. Several phytoplankton species can additionally enter a resting phase, in which they can survive in a dormant state for weeks, months, or hundreds of years. Studies of how phytoplankton respond to deep mixing events are rare. However, the limited evidence suggests that mixing events strongly control phytoplankton growth and there is considerable inter-taxa variation in their ability to survive and recover on re-illumination.

Short time-scale turbulent mixing is driven by wind speed and wave height, which have been increasing as climate change progresses. In addition, the mixed layer depth of the oceans shows an deepening trend over recent decades. Thus, to understand how the phytoplankton are going to respond to climate change, we need to know more about their capacity to survive and thrive in different mixing regimes and the cellular mechanisms that underpin these traits. The knowledge gained may also help us understand how phytoplankton survive the winter or polar night, and even shed light on events in the distant past, such as the survival of certain plankton groups in the prolonged darkness of the end Cretaceous mass extinction event.

This project will systematically investigate the cellular physiology of deep mixing in several phytoplankton groups, with a focus on how carbon and nutrient reserves are used to aid survival, and the role of the circadian clock in regulating the use of these reserves. Dark survival on different time scales and recovery of growth on reillumination will be measured. This will be linked to the following traits to understand the cellular basis of the differences found:

i) The coupling between the circadian clock and physiological processes
ii) The light-compensation and saturation points of photosynthesis
iii) The extent of phagocytosis or osmotrophy for carbon and nutrient acquisition
iv) Dark respiration rates
v) Types of carbon storage reserves and their patterns of use
vi) Differentiation to dormant cell types
vii) Phycosphere microbiome composition

The results from the physiological studies will be used to plan transcriptomic experiments for key species and timepoints, and the data analysed to identify genes diagnostic of particular physiological states.

Ocean water samples from different mixing regimes will be obtained from colleagues taking part in research cruises, and there may be opportunities for the student to participate in research cruises in the Atlantic or further afield. The expression of genes identified through lab transcriptomic experiments will be interrogated by qPCR, to see if the processes identified in the lab apply in the open ocean.

The state-of-the-art controlled environment facilities at the University of Stirling will be used to simulate deep-mixing events and the student will become skilled in algal culture. The student will use oxygen electrodes and fluorometry to measure respiration and photosynthetic parameters such as the light compensation point of photosynthesis, delayed chlorophyll fluorescence and non-photochemical quenching. The latter two parameters are generally under circadian clock control, and will be used to assess the strength of coupling between the internal circadian timer and physiological processes. Phagotrophy will be assessed by assaying the uptake of fluorescent beads and fluorescently labelled bacteria. Biochemical assays for carbon stores such as beta-glucans and lipids will allow the student to assess how carbon stores are used in prolonged darkness. Light and electron microscopy will be employed to study how cell morphology changes during darkness, while next generation sequencing will be used to examine changes in the phytoplankton-associated microbiome. Transcriptomics will be employed to identify marker genes for key physiological states and the expression of these genes will be studied by qPCR in samples from research cruises, collected across different mixing regimes. We will apply for funding for the student to participate in sample collection on a cruise, but otherwise samples will be provided by colleagues working on these cruises.

Year 1

The project will start with training in the essential skills: algal culture, measuring algal growth, light microscopy, SEM, and the use of apparatus to measure gas exchange. The PhD student will also conduct a literature review and carry out project planning in this period. They will meet all the project partners and become familiar with the scientific drivers and practical constraints of the project and choose a panel of relevant phytoplankton species for experimentation. Subsequently the PhD scholar will begin experiments examining the limits of dark survival and recovery in a variety of phytoplankton, while gaining familiarity with the range of methods necessary to tackle the project.

Year 2

The focus of year 2 will be data collection in the lab. Having already gained competence in the methods to measure the key traits of interest, and optimised these where necessary, the student will apply the methods to the panel of phytoplankton species over a set of standardised deep mixing simulations.

During year 2 or year 3 there may be opportunities to participate in a research cruise. Preparation, the cruise and sample processing would be expected to take around 6 months.

Year 3

The results from the physiological experiments will be used to plan transcriptomic experiments for key species and timepoints, and the data analysed to identify genes diagnostic of particular physiological states. These expression of these genes in environmental samples from diverse mixing regimes will be interrogated by qPCR, to see if the processes identified in the lab apply in the open ocean.

Year 3.5

The last six months will be dedicated to finalising data analyses, writing manuscripts and writing the PhD thesis. In year 3 or year 3.5 there will be an opportunity to present the results at national or international conferences.

The PhD scholar will gain a wide range of skills, placing them in an excellent position to pursue a career at the interface of environmental science and the molecular biosciences. Technical skills gained will include: algal culture, light and fluorescence microscopy, scanning electron microscopy, photosynthesis and respiration measurements, biochemical assays for carbon storage compounds and qRT-PCR. Skills will be gained in 16S metabarcoding and transcriptome sequencing and associated data analysis using specialised bioinformatic software and R. There may be the opportunity to gain field work experience, and the skills associated with sample collection and processing on a research vessel.

The PhD student would be integrated within the Environmental Molecular Microbiology research group at the University of Stirling, as well as the Ocean Carbon and Nutrient Dynamics (CANDY) research group in the Lyell Centre at Herriot Watt University, and have the opportunity to attend regular group meetings and seminars at both institutions. They will also interact with colleagues in the Aquatic Ecology lab at the University of Glasgow. They will be expected to make use of the diverse training opportunities offered by the IAPETUS consortium, and the UoS in key scientific and transferable skills, including scientific writing, coding and presentation skills.

The supervisory team combines expertise from multiple disciplines, including algal genetics, biochemistry and bioinformatics (Skeffington), biological oceanography, plankton ecology and biogeochemistry (Poulton), algal physiology and theoretical ecology (Spatharis) and marine microbiology (Bird). We have a large network of collaborators, both within the UK and internationally, providing opportunities for field work (e.g. research cruises) and advanced training.

This PhD lends itself to public engagement, and there will be opportunities to develop outreach activities via the Stirling and Glasgow science festivals.