Tropical peatland ecosystems through time: a joint biomarker-pollen approach.


Summary: This PhD project will lead to a step-change in our understanding of tropical peatland ecosystem function, development, and vulnerability, improving our ability to map peatland properties, and to model and predict peatland responses to climate change and anthropogenic pressures. The project will apply a “finger-printing” approach, using a novel combination of vegetation composition, biomarkers and pollen analysis, to characterise and understand the mechanisms at work in determining the functioning of present day peatland ecosystems. These fingerprints will then be used to reconstruct the long-term functional dynamics of peatlands, contributing to our understanding of, and ability to model, their role in the global carbon cycle.
Background and rationale: In the last decade there has been a rapid expansion of scientific interest in tropical peat-forming wetlands, fuelled by new discoveries in Amazonia and the Congo Basin (partly led by researchers at St Andrews [1,2,3]). Much of this research has focused on the value of the huge carbon stocks locked up in the peat – accumulations of dead plant material, built up over millennia underneath the swamp forests and fens. Urgent research is now underway to understand how to preserve these carbon stocks, and the characteristic fauna and flora of the peatlands, in the face of expanding human pressures, with a focus on mapping the present distribution of peat and modelling its response to 21st century climate change. But our scientific understanding of these newly recognized ecosystems and the mechanisms behind their vulnerabilities and, importantly, how to recognise long-term historical changes in these ecosystems, is still at an early stage.
Peatlands are highly structured ecosystems which form strong geographical (spatial) and developmental (temporal) patterns. Typically, a peatland may begin with a lake, such as an abandoned river channel, which progressively fills in with plant litter and sediment, laterally as well as vertically. Over centuries or millennia, a succession of different vegetational communities colonizes different parts of the site as physical and chemical conditions change [4,5]. External changes can also cause shifts in peatland ecosystem function; changes in climate, fluvial dynamics, drainage, felling and burning, can all cause changes in the physical and chemical balance which allows peatlands to function as active carbon stores and sinks.
For more than a decade, our team has been describing these patterns in Amazonian peatlands in space (using vegetation census plots and remote sensing) and in time (by analysing the sub-fossil pollen grains preserved in the peat itself as it accumulates), allowing us to map and quantify the peatland carbon store and understand how it has changed over time. More recently, we have begun research on the potential of biogeochemical markers (biomarkers) as indicators of fine-scale peatland processes [6]. The discovery of clear process indicators would open up the possibility of rapidly assessing aspects of peatland function at lots of sites across the basin and beyond, making it feasible to scale up measurements which are currently slow to carry out. Pilot work on peat in the Pastaza-Maranon Basin (PMFB) in Peruvian Amazonia, has revealed associations between particular suites of biomarkers and key functional characteristics of these peatlands (for example, substrate oxygen levels, methane production, vegetation type, and water table fluctuation) [7]. The proposed project will test a selection of these initial observations, systematically identifying relationships between the chosen biomarkers and peatland functional properties, with particular focus on the mechanisms behind peatland vulnerabilities. For example, methanogens are less abundant where Mauritia flexuosa palms are present because they increase oxygen levels in the surface peat, raising the possibility that felling the palms will increase methane production.
Project overview: The proposed project aims to apply a fingerprinting approach to characterising, and understanding the processes operating within, peatland ecosystems. The potential of three measurable characteristics (vegetation composition, biomarker signatures, and palynological assemblages) to be developed into proxy indicators of key peatland functions will be assessed, then applied down-core to understand how peatland function develops over millennial timescales. The ultimate aim is to provide a stronger foundation for understanding the mechanisms underlying important functional properties, such as carbon storage and biodiversity, opening the way for more insightful interpretation of remote-sensing data and better process-based peatland development models, which in turn will inform conservation and management.

Click on an image to expand

Image Captions

IMG_5874.JPG: “Mauritia flexuosa growing in a peatland palm swamp in Peruvian Amzonia.” Reproduced with kind permission of Dr Lydia Cole, University of St Andrews.
IMG_5702.JPG: “After field work in a swamp, the washing.” Reproduced with kind permission of Dr Lydia Cole, University of St Andrews.
IMG_5765.JPG: “Transport to an Amazon peatland field site.” Reproduced with kind permission of Dr Lydia Cole, University of St Andrews.


The study will focus on sampling environmental (primarily hydrological) and ecological (primarily successional) gradients in the Pastaza-Maranon Basin (PMFB) in northern Peru, the largest peatland complex in Amazonia. An existing network of permanent forest census plots, palaeoecological records, previously installed water level loggers, and inorganic geochemical analysis will provide secondary data for the project and inform the sampling strategy. New surface peat samples will be taken along the relevant gradients, for biogeochemical (biomarker) analysis at the BECS lab at the University of Glasgow, and for pollen/vegetation analysis in the SGSD University of St Andrews. Pollen analysis in the same set of surface samples will show how the vegetation is represented by its pollen rain. Combined biomarker and pollen analysis will then be applied down-core to a c. 4,000 year-long peat record to reconstruct the long-term functional dynamics of a typical peatland. If travel to the field area is possible, new samples will be collected. Otherwise, the supervisors have archived a range of surface samples and cores, representing suitable environmental gradients, and these will be made available for the project.

Project Timeline

Year 1

Literature review: peatland development and function, tropical peatland ecosystems, biogeochemistry in peatlands, biomarker methods, palynological methods. Design experiment and develop sampling strategy. Field and/or lab work planning. Begin learning lab techniques using archived samples. Field work (if possible) in summer end of year 1 to collect surface samples with opportunity to re-census forest plots and install further water table level-loggers.

Year 2

Lab analyses: biomarker and pollen analysis in surface samples (approximately 5 months on each). Statistical analysis of vegetation data. Summer end of year 2: field work to collect core and download level-logger data. Write-up findings for publication.

Year 3

Down-core biomarker and pollen analysis (approximately four months on each). Apply for radiocarbon age determinations (first quarter). Apply findings from surface sample work to interpret down-core data. Assess implications for modelling of peatland carbon cycle.

Year 3.5

Complete write up for publication of paper about down-core analysis. Complete thesis and submit.

& Skills

Specialist training in palynology will be provided by primary supervisor Dr Katy Roucoux, and biomarker analysis by second supervisor Prof Jaime Toney. Dr Ian Lawson with provide training in statistical analysis of environmental data, and access to existing peatland data sets from the PMFB. Prof Tim Baker will provide training in vegetation analysis (including use of the data base) and access to level logger and forest census data from appropriate sites. General research and teaching skills training courses are available to postgraduate students at the University of St Andrews in the organised GRADSkills programme offered by St Leonard’s Postgraduate College (of which all postgraduates at St Andrews are members). Support will be provided by the supervisors in publishing and disseminating the project findings through suitable conferences and peer reviewed journals. The student will also be included in our impact and policy-facing networks which include UN-FAO Peru, Peruvian Ministry of Environment, Global Peatlands Initiative, and the Institute for Research in the Peruvian Amazon (IIAP), providing the opportunity to develop an impact pathway to the research in addition to the academic outputs.

References & further reading

[1] Roucoux et al. (2017) Threats to intact tropical peatlands and opportunities for their conservation. Conservation Biology, 31(6), 1283-1292.[2] Draper et al. (2014) The distribution and amount of carbon in the largest peatland complex in Amazonia. Environmental Research Letters, 9(12), 124017.[3] Dargie et al. (2017) Age, extent and carbon storage of the central Congo Basin peatland complex. Nature, 542(7639), 86-90.[4] Roucoux et al. (2013) Vegetation development in an Amazonian peatland. Palaeogeography, Palaeoclimatology, Palaeoecology, 374, 242-255.[5] Lawson et al. 2014 The geochemistry of Amazonian peats. Wetlands 34, 905-15.[6] Naafs, B.D.A., et al. (2019) The potential of biomarker proxies to trace climate, vegetation, and biogeochemical processes in peat: A review. Global and Planetary Change, 179, 57-79.[7] Amariei, A. (2018) The potential of biomarkers for reconstructing long-term ecohydrological and microorganism community changes in newly discovered Amazonian peatlands. MSc thesis, University of Glasgow.

Further Information

Dr Katherine H. Roucoux, School of Geography and Sustainable Development, University of St Andrews, Irvine Building, North Street, St Andrews, Fife, Scotland, KY16 9AL., 0113 4644025
Prof Jaime Toney, School of Geographical and Earth Sciences, Room 513 Gregory Building, University of Glasgow, Glasgow.
Dr Ian T. Lawson, School of Geography and Sustainable Development, University of St Andrews, Irvine Building, North Street, St Andrews, Fife, Scotland, KY16 9AL., 0113 4644023
Prof Timothy R. Baker, School of Geography, University of Leeds, Leeds. LS2 9JT.

Apply Now