school of earth and environment › ... › essi › essi_projects_2017.pdf · school of earth and...

52
ESSI PhD Projects 2017 School of Earth and Environment University of Leeds http://www.see.leeds.ac.uk/research/essi/ @ESSILeeds

Upload: others

Post on 31-May-2020

3 views

Category:

Documents


0 download

TRANSCRIPT

ESSI PhD Projects 2017

School of Earth and Environment

University of Leeds

http://www.see.leeds.ac.uk/research/essi/

@ESSILeeds

Contents

Signals of the Ice Age in the tropics – new records from the Uruguayan Margin .................................. 1

Long-term management of leachates produced from highly alkaline bauxite residues. ....................... 5

Biodiversity in the extreme world of Pangea.......................................................................................... 9

Methane from herbivores: Impact on modern and ancient climate change. ...................................... 11

Wavy Jets and Arctic Climate Change ................................................................................................... 15

The Ocean Giant of the Warm World: Pliocene Changes in Pacific Palaeogeography ......................... 18

Oceanic anoxic event conundrums: reconciling palaeontology and geochemistry ............................. 22

Seeing the trees for the forest: a comparison of methods for inferring the tree of life ...................... 25

Keeping carbon in the ground: Coupled cycling of organic carbon and metal oxides (Fe, Mn, Al) in UK

upland soils ........................................................................................................................................... 28

How did the first animals and plants change our planet? .................................................................... 32

The Elephant in the Room: Ocean Sulphate Control on the Marine Carbon Cycle Since the Early

Jurassic .................................................................................................................................................. 36

Investigating the role of marine sediments in the global oceanic cycling of nutrient trace metals. ... 40

Constraining Nutrient Cycling in Modern Anoxic Lakes: Implications for Primary Productivity and

Oxygenation on the Early Earth ............................................................................................................ 45

The Rise of Black Shale Giants .............................................................................................................. 48

1

Signals of the Ice Age in the tropics – new records from the Uruguayan

Margin

Supervisors: Dr Tracy Aze, Dr Jason Harvey and Dr Ruza Ivanovic

School of Earth and Environment, University of Leeds

Contact email: [email protected]

Background:

The Last Glacial Maximum (LGM) ~26-19 thousand years ago was the most recent glacial period on Earth and was typified by extensive northern hemisphere glaciation, average global temperatures around 4 °C cooler than today and global sea levels were 130 m lower than the present. As climate warmed towards the present day and the vast northern ice sheets shrank, large volumes of meltwater flooded to the coasts, raising sea level and disrupting global-scale ocean circulation, and rapid changes in surface topography reorganized patterns of atmospheric circulation. Known as the last deglaciation, this period was an exciting time of abrupt changes in surface climate (including warming and cooling events) and the oceans.

Thus, the Last Glacial Maximum and subsequent deglaciation is the focus of much current research as we attempt to reach a better understanding of how the climate system responds to rapid climate fluctuations and better predict future climate change. This is principally achieved via improving and refining models based on primary data and knowledge of climate feedbacks and processes. The most recent assessment report from the Intergovernmental Panel on Climate Change (IPPC AR5) has stated that a number of issues remain regarding our understanding of the Last Glacial Maximum; namely the mismatch between proxy data and models regarding temperature estimates, the uncertainty surrounding the magnitude of tropical sea surface cooling, and the role of seasonal productivity and response of proxy-hosting plankton to variations in water column temperature and vertical stratification.

This project will focus upon direct sampling and analysis of cores donated by BG Group that have been collected from the Uruguayan Margin. The student will perform a number of geochemical and micropalaeontological investigations upon material spanning the Last Glacial Maximum and subsequent deglaciation. Specifically the student will:

i. Produce new tropical sea surface and bottom water temperatures estimates for the S.W. Atlantic Ocean using carbon and oxygen isotope and Mg/analysis of foraminifer shells.

ii. Produce new records of the changing nature of surface and deep oceanic water masses using stable isotope, eNd and trace metal analysis of foraminifer shells.

iii. Produce new records of the influence of seasonality on productivity and depth migration of planktonic foraminifera throughout the LGM and deglaciation using assemblage composition and carbon and oxygen stable isotope and trace metal analyses.

The project will make use of the state-of-the-art laboratory facilities at the University of Leeds, both in the Micropalaeontology Laboratory (sediment processing and microfossil imaging) and the Cohen Geochemistry Laboratories (C and O isotopes, eNd and Mg/Ca and other trace metal analyses on benthic and planktonic foraminifera and bulk sediments).

Impact of the Research and Publications:

The project is designed to test a number of clear hypotheses, with each work package designed towards the publication of a paper, which have clear potential for impact on the international scientific community.

2

An Excellent Training and Research Environment:

This interdisciplinary project will provide the successful PhD candidate with highly valued and sought-after tools for investigating palaeoceanography, past climates and species interactions with their environments, such as: analytical geochemistry, morphometrics and taxonomy and environmental modelling. This will equip the student with the necessary expertise to become the next generation of palaeontological and climate scientist, ready to carry out their own programme of innovative scientific research. The student will benefit from working within and collaborating with dynamic scientists within the multidisciplinary Palaeo@Leeds group (e.g. Gregoire, Haywood, Little, Wignall), and the Cohen Geochemistry Group (e.g. Mearz, Newton, Peacock, Poulton). There will be opportunities to present results at major, international conferences, e.g. AGU (San Francisco), EGU (Vienna), GSA, PalAss, and attend residential summer-schools (e.g. in Italy, USA, UK) and in-house workshops and courses.

Entry requirements:

A good first degree (1 or high 2i), or a good Master’s degree in geological or environmental sciences with a focus towards palaeontology or palaeoceanography, experience in micropalaeontology and programming (e.g. R, Python) is an advantage.

Further Reading:

Annan, J. D. and Hargreaves, J. C. 2013. A new global reconstruction of temperature changes at the Last Glacial Maximum. Climates of the Past. 9, 367-376.

Clark, P. U., Dyke, A.S., Shakun, J. D., Carlson, A. E., CLark, J., Wholfarth, B., Mitrovica, J.X., Hostetler, S. W. and McCabe, A. M. 2009. The Last Glacial Maximum. Science. 325, 710-714.

Harvey, J. and Baxter, E. F. 2009. An improved method for TIMS high precision neodymium isotope analysis of very small aquilots (1-10 ng). Chemical Geology. 258, 251-257.

Ivanovic, R. F., Gregoire, L. J., Kageyama, M., Roche, D. M., Valdes, P. J., Burke, A., Drummond, R., Peltier, W. R., and Tarasov, L. 2016. Transient climate simulations of the deglaciation 21–9 thousand years before present (version 1) – PMIP4 Core experiment design and boundary conditions. Geoscience Model Development. 9, 2563-2587.

Masson-Delmotte, V., M. Schulz, A. Abe-Ouchi, J. Beer, A. Ganopolski, J.F. González Rouco, E. Jansen, K. Lambeck, J. Luterbacher, T. Naish, T. Osborn, B. Otto-Bliesner, T. Quinn, R. Ramesh, M. Rojas, X. Shao and A. Timmermann, 2013: Information from Paleoclimate Archives. In: Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Stocker, T.F., D. Qin, G.-K. Plattner, M. Tignor, S.K. Allen, J. Boschung, A. Nauels, Y. Xia, V. Bex and P.M. Midgley (eds.)]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA.

3

Figure 1. Agumented Masson-Delmotte et al. (2013). “Changes in surface temperature for the Last Interglacial (LIG) as reconstructed from data and simulated by an ensemble of climate model experiments in response to orbital and well-mixed greenhouse gas (WMGHG) forcings. (a) Proxy data syntheses of annual surface temperature anomalies as published by Turney and Jones (2010) and McKay et al. (2011). McKay et al., (2011) calculated an annual anomaly for each record as the average sea surface temperature (SST) of the 5-kyr period centred on the warmest temperature between 135 ka and 118 ka and then subtracting the average SST of the late Holocene (last 5 kyr). Turney and Jones (2010) calculated the annual temperature anomalies relativeto 1961–1990 by averaging the LIG temperature estimates across the isotopic plateau in the marine and ice records and the period of maximum warmth in the terrestrial records (assuming globally synchronous terrestrial warmth). (b) Multi-model average of annual surface air temperature anomalies simulated for the LIG computed with respect to preindustrial. The results for the LIG are obtained from 16 simulations for 128 to 125 ka conducted by 13 modelling groups (Lunt et al., 2013).”

The red box in (b) highlights the lack of data for the LGM in the South West Atlantic Ocean.

4

Figure 2. A Google Earth image of the Ururguayan Coast. Left inset is a map showing the location of the 200

gravity cores that have been donated by BG Group. Right inset is a diagramtic representation of the different

water masses that currently affect this region against depth. NADW= North Atlantic Deep Water, AIW =

Antarctic Intermediate Water, UCDW = Upper Circumpolar Deep Water. The project will use geochemical tools

such as carbon and oxygen isotopes and eNd to investigate the behaviour of the various different

5

Long-term management of leachates produced from highly alkaline bauxite

residues.

Supervisors: Dr Ian T. Burke 1, Dr William M. Mayes2, Professor Douglas I. Stewart3, Amiel

Boullemant4

1 School of Earth and Environment, University of Leeds, 2 Centre for Environmental and Marine Sciences, University of Hull 3 School of Civil Engineering, University of Leeds 4 Rio Tinto Legacy Management

Contact email: [email protected]

Background and Rationale

There is a global legacy of mining and mineral processing residues and wastes produced by the ever

expanding need for raw materials. As former industrial and mining sites reach the end of their period

of economic production, attention switches to the needs of long-term management of residues and

the potential for site remediation. Some types of mineral processing residues contain toxic

chemicals and produce leachates which can be harmful to the environment if not properly managed.

Expectations from government and communities that these sites will be managed sustainably has

never been higher.

This project is focused on the management of large volumes of residues produced during the

worldwide production of aluminium. The manufacture of aluminium begins with extraction of

alumina (Al2O3) from bauxite ore, which produces 1-2 tonnes of ‘red mud’ residue for each tonne of

alumina produced. Rehabilitation of red mud sites is challenging and needs to be based on best

scientific understanding of the geochemical evolution of leachates and mineralogy of the specific

residues involved. Bauxite residues (red mud) and their associated leachates that are highly alkaline

and contain high concentrations of oxyanion forming elements (e.g. Al, As, Mo, V), which can be

problematic if released into the environment (Mayes et al., 2011; 2016). Although there is also

potential for removal and recovery of some of these elements (Gomes et al., 2016), vanadium (as

vanadate) is particularly recalcitrant to treatments (e.g. neutralisation) and can still pose an

environmental risk in treated leachates (Burke et al., 2012; 2013). Therefore, there is need to

investigate the fate and behaviour of trace elements during residue management and treatment,

seeking to produce systems (if possible at relatively low cost) that are effective for, alkalinity

reduction, metal(loid) retention, red mud stabilisation and site revegetation.

Figure 1:Rehabilitation of Rio Tinto’s old red mud impoundments a Mt. Rosser and Kirkvine, Jamaica.

6

Project Aim

This project will investigate the behaviour and mobility of selected trace elements during residue

storage and leachate management. It will employ a range traditional laboratory and field based

geochemical investigations, along with state of the art synchrotron and electron microscope based

methods to determine the precise chemical form of the trace elements in all parts of the storage and

management system (i.e. residues, leachates, precipitates). We will also investigate the likely fate of

trace elements (chiefly V) in natural environments where interaction with soil minerals and organic

matter is likely to control their environmental behaviour. We will seek to use this new understanding

of trace element fate and behaviour to explain the observed concentrations of trace elements in on

site processes and to help design future management systems with better performance and lower

costs.

Figure 2: Potential environmental issues and opportunities associated with the management of

alkaline red mud residues.

Project Objectives

1. Investigate the fate and mobility of soluble metals (Al, As, Mo. V) in relevant leachate

management systems (e.g. neutralisation, re-circulation) using a combination of on-site

measurement and laboratory experimentation (with synchrotron and electron microscopy

based characterisation of metal(loid) speciation in the solid phases produced).

2. Determine the effectiveness of residue treatments (e.g. in situ neutralisation, carbonation

reactions) for controlling trace metal(loid) leaching and their long-term role in promoting

residue stability and rehabilitation/ revegetation prospects.

3. Investigate the fate of released oxyanions (chiefly V) in natural environments receiving

treated leachates in order to understand the role of interactions with soil minerals and

organic matter in controlling metal(loid) mobility and risk.

Training

You will primarily work under the supervision of Dr. Ian Burke and Prof Doug Stewart within the

Cohen Geochemistry Group at Leeds. You will receive specialist scientific training in state-of-the-art

geochemical, mineralogical, experimental and analytical techniques and synchrotron based

geochemical analysis. Dr Will Mayes will lead training in fieldwork aspects of the work at bauxite

residue legacy disposal sites. In addition, you will have the opportunity to be trained in a wide

variety of key transferable skills within the SPHERES NERC DTP, from computer programming and

modelling, to media skills and public outreach. You will also be encouraged and supported to present

your research at national and international scientific conferences.

7

Figure 3: Diamond Light source in Oxfordshire: a powerful new facility for molecular level studies of

contaminant behaviour and an example of the molecular bonding proposed for V(V) on an iron oxide

surface (Peacock and Sherman, 2004) . It is only when the molecular behaviour is understood that

large-scale environmental predictions can be made with certainty.

CASE partnership and fieldwork

This project has a Case (Collaborative awards in science and engineering) in place with Rio Tinto

legacy management and the project findings will feed directly into their program of red mud site

management at bauxite residue disposal areas across the world. The project will benefit from

£10,000 of additional support from the case partner (to support the student’s travel to residue sites

and laboratories, and, to enhance the student stipend). The student will be hosted by Rio Tinto for

up to 4 months during the project. This work will include fieldwork at Rio Tinto’s European legacy

sites (e.g. in Scotland and France), visits to analytical laboratories in the Netherlands, and desk based

study at Rio Tinto offices in Paris.

Eligibility

The applicant must satisfy the requirements to register as a doctoral student at the University of

Leeds, which involves holding appropriate Honours, Diploma or Masters Degree and having passed

the appropriate English language tests. Applications are invited from graduates who have, or expect

to gain, a good degree in chemistry, geology, environmental science, materials science, chemical

engineering or another relevant science discipline. Relevant Masters level qualifications are also

welcomed. The applicant should have a good command of both written and spoken English.

References

Burke I. T., Mayes, W. M., Peacock C. L., Brown A. P., Jarvis A. P. and Gruiz, K. Speciation of

arsenic, chromium and vanadium in red mud samples from the Ajka spill site, Hungary,

Environmental Science and Technology. (2012) 46, 3085-3092.

Burke I. T., Peacock C. L., Lockwood C. L., Stewart D. I., Mortimer R. J. G., Ward M. B.,

Renforth P., Gruiz, K. and Mayes, W. M. Behaviour of aluminium, arsenic and vanadium

during the neutralisation of red mud leachate by HCl, gypsum, or seawater. Environmental

Science and Technology (2013) 47, 6527-6535.

Gomes H. I., Jones A., Rogerson M., Burke I. T. and Mayes W. M. Vanadium removal and

recovery from bauxite residue leachates by ion exchange. Environmental Science and

Pollution Research (2016; in press).

8

Mayes, W. M., Burke I. T., Gomes, H. I., Anton A. D., Ujaczki E., Molnar M. and Feigl V.

Advances in understanding environmental risks of red mud after the Ajka spill, Hungary.

Journal of Sustainable Metallurgy (2016) DOI 10.1007/s40831-016-0050-z, pp1-12.

Mayes W. M., Jarvis A. P., Burke I. T., Walton M. Feigl, V., Klebercz, O. and Gruiz K. Dispersal

and attenuation of trace contaminants downstream of the Ajka bauxite residue (red mud)

depository failure, Hungary. Environmental Science and Technology. (2011) 45 (12) 5147-

5155.

Peacock C. L. and Sherman D. M. Vanadium(V) adsorption onto goethite (alpha-FeOOH) at

pH 1.5 to 12: A surface complexation model based on ab initio molecular geometries and

EXAFS spectroscopy. Geochimica et Cosmochimica Acta. (2004) 68(8), 1723−1733.

9

Biodiversity in the extreme world of Pangea

Supervisors: Dr Alex Dunhill1, Dr Erin Saupe2, Dr Daniel Hill1, and Professor Paul Wignall1

1 School of Earth and Environment, University of Leeds 2 Department of Earth Science, University of Oxford

Contact email: [email protected]

Background

The modern-day latitudinal diversity gradient (LDG) is a keystone ecological pattern based on the

decrease in biodiversity from the equatorial to polar regions. Understanding the processes that

generate the LDG is critical for predicting the loss of biodiversity as a result of climate change. The

fossil record provides a unique record on the evolution and dynamics of LDGs and suggests that the

modern-day distribution of

biodiversity has not been

consistent over the past 500

million years (Mannion et al.

2014).

One period of Earth history

where LDGs may have been

significantly different to the

present is during the late

Palaeozoic to early Mesozoic,

when the continents were

arranged in a single landmass

called Pangea. The Permian-

Jurassic represents a turbulent

period of Earth history with

fluctuating extreme icehouse-

greenhouse conditions and

frequent large-scale volcanic events, resulting in four major mass extinction events (Wignall 2015).

The aim of this project is to document how extreme climatic fluctuations and mass extinctions

through the Permian-Jurassic influenced LDGs, and to examine which latitudes were most vulnerable

to biodiversity loss under extreme climatic stress (e.g., such as the superhot world of the earliest

Triassic) (Sun et al. 2012). Such investigations will shed new light on the underlying mechanisms

producing latitudinal diversity gradients.

Hypothesis testing

The student will build a spatiotemporal fossil database, concentrating on tetrapods, marine

vertebrates and plants, from a variety of sources (including the Paleobiology Database, the scientific

literature, and museum collections) ranging from the Permian-Early Cretaceous. This database will

then be used to test the following hypotheses:

1. Pangean LDGs differ from modern LDGs because of harsh, low-latitude conditions.

2. The breakup of Pangea during the Jurassic initiated the establishment of the modern

LDG.

Figure 1: Distribution of Early Triassic vertebrate fossils

showing the response to extreme equatorial high temperature

suggesting a bi-model or reverse LDG (Sun et al. 2012).

10

3. LDG dynamics are sensitive to high temperature-driven mass extinctions, with

preferential extinction occurring at low latitudes.

4. Fossil LDGs can be recreated using climate-constrained LDG simulations.

Impact and publications

This project will represent a significant contribution to our understanding of how climate change

drives the distribution of biodiversity. The work is easily divisible into publications that will form

consecutive chapters of the PhD thesis (corresponding to hypotheses 1-4).

An excellent training and research environment

This interdisciplinary project will provide the successful PhD candidate with highly valued and

sought-after tools for investigating past climates and macroevolutionary processes. The student will

gain experience and expertise in database construction, fossil specimen taxonomy, statistical and

spatial modelling, and climate modelling. This skillset will equip the student with the necessary

expertise to carry out their own programme of innovative scientific research. The student will

benefit from working and collaborating with dynamic scientists in the multidisciplinary

Palaeo@Leeds group (Aze, Gill, Gregoire, Haywood, Ivanovic, Little, Lloyd, März, Newton). There will

be opportunities to present results at major, international conferences, e.g. IPC, GSA, PalAss, and

attend residential summer-schools (e.g. in Australia, USA, UK) and in-house workshops and courses.

Entry requirements

A good first degree (1 or high 2i), or a good Master’s degree in geological, mathematical, biological

or environmental sciences with a focus towards palaeobiology or evolutionary biology, experience in

programming (e.g. R, Python) is an advantage but not essential.

Further reading

Mannion, P. D., P. Upchurch, R. B. J. Benson, and A. Goswami. 2014. The latitudinal

biodiversity gradient through deep time. Trends in Ecology & Evolution 29(1):42-50.

Sun, Y. D., M. M. Joachimski, P. B. Wignall, C. B. Yan, Y. L. Chen, H. S. Jiang, L. N. Wang, and X.

L. Lai. 2012. Lethally Hot Temperatures During the Early Triassic Greenhouse. Science

338(6105):366-370.

Wignall, P.B. 2015. The worst of times: How life on Earth survived eighty million years of

extinctions. Princeton University Press.

11

Methane from herbivores: Impact on modern and ancient climate change.

Supervisors: Dr Fiona Gill1, Professor. Martyn Chipperfield1, Dr Daniel Hill1, Professor. Marcus

Clauss2, Professor. Jürgen Hummel3

1 School of Earth and Environment, University of Leeds 2 Clinic for Zoo Animals, Exotic Pets and Wildlife, University of Zurich 3 Ruminant Nutrition, Georg-August University Göttingen

Contact email: [email protected]

Methane is the second most important anthropogenic greenhouse gas and as such makes a major

contribution to climate change. It has been increasing in the atmosphere for the past 5000 years,

but the reasons for both past increases (Ruddiman, 2003) and recent increases (Nisbet et al., 2014)

are not fully understood. In addition, predictions of future atmospheric methane levels require an

accurate knowledge of all sources.

Figure 1: Global methane cycle (from Encyclopaedia Britannica).

Herbivorous animals, particularly ruminants and other foregut fermenters, make a significant

contribution to global methane emissions (Figure 1), but estimates of this contribution are poorly

constrained for the present (Ciais et al., 2013) and the archaeological past ( Fuller et al., 2011).

Existing methods can be used to measure the amount of methane produced by domesticated

ruminants such as cows and sheep. However, these methods cannot be readily applied to wild

animal populations, for animal welfare and logistical reasons.

Archaeol is a lipid produced by archaea including the methane-producing methanogens, such as

those found in the digestive tract of herbivores. Previous studies have shown that archaeol is

present in the faeces of foregut-fermenting herbivores (Gill et al., 2010) and that for cows on

contrasting diets, the concentration of archaeol in the faeces co-varies with the amount of methane

produced (Figure 2, Gill et al., 2011; McCartney et al., 2013; Schwarm et al., 2015). However, details

of the quantitative relationship between archaeol and methane production are currently poorly

12

understood (e.g. McCartney et al., 2014). This project seeks to address this knowledge gap by

quantifying archaeol and measuring methane in several key suites of samples. This will improve

understanding of the controls on faecal archaeol concentration, allowing a quantitative proxy for

methane emissions in herbivores to be developed. Such a proxy could be used to generate methane

estimates to be incorporated into existing atmospheric models of methane sources. This project will

also produce new estimates of the impact of livestock on prehistoric methane levels, through the

use of the global climate models with changes in atmospheric methane levels across the last 5000

years.

Figure 2: modified

from Gill et al.

(2011), showing

that faecal

archaeol and

methane emissions

co-vary for cattle

on contrasting

diets.

Objectives

In this project, you will work with leading scientists at the University of Leeds and elsewhere to:

1. Carry out in vitro fermentation experiments on a range of herbivore feeds and quantify the

methane and archaeol produced.

2. Quantify archaeol in samples from the digestive tract of goats, cattle, llamas, horses and

rabbits and compare with PCR data on methanogens where available.

3. Quantify archaeol from an extensive range of herbivore faecal samples, spanning multiple

taxa and digestion types, and compare with methane emission data where available.

4. Integrate results to develop a faecal lipid proxy for methane emissions.

5. Test the proxy at a local (University of Leeds farm) and regional scale.

6. Simulate the dispersion of methane from herbivores in the atmosphere using numerical

models, and compare the simulations with recent in-situ CH4 observations.

7. Assess the role of herbivore CH4 emissions in present-day climate change and test its

potential role in climate changes of the past 5000 years.

Potential for high impact outcome

This interdisciplinary project brings together scientists with a wide range of expertise to address the

issue of quantifying herbivore methane emissions. Results will contribute to global greenhouse gas

inventories and provide novel insights into the carbon budget, to aid understanding of past and

present climate change and future changes. This project has the potential generate several

publications and given the topic, at least one is likely to be suitable for submission to a high impact

journal.

0

50

100

150

200

250

300

350

400

Methane production, g/day Faecal archaeol, mg/kg DM

concentrates

silage

13

Training

The student will work under the supervision of Dr Fiona Gill within the Earth Surface Science

Institute and Professor Martyn Chipperfield and Dr Daniel Hill within the Institute of Climate and

Atmospheric Science in SEE. The project provides training in:

i. Organic geochemistry – extraction of archaeol and other lipids from faeces and fermented

feed samples and analysis by gas chromatography-mass spectrometry (SEE).

ii. Dissections of the digestive tract of cattle, llamas, rabbits and horses. To be carried out

under the supervision of Prof. Marcus Clauss at the University of Zurich, Switzerland.

iii. In vitro fermentation experiments and quantification of methane using gas chromatography.

To be carried out under the supervision of Prof. Jürgen Hummel, Georg-August University,

Göttingen, Germany.

iv. Development and use of atmospheric models. Existing 3-D models, available within ICAS, will

be used to simulate the dispersion of methane emissions in the atmosphere. Comparison of

the models with recent ground and aircraft borne CH4 observations will be use to evaluate

the new estimates of emissions from herbivores.

v. The use of global climate models and the simulation of climate change over the last 5000

years under alternative greenhouse gas forcing scenarios. These simulations will be run on

high performance computing at the University of Leeds, under the supervision of Dr. Daniel

Hill. They will give the student hands on experience of the use of computer models and in

the processing and analysis of large data sets.

The successful PhD student will be a member of both the Cohen Geochemistry research group and

the Atmospheric Chemistry research group and will receive excellent hands-on training in both

experimental techniques and computer modelling. The student will also have access to a wide range

of training courses for both project specific and general skills

(http://www.emeskillstraining.leeds.ac.uk/).

Student profile

Applicants should have a background in a relevant subject, such as biology, chemistry, Earth or

environmental science, with an interest in global environmental problems.

References

Ciais, P., C. Sabine, G. Bala, L. Bopp, V. Brovkin, J. Canadell, A. Chhabra, R. DeFries, J.

Galloway, M. Heimann, C. Jones, C. Le Quéré, R.B. Myneni, S. Piao and P. Thornton, 2013:

Carbon and Other Biogeochemical Cycles. In: Climate Change 2013: The Physical Science

Basis. Contribution of Working Group I to the Fifth Assessment Report of the

Intergovernmental Panel on Climate Change [Stocker, T.F., D. Qin, G.-K. Plattner, M. Tignor,

S.K. Allen, J. Boschung, A. Nauels, Y. Xia, V. Bex and P.M. Midgley (eds.)]. Cambridge

University Press, Cambridge, United Kingdom and New York, NY, USA.

https://www.ipcc.ch/pdf/assessment-report/ar5/wg1/WG1AR5_Chapter06_FINAL.pdf

Fuller, D.Q., van Etten, J., Manning, K., Castillo, C., Kingwell-Banham, E., Weisskopf, A., Qin,

L., Sato, Y-I. and Hijmans, R.J. (2011) The contribution of rice agriculture and livestock

pastoralism to prehistoric methane levels: An archaeological assessment. doi:

10.1177/0959683611398052

Gill, F.L., Dewhurst, R.J., Dungait, J.A.J. Evershed, R.P., Ives, L., Li, C.S,; Pancost, R.D., Sullivan,

M., Bera, S., Bull, I.D. (2010) Archaeol - a biomarker for foregut fermentation in modern and

ancient herbivorous mammals?, Organic Geochemistry, 41, pp.467-472. DOI:

10.1016/j.orggeochem.2010.02.001

14

Gill, F.L., Dewhurst, R.J., Evershed, R.P., McGeough, E.; O'Kiely, P.; Pancost, R.D.; Bull, I.D.

(2011) Analysis of archaeal ether lipids in bovine faeces, Animal Feed Science and

Technology, 166-67, pp.87-92. http://dx.doi.org/10.1016/j.anifeedsci.2011.04.006

McCartney, C.A., Bull, I.D., Yan, T., Dewhurs,t R.J. (2013) Assessment of archaeol as a

molecular proxy for methane production in cattle. Journal of Dairy Science 96 1211-1217

http://dx.doi.org/10.3168/jds.2012-6042

McCartney, C.A., Bul,l I.D., Dewhurst, R.J. (2014) Using archaeol to investigate the location of

methanogens in the ruminant digestive tract. Livestock Science 164:39-45,

http://dx.doi.org/10.1016/j.livsci.2014.02.020

Nisbet, E.G., Dlugokencky, E. and Bousquet, P. (2014) Methane on the Rise—Again, Science,

343, 493-495, doi:10.1126/science.1247828

Ruddiman, W.F., 2003. The anthropogenic greenhouse era began thousands of years ago.

Climatic Change, 61, 261-293. doi 10.1023/B:CLIM.0000004577.17928.fa

Schwarm, A., Schweigel-Röntgen, M., Kreuzer, M., Ortmann, S., Gill, F., Kuhla, B., Meyer, U.,

Lohölter, M., Derno, M. (2015) Methane emission, digestive characteristics and faecal

archaeol in heifers fed diets based on silage from brown midrib maize as compared to

conventional maize. Archives of Animal Nutrition 69:159-176, doi:

10.1080/1745039X.2015.1043211

15

Wavy Jets and Arctic Climate Change

Supervisors: Prof Alan Haywood1, Dr Dan Hill1, Dr Jochen Voss2 and Dr Aisling Dolan1

1School of Earth and Environment, University of Leeds

2School of Mathematics, University of Leeds

Project partner: Participants of the Pliocene Model Intercomparison Project Phase 2

Contact email: [email protected]

Rising temperatures due to the emission of greenhouse gases may be changing atmospheric circulation (Petrie et al. 2015). This is being observed through changes in regional weather patterns, and in the frequency and intensity of extreme weather events (Dong et al. 2013). One of the most critical components of atmospheric circulation influencing European climate is the jet stream, which consists of ribbons of strong winds that move weather systems across the continent.

Over the last several years patterns of unusually persistent dry/warm or wet weather across Europe have been attributed to the behaviour of the jet stream (Dong et al., 2013). The unusual jet stream behaviour is potentially linked to changing conditions in the Arctic with reduced sea-ice extent and increased temperatures (Francis & Vavrus, 2015; Petrie et al., 2015). Therefore, understanding the changing nature of the Arctic, its relationship to jet stream behaviour, and European weather/climate is very important.

Warm intervals in Earths past provide a natural laboratory in which to investigate long-term environmental change, and climate models have been used to enhance our understanding of atmospheric, oceanic and ice sheet behaviour (Haywood et al., 2016a). The most recent interval of Earths past known to have had a comparable atmospheric carbon dioxide (CO2) level to today (~400 ppmv) is the Pliocene (~3 million years ago). It was an interval known to be warmer than the pre-industrial era, with reduced Arctic sea-ice extent (Figure 1 & 2), and shares a number of parallels to model predictions of climate at the end of the century (Haywood et al., 2016a).

In the context of a broader international climate modelling effort (see international partners section below), this project will use climate model simulations to investigate the nature of the jet stream and connections to the Arctic in the Pliocene to greatly enhance our knowledge and understanding of past warm climates, and critically, their significance in the context of future climate change.

Figure 1: Mean Arctic sea ice concentrations (%) during summer in the pre-industrial simulated by 8 different climate models (Howell et al., 2016).

16

Figure 2: Mean sea ice concentrations (%) during summer in the Pliocene simulated by 8 different climate models (Howell et al., 2016).

Objectives

Investigate and develop appropriate methods to diagnose the behaviour and variability of jet stream flow.

Examine the relationship between the large-scale features of Northern Hemisphere climate and jet stream behaviour.

Assess model differences in the representation of the jet stream for the Pliocene through multi-model comparison.

Examine the effect that different scenarios of Arctic warming have on model predictions of jet stream behaviour.

Compare and contrast climate simulations for the European region during the Pliocene, which display different characteristics of jet stream flow, to available geological climate data.

Compare and contrast Pliocene results with predicted jet stream behaviour using model experiments designed to simulate the climate of this century.

Potential for high impact outcomes

Understanding the relationships between Arctic sea-ice cover and jet stream behaviour for a climate of the past that has elevated concentrations of CO2 will provide valuable insights into weather and climate variability of the near future. The student will be guided by a brand new science plan recently formulated for the 2nd Phase of the Pliocene Model Intercomparison Project (Haywood et al., 2016b). Phase 1 led to the publication of numerous high impact papers in Nature journals. Phase 2 experiments are underpinned by the very latest syntheses of geological information available. The proposed research has the potential to contribute to the next Intergovernmental Panel on Climate Change Assessment Report.

Training

The PhD student will be embedded within a vibrant and dynamic research group in the School of Earth and Environment (Palaeo@Leeds). Palaeo@Leeds has experts in past climate and ice sheet modelling, as well as specialists in marine and terrestrial palaeoenvironments. The student will be supported and fully trained in coupled ocean-atmosphere modelling, gaining programming skills. The student will analyse existing climate model simulations, learn to perform new experiments, learn how to compare results from different models, and learn appropriate methods for diagnosing the behaviour of the jet stream. As such the student will become an expert in assessing atmospheric

17

circulation relating to jet streams. Our link to Jochen Voss in the School of Mathematics will provide valuable expertise in numerical analysis of model results and statistics. The student will attend the Urbino Summer School in Palaeoclimatology (Italy) and have the opportunity to attend various conferences during the project (e.g. American Geophysical Union and European Geoscience Union). Through our established collaborations the student will also have an opportunity to visit and work with scientists from the Unites States Geological Survey as well other international modelling groups involved in the Pliocene Model Intercomparison Project Phase 2 (led by the University of Leeds and the U.S. Geological Survey) in the U.S., France, Germany, Norway and China. The research has the potential to make a highly valuable contribution to the next Intergovernmental Panel on Climate Change Assessment Report.

Student Profile

It is necessary for the candidate has an undergraduate degree (2.1 or higher) in Atmospheric Science, Environmental Science, Earth Sciences, Mathematics or Physics. A strong interest in climate modelling with previous programming experience is desirable, although previous experience is not required as our training will equip the student with the skills necessary to use climate models.

International Partners

Through our established collaborations the student will have an opportunity to interact and work with scientists from the Unites States Geological Survey as well other international modelling groups involved in the Pliocene Model Intercomparison Project Phase 2 in the U.S., France, Germany, Norway and China.

References

Dong, B., Sutton, R. and Shaffrey, L. (2014). The 2013 hot, dry summer in Western Europe. Bulletin of the American Meteorological Society, 95 (9). S61-S66. ISSN 1520-0477.

Francis J.A. and Vavrus, S.J. (2015). Evidence for a wavier jet stream in response to rapid Arctic warming. Environmental Research Letters, 10, 014005.

Haywood, A,M., Dowsett, H.J., Dolan, A.M. (2016a). Integrating geological archives and climate models for the mid-Pliocene warm period, Nature Communications, 7, doi: 10.1038/ncomms10646

Haywood, A,M., Dowsett, H.J., Dolan, A.M., Rowley, D., Abe-Ouchi, A., Otto-Bliesner, B., Chandler, M.A., Hunter, S.J., Lunt, D.J., Pound, M., Salzmann, U. (2016b). The Pliocene Model Intercomparison Project (PlioMIP) Phase 2: Scientific objectives and experimental design, Climate of the Past, 12, pp.663-675. doi: 10.5194/cp-12-663-2016.

Howell, F,W., Haywood, A.M., Otto-Bliesner, B.L., Bragg, F., Chan, W.L., Chandler, M.A., Contoux, C., Kamae, Y., Abe-Ouchi, A., Rosenbloom, N.A., Stepanek, C., Zhang, Z. (2016). Arctic sea ice simulation in the PlioMIP ensemble, Climate of the Past, 12, pp.749-767. doi: 10.5194/cp-12-749-2016.

Petrie, R. E., Shaffrey, L. C. and Sutton, R. T. (2015). Atmospheric impact of Arctic Sea ice loss in a coupled ocean–atmosphere simulation. Journal of Climate, 28 (24). pp. 9606-9622. ISSN 1520-0442.

18

The Ocean Giant of the Warm World: Pliocene Changes in Pacific Palaeogeography

Supervisors: Dr Daniel Hill, and Prof Alan Haywood

School of Earth and Environment, University of Leeds

Contact email: [email protected]

The impacts of the Pacific Ocean on contemporary climate change and natural warming since the last Ice Age are increasingly being recognised (Kosaka and Xie, 2013; Skinner et al., 2015). However, its state and role in the warmer-than-modern climates of the recent geological past are still debated (Rickaby and Halloran, 2005; Wara et al., 2005; Li et al., 2011; Zhang et al., 2014). The Pliocene is the last period of Earth history with elevated surface temperatures and atmospheric carbon dioxide concentrations close to today (Pagani et al., 2010; Haywood et al., 2013). The North Atlantic has long been investigated for its role in the warm climate of the Pliocene (Dowsett et al., 1992; Raymo et al., 1996), but evidence that the Pacific Ocean also played a key role has emerged in recent years (Federov et al., 2013; Nie et al., 2014). There are, however, many uncertainties in the palaeogeography of the surrounding continents, ocean gateways and shallow seas (Figure 1). These have yet to be systematically incorporated into models of the Pliocene climate and may significantly impact the state of the Pacific Ocean.

Figure 1 Circum-Pacific palaeogeographic changes in the Pliocene. (A) Indonesian archipelago and throughflow

currents (Karas et al., 2009), (B) Antarctic ice sheets (Haywood et al., 2010), (C) topography in the Rockies and

Andes mountain chains (Haywood et al., 2010), (D) Central American Seaway prior to the final uplift of the

Isthmus of Panama (Coates et al., 2014), (E) a closed Bering Strait during the Pliocene (Haywood et al., 2016) and

(F) and the Japanese archipelago (Kamado and Kato, 2011).

19

The discrepancy between proxy sea surface temperature reconstructions in the Pliocene Pacific Ocean have been used to suggest that climate models are unable to reproduce the behaviour of the Pacific Ocean under warm climates of the past. Various mechanisms and possible changes in the Earth system have been suggested as a solution to this discrepancy, including altered ENSO dynamics (Rickaby and Halloran, 2005; Wara et al., 2005), enhanced ocean mixing (Federov et al., 2010) and altered cloud albedo impacts (Burls and Federov, 2014). If one or more of these mechanisms is indeed important for correctly simulating warmer than modern climates, then they could also be an important mechanism for simulating future climate warming. However, there has never been a comprehensive analysis of the potential impacts of palaeogeographic changes in the region to test whether models would reproduce the reconstructed temperatures given other plausible Pliocene boundary conditions, without having to invoke changes in the observed operation of climate.

This project will build an ensemble of General Circulation Model (GCM) simulations, using the Hadley Centre climate model, incorporating the circum-Pacific palaeogeographic changes. These will be used to investigate the state of the Pliocene Pacific Ocean and its sensitivity to the nature of these changes. Many different aspects of the Pacific Ocean will be investigated, including the oceanic temperatures and circulation, the internal variability of the El Niño Southern Oscillation (ENSO) and the impact of Pacific temperatures on the neighbouring monsoonal systems (Asian, Australian, South American and African). The project will also draw on the international Pliocene climate modelling project, with the PhD candidate able to lead on the Pacific Meridional Ocean Circulation analysis within PlioMIP (Pliocene Model Intercomparison Project).

Objectives:

The student will undertake a systematic modelling study of the Pliocene Pacific Ocean, in collaboration with their supervisors, the Palaeo@Leeds research group and palaeoclimate modellers from across the globe. There is plenty of scope for the student to tailor the project and prioritise the various aspects of the project according to their own interests. However, the following would be a reasonable expectation for the project.

1. Produce an ensemble of Pliocene climate model simulations, incorporating circum-Pacific palaeogeographic changes. These will include changes in the Indonesian Archipelago, Japan Sea, Bering Strait, Rockies, Andes and Antarctica.

2. Analyse the results of the ensemble in terms of the mean state of the Pacific and the climate variability in the region. Records of ocean temperature, circulation, ENSO and monsoons will test the impact of Pliocene palaeogeographic change in the Pacific region on global climate. This will also provide a test of whether the observed changes in the Pliocene Pacific are within the bounds of palaeogeographic uncertainties or require changes in the operation of climate in warmer than modern palaeoclimates.

3. Investigate the Pacific Ocean climate in PlioMIP phase 2 ensemble, testing the model dependency of Pliocene climate simulations. The student will lead the analysis of the Pacific Ocean circulation in PlioMIP phase 2.

Potential for high impact outcome

The Pliocene Pacific Ocean has been a hot topic in palaeoclimatology and palaeoceanography for a number of years (Rickaby and Halloran, 2005; Wara et al., 2005) and continues to produce high impact papers (Zhang et al., 2014). New International Ocean Discovery Programme (IODP) cores from the Western Pacific Warm Pool will keep this topic high on the scientific agenda (Rosenthal et al., 2016). Not only will the project produce a unique and important modelling ensemble, which will have important implications for new proxy reconstructions, but it will be able to draw on PlioMIP

20

Phase 2, enabling the student to lead an aspect of the analysis of at least 14 climate models from around the world (Haywood et al., 2016).

With the supervisors’ long history of simulating the Pliocene climate using these models, it is anticipated that the student will get up to speed quickly and will soon be presenting relevant results at international conferences and in publications. The publication strategy would depend on the results that are produced, but at least 2 high impact publications (palaeogeographic changes and PlioMIP results) would be anticipated from the project.

Training

The successful candidate will work closely with supervisors, Daniel Hill and Alan Haywood, and will play an active role in Palaeo@Leeds research group. Interacting with this group will give the student a broad education in cutting edge palaeoclimate and palaeontological research. Specific training in the use of climate models and high performance computing will be given both in Leeds and at external training courses. Being part of the Leeds/York NERC DTP (Natural Environment Research Council Doctoral Training Programme) will also give the student access to lots of training in general research and academic skills. Being part of the PlioMIP project will give the student experience of working will lots of different climate models and handling large data sets. The student will also be expected to interact with lots of different scientists and disciplines that work on the Pacific Ocean and the Pliocene Epoch. This will be facilitated by attendance and presentation at a series of major international conferences. The Urbino summer school in Italy provides general training in palaeoclimate research and the student would be expected to apply to attend the course in summer 2018.

Student profile

Palaeoclimate modelling is by necessity a multi-disciplinary research area and no candidate will have existing skills in all the necessary disciplines. Applications are particularly encouraged from candidates with a background in physical science, mathematics, Earth science or oceanography. However, as all training will be given to successful candidates, those with any quantitative scientific background would also be suitable.

References

Burls, N.J. and Fedorov, A.V., 2014. Simulating Pliocene warmth and a permanent El Niño-like state: the role of cloud albedo. Paleoceanography, 29, 893-910.

Coates, A.G., Collins, L.S., Aubry, M.-P. and Berggren, W.A., 2004. The geology of the Darien, Panama, and the Miocene-Pliocene collision of the Panama arc with northwestern South America. Geological Society of America Bulletin, 116, 1327-1344.

Dowsett, H.J., Cronin, T.M., Poore, R.Z., Thompson, R.S., Whatley, R.C. and Wood, A.M., 1992. Micropaleontological evidence for increased meridional heat-transport in the North-Atlantic Ocean during the Pliocene. Science, 258, 1133-1135.

Federov, A.V., Brierley, C.M. and Emanuel, K., 2010. Tropical cyclones and permanent El Niño in the early Pliocene epoch. Nature, 463, 1066-1070.

Federov, A.V., Brierley, C.M., Lawrence, K.T., Liu, Z., Dekens, P.S. and Ravelo, A.C., 2013. Patterns and mechanisms of early Pliocene warmth. Nature, 496, 43-49.

Haywood, A.M., Dowsett, H.J., Otto-Bliesner, B., Chandler, M.A., Dolan, A.M., Hill, D.J., Lunt, D.J., Robinson, M.M., Rosenbloom, N., Salzmann, U. and Sohl, L.E., 2010. Pliocene Model Intercomparison Project (PlioMIP): experimental design and boundary conditions (Experiment 1). Geoscientific Model Development, 3, 227-242.

Haywood, A.M., Hill, D.J., Dolan, A.M., Otto-Bliesner, B.L., Bragg, F., Chan, W.-L., Chandler, M.A., Contoux, C., Dowsett, H.J., Jost, A., Kamae, Y., Lohmann, G., Lunt, D.J., Abe-Ouchi, A., Pickering, S.J., Ramstein, G., Rosenbloom, N.A., Salzmann, U., Sohl, L., Stepanek, C., Ueda, H.,

21

Yan, Q. and Z. Zhang, 2013. Large-scale features of Pliocene climate: results from the Pliocene Model Intercomparison Project. Climate of the Past, 9, 191-209.

Haywood, A.M., Dowsett, H.J., Dolan, A.M., Rowley, D., Abe-Ouchi, A., Otto-Bliesner, B., Chandler, M.A., Hunter, S.J., Lunt, D.J., Pound, M. and Salzmann, U., 2016. The Pliocene Model Intercomparison Project (PlioMIP) Phase 2: scientific objectives and experimental design. Climate of the Past, 12, 663-675.

Kameda, Y. and Kato, M., 2011. Terrestrial invasion of pomatiopsid gastropods in the heavy-snow region of the Japanese archipelago. BMC Evolutionary Biology, 11, 118.

Karas, C., Nürnberg, D., Gupta, A.K., Tiedemann, R., Mohan, K. and Bickert, T., 2009. Mid-Pliocene climate change amplified by a switch in Indonesian subsurface throughflow. Nature Geoscience, 2, doi: 10.1038/NGEO520.

Kosaka, Y. and Xie, S.-P., 2013. Recent global-warming hiatus tied to equatorial Pacific surface cooling. Nature, 501, 403-407.

Li, L., Li, Q., Tian, J., Wang, P., Wang, P. and Liu, Z., 2011. A 4-Ma record of thermal evolution in the tropical western Pacific and its implication on climate change. Earth and Planetary Science Letter, 309, 10-20.

Nie, J., Stevenes, T., Song, Y., King, J.W., Zhang, R., Ji, S., Gong, L. and Cares, D., 2014. Pacific freshening drives Pliocene cooling and Asian monsoon intensification. Scientific Reports, 4, 5474.

Pagani, M., Liu, Z., LaRiviere, J. and Ravelo, A.C., 2010. High Earth-system sensitivity determined from Pliocene carbon dioxide concentrations. Nature Geoscience, 3, 27-30.

Raymo, M.E., Grant, B., Horowicz, M. and Rau, G.H., 1996. Mid-Pliocene warmth: stronger greenhouse and stronger conveyor. Marine Micropaleontology, 27, 313-326.

Rickaby, R. and Halloran, P., 2005. Cool La Niña during the warmth of the Pliocene? Science, 307, 1948-1952.

Rosenthal, Y., Holbourn, A., and Kulhanek, D.K., 2016. Expedition 363 Scientific Prospectus: Western Pacific Warm Pool. International Ocean Discovery Program. http://dx.doi.org/10.14379/iodp.sp.363.2016.

Skinner, L., McCave, I.M., Carter, L., Fallon, S., Scrivner, A.E. and Primeau, F., 2015. Reduced ventilation and enhanced magnitude of the deep Pacific carbon pool during the last glacial period. Earth and Planetary Science Letters, 411, 45-52.

Wara, M.W., Ravelo, A.C. and Delaney, M.L., 2005. Permanent El Niño-like conditions during the Pliocene Warm Period. Science, 309, 758-761.

Zhang, Y.G., Pagani, M. and Liu, Z., 2014. A 12-million-year temperature history of the tropical Pacific Ocean. Science, 344, 84-87.

22

Oceanic anoxic event conundrums: reconciling palaeontology and

geochemistry

Supervisors: Dr Crispin Little, Professor Simon Poulton, Dr Christian März, Dr Fiona Gill

School of Earth and Environment, University of Leeds

Contact email: [email protected]

One of the many detrimental effects of future climate warming will be the expansion of oxygen

minimum ‘‘dead zones’’ in shallow marine areas, leading to the loss of commercially important fish

and invertebrate stocks (1). General circulation models predict that climate change will directly

deplete oceanic dissolved oxygen levels by increasing stratification and warming, as well as indirectly

by causing changes in rainfall patterns, nutrient run-off and shelf eutrophication; all of which will

increase marine areas affected by hypoxia and anoxia. Hypoxia can occur at a variety of temporal

and spatial scales. Only the smallest temporal and spatial scales may be readily

observed or recreated experimentally, and it is unclear whether these results are applicable at larger

scales. Data from the largest temporal, spatial and ecological scales can, however, be

sourced from the fossil record, which provides an archive of natural data from a number of past

episodes of climatic and environmental change. A detailed fossil record with good temporal

resolution that spans past climate change events can help in forecasting future ecosystem changes,

especially if predicted climate changes move outside the parameters experienced by modern

ecosystems and into regimes known only from the deeper geological record. Rocks spanning the

Pliensbachian-Toarcian interval of the Early Jurassic (185-181 Ma) are an archive of natural data

from one of these past episodes of global warming and anoxia (2). Temperatures are estimated to

have increased by 2–3.5 degrees C in subtropical areas and 6–8 degrees C at higher latitudes, values

which are similar to the increases forecast for the end of the 21st century. In many early Toarcian

shallow, epicontinental basins worldwide, laminated, organic-rich, black shales (Fig. 1), which

formed under reduced oxygen conditions, were deposited, and so this event is widely referred to as

the Toarcian Oceanic Anoxic Event (TOAE)(3). In some localities, there is evidence that anoxia

temporarily spread into the lower photic zone, together with euxinia, as indicated by the presence of

biomarkers of green sulphur bacteria in some black shales. Marine ecosystems were adversely

affected by these climate driven environmental changes, and early Toarcian strata record a major

extinction of marine organisms, particularly amongst the infaunal benthos. However, for the TOAE

(as for many Oceanic Anoxic Events) there are significant discrepancies in the estimation of water

column and sediment oxygenation using palaeontological and geochemical data (4). For example,

prior to the main TOAE laminated black shale event there are several shorter intervals of laminated

black shale deposition (Fig. 2), which are not associated with basin-wide extinction events, and

within the main thickness of Toarcian black shales containing the geochemical evidence for greatest

oxygen reduction, including photic zone euxinia, are numerous shell beds of epifaunal benthic

bivalves (usually mono-specific).

23

Figure 1. Cliff exposure of lower Toarcian

bioturbated grey shales (recessed) and

laminated black shales (projecting), Kettleness,

N. Yorkshire.

Figure 2. Transition from laminated black shales

to bioturbated grey shales, ‘Sulfur Band’,

Kettleness, N. Yorkshire.

Aims and outcomes

The project will investigate the sometimes contradictory interpretations of sediment and water

column redox states obtained from palaeontological and geochemical analysis of black shale

sequences during the TOAE, where the geochemical evidence suggests greater oxygen restriction

than the fossil evidence. It will do so by studying rapid redox transitions from massive or bioturbated

(oxygenated) shales into laminated black shale (oxygen-depleted) facies, using benthic macrofauna

combined with modern geochemical redox proxies, including Fe abundance (Fe/Al) and Fe-S

speciation, trace metal (e.g. U, Mo, Re and V) enrichments, and the biomarkers for green and purple

sulfur bacteria (e.g. okenone and isorenieratane), as well as applying this methodology to ‘event

layers’ of benthic macrofauna within laminated black shale facies. The issues may relate to the

temporal resolution that the proxies (palaeontological and geochemical) are recording in the

sediment, which can likely be resolved by sampling at high resolution (cm to mm). The focus of the

study will be Toarcian material from outcrops on the Yorkshire Coast (Figs. 1&2), supplemented by

samples from existing (e.g. Schandelah-1, N. Germany) and soon-to-be-drilled Pliensbachian-

Toarcian core material (e.g. Mochras 2, N. Wales).

The expected results from the project will be: (i) improved understanding of the response of benthic

animals to rapid redox transitions; (ii) resolution of the common mismatch between palaeontological

and geochemical interpretations of redox in laminated black shale facies in Mesozoic Oceanic Anoxic

Events; (iii) better knowledge of what ‘event layers’ of benthos mean in a basinal content.

24

Potential for high impact outcome

The project addresses the NERC societal challenge of ‘managing environmental change’ as the

triggers, temporal and geographic extent of future oxygen minimum ‘‘dead zones’’ in shallow marine

areas are poorly understood.

Training

The project is interdisciplinary and the student will work within the Earth Surface Science Institute

(ESSI) under the supervision of Dr. Crispin Little (macrofossil palaeontology), Professor Simon

Poulton (Fe-S speciation), Dr. Christian März (trace metals) and Dr. Fiona Gill (organic geochemistry).

As a member of two research groups within ESSI (Palaeo@Leeds and Cohen Geochemistry), the

student will have access to a broad spectrum of relevant expertise, which will be supplemented by

an extensive range of research and personal development workshops delivered by the University of

Leeds, from numerical modelling, through to managing your degree, and preparing for your viva

(http://www.emeskillstraining.leeds.ac.uk/).

References

UNEP, United Nations Environment Programme website (2004) GEO Year Book 2003. GEO

Section/UNEP, Nairobi. Available: http://www.unep.org/yearbook/2003/.

Danise, S., Twitchett, R.J., and Little, C.T.S. (2015) Environmental controls on Jurassic marine

ecosystems during global warming. Geology 43:263-266.

Wignall, P.B., Newton, R.J. and Little, C.T.S. (2005) The timing of paleoenvironmental change

and cause-and-effect relationships during the early Jurassic mass extinction in Europe. Am. J.

Sci. 305: 1014-1032.

Friedrich, O. (2010) Benthic foraminifera and their role to decipher paleoenvironment during

mid-Cretaceous Oceanic Anoxic Events – the ‘anoxic benthic foraminifera’ paradox. Rev.

Micropal. 53: 175–192.

25

Seeing the trees for the forest: a comparison of methods for inferring the

tree of life

Supervisors: Dr Graeme T. Lloyd1, Dr Katie E. Davis2, Professor Paul Wignall1

1 School of Earth and Environment, University of Leeds 2 Department of Biology, University of York

Contact email: [email protected]

A central goal of biology is to uncover the tree of life – determining how all species, extinct and

extant, are ultimately related. Here the student will investigate how different approaches to

inferring this tree can be compared. Pre-existing databases of primarily animal trees, but with strong

focuses on arthropods (e.g., insects, crustaceans) and tetrapods (e.g., birds, dinosaurs, ichthyosaurs,

lizards, plesiosaurs, pterosaurs, mammals) will be expanded and developed, allowing the broadest

possible set of comparisons to be made. The student will also have the option to develop tree(s) of

their own. Comparisons will be made using methods that compare the branching order of trees with

the appearances of taxa in the fossil record. Thus only groups with fossil records will be used.

Because the branching order of different phylogenies and the appearance of taxa in the fossil record

are independent estimates of the same thing their mutual agreement is suggestive of accuracy (and

by extension, disagreement of inaccuracy). A suite of metrics has been produced to make such

comparisons (summarised in Bell and Lloyd 2015). These allow competing phylogenies to be

compared. Although so far limited headway has been made in this area (but see Brochu and Norell

2001). Instead these metrics have been applied to different groups and time periods to see if any

major patterns emerge (for a recent summary see O’Connor and Wills 2016).

Comparison of competing phylogenies is important as there is disagreement on the best methods to

use in inferring them. Palaeontologists have traditionally relied on parsimony – algorithms that

attempt to select trees that minimise the number of evolutionary “steps”. However, more recently

model-based approaches that make particular assumptions about evolutionary change have been

employed. Similarly, different statistical paradigms are in use. For example, the Bayesian approach,

which requires a number of guesses to be made about the tree before analysis proceeds. Yet other

approaches combine the outputs of individual analyses into larger “supertrees” (Davis and Page

2014; Hill and Davis 2014; Lloyd et al in press). Being able to compare the outputs of trees generated

from such disparate approaches should help aid in establishing a “best practice” in the field, and

hence the project has the potential to be highly influential.

The student will primarily use the software package “strap” (Bell and Lloyd 2015) to make their

comparisons, for which the main supervisor is an author. Other software produced by, or otherwise

familiar to the supervisors will also be employed (e.g., The Supertree Toolkit 2; Hill and Davis 2014),

allowing the student the best possible access to cutting edge techniques.

Objectives

As part of the project the student will be able to test a number of hypotheses that would correspond

to both a thesis chapter and a publication. Specific possibilities include:

26

1. Simulation studies suggest that model-based phylogenetics are superior to methods that

attempt to minimise the number of evolutionary steps on a tree (Wright and Hillis 2014;

O’Reilly et al 2016). However, so far there has been no comparison between empirical

data sets. Here the student will re-analyse a series of data sets, applying both methods

to infer trees, and then comparing the results using stratigraphic fit to establish whether

the same is true for empirical data.

2. Empirical studies suggest that morphological characters based on soft parts are more

congruent with molecular trees than those based on hard parts (Sansom and Wills

2013). Here the student will compare the stratigraphic fits of trees produced from

different partitions of the same data set. This could encompass a number of different

projects representing their own chapters or papers, for example: morphology versus

molecules (the latter thought to be superior), hard parts versus soft parts (the latter

thought to be superior), or head versus body characters (the former thought to be

superior),

3. Generating very large trees can be problematic and so is often achieved by combining

smaller trees together as “supertrees” (e.g., Hill and Davis 2014; Lloyd et al in press).

However, it is not clear whether this is superior to combining the original data instead

(“supermatrices”), nor whether this process leads to poorer stratigraphic fits in the final

tree than it does in the smaller source trees. Here the student will explore whether the

extra effort of creating a supermatrix results in trees with superior stratigraphic fit.

Alternatively, or additionally, they will compare the fits of supertrees with their input

source trees to see if there is a resulting loss in stratigraphic “fidelity” or not.

4. Stratigraphic congruence has seen very limited usage when comparing competing

phylogenies for controversial areas of the tree of life (but see Brochu and Norell 2001).

Here the student will compare major controversies using stratigraphic congruence. For

example, the controversial relationships of squamates (lizards and snakes) and the

position of turtles in the tetrapod tree.

5. Recently developed methods are allowing palaeontologists to employ time in inferring

phylogenies (e.g., Bapst et al 2016), theoretically biasing trees towards greater

stratigraphic congruence. Even more recently it has been suggested that geography also

be incorporated in inference (De Baets et al 2016; Landis in press). Here the student will

have the opportunity to develop new method(s) that exploit the parallels between time

and space to compare trees based on their implied number of biogeographic dispersal

events as an alternative to stratigraphic congruence.

Potential for high impact outcome

This project will allow the student to address three major areas: 1) comparing methods for inferring

phylogenetic trees, 2) comparing different data types for inferring phylogenetic trees, and 3)

comparing conflicting and controversial phylogenetic trees. These all offer excellent opportunities

for high impact results.

Training

Over the course of the project we expect the student to pick up a wide range of practical skills,

including: databases, phylogenetics, and programming (mainly in the R language). These can be

taught directly by the supervisory team although attendance of formal courses will also be strongly

encouraged. It is expected that by the end of the PhD the student will have a strong set of

transferrable skills and subsequent broad employment opportunities.

27

Student profile

The project will suit a student who has a first degree in either geology or biology (a Masters is

desirable but not essential). Proficiency with computational and numerical skills will be helpful, but

these can also be taught by the supervisory team. Strong organisational skills will also be important.

References

Bapst, D. W., Wright, A. M., Matzke, N. J. and Lloyd, G. T., 2016. Topology, divergence dates

and macroevolutionary inferences vary between different tip-dating approaches applied to

fossil theropods (Dinosauria). Biology Letters, 12, 20160237.

Bell, M. A. and Lloyd, G. T., 2015. strap: an R package for plotting phylogenies against

stratigraphy and assessing their stratigraphic congruence. Palaeontology, 58, 379-389.

Brochu, C. A., and Norell, M. A., 2001. Time and trees: A quantitative assessment of

temporal congruence in the bird origins debate. pp. 511-535 in J. A. Gauthier and L. F. Gall

(eds.), New Perspectives on the Origin and Early Evolution of Birds, Peabody Museum of

Natural History, New Haven, CT.

Davis, K. E. and Page, R. D. M., 2014. Reweaving the tapestry: a supertree of birds. PLOS

Currents Tree of Life, 1.

De Baets, K., Antonelli, A. and Donoghue, P. C. J., 2016. Tectonic blocks and molecular clocks.

Philosophical Transactions of the Royal Society B, 371, 20160098.

Hill, J. E. and Davis, K. E., 2014. The Supertree Toolkit 2: a new and improved software

package with a Graphical User Interface for supertree construction. Biodiversity Data

Journal, 2, e1053.

Landis, M. J., in press. Biogeographic dating of speciation times using paleogeographically

informed processes. Systematic Biology.

Lloyd, G. T., Bapst, D. W., Friedman, M. and Davis, K. E., in press. Probabilistic divergence

time estimation without branch lengths: dating the origins of dinosaurs, avian flight, and

crown birds. Biology Letters.

O’Connor, A. and Wills, M. A., 2016. Measuring stratigraphic congruence across trees, higher

taxa and time. Systematic Biology, 65, 792-811.

O’Reilly, J. E., Puttick, M. N., Parry, L., Tanner, A. R., Tarver, J. E., Fleming, J., Pisani, D. and

Donoghue, P. C. J., 2016. Bayesian methods outperform parsimony but at the expense of

precision in the estimation of phylogeny from discrete morphological data. Biology Letters,

12, 20160081.

Sansom, R. S. and Wills, M. A., 2013. Fossilization causes organisms to appear erroneously

primitive by distorting evolutionary trees. Scientific Reports, 3, 2545.

Wright, A. M. and Hillis, D. M., 2014. Bayesian analysis using a simple likelihood model

outperforms parsimony for estimation of phylogeny from discrete morphological data. PLoS

ONE, 9, e109210.

28

Keeping carbon in the ground: Coupled cycling of organic carbon and metal

oxides (Fe, Mn, Al) in UK upland soils

Supervisors: Dr Christian März1, Dr Sheila Palmer2 and Dr Caroline Peacock1

1 School of Earth and Environment, University of Leeds 2 School of Geograpphy, University of Leeds

Contact email: [email protected]

Background

Soil organic carbon (SOC) is a key parameter for healthy soil function, including its fertility, water

holding capacity, and carbon storage, and it has important repercussions on both food production,

flood/drought resilience, and the global carbon cycle (Lal, 2004). It is therefore of scientific, societal

and economic interest to better understand SOC dynamics, and especially its interactions with the

inorganic components of the soil system. This could ultimately lead to improved strategies of

engineering more fertile and resilient soil systems.

In natural soils, a lot of SOC is bound to inorganic particles, especially to Al, Fe and Mn

(oxyhydr)oxides. Numerous recent studies (e.g., Wagai and Mayer, 2007; Lalonde et al., 2012;

Palmer et al., 2013; Riedel et al., 2013; Johnson et al., 2015; Estes et al., 2016; Shields et al., 2016)

have examined the role that Fe and Mn (oxyhydr)oxides play in stabilising significant amounts of

organic matter, both in soils and marine sediments (Fig. 1).

Figure. 1: Relative percentages of organic carbon associated with Fe oxides (OC-Fe) in marine

sediments worldwide, reaching 15-30% in most places (Lalonde et al., 2012)

29

However, in different climate change scenarios, flooding or drying the soil will directly translate into

changing pH and redox conditions, with immediate but poorly constrained effects on the stability of

Al, Fe and Mn oxides and their capacity to retain SOC within the soil system (e.g., Schwertmann,

1966; Thompson et al., 2006; Lehmann and Kleber, 2015; Emsens et al., 2016). Organic matter can

be chemically transformed and then get released from the soil, either in particulate form or as

organo-metallic complexes. How stable these organo-metallic complexes are under changing

environmental conditions has implications for the long-term burial of carbon in soil systems or

streambeds. There are also implications for the water industry as dissolved or colloidal organo-

metallic complexes can contribute to unwanted coloration of water and affect its subsequent

treatment for drinking water purposes.

In this project, the spatially and temporally dynamic coupling between SOC and Al, Fe and Mn oxides

will be investigated in globally important carbon-rich soil types, such as peats and organomineral

upland soils (Fig. 2), that have a recognised relevance as terrestrial carbon stores and within the UK

are sources for much of our drinking water. The successful candidate will join a team of geochemists

with long-standing experience in carbon and metal cycling in the environment.

Figure 2: Eroded peat hags in the Pennines

Objectives

1. Determining the quantity and relative contribution of SOC bound to Fe, Mn and Al

(oxyhydr)oxides in UK upland soil systems

2. Trace changes in this specific SOC pool in relation to soil depth, underlying

lithologies, dry versus flooded areas.

3. Quantify changes in this specific SOC pool along hydrological pathways, e.g, small

stream, river banks, river sediments.

4. Determine stability of this SOC pool under changing environmental conditions, e.g.,

wet versus dry, hot versus cold.

Approach & training

Sampling locations will be uplands in the north of the UK (Fig. 2) where Dr Palmer and her group

have long-standing research experience (Palmer et al., 2013). Sampling will include soil profiles and

cores, soil moisture sampling, river cuttings, river sediments and suspension load to get a full picture

30

of different stores and transport pathways of different carbon and metal fractions. The analytical

approach will include geochemical analyses of the bulk sediment and water samples (dissolved and

particulate organic carbon, metals, nutrients) and sequential leaching methods to extract different

metal phases and the associated carbon fractions. Selected natural samples, and analogue samples

created in the laboratory, will be analysed at very high spatial and chemical resolution using the

latest synchrotron nanoprobes, to further investigate the mineral-organic couplings and how these

might promote carbon stabilization and burial.

The student wil be trained in the laboratory procedures and analyses by Drs März, Palmer and

Peacock who have substantial experience in the extraction and analytical methods to be applied

(including extracting different metal phases from soil and sediment samples and total acid

diegstions, analysis of dissolved phases using AAS, ICP-OES and ICP-MS, and of solid samples using

XRD, CNS combustion analysis and synchrotron-based spectroscopy). Hands-on training and support

will further be provided by highly qualified technicians both in the Cohen Laboratories (School of

Earth and Environment) and in the School of Geography. The successful candidate will have access to

a wide range of training workshops (scientific writing and presentation skills, statistics, science

communication and outreach), and will be supported by the supervisors in preparing conference

presentations and peer-reviewed publications.

Student qualification

The successful candidate should have an excellent degree in an Earth Sciences, Environmental

Sciences, or Soil Science discipline, a strong background and keen interest in fieldwork and analytical

skills, ideally experience in conducting a research project and presenting research results to the

wider scientific community.

Further reading

Emsens W-J, Aggenbach CJS, Schoutens K, Smolders AJP, Zak D, Van Diggelen R (2016) Soil

iron content as a predictor of carbon and nutrient mobilization in rewetted fens. PLoS ONE

11, e0153166.

Estes ER, Andeer PF, Nordlund D, Wankel SD, Hansel CM (2016) Biogenic manganese oxides

as reservoirs of organic carbon and proteins in terrestrial and marine environments.

Geobiology, doi:10.1111/gbi.12195

Johnson K, Purvis G, Lopez-Capel E, Peacock C, Gray N, Wagner T, März C, Bowen L, Ojeda J,

Finlay N, Robertson S, Worrall F, Greenwell C (2015) Towards a mechanistic understanding

of carbon stabilization in manganese oxides. Nature Comm. 6, doi: 10.1038/ncomms8628.

Lalonde K, Mucci A, Ouellet A, Gelinas Y (2012) Preservation of organic matter in sediments

promoted by iron. Nature 483, 198−200.

Lehmann J, Kleber M (2015) The contentious nature of soil organic matter. Nature 528, 60-

68.

Palmer SM, Clark JM, Chapman PJ, Van der Heijden GMF, Bottrell SH (2013) Effects of acid

sulphate on DOC release in mineral soils: the influence of SO42− retention and Al release. Eur.

J Soil Sci. 64, 537-544.

Riedel T, Zak D, Biester H, Dittmar T (2013) Iron traps terrestrially derived dissolved organic

matter at redox interfaces. PNAS 110, 10101-10125.

Schwertmann U (1966) Inhibitory effect of soil organic matter on crystallization of

amorphous ferric hydroxide. Nature 212, 645−648.

31

Shields MR, Bianchi TS, Gélinas Y, Allison MA, Twilley RR (2016) Enhanced terrestrial carbon

preservation promoted by reactive iron in deltaic sediments. Geophys. Res. Lett. 43, 1149–

1157.

Thompson A, Chadwick OA, Rancourt DG, Chorover J (2006) Iron-oxide crystallinity increases

during soil redox oscillations. Geochim. Cosmochim. Acta 70, 1710-1727.

Wagai R, Mayer LM (2007) Sorptive stabilization of organic matter in soils by hydrous iron

oxides. Geochim. Cosmochim. Acta 71, 25−35.

32

How did the first animals and plants change our planet?

Supervisors: Dr Benjamin Mills1, Professor Simon Poulton1, Dr Rob Newton1, Supervisor at British

Geological Survey to be confirmed.

1 School of Earth and Environment, University of Leeds

Contact email: [email protected]

This is a CASE award project

The CASE partner is British Geological Survey

Introduction

This project aims to understand and quantify the changes in Earth’s surface conditions during the

Early Paleozoic era, which saw the evolution of land plants and the rapid diversification of animal

life. Specifically we will focus on proposed large shifts in atmospheric CO2 and O2 concentrations,

which have been linked to the evolution of the terrestrial and marine biospheres and their effects on

the delivery and cycling of the key limiting nutrient phosphate [Lenton et al., 2016; Boyle et al.,

2014]. This will be achieved using a combination of state-of-the-art geochemical analyses of ancient

sedimentary rocks and the application of mathematical models, with the potential for targeted

fieldwork to collect additional samples covering specific periods of interest.

Background

The geological record of the Cambrian period (541-485 million years ago, Ma) documents the

explosion of animal life on planet Earth, and the following Ordovician and Silurian periods (together

485-416 Ma) saw the evolution of the first land plants and terrestrial arthropods. Until recently, it

has been thought that these newly developed terrestrial and marine ecosystems did not significantly

impact the global elemental cycles that regulate climate, but this assumption has now begun to be

questioned.

Figure 1. Artists’ impressions of the Cambrian marine (a) and Silurian terrestrial (b) ecosystems.

Modified from Wikimedia commons.

The early Paleozoic is characterised by widespread ocean anoxia, uncertain fluctuations in

atmospheric oxygen, and substantial glacial episodes. Current research suggests that these changes

in surface conditions may be related to the evolution of both the animal [Boyle et al., 2014] and

plant [Lenton et al., 2016] kingdoms over this timeframe, and recently developed laboratory

techniques and computer models will allow quantification and testing of these ideas.

33

Aims and approach

This project aims to improve the geochemical record of ocean redox conditions, in addition to

applying novel geochemical techniques to evaluate changes in the oceanic influx of nutrients and

their behaviour, during the early Paleozoic. Via biogeochemical modelling of these analyses, the

project aims to elucidate the mechanisms behind long term global environmental change during this

pivotal period of Earth history.

The following key questions will guide the research:

1. Did changes in global phosphorus cycling accompany the expansion of the terrestrial

and marine biospheres in the Paleozoic?

2. What were the dynamics of deep ocean oxygenation throughout the Cambrian,

Ordovician and Silurian periods?

3. Did the initial expansion of plant and animal species drive long term climate shifts,

or can these be attributed to tectonic or geomorphological factors?

The initial focus of the project will be the sampling of excellently preserved continuous drill core

sections held by CASE partners British Geological Survey. Measurements of the speciation of iron

and phosphorus will provide unprecedented insight into ocean redox conditions and their influence

on marine nutrient cycles. These analyses will be combined with bulk element analyses and isotopic

ratios of carbon and sulphur, which respond to changes in global tectonic processes, weathering and

biogeochemical cycling. There is also potential for high-resolution redox geochemistry and dating of

appropiate intervals using the BGS core scanning equipment.

Some of these techniques have been developed by the project team, and research at Leeds will be

carried out in the modern and well-equipped Cohen Geochemistry Laboratories within the School of

Earth and Environment. There will be opportunities to visit field sites and collect additional

carbonate and black shale samples as the project progresses.

Earth system ‘box’ models link the global cycles of carbon, sulphur, oxygen and phosphorus (among

others) to reconstruct long term climate [Berner, 2006; Bergman et al., 2004; Figure 2]. The

researcher will work to improve the ongoing modelling efforts of the project team [e.g. Mills et al.,

2016] by investigating more detailed ocean modelling [e.g. Wallman, 2003; Clarkson et al., 2015] and

new functions representing the evolving global biota [Lenton et al., 2016].

The models can be ‘driven’ using the geochemical data obtained in the project (e.g. δ13C, δ34S,

Figure 2: Model

predictions for relative

atmospheric oxygen (a)

and CO2 (b) concentrations

[GEOCARB: Berner, 2006;

COPSE: Bergman et al.,

2004]. Shaded area shows

the timeframe of interest,

where current models

disagree substantially.

34

chemical index of alteration) in order to investigate the potential changes in biogeochemical cycling,

and may also be used as a predictive tool whereby the geochemical records are estimated for a

given hypothesis and then compared to data (for the redox state of the deep ocean, for example).

Impact of the research

The question of the ability of life to alter and regulate climate on a global scale is a top priority in the

Earth sciences, and papers on this subject appear regularly in top geoscience journals, as well as

leading interdisciplinary publications such as Science and Nature. Moreover, the field of Earth

systems science is relatively new, and many topics remain unaddressed. This project will not only

provide an excellent suite of geochemical data for an exciting period in Earth history, it will directly

address some of the key questions in the field that are also of interest to the general public. We

therefore expect the impact of this project to be highly significant within the scientific community

and beyond.

(Click to see recent research in this field co-authored by Dr Mills in the Guardian newspaper)

Training

There is scope within this project to develop a wide skill set, which is multidisciplinary in nature yet

inextricably linked: the researcher will receive training in both numerical modelling and cutting edge

laboratory techniques from world leaders in these fields, and will have the opportunity to collect

additional samples with the help of expert geologists. The researcher will also be trained in the

scientific method, concise writing and presentation, along with a broad range of additional courses

offered by Faculty Graduate School.

Partners and collaborators

The project will benefit from the expertise of an external supervisor at British Geological Survey. This

will include a minimum 3 month placement at BGS and additional funding for travel, subsistence and

general support.

Entry requirements

A good degree in the physical sciences, mathematics or computing is required, and the candidate

should have a strong interest in Earth history and geoscience. Formal training in laboratory

geochemistry, geology or numerical techniques is not essential, but experience in at least one of

these fields is advisable. All necessary training will be provided as part of the project.

Funding

This project is CASE funded in principal by the British Geological Survey.

References and further reading

Bergman, N. M., Lenton, T. M. & Watson, A. J. COPSE: A new model of biogeochemical

cycling over Phanerozoic time. American Journal of Science 304, 397-437 (2004).

Berner, R. A. GEOCARBSULF: A combined model for Phanerozoic atmospheric O2 and CO2.

Geochimica et Cosmochimica Acta 70, 5653-5664 (2006).

Boyle, R. A., Dahl, T. W., Dale, A. W., Shields-Zhou, G. A., Zhu, M., Brasier, M. D., Canfield, D.

E. & Lenton, T. M. Stabilization of the coupled oxygen and phosphorus cycles by the

evolution of bioturbation. Nature Geoscience 7, 671-676 (2014).

35

Lenton, T. M., Dahl, T. W., Daines, S. J., Mills, B. J. W., Ozaki, K., Saltzman, M. R. & Porada, P.

Earliest land plants created modern levels of atmospheric oxygen. Proceedings of the

National Academy of Sciences of the United States of America 113, 9704-9709 (2016).

Mills, B. J. W., Belcher, C. M., Lenton, T. M. & Newton, R. J. A modelling case for high

atmospheric oxygen concentrations during the Mesozoic and Cenozoic. Geology (accepted).

Wallmann, K. Feedbacks between oceanic redox states and marine productivity: A model

perspective focused on benthic phosphorus cycling. Global Biogeochemical Cycles 17, 1-18

(2003).

Clarkson, M. O., Kasemann, S. A., Wood, R. A., Lenton, T. M., Daines, S. J., Richoz, S.,

Ohnemueller, F., Meixner, A., Poulton, S. W., Tipper, E. T. Ocean acidification and the Permo-

Triassic mass extinction. Science 348, 229-232 (2015).

36

The Elephant in the Room: Ocean Sulphate Control on the Marine Carbon

Cycle Since the Early Jurassic

Supervisors: Dr Robert Newton, Dr Benjamin Mills, and Dr Tracy Aze

School of Earth and Environment, University of Leeds

Contact email: [email protected]

Sulphate is the most important oxidant for organic matter in ocean sediments after dissolved oxygen. The continental shelves are the most significant location for marine carbon burial and sulphate can account for up to 80% of organic matter oxidation in these settings. Changes in the concentration of sulphate in the oceans are therefore likely to exert a profound effect on the cycling of carbon in ocean sediments. Specifically, ocean sulphate concentration plays a pivotal role in the ocean methane cycle: In the modern world high concentrations of sulphate cap methane emissions from sediments via the process of anaerobic methane oxidation. It’s known in a general way that ocean sulphate has been much lower at certain times in the past but these records only exist at low resolution, have large error bars, are sometimes poorly dated and different approaches produce different values. The reliance of oceanic methane emissions on sulphate concentration makes understanding past changes in marine sulphate a key goal of predicting atmospheric methane. The most direct method of estimating past ocean sulphate is from the chemistry of fluid trapped in halite crystals formed in evaporitic environments (fluid inclusions), but these records are sparse, and have large error bars in both concentration and dating (Figure 1; Holt et al., 2014; Horita et al., 2002). The latter is especially important as we are beginning to appreciate that ocean sulphate concentrations may have changed much more rapidly in the past than we previously thought (e.g. Wortmann and Paytan, 2012) with the potential to drive more rapid changes in oceanic methane emissions. The drivers for these rapid changes as well as their effects are also poorly understood. To address this knowledge gap, the student will explore two novel methods for deriving much higher resolution records of ocean sulphate concentrations from the beginning of the Jurassic to the present day based on the substitution of sulphate into phosphate and carbonate minerals. This time period is chosen because current records indicate it encompasses an approximately three-fold increase in ocean sulphate. In tandem, the student will use a various modelling approaches to explore the controls on the oceanic sulphur cycle and its effect on the marine carbon cycle and methane production.

Figure 1. A compilation of Phanerozoic ocean concentrations of sulphate and calcium (left) derived from the chemistry of fluid inclusions. Note the scarcity of coverage. Black bars are new data from Carboniferous evaporite deposits. Error bars on ages are not shown but are on the order of a few

37

million years. Primary fluid inclusions in primary halite shown to the right (both figures from Holt et al., 2014)

Francolite or hydroxyapatite are the main minerals in phosphorite deposits and phosphate nodules. Sulphate substitutes into the structure of these minerals in proportion to the concentration of sulphate in the solution from which they are formed (McArthur, 1985). Phosphate minerals can form in a variety of ways but often within the sediment in environments where pore-water sulphate is depleted by microbial sulphate reduction (MSR; Föllmi, 1996). This effect will be excluded by extracting and analysing the sulphate for its isotopic composition, which is strongly affected by MSR (Chambers and Trudinger, 1979; Piper and Kolodny, 1987). Additional information on the environment of formation will be derived from the isotopic composition of its structurally substituted carbonate (Benmore et al., 1983). Similar methods have only previously been applied to samples from the Cambrian (Hough et al., 2006) but pilot work by the lead supervisor has derived estimates for the Cretaceous that overlap those from fluid inclusion studies.

Figure 2. Left: Phosphorite S:P ratio plotted against the sulphur isotope composition of the sulphate substituted into the phosphorite lattice from the late Permian Phosphoria Formation (adapted from Piper and Kolodny, 1987). Where the sulphur isotope composition records seawater, the S:P ratio reflects the sulphate concentration of the ocean. Right: Scanning electron microscope image of the foraminifera Globigerinella siphonifera from the S.W. Indian Ocean.

Sulphate substituted into carbonate minerals is already widely employed as a proxy for the sulphur isotopic composition of ancient oceans, but the controls on the amount of sulphate contained in the mineral lattice are only understood from experimental work (e.g. Busenberg and Plummer, 1985). Recent work on cultured foraminifera suggest a clear relationship between S/Ca in the shell and the sulphate concentration of the water they were growing in (Paris et al., 2014). The student will explore the controls on the sulphate concentrations in foraminiferal calcite (e.g. Figure 2) first in the Holocene, then moving on to the rest of the Cenozoic. Factors to be assessed include species, temperature, growth rate, sulphate concentration and carbon chemistry.

Many of the samples necessary for the project are held in collections either in Leeds or with project partners. Additional sample collections will be made to improve the time resolution of the phosphorite records during fieldwork to Morocco and Bulgaria where phosphorite deposits are common in the Palaeogene, and Jurassic to Cretaceous respectively.

The student will integrate the results of the analytical phases of the project with other published information by developing a box model of marine sulphur cycle (Figure 3) and the sedimentary carbon cycle. The modelling will be based on well-established methods (see Garrels and Lerman, 1984) used to compute past seawater sulphate concentrations from variation in δ34S, and will draw

38

on more recent approaches, which model fluxes of the major components of seawater under changing biogeochemical and tectonic processes (Arvidson et al., 2013). This will allow a quantitative appraisal of the various factors that may be influencing changes to the marine sulphur and carbon cycles on a range of time scales.

Figure 3. A schematic representation of the global sulphur cycle illustrating the controls on ocean sulfate concentrations. The size of the solid boxes is proportional to the size of the reservoirs. Organic carbon is consumed during bacterial sulphate reduction (BSR). Only a small proportion of the sulphate that is reduced to sulphide goes on to be buried as pyrite. Dashed boxes and lines represent variable or poorly constrained reservoirs or fluxes. MOR – mid ocean ridge (Newton, unpublished)

Aims and Objectives

The aims of the project will be to: 1. Derive a high resolution record of sulphate concentrations across the last 200 million

years 2. Explore the controls on the preservation of the new proxies 3. Investigate the controls on marine sulphate concentrations and the implications for

the sedimentary carbon cycle.

This will be achieved by:

1. Analysing a suite of phosphorite samples for their S:P ratio and the d34S of their structurally substituted sulphate. This will also entail SEM work and other techniques to constrain the presence of pyrite or other sulphur phases which may pose a risk of contamination.

2. Undertaking fieldwork in Bulgaria and Morocco to supplement the pre-existing collections of phosphorite samples to improve the time resolution of the record. This work will exploit pre-existing links to help with local logistics and permissions.

3. Selecting and analysing a suite of foraminiferal samples for their S:Ca ratio to test a range of possible controls on sulphate incorporation e.g. a range of species, cosmopolitan species from sites with a range of temperatures, etc. Possible diagenetic controls on the preservation of pristine S/Ca ratios will also be assessed using a range of standard techniques.

4. Developing a box model for ocean sulphate concentrations and the marine sedimentary carbon cycle across the studied time interval constrained by the new information from 1) and 3) above and supplemented by previously published proxy records (e.g. marine sulphate isotope record).

Potential for high impact outcome

The project will address fundamental questions about the detailed chemical evolution of the oceans, one of the most important components of Earth’s biogeochemical cycles. It is also has the potential for significant impact on our understanding of the Earths atmospheric methane budget over time, a

39

key component of the climate system. We therefore expect the project to result in a number of significant papers in the field with at least one or more being suitable for a high impact journal.

Training

The student will be trained in the wet chemical techniques used to measure the element ratios of interest, isotope geochemistry, foraminiferal identification and box modelling. Techniques which will form an integral part of the project are stable isotope mass spectrometry, ion chromatography, ICP-MS, ICP-OES, SEM, and XRD. All of these techniques are available in the School. The supervisory group is made up of expertise on geochemistry and stable isotopes (Dr Robert Newton), micropalaeontology (Dr Tracy Aze) and numerical modelling (Dr Ben Mills) providing a high level of specialist training in all aspects of the project work. The student will become part of the Earth Surface Science Institute in the School and the Cohen Geochemistry and Palaeo@Leeds research groups. This organisational framework provides a broader supportive environment which allows the cross fertilisation of ideas and expertise. In addition to the bespoke high level training for the PhD the student will have access to a wide range of other training and support. Examples would include other useful scientific skills such as programming or statistics, transferable skills such as time management, writing and giving presentations, and skills specific to a PhD programmme such as managing your degree and preparing for your viva (http://www.emeskillstraining.leeds.ac.uk/).

References

Arvidson, R.S., Mackenzie, F.T., Guidry, M.W., 2013. Geologic history of seawater: A MAGic approach to carbon chemistry and ocean ventilation. Chemical Geology, 362: 287-304.

Benmore, R.A., Coleman, M.L., McArthur, J.M., 1983. Origin of sedimentary francolite from its sulphur and carbon isotope composition. Nature, 302(5908): 516-518.

Busenberg, E., Plummer, L.N., 1985. Kinetic and thermodynamic factors controlling the distribution of SO4

2- and Na+ in calcites and selected aragonites. Geochimica et Cosmochimica Acta, 49(3): 713-725.

Chambers, L.A., Trudinger, P.A., 1979. Microbiological fractionation of stable sulfur isotopes: A review and critique. Geomicrobiology Journal, 1(3): 249-293.

Föllmi, K.B., 1996. The phosphorous cycle, phosphogenesis and marine phosphate-rich deposits. Earth-Science Reviews, 40: 55-124.

Garrels, R.M., Lerman, A., 1984. Coupling of the sedimentary sulfur and carbon cycles; an improved model. American Journal of Science, 284(9): 989-1007.

Holt, N.M., García-Veigas, J., Lowenstein, T.K., Giles, P.S., Williams-Stroud, S., 2014. The major-ion composition of Carboniferous seawater. Geochimica et Cosmochimica Acta, 134(0): 317-334.

Horita, J., Zimmermann, H., Holland, H.D., 2002. Chemical evolution of seawater during the Phanerozoic: Implications from the record of marine evaporites. Geochimica et Cosmochimica Acta, 66(21): 3733-3756.

Hough, M.L. et al., 2006. A major sulphur isotope event at c. 510 Ma: a possible anoxia–extinction–volcanism connection during the Early–Middle Cambrian transition? Terra Nova, 18(4): 257-263.

McArthur, J.M., 1985. Francolite geochemistry--compositional controls during formation, diagenesis, metamorphism and weathering. Geochimica et Cosmochimica Acta, 49(1): 23-35.

Paris, G., Fehrenbacher, J.S., Sessions, A.L., Spero, H.J., Adkins, J.F., 2014. Experimental determination of carbonate-associated sulfate δ34S in planktonic foraminifera shells. Geochemistry, Geophysics, Geosystems, 15(4): 1452-1461.

Piper, D.Z., Kolodny, Y., 1987. The stable isotopic composition of a phosphorite deposit: d13C, d34S, and d18O. Deep Sea Research Part A. Oceanographic Research Papers, 34(5-6): 897-911.

Wortmann, U.G., Paytan, A., 2012. Rapid Variability of Seawater Chemistry Over the Past 130 Million Years. Science, 337(6092): 334-336.

40

Investigating the role of marine sediments in the global oceanic cycling of

nutrient trace metals.

Supervisors: Dr Caroline Peacock1, Professor Simon Poutlon1, Dr Amy Atkins2, and Dr Stefan Lalonde3

1School of Earth and Environment, University of Leeds 2Swiss Federal Institute of Technology 3 European Institute for Marine Studies, University of Brest

Contact email: [email protected]

This project will investigate the mobility and fate of the nutrient trace metals during the diagenesis

of marine sediments to determine whether marine sediments provide a net sink or a net source of

these bioessential metals to seawater.

Project Background

The nutrient trace metals, including nickel, copper, zinc and cadmium, are required for

photosynthesis, which is the main process regulating the short-term carbon cycle and the

atmospheric concentration of CO2. Over half the Earth’s photosynthesis takes place in the oceans by

marine photosynthetic algae. Understanding what controls the concentration of nutrient metals in

seawater therefore helps us understand the links between marine biology, seawater chemistry and

ultimately the Earth’s carbon cycle and climate.

At the global scale most approaches to investigating the oceanic cycling of nutrient metals start by

trying to identify the major metal reservoirs, for example seawater and marine sediments, and the

major fluxes between these reservoirs, for example scavenging of metals from seawater onto

particles that settle into the sediments. Then the concentration of the metals, and increasingly the

isotopic composition of the metals, in these reservoirs and fluxes are either measured or calculated.

This information is then used to construct a global oceanic metal cycle, where, if our understanding

of the metal behaviour is complete, there will be a mass balance between the major sources and the

major sinks of metals to seawater (Fig. 1a).

Figure 1: Cartoons representing a) a global model for nutrient trace metal cycling in seawater and b)

the complex biogeochemical processes that go on inside the marine sediment reservoir and between

the sediments and seawater.

A

B

41

In reality however this is a hugely challenging task, in large part because we have only a very limited

understanding of the detailed biogeochemical processes that go on inside the reservoirs (Fig. 1b). It

is these biogeochemical processes that determine what parts of the environment act as metal

reservoirs, whether these reservoirs act as sinks or sources of metals to other parts, and how large

the associated fluxes of the metals are.

Despite our lack of detailed understanding however, there is one important fact that ties almost all

of the biogeochemical processes together – they all involve metal interactions with freshly

precipitated iron and manganese minerals.

Indeed for many of the nutrient metals, iron and manganese (hydr)oxide minerals present in marine

sediments appear to be the primary reservoir for these nutrients in the modern oceans. These

minerals are ubiquitous in pelagic muds, as dispersed nanoparticulate phases, and present

throughout the oceans concreted into ferromanganese crusts and nodules (Fig. 2a,b). And whilst

they may only be present in very small amounts in pelagic muds, they are arguably the strongest

naturally occurring metal scavengers in the environment (Fig. 2c ). This means that in both muds and

crusts, these scavengers are able to control the concentration, isotopic composition and ultimately

the bioavailability of nutrient metals in seawater.

Unfortunately however the freshly precipitated iron and manganese (hydr)oxides are transient

phases and as they age during the diagenesis of marine sediments they transform into new, often

more crystalline, minerals.

This leads us to a fundamental question that is crucial to understanding the oceanic cycling of the

nutrient metals:

A

B B

C

Figure. 2: Images of a) ferromanganese crusts

precipitated on hard rock surfaces at the ocean

floor and b) ferromanganese nodules precipitated

at the sediment-seawater interface; these nodules

carpet large areas of the Pacific ocean, c) cartoon

showing metals scavenged to the surface and into

the structure of a freshly precipitated iron

(hydr)oxide mineral.

42

What is the mobility and fate of nutrient trace metals during the aging and transformation of iron

and manganese (hydr)oxides?

i. Are the metals that are initially scavenged by the freshly precipitated minerals

retained in the newly formed phases, and thus retained in the sediments?

ii. Are the initially scavenged metals released during the mineral transformation into

sediment porewaters, but then re-scavenged by other phases present in the

sediments?

iii. Or are the initially scavenged metals released during mineral transformation and

escape from the porewaters into the overlying seawater?

These questions are of upmost importance because in the first two scenarios the sediments provide

a net sink of metals from seawater, but in the final scenario they provide a net source of metals to

seawater. And in order to track metal cycling in the oceans, and link metal abundance to biological

activity and carbon cycling, we must know which way the sediments behave.

Objectives

This project will investigate the mobility and fate of nickel, copper, zinc and cadmium during the

aging of iron and manganese (hydr)oxides to determine whether marine sediments provide a net

sink or a net source of these bioessential metals to seawater.

1. Prepare synthetic iron and manganese (hydr)oxide minerals in the laboratory and dope

these with nickel, copper, zinc and cadmium to produce synthetic samples that are

analogous to iron and manganese (hydr)oxides found in marine sediments.

2. Age these metal-mineral samples in laboratory experiments designed to simulate the

diagenesis of marine sediments. During aging take samples of the experimental solution and

the metal-mineral solids to form a time series of samples.

3. Analyse the solution and solid time series samples with a suite of state of the art

geochemical techniques, including ICP MS for the concentration of metals in solution, XRD,

SEM and TEM for the concentration of metals in the solids, and MC ICP MS for the isotopic

composition of the metals in both the solution and the solids, to determine the amount of

the metals that are released into solution vs the amount that are retained in the newly

formed mineral products.

4. Analyse the solid time series samples in detail using synchrotron spectroscopy to determine

how and why the metals are released or retained in the newly formed mineral products.

5. Investigate metal concentrations and isotopic compositions in a suite of natural marine

ferromanganese sediments deposited in a range of diagenetic regimes, to relate the

experimental results to real-world environments.

6. Conclude whether marine sediments provide a net sink or a net source of nutrient metals to

seawater.

43

Training

You will work under the supervision of Dr. Caroline Peacock and Prof. Simon Poulton within the

Cohen Geochemistry Group at Leeds, and, depending on your interests, you will have the

opportunity to work with Dr. Amy Atkins at the Swiss Federal Institute of Technology and Dr. Stefan

Lalonde at the European Institute for Marine Studies in Brest, where you will engage with a wide

variety of Earth scientists. You will receive specialist scientific training in state of the art

44

geochemical, mineralogical, experimental and analytical techniques and computational geochemical

modelling. Specifically you will also have the opportunity to analyse your samples using world-

leading synchrotron spectroscopy techniques at the UK synchrotron Diamond Light Source.

In addition, you will have the opportunity to be trained in a wide variety of key transferable skills

within the SPHERES NERC DTP, from computer programming and modeling, to media skills and

public outreach. You will also be encouraged and supported to present your research at national and

international scientific conferences, for example the premier geochemistry conference Goldschmidt

next year held in Japan.

Eligibility

The applicant must satisfy the requirements to register as a doctoral student at the University of

Leeds, which involves holding appropriate Honours, Diploma or Masters Degree and having passed

the appropriate English language tests. Applications are invited from graduates who have, or expect

to gain, a good degree in chemistry, geology, environmental science, materials science, or another

relevant science discipline. Relevant Masters level qualifications are welcomed. The applicant should

have a good command of both written and spoken English.

Recommended Reading (copies available on request)

Atkins A.L., Shaw S., Peacock C.L. (2016) Release of Ni from birnessite during transformation

of birnessite to todorokite: Implications for Ni cycling in marine sediments. Geochim.

Cosmochim. Acta 189, 158-183.

Atkins A.L., Shaw S., Peacock C.L. (2014) Nucleation and growth of todorokite from

birnessite: Implications for trace-metal cycling in marine sediments. Geochim. Cosmochim.

Acta. 144, 109-125.

Gall L., Williams H.M., Siebert C., Halliday A.N., Herrington R.J. and Hein J.R. (2013) Nickel

isotopic compositions of ferromanganese crusts and the constancy of deep ocean inputs and

continental weathering effects over the Cenozoic. Earth. Planet. Sci. Lett. 317, 148-155.

Konhauser K.O., Pecoits E., Lalonde S.V., Papineau D., Nisbet E.G., Barley M.E., Arndt N.T.,

Zahnle K. and Kamber B. S. (2009) Oceanic Ni depletion and a methanogen famine before

the great oxidation event. Nature. 458, 750-753.

Koschinsky A. and Hein J.R. (2003) Acquisition of elements from seawater by

ferromanganese crusts: Solid phase associations and seawater speciation. Marine Geol. 198,

331-351.

Peacock C.L. and Sherman D.M. (2007) Sorption of Ni by birnessite: equilibrium controls on

Ni in seawater. Chem. Geol. 238, 94–106.

Peacock C.L. (2009) Physiochemical controls on the crystal chemistry of Ni in birnessite:

genetic implications for ferromanganese precipitates. Geochim. Cosmochim. Acta 73, 3568–

3578.

Post J.E. (1999) Manganese oxide minerals: crystal structures and economic and

environmental significance. Proc. Natl. Acad. Sci. U. S. A. 96, 3447–3454.

Usui A. (1979) Nickel and copper accumulation as essential elements in 10Å manganite of

deep-sea manganese nodules. Nature. 279, 411-413.

Waychunas G.A, Kim C.S. and Banfield J.F. (2005) Nanoparticulate iron oxide minerals in soils

and sediments: unique properties and contaminant scavenging mechanisms. J. Nanopart.

Res. 7, 409-433.

45

Constraining Nutrient Cycling in Modern Anoxic Lakes: Implications for

Primary Productivity and Oxygenation on the Early Earth

Supervisors: Professor Simon Poulton, Dr Caroline Peacock

School of Earth and Environment, University of Leeds

Contact email: [email protected]

Project Background and Rationale

Understanding the input and recycling of major nutrients (e.g. P, N) and bioessential trace metals

(e.g. Fe, Ni, Cu, Mo) in the oceans has major implications for the regulation of primary productivity,

organic carbon burial and oxygen production in both modern and ancient environments. One of the

main geochemical processes that affects the bioavailability of these elements is uptake by reactive

Fe minerals. Subsequently, the behaviour of Fe minerals and associated elements during early

diagenesis exerts the dominant control on whether nutrients and bioessential trace metals are

either sequestered in the sediment or released back into the water column. Clearly, the fixation of

elements in the deposited sediment effectively limits their bioavailability, and thus it is crucial to

understand the behaviour of nutrients during uptake by minerals under ferruginous conditions and

during early diagenesis in order to evaluate implications for primary production and ultimately the

rise of oxygen early in Earth’s history.

The modern ocean is largely characterized by an

abundance of dissolved oxygen, and as a result,

Fe oxides are the major group of Fe minerals that

have been widely examined in terms of their

uptake capacity for major and trace metal

nutrients. However, recent research suggests

that, considering the entirety of Earth history,

the ocean has dominantly been free of oxygen

(anoxic) and rich in dissolved Fe (ferruginous).

Development of these anoxic non-sulphidic

conditions in the water column is also a major

concern with regard to the future impact of

modern climate change on oxygen levels in the

ocean. There is growing evidence that major

initial Fe precipitates under ferruginous

conditions may be iron phosphate (viviantite) or

green rust (GR; Fig. 1), dependent on the precise

chemistry of the anoxic waters. However, controls on the formation of these minerals, and on the

behaviour of phosphorus and bioessential trace metals during their formation and transformation is

poorly understood, particularly in terms of processes likely to operate under ferruginous oceanic

conditions and during early diagenesis in anoxic porewaters.

Aims, Objectives and Key Hypotheses

This project will focus on the uptake of phosphorus and trace metal nutrients to minerals formed

under ferruginous water column conditions, and will investigate the subsequent potential for these

Figure 1: Green rust particles

46

elements to be fixed in the sediment or released to solution during early diagenesis. A dual approach

will be taken, involving detailed laboratory experiments, coupled with studies of modern ferruginous

lakes with differing P contents in Spain and other appropriate localities. The ultimate goal will be to

build an understanding of the role of Fe minerals in the biogeochemical cycling of elements such as

P, Ni (essential for methanogenesis), and Cu (essential for aerobic methanotrophy) under

ferruginous conditions. This, in turn, will provide greater understanding of the potential for these

elements to limit key biogeochemical processes in the ancient and future ocean. The main

hypothesis to be tested is whether the multitude of experimental data that currently exists with

regard to elemental adsorption to Fe oxides is really appropriate in terms of processes operating

under anoxic, ferruginous water column conditions.

Figure 2 Lake La Cruz, Spain.

Methodology

The initial experimental phases will examine nutrient and trace metal uptake during the synthesis of

green rust, in addition to examining controls on the formation of green rust versus vivianite under

different environmentally relevant conditions. Controlled experiments will be performed to oxidise

Fe(II) in the presence of different elements. These experiments will be conducted in different media,

and will be compared to the results of separate adsorption experiments to pre-formed GR. The final

experimental phase will be aimed at investigating the release and/or fixation of adsorbed elements

during conditions encountered during early diagenesis. The field-based phase of the project will

involving sampling and characterizing particulate and dissolved species in the anoxic and ferruginous

Lake La Cruz and Lake Montcortés, Spain (Fig. 2), with the potential to expand this research to other

lake systems. Geochemical extraction techniques (e.g. Fe and P speciation) will be combined with a

range of mineralogical techniques available at Leeds (e.g. XRD, TEM), with the potential for further

characterization of minerals at the Diamond Light Source Facility, UK.

Training

The student will receive training in a wide variety of state-of-the-art experimental and sedimentary

geochemical and mineralogical techniques, including techniques that the project supervisors have

47

been personally responsible for developing. In addition, the student will be trained in a wide variety

of key transferable skills within the Faculty Graduate School.

Opportunity for Travel

The student will undertake fieldwork in Spain and potentially at other international sites. The

student will also be encouraged to present their research at national and international conferences

in Europe and North America (for example, the International V.M. Goldschmidt Conference).

References and Further Reading (copies available on request)

Zegeye, A., Bonneville, S., Benning, L.G., Sturm, A., Fowle, D.A., Jones, C, Canfield, D.E., Ruby,

C., Maclean, L., Nomosatryo, S., Crowe, S.A., Poulton, S.W. (2012) Green rust formation

controls nutrient availability in a ferruginous water column. Geology, 40, 599-602.

Poulton, S.W. and Canfield, D.E. (2011) Ferruginous conditions: A dominant feature of the

ocean through Earth’s history. Elements, 7, 107-112.

Canfield, D.E., Poulton, S.W., Knoll, A.H., Narbonne, G.M., Ross, G.M., Goldberg, T. and

Strauss, H. (2008) Ferruginous conditions dominated later Neoproterozoic deep water

chemistry. Science, 321, 949-952.

Crowe, S.A. et al. (2008) Photoferrotrophs thrive in an Archean ocean analogue. Proceedings

of the National Academy of Sciences, 10

48

The Rise of Black Shale Giants

Supervisors: Professor Paul Wignall, Professor Simon Poulton and Dr. Rob Newton

School of Earth & Environment, University of Leeds

Contact email: [email protected]

Carbonate platform formation is often abruptly terminated by the onset of thick black shale deposition. The reason(s) for this fundamental change in depositional style is unclear and contentious and yet it is of great geoloigcal and economic significance because some of most economically-important hydrocarbon source rocks are formed in this way. The most spectacular example of this transition in the geological history of the British Isles occurred in the middle of the Carboniferous when shallow-water carbonates, that had been accumulating for tens of millions of years, were replaced by hundreds of metres of black shales - one of the thickest successions of this rock type ever to accumulate. Thus, the Dinantian Limestones of northern England are succeeded by up to 300 m of black shale belong to the Bowland Shale and in Ireland a similar thickness of Clare Shales occurs at the same level following the regional cessation of limestone formation. Equally intriguing the limestone and shale are

Figure 1. The Clare Shale Formation: large cliffs of black shale seen in Co. Limerick, western Ireland. often separated by a thin bed of phosphatic pebbles whose origin is poorly understood.

This project aims to evaluate what happened at this transition and what depositional conditions were like during black shale deposition. The study will focus on the well-exposed Carboniferous outcrops in western Ireland where Lower Carboniferous (Dinantian) Limestones are overlain by hundreds of metres of black shale belonging to the Clare Shale Formation (Fig. 1). Comparison will also be made with the equivalent strata in the Pennines of northern England where similar limestones are succeeded by the thick Bowland Shales. The tectono-sedimentary situation in both regions was very different - the western Irish area probably saw a change from transtensional to foreland basin style subsidence, whilst subsidence style changes in the Pennines were governed by the transition from a syn-rift to post-rift transition in an extensional basin. Despite these different underlying tectonic controls, both regions experienced the same change in sedimentation style pointing to an overriding control by water column conditions, that was perhaps climatically driven. The onset of black shale deposition is the start of a prolonged period of clastic deposition that presumably heralds the onset of rainfall in the hinterlands. However, a humidity increase alone is

49

not sufficient to shut down carbonate formation. For example, the late Dinantian sedimentation in north-eastern England consists of regular alternations of clastic and carbonate lithologies (Yoredale Cyclothems) showing that heterolithic sedimentation was occurring to the north of the black shale basins.

Objectives

This project will focus on the environemntal changes responsible for the carbonate-to-black shale transition using state-of-the-art approaches to determine water column oxygenation, including sedimentary logging, sedimentary petrography and the latest geochemical techniques to assess both redox and primary productivity. The student will specifically focus on pyrite framboid size distributions, Fe speciation and trace metal techniques to evaluate local and regional water column redox conditions. Many of these techniques were developed by the supervisory team (Wignall & Newton, 1998; Poulton & Canfield 2005) and have recently been calibrated for application to carbonate as well as black shale successions (Bond & Wignall, 2010; Clarkson et al.., 2014). This detailed evaluation of marine oxygenation levels will set the premise for understanding controls on the supply and recycling of the key nutrient phosphorus across the carbonate-black shale transitions. This will be one of the first times such an analysis has been possible thanks to the availability of novel P speciation techniques that have recently been developed by the supervisory team at Leeds for application to ancient marine rocks.

Training i. Sedimentary logging in order to collect and measure the Mid Carboniferous strata

spanning the carbonate-to-black shale transition in western Ireland and the Pennines.

ii. Pyrite petrographic analysis on a scanning electron microscope combined with sulphur isotope analysis. These data can help evaluate water column conditions and determine the presence of sulfidic (euxinic) water column.

iii. analyse water column redox controls on P cycling using Fe and P speciation, organic carbon contents and trace metal ratios.

iv. Construction of regional depositional history using these datasets and a model to explain the mechanisms of carbonate platform shut down and the subsequent prolonged deposition of highly organic rich mudrocks.

References

Bond, D.P.G. & Wignall, P.B. 2010. Pyrite framboid study of marine Permo-Triassic boundary sections: a complex anoxic event and its relationship to contemporaneous mass extinction. Bulletin of the Geological Society of America, 122, 1265-1279.

Clarkson, M.O., Poulton, S.W., Guilbaud, R. & Wood, R.A. 2014. Assessing the utility of Fe/Al and Fe-speciation to record water column redox conditions in carbonate-rich sediments. Chemical Geology 382, 111-122.

Poulton, S.W. & Canfield, D.E. 2005. Development of a sequential extraction procedure for iron: implications for iron partitioning in continentally derived particulates. Chemical Geology 214, 209-221.

Wignall, P.B. & Best, J.L. 2000. The Western Irish Namurian Basin Reassessed. Basin Research, 12, 59-78.

Wignall, P.B. & Newton, R. 1998. Pyrite framboid diameter as a measure of

oxygen deficiency in ancient mudrocks. American Journal of Science, 298,

537-552.

Wignall, P.B. & Newton, R. 2001. Black shales on a basin margin: a model based on examples from the Upper Jurassic of the Boulonnais, northern France. Sedimentary Geology, 144, 335-356.