Tales from the Alice Holt forest: carbon fluxes, data assimilation and fieldwork

Email: ewan.pinnington@gmail.com

Forests play an important role in the global carbon cycle, removing large amounts of CO2 from the atmosphere and thus helping to mitigate the effect of human-induced climate change. The state of the global carbon cycle in the IPCC AR5 suggests that the land surface is the most uncertain component of the global carbon cycle. The response of ecosystem carbon uptake to land use change and disturbance (e.g. fire, felling, insect outbreak) is a large component of this uncertainty. Additionally, there is much disagreement on whether forests and terrestrial ecosystems will continue to remove the same proportion of CO2 from the atmosphere under future climate regimes. It is therefore important to improve our understanding of ecosystem carbon cycle processes in the context of a changing climate.

Here we focus on the effect on ecosystem carbon dynamics of disturbance from selective felling (thinning) at the Alice Holt research forest in Hampshire, UK. Thinning is a management practice used to improve ecosystem services or the quality of a final tree crop and is globally widespread. At Alice Holt a program of thinning was carried out in 2014 where one side of the forest was thinned and the other side left unmanaged. During thinning approximately 46% of trees were removed from the area of interest.

Figure 1: At the top of Alice Holt flux tower.

Using the technique of eddy-covariance at flux tower sites we can produce direct measurements of the carbon fluxes in a forest ecosystem. The flux tower at Alice Holt has been producing measurements since 1999 (Wilkinson et al., 2012), a view from the flux tower is shown in Figure 1. These measurements represent the Net Ecosystem Exchange of CO2 (NEE). The NEE is composed of both photosynthesis and respiration fluxes. The total amount of carbon removed from the atmosphere through photosynthesis is termed the Gross Primary Productivity (GPP). The Total Ecosystem Respiration (TER) is made up of autotrophic respiration (Ra) from plants and heterotrophic respiration (Rh) from soil microbes and other organisms incapable of photosynthesis. We then have, NEE = -GPP + TER, so that a negative NEE value represents removal of carbon from the atmosphere and a positive NEE value represents an input of carbon to the atmosphere. A schematic of these fluxes is shown in Figure 2.

Figure 2: Fluxes of carbon around a forest ecosystem.

The flux tower at Alice Holt is on the boundary between the thinned and unthinned forest. This allows us to partition the NEE observations between the two areas of forest using a flux footprint model (Wilkinson et al., 2016). We also conducted an extensive fieldwork campaign in 2015 to estimate the difference in structure between the thinned and unthinned forest. However, these observations are not enough alone to understand the effect of disturbance. We therefore also use mathematical models describing the carbon balance of our ecosystem, here we use the DALEC2 model of ecosystem carbon balance (Bloom and Williams, 2015). In order to find the best estimate for our system we use the mathematical technique of data assimilation in order to combine all our available observations with our prior model predictions. More infomation on the novel data assimilation techniques developed can be found in Pinnington et al., 2016. These techniques allow us to find two distinct parameter sets for the DALEC2 model corresponding to the thinned and unthinned forest. We can then inspect the model output for both areas of forest and attempt to further understand the effect of selective felling on ecosystem carbon dynamics.

Figure 3: Model predicted cumulative fluxes for 2015 after data assimilatiom. Solid line: NEE, dotted line: TER, dashed line: GPP. Orange: model prediction for thinned forest, blue: model prediction for unthinned forest. Shaded region: model uncertainty after assimilation (± 1 standard deviation).

In Figure 3 we show the cumulative fluxes for both the thinned and unthinned forest after disturbance in 2015. We would probably assume that removing 46% of the trees from the thinned section would reduce the amount of carbon uptake in comparison to the unthinned section. However, we can see that both forests removed a total of approximately 425 g C m-2 in 2015, despite the thinned forest having 46% of its trees removed in the previous year. From our best modelled predictions this unchanged carbon uptake is possible due to significant reductions in TER. So, even though the thinned forest has lower GPP, its net carbon uptake is similar to the unthinned forest. Our model suggests that GPP is a main driver for TER, therefore removing a large amount of trees has significantly reduced ecosystem respiration. This result is supported by other ecological studies (Heinemeyer et al., 2012, Högberg et al., 2001, Janssens et al., 2001). This has implications for future predictions of land surface carbon uptake and whether forests will continue to sequester atmospheric CO2 at similar rates, or if they will be limited by increased GPP leading to increased respiration.


Wilkinson, M. et al., 2012: Inter-annual variation of carbon uptake by a plantation oak woodland in south-eastern England. Biogeosciences, 9 (12), 5373–5389.

Wilkinson, M., et al., 2016: Effects of management thinning on CO2 exchange by a plantation oak woodland in south-eastern England. Biogeosciences, 13 (8), 2367–2378, doi: 10.5194/bg-13-2367-2016.

Bloom, A. A. and M. Williams, 2015: Constraining ecosystem carbon dynamics in a data-limited world: integrating ecological “common sense” in a model data fusion framework. Biogeosciences, 12 (5), 1299–1315, doi: 10.5194/bg-12-1299-2015.

Pinnington, E. M., et al., 2016: Investigating the role of prior and observation error correlations in improving a model forecast of forest carbon balance using four-dimensional variational data assimilation. Agricultural and Forest Meteorology, 228229, 299 – 314, doi: http://dx.doi.org/10.1016/j.agrformet.2016.07.006.

Heinemeyer, A., et al., 2012: Exploring the “overflow tap” theory: linking forest soil co2 fluxes and individual mycorrhizo- sphere components to photosynthesis. Biogeosciences, 9 (1), 79–95.

Högberg, P., et al., 2001: Large-scale forest girdling shows that current photosynthesis drives soil respiration. Nature, 411 (6839), 789–792.

Janssens, I. A., et al., 2001: Productivity overshadows temperature in determining soil and ecosystem respiration across european forests. Global Change Biology, 7 (3), 269–278, doi: 10.1046/j.1365-2486.2001.00412.x.

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Understanding the urban environment and its effect on indoor air.

Email: h.l.gough@pgr.reading.ac.uk

Recent estimates by the United Nations (2009) state that 50 to 70 % of the world’s population now live in urban areas with over 70 % of our time being spent indoors, whether that’s at work, at home or commuting.

We’ve all experienced a poor indoor environment, whether it’s the stuffy office that makes you sleepy, or the air conditioning unit that causes the one person under it to freeze. Poor environments make you unproductive and research is beginning to suggest that they can make you ill. The thing is, the microclimate around one person is complex enough, but then you have to consider the air flow of the room, the ventilation of the building and the effect of the urban environment on the building.

So what tends to happen is that buildings and urban areas are simplified down into basic shapes with all the fine details neglected and this is either modelled at a smaller scale in a wind tunnel or by using CFD (computer fluid dynamics). However, how do we know whether these models are representative of the real-world?


This is Straw city, which was built in Silsoe U.K during 2014. You can just see the car behind the array (purple circle), these cubes of straw are 6 m tall, or roughly the height of an average house. Straw city is the stepping stone between the scale models and the real world, and was an urban experiment in a rural environment. We measured inside the array, outside of the array and within the blue building so we could see the link between internal and external flow: which meant the use of drones and smoke machines! The focus of the experiment was on the link between ventilation and the external conditions.

Smoke releases, drone flying, thermal imaging and tracer gas release: some of the more fun aspects of the fieldwork

After 6 months of data collection, we took the straw cubes away and just monitored the blue cube on its own and the effect of the array can clearly be seen in this plot, where pink is the array, and blue is the isolated cube. So this is showing the pressure coefficient (Cp),  and can be thought of as a way of comparing one building to another in completely different conditions. You can see that the wind direction has an effect and that the array reduces the pressure felt by the cube by 60-90 %. Pressure is linked to the natural ventilation of a building: less pressure means less flow through the opening.


Alongside the big straw city, we also went to the Enflo lab at the University of Surrey to run some wind tunnel experiments of our own, which allowed us to expand the array.

Photos of the wind tunnel arrays. Left is the biggest array modelled, centre is the Silsoe array, top right is the wind tunnel and roughness elements. Bottom right is the model of the storage shed at the full-scale site and centre is the logging system used.

So we have a data set that encompasses all wind directions and speeds, all atmospheric stabilities, different temperature differences and different weather conditions. It’s a big data set and will take a while to work through, especially with comparisons to the wind tunnel model and CFD model created by the University of Leeds. We will also compare the results to the existing guidelines out there and to other similar data sets.

I could ramble on for hours about the work, having spent far too long in a muddy field in all weathers but for more information please email me or come along to my departmental seminar on the 8th November.

This PhD project is jointly funded by the University of Reading and the EPSRC and is part of the Refresh project: www.refresh-project.org.uk

NAWDEX Campaign – Experiencing the Jet Stream

Email:  j.maddison@pgr.reading.ac.uk

NAWDEX (North Atlantic Wave and Downstream impact Experiment) was an International field campaign led by Ludwig-Maximilians-Universität (LMU) Munich and the Deutsches Zentrum für Luft- und Raumfahrt (DLR) Oberpfaffenhofen in cooperation with the Eidgenössische Technische Hochschule (ETH) Zurich and the Office of Naval Research in the USA, with many other international collaborators. Multiple aircraft were deployed from Iceland (the HALO aircraft and the DLR and Safire Falcons) and the UK (the FAAM aircraft) to take meteorological measurments with the aim of providing knowledge of mid-latitude dynamics and predictability. There was involvement from across the UK, including the University of Reading, the University of Manchester, and the Met Office as well as from the FAAM.

The NAWDEX operations centre was based in Keflavik, Iceland (number 27 in Figure 1), which I visited for a week to join the campaign as one of the representatives from the University of Reading, UK. I was tasked with being the ground-based observation coordinator.


Figure 1: Radiosonde launch locations for the campaign.

A Europe-wide network of radiosonde launch locations (Figure 1) had been readied for additional launches during the NAWDEX period. Our role was to choose sites to launch sondes from that would complement measurements taken by the aircraft and/or support one of the NAWDEX objectives. Of particular interest was downstream high impact weather events over Europe. It was great to be given real responsibility and be able to actually contribute to the NAWDEX project.

Below is a typical daily schedule I would have in Iceland:

Daily schedule:

UK call: 8:30am Icelandic. Conference call between UK parties discussing plans for the coming days and any updates from Iceland or the UK.

General meeting: 12pm Icelandic. Go over brief weather summary, instrument status reports, flight plans for the coming days and reports of previous flights.

Weather meeting: 4pm Icelandic. Detailed look at the weather situation for the short and medium-ranges, highlighting key features that would be of interest to fly into, e.g. extratropical transitions of tropical cyclones (which we were fortunate to observe more than once). Radiosonde launch updates.

In between: assessing forecasts and flight plans for the coming days and meeting with scientists for their input to decide where we want to launch radiosondes from. Along with preparing slides to present to the group proposed launch locations and emailing various meteorological services to request the launches (the most time consuming).

My time in Iceland was a great learning experience. Working with some of the pre-eminent scientists in the fields of dynamics and predictability (and spending most of the day discussing the weather!) really helped improve my understanding of the development of mid-latitude weather systems and better understand their predictability.


Figure 2: On-board the FAAM aircraft.

After returning from Iceland I got the opportunity to fly on the FAAM aircraft (Figure 2) whilst it was on a mission for another project. The flight aim was to perform a radiometer inter-comparison by taking coordinated measurements of deep-frontal cloud to the north of Scotland with the HALO and Safire aircraft. The flight was remarkably turbulent free (I‘d been hoping for more of a roller coaster ride), although we did perform a profile right through the cloud to an altitude of less than 50 ft, which was pretty fun! Whilst on the aircraft we were also able to plot measurements being taken in real time on an on-board computer.


Figure 3: Flying at an altitude of 35 ft.

NAWDEX was a great opportunity to get first-hand experience of a major international field campaign (and see some of Iceland).


NERC Course on Polar Fieldwork Skills

Email: r.frew@pgr.reading.ac.uk

The aims of the NERC funded BAS run course, “A skills framework for delivering safe and effective fieldwork in the polar regions”, were to learn how to safely and effectively plan and carry out fieldwork at the poles. And in doing so, to give 16 early career polar scientists across a range of disciplines the opportunity to go to the Arctic and learn practical fieldwork skills that we don’t pick up from our day to day office work.

The first part took place at Madingley Hall in Cambridge where we were briefed as an entire cohort on planning, logistics, instrumentation, risk assessment, GPS mapping, health and safety, and were exceedingly well fed as part of the process….

The sunny early morning views that greeted us into Ny Ålesund.

Next we set off to put what we had learnt into practice in Ny Ålesund, on the Island of Spitzbergen (translates as ‘pointy mountains’) in Svalbard. Ny Ålesund is a small international village predominantly inhabited by scientists, with a peak population in summer of around 150, and a hardy winter population of 35 toughing out the minimal daylight hours and chilling temperatures, which reach minimums of around -20°C! Our journey began with three flights, and a stopover in Longyearbyen, also known as Santa Claus town, although it looks a lot more industrial than the name implies. We then had a 3.30am start which was aided by the 24 hour daylight to get the boat to Ny Ålesund. After 4 hours of queasiness we arrived at the NERC UK Arctic research station in Ny Ålesund.

The group all kitted out in front of the NERC UK Arctic Research Station. Photos courtesy of Simon Morley.

The first task we had to do after arrival was the rifle training course. This felt like a dangerous activity to be doing at 2pm in the afternoon after a 3.30am start. However it is safe to say we were all sufficiently awake after the first gun shot… We never left the NERC Arctic base without a massive rucksack full of layers, food, water, flask etc and most importantly a rifle and flare gun in case of running into a polar bears. As we are essentially trespassing on the bears’ territory, it is up to us to avoid disturbing them and to use rifles for self-defence as a last resort.

Terrestrial wildlife around Ny Ålesund. The greatest wildlife threat we faced was the cheeky Arctic fox stealing our sandwiches!

In Ny Ålesund you are very far removed from civilisation, even via digital means as there is no wifi (due to a large experiment detecting quasars) or phone signal. Therefore life in Ny Ålesund feels timeless, as outside events that rampage on social media feel far removed and irrelevant. However signatures of global warming are evident, with the extent of glaciers noticeably retreating each year, and sea ice becoming a rarer and rarer occurrence in the fjord within the living memory of residents of Ny Ålesund.

From left to right: View of Ny Ålesund, the closest we came to a polar bear in the doorway of the mess building, old hut from the mining industry.

The past mining infrastructure is evident everywhere, and classified as ‘heritage’, meaning that despite thinking of them as eyesores, in the otherwise immaculate views the run down infrastructure is actually protected as part of Ny Ålesund’s history. The NERC UK Arctic base was very cosy, we definitely weren’t roughing it like all those early polar explorers! The base is run by station manager Nick Cox, who was full of stories about everything and anything. Most evenings ended with everyone staying at the base gathering together for storytime with Nick in the living room of the UK Arctic base. Everyone in Ny Ålesund went to the mess building (best view I’ve ever had whilst eating breakfast!) in the centre of Ny Ålesund for meals, and on Saturdays everyone makes more of an effort to change out of work clothes and enjoy good food and wine together before heading to the small pub which opens on Saturday nights for people to gather to drink, chatter and dance.

Every time we left the UK station we had to take an enormous rucksack filled with food (packed lunch and lots of snacks, Mars bars disappeared like gold dust), waterproofs, spare layers, emergency blanket, first aid kit, temporary shelters, spare batteries for any equipment needed, flare gun, rifle, bullets, a satellite phone (one between the group), radio (at least one for each separate group). Keeping in contact via radio is very important, even if our group was going to be just 15 mins late we had to radio in and let the people at the station now so they can amend the signing out book. There was also a radio line for all of the stations in Ny Ålesund, so everybody would know if somebody was in trouble or extra help was needed. All the extra layers were essential. In just the five days we were there, we saw sun, rain, snow, sometimes all in one day! Preparing for all eventualities and all of the `what ifs’ is essential for polar fieldwork.

We had two main projects that required fieldwork planning and execution. The first was a two day marine biology project (led by Simon Morley from BAS) which was undertaken in two boats followed up by lab work. We took sediment grabs, plankton nets, CTD profiles (measurements of salinity, temperature and density), put down traps overnight. The aim was to investigate the difference between near rivers and near glaciers, and build up a picture of the food web there. Understanding the small marine creatures at the base of the food web and their temperature tolerance has important implications for larger marine and terrestrial creatures higher up the chain.

Left to right, getting our hands dirty sieving the sediment samples on the boat, putting on the immersion suits before getting onto the smaller boat in case of falling in! Photos courtesy of Simon Morley and Ed King.

The second two day task (led by Ed king from BAS) was to investigate the retreat of a glacier about 4-5km from Ny Ålesund called Midtre Lovénbreen. We carried out was to do a ground penetrating radar survey along and across the nearest glacier to Ny Ålesund to measure the ice thickness. Also, we mapped out the snout of the glacier and took photos to compare the glacier to previous years. A 15-20m retreat of the snout of the glacier relative to last year was measured!

Clockwise from left: Setting up the geophysics kit for a transect on the glacier, Midtre Lovénbreen in 1999, Midtre Lovénbreen September 2016. Glacier photos courtesy of Ed King.

The five or so days we had in Ny Ålesund flew by and before we knew it, it was time for us all to take the (very choppy) boat journey back to Longyearbyen before heading back to the UK. I really, really enjoyed the course, and I would highly recommend to any PhDs or Postdocs who study the poles to consider applying for the course in 2017!

Thanks to everyone at BAS involved in organising the course, in particular Alistair Crane, Blair Fyffe, Simon Morley, Ed King, Nick cox, and of course Ali Teague for organising all of the logistics and ensuring we all got there and back as smoothly as possible!