Source, transport and fate of soil organic matter inferred from microbial biomarker lipids

06/09/2016 UPDATE: The paper has been accepted and is now published. The final version is available from the journal.

Our international team of East Siberian researchers currently has a paper in open review at Biogeosciences. The discussion paper, and its interactive comments, can be downloaded from the  journal website.

The paper studies a group of compounds called “bacteriohopanepolyols” (BHPs for short), which are found in the cell membranes of a range of microbes and are therefore one of the most common organic compounds around. They are found in modern and ancient sediments from all over the world. This study has concentrated on two groups of these. Group 1 is the soil marker compounds. These are only found in soils, and so have been used as tracers for soil material in rivers, lakes and offshore. Here is how they are spread across the East Siberian Artic Shelf:

BHPfig2a (Custom)
Soil marker compounds across the Arctic Shelf

Note how the soil marker concentrations are highest (orange colours) near to the rivers and coastlines. By measuring the concentration next to the river mouths, and in the sediments being washed away by coastal erosion, we show that it is not just rivers that are delivering the soil markers to the Arctic Ocean.

There is no single compound that is a true tracer for carbon produced in the ocean itself, but the compound bacteriohopanetetrol (BHT) is most abundant in marine settings despite being found in soils as well. Therefore if your sample is rich in BHT, and poor in soil markers, it is likely dominated by carbon from the ocean. Here’s a map of BHT across the East Siberian Arctic Shelf:

BHPfig2b (Custom)
BHT, a marine marker, is present across the Arctic Shelf

The BHT results show a fairly constant amount across the ocean floor. If we compare the soil marker concentrations to the BHT concentrations, we can see which areas are rich in soil carbon (more soil markers than BHT) and which are rich in marine carbon (more BHT than soil markers). This comparison is called the R’soil index, and is shown below:

R'soil index on the Arctic Shelf
R’soil index on the Arctic Shelf

The R’soil index shows that all along the East Siberian Arctic coastline, offshore sediments are dominated by carbon from the land. As you go further offshore, especially in eastern parts nearer to the Pacific Ocean, marine carbon is more important. This result shows a similar pattern to that seen using stable carbon isotopes, but is different to the pattern shown by the BIT index. Therefore these two indices, both based on microbial biomarkers, are tracing different parts of the carbon cycle.

Preservation of terrestrial organic carbon in marine sediments offshore Taiwan

This paper was published in the open access journal Earth Surface Dynamics, and is available through the journal website and the MMU e-space repository.

The paper is a combined effort from a large team of researchers interested in the way that organic carbon is exported from small tropical islands. These islands are very biologically productive, the forest grows quickly in the warm, wet climate. They are also responsible for delivering large amounts of sediment to the ocean. Rocks are weakened by earthquakes and then eroded by the frequent tropical storms that hit the islands. This washes sediment and carbon out to sea via two mechanisms. High sediment concentrations lead to ‘hyperpycnal’ plumes of material flowing along the ocean floor, lower sediment concentrations cause ‘hypopycnal’ flows that stay at the ocean surface. Both systems can spread sediments and carbon a long way offshore.

Marine sediment cores look very similar to the sediment coming out of the rivers
Marine sediment cores look very similar to the sediment coming out of the rivers

It had long been thought that hyperpycnal delivery of sediment, which usually only occurs in the most extreme weather conditions when floods deliver vast amounts of sediment to the ocean in a short period of time, were efficient methods of organic carbon preservation. Our data confirmed this hypothesis, showing that little terrestrial organic carbon was lost during transport, and little marine carbon added to the mixture.

However, the dataset also investigated how efficient hypopycnal delivery can be. Sediment and carbon are delivered throughout the year, in smaller floods and less extreme storms, and it had been suspected that this mechanism exposed the carbon to oxidising conditions where it could be degraded and released as CO2. We showed that in Taiwan, where hypopycnal conditions exist but are still receiving and accumulating a large amount of sediment, the burial efficiency of carbon in hypopycnal conditions is still very high. Marine carbon is mixed into the sediments, but at least 70% of the terrestrial carbon survives.

This means that small tropical islands are even better at exporting and burying carbon than was previously thought, and therefore better at sequestering atmospheric CO2. We estimated that more than 8 Teragrams (million tonnes) of carbon could be buried each year throughout Oceania.


Decadal carbon discharge by a mountain stream is dominated by coarse organic matter

This paper, with Jens Turowski and Bob Hilton, was recently published as an open-access article in Geology and is available from the journal website and via the MMU e-space repository. In it we show that erosion and transport of large woody material (coarse particulate organic carbon; CPOC) is very important in terms of the overall carbon cycle, but is concentrated in very extreme events.

The research is based in the Erlenbach, a small river in the Alps that has been studied by Swiss researchers for several years. They have built a very sophisticated stream sampling station, which can capture everything that flows down past a gauging station. There is a large retention pond that catches the logs/pebbles/sediments and a shopping-trolley sized wire basket that can be moved into the middle of the stream to catch a particular time point (for example the middle of a large storm). The photo below was taken during winter when the river was frozen over, but you can see the v-shaped river channel, the three wire baskets ready to move into position to catch material, and the snow in the foreground covering the retention pond.

The sampling system in the Erlenbach River during winter
The sampling system in the Erlenbach River during winter

This sampling system led to Jens observing that there was a lot of CPOC coming down the river and piling up in the retention pond. A quick calculation suggested that this was a significant portion of the total carbon coming out of the river catchment, but the scientific consensus was that actually more carbon came through as fine particles than CPOC. An experiment was designed to test this.

Across a wide range of river flow speeds, the amount and size of woody debris flowing down the river was measured, both waterlogged and dry material. This allowed a rating curve to be defined – that is for a given river flow speed, how much organic carbon would be expected to flow down the river? The rating curve was very biased towards the high-flow end for CPOC, much more so than for fine carbon (FPOC) or dissolved carbon (DOC). At low flow rates, very little CPOC is moved, but at high flow rates a very large amount is mobilised.

Rating curve of organic carbon types vs. river discharge
Rating curve of organic carbon types vs. river discharge

During the 31 years of data collection there were four particularly large storms. Integrating over the rating curve shows two things. Firstly, if the large storms are ignored then the Erlenbach is already a major source of CPOC, about 35% of the total carbon, with CPOC being roughly equal to the FPOC estimate. Thus it is much more important than might previously have been imagined. If the extreme events are included, the CPOC becomes ~80% of the total organic carbon transported by the river.

A majority of the CPOC transported by the river was waterlogged, having sat on the river bank or behind a log jam while waiting for a large storm to wash it downstream. Waterlogging increases the density of the wood and makes it more likely to sink when it reaches a lake or the sea. My contribution to the paper was to provide evidence of this process. My PhD work in the Italian Apennines found CPOC, from millimetre scale up to large tree trunks, that had been preserved in ocean sediments for millions of years. Again, a lot of this CPOC is too large to measure using standard techniques, and suggests that rivers can deliver organic carbon from mountains to the ocean far more efficiently than previously thought.

Elephant Moraine 96029, a very mildly aqueously altered and heated CM carbonaceous chondrite

This paper is a result of collaboration with researchers at the University of Glasgow who I met while interviewing for a position. I didn’t get the job, but I did get talking to Paula Lindgren and we discovered a common interest in using Raman Spectroscopy to study organic carbon. This publication is the first result of that, and is available as an open-access article.

A little bit of meteorite, under an electron microscope
A little bit of meteorite, under an electron microscope

The paper is a comprehensive study of a meteorite collected from Antarctica. Antarctica is a great place to find meteorites because they sit on top of the ice and are easy to spot – sometimes the flow of ice even concentrates them into particular areas to makes things even easier. This meteorite is classified as a “CM carbonaceous chondrite” and has experienced very little change since it was part of the protoplanetary disc billions of years ago. Therefore we can use it like a time capsule to look at what the early solar system was like.

However, some meteorites are better time capsules than others. As they float around the solar system, they can build up ice, which can then be melted by radioactivity and the water released can alter the crystallography of the meteorite. Our paper uses a wide range of techniques to characterise the meteorite and show that it is one of the least altered carbonaceous chondrites ever found.

The techniques used included electron microscopy (both scanning and transmission techniques; SEM and TEM), X-ray analysis, X-ray diffraction, thermogravimetric analysis (TGA), oxygen isotope measurements and Raman Spectroscopy. My contribution was to use my automatic Raman processing technique to determine how crystallised the carbon in this meteorite was in comparison to carbon in other meteorites.

Mobilization and transport of coarse woody debris to the oceans triggered by an extreme tropical storm

This paper, led by Josh West and colleagues in Taiwan, was published in Limnology and Oceanography. The full text is available via the journal website, since all L&O papers become open access after three years, and through the MMU institutional repository.

The island of Taiwan, in the South China Sea, has an interesting, yet devastating, combination of climate, biology and geology. It sits on the plate boundary between Eurasia and the Phillipines, which are moving into each other and causing the island to rise out of the ocean. This leads to earthquakes as the land is pushed up, and rapid erosion as the mountains get steeper and taller. The mountain sides collapse as landslides, producing sediment that is prone to being washed away by Taiwan’s many rivers. These rivers may not be the longest in the world, but they carry a lot of water, because Taiwan sits in the tropical zone where the year-round high levels of rainfall are topped up by several typhoons each year. The final piece of this jigsaw is the biology – being in a warm, wet region means that Taiwan is very biologically productive, with extremely fast forest growth rates.

A Taiwanese reservoir after Typhoon Morakot
A Taiwanese reservoir after Typhoon Morakot

Coupling all of these features together leads to a heavily forested mountainous island on which the hillsides are regularly landsliding and generating woody debris (tree trunks, branches, shrubs etc.) The large typhoons that hit the island each year provide water which washes the woody debris into the rivers and then out to the ocean.

In 2009, Taiwan was struck by a particularly devastating tropical cyclone, Typhoon Morakot. The island received about 4 metres of rainfall in just a couple of days, enough to cause rivers to burst their banks, washing away entire villages and unfortunately leading to several deaths. I visited the island a few months later, and the clear-up operation was still going on. Beside the rivers was up to a metre of chaotic sediment with tree branches sticking out of it, since the waters had carried everything off the hillside and dumped it when the floods receded. A lot of the tree trunks made it all the way through the river, out to the sea. They washed up on the shoreline around Taiwan, and were reported as far away as Japan.

A Taiwanese river channel filled with logs after the storm
A Taiwanese river channel filled with logs after the storm

These trees contain a lot of carbon, which has been moved from the hillside to the floodplain and out to the sea. Our study tried to work out just how much carbon, in the form of coarse woody debris, was being transported during this storm. Single river channels, such as the picture above, could contain 40 million tonnes of carbon – how much carbon was washed away by the whole storm?

There were two independent methods used to make the carbon estimates. The first one compared aerial photography before and after the storm to look at how much area was affected by landslides, and how much of the island was covered in forest. If you combine the forest cover data with the landslide map, and correct for areas where landslides do not deliver the woody debris to the river network, an estimate of carbon mobilisation can be made

The second method used reservoirs as sampling facilities. Reservoirs have filters to stop large trees going through their exit pipelines, and so any woody debris reaching the reservoir will be stopped at the dam (see the top picture for an extreme example). Knowing the area of land that drains into the reservoir, and the amount of wood trapped at the dam, you can scale up to the area of the entire river catchment.

Both of these methods produced similar results, they agreed that there was a shocking amount of carbon washed to the ocean during the storm. The storm delivered 3.8 – 8.4 Teragrams of woody debris from Taiwan to the ocean, which represents 1.8 – 4.0 Teragrams of carbon. This is about 1/4 the annual delivery of carbon from the Amazon River, but most of that is as small particles. The woody debris delivery in these few days was over 10 times greater than the annual woody debris delivery from the Amazon. So one single event on a small island was significant from a global point of view, but how much carbon is a Teragram?

One Teragram is equal to one million tonnes; an oil tanker can carry 300 000 tonnes of oil (mostly carbon) and therefore the storm delivered 10 oil tankers worth of carbon to the ocean. Obviously this event is not as disastrous as an oil tanker spill – the woody material will rot down and provide food for ocean-living creatures as well as potentially being buried safely in the sediments.

Our paper shows just how much carbon can be washed away by a single storm, and highlights that large pieces of woody debris, too large to analyse by most techniques, are an important and probably under-studied element of the organic carbon cycle.

Out for Review: Macromolecular organic matter across the East Siberian Arctic Shelf

Following the successful experience of publishing in Biogeosciences, our latest paper has been submitted to their sister journal “The Cryosphere”, where it is currently out for open review. The Cryosphere is another fully open access journal from the European Geosciences Union where the review process is carried out in full view of anyone interested. This allows any reader to make comments on our paper, which I would encourage you to do. We will respond to comments through the journal webpage. The paper itself can be downloaded from the journal webpage.

Map of radiocarbon ages across the ESAS
Map of radiocarbon ages across the ESAS

The study continues our work on the East Siberian Arctic Shelf, and contains two new datasets. The first is a radiocarbon study, measuring the age of organic matter on the shelf using carbon dating (see map above). By measuring the age, we can determine whether the carbon has come from the ocean (very young), the topsoil (quite young) or the coastal permafrost (thousands of years old). We combined our results with those already measured on the shelf to form the most complete radiocarbon map for this area. The high-resolution map shows that areas close to the shore and away from the major rivers are home to very old carbon, almost certainly sourced by erosion of old permafrost cliffs. Elsewhere on the shelf, the carbon is younger but not as young as modern topsoils or ocean carbon. Therefore the coastal erosion carbon is having an influence right across the shelf.

A pyrolysis probe can heat samples to 900 C in milliseconds
A pyrolysis probe can heat samples to 900 C in milliseconds

Our second technique is pyrolysis GCMS, where samples are smashed into small pieces using high temperatures and the small pieces are then analysed using GCMS. This technique generates a large amount of small pieces, too many to analyse each one individually, and so we decided to concentrate our efforts on a few target molecules. These included Phenols, which are probably sourced from lignin, a major component of land plants, and Pyridines, which are nitrogen-containing compounds probably sourced from proteins. We think that a lot of the Pyridines in the Arctic Ocean will come from organisms living in the ocean itself, and therefore the Pyridines are a potential tracer for marine organic matter. By comparing the concentrations of Phenols and Pyridines, we can estimate the amount of terrestrial and marine organic carbon in a sample.

Phenol-Pyridine ratio on the Arctic Shelf
Phenol-Pyridine ratio on the Arctic Shelf

In the map above, red areas are dominated by Phenols and are therefore rich in terrestrial carbon, blue areas are dominated by Pyridines and are therefore rich in marine carbon. This pattern matches very well with our previous work in the region, showing that there is a transition from terrestrial to marine conditions across the Arctic Shelf, and that the transition zone lasts for hundreds of kilometres offshore. This means that there is a lot of terrestrial carbon being deposited, and hopefully buried, on the shelf, rather than all of the eroded carbon being degraded and released as CO2.


GDGT distributions on the East Siberian Arctic Shelf

Our paper, “GDGT distributions on the East Siberian Arctic Shelf: implications for organic carbon export, burial and degradation” has now been published. You can download the paper, and the underlying data, from the Biogeosciences website here.

As I mentioned before, this paper has been submitted, reviewed and published completely open-access. This means that the original paper, the reviews and our response are all archived online forever. All of this is available freely to anyone, without the need to pay for access. You are free to copy, distribute and make use of the data and graphs as long as the original paper is cited (also known as a CC-BY copyright license)

Boxplots showing how GDGT biomarkers vary offshore
Boxplots showing how GDGT biomarkers vary offshore

In the paper we show the first map of GDGT biomarkers from the East Siberian Arctic Shelf. This region is extremely remote yet very important within the global carbon cycle. Our work shows that this is an area of complex interaction between rivers, coastal erosion and open ocean productivity. The GDGT biomarkers are very useful here as a tracer of carbon being washed away by the rivers and being produced in the oceans, and this allowed me to make a model of the Arctic Ocean in this region to better understand how all of the different processes interact.

Our model of biomarker export across the Arctic Shelf
Our model of biomarker export across the Arctic Shelf

As an author, the publishing process for Biogeosciences was interestingly different. There was a reasonable amount of time between submitting the paper and final publication, but that was mostly due to the interactive public discussion stage which most journals do not have. During this time the paper was available and citable, which means that although it was relatively slow progress towards final publication the story was out there very quickly. I’m keen to go for this style of publishing again in the future.

Redistribution of multi-phase particulate organic carbon in a marine shelf and canyon system during an exceptional river flood

I have recently had a paper accepted in the journal “Marine Geology“, which looks the transport of organic carbon during a major typhoon in Taiwan: “Redistribution of multi-phase particulate organic carbon in a marine shelf and canyon system during an exceptional river flood: Effects of Typhoon Morakot on the Gaoping River–Canyon system”.

Typhoon Morakot was a particularly severe tropical cyclone that hit the island in 2009, causing flooding, mudslides and hundreds of deaths. From an organic geochemistry perspective, it also transported sediment and organic carbon from the hillsides and floodplains out to the South China Sea. Some of this carbon was “fresh” material, coming from trees, grass, shrubs and soil. Other parts of the carbon was “fossil” carbon, sourced from the mountains running down the centre of the island, or from sedimentary rocks in the foothills and floodplains. It is important for the global carbon cycle to understand how much of the land-sourced (terrestrial) carbon makes it to the ocean floor, because this process can lead to carbon being stored in the sediments for millions of years.

Out at sea, all of this organic carbon and sediment was mixed together with material produced in the water column, by algae and plankton. Mixing three carbon sources together makes it very difficult to work out how much of each one is present in a sample, which is where my work comes in. By combining measurements of the nitrogen to carbon ratio with the carbon-13 to carbon-12 isotope ratio, these three inputs can be identified. I did this for samples collected in the Gaoping Canyon, a deep submarine channel running from the island out to the deep sea. I found that terrestrial organic carbon was the dominant form of carbon present in the canyon and that therefore millions of tonnes of carbon were transported to and buried in the ocean by the typhoon.

Figure from the paper
Unmixing plant matter, bedrock OC and marine carbon


This carbon will most likely be locked away in these sediments for thousands or millions of years, while on the island more trees will grow to replace the ones washed away in the storm. In the process, carbon dioxide will be taken out of the atmosphere, so the storm-flood-burial cycle should go some way towards slowing the rate of climate change.

If you would like to download the paper, it is available freely via open access or as a PDF.

GDGT distributions on the East Siberian Arctic Shelf: Discussion paper

My last post talked about Open Access publishing, and the various philosophies for spreading (and/or making money from) academic knowledge. Now there is a chance to play an active part in the publishing process. My latest paper has been submitted to a journal called “Biogeosciences” which is administered by the European Geosciences Union (EGU). Their journals are published using a super open process, where more than just the final paper is released free-of-charge to the world. Whereas in regular Open Access publishing anyone is free to read the final reviewed work, in EGU journals the initial version is also made available. Two reviewers are selected from the community, and their reviews are shown on the website as well. Everyone else is free to read and comment on the paper, raising questions that the authors have to respond to. It is hoped that this system is a) transparent b) open to more (constructive) criticism than the standard two-review system and c) faster, since the paper is available for people to read at an earlier stage of the process.

A figure from the paper showing land-sourced GDGT molecules
A figure from the paper showing land-sourced GDGT molecules

Our paper discusses the distribution of GDGT biomarkers on the East Siberian Arctic Shelf. We measured these biomarkers to determine whether the organic matter deposited on the shelf came from land or ocean sources. When we had made these measurements, a model was created to try and explain the observations and work out the budget for carbon being delivered to the shelf from large Arctic rivers.

If you want to read and comment on the paper it is available on the Biogeosciences website

What is: Open Access publishing?

Peer review is generally accepted to be the least-worst way to generate trust in the scientific publishing process. By allowing experts in the field to read, critique, confirm, challenge and improve your work before it enters the mainstream body of science, poor quality or erroneous work should be filtered out before it gets the chance to distort public perception and policy. However, it’s not without its critics. Anonymous reviews allow reviewers to partake in spiteful and/or personal attacks which do nothing to improve the science behind the work, and can delay or even prevent publication of perfectly acceptable work. Also, the system is based on a financial system that only seems to benefit the publishing companies. In traditional journals, scientists relinquish their copyright to a company that then charges them and their colleagues to read the work, restricting access to those in universities or with big budgets (individual papers can cost $30 or more, subscriptions run to the thousands). Journal reviewers and editors work for free, considering the process as part of their community obligation despite the for-profit journal getting the real benefits.

Recently, open-access publishing has started to change the way that ordinary people can read the research that they, through their taxes and charity donations, have paid for, but the business model for the publishers is generally similar. In a typical open access publishing workflow, the researchers submitting the paper pay an “article processing charge” (APC) once the work has been accepted. Paying this charge, which is often £1000 or more, allows them to retain the copyright, and lets anyone, anywhere in the world, read the paper for free. It shifts the costs for access from the distributed consumers, who would often lack the resources to pay for the research, to the universities producing the work in the first place. Most research grant bodies now request open access publishing, and have provided some funds to cover the APCs, for now at least. Reviewers and editors are still unpaid, and publishers still make a profit, in fact since many articles are not open access then universities (i.e. taxpayers) are on the hook for both the journal subscriptions and the APCs.

So why are researchers still paying these companies such large amounts of money (profit margins are amongst the best of any industry)? Well, academic promotion is mostly decided by your publication history; the easiest way to judge a publication history is to look at the journals that a researcher publishes in, rather than reading the papers themselves. Therefore the pressure is on, especially for young researchers, to publish in the most prestigious journals, and they tend to be the most expensive ones, where articles are either restricted access or have high APCs.

Recently, there has been a shift towards more open and accountable publishing systems, with journals allowing researchers to publish either draft versions or even the finished paper on their website without violating copyright. Many universities have created online repositories to let researchers store and share their work (mine is available through my Manchester profile page), which are imperfect, since it’s often hard to find the papers, but better than nothing.

Even within my short career, the way that people publish and access science has changed; open publishing is still in development and it’s likely that further innovation in the next 5-10 years will change the landscape even further.