How deep is your mud? Pinpointing hidden transitions in restored saltmarsh sediments to support robust assessment of carbon stocks

Knowing how much sediment has been deposited is really important for carbon monitoring, reporting and verification. Here we tested some cost-effective ways to determine the depth to pre-existing soil after a saltmarsh has been created. The work is published in Estuaries and Coasts.

Tidal inundation of saltmarshes can mitigate anthropogenic carbon dioxide emissions by rapidly accumulating carbon-rich sediment, with the potential to sequester this “blue carbon” for thousands of years. The desire to remove atmospheric carbon, alongside increased flood risk from sea-level rise, is driving scientific and financial interest in restoring low-lying land into saltmarshes. Saltmarsh restoration buries agricultural fields with marine or estuarine sediment, yet the transition from agricultural soil to saltmarsh sediment is often difficult to observe in sediment cores. Quantifying sediment accumulation is critical for calculating the carbon benefits of saltmarsh restoration, and a pre-requisite for generating financial returns.

At Bleadon Levels, a restored saltmarsh in Somerset, UK, we tested several methods to determine the transition between agricultural soils and saltmarsh sediments. Calcium (Ca) and inorganic carbon (IC) were significantly more concentrated in the upper parts of cores, interpreted as marine carbonates within saltmarsh sediment deposits. The biomarker-based Rsoil index agreed with Ca and IC data. Organic carbon (OC) measurements did not show matching changes, demonstrating that OC variations with depth do not reliably identify transitions from saltmarsh to agricultural layers. Thus, saltmarsh sediment depth can be determined using relatively simple, cost-effective Ca and IC concentration measurements, and restoration schemes should consider these techniques in their monitoring, reporting and verification procedures.

Comparing loss-on-ignition, acid decarbonation and combustion elemental analysis for measuring organic carbon concentrations – recommendations for best practice

After testing various lab protocols we have a strong preference for coupling accurate and precise instrumental measurements with combustion pre-treatments to isolate and measure organic carbon. This work was published in Organic Geochemistry.

Quick and cost-effective measurements of organic carbon concentration are fundamental for a variety of environmental projects, but not all methods produce reliable results. Poor quality baseline data could compromise an entire study.

Measuring the total amount of carbon in a sediment sample is usually carried out by an elemental analyser, which makes quick, accurate measurements of carbon and nitrogen. However, sediments can contain carbon in a range of forms – plant matter, mineral-bound organics, microbial biomass, shells, carbonate minerals, and more. Sometimes distinguishing all these sources might be criticial, but often the split between organic and inorganic carbon is sufficient, and important since the organic and inorganic carbon cycles are very different.

For this study, we investigated three ways of measuring the amount of organic and inorganic carbon in a sediment, with a focus on young materials such as saltmarsh carbon.

  1. Loss-on-Ignition: Burning the samples a fixed temperatures to combust the organic matter (at about 500 °C) and decompose inorganic carbon (at 800 – 900 °C). Use the change in mass to estimate the amont of carbon present.
  2. Acid digestion followed by elemental analysis: Removing the inorganic carbon by reacing with acid, and then measuring the remaining organic carbon.
  3. Combustion followed by elemental analysis: Remove organic carbon in the furnace, measuring the remaining inorganic C, calculating the OC lost.

Perhaps the most important finding should not have been a surprise – Loss-on-Ignition relies on combusting organic matter, but wants to measure organic carbon, therefore a conversion between the two is needed. There are lots of conversions in the literature, and they all produce different results. Our testing showed that some common conversions are out by more than 50%, and we cannot recommend using Loss-on-Ignition for current or future work.

We also showed that using acid to remove inorganic carbon also removed up to 40% of the organic carbon, so we would avoid using this technique unless it’s imperative to measure the organic matter directly, for example in stable carbon isotope analysis.

As a final observation, this work was enhanced by contributions from a cohort of undergraduate student co-authors who generated real-world saltmarsh data. For this, I am very grateful.

Enhanced petrogenic organic carbon oxidation during the Paleocene-Eocene thermal maximum

This collaboration with the University of Southampton used Raman spectroscopy to investigate cores from an ancient climate event. The study was published in Geochemical Perspectives Letters.

The PETM event caused major, rapid global warming of 4-6 °C, which also released large amounts of carbon into the atmosphere. The climate change associated with the event altered hydrological cycles and may have driven erosion and degradation of petrogenic organic carbon (OCpetro), which may have been a further positive feedback in the PETM climate system.

This is the first study to use Raman spectroscopy to investigate OCpetro oxidation at the PETM. We found that there was an increased contribution of graphite during the PETM, likely caused by intensified physical erosion and enhanced OCpetro oxidation.

In areas where there is a range of OCpetro inputs, both graphitic and disordered, Raman spectroscopy appears to be a very promising tool for investigating past changes in the carbon cycle.

Allochthonous carbon primarily of marine origin in Irish saltmarshes: Novel insights from bacteriohopanepolyol biomarkers

This collaboration with the BlueC project at University College Dublin measured organic carbon and BHP biomarkers in saltmarshes from the East and West coasts of Ireland. The paper is published in Sustainable Microbiology.

A map of sample sites used in this study

Organic carbon concentrations were high and very variable, from 0.26% up to 26%, a 100 times increase. Concentrations were particularly high at the top of cores from the upper marsh (furthest from the sea). Comparing this to the BHP data showed that these samples were rich in marine organic matter. Terrestrial BHPs were only found in high concentrations at depth in the oldest cores. Therefore, most of the carbon in the saltmarsh sediments has been brought in on the tide, and the influence of tidal sediment supply on saltmarshes is important for their growth and survival.

This is our first study using BHPs to investigate saltmarshes. The oldest, high-marsh sediments had terrestrial BHP signatures, but everywhere else the source appears to be marine.

Past and present bacterial communities in deglaciating northern latitude catchments reveal varied soil carbon sequestration potential

My first PhD student, Saule Akhmetkaliyeva, has published her thesis in Science of the Total Environment. Her study compares organic carbon and bacterial communities across three deglaciating Arctic catchments.

Graphical abstract from Akhmetkaliyeva et al., 2025

After a glacier thaws and retreats, the exposed land is usually quite bare and carbon poor. Saule visited deglaciating sites in Sweden, Iceland and Greenland to measure the amount of carbon present in the sediments and the development of soil bacterial communities over time. She found that bacterial communities change as the soil develops and the organic carbon content rises.

Soil sampling in Tarfala Valley, Sweden

In Sweden, the deglaciation was very recent and the soil very thin, with lowest carbon contents and very few soil biomarkers. Iceland had some very young soils, but also some older moraines with age estimates – older moraines had higher carbon contents and a more developed soil bacterial community. In Greenland, the catchment had been deglaciated for thousands of years and a fully-developed ecosystem was present, with the highest amount of organic carbon, plenty of soil-specific biomarkers, and a stable microbial community.

Older, developed soils in Iceland had higher concentrations of organic carbon and a greater proportion of soil-specific BHP biomarkers

The paper is available, open access, from the journal website and via MMU e-space

Sharing our Standard Operating Procedures

A lot of science is like baking – you follow a procedure (recipe) and generate a batch of data (cake). If the same sample is analysed following the same procedure in two different laboratries, the data generated should be the same. This is not always the case, but standardising the approach across a research community reduces the scope for variability between datasets and allows for comparison between studies.

In a lot of cases, protocols are generated by carefully reading the methods section of a published paper, but publications are often written very concisely and some of the steps taken in the lab could be left out or hard to follow. The step-by-step protocol is less likely to be published, but could be much more useful for those trying to build upon published studies.

To avoid that confusion, I have created a new section of the website dedicated to publishing the latest version of our laboratory standard operating procedures. These are published under a Creative Commons CC-BY 4.0 license so you are allowed – encouraged in fact – to use, adapt, improve and share these protocols.

I also welcome feedback regarding the protocols. Comments are enabled on each one and you are welcome to highlight steps that are unclear or could be improved.

Rapid carbon accumulation at a saltmarshrestored by managed realignment exceeded carbon emitted in direct site construction

In the last few years, I have expanded my research into the burial of carbon in saltmarsh environments, especially around the UK. This is the first paper I have published on the topic. The paper is available Open Access via the journal website.

A composite map/aerial image of the Steart Marshes saltmarsh site

Saltmarshes, which is an coastal wetland which is flooded and drained by saltwater brought in on the high tide, are natural features acrosst the UK and around the world. In the UK, many saltmarshes were drained to form farmland, with a sea defence built between the drained marsh and the river or estuary. Rising sea levels threaten the reclaimed marshes, and the nearby fields, towns and villages, with flooding. Often it is decided that retreating from the drained land is the best way to protect other, more valuable, assets nearby. Through a process called “managed realignment”, the sea defences are breached and the tide returns to the saltmarsh.

Realigned saltmarshes are often lower than the local high tide level, and are rapidly filled with sediment and saltmarsh plants when the water returns. This creates a habitat that can attract wetland birds and, since the sediment has organic carbon associated with it, also generates and opportunity to bury carbon in the marsh.

This paper investigates two things: how much organic carbon was buried on a realigned saltmarsh in the first years after it was created, and how does this carbon burial compare to the emissions generated by the construction of the site.

Samples were collected from Steart Marshes, a site in Somerset, UK, that was flooded in 2014. The samples were analysed for their total carbon and organic carbon content using analytical facilities here at Manchester Met. The carbon concentrations were scaled up to the entire site using sedimentation data calculated from laser scans of the marsh collected at different time points.

There has been a very rapid build-up of sediment at Steart Marshes since the sea defences were breached

We found that the organic carbon burial rate (19 tonnes per hectare per year) was very high compared to other saltmarsh sites, mostly because the sediment built up very rapidly (75 mm per year) after the sea defences were breached. The organic carbon buried on site is much greater than the carbon emissions generated by the diggers and bulldozers used to make the new marsh, and so it seems that there has been a net climate benefit by creating the marsh.

However, the next piece of the puzzle is to fully understand the types of organic carbon being buried on the site. Not all carbon has the same climate benefit associated with it, and so further work is required to properly calculate the climate change mitigation potential of restoring saltmarshes.

Characterization of diverse bacteriohopanepolyols in a permanently stratified, hyper-euxinic lake

This paper is available Open Access via the journal website.

Water filters, extracts and column chromatography for the samples from Mahoney Lake

This publication, led by Molly O’Beirne from the University of Pittsburgh is a really exciting look at BHP biomarkers and microbes in an unusual Canadian lake. My role was to measure and identify the BHPs present in the lake, including finding a ‘new’ BHP that had not been described before.

Mahoney Lake, British Columbia, is a small lake with a really high concentration of sulfur, and a low concentration of oxygen. This classifies it as ‘euxinic‘, and Mahoney Lake is 100 times more sulfidic than the Black Sea. Not only that, but the lake switches from oxic to euxinic within the top 7-8 metres, meaning that sunlight can penetrate into the euxinic layer. This study looked at the changing bacterial communities and BHP biomarkers present in the different layers of the lake.

Water filter samples were collected at a series of depths in the lake, from the oxic layer, through the changeover to euxinia (the ‘chemocline’), down to the sediment at the bottom. At the chemocline, a large community of purple sulfur bacteria were collected which made the filters turn a bright pink-purple colour (see the picture above), which makes a nice change from the usual brown-grey water filters usually collected from lakes and rivers.

Chromatogram and mass spectrum showing the novel BHP with m/z 710

Back in the lab in Pittsburgh, these filters were extracted using solvents and the BHP molecules were separated out from everything else, transferred into small vials, and posted across the Atlantic. After a few days in customs, they made it to Manchester Metropoltian to be analysed on the LC-MS. When looking through the data, there were several common BHPs present, but also a large amount of a previously unknown BHP molecule. It was seen on the chromatogram at a similar time to the ubiquitous ‘aminotriol’ BHP, but careful analysis of the mass spectrum showed that the molecule and its fragments were four mass units ligher than aminotriol, with m/z (mass to charge ratio) 710 rather than 714. We think that this molecule has the same structure as aminotriol, but has two carbon-carbon double bonds in the structure.

Since this molecule was only found in the lower parts of the lake, we think it could be directly linked to euxinic environments. In future work, I will look for this molecule in other euxinic and oxic lake samples to test whether it is a reliable biomarker for euxnia. If it is, BHP 710 can be used to identify euxinia in ancient lakes throughout the geological record.

To find out which bacteria might be making these molecules, Trinity Hamilton from the University of Minnesota sequenced the bacterial genomes present in the lake filters. Genes that produce BHPs were found in samples from the lower parts of the lake, and the BHP producing bacteria are probably Deltaproteobacteria, Chloroflexi, Planctomycetia, and Verrucomicrobia.

At the bottom of the lake, the BHPs present change again. Bacteriohopanetetrol (BHT) is the most common, and methylated BHTs are only found in the lake sediments. This makes us think that bacteria living in the oxygen-free sediments at the bottom of the lake are the source of the methylated BHTs, rather than bacteria living in the oxygenated upper layer of the lake.

Overall, this has been a really fun and interesting study to be part of, and provides loads of new research questions as well as answers. Other researchers looking to analyse BHPs in their samples are welcome to get in touch to discuss collaborations.

The quantification of di-octyl terephthalate and calcium carbonate in polyvinyl chloride using Fourier transform-infrared and Raman spectroscopy

This article is available Open Access via the journal.

Typical results when measuring PVC using Raman spectroscopy

A slight detour from my usual environmental chemistry work, this paper was led by PhD student Kate Irvin and looks at characterising PVC samples in an industrial setting, finding ways to optimise the product development process.

When developing a new polymer product, it is important to regularly test its properties and confirm its ingredients. Typical tests take hundreds of hours and can delay the development cycle, adding costs to the process. In this paper we demonstrate some rapid, non-destructive techniques for quantifying the amount of plasticiser (dioctyl terephthalate) and filler (calcium carbonate) within a PVC sample.

Fourier transform-infrared spectroscopy and Raman spectroscopy were used, since they are quick, easy-to-use and non-destructive methods of identifying samples. The time savings alone of using these methods compared to using traditional hardness, softness and tensile tests could reduce product development costs by 50%.

Methanotroph-derived bacteriohopanepolyol signatures in sediments covering Miocene brown coal deposits

This paper is available Open Acess via the journal website.

When I joined Manchester Metropolitan University in 2016, I was awarded a small grant to set up an analysis facility measuring a group of molecular biomarkers, bacteriohopanepolyols (BHPs), that are found in environments throughout the world. This paper is the first to be published on BHPs measured at Manchester Met.

Cores of polish lignite used in this study

In this paper, led by Anna Pytlak, samples from two Polish lignite deposits were analysed via LC-MS to see which BHPs were present in the samples, and whether these could be linked to methane-generating bacterial living in the rocks now, or millions of years ago.

My role, along with PhD student Saule Akhmetkaliyeva, was to extract the BHP biomarkers from the sediment samples and analyse them on the time-of-flight mass spectrometer at Manchester Met. The molecules found in the mass spectrometer were compared against known BHP results, and identified as being from various types of bacteria. This included both Type I and Type II methanotrophs (bacteria that consume methane), including some living methanotrophs.

BHP concentrations were higher in the lignite than the surrounding mineral soil, suggesting some form of active bacterial commuity supported by the lignite deposits that cannot be sustained in regular soil. Living methanotrophs means that there’s a chance some of the methane released over time by the lignite is eaten by the bacteria and not released to the atmosphere.

If you would like to measure BHPs in your own samples, please get in touch to discuss collaborations!