Researchers from the Connecticut Agricultural Experiment Station and the University of Massachusetts have pioneered the use of tomography for assessing carbon storage in trees. While assessing this technique’s capabilities, they found that tree damage caused by wood-decaying fungi means that forests store less carbon than previously thought. As forests play a vital role in sequestering atmospheric carbon, the team’s work has important implications in the fight against climate change. Their results suggest that tomography could offer greater insight into forest carbon cycles, allowing decision makers to implement more effective policies to mitigate climate change.

Wood-Decaying Fungus and Carbon

Human-induced climate change is arguably the most pressing issue facing society today. Its main driver is an increased concentration of atmospheric carbon dioxide, which traps heat energy and causes the planet to warm, leading to an array of negative consequences. In fact, carbon dioxide levels have risen by almost 45% over the past two centuries, primarily caused by humans burning fossil fuels.

The world’s forests play a vital role in absorbing carbon dioxide from the atmosphere and storing this carbon as wood, during the process of photosynthesis. Widespread deforestation means that this process is severely reduced, causing levels of atmospheric carbon dioxide to rise further. Therefore, today’s most commonly-used climate models take forests and future deforestation into account when predicting future atmospheric carbon levels and climate scenarios.

However, one factor that has been overlooked in our current climate models is internal wood decay, which is the process whereby fungi decompose wood inside of living trees, resulting in the release of carbon dioxide back into the atmosphere, partially offsetting the amount of carbon that trees absorb. As part of a collaborative project, researchers from the Connecticut Agricultural Experiment Station and the University of Massachusetts have found that the amount of carbon absorbed by forests may be significantly overestimated in climate models, due to their failure to accurately account for carbon lost through internal decay in living trees.

In order to obtain a more accurate picture of the planet’s future climate, and to identify the most effective solutions to climate change, this important factor must be accounted for. ‘However, wood-decaying fungi are some of the most difficult plant pathogens to study because they are mostly hidden to us,’ notes Dr Nicholas Brazee of the University of Massachusetts. ‘Specifically, many of these fungi live within trees, making it challenging to diagnose decay with simple visual assessments.’

Dr Brazee and Dr Robert Marra of the Connecticut Agricultural Experiment Station, who leads the project, set out to find an accurate and non-destructive method of testing trees for internal decay, which could be used to measure the scale of such decay in the world’s forests.

The PiCUS sonic tomograph established on the lower trunk of a pin oak

Observing Decay

Over the past few decades, researchers have attempted to measure internal decay in trees without causing too much damage. Previous methods have all involved drilling into trees, which has the potential to compromise their long-term health. In contrast, more recently developed methods are minimally invasive, causing little if any damage to the health of the tree.

One such method is called sonic tomography, which measures the speed of sound waves as they travel through wood. Because sound waves travel slower through lower density materials, this technique is able to identify decayed wood, which is less dense than non-decayed wood. Complementing sonic tomography, electrical-resistance tomography measures the electrical conductivity of wood: moisture builds up in wood as it decays and its electrical conductivity increases.

Based in Germany, the company Argus Electronic GMBH recently developed a piece of equipment called the PiCUS Tools Box, which employs both sonic tomography and electrical-resistance tomography in tandem. ‘Theirs may be the only equipment that uses both sonic and electrical-resistance tomography synergistically to more accurately assess the internal condition of a tree,’ states Dr Marra. Although the PiCUS Tools Box is primarily used by arborists to identify internal decay and cavities in trees, and assess the associated risks, Dr Marra and Dr Brazee wished to test the feasibility of using the equipment to identify and measure the volume of decay and cavities. They then used these data to develop a method for estimating the resulting loss of carbon.

In an initial study, Dr Brazee, Dr Marra and two other colleagues assessed the equipment’s ability to identify and measure decay and cavities in three hardwood species in Connecticut. After collecting sonic and electrical-resistance tomographic data on nine trees (three of each species), the team then felled the trees and cut their trunks into sections to assess how accurate the results were.

The team found that the tomographic results were remarkably well matched to what they observed inside the trees. As it employs both sonic and electrical-resistance tomography, the PiCUS Tools Box provided a far more accurate and detailed assessment of the trees compared with using either of these techniques on their own. For five trees that showed decay, the team was also able to accurately quantify the amount of decay. Furthermore, the researchers were able to estimate the amount of carbon that had been lost due to the decay observed in the tomographed portion of the trees.

After this successful initial study, the researchers were hopeful that this combination of sonic and electrical-resistance tomography could be used to dramatically improve our knowledge of the extent of decay in forests worldwide, and the resulting loss of carbon.

Dr Brazee generating a sonic tomogram on an American elm

A Deeper Look at Carbon Loss

Several years later, with funding from the National Science Foundation, Dr Marra and Dr Brazee more thoroughly investigated the carbon loss resulting from internal decay in trees. Using the PiCUS Tools Box, they expanded on their initial study by investigating 72 northern hardwood trees.

First, the researchers further refined their methodology for identifying and quantifying decay. Employing the PiCUS Tools Box, and optimised mathematical models, they demonstrated that they could accurately measure the incidence and severity of internal decay, and also distinguish actively decaying wood from hollow cavities. They did this by comparing their tomographic data to 105 cross-sectional samples taken from 47 of the study’s 72 trees. Overall, the technique was able to effectively identify varying degrees of decay in 95 of the 105 cross-sections; tomography misidentified small cavities as active decay in the remaining 10 cross-sections.

Then, by measuring the amount of carbon in the non-decayed and decayed wood samples and comparing these results with their tomographic data, Dr Marra and Dr Brazee developed a method for calculating carbon loss. On average, they found that the carbon density of actively decaying wood was 27% lower than that of non-decayed wood. Using these data, they estimated varying degrees of carbon loss, with some of the study’s trees having lost as much as 34% of their carbon due to active decay and cavities. 

Climate Change and Reforestation

‘Our results show that internal decay has the potential to be an important countervailing force to sequestration, reducing overall carbon storage in living trees,’ says Dr Marra. ‘This has important implications for current carbon storage models, which currently do not accurately account for internal decay, and the consequent loss of stored carbon.’

Improving current understanding of these processes is vital, if we are to make accurate predictions and take the best course of action against climate change. ‘Forests are increasingly being recognised for their role in the global carbon cycle, by reducing greenhouse gases through carbon sequestration,’ explains Dr Marra. However, if internal decay is not accurately accounted for in models that quantify carbon storage rates in forests, then such rates may be overestimated.

The researchers’ work also has important implications for reforestation efforts. Currently, older forests are believed to have a greater impact on carbon dioxide levels than new forests, as older trees absorb and store more carbon. However, the likelihood of decay also increases with age, partially offsetting this effect. If internal decay turns out to be widespread in forests across the globe, the difference in the amount of carbon captured and stored between older and younger forests could be less significant. Therefore, reforestation initiatives may be comparably more effective than previously thought at tackling climate change.

An American beech (Fagus grandifolia) from the Great Mountain Forest study, alongside the sonic (left) and electrical-resistance (centre) tomograms taken at 50, 100, and 150 cm above the forest floor, and the corresponding stem-disks (right) excised from the tree

Public Safety and Tree Conservation

In addition to estimating forest carbon stocks, the team also wished to apply tomography and adapt their methodology for the purpose of ensuring the safety of trees in populated areas. In a study led by Dr Daniel Burcham of the Centre for Urban Greenery and Ecology in Singapore, the research team used the data obtained in their study of 72 hardwood trees to develop effective methodology for assessing the strength – or ‘load-bearing capacity’ – of decaying trees.

Taking tomographic data and cross-sectional photos of trees containing regions of decay, Dr Burcham used a colour scale to represent the speed of the sound as it travelled through the wood. The fastest sound speeds in the non-decayed wood were depicted as varying shades of brown, while slower speeds were depicted as green, violet and blue, in order of increasing wood decay. The team tested out several mathematical models, incorporating regions of varying degrees of decay, as depicted by the colours. In doing so, they were able to find a mathematical model that most accurately predicted the loss of load-bearing capacity, which could be used to determine whether a tree poses a risk to public safety.

The above study focused on three hardwood species – American beech, sugar maple and yellow birch. Another tree that the researchers were interested in is the American elm, as it is found in many populated areas in the US. This species is under severe threat from a fungal infection known as Dutch elm disease, which has given rise to safety concerns.

Spread by both native and invasive bark beetles, this serious condition affects the tree’s water transport system, causing the branches to wilt and die. To prevent the spread of the disease, many American elms are routinely injected with a fungicide treatment. However, many believe that colonisation by fungal pathogens through the site of the injection may lead to a greater risk of internal decay. As Dr Brazee explains, ‘there are widespread concerns that the adverse effects of injection may outweigh the benefits.’

Therefore, Dr Brazee and his colleagues set out to investigate the effect of these regular injections on the long-term health of elms. Using the PiCUS Tools Box, and with funding from the US Department of Agriculture, the team assessed 210 American elms – about half of which had been receiving regular injections, the rest of which had not. The researchers found that 31% of the elms that had been receiving regular treatment were decayed, compared to 29% of those that been receiving irregular or no treatment. They found that this difference was statistically insignificant, meaning that the injections do not damage the structural integrity of trees and should be continued.

In addition to ensuring the safety of these trees in populated areas, Dr Brazee explains that the American elm is a culturally significant tree in the US. Therefore, tomography could also benefit its conservation. ‘As culturally and historically significant trees, American elms have a unique place in the urban forests of the northeast and preservation of these is a high priority,’ he says.


The work undertaken by Dr Marra, Dr Brazee and their colleagues has advanced our understanding of the extent of fungal decay in many different tree species and locations. The team hopes that their work will lead to better carbon and climate predictions, forestry management strategies and tree conservation worldwide.


Meet the researchers

Dr Nicholas J. Brazee
Plant Diagnostic Laboratory
Center for Agriculture, Food and the Environment
University of Massachusetts
Amherst, MA

Dr Nicholas Brazee is an extension plant pathologist at the University of Massachusetts, where he directs the UMass Plant Diagnostic Lab. His duties include woody plant disease diagnostics, outreach with green industry professionals and research on pathogens of landscape and forest trees. His primary research interest focuses on wood-rotting fungal pathogens of landscape and urban trees. Dr Brazee earned his PhD in forest pathology (UMass) before working as a post-doctoral researcher with the US Forest Service at the Center for Forest Mycology Research.



Dr Robert E. Marra
Department of Plant Pathology and Ecology
The Connecticut Agricultural Experiment Station
New Haven, CT

Dr Robert Marra is an Associate Scientist in the Department of Plant Pathology & Ecology at The Connecticut Agricultural Experiment Station, based in New Haven, where his research focuses on fungal plant pathogens and forest pathology. In addition to research on the dynamics of carbon loss associated with internal decay, he also studies the population genetics of two fungal pathogens: Fusarium palustre, associated with Sudden Vegetation Dieback in eastern North American salt marshes, and Neonectria ditissima, a forest pathogen causing cankers on a broad range of tree species. Following his PhD in plant pathology at Cornell University, Dr Marra did postdoctoral research in evolutionary biology at the University of Arizona, and medical mycology at Duke University.




Shawn Fraver, Dan Burcham, Brian Kane, Lothar Gocke, Philip Van Wassanaer


McIntire–Stennis Cooperative Forestry Research Program

US Department of Agriculture

US National Science Foundation


NJ Brazee, RE Marra, Incidence of internal decay in American elms (Ulmus americana) under regular fungicide injection to manage Dutch elm disease, Arboriculture and Urban Forestry, 2019, in press.  

DC Burcham, NJ Brazee, RE Marra, B Kane, Can sonic tomography predict loss in load bearing capacity for trees with internal defects? A comparison of sonic tomograms with destructive measurements, Trees: Structure and Function, 2019, 33, 681–695.  

RE Marra, NJ Brazee, S Fraver, Estimating carbon loss due to internal decay in living trees using tomography: implications for forest carbon budgets, Environmental Research Letters, 2018, 13, 105044.

NJ Brazee, RE Marra, L Göcke, P van Wassanaer, Nondestructive assessment of internal decay in three hardwood species of northeastern North America using sonic and electrical impedance tomography, Forestry, 2011, 84, 33–39.

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