Forestry: Measuring nature using the power of DNA

Published: 12th April 2022

This article originally appeared in Forestry & Timber News, April 2022, Issue 110.

What gets measured, gets managed and until now, biodiversity has had a measurement problem. Stefanie Kaiser of green tech company NatureMetrics outlines how DNA-based methodologies can open the path to robust biodiversity assessments at scale.

Triggered by a powerful combination of recent extreme weather events, a ‘return-to-nature’ sentiment in society during lockdown, media attention around COP26 and the release of the Dasgupta Report on the Economics of Biodiversity, the penny has eventually dropped – both the climate and nature emergency have to be addressed, and quick. Governments and private businesses have to change their mindset and start seeing ‘nature’ as the fundamental resource our economy is built on. Basically, environmental costs and benefits need to make their way into corporate balance sheets.

“Using traditional methods, we can only measure what we see – that is a tiny fraction of biodiversity and it’s often not measuring the things that are really driving the functioning of the ecosystem.”

A symptom of this trend, in particular in the forestry and wider land use sector, has been a striking interest in nature-based solutions and carbon markets; within the Confor membership, several new businesses have started dedicated carbon forestry ventures in the last few years. Land agents have reported a rise in the value of natural assets overall, which is reflected in soaring sales prices for not only commercial woodlands but also land suitable for afforestation or peatland restoration. Simon Hart of John Cleggs & Co says “even poor ground in Scotland is now selling at £5000/ha and more, which is more than treble values seen in the recent past”.

For climate change mitigation, more or less robust market-based incentives in the form of carbon credit schemes exist, and National net zero strategies provide a strong framework and pull for companies to take tangible climate action.

However, climate change and the deterioration of nature and biodiversity are strongly interlinked. In the last six months, many in the business and finance community have woken up to the need to monitor impacts on nature. Biodiversity regulations and certification requirements are likely to tighten resulting in the need for robust and scalable metrics.

Biodiversity – Digging Deeper

Soil biodiversity underpins the health and resilience of a forest ecosystem.

Many people will intuitively relate the term  biodiversity’ to charismatic and potentially endangered species. Think red squirrels, pine martens, dormice and rare butterflies. However, it is mostly the less visible communities of bacteria, fungi and  vertebrates that underpin the health of an ecosystem. Understanding soil biodiversity is a good proxy for understanding the overall ecosystem health of a forest. For example, there is increasing evidence that tree health is highly dependent on well-functioning fungal communities. However, Fungi can be tricky to visually survey unless they have above ground mushrooms, and these are only visible at certain times of year. eDNA can overcome this barrier.

Can we measure nature?

The measurement of biodiversity is extremely difficult due to its complexity, diversity and its interconnectedness to other aspects of the environment.

Standardised monitoring of forest biodiversity at wide spatial scales and/or at repeat intervals is a significant challenge. The number of forest-dwelling species is immeasurable in itself, and we must resort to the careful selection of a subset of taxa or ‘proxy’ measures to represent forest species in their entirety

Nadia Barsoum, Forest Ecologist, Forest Research

Molecular methods based on the detection of environmental DNA are revolutionizing the way we can understand our impact on biodiversity and habitats. At NatureMetrics, we are building strong methodologies to robustly assess and manage nature with eDNA.

What is eDNA based biodiversity monitoring?

NatureMetrics has developed a cheap, easy and highly effective way to measure biodiversity in an area using DNA from water, soil and insect samples that can be collected by anyone. It can provide data on biodiversity at unprecedented scales and resolutions.

Opportunities for Biodiversity Monitoring in the Forestry Sector

There are many ways that molecular methods can be used to complement conventional monitoring methods.

1. Assess Soil Health

Understanding differences in soil fauna, bacteria and fungi can give an idea of the effect of land management on ecosystem health and resilience. NatureMetrics currently focuses on providing data on composition and richness, rather than on long lists of species, for the assessment of bacteria, fungi and soil fauna from soil samples.

2. Compare impacts of management regimes and forest types

This can be useful to manage reputational risk, to inform grant or certification applications or to assess the effectiveness of new treatment or management regimes. It can also compare differences in land management such as:

  • Certified vs non-certified
  • With or without pesticide treatment
  • Clearfell vs non-clearfell
  • Different tree species compositions
  • Monoculture vs mixed stands
  • Woodlands on sites with different site factors (eg soil types, water etc)
  • Compare productive forests with previous land use (eg sheep pasture)

eDNA Derived Metrics

Currently, the main output from eDNA analysis would be a list of all species detected in a sample. Data is presented to visualise key patterns that might facilitate interpretation of ecological meaning. NatureMetrics is working with clients and partners to develop a range of derived metrics that require no further ecological expertise for interpretation.

Examples of metrics:

  • Species richness
  • Difference in species composition between sites
  • Functional and phylogenetic diversity
  • Fungal:bacterial ratio (soil stability)
  • Endangered or vulnerable species

3. Detect specific vulnerable, invasive or elusive species

eDNA is a great tool for detecting the presence or absence of a particular species. This might be required for diverse certification and permit audits, when dealing with Sites of Special Scientific Interest in response to eNGO campaigns. Elusive or cryptic species can also be easier and more effective to detect using molecular methods, compared to conventional ecological surveying techniques. For the detection of specific species, molecular and traditional methods can complement each other, depending on species type and ecology. Many priority species such as mammals, birds and amphibians are currently only detected from water samples, but detection from soil samples is currently in development.

4 Data for biodiversity KPIs

Currently, eDNA-based monitoring methods can provide the data that can inform the development of biodiversity indicators and metrics: For impact reporting and monitoring; For accessing grant funding or ‘green’ finance and for emerging biodiversity markets.

5. Assess environmental impact of operations

Pesticides, fuel residues or machinery lubricants can enter nearby streams or lakes and potentially have a negative impact on water biodiversity. eDNA biodiversity data and metrics from water samples can give clarity on environmental impact and change over time.

6. Pest detection

Currently, insect or soil samples can be DNA tested to detect key tree pests and diseases on site, for example Ips typographus, Emerald ash borer or fungal pest species. There is also potential to develop DNA-based rapid detection kits for a variety of pest species; this could enhance and calibrate existing plant health monitoring frameworks and remote sensing methods.

Trialling eDNA-based Biodiversity Monitoring and Assessment for the Forestry Sector

At present there is a heavy reliance on the use of proxy measures of forest biodiversity, such as indicator species or structural features (eg volume of deadwood) that are known to correlate well with levels of biodiversity. The National Forest Inventory, for example, uses a suite of surrogate measures of biodiversity to assess inter-regional and temporal variations in ‘woodland condition’ as an indirect measure of biodiversity performance. These surrogate measures provide a measure of potential rather than actual, direct measures of biodiversity. Thus, they do not provide information on how the presence or absence of given species might influence forest ecosystem resilience and functioning. They also do not distinguish between different forest types (eg a wet woodland is assessed in the same way as a Sitka spruce woodland), or stages of development which can skew results unless variation causedby woodland type and age are properly accounted for. With funding from Forestry England and Defra’s Natural Capital Ecosystem Assessment Programme, Forest Research is currently undertaking a series of pilot studies that explore the potential for an eDNA approach to facilitate and increase the depth of direct forest species information acquired in national forest biodiversity monitoring schemes, but also in targeted forest regeneration projects, helping to account for no net loss in biodiversity. More on this in a follow up article this summer.

Nadia Barsoum, Forest Ecologist, Forest Research

eDNA Vs Conventional Surveying Methods

eDNA-based monitoring technologies have a range of unique advantages over conventional surveying methods, but also come with limitations. However, the technology is advancing all the time.

Species reference libraries used for identification are evolving and ongoing research on machine learning techniques will further expand what eDNA based monitoring can do.

Advantages

  • Large number of species detected, including elusive or cryptic species
  • Scalable standardised data collection that is cost-effective relative to traditional approaches and enables consistency when sampling whole landscapes.
  • Objective measurement and reporting– eDNA measures biodiversity directly, removing error introduced by observers and proxies.
  • Auditable outcomes – eDNA samples can be stored for independent verification of outcomes, thus establishing the credibility of claims.
  • Cost-efficiency – eDNA removes the need for experts in the field and reduces sampling time whilst returning high-quality data.
  • Community engagement – NatureMetrics sampling kits have been designed to maximise ease-of-use and have been used extensively by on-expert samplers

Limitations

  • Currently no robust data on species abundance (but relative abundance may be possible)
  • No data on age or size distribution in population
  • There can be uncertainty on spatial distribution
  • Genetic reference data not available for all species

Better Biodiversity Data is Essential to Understand the Impact of Forestry Management

The production of timber is a key objective in forest management, as it provides society with a supply of renewable raw materials and the owner with a source of income. As a result, we use a range of techniques for forecasting and measuring productivity and timber volumes, with a high degree of precision.

However, we also manage our forests to achieve other objectives, such as biodiversity. Our observation is that levels of biodiversity within productive forests is much greater than generally supposed and that it increases with time. We frequently identify species, including rare and protected species which biodiversity records suggest should not be present and have not previously been recorded on the site.

We thought that it would be useful to build on this anecdotal evidence and attempt to quantify the levels of biodiversity within the forests which we manage. The attraction of eDNA is that it offers a way in which this can be carried out in a systematic and quantitative way. If we are able to gather such information, then we could use it as baseline, so that we could record the impact of changes in management. We could also use it to better understand how the biodiversity in productive forest ecosystems changes as the forests develop. This could be used to compare against other land-uses and help to inform management at the landscape level.

If we are serious about biodiversity, then it is essential that we learn to measure it in a precise way. Only then, can we be confident about the impacts of our management.

Jason Sinden, Investment Director, Gresham House

Get Involved

Be ahead of the curve.

The eDNA biodiversity monitoring technology is booming across sectors but is still not widely adopted within the forestry sector.

Get in touch if:

  • you have water on your site and want to tell stories about key species on your site;

  • you want to understand how your management decisions affect soil health and soil microbiome that underpins the health of the forest;
  • you are interested in using eDNA for early detection of pests and pathogens and would be interested in being a R&D partner for NatureMetrics.

Contact

Stefanie.Kaiser@naturemetrics.co.uk

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