High-throughput, DNA-based biodiversity assessment and detection for the environmental consultancy market

Does a proposed housing development contain protected species? Has a mining operation polluted a watershed? How can we be certain that the organic fruit we pay extra for is from nature-friendly farms? Which restoration treatment is most effective at restoring brownfield sites? Industries that have a large impact on the environment, such as mining, oil & gas, agriculture, aquaculture, and construction, need to measure the 'state of nature' as part of their operations, because failure to detect environmental damage is a source of reputational risk and legal liability, while success in protecting the environment can enhance reputation and result in premium pricing.

However, environmental surveys are notoriously difficult to carry out because nature is diverse, and most species are difficult to detect, especially out of season, and to identify reliably and quickly. The standard method of identifying species by their morphologies consumes expensive field time for collections, requires scarce taxonomic expertise, is error-prone and difficult to standardise over long time series, and most importantly, is nearly impossible to verify to third parties, which impedes dispute resolution.

The good news is that the world is permeated with DNA molecules that have been liberated from their original owners in the form of skin, mucous, saliva, sperm, eggs, faeces, urine, blood, secretions, roots, leaves, fruit, pollen, and rotting bodies, which is collectively known as environmental DNA or eDNA. It is also straightforward to collect and to extract DNA from bulk samples of plant material and mass-trapped arthropods (including the DNA of mammals and other vertebrates from blood that has been stolen by parasitic invertebrates).

Recent technological advances have now made it feasible to read biodiversity from eDNA and bulk samples, giving us lists of hundreds to thousands of animal, plant, or fungal species, which can reveal the presence of protected and/or undesirable species. Also, changes in species lists tell us when the environment has changed for the better or for the worse, letting us detect pollution events, assess the outcome of restoration interventions, and track the state of nature in general. These DNA-based methods are many times faster than even expert taxonomists and are powerful at detecting hidden species. As a result, DNA-based methods promise to greatly reduce the costs of environmental monitoring while also increasing information content. This combination will confer competitive and reputational advantages on businesses able to take advantage of this new set of technologies.

In 2012, the estimated global market for Environmental Consultancy was $27.4B, and the estimated UK market was £1.32B, of which £219M was spent on Environmental Impact Assessments (EIA), an 11.9% growth over 2011. In 2014, Natural England galvanised the consultancy sector by announcing that it would accept eDNA evidence to detect the endangered Great Crested Newt (a European Protected Species that features heavily in EIAs), due to eDNA's greater speed and reliability compared with visual surveys.

We propose to start a company, NatureMetrics, that will provide a range of DNA-based environmental services on a white-label basis to environmental consultancies. We will use FoF funding to set up business and laboratory procedures so that we can reliably process large numbers of samples with rapid turnaround time and at lower costs. We have partnered with four UK environmental consultancies, and our four partners will market these services within their own product lines, which will increase the effectiveness of environmental management in general.

Keywords: Biodiversity; biomonitoring; metabarcoding; mitogenomics; environmental DNA; pollution; freshwater; protected species; pollinators; environmental consultancy; infrastructure and construction; mining; oil & gas; water quality; agriculture; horticulture; forestry; conservation organisations

In theory, any decent molecular lab can provide qPCR, metabarcoding, or mitogenomic analyses for environmental biomonitoring. But in practice, there are severe managerial and financial obstacles to commercial uptake and adoption. The example of eDNA for Great Crested Newt detection provides an instructive example. Despite regulatory approval early in 2014, the six laboratories that advertised their services for GCN were only able to provide months-long turnaround times, rendering the method largely valueless. Demand for GCN detection is highly seasonal, and any service provider that staffs up to meet peak demand must somehow find a way to amortise high fixed salary costs over a whole year. We believe the way to do this is to provide a suite of services that can be used by a range of clients that carry out contracts in multiple geographic locations and over the whole calendar year.

However, it is difficult to establish a full-service provider. Existing environmental consultancies do not have the necessary molecular skills in-house, especially at the management level. Any consultancy that tries to grow these skills in-house and organically will be rapidly outcompeted by consultancies that choose instead to ally with a service provider. University research groups can certainly learn the methods that we will use, but as we have discovered ourselves, university research groups face structural impediments to maintaining a technical staff that can process large numbers of samples in a consistent way over long time periods. Pure sequencing centres have the basic laboratory and bioinformatic skills and the ability to keep staff long-term, but they do not have the experience in ecology to be able to tailor their services to this market or to train end-users. Our experience is that even very experienced environmental consultants need to be taught from scratch how to collect and handle samples for DNA work.

Commercial analytical labs that provide food-quality or water-quality monitoring are the businesses that are most likely to be able to enter this market. But these businesses would also have to gain a deep understanding of ecology and how to use biodiversity data to conduct biomonitoring. It is currently unclear whether any existing analytical lab has the capacity to enter the biomonitoring market, and more importantly, whether existing analytical labs will be able to keep up with the still-rapid technical developments in this field. Thus, what we are proposing is to establish a commercial analytical lab that can draw upon our years of experience in biodiversity genomics and ecological analysis.

We believe that Follow-on-Fund support will therefore accelerate the uptake of DNA-based methods for environmental biomonitoring, with all its attendant economic and societal benefits, by supporting the establishment of the first full-service business in this space and, as a consequence, by providing a model for other companies to follow.

The commercial availability of high-volume biodiversity assessments will benefit not only environmental consultancies but also research scientists, conservation organisations, and the government, and through all these entities, the wider public, which will benefit via increased efficiency and effectiveness of environmental monitoring. An excellent potential example of this wider impact is the proposal for a national pollinator monitoring programme in the UK's National Pollinator Strategy. Our bee mitogenomic pipeline, if coupled with the commercial capacity to process large numbers of samples, will make such a monitoring programme feasible.