10th Anniversary Volume 7: The ecologist’s field guide to sequence‐based identification of biodiversity

Post provided by Si Creer, Kristy Deiner, Serita Frey and Holly Bik

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature in the Methods.blog. For Volume 7, we have selected ‘The ecologist’s field guide to sequence‐based identification of biodiversity’ by Creer et al. (2016).

In this post, the authors share their motivation behind the paper and discuss advances in sequencebased identification of biodiversity.

From sorting specimens to sorting sequences

It’s reasonable to assume that not all molecular ecologists were born that way, but instead most of us started out with an interest in biodiversity, morphological taxonomy or ecology, but perhaps were frustrated with the vast amount of time that is needed to identify and count different species from diverse habitats. A number of us were propelled into the field of environmental or community DNA metabarcoding, because realistically there were no other options to assess the biodiversity of microscopic organisms inhabiting marine sediments or soils. Others were inspired into the field because they wanted to understand, for example, freshwater biodiversity, at massive taxonomic and geographic scale (studies that were not possible with slow, manual microscopy approaches). Another group of us could see the amazing value of environmental DNA (eDNA) analyses for non-invasive sampling, where traditional approaches are either not possible, or destructive to the biodiversity in question. Either way, it is difficult not to be impressed by a metabarcoding dataset that features the diversity of many phyla and families, taken from environmental sources such as filtering water, air, soil, or blood meal samples, from actual communities of organisms from (e.g.) Malaise or pitfall traps, or gut contents.

Si doing the eDNA kit evening shift at Mopiri Camp, after a long day sampling in the Okavango Delta, courtesy of Sophie von der Heyden and the National Geographic Okavango Wilderness Project.

Collectively, eDNA approaches provide a massive lens into the patterns and processes underpinning biodiversity, in addition to revealing interactions between taxa. Our paper and Thematic Symposium in Lille, 2014 coincided with a series of exciting US meetings held at the Universities of Florida, UC Davis and meetings in Durham, North Carolina, Fort Lauderdale and Sacramento (SMB/ESA – 2009-2015), mostly facilitated by NSF Research Collaboration Network (EukHiTS) and NESCent Catalysis grants. Indeed, the (at the time) meiofauna group’s (Holly, Si, Dorota and Kelley) metabarcoding journey started with a memorable analysis workshop where we stayed in a trailer in the grounds of the University of Florida. The symposium in Lille offered a chance to forge further links with established (e.g. Pierre) and emerging (e.g. Kristy) leaders from our European network, thereby consolidating the author team with additional collaborators.

Motivation behind the article

Left to right, Si, Dorota, Holly and Serita enjoying the chilly night life of Lille.

The aim of the “The ecologist’s field guide to sequence-based identification of biodiversity” paper was inspired by a desire to provide an easy-to-use reference point for ecologists interested in using all forms of environmental sequencing analyses to understand biodiversity and hopefully to foster closer links between molecular ecology and traditional ecological fields. Importantly, we felt that clear explanation of terminology and approaches, including field, lab and informatics lingo would help promote future collaborations, so that all parties would be on the same page when it came to experimental design, costs, study foci and goals. Regarding aspirations, the paper and others that followed focused on effective stakeholder/end user engagement – a mission that we still strive for, via engagement with statutory groups and associated DNA Working Groups (e.g. UK Defra DNA Centre of Excellence, DNAqua.net, and the California Water Quality consortium). There is now a huge community of academics and end users that acknowledge that eDNA analyses provide paradigm shifting abilities in the realm of biomonitoring – the challenge now is how to integrate that power into existing regulatory frameworks.

The future of eDNA

The field of sequence-based identification of biodiversity and, in particular eDNA metabarcoding, has exploded in recent years, a move that coincided with our paper and others that many of the authors have pioneered. It is also great to see the engagement of more traditional ecologists, leveraging the power of the molecular ecologist’s toolkit. Further advances that are immediately apparent are the breadth of substrates that are employed to measure different aspects of biodiversity interactions, ranging from soils, to flowers, to honey, to cobbles in the oceans. Building on the successes with eDNA, we are even dipping our toes into the idea that environmental RNA (eRNA) can reveal the transcriptome of whole communities.  Importantly, we are using these approaches to address real world questions in relation to phenomena such as pollution, human allergies, and of course, making impacts in the field of  environmental biomonitoring via global networks such as the EU Cost Action DNAquanet.

Home working through the Covid-19 pandemic. Blog co-authors Simon Creer (top left), Holly Bik (top right), Kristy Deiner (bottom left) and Serita Frey (bottom right).

The field is not static of course and notwithstanding a catalogue of knowledge that is being developed regarding the ‘ecology’ of environmental DNA, work is emerging that captures genomic level diversity from freshwater and pollen samples. A tempting glance round the corner also asks the question as to whether or not we can assess species and population genetic diversity simultaneously using eDNA metabarcoding approaches.

One day, it would be good to revisit the new knowledge and use of molecular biology insights across the field of ecology and update the ‘omics toolbox’ of our field guide.

To find out more about sequence-based identification of biodiversity, read the Methods in Ecology and Evolution article, The ecologist’s field guide to sequence-based identification of biodiversity.

Find out about the Methods in Ecology and Evolution articles selected to celebrate the other volumes and our editors’ favourite papers in this collection of MEE blog posts.

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