To BOLDly Go

To BOLDly Go

Illuminations

Catalog all of Earth's multicellular lifeforms—tens of millions of species—in one giant DNA library.

November 14, 2019

By Kat Pyne and Josh Silberg, Hakai Institute – hakai.org

Space may be the final frontier, and yet we still have light years to go before we fully understand the rich diversity of life at home. The current mission? Catalog all of Earth’s multicellular lifeforms—tens of millions of species—in one giant DNA library.

Imagine this: just as you would scan a cereal box’s barcode at the grocery store, the same thing could be done with any plant or animal’s DNA to find out its species. It may sound like science fiction, but scientists around the world are working toward that reality. Their goal? To create an international barcode of life!

So just how are scientists stocking the library’s shelves? Come with us to British Columbia and California to find out!

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Reconstructing the diet of an elusive wood grouse (western capercaillies) using metagenomics

Reconstructing the diet of an elusive wood grouse (western capercaillies) using metagenomics

Illuminations

Environmental DNA provides a non-invasive and simple means of biomonitoring

By Physilia Chua

Spotted! A male capercaillie displaying its magnificent tail feathers

PHOTO CREDIT: Per Gätzschmann

Gone are the days when researchers needed to spend countless hours observing an animal in the wild to understand its behaviour and ecology. As we demonstrate with our study, valuable data can be gathered by simply examining faecal samples with powerful metagenomics approaches.

The need for data that effectively informs biological conservation is intensifying as the rate of biodiversity loss increases. Traditionally, scientists have endured long hours in the field, often hiding uncomfortably in bushes or traversing dangerous and hard-to-reach places, all for the purpose of observing elusive animals.

Searching for capercaillies in the midst of a snow storm in the Norwegian boreal forests

Photo credit: Physilia Chua

With the advent of next-generation sequencing (NGS) technologies – those that effectively provide large amounts of DNA sequence data – it is now possible to obtain a wealth of ecological information from just a single faecal sample. The ease of collecting such samples circumvents some of the challenges of studying animals otherwise hard to find.

One such NGS approach is metagenomics shotgun sequencing (MSS), which determines the nucleotide composition of large amounts of random DNA molecules recovered from complex samples of DNA from various sources. This method makes it possible to simultaneously retrieve information about the host’s diet, microbiome, gut parasites, as well as the population structure of the species1. While it has vast potential for conservation biology, few studies have utilised MSS to reconstruct the diet of animals, and none have done so for herbivorous birds.

A typical day out in the fields high above the Arctic Circle in Tromsø, Dividalen National Park, Norway

Photo credit: Physilia Chua

The western capercaillie (Tetrao urogallus), or wood grouse, is an emblematic species which can be found in the coniferous forest of Eurasia. Highly susceptible to the increased levels of habitat destruction and fragmentation, their declining population has placed them on the International Union for Conservation of Nature (IUCN) Red-list throughout most of western and central Europe2. By studying the wood grouse’s diet, we could gain clues about the resources it requires and the other species it interacts with in its habitat, informing better conservation strategies. By observing the animal and morphologically identifying plant remains from their faecal samples, it was determined that the capercaillie’s diet consists of mostly pine needles in the winter, and Vaccinium species in the summer3.

A pile of capercaillie scat

Photo credit: Physilia Chua

Capercaillie’s favourite food? Pine needles (left) and Vaccinium sp. (right)

Photo credit: Physilia Chua

However, preliminary results from our study show promising signs that the capercaillie’s diet is more diverse than once thought. Other than plants, we have also discovered parasitoid wasps and several species of mites, which could have been accidental ingestion while feeding or preening. And with the use of metagenomics, there is also the possibility of obtaining more detailed quantitative information about its diet that can be used to inform habitat management choices. Their gut microbiome, intestinal parasites, and population genetics are also currently being analysed.

Unexpectedly, we were also able to detect the presence of plant-pathogenic fungus and nematodes from their faecal samples, providing some interesting ecological insights about the capercaillie’s habitat. Even though our research is still in its infancy, by using metagenomics shotgun sequencing on faecal samples, our initial study has already yielded a wealth of data. There is truly an untapped potential for its application in conservation biology and biomonitoring, which should be further explored.

The road less travelled might lead to unexpected discoveries

Photo credit: Physilia Chua

AcknowledgementS:

I thank my supervisors Kristine Bohmann, Sanne Boessenkool, and Inger Greve Alsos for their guidance in every step of this research, without whom this study would not have been possible. I am deeply grateful to Torbjørn Ekrem for his invaluable support both in and outside of fieldwork. I am indebted to my collaborators Kat Bruce and Alex Crampton-Platt for taking me into their team at NatureMetrics and making bioinformatics look so easy. Lastly, my sincere gratitude to the members of the eDNA group at the Section for Evolutionary Genomics, University of Copenhagen, and also to my fellow Plant.ID ESRs for keeping me in the right headspace. This project is part of the H2020 MSCA-ITN-ETN Plant.ID network and has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 765000.

References:

1. Srivathsan A, Sha JCM, Vogler A, Meier R (2015) Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus). Molecular Ecology Resources 15(2): 250–261. https://doi.org/10.1111/1755-0998.12302

2. Storch I (2000) Grouse: status survey and conservation action plan 2000-2004. IUCN/SSC Action Plans for the Conservation of Biological Diversity. Retrieved from http://www.iucn.org/dbtw-wpd/edocs/2000-031.pdf

3. Picozzi N, Moss R, Catt DC (1996) Capercaillie habitat, diet and management in a Sitka spruce plantation in central Scotland. International Journal of Agriculture and Forestry. 69(4): 373 – 388. https://doi.org/10.1093/forestry/69.4.373

Written by

Physilia Chua

Physilia Chua

Department of Biology, University of Copenhagen, Copenhagen, Denmark.

November 12, 2019
https://doi.org/10.21083/ibol.v9i1.5725

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The Barcode Bulletin moderates comments to promote an informed and courteous conversation. Abusive, profane, self-promotional, or incoherent comments will be rejected.