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

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

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

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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Scat Raiders Unravel Animal-Plant Interactions in Lebanon Using DNA Barcoding Tools

Scat Raiders Unravel Animal-Plant Interactions in Lebanon Using DNA Barcoding Tools

Scat Raiders Unravel Animal-Plant Interactions in Lebanon Using DNA Barcoding Tools

Using DNA dietary analysis on Eastern Mediterranean wildlife to explore the role of animals in ecological restoration processes.
Plant collection in Ehden Nature Reserve – north Lebanon. PHOTO CREDIT: Saint Joseph University

Lebanon is considered a hotspot for biodiversity in the Mediterranean basin likely due to its geographic position at the transition of two major landmasses (that is Eurasia and Africa). The Lebanese territory is divided between mountainous slopes with fertile valleys separating the two mountain chains that run parallel with the sea and the steppe areas in the north-east. Deep canyons and numerous rivers characterize this mountainous landscape.

These geomorphological regions give rise to many bio-climatic zones and several habitat types that are home to more than 9,116 described species (4,486 for fauna and 4,630 for flora from which 91 are endemic). However, major taxonomic groups like insects and fungi are understudied and taxa are underrepresented within public data platforms. For example, according to the Barcode of Life Data System (BOLD), only 345 Lebanese specimens with sequences are published, forming 151 BINs and, of these records, only 108 have species names.

In September 2018, the Faculty of Science at Saint Joseph University of Beirut joined the iBOL Consortium providing us with the opportunity to unravel Lebanese biodiversity by DNA barcoding both small and large mammals as well as the main trees and shrubs used in reforestation programs. We will also target endemic plant species.

Animals are a crucial component for the resilience of forest ecosystems and an important factor in forest restoration projects as they promote the sustainability of reintroduced plants, as well as seed dispersal. However, we still need to identify the animals present in restored areas.

Animal scat collection. PHOTO CREDIT: Saint Joseph University

In addition, knowing what each animal eats and which plant seeds are being dispersed is crucial for reforestation schemes that promote wildlife and ensure ecosystem sustainability. The information needed to study the diets of animals can be found hidden in their scat which contains not only the animal’s DNA, but also what that animal has eaten. With the powerful technique of DNA metabarcoding, we now have the necessary tool to efficiently unravel the genetic information hidden in animal scat. The DNA sequences obtained from such material are identified by comparison to a reference library of animals and plants of the Eastern Mediterranean countries.

 

Constructing the Reference Library – DNA isolation. PHOTO CREDIT: Saint Joseph University
This reference library was prepared from leaves collected in the wild and from DNA isolated from dead animals found along roads or from private museums. Thus, we have generated sequences for 51 plants and 18 mammals. This study conducted in collaboration with the Smithsonian Conservation Biology Institute and the University of Otago is the first to employ a DNA dietary analysis on wildlife in the Eastern Mediterranean Region and explicitly considering the role of wildlife in ecological restoration processes. Our results will inform management strategies to help with the conservation efforts of these imperiled species.

Written by

Carole Saliba

Carole Saliba

Faculty of Science, Saint-Joseph University

Liliane Boukhdoud

Liliane Boukhdoud

Faculty of Science, Saint-Joseph University

Magda Bou Dagher Kharrat

Magda Bou Dagher Kharrat

Faculty of Science, Saint-Joseph University

April 7, 2019
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https://doi.org/10.21083/ibol.v9i1.5489

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HOW BIOSCAN IS INSPIRING THE NEXT GENERATION OF RESEARCHERS

They were enlightened by the idea of discovering new species and by the possibility of doing so using DNA barcoding tools.”

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