Understanding how wetland species became rare or locally extinct using sedimentary DNA and stable isotopes – supporting future ecological restoration by uncovering the past.

Overview

Extensive coastal and floodplain wetlands were a feature of lowland Britain in the past. Wetland complexes such as the East Anglian Fens, the Somerset Levels and the Humberhead Levels each comprised hundreds to thousands of square kilometres. Since Roman times there has been a ca.90% reduction in wetland extent, with consequent loss of biodiversity but also the ecosystem services that wetlands provide. It is thought that around 20 bird species and perhaps three amphibian species were lost from lowland Britain during this period. The 25-year Environment Plan and associated initiatives around Nature Recovery Networks and rewilding envisage the restoration of some of these wetlands on a scale not previously seen. This creates an exciting opportunity to reverse some of the losses of wetland species from lowland Britain, and recent restoration projects for Eurasian beaver Castor fiber, White Stork Ciconia ciconia and Common Crane Grus grus provide a glimpse of what is possible.

Reintroduction guidelines dictate that in order to progress this species restoration agenda, clear information is needed on which species are genuinely native, where they occurred and what drove their extirpation. However, this information is currently lacking, with what little evidence there is typically limited to archaeological remains associated with anthropogenic sites and some documentary sources. This lack of historical context presents a significant barrier to potential ecological restoration, yet new technologies have transformed our ability to reconstruct past ecology, and could resolve many of these uncertainties.

This project aims to develop methods that will enable conservation practitioners to look back in time and establish historic distributions of locally extinct wetland species such as Dalmatian pelican Pelecanus crispus, night heron Nycticorax nycticorax, Moor Frog Rana arvalis and Burbot Lota lota. It will explore how eDNA in lake sediment cores can be used track changes in species presence at key sites over several hundred years. With Prof Darren Evans (NCL) and Dr Laura Epp (University of Konstanz) we will use specific primers to target DNA of vertebrate and invertebrate species preserved in sediment samples (Epp et al., 2012). Change in the composition of invertebrate communities through time will be investigated under supervision of Dr Maarten van Hardenbroek (NCL) and Dr Hannah Robson (CASE partner the Wildfowl and Wetland Trust (WWT)) using sedimentary remains of invertebrates. Stable carbon/nitrogen isotope analysis of these invertebrate remains will be used to trace changes in resources and food web structure through time (pilot data presented in van Hardenbroek et al. (2018) indicate the potential of this approach) in collaboration with Dr Jack Lacey (BGS).
CASE partner WWT, has a track record of work on wetland restoration and species recovery in the UK and around the globe: it will directly use the results of this project to prioritise and plan future projects. At its UK wetland centres, WWT has a captive collection of water birds and ponds which will be used establish the pathways of DNA preservation and loss from animal to sediment under controlled conditions. The methodology will be further tested on sites with species which are currently present in the UK but have shown distinct changes in abundance, for example the Eurasian Otter Lutra lutra (rapid decline in mid-late 20th century, subsequent recovery) and Water Vole Arvicola amphibius (catastrophic decline through mid 20th century to present). Finally, the methodology will be applied on sediment cores from sites in the Fens and Somerset levels.

Key research questions in this project are:

  • How can eDNA in water and sediments be used to identify current site use by elusive/hard to monitor wetland species?
  • How can sedimentary DNA contribute to establish historical wetland occupation of species that are currently rare or extinct?
  • Can we estimate rates and causes of decline by combining sedimentary DNA, stable isotopes and traditional palaeolimnological approaches?

Click on an image to expand

Image Captions

Now locally extinct birds in the UK: dalmatian pelican, night heron, white stork. All images used under creative commons licence.

Methodology

Water samples, surface sediments, and wide-diameter sediment cores will be obtained from ponds with captive birds at WWT, from sites with documented changes in otter and water vole occupancy, and from ca. 10 small lakes and ponds in the Fens and Somerset Levels with known (historical) populations of now locally extinct birds.

Sediment cores will be dated to ~1850 using spheroidal carbonaceous particles (SCPs: Rose, 2008), using radiocarbon dating for sediments >500yr old. Elemental composition of sediments (including heavy metals) will be analysed via X-Ray Fluorescence (XRF) and bulk sediment stable carbon and nitrogen isotopes.

Sedimentary DNA will be analysed via metabarcoding using short primer pairs to identify bird and mammal taxa (Epp et al 2012), in collaboration with Dr Laura Epp (University of Konstanz).

Invertebrate remains will be manually picked from sediment samples, identified and analysed for stable carbon and nitrogen isotopes to give insight into the relative position of different invertebrate groups in the aquatic food web (van Hardenbroek et al. 2018).

Multivariate statistics and structural equation modelling will be used to identify the key drivers of changes in wetland community composition and food web interactions.

Project Timeline

Year 1

Background reading and literature review .
Fieldwork to collect lake sediment cores from up to 10 lakes, with CASE partner WWT.
Lake sample processing and analysis for elemental chemistry (XRF).
Dating of sediment cores by analysis of spheroidal carbonaceous particles (SCPs) and preparing material for radiocarbon dating.

Year 2

Begin sedimentary ancient DNA extraction and amplification using selected primers, possible lab visit to Dr Laura Epp (University of Konstanz).
Pick out and identify aquatic invertebrate remains; prepare invertebrate remains and bulk sediment samples for stable carbon and nitrogen isotope analysis at BGS.

Year 3

Complete stable isotope analyses, reconstruct lake food web interactions at different time slices.
Complete sedimentary ancient DNA extraction/amplification and sequence DNA samples and complete bio-informatics analysis and interpretation.
Undertake multivariate analysis of data and structural equation modelling to understand cause and effect between environmental drivers and change in wetland species occurrence.

Year 3.5

Completion of data analysis.
Integration of all results and thesis writing.

Training
& Skills

Skills training provided:
(1) palaeo/limnological sampling/coring and creating chronologies for lake sediment records using spheroidal carbonaceous particles (SCPs) and radiocarbon;
(2) molecular techniques including extraction, PCR amplification, library preparation for sequencing or nanopore, bioinformatics;
(3) preparation and analysis of samples for stable isotopes;
(4) multivariate statistics and structural equation modelling using R.

References & further reading

Epp et al. (2012) New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Mol. Ecol. 21: 1821-1833.

Rose (2008) Quality control in the analysis of lake sediments for spheroidal carbonaceous particles. Limnol. Oceanogr. Meth. 6: 172-179.

van Hardenbroek et al. (2018) The stable isotope composition of organic and inorganic fossils in lake sediment records: Current understanding, challenges, and future directions. Quaternary Sci. Rev. 196: 154-176.

Further Information

Please contact Dr Maarten van Hardenbroek (maarten.vanhardenbroek@ncl.ac.uk) for further information.

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