Adapting to life in an increasingly acid world: understanding tolerance to acidic waters in populations of trout (Salmo trutta). PhD in Biosciences(NERC FRESH).

The NERC Centre for Doctoral Training in Freshwater Biosciences and Sustainability (GW4 FRESH CDT) provides a world-class doctoral research and training environment, for the next generation of interdisciplinary freshwater scientists equipped to tackle future global water challenges. GW4 FRESH harnesses freshwater scientists from four of the UK’s most research-intensive universities (Bath, Bristol, Cardiff and Exeter) plus world-class research organisations the Centre for Ecology and Hydrology (CEH) and British Geological Survey (BGS).

For an overview of the GW4 FRESH CDT please see website www.gw4fresh.co.uk

Full Project Description

During the freshwater phases of their lifecycles, brown trout (Salmo trutta) and Atlantic salmon (Salmo salar) inhabit a broad range of environments, ranging from acidic upland streams to neutral-alkaline chalk streams. Due primarily to the impacts of human-driven ecological perturbations, e.g. forestry clearance and acid run-off, the pH of many of these systems is now fluctuating far beyond previously recorded levels.

Dartmoor National Park is a unique upland habitat in southwest England. Flowing over granite and peat, many rivers of the region are markedly acidic; nonetheless, compared to similar upland streams elsewhere in Britain and Ireland, local management activities, e.g. forestry clearance, have led to large fluctuations in pH, with readings of less than pH 4 being recorded. Despite this, most Dartmoor streams host healthy populations of trout and salmon, and molecular analysis shows trout from acid rivers to be genetically distinct (Griffiths et al. 2009).

This project aims to identify the basis of tolerance to acid waters in brown trout through analysis of single nucleotide polymorphisms (SNPs) and changes in gene expression. We propose to use the complementary approaches of restriction site associated DNA sequencing (RADseq) and transcriptomics (RNA sequencing [RNAseq]) to study trout populations inhabiting acid, neutral and alkaline rivers in southern Britain. This will allow us to explore common/convergent evolutionary ’solutions’ to acid tolerance. Additionally, the student will gain field experience and work with a modern conservation organisation.

Our primary objective is to understand the genetic basis of acid tolerance in brown trout. We propose to use RADseq analysis of fish from rivers with low pH (Dartmoor streams), neutral rivers (other rivers in Cornwall and Devon) and more alkaline waters (chalk streams, Dorset/Hampshire). We already hold tissue samples from resident trout collected from across these regions, and the student will have the opportunity to partake in fieldwork to collect additional trout tissue samples. The sampling design includes fish from tributaries running off acid high-moor sites and neutral lowland locations (allowing us to eliminate the effects of differential genetic drift and catchment-specific selective pressures). This will allow us to identify SNPs that segregate definitively between the ecotypes and to identify regions of the trout genome associated with adaptations to living in a low pH environment. The study will provide a better understanding of the basis of acid tolerance in salmonids and addresses long-standing questions regarding persistence of this species in an otherwise species-poor (highly acid) ecosystem. It also offers the potential to reveal the mechanisms of local adaptation and the genetic architecture underlying this process. Such information will also be of value in fish conservation and aquaculture in the face of global pressures on aquatic systems, e.g. the acidifying effects of increased atmospheric CO2 (Hasler et al. 2016).

Collaboration with the CASE partner, Westcountry Rivers Trust, and The Game & Wildlife Conservation Trust also provides a rare opportunity to look for changes in gene expression in relation to exposure to highly acidic conditions. For the first time, permission was recently granted to add lime to an extremely acid stretch of river on Dartmoor, thereby artificially increasing the pH. Samples of gill and kidney will be collected from trout at the treatment site, alongside those in more acidic water immediately upstream. Analysis by RNAseq will then characterise changes in gene expression related to acidity, identifying genes important to physiological responses in wild trout populations. By combining population genomic and gene expression approaches, this exciting studentship offers the potential to address broader questions of acid tolerance and adaptation in this fish. The team at Exeter and Bristol have extensive experience in this field and we anticipate that our research findings will be used by fisheries managers, conservationists and other stakeholders to help in monitoring at-risk environments and detecting changes in water quality that may threaten fish health and population numbers.

Project specific enquiries should be directed to the lead supervisor, Dr Jamie Stevens.