WTT Blog Posts

Communities created by crowfoot?

There are few more captivating sights than a river reach swathed in water crowfoot flowers, for what delights might be hidden beneath?  William Barnes (1801–1886) was certainly inspired:

O small-feac’d flow’r that now dost bloom,
To stud wi’ white the shallow Frome,
An’ leäve the clote to spread his flow’r
On darksome pools o’ stwoneless Stour,
When sof’ly-rizèn airs do cool
The water in the sheenèn pool,
Thy beds o’ snow white buds do gleam
So feäir upon the sky-blue stream,
As whitest clouds, a-hangèn high
Avore the blueness of the sky

This humble member of the buttercup family is considered by ecologists as an autogenic engineer: it can change the surrounding environment via its own physical structure. While many people have tried to study where and why water crowfoot grows, especially in relation to nutrients, few have considered how the plant influences the assemblages of organisms around it. Cue Jessica Marsh’s PhD study….

I am working with Queen Mary, University of London’s  River Communities Group and Game & Wildlife Conservation Trust’s Fisheries team to better understand the role of water crowfoot (Ranunculus spp) in southern chalk stream ecosystems. My PhD project will focus on studying the relationships between water crowfoot and the other plants, invertebrate and salmonid communities in chalk streams. Data will be collected from in-river experiments in the River Frome, Dorset to understand how the presence of water crowfoot drives the variability of other flora and fauna.

Wading through high water crowfoot cover on the north stream of the River Frome, Dorset

So, why chalk streams and water crowfoot? Well, unique in the stability of their thermal, chemical and physical conditions, lowland chalk stream habitats are of both national and international importance. Chalk streams sustain a high diversity of flora and fauna including species of conservation concern such as water vole, European eel, and white-clawed crayfish. They also support the important salmonid game fish species, Atlantic salmon and brown trout.

The high biodiversity supported by chalk streams is thought to be due to the presence of water crowfoot family. These macrophytes are the dominant in-river plant species throughout chalk stream catchments and are described as pioneer species for their ability to colonise a variety of habitats.

The presence of water crowfoot subsequently creates habitats for other flora and fauna. The plant greatly reduces water velocity within and immediately down-stream of the plant stands, whilst increasing velocity elsewhere by directing water around its cover, thereby altering flow dynamics within the river. The reduction in flow results in an increase of fine sediments being deposited downstream of the plant structure. This encourages growth of other macrophyte species, such as watercress and starworts, that may otherwise be unable to establish themselves due to a lack of organic material or high flow rates. Conversely, increased flow elsewhere keeps gravels free from fine silts.

Flowering water crowfoot on the River Frome, Dorset. Photo taken by Bill Beaumont.

This results in the creation of more complex habitats within the river which, in turn, is linked to the abundant and diverse invertebrate communities that are present in chalk streams by providing diverse food sources and refugia. For example, the submersed parts of macrophytes provide a large surface area for suspension-feeding invertebrates, such as black fly larvae and certain caddis fly larvae, to attach to and feed on organic particles. The mosaic of macrophyte species provides suitable habitat for many different insects during their larval stage, such as damselflies and dragonflies.

High invertebrate production, in turn, generates large numbers of potential prey for juvenile salmonids, including mayfly and blackfly larvae. The absence of any naturally occurring large substrate in lowland streams for physical shelter also makes submerged macrophytes a fundamental requirement for juvenile salmonids; to reduce energy consumption and provide refugia from predators.


Whilst the importance of water crowfoot in driving diversity in chalk stream ecosystems is acknowledged, existing studies on this family are often limited in duration and physical scale and most previous studies have only encompassed single components such as macrophytes, invertebrates or fish, rather than the whole stream ecosystem.

One aim of my project is to establish patterns in the number of juvenile salmon and brown trout, and diversity and density of invertebrate species in areas with varying amounts of water crowfoot. The first of three years of data on macrophyte cover, substrate structure, and invertebrate and fish communities was collected from sites spread throughout the Frome catchment in 2015. The data were collected during the GWCT Fisheries Team’s annual parr-tagging event, where 10,000 juvenile fish are caught, tagged and released, providing critical population data.

GWCT Fisheries team and volunteers electro-fishing on the river Frome, Dorset during annual parr-tagging

Preliminary results of this initial data collection show a significant, positive association between increasing cover of water crowfoot and an increase in juvenile salmon density, as well as an increase in cover of other macrophyte species. The findings suggest that an increase in water crowfoot cover, to a certain extent, is beneficial to other chalk stream ecosystem components. The next stage of the research will be to explore these correlative relationships through two-year long manipulation experiments. These in-stream studies aim to elucidate the mechanisms behind the patterns discovered by altering existing water crowfoot assemblages and monitoring the effects on juvenile salmon and brown trout densities, invertebrate communities, other macrophyte species, and the interaction between all of these groups.

Collecting an invertebrate sample with a Surber net - an underwater quadrat!

Gaining an understanding of such relationships is essential in order to develop effective river management strategies and to direct successful conservation of chalk stream ecosystems.

Please feel free to contact me if you have any questions, or would like further information on my work

Jess (jmarsh@gwct.org.uk)

Should I stay or should I go?

'Can I migrate?' is a question that we at WTT often raise on behalf of fish. In most instances, this question is associated with two physical factors. One is whether there is sufficient water in the river for fish to move through; a problem exacerbated in the southern parts of the UK by abstraction pressures. The other is whether there are any barriers or obstacles to free fish passage - and there are usually plenty! But 'Should I migrate or not?'  is an interesting one that does not get asked very often. Luckily I know someone who does ask such questions! With great pleasure, I hand over to Kim Birnie-Gauvin from the National Institute for Aquatic Resources at the Technical University of Denmark who is conducting her PhD research within the AMBER project.

Physiology & partial migration: from the free radical theory of ageing to residancy and migration in brown trout....

As many of you probably already know, brown trout (Salmo trutta) is a partially migrant species. This means that within a single population, some individuals will migrate to sea and become ‘sea trout’ while others will stay put and become ‘residents’. Many hypotheses have been formulated in an attempt to explain the evolution of such patterns, but today we still have a poor understanding of the mechanisms at play in choosing residency or migration.

Figure 1. Adult resident (A) and migrant (B) brown trout, Salmo trutta capture in a Danish stream (Images by Kim Birnie-Gauvin).

As an animal physiologist by training who has joined the field of fish ecology in recent years, my interests lay in understanding the physiological mechanisms that lead to ecological patterns as well as how fish cope in a human-dominated world. Currently, I am investigating the physiology that underlies residency and migration choices in brown trout. What makes an individual decide to stay in a river its whole life? What makes a seemingly identical individual decide to migrate to marine environments?

With growing evidence suggesting that oxidative stress processes were linked to life-history strategies, I investigated the role of these processes in brown trout partial migration. If you are not familiar with the term, oxidative stress is essentially what makes you wrinkle (also termed the free radical theory of aging) – it is a slow process which takes place when pro-oxidants (‘bad stuff’) are present in greater amounts than antioxidants (‘good stuff’), and damages your proteins, lipids and DNA. You might be wondering how wrinkling might have anything to do with migration… It’s a little more complicated than that, but it essentially has to do with how well a fish can cope with the demands of migration. Hence, you would expect that fish with higher antioxidants have a greater capacity to cope with migration, and may therefore migrate. Similarly, a fish with a lesser ability to cope with the demands of migration (i.e. lower antioxidant) may stay and assume residency.

This is exactly what my study showed.  Here’s what I did: I captured over 500 juvenile brown trout, obtained a blood sample from each of them and tagged them using PIT tags (passive integrated transponder tags). These are small tags that allow us to identify each individual with a unique identification. I then used the red blood cells to evaluate antioxidant capacity (which essentially requires a lot of time in a lab). 

Figure 2. Study design: electrofishing (A), 23mm PIT tag (B) and blood sampling (C) (Images by Kim Birnie-Gauvin).

The analysis showed the migrants had a higher antioxidant capacity, and perhaps enhance these antioxidants as part of the smoltification process in preparation for migration. We also found that within migrant individuals, fish that migrated earlier had higher antioxidants than those that migrated later – this may reflect a fish’s readiness to migrate. Do brown trout plan ahead?

Figure 3. Antioxidant capacity in resident and migrant brown trout (Salmo trutta).

So far, this has been the first evidence suggesting a link between oxidative stress processes and partial migration, not only in fish but in all animals. Though this is only the first step, my team and I are excited for what will come of this.

If you have any questions, please don’t hesitate to contact me by email at kbir@aqua.dtu.dk

Kim (@kbg_conserv)

Woodplumpton Brook Restoration: Baffle-ing Results!

With my ‘Research’ & Conservation Officer cap on, I can straddle the often hefty divide between academia and NGO/grass roots conservation groups and do a little bit to pull them together. Queen Mary University of London buy out some of my time and expertise from WTT to give their aquatic ecology MSc students practical training and experience in the field. As a part of a week-long fieldcourse based in the Lake District, I have forged a link between them and Wyre Rivers Trust but I’ll let some of the excellent members of this year’s cohort tell you about it, below. Thanks to Dr Christophe Eizaguirre and the rest of the students who worked efficiently on the day to provide the data, and of course, to Tom Myerscough from Wyre RT for sorting out the relevant permissions.

The Wyre is one of the key rivers of Lancashire, with its catchment covering much of the North of the county. It has historically been known as one of the best sea-trout fisheries in England. However, in the post-war 20th Century, like most rivers it suffered from intensified agriculture, urbanisation and new engineering methods, and these changes have cumulatively affected fish communities.

Brown trout, a fish which requires a diverse range of habitats to complete its lifecycle (loose gravel in which to lay its eggs, instream and overhanging vegetation to hide its fry, deeper pockets to hold larger adults) has been notably impacted. The Wild Trout Trust labels the brown trout as a sentinel species; its requirements mean that healthy trout populations are indicative of a healthy ecosystem (from the freshwater invertebrates to riverbank birds) so if it isn’t there, then something is likely to be wrong!

A river is only as good as its catchment, and starting small can make the task of river restoration less daunting. Hence, Woodplumpton Brook has been chosen as one of the Wyre River Trust’s target sites for improvement. Aerial photographs reveal how this stream has been straightened and channelised since the 1940s, processes which greatly reduce the diversity of habitats needed for fish to survive. No trout have been seen here for 20 years.

One issue, in particular, is that of artificial barriers to fish movement. On Woodplumpton Brook, a road-bridge culvert speeds up the water as it glides over a concrete slab. Under normal flow conditions, this creates a very shallow and uniform area of fast water for 15m which hinders the free movement of fish upstream, especially larger individuals. Structures like this impair other restoration efforts upstream, such as fencing off livestock, addition of woody debris and planting of willow, by preventing recolonisation by larger fish. Even seemingly small obstructions like this can have a large effect (e.g. Jeroen Tummers WTT blog).

A restoration intervention was put in place last year to reduce these connectivity issues. Baffles, large pieces of wood anchored to the concrete, were fitted in the culvert. They slow the flow by increasing sinuosity and creating slack water refuges, and increase the water depth, allowing fish to make their way from baffle to baffle and hence upstream.  

Several cohorts of Freshwater and Marine Ecology Masters students from Queen Mary University of London have conducted sampling to assess the impact on the fish communities both before and after baffle installation. Our data will contribute to the long term monitoring of changes at this site as a result of this installation and other restoration techniques that have been put in place over recent years. We got to learn and practice new techniques and at the same time contribute useful data for Wyre Rivers Trust; a win-win situation!

To determine whether the baffles are actually helping, electrofishing was carried out both upstream and downstream of the culvert. To gain a representative population estimate, 50m stretches containing similar habitat features were cordoned off using stop nets, and 3-run depletion sampling was conducted in each section.  Each fish was identified and its length carefully recorded. After each run, the caught fish were released outside of the survey area to prevent recounts of the same individuals.

Last year, i.e. prior to the baffle installation, the group surveying the fish community in the Brook found that the communities downstream and upstream were significantly different (Fig. 1), and that the average fish size upstream was significantly smaller than downstream (Fig. 2). This implies that bigger fish were discriminated against, i.e. that they struggled to swim upstream through the culvert.

Fig 1: Stacked bar chart showing the proportions of each species to the fish community at sites either side of the baffles per year. The 2017 sites (after restoration) are much more like each other than the 2016 sites (before restoration), suggesting that the baffles are doing their job, improving fish passage through the culvert.

This year, however, we discovered that the fish communities were more similar upstream and downstream (Fig. 1). In addition, the fish were of similar size downstream and upstream (Fig. 2). Together, this indicates that the fish can move more freely up and down the Brook.

Fig 2: Average fish length (± Standard Error), up (blue) and downstream (red) per year. In 2016 (before restoration), larger fish were typically downstream of the culvert, but in 2017 (after restoration) we found the opposite: the baffles have allowed big fish to migrate upstream of the culvert.

Additionally, the overall community was quite different from last year. One of the most exciting discoveries was that we recorded a brown trout – the first in Woodplumpton for twenty years, and perhaps a sign of the overall recovery of the Brook. However, chub and dace were found in abundance last year, whereas this year there were very few. Furthermore, this year stickleback and stone loach were most abundant, whereas last year they were not present or found in very low numbers. These differences, in conjunction with us collecting several recently dead chub specimens (including larger individuals in the upstream section), suggest that although the restoration works are improving connectivity and habitats within the Brook, pollution events undermining the work and altering the community structure.

The first brown trout for 20 years!

Thus, despite apparent success of the baffles in mixing fish populations, it appears that overarching factors are impairing the true restoration impact and that Wyre Rivers Trust still have some work to do with local landowners. It should be noted that this is only the first year of data collection after installation of the baffles, and it will be interesting to see what future cohorts of our MSc will find in subsequent years.

Liam Nash, Abbie Nye, Thomas Del Santo O'Neill, Pascaline Francelle & Alice Goodwin

If you have any questions re our report or the work of the Wyre RT on Woodplumpton Brook, please contact Dr Christophe Eizaguirre or Tom Myerscough, respectively.

Where in the sea are sea trout?

As anglers, we often struggle to find fish in a stream, river or lake / loch, and we're generally seeking the bigger fish! Keeping track of the vulnerable juvenile life-stages is even more tricky, and then imagine translocating that problem to the sea.... OK, so with advances in acoustic telemetry, the boffins have a few tricks up their sleeves and are making some headway but the logistics of tracking in such a potentially vast environment are nonetheless challenging. Isabel Moore from the Scottish Centre for Ecology & The Natural Enviornment has risen to that challenge during her PhD and outlines one aspect below.

The brown trout is a remarkably diverse species; it can utilise multiple life-history strategies, ranging from freshwater residency through to migration into marine environments for a period of time before returning to freshwater to reproduce (i.e. anadromous sea trout). Unfortunately, this iconic species has been faced with significant population declines in recent decades across the UK and other parts of the world. A significant portion of the anadromous population decline is thought to occur in marine environments. However, the sheer areal extent of habitats utilised by sea trout makes the monitoring of their movements very difficult, leaving many unanswered questions about the types of challenges that sea trout face and how those challenges might affect the their survival rates. Both environmental (i.e. predation, climate change, etc.) and anthropogenic influences (i.e. overfishing, aquaculture, etc.) have been identified as potential sources of increased mortality, but further research is required to determine the effect of each on wild sea trout.

Resident brown trout (left) and anadromous sea trout with acoustic tag on the rule below (right)

High mortality is thought to occur during the initial marine phase of the smolt life stage. However, we actually know relatively little of their whereabouts during this period. Recent advances in acoustic telemetry equipment have created opportunities to observe the movement of sea trout in marine environments. Such studies have been conducted in Norway and have found several interesting trends, such as preference of young smolts to stay in coastal areas near to their natal streams, and the impacts of high salmon lice loads on the behaviour of sea trout (i.e. early returns of sea trout to freshwater in order to “de-louse” themselves).

One aspect of my PhD at the University of Glasgow is focused on the spatial movements and habitat use of young sea trout smolts as they first leave their natal rivers, and what level of interaction they might have with anthropogenic structures such as fish farm facilities. An acoustic telemetry project at this level of fine-scale movement of sea trout smolts has not been carried out in Scotland before and it is hoped that it will shed some light on the current problems facing our local wild fish.

For this project, we chose two adjacent sea lochs on the Isle of Skye in Scotland: Loch Snizort and Loch Greshornish. An active fish farm facility is located within Loch Greshornish. In April 2017, in time with the natural smolt run, 30 sea trout smolts were captured from rivers in both sea loch systems using a combination of fyke netting and electrofishing.

Fyke netting for smolts in the R Snizort (left) and some of the hardware to anchor my telemtry receivers into the lochs (right)

All 60 smolts were anesthetised then tagged with a small acoustic tag that was surgically implanted, before being released back into the site they were captured from. Each tag emits a unique acoustic “ping” that can be “heard” by an acoustic receiver up to ~200m away. These data can then be used to identify when and where a specific smolt was located during the course of the study. The information is stored in the receiver until it is downloaded onto a computer.

Locations of the acoustic telemetry receivers in Loch Greshornish (left) and Loch Snizort (right)

A total of 40 acoustic telemetry receivers were split between the two sea lochs and placed in strategic lines across the lochs. Several “double curtain” receiver arrays were also used to gather information about swimming speed and directionality.

The limiting factor to my study is the battery life of the tags put into the smolts. Unfortunately they only last for ~80 days, so the length of the study was constrained from the end of April until the end of July.

Although the data have not been fully analysed yet, an initial glimpse has identified at least one fish that was successfully recorded moving between the two monitored sea lochs, and several fish that were identified near the fish farm facility in Loch Greshornish. Once the data analysis has been completed, a paper will be published with the final results.

If you have any questions, please feel free to contact me directly.

Isabel Moore (i.moore.2@research.gla.ac.uk or @izzy_moore89)

Capturing Catchment Connectivity Issues

Here at WTT, we're (no pun intended!) all for reconnecting fragmented systems: see recent news items from Tim Jacklin's work on letting the Dove flow, applications of Mike Blackmore's patented #weirbegone, or some of my recent work with Aire Rivers Trust as just a few examples. Europe wide, indeed globally, there is growing recognition of such issues but do we know even the true extent of the problem? Hence, it's great to hear from Siobhán Atkinson regarding her current PhD research.

River connectivity is vital for sustaining healthy freshwater ecosystems. It is important for maintaining resident as well as migratory fish populations, natural sediment movement, and habitat for macroinvertebrate communities and other aquatic organisms. Despite this, few rivers remain uninterrupted across Europe.

Obstacles, or barriers such as culverts, dams, weirs etc. are fragmenting river systems and can be quite extensive. For example, 508 structures with the potential to inhibit fish movement have been recorded in the Nore catchment alone in Ireland. These structures are typically perched culverts, bridge aprons, weirs or fords. To address this issue, an Environmental Protection Agency (EPA) funded project (Reconnect) is being undertaken in Ireland. The goal of Reconnect is to harness knowledge on the distribution, types and impacts of obstacles on Irish rivers, and to develop a methodology for prioritising their modification or removal. The project results will advance efforts to improve the physical and ecological integrity of Ireland’s rivers and will inform the choice of measures to address policy requirements. My PhD focuses on mapping and characterising obstacles in Irish rivers, and studying their ecological impacts.

Figure 1. Examples of different river obstacle types, showing (a) a bridge apron, (b) a natural waterfall, (c) a pipe culvert, (d) a weir and (e) a ford crossing.

The logical first step in addressing the issue of obstacles in rivers is knowing where they are located. This can help managers make informed and targeted decisions on which obstacles to invest removal or remediation measures on. Unfortunately, in Ireland, we do not have a detailed georeferenced map layer of where these structures are. The first part of my PhD is assessing methods of locating obstacles in rivers, and using these methods to map and characterise obstacles in selected sub-catchments. Discovery Series maps, historic maps and satellite imagery are used in combination to locate obstacles. In addition, I am encouraging citizen scientists to use a mobile phone app called River Obstacles (https://www.river-obstacles.org.uk/) to help with the mapping.

Figure 2. The selected sub-catchments where I will map and survey river obstacles.

While the impacts of obstacles on fish movement have been quite well studied, less research has been carried out on their hydromorphological impacts, i.e. impacts on the physical environment, and the resultant consequences for fish and macroinvertebrates. Weirs in particular can change the hydromorphology of a river by impounding a length of channel above the weir. In order to understand the impact of this impoundment on the ecology of a river, I am sampling both fish and macroinvertebrates in impounded and in natural river habitats.

Figure 3. One of my study sites; the weir pictured is approximately 3m high, and the sea trout was caught immediately below it.

The final part of my PhD focuses on the use of an alternative, non-invasive and potentially more efficient approach for assessing the passability of a river obstacle, specifically environmental DNA (eDNA) analysis. This involves collecting water samples that contain DNA shed from organisms inhabiting the river.  The DNA is extracted from these water samples and can be used to detect the presence and relative abundance of target species.  I will test the effectiveness of this tool to detect the presence of Atlantic salmon upstream and downstream of specific obstacles. The results of these analyses will be compared with the results of the electrofishing surveys.

Stay tuned for updates on my progress! Please also download the River Obstacles app and join the mapping effort throughout the UK and Ireland.

Siobhán (siobhan.atkinson@ucdconnect.ie or @ShivAtkinson)


Malcolm Greenhalgh's September Blog


I am writing this blog on the 28th, and in the 28 days thus far we here in northwest England have had rain on 25 of them, thus ensuring that the year’s trout season has been the worst I have known over the past 45 years.

It started well on the 1st, when Mick Addison took me to the Dee near Corwen as his guest. It was a beat I had never fished before, on the outside of a huge meander bend. Thus the deeper water was directly under our bank so that there was little need to wade and the chief use of my chest waders was to prevent my bum from getting wet! The day was quite pleasant weatherwise, other than for a downstream breeze that occasionally strengthened to a strong wind, and in the afternoon it was quite balmy. There was a nice little hatch of pale wateries, with a few BWOs and large dark olives, and a very good hatch (in the marginal vegetation) of needle flies. Unfortunately the river was up a couple of inches and had a tinge of peat, otherwise there would have been more fish rising. As it was I had some nice grayling to 14”, most on Sturdy’s Fancy, and cracking brown trout on a grey-bodied Klinkhamer.

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Some while ago I curated the freshwater specimens in the Manchester Museum’s (part of the University of Manchester) entomology  collection, and still keep in contact with the staff there. They asked if I would give a hand to a group of fly-fishers who were looking at the streams in the Mersey/Irwell system.

Up to the 1980s this major river network was as badly polluted as any – Rhine, Douglas, Thames...you name it! But the Mersey Basin Trust moved to change that with massive lobbying to get the foul streams made clean. So it was in 1990, when I was asked by a now defunct magazine Environment Now to cover the stocking of Salford Quays, and thus the Mersey/Ship Canal with coarse fish (mainly bream, roach and carp) by Prime Minister Thatcher’s Environment Minister, David Trippier. I also interviewed the leaders of the MBT who said that their aim was to get the river clean enough to attract salmon back running and spawning there by the new millennium.

“Some chance!” I thought.

I was wrong to think thus. By 2000 the EA had recorded salmon and sea trout ascending the weir at Warrington, and on 2nd April 2015, when I had to waste time in Warrington while my car was being serviced, I even saw two silver salmon, moving upstream under the A49 road bridge. I was also hearing of tales of brown trout spreading downstream through both Mersey and Irwell as the two rivers became cleaner, mirroring the spread of dippers into streams like the Croal, which runs through the town centre of Bolton.

[The same has happened on the River Douglas, a once foul waterway that passes through the centre of Wigan before emptying into the Ribble estuary. Brown trout are moving down the river from the clean sources in the west Pennine Moors and sea trout are running the Yarrow, a major tributary. The Douglas is culverted through the town centre and this year dippers nested just downstream of the culvert.]

So on the 17th eight of us met at the education centre in Philips Park between Prestwich and Whitefield, and sampled a small, once polluted stream called Bradley Brook. There Baetis (olive) nymphs and Silulium (blackfly) larvae were abundant, and we also obtained some caseless caddis larvae and one stonefly species. We also looked at some samples I had collected from the upper Lune and Aire, which had, as expected, a much greater range of clean water species. The experiences of those who came of the streams they had been examining together with the discussion we had led us to consider a hefty survey of all the Mersey/Irwell system. This could provide a new base line on the state of cleanliness of this once badly polluted system.

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It is now six years since an Environment Agency bailiff asked to see my England & Wales rod licence. Go back forty years and if you went fishing the upper Lune it was a rare day that the bailiff would appear and examine your licence, and go back fifteen years and bailiff Andy would appear by the Hodder one visit in four.

That a warranted bailiff was likely to appear to examine your credentials as an angler on that beat of that river meant that daytime poaching was rarely carried out. But more importantly, when a bailiff was regularly patrolling the river potential (and actual) pollution incidents would be spotted quickly and action taken. Some bailiffs (and Mr Staveley, the upper Lune bailiff I have mentioned was a great instance) even helped maintain the fishery by trapping mink and monitoring the number of salmon and sea trout caught; go back 40 years ago and many anglers did not declare all their catches.

Because the EA cannot afford to pay bailiffs (though they have famously wasted large funds recently ruining excellent cover for brown trout on some rivers) we anglers must take on the role. We must walk the river with an eye open to potential and actual problems. ‘Potential?’ A couple of years ago two of us found a spillage of creosote that was dribbling towards a tiny stream leading down to the river. A phone call and the EA pollution department were informed and dealt with it. ‘Actual?’ More recently, my son Pete found a poacher’s net in the river that had already trapped a brown trout and couple of chub. A quick phone call and the EA responded.

All fly-fishers in England & Wales should carry their rod licences with them, and on the back is the relevant number. From the back of my licence: “Report incidents on 0800 807060”.

We owe it to our rivers and the fish.

How do chalk stream fish respond to flow and habitat restoration?

At the WTT Annual Get Together earlier this year, I had the pleasure of bumping into a former MSc student of mine, Simon Whitton, who now works at Affinity Water and is collaborating with colleagues at Cranfield University, supervising PhD students of his own; a perfect opportunity for another guest blog or four! Since abstraction and chalk streams have hit the headlines repeatedly and this year especially, we should follow Mickaël's progress with interest (and that of Jess Picken too)....

Chalk streams are highly important ecosystems and are a fundamental component of the landscape in the south and east of England. They are hotspots of ecological diversity and support important fisheries for trout and dace amongst others. However, the water that feeds chalk streams originates from groundwater, which is under increasing pressure from abstraction to supply our expanding urban populations. This conflict puts chalk streams squarely in the sights of environmental regulators and water companies as they try to find the best ways to preserve the ecology and the water supply. Hence, my project is sponsored by Affinity Water, and the Environment Agency, and is a part of Cranfield University’s Industrial Partnership PhD studentship programme.

My research aims to investigate the effect of habitat restoration and flow restoration on fish communities. To do this, I am using a broad set of techniques to monitor hydromorphological change (river habitat change) and biological change with a specific focus on fish communities. My study sites are on the rivers Beane and Mimram.

To put the information gathered from my field studies into context, a set of reference sites on six chalk streams has been chosen: Misbourne, Chess, Gade, Ver, as well as elsewhere on the Mimram and Beane. Data collected previously on the fish community and habitats of these rivers is being used as a baseline against which future change will be assessed.

The ultimate aim is to provide river managers with evidence on the links between fish, river flows and physical habitat. Information on how fish (and particularly coarse species) use habitats, will help us to decide which types of features to bring back into the river (plants, riffles, etc) to encourage colonisation of sites or to sustain fish populations and ensure resilience in the future.

At the moment, we have completed a first cycle of surveys. At Singlers Marsh in Welwyn, the public was amazed to see fish being caught in the stream, from small bullhead up to a nice-sized brown trout.

We have faced some challenges along the way, such as finding one of the rivers chosen for our survey to be dry in its upper reach. Unfortunately, this situation appears to have been all too common this year, as reported elsewhere on the WTTblog (e.g. Long term abstraction and fishery collapse). While I could not say much about the fish community at the time (cows were more prevalent), I could still assess the dry reach for potential habitat features which are likely to ‘re-emerge’ as the flow returns.

From the techniques we have chosen to monitor our sites, some of the most interesting use cameras to capture images from fixed points both above and below water; this will be the focus of another blog in the near futur

Further information about this specific project and about river-related research from my colleagues at Cranfield University can be found on the following websites:



Or please contact me for more information

Mickaël Dubois (Mickael.Dubois@cranfield.ac.uk, @Mickael_bio_be)

Genetics to underpin effective management

As WTT Conservation Officers, we are asked to make assessments on what is good and bad habitat for trout populations based upon visual observation and expert judgement; this is the basis of a typical Advisory Visit Report. If we had the time and resource, we'd look to the fish themselves to tell us! In this latest blog from current researchers, Jess Fordyce from the University of Glasgow Scottish Centre for Ecology and the Natural Environment outlines how an understanding of the genetic diversity within a catchment can inform more efficient management strategies for safe-gaurding trout populations.

The brown trout, Salmo trutta, is an extremely diverse species in terms of behaviour, physiology, genetics and morphology. Brown trout can adopt a range of life-history strategies which include freshwater residency in rivers and/or lakes, or anadromy – the movement from fresh to saltwater and back again (ie sea trout). The diversity of brown trout in terms of genetics and morphology was the focus of my PhD which was funded by an EU project called IBIS (Integrated Aquatic Resource Management Between Ireland, Northern Ireland and Scotland) and the Atlantic Salmon Trust. My study site was the Foyle catchment which is a large dendritic (branching) system with an area of around 4500km2 located in both Ireland and Northern Ireland. This catchment is managed by the Loughs Agency. Like other catchments across Britain and Ireland, sea trout numbers have been sharply declining over the last few decades. Therefore, it is important to understand the genetic population structuring of brown trout (the pattern of genetic variation) and which environmental factors shape such structuring. From this information, it is possible to detect exactly which populations contribute significantly to the production of sea trout and hence provide focused management.

WTT blog sea trout PhD research population geneticsWTT blog PhD research trout genetics population

An anadromous (‘sea’) trout (left) and juvenile resident brown trout (right)

I aimed to address several objectives throughout my PhD, but here I will only discuss two of them. The first of these aims was to determine the spatial scale at which genetic populations could be detected. In other words, do brown trout form genetically different populations between sampling sites >1km apart, >10km apart etc, and which environmental factors could be driving such genetic diversity? The spatial scales I focused on were:

  • Large - comparison of sampling sites between sub-catchments;
  • Medium - comparison of sampling sites between tributaries within sub-catchments and
  • Small - comparison of sampling sites within tributaries.

It is important for management to know at which spatial scale that genetic population structuring occurs to conserve the maximum amount of important genetic variation within each sub-catchment and which environmental variables drive such variation.

PhD blog WTT research

Illustration of spatial scales used to determine population structuring.

With a team of three or four people, we electrofished ~1 km stretches of 28 sampling locations to catch ~60 juvenile brown trout at each sampling location. Those ~1km stretches of river were to ensure the brown trout we sampled represented more than a few families. The trout were then anesthetised and a non-destructive genetic sample (fin clip of adipose fin) from each was placed in ethanol.

Map showing the location of the Foyle catchment and sampling sites. Highlighted in orange for the next aim I will discuss is the River Faughan and the star shows the location of the Rotary Screw Trap.

I then processed the genetic samples at Queens University, Belfast using a suite of 21 microsatellite markers. Each microsatellite marker targets a short-repeated sequence of DNA, from which the genetic variation of each individual brown trout can be compared. Using the genetic variation, I determined the genetic population structuring of brown trout in the Foyle catchment and which environmental variables could be driving this population structuring. I found extensive genetic population structuring which varied with spatial scale and was driven by environmental variables. This work will be published soon I hope so stay tuned for the details.

Electrofishing one of my sampling locations… it wasn’t always this sunny!

To address another aim of my PhD, I used the genetic information gained from the population structuring of brown trout, described above, to determine which tributaries within the River Faughan produce sea trout. The River Faughan is one of the best sea trout producing rivers in the Foyle catchment and determining where exactly the sea trout are being produced is important for effective and efficient management and conservation.

I used a Rotary Screw Trap in the lower reaches of the River Faughan to capture sea trout smolts during their downstream migration to sea in 2014. The RST has a large cone shaped barrel which is turned by the flow of the water. This rotating barrel allows fish to swim in but they are unable to swim back out and are held in a holding tank at the back of the trap. We would then check the trap every day, collecting fin clip samples for genetics from sea trout smolts and releasing all fish to continue their downstream migration. The fin clips from these smolts and archived genetic samples (scales) from sea trout smolts caught in the same trap between 2005 and 2008 were used to determine which tributaries within the River Faughan produce sea trout.

Rotary screw trap in the lower reaches of the River Faughan.

I processed the genetic samples from sea trout smolts using the same suite of microsatellite markers that I used to determine the genetic population structure described above.  In doing so, I could assign individual sea trout to their tributary or population of origin by using the genetic diversity of each population as a genetic ‘baseline’. Each population represents a different tributary, therefore, the genetic variation of each sea trout smolt can then be matched to the tributary with the most similar genetic variation. Hence I could estimate the proportion of the smolts originating from each tributary and identify the most producitve spawning grounds. Again, these data are in the final throes of the publication process so I cannot yet reveal the fine details but will do so in the near future.

In the meantime, if you have any comments or specific questions, please feel free to contact me.

Jess (j.fordyce.1@research.gla.ac.uk or @JessicaRFordyce)


Stocked fish or native invader?

Anyone with an interest in rivers or lakes and the life within them, be it from a conservation, management, or angling perspective (and of course those three are not mutually exclusive) will be aware of invasive non-native species (INNS), the impacts they may cause in certain situations, and the importance of biosecurity. Ecologists with a particular interest in invaders differentiate between non-native (i.e. those species introduced beyond their original distribution range, a pertinent example being pink salmon) and native invaders (referring to species that add to existing or establish new populations within their native range). The artificial stocking of salmonids into waterbodies is one such example of the deliberate introduction of native invaders, to allegedly enhance commercial and recreational fisheries, as well as for conservation purposes in some instances. The evidence accruing as to the benefits of this approach makes interesting reading.

In 2016, Buoro and colleagues used the global-scale introductions of salmon and trout as a robust biological model (i.e. lots of studies with plenty of data to analyse) to investigate the ecological effects of changing intraspecific (within species; e.g. stocking farmed brown trout in to rivers containing wild brown trout populations) and interspecific (between species; e.g. stocking rainbow trout into lakes with Arctic char) diversity. The enormity of the dataset collated from the literature allowed them to look at various levels of organisation which introduces a lot of complexity. However, the take home message was that, overall, introduction of native invaders resulted in stronger ecological effects than those associated with changes in interspecific diversity caused by non-native species.

Sifting through the results revealed that physiological traits (mainly associated with stress response) were most impacted by native invaders, and probably the basis of the initial response of for example, wild brown trout facing introduced farmed brown trout. Furthermore, the study also revealed significant impacts of native invaders on growth and condition, suggesting that there may be evolutionary consequences further down the line. This is aside from the more direct impacts at the genetic level resulting from interbreeding and the introduction of less ‘fit’ genes if diploid (fertile) native invaders are stocked.

Buoro et al highlighted that actually, there is a significant knowledge gap regarding the wider ecological consequences of introduced native salmonids on recipient communities and ecosystems. A paper published this week by Hasegawa and colleagues has taken up that challenge using the introduction of hatchery chum salmon fry on top of the wild masu salmon fry population, as well as their benthic invertebrate prey, and the algal food of those invertebrates.

They assessed the impacts of a single stocking event, the release of 3 million fry into the Mamachi stream, Hokkaido, northern Japan. As was revealed in the previous meta-analysis (above), the foraging efficiency and growth of wild masu salmon fry was reduced following the introduction of the chum salmon fry (the native invader). There was a marked decrease in abundance of various mayfly and caddis species via predation pressure from the fish. This induced an apparent ‘trophic cascade’ across the various links in the food-chain: Lots of fish induced high predation pressure on the invertebrates, reducing their overall number and therefore reducing the grazing pressure on algae at the bottom of the chain. As a consequence, algal biomass increased although the extra nutrients recycled via stocked fish excretion has also been shown to promote algae.

Together, these findings highlight the need to consider the more subtle ways that introduced native organisms like stocked trout and salmon can potentially change the ecology of a waterbody, as well as the more obvious detriment caused to wild populations of salmonids. The Wild Trout Trust always urges caution and consideration when asked about stocking: our position paper and an ever increasing number of case studies from clubs that have ceased stocking are available on our web pages. Click the green links above.

Tags under trees tell a tale

In science, new questions are always arising from serendipitous discoveries. Angus Lothian tells us of some interesting data on fish predation that has come to light as a part of his PhD project at Durham University, assessing trout behaviour at fish passes.

Every year, Atlantic salmon (Salmo salar) and sea trout (Salmo trutta) undertake an upstream migration in autumn. People watch these fish ‘heavy-weights’ leap, or at least attempt to, over barriers after having already completed maybe tens of miles on their journey to and from sea. Such a migration allows the fish to use rich marine feeding areas to grow larger than they might achieve by staying in freshwater, thus increasing their fecundity or egg production for when they return to their natal rivers. But there are trade-offs. The migration between freshwater and saltwater is filled with risk, resulting in large annual mortality affecting fish populations. For example, for my MRes, I studied the emigration of salmon smolts from rivers, and their behaviour strongly reflected predator avoidance tactics.

But closer to home, the year-round, river-resident brown trout – the same species as sea trout – can also exhibit an annual migration.  Similar to their anadromous counterparts (those fish that move from freshwater to saltwater), brown trout also move to areas of increased nutrient abundance within freshwater environments to grow more efficiently which will be different to where they spawn.  Although on a much smaller scale, substantial risks are also faced by river-resident individuals on their potadromous (within river) migrations.

Last autumn at Durham University, we performed a small study monitoring the spawning migration of adult brown trout in a local river. We fitted sixteen fish with radio transmitters which were subsequently tracked for two months, from mid-October to mid-December 2016.  Two remote logging stations were placed approximately 1.5 km apart on the River Deerness, a sub-tributary of the River Wear, with further manual tracking taking place four times a week.  This involved walking along the river bank for a minimum of 5 km with a radio receiver and antenna to precisely locate each individual fish.  Manual tracking meant we could record exactly where each individual fish was in the river, how far they had moved, and in which direction.

The manual tracking also proved to be useful in a different and unexpected manner.  Radio tags actually function better in air than in the water; not something that you generally need to consider when monitoring fish movement!  On one survey, I could not get a strong fix on a tag in the river.  After several minutes of pacing the river bank, I was about to give up, when I turned around and heard a clearer *beep* in my headset.  Using our unidirectional antenna, it did not take me long to find the tag underneath a tree only 5 m from the river edge.  Even more exciting, the tag was actually encapsulated within a heron pellet!

Over the course of the next month, we made several more visits to the same tree, recovering four of our 16 radio tags, along with some PIT (Passive Integrated Transponder) tags that had been inserted into trout parr in 2014 for a different study.  This means that a heron has used this feeding spot for at least two years.  Further, another three radio tags were found downstream; one of which was found in a heron pellet, but the other two were never retrieved due to being lost in a woodpile and in a relatively large pond.  We know that at least 31.3% of our tagged fish were definitely eaten by herons, and potentially up to 43.8% had succumbed to predation within this 2 month period.  Extrapolating this figure implies that a large proportion of the trout population in the Deerness at least, ranging in size from small parr to larger adults, can be removed by an avian fish predator.

Several questions spring to mind: is this one heron with a good fishing spot? Or, are there several predators along the river that enjoy a fishy snack?  As part of a larger study in the upcoming autumn (2017) - the behaviour of parr, adult brown trout and sea trout at a newly constructed fishway - we will also focus some of our efforts on understanding the potential impact of predation on the trout population of the catchment.  Piscivorous birds along the river will be counted during manual tracking exercises, and frequent searches at their known feeding sites for regurgitated tags will be undertaken.

I hope to bring you an update on how things are going later but in the meantime please contact me if you have any questions or comments regarding my project.

Angus Lothian (angus.j.lothian@durham.ac.uk or @AngusJLothian)

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