ENHANCEMENT OF ATLANTIC SALMON POPULATION and Biodiversity Considerations of Habitat Restoration in SACs Drawing on the Experience of MulkearLIFE 2009 to 2014 BEST PRACTICE GUIDE NUMBER ONE
Introduction The following guidance document is based on the experience of MulkearLIFE, the European Commission funded LIFE+ Nature project (LIFE07/NAT/IRL/000342 IShannonSACLAEO). It provides an introduction to MulkearLIFE s work on habitat enhancement for Atlantic salmon in Mulkear catchment. It also focuses on the designation of sites of conservation importance, in addition to the habitat, ecological and water quality issues that impact on salmon populations in freshwater. The guide will be of assistance to agencies, local authorities, land owners and others, to assist them to play a proactive role in the conservation management of Atlantic salmon and the protection of river catchments for future generations. The Mulkear River is considered one of the most important salmon rivers on the Shannon system Overview of MulkearLIFE MulkearLIFE (www.mulkearlife.com) was established in Ireland and ran for a five-year period between 2009 and 2014. The main project objective was to restore, through in-stream rehabilitation works, degraded habitats along stretches of the Mulkear River and its main tributaries for Atlantic salmon, sea lamprey and European otter. Inland Fisheries Ireland (IFI) was the co-ordinating project partner, together with the Office of Public Works and Limerick County Council. The National Parks & Wildlife Service (NPWS) provided funding support. Other important supporters included Coillte, ESB Fisheries, Teagasc, anglers and local farmers. 01
BEST PRACTICE GUIDE NUMBER 1 Enhancement of Atlantic Salmon Population and Biodiversity Considerations of Habitat Restoration in SACs Key Achievements of MulkearLIFE: Installation 28 rubble mats on 10 km of the Mulkear River, utilising over 5,000 tonnes of rock, which enhanced habitat for salmonids and lamprey species by improving instream and riparian biodiversity. Enhancement of over 15km of river channel through additional instream measures (random boulders, vortex and stone weirs) using 1,500 tonnes of rock which added additional beneficial flow complexity. Research, design, manufacture and successful installation of lamprey passes to assist sea lamprey ascend Annacotty weir, which was a major barrier, on the Lower Mulkear River. Following 15 months planning and consultation, the partial removal Ballyclogh weir as a barrier to salmonid and sea lamprey passage, opening up 184km of river channel and improving upstream habitat. Treatment of over 200 kms of river bank (riparian habitat) to control non-native invasive plant species (with focus on giant hogweed & knotweed species) and the manual removal of other invasives (Himalayan balsam and pheasant berry) from High Nature Value (HNV) sites in the catchment. Improvement of otter habitat through tree planting, enhancement of river connectivity and installation of artificial otter holts at sites degraded in past historical drainage programmes. Establishment of the Mulkear Conservation Volunteers to undertake practical, river and riparian based, conservation activities: 47 outings (amounting to over 1,120 unit days) improving river biodiversity. Establishment of a river based an Environmental Education Programme. This included 74 classroom engagements and separate, river based, field trips with almost 2,000 schoolchildren and their teachers. Delivering training workshops and field-trips for 360 people and 66 illustrated talks to 2,120 people. Worked directly with local farmers to address water quality concerns and installed alternative watering solutions away from rivers. Established 12 pilot learning sites on farms with extensive river frontage. 02
Mulkear River Catchment Overview The Mulkear catchment as part of the Lower Shannon SAC The Lower Shannon SAC The Lower Shannon is designated as a Special Area of Conservation (SAC) of international nature conservation importance, for a range of species including, Atlantic salmon (Salmo salar), Sea Lamprey (Petromyzon marinus) and European otter (Lutra lutra). This SAC forms part of an EU wide network of nature protection areas established under the Habitats Directive and is one of 430 SAC s in Ireland, that we, as a nation, are legally obliged to protect. The Mulkear River forms part of this SAC. The work of MulkearLIFE, under the auspicious of the EU LIFE programme, has been designed to help develop and inform an overall conservation strategy for the Lower Shannon SAC, to deliver the objectives of the Habitats Directive. MulkearLIFE s work programme has been implemented to establish a framework for the positive management of the Mulkear catchment in order to safeguard the long-term survival of salmon populations. The Mulkear River The Mulkear River rises in the Slievefelim and Silvermine mountains and flows through counties Tipperary and Limerick, before joining the Shannon River below Annacotty in County Limerick. The catchment consists of upland and lowland habitats, typical of many Irish river systems. The upland areas are extensive, with mountains in excess of 400m. The lowland areas are largely flat river plains, with surrounding agricultural pastures and a scattering of small towns and villages. The main channel of the Mulkear River is approximately 21.5 km long and together with its tributaries, it drains a catchment area of approximately 650 km². The principal tributaries are the Dead, Bilboa and Newport rivers. Within the catchment, there are 10 Special Areas of Conservation (SAC s) which have been designated as part of the Natura 2000 Network of designated European sites. The qualifying species include Atlantic salmon, lamprey, European otter and other species and habitats. They also contain a wide range of supporting biodiversity important to the conservation objectives of the EU including species of interest like the European eel. 03
BEST PRACTICE GUIDE NUMBER 1 Enhancement of Atlantic Salmon Population and Biodiversity Considerations of Habitat Restoration in SACs Background The Habitats Directive The Habitats Directive is one of the main tools through which the European Union safeguards its natural heritage and it aims to conserve biodiversity through maintaining and restoring habitats and species, while taking account of economic, social, cultural and regional requirements. This is achieved through a series of measures, including the creation of a network of protected sites across Europe, known as Natura 2000. The Natura 2000 network aims to maintain the European Union s overall biodiversity by ensuring that activities and developments taking place in protected sites are sustainable for the designated habitats and species. The Habitats Directive details specific habitats and species of conservation importance. These include specific habitat types (listed in Annex I of the directive) and the habitats of vulnerable species (listed in Annex II of the directive), species in need of strict protection (Annex IV) and species whose taking from the wild can be restricted by European law (Annex V). The Natura 2000 network also includes Special Protection Areas (SPAs) which are sites designated under the Directive on the Conservation of Wild Birds (79/409/EEC). The Upper Mulkear Catchment also adjoins several SPAs. Protection of Natura 2000 interest features The Habitats Directive and Habitats Regulations apply a common protection regime to all Natura 2000 sites (SACs and SPAs).The main requirements of the Habitats Directive are: Member states shall establish the necessary conservation measures (for example, development appropriate management plans) and appropriate statutory, administrative or contractual measures which correspond to the ecological requirements of the qualifying feature(s) Member states shall take appropriate steps to avoid deterioration of natural habitats, habitats of species and disturbance of species for which the site has been designated Activities, plans or projects, whether within or outside the European site, likely to have significant effects on the conservation status of the site s qualifying feature(s) shall be subject to assessment. The competent authority shall only agree to the plan or project if it is ascertained it will not adversely affect the integrity of the site, or if there are imperative reasons of overriding public interest (such as social and economic reasons) A surveillance programme of the interest feature(s) should be undertaken, to monitor the condition of qualifying features and to assess the effectiveness of management measures undertaken. Salmon jumping Annacotty Weir (Eamonn Pearce) 04
The duty of competent authorities The Habitats Regulations place a duty on the Irish Government to undertake functions related to nature conservation in accordance with the requirements of the Habitats Directive. In the case of the Lower Shannon SAC this is primarily through the National Parks and Wildlife Service (NPWS) and Inland Fisheries Ireland (IFI). There is also a duty on every competent authority in the exercise of any of their functions to have regard to the Habitats Directive. Competent authorities are obliged to consult with NPWS / IFI over plans or projects that are likely to have a significant effect on a European site, and not to permit developments or operations unless it can be demonstrated that they will not have an adverse impact on the integrity of the site or, if they will that there are imperative reasons of overriding public interest (social and economic). Competent authorities are defined as including any minister, government department, public or statutory undertaker, public body of any description or person holding a public office. Any activities and operations that may have a significant effect on Natura 2000 sites, species or habitats, are subject to appropriate assessment. An assessment by any competent authority as to whether a plan or a project may have a significant adverse effect on the site, and therefore should not be permitted to go ahead, must be made against the site s conservation objectives. These projects or plans are only permitted if they are found to cause no significant impact to the features of interest, unless it can be demonstrated that there are imperative reasons of overriding public interest. The Mulkear river and it s tributaries flow through a rich agricultural landscape 05
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The Atlantic salmon Population decline of Atlantic salmon Salmon jumping (Martin O Grady, IFI) The Atlantic salmon (Salmo salar) is an internationally important species, protected under the Bern Convention, and annexes II and V of the Habitats Directive. The species used to be widely distributed in all countries whose rivers enter the North Atlantic, but the species has undergone dramatic decline and has become extinct in many rivers throughout its range. The species is also covered by the Convention for the Conservation of Salmon in the North Atlantic Ocean which entered into force on 1 October 1983. This multilateral convention aims to promote the conservation, restoration, enhancement, and rational management of salmon stocks in the North Atlantic Ocean and is managed by the North Atlantic Salmon Conservation Organization (NASCO). Recent studies indicate the abundance of Atlantic salmon is at a historically low level in some rivers in Europe and in a very unfavourable condition. The analysis carried out by the Irish Standing Scientific Committee on Salmon in 2014, indicates that the number of rivers with healthy populations on the basis of attainment of Conservation Limits for 2015 has risen to 55 rivers, from 43 in 2007. In the second Article 17 report on the status of Irish salmon stocks, submitted as a requirement under the Habitats Directive in 2013, factors considered as threats to salmon populations are described. These include factors such as agricultural intensification, diffuse pollution to surface waters (resulting from factors such as inadequate sewage treatment, agricultural enrichment, acidification, erosion and siltation), forestry related pressures, pressures related to intensive fish farming and peat extraction, and poaching. Concerns were expressed about the poor levels of marine survival; despite the removal of the drift net fishery from Irish coastal waters in 2006 salmon numbers have not increased. The range where salmon were found was classified as favourable, the population size was considered stable, habitat condition was considered favourable with future prospects considered stable. The overall classification for the Atlantic salmon in Ireland was therefore described as Stable, an improvement on the 2007 overall classification of Bad status. It was noted that this current period of stability has to be set against the context of a long trend of population decline. 07
BEST PRACTICE GUIDE NUMBER 1 Enhancement of Atlantic Salmon Population and Biodiversity Considerations of Habitat Restoration in SACs The Atlantic salmon Life Cycle The salmon is anadromous, i.e. born in fresh water, spends most of its life in the sea and returns to fresh water to spawn. The Lower Shannon SAC and the Mulkear catchment in particular, comes to life from late autumn to early winter as adult salmon return to spawn. Mature fish returning to rivers to spawn after one winter at sea are referred to as one-sea-winter (1SW) salmon (or grilse). Non-maturing fish returning after two or more winters at sea and are referred to as multiseawinter (MSW) salmon. The adults spawn in their natal river or upland stream by cleaning and excavating gravel on the river bed and depositing eggs in depressions in the gravel bed, excavated by the female salmon called redds. The eggs are then fertilised by the male. Approximately 1,100 eggs are laid per kilogram of adult female body mass. Following spawning, the majority of adults, known as kelts, will die, although some may descend downstream back to the sea. Several of these will return to the river the following year to spawn again. The eggs develop in the redds over winter and hatch between March and late April the following year. Atlantic salmon life cycle courtesy of Atlantic Salmon Trust and Robin Ade 08
The newly hatched salmon, called alevins, remain within the redd, dependent on their yolk sacs for food, until they emerge to feed independently. Following emergence, the juvenile salmon is called a fry. The mortality rate at this stage is high, due to predation and competition for space and food resources. Migration takes place between April and June, when the parr begin to turn silver and become smolts. Only very few fry will survive and grow on to become parr (more than one year old). Salmon fry and parr are territorial, feeding primarily on aquatic insect larvae and some terrestrial insects. Juvenile salmon in the Mulkear system usually remain in the freshwater system for between two and four years, before entering the Shannon River and migrating down the Shannon Estuary and out to sea. During the smoltification process salmon undergo a number of behavioural, morphological and physiological changes, in preparation for life at sea. Upon reaching the sea, salmon grow rapidly, feeding on a variety of small fish including capelin, herring, sand eels and sprat. A proportion of male salmon adopt a slightly different life cycle, as they become sexually mature before going to sea. These precocious males may be responsible for fertilising a proportion of the eggs of returning adult females. The following spring the precocious males smoltify, go to sea and later return to their natal river to spawn again. The installation of rubble mats on the Mulkear River helped to improve habitat for juvenile salmon 09
BEST PRACTICE GUIDE NUMBER 1 Enhancement of Atlantic Salmon Population and Biodiversity Considerations of Habitat Restoration in SACs Management Guidelines Factors behind the decline in stock numbers In an Irish context, studies have indicated that a number of interrelated factors have all contributed to the dramatic reduction in stock abundance over the past 30 years. Causes can be found in both freshwater and in the sea. Key threats to the freshwater phase are poor water quality resulting from the adverse effects of agriculture, forestry and pollution, amongst other factors. Habitat loss and degradation of juvenile and spawning habitat are all considered significant threats. These threats have arisen due to an intensification of commercial agriculture, water abstraction, development projects and in-stream engineering works including drainage works. In the marine phase there is evidence that the main causes for reduced marine survival include changes in sea surface temperatures, brought about by climate change, over-exploitation of the stock, predation and, in some areas, the negative impact of fish farming, including parasite infestation and the impact of farmed salmon on wild stock. The Mulkear catchment is considered to support a healthy population of salmon. Ecological requirements The main requirements for salmon (as for other anadromous species) during the freshwater part of their lifecycle are a clean and plentiful supply of water, good habitat conditions, free upstream passage for adult fish and downstream passage for smolts (juvenile fish) and an adequate food supply. The ecological requirements can be directly correlated to the factors that have given rise to the decline in the Atlantic salmon. Of key importance to the well-being of the salmon are water quality, flow and the riverbed substrate. The water quality needs to be high, typical of that found in upland streams. The water flow should be sufficient to allow migration to spawning and nursery areas and to negotiate barriers, but not so high that is causes wash out of redds and scouring of suitable spawning and nursery substrate. Summer flows must be sufficient to maintain adequate depth and velocity in juvenile rearing areas. Natural freshets, or sudden increases in water flow, during low summer and autumn flow periods are of great importance in providing the stimulus to initiate upstream migration of adults into freshwater. Adequate habitat diversity of the type provided by the typical riffle/pool sequence is important for both juvenile and adult salmon. The pools provide the deeper holding areas required by the adults while the riffles provide the fry and parr habitat, and suitable spawning sites are provided at the point where a pool shallows into a riffle and water velocity increases. Pebbly riffles without boulders are considered prime nursery habitat for salmon less than 7 mm long. As fry grow their preference for deeper and swifter parts of riffles increases and larger (boulder and cobble sized) substrates become important for providing cover. Riparian vegetation can be important in providing cover and food for juvenile salmon, as well as maintaining riverbank stability and reducing erosion. Dense shading of the riverbank should, however, be avoided, as it can lead to a reduction in juvenile salmon density, through a reduction in aquatic plant cover which attract many animals that juvenile salmon prey upon. MulkearLIFE has attempted to address all of these factors in its work programme over the past five years. 10
The placement of random boulders on the Newport River has helped to improve habitat for juvenile salmon The main focus of MulkearLIFE was the conservation of Atlantic salmon as well as sea lamprey and European otter, which had become seriously threatened. Modifications to the river, such as straightening its course and installing weirs, represented particular obstacles to the conservation of these species. The planting of conifers and the spread of invasive plants can negatively impact salmon spawning beds with sediments. The objective of MulkearLIFE was to enhance habitat for salmon and sea lamprey using best practice techniques through in-stream habitat rehabilitation. The specific measures carried out by the project are designed to mimic the conditions typically found in a natural river or an undrained river. These works alter the river flow, gradient, bed, channel or banks. All of MulkearLIFE s instream work was carried as part of a holistic restoration plan, to improve habitats and enhance instream complexity of the river environment for Atlantic salmon and other species. As part of the project, 28 rubble mats were installed to rehabilitate over 10 km of the main channel of the Mulkear River. This utilised over 5,000 tonne of rock. Additionally, the project used more than 1,500 tonne of locallysourced rock to improve habitat in over 15 km of river channel in the Dead, Bilboa, Newport, Clare- Annagh and Killeengarriff rivers. The project also installed other in-stream measures such as random boulders, paired deflectors and vortex weirs - to increase flow and habitat variability. In addition, considerable bank protection work was undertaken at sections of various river in the catchment. 11
BEST PRACTICE GUIDE NUMBER 1 Enhancement of Atlantic Salmon Population and Biodiversity Considerations of Habitat Restoration in SACs MulkearLIFE undertook extensive monitoring of all its work in relation to Atlantic Salmon. This included walkover surveys of reeds, water quality monitoring work and monitoring of instream measures. The most important monitoring work was the annual fish stock survey. This was one of the most comprehensive fish stock survey programmes every undertake anywhere in Ireland. The LIFE project provided an unprecedented opportunity to carry out detailed monitoring at thirty-five sites throughout the Mulkear catchment. IFI staff undertaken electrofishing survey work During the operational phase of MulkearLIFE (2010-2014) a staggering 11,471 fish were processed for monitoring purposes. The data generated will be invaluable in the AfterLIFE phase of the project. Electrofishing survey work on the main channel of the Mulkear River in 2011, prior to the installation of rubble mats, clearly demonstrated that the proposed sites were not being used by salmon fry. With new rubble mats in place, within three years, the average salmon parr density has more than tripled. Results for the 2013 and 2014 seasons indicate the average density at the rubble mat sites to be 0.72 fry/m². IFI staff at work on the Killeengarriff River Explaining the life cycle of Atlantic salmon Habitat Issues Atlantic salmon usually return to their natal stream for reproduction, but barriers, such as dams and weirs, as well as river modifications, have become an increasing problem in recent decades. Habitat deterioration, commercial fishing and decreasing water quality are also factors explaining local extinctions. Changes in the freshwater habitat can have a detrimental effect on the carrying capacity of a river for Atlantic salmon. Increased siltation and sedimentation resulting from activities such as poor agricultural practices (lack of buffer zones, cattle poaching etc.) forestry, road development, in-river engineering, construction, gravel and peat abstraction, quarrying and urban runoff etc., can have a detrimental impact on in stream spawning and fry substrates, resulting in smothering of essential habitats and changes in flow regime. Loss of shelter and cover from activities such as removal of riparian and in-river vegetation and substrate alteration can result in the increasing of summer water temperatures, while overplanting of riparian vegetation can result in tunnelling and inhibiting the growth of aquatic vegetation. The creation of physical barriers to migration resulting from activities such as dams, poorly designed river crossings, culverts, weirs and hydroelectric power stations can result in entire sections of rivers, which could normally support a healthy salmon population, being devoid of salmon as a result of poor ecological design. 12
Water Quality Issues Good water quality that supports a healthy and varied aquatic biodiversity is essential for all freshwater stages of Atlantic salmon. Clean, well oxygenated water at relatively low temperatures is essential for salmon and negative changes in water quality through the addition of nutrients and chemicals from activities such as agriculture, industrial and domestic waste water discharges and forestry can impact negatively on salmon. Eutrophication can result in a substantial increase in aquatic vegetation and phytoplankton which contribute to fluctuations in oxygen levels, particularly at night. Aquatic invasives outcompeting native species can result in the altering of aquatic ecosystems, leading to a reduction in the abundance of species that provide food for salmon. Climate change is currently and will in the future, impact on salmon survival and the carrying capacity of rivers through, for example, increased flooding events removing spawning gravels, increasing siltation and summer temperatures. These changes make salmon even more sensitive to the other issues outlined above and the practical management of rivers needs to take this into account. Improving water quality greatly assists salmon Bank erosion leads to increased siltation Ecological Issues Invasive plant species can alter the riparian vegetation leading to changes in invertebrate quality and quantity and structural changes in banks, leading to bank erosion and siltation problems. Genetics and Tagging The life cycle of Atlantic salmon, their homing instincts and the way that they spawn in natal streams and rivers lends itself very well to the use of genetics as a management and conservation tool. The use of genetic markers can help separate distinct populations to, not only observe populations in the freshwater environment but also offshore where not much is known of their behaviour. Distinct migration routes can be tracked and with advances in tagging new insights into the role and effect anthropogenic influences including fishing, aquaculture, habitat modification can be determined. Addressing invasives can assist Atlantic salmon 13
BEST PRACTICE GUIDE NUMBER 1 Enhancement of Atlantic Salmon Population and Biodiversity Considerations of Habitat Restoration in SACs Improving Atlantic salmon survival in freshwater environments There are significant pressures from a habitat, ecological and water quality perspective, impacting on salmon in the freshwater and marine environment. Addressing these issues in freshwater requires understanding the requirements of salmon and addressing concerns in a systematic and catchment based approach. As outlined by NASCO where salmon habitat has been degraded or lost, options for its restoration should be identified and prioritised. Priority should be given to management options that will have the greatest direct (increase in productive capacity) and indirect (overall value of ecosystem services, public relations aspects) benefits relative to the costs of the improvement work. Restoration activities should be evaluated to assess achievement of the objectives and to inform future activities. Wherever possible, restoration initiatives should include community participation and the restoration of habitat should generally take precedence over habitat enhancement. In terms of recreational angling more fisheries are now applying catch and release as a conservation measure in conjunction with salmon tagging, which limits the number of adult salmon that may be taken on rod and line. The Mulkear River went to catch and release in 2015 14
www.mulkearlife.com Other Best Practice Guides in this series: - Management of Upstream Passage for Adult Sea Lamprey in SACs - Management Guidelines for European Otter (Lutra lutra) in SACs - Management of Riparian Zones in SACs with particular reference to the management of Non-Native Invasive Plant Species - Guide to Sustainable Water Management on Farms in Close Proximately to SACs designed at copperreed.com Front cover image by Lette Moloney, remaining images by Ruairí Ó Conchúir unless otherwise stated