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Using Hydroacoustics to Spatially Quantify Productive Capacity in Freshwater Ecosystems

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My MSc. thesis proposal.

My MSc. thesis proposal.


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  • 1. Using Hydroacoustics to Spatially Quantify Productive Capacity in Freshwater Ecosystems A Thesis Proposal Submitted by Riley Pollomin Partial Fulfillment of the Requirements for the Master’s of Science Degree in Biology at Memorial University of Newfoundland Advisor: Dr. George A. Rose – Director, Centre for Fisheries Ecosystems Research (Fisheries and Marine Institute of Memorial University) Committee: Dr. Daniel Boisclair – Professor, Département de Sciences Biologiques(Université de Montréal); Scientific Director, NSERC HydroNet Strategic Network Dr. RodolpheDeVillers – Professor, Department of Geography (Memorial University)Statement of Purpose
  • 2. It is the purpose of this MSc. thesis to determine hydroacoustic methods to evaluatethe productive capacity of fish habitats in freshwater lakes and reservoirs in Manitoba, andto discover how this productive capacity varies over space within and between natural andreservoir systems. This research is part of NSERC’s HydroNet research program(Smokorowskiet al. 2011).Introduction Freshwater ecosystems of the world provide people with a vast amount ofecosystem services that are vital to our survival and well-being(Braumanet al. 2007). Oneof the most salient services provided by these ecosystems is the production of fish forhuman consumption and recreation. Increasingly, freshwater systems and the servicesthey provide - includingfish productivity -are under threat from multiple stressors(Ormerodet al. 2010). One of the major ways in which the productive capacity of fishhabitats (i.e. the total production of all stock during the time they spend any part of theirlife history in that habitat; Minns 1997)is altered is through the creation and operation ofhydropower facilities (Rosenberg et al. 1997). In Canada there is a federal mandate to protect fish habitat and productive capacitythrough a ‘no net loss’ approach (DFO 1986), however it remains prohibitively challengingto measure such capacity in the field (Randall and Minns 2002; Smokorowskiet al. 2011).Challenges include the need for long-term monitoring and the necessary measurement ofmultiple ecosystem components such as plankton production and interactions amongtrophic levels. Even when such comprehensive studies are undertaken, they can lead to
  • 3. ecosystem disturbances and fish mortality that can contradict the ultimate goals of theproject (Argent and Kimmel 2005). Hydroacoustics offer a substantial contribution to the amelioration of the challengesfor assessing aquatic production. The technology allowsresearchers to study multiplefacets of ecosystems including fish, plankton, macrophytes, and bathymetry relativelyquickly over large areas andwith minimal impact to the studied environment (Simmondsand MacLennan 2005). Hydroacoustics have long been used in marine environments forstudying fish (e.g. Trout et al. 1952; Tungate 1956; Robichaud and Rose 2002), and havemore recently been applied to the study of freshwater environments in northern Europe(e.g. Mehneret al. 2007;Godlewskaet al. 2009), the Pacific Northwest (e.g. Ransom et al.1998;Scheuerell and Schindler 2004), and the Laurentian Great Lakes (Rudstamet al.2009). Although hydroacoustics have traditionally been used only for fish surveys,scientists studying smaller planktonic organisms have recently adopted the technology.Euphasiid shrimp (Amakasu and Furusawa 2006), smaller-bodied zooplankton(Georgakarakos and Kitsiou 2008), and even phytoplankton (Selivanovskyet al. 1996) havebeen assessed using hydroacoustics. This versatility of the technology allows for acomprehensive examination of pelagic aquatic ecosystems at relatively low cost in terms ofboth man-hours and subject mortality. Another advantage of hydroacoustics is the spatial resolution of the data collected.Integrated GPS and a high ping rate (the number of sound waves sent per unit time)provide data for analysis at various spatial scales, including across an entire lakeas well asat meso- and microscale habitat patches. This presents the opportunity to
  • 4. appreciatepattern and process at multiple levels, and to understand the aquatic ecosystemmore fully (Rose and Leggett 1990; Levin 1992). One of the major potential drawbacks of using hydroacoustics is the difficultyassociated with species identification (Horne 2000).The echograms produced through theuse of hydroacoustic deviceseffectively depict the body size of an organism (as a function oftarget strength, or TS), but it is very challenging to be confident in the actual identificationof fish species, and the possibility of identifying plankton is even more remote. Body sizehas been seen, however, as fundamental to the ecology of individuals for many decades(Elton 1927). Recent literature strongly suggests that the binomial species classification oforganisms may not be as crucial as body size data when studying structure and function inecosystems, especially in aquatic environments (Kerr and Dickie 2001; Hildrewet al. 2007;Belgrano and Reiss 2011). The theoretical foundations for using organismal body size as a primary avenue forunderstanding ecosystems are found in the close linkages between this trait, metabolism,and energy flux through ecological communities (Woodward et al. 2005). It has even beensuggestedthatthe concepts surrounding body size lie at the heart of a unified theory ofecology as a discipline (Allen and Hoekstra 1993; Brown et al. 2004). Body size shows a consistent relationship to metabolic rate across all ecosystems attheindividual level,resulting in strong implications in terms of resource allocation(Brownet al. 2007; Yvon-durocheret al. 2011). Aquatic ecosystems in particular have providedevidence to support this theory of size structure, owing largely to the gape-limitation thatonly permits efficient feeding for a certain predator-prey body size ratio (Jennings et al.2001). Body size is thus robustly indicative of the ecology of individuals and the flux of
  • 5. energy through an ecosystem (White et al. 2007), and can accurately reveal patterns in theproductive capacity of fish habitat at multiple scales. It is the overarching goal of the present study to use hydroacoustic methods(combined with a limited amount of traditional sampling techniques for groundtruthing) tofirst spatially quantify fish productivity in Lac du Bonnet and Lake Manigotagan, Manitoba,and then to analyze how this productivity relates to other functional characteristics of theecosystem, namely the distribution of organisms at lower trophic levels. Finally,individualsize distributions (ISDs – i.e. a histogram of log10Abundance vs. log10Body Size, sensu Whiteet al. 2007) will be used to determine how resources are divided across body size classeswithin each ecosystem.MethodsStudy Sites Hydroacoustic surveys will be conducted over two summers on one natural lake(Lake Manigotagan) and one reservoir (Lac du Bonnet), both of which are a part of theWinnipeg River system in southeastern Manitoba. The much smaller Lake Manigotagan islocated at 50° 52’N 95° 37W in Nopiming Provincial Park. It is a naturally formed,undammed lake, and the only human settlements on it are a modest fishing lodge and somesmall cabins. Lac du Bonnet is located at 50° 22’N 95° 55’W. It is a reservoir which isdammed at both ends and is highly developed, with many large summer homes,campgrounds, and a small town on its banks. Each system has a maximum depth ofapproximately 30 metres, and summer surface temperature is approximately 22°C.
  • 6. Both Lac du Bonnet and Lake Manigotagan lie over the Canadian Shield in thetransition zone between aspen parkland and boreal forest, and can be classified asmesotrophic. Each is characterized by larger fish such as walleye (Sander vitreus), sauger(Sander canadensis), northern pike (Esoxlucius), lake whitefish (Coregonusclupeaformis)and burbot (Lotalota), as well as smaller cisco (Coregonusspp.) and shiners(Notropisspp.)(Stewart and Watkinson 2004; personal observation August 2011).Hydroacoustic Surveys Acoustic surveys will be performed in July and August of 2011 and 2012 in bothsystems. Parallel straight-line transects will be run along the short axis of the basin gettingas close to the shoreline as possible in order to cover the most ground. Space betweentransects will be one nautical mile for Lac du Bonnet and 500m for Lake Manigotagan, withvessel speeds of 6kts and 4kts, respectively. Areas with high densities of fish targets will beadaptively sampled with increased transect frequency to capture more variability. A BioSonicssplitbeam DTX echosounder will be used with 200kHz, 430kHz and1000kHz transducers mounted on a 17’ Boston Whaler. The vessel will have a foam-coredhull and a four-stroke engine, and will use battery power to reduce noise interference. Thetransducers will be deployed on an aluminum arm between 40 and 50cm below the watersurface. Transducers will be calibrated using well-established standard methods (Foote1982). All acoustic data will be georeferenced with an integrated GPS and collected usingVisual Acquisition Software version 6.0.2 (BioSonics Inc., Seattle, WA, USA).Acoustic fishtarget signals will be ground-truthed haphazardly using a combination of gill-netting and
  • 7. line fishing at sites that are identified as having high fish densities or unique acoustic fishsignal.Target Strength Experiments In situ target strength experiments will be performed in order to quantify therelationship between target strength and body size for the more important species in thestudy sites. Fish of a known size will be enclosed in a mesh bag beneath the transducers fora period of time to record target strength. An underwater camera will be used to helpquantify any deviations in target strength due to fish movement (Gauthier and Rose 2001).This technique may also shed light on what some of the species that are actually observedwith the hydroacoustics, furthering our understanding of how the ecosystems arestructured.Plankton Sampling Plankton sampling to ground-truth acoustic signals will occurhaphazardly at siteswith interesting or unrecognized signals (collected with the 1000kHz transducer), withenough replication to ensure each signal type is consistently identifiable. Vertical tows willtake place with an 80µm plankton net. Zooplankton will be counted, measured andidentified in the lab. A fluorometer will be used to systematically measure chlorophyll alevels in the water as a proxy for phytoplankton densities. Maps portraying bothzooplankton andphytoplankton distributions will be created using ArcGIS 10 Software(ESRI Inc., Redlands, CA, USA).
  • 8. Fish Tagging During the summer of 2012 several individual fish will be tagged and tracked withthe Vemco VRAP acoustic telemetry system (Amirix Systems Inc., Halifax, NS, Canada) inorder to determine the movement patterns of fish within each system.Data Analysis All acoustic data will be edited and analyzed using Echoview version 5.0 (MyriaxInc., Hobart, TAS, Australia). All noise in the data, including that arising from air bubbles orwave action will be removed prior to analysis, and bottom lines will be corrected in all datafiles. Abundance and biomass estimates of fish will be analyzed, while only biomassestimates of plankton will be looked at due to logistical difficulties associated withobtaining count data. Spatial data will be analyzed using intrinsic geostatistical methods(Rivoirardet al. 2000) with ArcGIS 10 (ESRI).Potential Results The results from the first portion of the study will be largely descriptive in nature,and will lead into the more biologically interesting topics addressed later on. Echograms(see Figure 4) will be used to create fish and plankton distribution maps for Lac du Bonnetand Lake Manigotagan. GIS will be used in order to visualize general patterns inproductivity that occur in each system. Biomass estimates will be performed on both fishand plankton to determine relative abundances and to visualize the system from a ‘bird’s-eye view’. At this point it may become apparent that fish are avoiding the vessel inshallower areas, or that different portions of the lake or reservoir are supporting more
  • 9. biomass. Variability in the biomass estimates from the acoustic surveys may prove to bequite high. Repetition of surveys will hopefully deal with this problem effectively. Inaddition, the fish and/or plankton may display variability in habitat selection, failing toreveal a particular pattern. Geostatistical analysis has the potential to reveal different patterns at differentscales in terms of the correlation between fish and plankton biomass. On a small scale, itmay be apparent that fish are not closely associated with food sources, while at a largerscale they may be more closely linked (i.e. smaller fish or plankton avoid predators, butpredators are always close enough to food sources to access them when necessary). It maybe possible to recognize that fish are associated with a particular plankton species or bodytype. Differences between day and night surveys due to diel migrations will becomeevident as well. In terms of the body size analysis, it can be predicted that a hierarchical trophicpyramid will be exposed, one in which organisms with a much larger body size are muchless abundant and/or make up less biomass in the ecosystem due to metabolic scaling anddifferences in energy use and availability. Predicted values for the relationship betweenabundance and body mass can be calculated using the equation Log Abundance = log a +b log Mass ,wherea is a coefficient different for each group, and b (the slope of the regression line) isapproximately equal to -¾ (Boudreau and Dickie 1987). Observed data may deviate fromthis as organisms can experience influences that affect their numbers outside of the bodymass – metabolism – energy flux framework, including competition from fish or other
  • 10. species that are transient in the system, and obtaining resources from outside the system.In addition, patterns may only be observable at certain scales, and the estimate of body sizeused in this case may not capture everything (Hildrewet al. 2007a). In conclusion, this thesis should provide a general understanding of how thestructure of the aquatic community can be described and analyzed using hydroacoustics.Patterns of organism distribution will be better understood in both freshwater systems,and the role of body size on the partitioning and movement of energy throughout theecosystem will be exposed.In general the project will help to better understand theproductive capacity of fish habitats and how to assess it. This will lead to furtherknowledge about the impacts of hydropower projects on aquatic ecosystems.
  • 11. FiguresFigure 1.Photo of study site at Lake Manigotagan, Manitoba.
  • 12. Figure 2.Photo of study site at Lac du Bonnet, Manitoba.
  • 13. Figure 3.Photo of the deployment system for the acoustic transducers. The arm swings down into the water, orienting the transducer faces toward the lake bottom.
  • 14. Figure 4.200 kHz echogram displaying bathymetry, plankton and fish targets in Lake Manigotagan, Manitoba. Hotter colours represent stronger sound wave backscatter detection by the transducer. The lake bottom is the large yellow-green band. Light blue fish targets are visible, and dark purple flecks represent plankton signal, evidently beginning at the thermocline or about eight metres depth. Maximum depth is approximately 25m.
  • 15. Timetable and Milestones Milestone Description Timeframe Attend workshops in Seattle to learn hydroacoustics basics, how Acoustic Training to use BioSonics DTX system, how to use Echoview software January 2011 program. MED-A1 Complete Marine Emergency Duties course January 2011 Research Aboard the RV Taking part in cod acoustic and trawl surveys with other CFER February 2011 Celtic Explorer members aboard the RV Celtic Explorer Complete Transport Canadas Small Vessel Operators SVOP April 2011 Proficiency course Complete multiple acoustic surveys of both LakeManigotagan First Field Season and Lac du Bonnet; Collect first set of plankton data; Perform July & August 2011 some gillnetting to groundtruth acoustic fish signals. Complete MSc. coursework at MUN including Biology 7220: Model-based Statistics in Biology; Biology 7000: Graduate Core September-December Course Work Seminar; and Fisheries Resource Management 6009: Overview 2011 of World Fisheries. Complete comprehensive research proposal for peer review and Research Proposal November 21st, 2011 editing. Present proposal to Biology 7000 classmates and instructors forResearch Proposal Seminar November 28th, 2011 critiquing. Departmental Research Present proposal to MUN Biology Department. December 5th, 2011 Proposal Seminar Edit and analyze data using Echoview. Map plankton and fish Data Editing and Analysis distributions using ArcGIS. Perform geostatistical analyses. January-May 2012 Preliminary thesis preparations. Research Aboard the RV Taking part in cod acoustic and trawl surveys with other CFER May 2012 Celtic Explorer members aboard the RV Celtic Explorer Complete multiple acoustic surveys of both Lake Manigotagan and Lac du Bonnet; Collect more comprehensive plankton data; Perform gillnetting to groundtruth acoustic fish signals; Use Second Field Season July & August 2012 VRAP telemetry system to track several fish species in each system; Perform in situ target strength experiments to relate target strength to fish body size. Edit and analyze data using Echoview. Map plankton and fish September-November Data Editing and Analysis distributions using ArcGIS. Perform geostatistical analyses. 2012 Submit First Draft of December 2012 Thesis January-February Thesis Revisions 2012 Convocation June 2013
  • 16. Literature CitedAllen, T. F. H. And T. W. Hoekstra. 1992. Toward a Unified Ecology. New York, NY, USA: Columbia University Press.Amakasu, K. and M. Furusawa. 2006. The target strength of Antarctic krill (Euphasia superb) measured by the split-beam method in a small tank at 70 kHz. ICES Journal of Marine Science 63:36-45.Argent, D. G. and W. G. Kimmel. 2005. Efficiency and selectivity of gill nets for assessing fish community composition of large rivers. North American journal of Fisheries Management 25:1315-1320.Belgrano, A. and J. Reiss.eds. 2011.Advances in Ecological Research Volume 45: The Role of Body Size in Multispecies Systems. Waltham, MA, USA: Academic Press.Brauman, K. A., G. C. Daly, T. K. Duarte, and H. A. Mooney. 2007. The nature and value of ecosystem services: An overview highlighting hydrologic services. Annual Review of Environment and Resources 32:67-98.Brown, J. H., A. P. Allen and J. F. Gillooly. 2007. The metabolic theory of ecology and the role of body size in marine and freshwater ecosystems. In Body Size: The Structure and Function of Aquatic Ecosystems (Hildrew, A., D. Rafaelli and R. Edmonds-Brown, eds), pp. 1-15, Cambridge University Press.Brown, J. H., J. F. Gilooly, A. P. Allen, V. M. Savage and G. B. West. 2004. Toward a metabolic theory of ecology. Ecology 85(7):1771-1789.Dickie, L. M., S. R. Kerr and P. R. Boudreau. 1987. Size-dependent processes underlying regularities in ecosystem structure. Ecological Monographs 57(3):233-250.Elton, C. 1927. Animal Ecology. Chicago, IL, USA: The University of Chicago Press.Foote, K. G. 1982. Optimizing copper spheres for precision calibration of hydroacoustic equipment. Journal of the Acoustical Society of America 71(3):742-747.Gauthier, S. and G. A. Rose. 2001. Target strength of encaged Atlantic redfish (Sebastesspp.). ICES Journal of Marine Science 58:562-568.Georgakarakos, S. and D. Kitsiou. 2008. Mapping abundance distribution of small pelagic species applying hydroacoustics and Co-Kriging techniques. Hydrobiologia612:155- 169.Godlewska, M., M. Colon, L. Doroszczyk, C. Verges, and J. Guillard. 2009. Hydroacoustic measurements at two frequencies: 70 and 120 kHz – consequences for fish stock estimation. Fisheries Research 96:11-16.Horne, J. 2000. Acoustic approaches to remote species identification: a review. Fisheries Oceanography 9(4):356-371.
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