How BioBase is Helping Fish Conservation

BioBase EcoSound is helping State Fisheries Departments and Research Institutions across the US and UK to better manage Fisheries by providing important information about fish habitat.  See below for a short description of these ongoing investigations.Precision bathymetric mapping to estimate concentrations of a fish toxin (rotenone) to kill invasive fish in a Nebraska backwater lake. … Continue reading “How BioBase is Helping Fish Conservation”

BioBase EcoSound is helping State Fisheries Departments and Research Institutions across the US and UK to better manage Fisheries by providing important information about fish habitat.  See below for a short description of these ongoing investigations.

Precision bathymetric mapping to estimate concentrations of a fish toxin (rotenone) to kill invasive fish in a Nebraska backwater lake.

Principal Investigator (PI): Jeff Schuckman, District Fisheries Manager.
Nebraska Game and Parks

Success story described in this blog.

Using cloud based software and GIS automation to quantify and evaluate changes in aquatic vegetation and substrate composition following the infestation of zebra mussels in the Iowa Great Lakes

PI: Jonathan Meerbeek
Iowa Department of Natural Resources
In collaboration with Iowa Lakeside Laboratory

In 2012, four live juvenile zebra mussel Dreissena polymorha were discovered in the Iowa Great Lakes. By 2013, both juvenile and adult zebra mussels were found in several of the interconnected lakes, confirming the presence of a reproducing population. Zebra mussels are known as ecosystem engineers because their intense filtering behavior can modify the physical environment by increasing light penetration, thus likely influencing distribution and diversity of submersed macrophytes. Effects of aquatic invasive species can be documented by monitoring macrophytes as they are a well-suited indicator of ecological health due to their immobility and ease of sampling and identification. Limited detailed aquatic macrophyte vegetation mapping data for this diverse chain of lakes exists. Recent advances in GPS and sonar technology coupled with cloud-based software have substantially expanded the ability for fisheries managers to conduct lake-based bathymetric and habitat evaluations with limited time and investment. In 2014 and 2015, we mapped each lake with a Lowrance HDS sonar unit and uploaded files to a web-based server so data could be post-processed and viewed. In addition, physical estimates of aquatic macrophyte density and diversity were collected using the point intercept sampling method in each lake. Average aquatic plant biovolume (percent of water column taken up by vegetation) ranged from 1.3% in Little Spirit Lake to 26.6% in Lower Gar Lake. Distinct vegetation beds in shallow bays and deeper weed lines were well represented using 35m-100m transect spacing. Collectively, we sampled 3,807 vegetation points during the first two years of the study and identified 19 species ranging in abundance from <1% of rake coverage to well over 100% (i.e., mats of vegetation). We plan to repeat this study in 2016 and periodically after that so macrophyte-based IBI’s (i.e., maximum depth of plant growth, 95% occurrence, percentage of littoral zone vegetated, number of species with frequency over 10%, relative frequency of submersed species, relative frequency of sensitive species, relative frequency of tolerant species, and number of native taxa) can be calculated and tracked over time to document changes in the ecological health of the Iowa Great Lakes.

Largemouth Bass in northeastern Minnesota: regulators and impacts of abundance

PI: Bethany Bethke: Fisheries Research Biologist
Minnesota Department of Natural Resources
Study 635 F-26-R-4

Minnesota is currently undergoing long-term shifts in climate resulting in warmer and more variable weather patterns (Johnson and Stefan 2006, Novotny and Stefan 2007).  Aquatic ecosystems are likely responding to these shifts, although their specific responses are unknown and have not been biologically quantified.  Some fisheries managers and researchers suspect that warmer air temperatures are resulting in warmer water temperatures, longer growing seasons for aquatic vegetation, and increased water clarity as a result of increased aquatic vegetation abundance (Lottig et al. 2014).  If occurring, these changes could favor Largemouth Bass.  Although lake survey methods measure these variables, the surveys may be too infrequent to detect changes and further our understanding of how those changes may affect Largemouth Bass growth and recruitment.

Quantifying aquatic plant community composition and abundance is difficult and time consuming and Area Management Offices have been using transect surveys to document vegetation in lakes, but these have many drawbacks.  The information collected with transect surveys is subjective and difficult to replicate, and does not provide reliable estimates of important statistics, such as maximum depth of emergent plant growth.  Maximum depth of emergent and submergent plant growth is an important metric in lakes because it indicates the extent of aquatic plant habitat in that system.  Fortunately, new technology allows for the application of hydroacoustic assessment of aquatic vegetation, which collects more accurate information about plant abundance more quickly than traditional methods (Valley and Drake 2005).

Benthic Habitat Mapping of Grand Lake Tributaries as it Relates to Paddlefish

PI: Jason Schooley
Biologist; OK Department of Wildlife Conservation
Study F11AF00318

Recent use of side scanning sonar to map the benthic habitat of streams has allowed resource management agencies to quantify and produce GIS maps of various habitat types (Rowe et al. 2002, Kaeser et al. 2013). This technology has proven to be effective and accurate in medium sized streams (overall classification accuracy of 77%), and is low-cost (Kaeser and Litts, 2010). The creation of a benthic habitat map of the Neosho and Spring rivers would allow ODWC paddlefish managers to classify and quantify available habitat types and assess how the quantity of each habitat type changes according to water level fluctuations (annual flow regime). Similar studies have successfully used GIS to quantifiy the spawning habitat of lake smelt Retropinna retropinna (Rowe et al. 2002) and white sturgeon Acipenser transmontanus (Parsley and Beckman 1994) under a range of water level fluctuations. Depth, substrate type, and composition play vital roles in the quantity and suitability of habitat for potadromous fishes in freely-flowing rivers (Parsley and Beckman 1994).

Hydroacoustic quantification and assessment of spawning grounds of a lake salmonid in a eutrophicated water body

PI: Dr. Ian Winfield
Centre for Ecology and Hydrology, Lancaster UK

Summarized in this blog and now published in the peer-reviewed journal Ecological Informatics.

Monitoring Important Fisheries and Habitats

PI: Kevin Johnson
Florida Fish and Wildlife Conservation Commission
Study F14F00915 2015 Progress Report

Techniques were developed to estimate lake-wide coverage of submersed and emergent vegetation. Sonar data were collected from four lakes to determine the transect spacing needed to provide an accurate representation of waterbody-wide percent coverage of submersed vegetation using the CI BioBase automated web-based processing software ( Based on this work, we determined that a transect spacing of 285 m will serve as our spacing maximum. Submersed vegetation mapping will begin next fiscal year by running a Lowrance sonar unit along parallel transects of a lake, collecting point-intercept aquatic plant samples for submersed vegetation speciation along these transects, and uploading the sonar data to the website for final outputs of percent area coverage (PAC) and percent volume infested (PVI) estimates.

Response of native and non-native aquatic macrophytes to invasive common carp removal in a North American shallow lake

PI: Dr. Raymond Newman
University of Minnesota

We investigated the response of an aquatic macrophyte community to common carp
(Cyprinus carpio) removal in Staring Lake, a 66 ha shallow lake in the North American Midwest. Adult carp were extremely abundant prior to removal (490 kg/ha) and the lake had few macrophytes; macrophyte frequency of occurrence was <15% and macrophyte dry biomass <2g/m2. Only eight aquatic macrophyte species were found, with invasive curlyleaf pondweed (Potamogeton cripsus) being the most common and occurring at ≤7% of sites. Carp density was reduced to 190 kg/ha in winter 2014. Macrophytes remained sparse in throughout 2012 and 2013, but increased to 29% occurrence in Spring 2014 and 40% in 2015 when carp density was further reduced to 100 kg/ha. Macrophyte biomass increased to 3 g/m2 in 2014 and 9 g/m2 in 2015. Curlyleaf pondweed remained the dominant macrophyte, increasing to 28% occurrence and 8 g/m2 in 2015 while native taxa such Canada waterweed (Elodea canadensis), narrowleaf pondweed (Potamogeton pusillus) and sago pondweed (Stuckenea pectinata) also increased and 13 species were found. Reduction of carp density allowed both native and invasive aquatic macrophytes to increase, but the increased abundance of invasive curlyleaf pondweed will require management to further restore a native macrophyte community.

Author: biobasemaps

BioBase is a cloud platform for the automated mapping of aquatic habitats (lakes, rivers, ponds, coasts). Standard algorithms process sonar datafiles (EcoSound) and high resolution satellite imagery (EcoSat). Depth and vegetation maps and data reports are rapidly created and stored in a private cloud account for analysis, and sharing. This blog highlights a range of internal and external research, frequently asked questions, feature descriptions and highlights, tips and tricks, and photo galleries.

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