Revised Protocols for Sampling Algal, Invertebrate, and Fish Communities as Part of the National Water-Quality Assessment Program Open-File Report 02-150 U.S. Department of the Interior U.S. Geological Survey B A C F D E Front Cover: A. Nymph of the stonefly Calineuria californica (Banks). (Photograph by James Carter) B. A crewmember scraping algae from a cobble. (Photograph by Mitchell Harris) C. The diatom Navicula lacustris Greg. (Photograph by Phycology Section, The Academy of Natural Sciences of Philadelphia) D. Crewmembers sampling fishes with barge electrofishing gear. (Photograph by Rodney Knight) E. The redfin darter, Etheostoma whipplei (Girard). (Photograph copyright Joseph R. Tomelleri) F. Two crewmembers sampling invertebrates with a Slack sampler. (Photograph by Dennis Sun) Revised Protocols for Sampling Algal, Invertebrate, and Fish Communities as Part of the National Water-Quality Assessment Program By Stephen R. Moulton II, Jonathan G. Kennen, Robert M. Goldstein, and Julie A. Hambrook Open-File Report 02-150 Reston, Virginia 2002 U.S. DEPARTMENT OF THE INTERIOR GALE A. NORTON, Secretary U.S. GEOLOGICAL SURVEY Charles G. Groat, Director The use of trade or product names in this report is for identification purposes only and does not constitute endorsement by the U.S. Government. For additional information write to: U.S. Geological Survey Chief, National Water-Quality Assessment Program 413 National Center 12201 Sunrise Valley Drive Reston, VA 20192 Information regarding the National Water-Quality Assessment (NAWQA) Program is available on the Internet at http://water.usgs.gov/nawqa/. Copies of this report can be downloaded from this address. FOREWORD The U.S. Geological Survey (USGS) is monitoring data will be available to determine trends at committed to providing the Nation with accurate and many of the Nation’s streams and aquifers. The next 10 timely scientific information that helps enhance and years of study also will fill in critical gaps in protect the overall quality of life and that facilitates characterizing water-quality conditions, enhance effective management of water, biological, energy, and understanding of factors that affect water quality, and mineral resources. Information on the quality of the establish links between sources of contaminants, the Nation’s water resources is critical to assuring the long- transport of those contaminants through the hydrologic term availability of water that is safe for drinking and system, and the potential effects of contaminants on recreation and suitable for industry, irrigation, and humans and aquatic ecosystems. habitat for fish and wildlife. Population growth and The USGS aims to disseminate credible, timely, increasing demands for multiple water uses make water and relevant science information so that the most availability, now measured in terms of quantity and current knowledge about water resources can be quality, even more essential to the long-term applied in management and policy decisions. We hope sustainability of our communities and ecosystems. this NAWQA publication will provide you with insights and information to meet your needs, and will The USGS implemented the National Water- foster increased citizen awareness and involvement in Quality Assessment (NAWQA) Program in 1991 to the protection and restoration of our Nation’s waters. support national, regional, and local information needs The USGS recognizes that a national assessment and decisions related to water-quality management and by a single program cannot address all water-resource policy. Shaped by and coordinated with ongoing efforts issues of interest. External coordination at all levels is of other Federal, State, and local agencies, the critical for a fully integrated understanding of NAWQA Program is designed to answer: What is the watersheds and for cost-effective management, condition of our Nation’s streams and ground water? regulation, and conservation of our Nation’s water How are the conditions changing over time? How do resources. The NAWQA Program, therefore, depends natural features and human activities affect the quality on advice and information from other agencies— of streams and ground water, and where are those Federal, State, interstate, Tribal, and local—as well as effects most pronounced? By combining information nongovernment organizations, industry, academia, and on water chemistry, physical characteristics, stream other stakeholder groups. Your assistance and habitat, and aquatic life, the NAWQA Program aims to suggestions are greatly appreciated. provide science-based insights for current and emerging water issues and priorities. NAWQA results can contribute to informed decisions that result in practical and effective water-resource management and strategies that protect and restore water quality. (signed) From 1991–2001, the NAWQA Program Timothy L. Miller completed interdisciplinary assessments in 51 of the Chief, NAWQA Program Nation’s major river basins and aquifer systems, referred to as Study Units. Baseline conditions were established for comparison to future assessments, and long-term monitoring was initiated in every basin studied. Financial constraints will reduce the number of Study Units that NAWQA can assess in the future; therefore, during the next decade, 42 of the 51 Study Units will be reassessed so that 10 years of comparable 0 5 1 2- 0 R F O — m a gr o Pr nt e m s s e s s A y alit u Q er- at W al n o ati N e h of t art P s a s e niti u m m o C h s Fi d n a e, at br e ert v n al, I g Al g n pli m a S or s f ol c o ot Pr d e s vi e R — s er h ot d n a n o ult o M CONTENTS Abstract ....................................................................................................................................................................................................... 1 Introduction ................................................................................................................................................................................................ 1 Overview of the NAWQA Program .............................................................................................................................................. 1 Purpose and scope ........................................................................................................................................................................ 1 Summary of revisions to original protocols ............................................................................................................................... 2 Acknowledgments ......................................................................................................................................................................... 2 Field protocols ............................................................................................................................................................................................ 3 1. Overview of the sampling approach ....................................................................................................................................... 3 1.1 Establishing the sampling reach ................................................................................................................................ 3 1.2 Types of samples collected ......................................................................................................................................... 3 1.3 Identifying instream-habitat types for sampling ...................................................................................................... 4 1.4 Factors determining when to sample......................................................................................................................... 4 1.5 Coordination of field activities .................................................................................................................................... 4 2. Pre-field activities ...................................................................................................................................................................... 5 2.1 Preparing a sampling plan ........................................................................................................................................... 6 2.2 Collecting permits ......................................................................................................................................................... 6 2.3 Supplies and chemicals ............................................................................................................................................... 6 2.4 Sample preservatives ................................................................................................................................................... 8 2.5 Sample identification and tracking ............................................................................................................................ 8 2.6 Sampling gear maintenance ....................................................................................................................................... 10 3. Safety in the field ........................................................................................................................................................................ 12 3.1 Personal and environmental safety ........................................................................................................................... 12 3.2 Chemical safety ............................................................................................................................................................. 13 3.3 Vehicles, boats, and sampling gear safety ............................................................................................................... 14 4. Algal sampling protocols .......................................................................................................................................................... 14 4.1 Algal sample types collected ...................................................................................................................................... 15 4.2 Identifying instream habitats for sampling ............................................................................................................... 15 4.3 Quantitative targeted-habitat sampling methods .................................................................................................... 16 4.4 Qualitative multihabitat sampling methods .............................................................................................................. 22 4.5 Sample processing procedures ................................................................................................................................. 24 4.6 Quality-control recommendations ............................................................................................................................. 28 4.7 Field data sheets ........................................................................................................................................................... 28 5. Invertebrate sampling protocols ............................................................................................................................................. 36 5.1 Invertebrate sample types collected ......................................................................................................................... 36 5.2 Identifying instream habitats for sampling ............................................................................................................... 36 5.3 Semi-quantitative targeted-habitat methods for sampling wadeable and nonwadeable streams ................ 37 5.4 Qualitative multihabitat methods for sampling wadeable and nonwadeable streams ..................................... 41 5.5 Sample processing procedures ................................................................................................................................. 42 5.6 Field data sheets ........................................................................................................................................................... 48 6. Fish Sampling Protocols ............................................................................................................................................................ 55 6.1 Overview of sampling methods .................................................................................................................................. 55 6.2 Sampling methods for wadeable streams ................................................................................................................ 56 6.3 Sampling methods for nonwadeable streams ......................................................................................................... 59 6.4 Alternative sampling methods .................................................................................................................................... 60 6.5 Sample processing procedures ................................................................................................................................. 60 6.6 Field data sheet ............................................................................................................................................................. 66 Contents V 7. Post-Field Activities ................................................................................................................................................................... 69 7.1 Logging samples into the Biological Transactional Data Base ............................................................................. 69 7.2 Replacing field sample labels ..................................................................................................................................... 69 7.3 Preparing packing lists and Analytical Services Request Forms ......................................................................... 69 7.4 Shipping samples to analytical laboratories ............................................................................................................ 69 Summary ..................................................................................................................................................................................................... 70 References cited ....................................................................................................................................................................................... 73 Appendix ..................................................................................................................................................................................................... 75 FIGURES 1. Sample identification code used to distinguish algal (top), invertebrate (middle) and fish (bottom) samples in the National Water-Quality Assessment Program .................................................................... 9 2. Examples of field sample labels used to uniquely identify algae ................................................................................ 11 3. Methods used to collect microalgal periphyton samples ............................................................................................ 17 4. Examples of common macroalgae ................................................................................................................................... 23 5. Steps followed in the field to process algal samples .................................................................................................... 25 6. Major steps in processing microalgal sample components in the field .................................................................... 26 7. Priority levels for determining the habitat type that is selected as the richest targeted habitat for semi-quantitatively sampling invertebrates ................................................................................................ 38 8. Samplers used to collect invertebrate samples ............................................................................................................. 39 9. Steps followed in the field to process invertebrate samples ...................................................................................... 43 10. Key steps in the collection and processing of invertebrate samples ........................................................................ 44 11. Steps followed in the field to process fish collections ................................................................................................. 61 12. Total and standard length measurements of a fish ....................................................................................................... 63 13. Deformities, eroded fins, lesions, and tumors noted on fish ........................................................................................ 65 TABLES 1. Hierarchical framework for geomorphic descriptors used to determine habitats from which algal and invertebrate samples are collected .................................................................................................... 5 2. Definition of character fields used to create sample identification codes for algae, invertebrates, and fish samples ............................................................................................................................ 8 3. Algal sample types, sample components, and subsamples collected ....................................................................... 15 4. Explanation of field data-sheet sections used to record information about algal sampling activities .......................................................................................................................................... 29 5. Generalized matrix of the 51 instream habitats .............................................................................................................. 37 6. Explanation of field data-sheet sections used to record information about invertebrate sampling activities ............................................................................................................................ 48 7. Two-letter codes used to denote external anomalies in fish ....................................................................................... 64 8. Explanation of field data-sheet sections used to record information about fish sampling activities ............................................................................................................................................ 66 VI Contents CONVERSION FACTORS, VERTICAL DATUM, AND ABBREVIATED WATER-QUALITY UNITS Multiply By To obtain Length micrometer (µm) 0.00003937 inch millimeter (mm) 0.03937 inch centimeter (cm) 0.3937 inch meter (m) 3.281 foot kilometer (km) 0.6214 mile Area square centimeter (cm2) 0.155 square inch square meter (m2) 10.76 square foot square kilometer (km2) 0.3861 square mile Volume liter (L) 1.057 quart liter (L) 0.2642 gallon milliliter (mL) 0.0338 ounce, fluid Flow centimeter per second (cm/s) 0.0328 foot per second Mass gram (g) 0.03527 ounce, avoirdupois Pressure kilopascal (kPa) 0.1450 pound-force per square inch Temperature Conversion Degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) by using the following equation: °F = 1.8 (°C) + 32 ABBREVIATIONS FREQUENTLY USED IN THIS REPORT AFDM ash-free dry mass QA/QC quality assurance/quality control ANSP Academy of Natural Sciences of Philadelphia QC quality control ASR analytical services request QMH qualitative multihabitat Bio-TDB Biological Transactional Data Base RTH richest-targeted habitat CHL A chlorophyll a SMCOD sample identification code DTH depositional targeted habitat USGS U.S. Geological Survey ID identification > greater than NAWQA National Water-Quality Assessment < less than NWQL National Water Quality Laboratory ≥ greater than or equal to PFD personal flotation device ≤ less than or equal to PHY phytoplankton ± plus or minus QA quality assurance Contents VII GLOSSARY Algae—Chlorophyll-bearing, nonvascular aquatic plants (for areas of low velocities, such as pools and side-channel example, diatoms, green algae, and red algae) including areas, where silt can deposit. the primitive photosynthetic bacteria (for example, blue- Epiphytic—Benthic habitat consisting of plants on which green algae). organisms are attached or loosely associated. Anadromous—Refers to fish species (for example, some Epipsammic—Benthic habitat consisting of sand-sized species of salmon) that live in the ocean as adults and (> 0.064 – 2 mm) particles on which organisms are return to freshwater to spawn. attached or loosely associated. Benthic—Refers to bottom; for example, benthic organisms External anomalies—Visible body surface or subcutaneous that live on or burrow into an aquatic substrate. disorders in fish, such as deformities, eroded fins, Brails—The poles supporting each end of a seine. lesions, and tumors. Coarse-grained substrates—Stream substrates (> 2 mm Fine-grained substrates—Stream substrates (< 2 mm wid- widest dimension) composed primarily of gravels, cob- est dimension) composed primarily of silt and sand. bles, and boulders. Fixed site—Sites on streams at which streamflow is mea- Component—See sample component. sured and samples are collected to assess the broad-scale Composite sample—See sample. spatial and temporal character and transport of inorganic Decant volume (algae only)—The volume associated with constituents of streamwater in relation to hydrologic con- decanting an algal sample or subsample in order to con- ditions and environmental settings. centrate the material by removing excess liquid. There Formaldehyde—As used for a preservative, the term are two types of decant volume: (1) before decant volume "formaldehyde" is marketed as a saturated water solution (BDV)—the volume before excess liquid is removed; and of formaldehyde gas (HCHO), representing a (2) after decant volume (ADV)—the volume after excess concentrated stock solution of formalin (37-percent liquid is removed. formaldehyde by weight). Also referred to as Depositional-targeted habitat (DTH)—A habitat targeted “concentrated formalin" or "100 percent formalin." for sampling in the reach where fine sediments (for Formalin—A mixture of formaldehyde and water. Ten- example, sand and silt) are deposited. A composited sam- percent formalin is prepared by mixing one part formal- ple from this habitat is referred to as a "DTH sample." dehyde with 9 parts water; this mixture is typically used Discrete collection—The material collected from a single for preserving invertebrate and fish samples. location within a reach. Discrete collections are compos- Galvanotaxis—A response by fish to swim toward the ited either physically (sensu invertebrates) or logically anode during application of direct current during electro- (sensu algae) to create a sample. For example, a single fishing. invertebrate RTH sample is composed of five discrete Geomorphic channel units—Fluvial geomorphic descrip- collections that are physically combined. Likewise, an tors of channel shape and stream velocity. Pools, riffles, algae QMH sample is composed of discrete collections and runs are three types of geomorphic channel units that are composited according to growth form (either considered for NAWQA Program ecological sampling. micro- or macroalgae) that then collectively form a logi- Habitat—In general, aquatic habitat includes all nonliving cal algal sample from the reach. (physical) aspects of the aquatic ecosystem (Orth, 1983), Discrete sample—See discrete collection. although living components like macrophytes and ripar- Ecological studies—Studies of biological communities and ian vegetation also are usually included. Measurements habitat characteristics to evaluate the effects of physical of habitat are typically made over a wider geographic and chemical characteristics of water and hydrologic scale than measurements of species distribution. conditions on aquatic biota and to determine how biolog- Hyporheic zone—The subbenthic habitat of interstitial ical and habitat characteristics differ among environmen- spaces between substrate particles in the streambed bor- tal settings in NAWQA study areas. dered by surface water above and true ground water Epidendric—Benthic habitat consisting of woody substrates below. This zone acts as a faunal reservoir and refugium on which organisms are attached or loosely associated. for aquatic invertebrates during floods, droughts, and Epilithic—Benthic habitat consisting of natural, coarse- extreme temperatures. grained substrates (for example, gravels, cobbles, or Invertebrates—Animals that do not have backbones, such boulders) or bedrocks, or artificial hard substrates such as as worms, clams, crustaceans, and insects. submerged concrete on which organisms are attached or Meandering stream—Typically a low gradient stream with loosely associated. high channel sinuosity. Epipelic—Benthic habitat consisting of silt-sized Motile—Refers to organisms that have the ability to move, (<0.064mm) streambed sediments on which organisms often rapidly and spontaneously. are loosely associated. This habitat is commonly found in VIII Glossary