In the Field - Sample Collection

On this page:

Permits and Approvals
Collection Methods
Preservation of Sample Integrity
Field Recordkeeping
Equipment and Safety Considerations
Fish Biopsy Plug Collection

Permits and Approvals

Permits are typically required for data or sample collection activities. Permits or documentation required for site access or sample collection should be part of a site packet of information.

Before collecting samples on public land, notify the relevant agency and secure permission if necessary. If access to public land necessitates crossing private lands, obtain permission to do so.

If samples are collected from private land, obtain permission from the owner to access the property. Communicate with the landowner when a field crew is on site. Obtain information in advance on things that could impede access (e.g., locked gates, pets, and livestock) and on activities in or near the sampling site such as active hunting, farming, and mining.

Collection Methods

Collection methods are divided into two major categories: active and passive. Active collection methods involve human or mechanical power to chase and capture target species. Passive collection relies on the movement of the fish into a net or trap that is left in place for a period before retrieval. Each collection method has a variety of devices, and each collection method has advantages and disadvantages.

Active collection methods (Table 1) are particularly useful in shallow waters. For deep water sampling, active collection methods require more field personnel and more expensive equipment than passive collection methods.

Passive collection methods (Table 2) generally require less effort than active methods for deep water. Fish captured in passive collection devices should be removed within 24 hours of deploying the device as caught fish can be vulnerable to predation.

Sampling procedures that apply to a variety of waterbodies are described in the field operations manuals for the National Aquatic Resource Surveys. These procedures are for large-scale programs but could be adapted for a smaller program.

For rivers and streams: Section 10.3 of the National Rivers and Streams Assessment 2018/19 Field Operations Manual Wadeable (pdf)
For lakes: Section 7.0 Lake Wide Fish Sample Collection of the National Lakes Assessment 2022 Field Operations Manual (pdf)
For coastal waters: Section 14.1 Ecological Contamination Fish Tissue Collection of the National Coastal Condition Assessment 2020 Field Operations Manual (pdf)

Table 1. Summary of Active Collection Methods

Organism	Device and Use	Advantages	Disadvantages
Fish	Electrofishing – shallow rivers, lakes, and streams	Efficient method. Minimal damage to fish. Adaptable to many sampling conditions (e.g., boat, wading, shorelines). Useful at sites where other active methods cannot be used (e.g., around snags and irregular bottom contours).	Nonselective (may include bycatch). Stuns or kills most fish. Cannot be used in brackish, salt, or extremely soft water. Requires extensive operator training. DANGEROUS when not used properly. More expensive than passive devices.
	Angling (hook and line)	Most selective method. Does not require use of large number of personnel or expensive equipment.	Can be time and/or personnel intensive.
	Dip net	Inexpensive. Doesn’t require special training or skills.	Requires high density or concentration of fish. Effective area limited to size of equipment and physical reach of the user.
Fish and Shellfish	Seines – shallow rivers, lakes, streams, and shoreline areas of estuaries.	Inexpensive and easily operated. Variety of mesh sizes available for target fish and crustacean (e.g., shrimp and crab) species. Non-target species can usually be released unharmed.	Nonselective. Cannot be used in deep water or over substrates with an irregular contour. Not completely efficient - fish can evade the net during seining operation.
Fish and Shellfish	Trawls – moderate to deep open bodies of water (≥10m depth)	Effective in deep waters inaccessible by other methods. Allows collection of a large number of samples.	Nonselective and may be lethal to non-target species. Requires boat and trained operators.
Shellfish	Double-pole-operated grab buckets – mechanical grab used from boat or pier. Most useful in shallow water areas less than 6m deep.	Very efficient means of sampling bivalves (e.g., clams and oysters) that are located on or buried in bottom sediments.	Pole-operated devices difficult to operate manually at depths greater than 6 meters.
	Tongs or double- handled grab sampler – mechanical grab generally used from a boat. Most useful in shallow water, lakes, rivers and estuaries.	Very efficient means of sampling oysters, clams, and scallops. Sediment is not captured which reduces the weight.	Pole-operated devices difficult to operate manually at depths greater than 6 meters.
	Ekman grab – line or cable operated grab bucket used from a boat or pier to sample soft or semisoft substrates.	Can be used in water of varying depths in lakes, rivers, and estuaries.	Incomplete closure of jaws can result in sample loss. Must be repeatedly retrieved and deployed. Grab is small and is not particularly effective in collecting large bivalves (clams and oysters).
	Petersen grab – line or cable-operated grab bucket used in deep lakes, rivers, and estuaries for sampling most substrates.	Large sample is obtained. grab can penetrate most substrates.	Grab is heavy, may require winch for deployment. Incomplete closure of jaws can result in sample loss. Must be repeatedly retrieved and deployed.
	Ponar grab – line or cable-operated grab buckets used in deep lakes, rivers, and estuaries for sampling sand, silt, or clay substrates.	Most universal grab sampler. Adequate on most substrates. Large sample can be obtained intact.	Incomplete closure of jaws can result in sample loss. Must be repeatedly retrieved and deployed.
	Orange peel grab – line or cable-operated grab buckets used in deep lakes, rivers, and estuaries for sampling most substrates.	Designed for sampling hard substrates.	Grab is heavy, may require winch for deployment. Incomplete closure of jaws can result in sample loss. Must be repeatedly retrieved and deployed. Grab is small and not particularly effective in collecting large bivalves (e.g., clams and oysters).
	Biological or hydraulic dredges – line or cable- operated grab buckets dragged along the bottom of deep waterbodies to collect large stationary invertebrates.	Allows for qualitative sampling of large area of bottom substrate and benthic community. Length of tows can be relatively short if high density of shellfish exists in sampling area.	Difficult to pinpoint exact location of sample collection area if the length of the tow is long. Bivalve shells may be damaged because of scouring operation of the dredge.
	Scoops or shovels used in shallow waters accessible by wading or SCUBA equipment for collection of hard clams or soft-shell clam.	Does not require a boat; sampling can be done from shore.	Care must be taken not to damage the shells of bivalves while digging in substrate.
	Scrapers – used in shallow water accessible by wading or SCUBA equipment for collection of oysters or mussels.	Does not require a boat; sampling can be done from shore.	Care must be taken not to damage the shells of bivalves while digging in substrate.
	Rakes – used in shallow waters accessible by wading or can be used from a boat.	Does not require a boat; sampling can be done close to shore. Can be used in soft sediments to collect clams or scallops, Can be used to dislodge oysters or mussels that are attached to submerged objects.	Care must be taken not to damage the shells of the bivalves while raking or dislodging them from the substrate.

Table 2. Summary of Passive Collection Methods

Organism	Device and Use	Advantages	Disadvantages
Fish	Gill nets – lakes, rivers, and estuaries where fish movement is expected or anticipated.	Effective for collecting pelagic fish species. Relatively easy to operate. Requires less fishing effort than active methods. Selectivity can be controlled by varying mesh size.	Not effective for bottom-dwelling fish or populations that do not exhibit movement patterns. Nets prone to tangling or damage by large and sharp spined fish. Gill nets will kill captured specimens, which, when left for extended periods, may undergo physiological changes. Must be checked frequently, every 24 hours. May cause bycatch mortality.
	Trammel nets – lakes, rivers and estuaries where fish movement expected or anticipated.	Slightly more efficient than a straight gill net.	Same as gill nets. Tangling problems may be more severe. Method of scaring fish into net requires more personnel or possibly boats in deep water areas.
	Hoop, fyke and pound nets – shallow rivers, lakes, and estuaries where currents are present or when movements of fish are predictable. Used in commercial operations.	Unattended operation. Very efficient in regard to long-term return and expended effort. Particularly useful in areas where active methods are impractical.	Inefficient for short term. Difficult to set up and maintain.
Fish	Minnow traps	Useful for catching small fish.
Fish and Shellfish	D-traps – used for capture of slow-moving bottom fish and crustaceans (crabs and lobsters) that move on or just above substrate.	Easy to operate and set. Unattended operation. Used in a variety of environments. Useful for capturing bottom-dwelling organisms in deep water or other inaccessible areas. Relatively inexpensive, can be handmade.	Catch efficiency is highly variable. Not effective for pelagic fish or fish that are visually oriented. Less efficient for all species when water is clear. Not a good choice for a primary sampling technique, but valuable as a backup for other methods.

If the collection doesn’t result in sufficient samples, purchasing or acquiring fish and shellfish from commercial or recreational fishers is acceptable and can supplement agency efforts and help to fill a data gap for the target waterbody. However, it is essential for quality control purposes that sample collection and handling procedures are followed by the commercial or recreational fishers, and documentation ensuring chain of custody records is provided. It is preferable to have a representative on the commercial boat, if possible, to ensure fish are collected and handled properly; however, there may be legal limitations depending on the location and/or fishing industry.

There could be opportunities for projects with commercial fishermen as collaborators. Some agencies obtain samples from the commercial seafood industry, but through seafood processors, not the fishermen.

Recreational fishers can provide fish from locations that are popular for recreational fishing but may not be easily accessible for sampling. This works best through pre-arrangement. If the fisher is a current or former department employee, there is increased confidence that the fish is collected and handled properly.

Preservation of Sample Integrity

Sample preservation is the most important quality assurance consideration in sample collection and should align with the monitoring objectives and contaminant analysis. After the sample is collected, field staff should ensure that processing and preservation are conducted as prescribed in sample collection protocols, with minimal chance of contamination. Sample integrity is preserved by preventing the loss of contaminants present in the tissues and by preventing cross contamination. The tissue contaminant analyses (metals or organics or both) should be considered when planning the materials to be used in the collection and handling steps to minimize cross contamination.

Contaminant loss: This can be prevented by ensuring that the skin on the fish specimens has not been lacerated by the sampling gear or that the carapace of crustaceans or shells of bivalves have not been cracked during sample collection. Any imperfections may lead to the loss of tissues and/or fluids that may contain contaminants. Similarly, fish and shellfish specimens should be carefully wrapped after they are collected and placed on wet or dry ice to limit fluid loss through dehydration. After the samples have reached the laboratory, further care must be taken during thawing (if specimens are frozen) to ensure that all liquids from the thawed specimens are retained with the tissue sample as appropriate.
Cross contamination: Samples should be protected from cross-contamination from sampling gear, bilgewater, sediment, crew supplies, grease from ship winches or cables, spilled engine fuel (gasoline or diesel), and engine exhaust. All potential sources of contamination in the field should be identified and appropriate steps taken to minimize or eliminate them. Consider using these good practices:
- During sampling, position the boat (or any other vehicle used while sampling) so that engine exhaust emissions do not contaminate samples on the deck.
- Put on clean nitrile gloves before handling the fish.
- Rinse potential target species/individuals in ambient water to remove foreign material from the external surface and place them in clean holding containers (e.g., livewells, buckets).
- Do not use sampling equipment that has obviously been contaminated by oils, grease, diesel fuel, gasoline, or anything else.
- Between sampling sites, the field collection team should clean each measurement device by rinsing it with ambient water. Keep boat decks and docks clear of devices and material not directly related to sample collection.
- Do not handle any food, drink, sunscreen, or insect repellant until after the fish has been collected, measured, and wrapped (or implement measures to reduce contamination by such chemicals if applied such as washing, wearing long gloves, etc.).

Field Recordkeeping

Thorough documentation of all field sample collection activities is necessary for proper interpretation of field survey results. Although paper data forms are still commonly used, weather-resistant electronic tablets with appropriate applications and data forms may also be used to document field work. Wireless capability data collection is ideal in the field, but electronic tablets should be equipped with a reliable battery and memory space to store forms to be downloaded later, if wireless capability is unavailable. If paper forms are to be used, it is advisable to use preprinted waterproof data forms, indelible ink or pencil, and writing implements that can function when wet or cold.

There are important field collection and sample tracking data that should be recorded for each sampling site to document field activities from the time the sample is collected through delivery to the processing laboratory. The example forms and labels show important field collection and sample tracking data elements, but format and content should be adapted based on specific study needs and objectives.

Field Record Forms (pdf) are available as tablet applications (apps), but some programs may still use paper forms. Recorded information should include date, location, weather conditions, hydrologic conditions, sample collection activities, problems encountered, sample ID, fish species, weight, and length.
Sample Identification Label (pdf) - Each sample should have a unique identification and this tag should stay with the sample (e.g., affixed to sample packaging) through the entire process. In this example, the label includes project name, date, time, site identification, sample identification, and specimen number. A portable label printer with indelible ink is useful when attached to the computer used to record data.
Chain of Custody Form (pdf) - This form tracks samples from the field to the laboratory. The information includes contact information, sample location, date, time, sample identification or station, preservative, number of containers, and signatures.
Sample Shipping Form (pdf) - This example includes a Site ID and Sample ID. A consistent format should be used that makes sense to the project team.

Equipment and Safety Considerations

Checklist of Field Sampling Equipment and Supplies (pdf) (95.96 KB)

Safety Considerations for Field Sampling Using a Boat

Fish Biopsy Plug Collection

Most programs collect fish to process as either fish fillet or whole fish samples. If a program only needs to monitor for mercury or selenium, fish plug samples could be collected in the field for tissue analysis. The U.S. Environmental Protection Agency recommends following the field procedures described in Section 11 of the National Rivers and Streams Assessment 2018/2019 Field Operations Manual Non-Wadeable Version 1.2.

Summary

In this section, you have:

Gained an understanding of the permit and approval process to ensure access to your site.
Determined which collection methods work best for your waterbody and target species.
Gained an understanding of the importance of sample preservation and the actions that can be taken to prevent contaminant loss and cross contamination.
Ensured you have all field forms and that safety measures are in place.