3.6: Sampling Living Organisms in the Sea

Almost all terrestrial species spend their entire lives within a narrow zone that extends from a few tens of meters above the tops of the trees to a few meters below the Earth’s surface. Therefore, terrestrial organisms are relatively easy to study, as they are readily accessible and visible to the scientist. In contrast, ocean life is present throughout the thousands of meters of ocean depth (pelagic species) and for several meters, or more, below the seafloor (benthos or benthic species).

Special Challenges of Biological Oceanography

Although pelagic marine life is concentrated in the ocean’s upper few hundred meters, scientists cannot readily enter the oceans to observe it. Therefore, most marine biological studies require capturing the undersea creatures and bringing them back to a research vessel or onshore laboratory. Collecting biological samples from a specific ocean location and depth is a daunting task that poses five major problems, which add to the general problems of working in the oceans discussed previously:

• Pelagic life is widely dispersed in three dimensions. Therefore, large volumes of water must be sampled or searched before representatives of all, or even most, species in any part of the ocean are captured.

• The species that make up ocean life range in size from microscopically small bacteria, archaea, and viruses to giant whales. Therefore, no single method of sampling can capture all important species in a particular study location.

• Many species of ocean life actively swim and avoid any sampling device lowered into their environment.

• Many species are extremely delicate and are literally torn apart by contact with sampling devices that are dragged through the water.

• Many species that live in the cold, dark, high-pressure, deep-ocean environment cannot survive the changes in temperature, pressure, or both as they are brought to the surface.

Nets, Water Samples, and Traps

Nets towed through the water are the sampling devices most often used to collect pelagic species. Nets of different overall sizes and mesh sizes are required to capture different types of organisms (Fig. 3-20). Small nets with very fine mesh are used to sample phytoplankton and zooplankton, and progressively larger nets and meshes are used to capture fishes and invertebrates. Net samples may be collected by simply lowering a net from a stationary ship and hauling it back on board. However, biologists usually want to collect samples from a specific depth, so most sampling with nets is performed by towing a weighted net slowly behind the research vessel.

Figure 3-20. Many different types of nets are used to sample pelagic and benthic organisms. (a) The otter trawl uses two "otter boards" that “sail” in the current created by the vessel's movement, forcing the end of the net to stay open as it is towed. (b) The purse seine is towed quickly around a school of fish and then drawn up under the fish, preventing their escape. (c) Plankton nets are extremely fine mesh nets with a jar or bucket attached at the narrow end to collect plankton as the net is towed through the water. Some plankton nets can be opened and closed on command to sample only selected depths and locations, and some have current meters attached to measure the volume of water sampled as it flows through the net. (d) Drift nets may be deployed for many kilometers across the ocean, where they catch anything too large to swim through the net. Large animals, such as dolphins and sharks, may be inadvertently entangled and die.

Biologists need to know the net depth, how much water passed through the net, and the exact distance the open net is towed. Nets can be let out on a known length of cable over the stern of the ship, towed for a time, and then retrieved. However, without instrumentation the biologist does not know the exact depth of the net tow, how much of the catch came from shallower depths as the net was let out or retrieved, or how much water passed through the net. Many sampling nets now have various types of gauges to measure the depth at which the net is towed. Biologists also need to know the amount of water passing through the net during a tow to calculate concentration or population density of the species in that area. To calculate the volume of water sampled by the net, the measured tow distance is multiplied by the cross-sectional area of the net opening. To provide an accurate length of the tow, many nets carry flow meters similar to impeller-driven current meters (Fig. 3-18a). Some modern nets can also be kept closed until reaching the desired sampling depth, and then opened, towed, and closed again before retrieval. The volume of water sampled by the net, the measured tow distance, is multiplied by the cross-sectional area of the net opening. Some nets are even equipped with video cameras to record species that evade the net.

The smallest pelagic organisms in the oceans (bacteria, archaea, viruses, and phytoplankton) can be sampled by collecting water in sampling bottles such as those described earlier. Plankton and microorganisms are often measured using surrogate parameters. For example, investigators often estimate the total biomass of photosynthetic plankton by measuring the total chlorophyll (CC14) concentration. Concentrations of some other groups of microorganisms are calculated by measuring the concentrations of other pigments similar to chlorophyll or by measuring the concentrations of specific types of genetic material such as DNA. Sharks, large fishes, and squid that avoid nets are sampled with fishing lines and lures. Small benthic organisms are collected by sediment collection devices such as grab samplers and box corers. Fishes and other large invertebrates that live on the seafloor are sampled with trawl nets towed across soft sediment bottoms (Fig. 3-20a) or by dredges similar to those used to collect rocks from the seafloor (Fig. 3-10). 

Fishes and invertebrates that are particularly adept at eluding nets can be caught in a variety of traps. The animals are attracted to the traps with bait or lures. In the dark deeper waters or at night, they may also be attracted by light. Many types of traps have been used. Almost all of the traps allow the organism to enter the trap easily in pursuit of the bait or lure, but make it difficult or impossible for the organism to escape. Figure 3-21 shows a commonly used lobster pot.

Figure 3-21. Lobster pots (or traps) are designed so the lobsters can crawl into the pot to eat the bait inside the pot, but then cannot escape.

Fragile Organisms

Fragile organisms that are easily damaged by nets are particularly difficult to collect and must be captured in closed bottles or jars. Such organisms are numerous in the oceans. Fragile organisms are especially common floating freely in near-surface open-ocean waters (Chap. 14), and in benthic communities at hydrothermal vents (Chap. 17). 

Fragile organisms from the upper layers of the open ocean can be collected by divers that guide interesting organisms into an open jar that they seal immediately. Fragile or elusive small fishes and other organisms can also be sampled by a simple syringe-like device called a “slurp gun.” The diver places the open mouth of the gun near the organism and simply sucks it into the slurp gun’s body by withdrawing a plunger. Slurp guns are particularly useful for collecting small organisms from within cracks and holes in coral reefs, and they are the most environmentally sound means of collecting small tropical fishes for aquariums.

In waters deeper than scuba divers can reach, fragile organisms are collected from research submersibles, ROVs, or AUVs. The collection methods are the same as those used by divers, but the jars, slurp guns, or other collecting devices must be manipulated by remote control or complex autonomous systems.

Migrations and Behavior

Although the occurrence or concentration of a species within a given area is an important parameter, it tells us little about the organism’s life cycle—including, for example, its migration, feeding, and reproduction. Observations by divers, submersibles, and remote cameras can provide some of this information, but only for species that remain relative local and stay in observable depths during the activity. However, many species, including whales and other marine mammals, turtles, and many fish species, swim large distances and dive to substantial depths to feed or reproduce, making them effectively impossible to directly observe. Some of these behaviors can be studied remotely. For example, schools of fish can sometimes be followed by sonar, and whales can be tracked by their songs, which can be heard at great distances. However, these are at best inadequate techniques for understanding their activities. Small sensing packages attached to an organism, for example, the skin of a whale, can gather data on time, depth, and temperature. The instrument package stays attached for some time, is released, floats back up to the surface, and is either recovered by researchers or transmits its data remotely. These instrument packages are becoming steadily more sophisticated and may include additional sensors or video cameras. A particularly interesting way to observe whales is a package that contains a microphone and motion recording device. Attached to whales, this device has been used to record the changes in diving behavior caused when a whale swims into the sound field generated by a surface sonar unit.