Researchers are working to explain a mysterious 10-year decline in the populations of a wide variety of organisms that live at the bottom of Puget Sound.

Studies in 1999 and 2009 showed a drop in the population of benthic invertebrates in central Puget Sound, according to a report released last summer by the Washington Department of Ecology. The analysis also showed a decline in the number of species that researchers found, a condition also seen in other areas of Puget Sound.

Toxic chemicals in the sediments don’t appear to be the driving factor for the decline, experts say. The actual cause has not been identified, but a number of ideas have been proposed.

“We’ve been talking to a lot of people and trying to figure out what could be influencing the benthos,” said Maggie Dutch, lead scientist for Ecology’s Puget Sound Sediment Monitoring Program.

As found in the study, chemicals measured were generally unchanged over the 10-year period, and measurable decreases were seen in the concentrations of lead, mercury, tin and polycyclic aromatic hydrocarbons from central Puget Sound. Laboratory tests showed only slightly greater problems over the decade when amphipods and sea urchin eggs were exposed to the sediments, so people were left wondering why the numbers declined and why some species went missing.

Benthic organisms — including a variety of tiny worms, clams and crustaceans — live in the mud and feed largely on dead matter that sinks to the bottom of Puget Sound. These tiny invertebrates, in turn, are eaten by other bottom-dwellers, such as crabs, shrimp, and by fish. They are one of the primary links into a food web that supports salmon, marine mammals and humans.

Gray whales eat the benthic creatures directly by swimming down, scooping up sediments and sifting the prey through the baleen around their mouths.

“Benthic invertebrates are overlooked by most people,” Dutch said. “They are in direct contact with the sediments. They live on them, feed on them. If there are contaminants, they will pick them up and pass them up through the food chain.”

When Ecology launched its long-range monitoring program in 1989, biologists generally assumed that the greatest problem for benthic organisms was the toxic contamination left behind by historical industries. In fact, chemicals are known to have serious effects on the benthos, as observed in several urban waterways. But declines in abundance also have been observed in some rural bays where relatively little chemical contamination exists. Such areas include Hood Canal, the Strait of Georgia, the Eastern Strait of Juan de Fuca and the San Juan Islands.

Over the past 25 years, some of the most toxic underwater sites have been cleaned in Puget Sound. Such projects often involve dredging to remove the worst of the contamination, followed by the addition of clean sediments to “cap” the pollution and keep it from escaping back into the environment.

Positive effects from the cleanups have been noted in some places, as shown in focused studies on the urban bays, Dutch said. For example, the general quality of sediments in Seattle’s Elliott Bay showed a positive shift from 1998 to 2007, with decreases in polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs).

In Kitsap County’s urban bays — namely Sinclair and Dyes inlets, Liberty Bay and Port Orchard Passage — concentrations of arsenic, lead and some PAHs decreased from 1998 to 2009, while concentrations of several metals and other PAHs increased.

But during that time, the total area of the bottom where benthos were judged as “adversely affected” increased from 9 percent in 1998 to 29 percent in 2009. In 1998, most of the “adversely affected” areas were found in Sinclair Inlet, but by 2009 all of Liberty Bay was similarly affected.

In most areas, toxic chemicals alone fail to explain the general decline in the benthos, Dutch said. The complexity of the Puget Sound ecosystem might preclude a simple answer to the mystery, but these are some factors under consideration:

Chemicals not tested: Unknown substances might be creating problems. For example, in Budd Inlet near Olympia, some areas had no benthic organisms at all, yet tests for 262 toxic chemicals revealed relatively low contamination. Now, experts believe that untested chemicals — possibly hazardous dioxins — could be to blame.

“Emerging chemicals”: Studies are just beginning to identify problems caused by pharmaceuticals and personal-care products, which can mimic hormones and disrupt growth, behavior and reproduction in exposed animals. Some of these chemicals have been found in Puget Sound sediments.

Planktonic shift: Christopher Krembs of Ecology’s Water Quality Monitoring Program has hypothesized that excess inputs of nitrogen from human sources might be reducing the abundance of one type of plankton (diatoms) in favor of another type (dinoflagellates). When they die, diatoms more readily sink to the bottom and feed the benthos.

Changes in sediments: Grain size and organic material are determining factors for what grows in the sediments. In some areas, changes in land use have affected the quality of the sediments, especially at river mouths. Large sediment loads can kill off sensitive species, leaving only those able to cope with dramatic change.

Low-oxygen conditions: Nitrogen also has been implicated in creating low-oxygen conditions, known as hypoxia. Excess nitrogen encourages the growth of plankton, which then die and decay. During decomposition, bacteria can use up the available oxygen, leaving deadly conditions for other organisms.

Increased acidification: Lower pH levels, associated with both hypoxia and climate change, can affect many species, especially those with calcium shells. An oyster hatchery on Hood Canal, operated by Taylor Shellfish Farms, was forced to alter its water intake in Quilcene Bay because of low-oxygen conditions. Experts found that the tiny oyster larvae were dying when they were unable to produce a healthy shell.

Natural oceanic cycles: Scientist have long studied cycles in ocean conditions, including the long-term Pacific Decadal Oscillation and the shorter-term El Niño/La Niña cycles. These cycles can shift temperature, acidity, nutrients and oxygen levels, but their effects on the benthos are not fully understood.

As the studies move forward, it has become clear that Ecology’s Sediment Monitoring Program must work more closely with the Water Quality Monitoring Program and other research efforts, said Dutch, who has worked for Ecology since 1989.

“Putting pieces of the puzzle together means communicating with others doing research in this area,” she said. “Various programs have grown and evolved to answer their own questions. But you get to the point where you start to see how all these parameters are connected.”

One can learn from other areas as well, she said, but Puget Sound has some of the greatest benthic diversity in the world. East Coast estuaries, such as Chesapeake Bay, has just one-fourth the number of species found in Puget Sound.

To help communicate the findings about sediment chemistry and benthic organisms, Dutch and her colleagues developed three numerical “indexes” to describe the health of sediments within a bay or across a region of Puget Sound.

One is the “sediment chemistry index,” which considers the levels of toxic chemicals in the waterway. Urban bays in Kitsap County had better scores than Seattle’s Elliott Bay or Tacoma’s Commencement Bay, but Elliott Bay has shown the greatest improvement from 1998 to 2007.

The second is the “sediment toxicity index,” which involves exposing amphipods and sea urchin eggs to the sediments taken from the waterway. Elliott Bay, Commencement Bay and Kitsap bays were all close in the first round of testing. But 10 years later only Elliott Bay had improved, and Kitsap bays had shown a 7 percent decline.

The third is the “sediment benthic index,” which looks at the numbers and species of bottom organisms found in the area. A numerical score is under development. For now, areas are described as either “adversely affected” or “unaffected.”

Finally, the three indexes are put together to create a “sediment quality triad index,” which is being used by the Puget Sound Partnership as a “vital signs indicator” to describe progress in cleaning up Puget Sound. Largely because of the mysterious declines in benthic populations and species, the overall triad index has declined in five of the six Puget Sound regions. That worsening trend must be reversed to meet the partnership’s 2020 target to improve sediments to an unimpaired status.