For the past 30 years, scientists have been studying the varied bottom-dwelling invertebrates that reside in the York River near its confluence with the Chesapeake Bay.

There has been a lot happening.

“We’ve seen species come and go, we’ve seen species become very abundant and then go back down in abundance, and we’ve seen species that were not abundant increase in abundance,” said Bob Diaz, of the Virginia Institute of Marine Science. “So there is almost any combination of patterns that you can think of going on.”

Diaz is one of a number of scientists who are working to understand the way in which small portions of the Bay’s ecosystem work — and how they fit into the Bay’s overall health. “What we’ve seen lately — probably from the 1970s — is sort of an increase in the number of certain species that would be characteristic of eutrophication,” Diaz said.

The Bay has an estimated 2,700 species; Diaz is studying a community with a few hundred of them. Altogether, they make up the Bay’s biodiversity.

Biodiversity, in some quarters, has become a flash point for controversy. It has been closely tied to arguments surrounding endangered species: That every organism is unique and should therefore be preserved — a concept that critics say equates ants with humans.

But biodiversity, as broadly defined by scientists, means more than just an accounting of all the millions of species on the planet. Harvard biologist Edward O. Wilson defines biodiversity as going beyond individuals to include “communities of organisms within particular habitats and the physical conditions under which they live.”

Communities are groups of species that occupy a specific habitat whose survival often hinges upon one another. In turn, they also exert some force on their surrounding environment and can affect other communities.

This biodiversity, writes Wilson in his book, "The Diversity of Life," is the key to the maintenance of the world as we know it.”

“Every habitat, from Brazilian rain forest to Antarctic bay to thermal vent, harbors a unique combination of plants and animals,” Wilson wrote. “Each kind of plant and animal living there is linked in the food web to only a small part of the other species. Eliminate one species, and another increases in number to take its place. Eliminate a great many species, and the local ecosystem begins to decay visibly. Productivity drops as the channels of the nutrient cycles are clogged. More of the biomass is oxygen-starved mud, or is simply washed away. Less competent pollinators take over as the best-adapted bees, moths, birds, bats and other specialists drop out. Fewer seeds fall, fewer seedlings sprout. Herbivores decline, and their predators die away in close concert.”

Biodiversity, then, is not a matter of just keeping all the parts of every community — in a natural system that would never happen — but a matter of keeping balance in the community. That requires not only a broad range of species — to form defacto “backup” systems when other species fail — but also that those species are present in great enough abundances to fulfill their roles. Wilson notes that certain “keystone” species, which are not always known, will exert more influence over the system than others.

Take the oyster, for example, which has dramatically declined in abundance in the Bay because of disease and overharvesting. Some scientists speculate that there used to be enough oysters to filter all the Bay’s water every few days; the task now takes the depleted stock about a year to accomplish.

The roles that such creatures play is often poorly understood. Sometimes it is not simply a matter of losing biodiversity that is important — the oyster, for instance, has not been totally “lost” — but changing the balance of species that make up that biodiversity through actions that hurt some species or communities while favoring others, said the National Research Council in a recent report, "Understanding Marine Biodiversity."

Citing the Chesapeake oyster as an example, the report cautioned that wholesale changes are taking place in the biological makeup of marine areas around the world — spurred by overfishing, pollution, the introduction of nonnative “exotic” species and other activities. Meanwhile, it said, the “depth and breadth” of marine biodiversity is largely unknown. At stake, the report said, is the capacity of the oceans to sustain fisheries, the ability of bays and estuaries to serve as nursery grounds, the availability of species for biomedical products, and the recreational value of oceans.

“Marine biological diversity is changing, and it does matter,” the report emphasized. “The dual issues of change and loss of marine biodiversity are not trivial and have unified marine scientists — oceanographers, ecologists, and taxonomists — in common cause.”

Although it never used the term biodiversity, the 1987 Bay Agreement bought into the concept. “The productivity, diversity and abundance of living resources are the best ultimate measures of the Chesapeake Bay’s condition,” it declared.

The agreement further stated that, “Some species of shellfish and finfish are of immense commercial and recreational value to man. Others are valuable because they are part of the vast array of plant and animal life that make up the Chesapeake Bay ecosystem on which all species depend. We recognize that the entire natural system must be healthy and productive.”

No one, though, is certain what that “healthy and productive” Bay would look like — what species it would contain, in what communities, and in what abundances. Too little is known about too many of the Bay species and the communities in which they live.

In the York River, for instance, Diaz ponders the significance of the changing diversity among benthic invertebrates. It could have ramifications all the way up the food chain. If the quality of food declines, then the quantify of fish produced could follow suit.

“The ideal food package to the fish is something that is big, easily caught and has lots of juicy meat on it,” Diaz said. “We’ve seen changes in some of the size structures of the invertebrate populations over the years. There is a tendency for things to be slightly smaller. Some of the species that are now very abundant are very small.”

Some of that change would happen regardless, he noted. Different species thrive from year to year and even from season to season. But, he added, “the watershed development has probably accelerated a lot of the species turnover, and has driven it in a certain direction — toward species that like to see more organic matter [nutrients] in the water column.”

While the Chesapeake Bay is a tremendously productive ecosystem, it does not have the range of diversity of some other marine systems, noted Kent Mountford, an ecologist with the EPA’s Chesapeake Bay Program Office. A sample taken from the Bay floor might yield 20 to 30 species, but one from a tropical or coral reef habitat might contain more than 250.

On a nutrient-poor coral reef, Mountford said, “each species, in relatively small numbers, is desperately trying to ‘make a living’ in some little niche where it can get a little bit of change, a little bit of leakage, or a little bit of nutrition that is coming off something else.” If you begin to fertilize a coral reef, he said, the diversity quickly breaks down as opportunistic organisms, able to capitalize on the increased nutrients, begin to take over.

In nutrient-rich estuaries, by contrast, that degree of specialization — and competition — is not needed; there are plenty of nutrients to go around. As a result, estuaries result in relatively large populations of fewer species. “That’s why we get lots of oysters, lots of crabs, lots of bluefish, lots of striped bass, lots of shad and all those things,” Mountford said.

In addition, the species that live in the Bay have to be “relatively tough,” Mountford said. Unlike a stable coral reef, where salinities, temperatures and nutrient levels are almost constant, estuarine species have to put up with large variations in all three. And the greater their range in the estuary, the more tolerant they must be of those stresses.

As a result, he said, there is less diversity where the Bay reaches into its tidal rivers and the water turns from a mixing zone of salt and fresh water — known as the “salt wedge” to an area of all fresh water. “There are tremendous stresses when you go between saltwater and pure freshwater,” he said.

Those stresses can be amplified from year-to-year as large “freshets” sometimes pour huge amounts of fresh water into the Bay, dramatically lowering salinity over large areas for long periods of time. By contrast, in unusually dry years, upper parts of the Bay become far saltier than normal.

Over the course of thousands of years, Mountford said, the variety of species in the Bay adapted to these conditions. “The ones that were good survivors in the low salinities were in the upper part of the Bay where they needed to be, and the ones that were less tolerant were down near the mouth of the Bay where they got these impacts less frequently.”

As the watershed became more developed and the land was cleared — and therefore retained less water — studies of bottom sediments indicate that the freshets became more frequent and more powerful, affecting larger portions of the Bay.

As time went on, pollution put organisms under further stress, allowing the tougher populations to survive. Mountford noted that some of the largest cities in the Bay region — Richmond, Washington and Baltimore — are located near the limit of salinity where natural stresses already deplete the number of species.

“Eventually, you come down to just a few species if, for example, you get near a sewage outfall,” Mountford said. “There are few species that can handle that. But they are extraordinarily abundant, something like hundreds of thousands per square meter. You get large populations of stress-tolerant organisms.” These are often worms and other organisms people typically don’t think of when they think of the Bay’s diversity.

The problem is that when a single species becomes this dominant, it becomes subject to collapse if a disease or other variable suddenly hits the population, and there is nothing left to take its place. In an unimpacted system, with greater diversity, the decline of one species is buffered by the presence of many others. This has been seen for example, in grass beds in the Bay; those beds dominated by single populations often greatly expand or contract in size in a single year, dramatically changing habitat conditions for other species.

“If you preserve the species and all the links in the chain, they will adjust to a mix that is generally in balance with the system, and it will fluctuate,” Mountford said.

In a sense, then, the natural system has some built-in redundancy; if one species fails, another is there to pick up the slack. But when diversity declines, the system’s ability to “bounce back” is reduced.

“Resilience is the term that a lot of ecologists use,” Mountford said. “The system as a whole is able to buffer the loss or decline in a few species and buffer itself against the impact of natural fluctuations.”

If the Bay actually were balanced, healthy and productive as the Bay Agreement called for, what would it look like? No one is certain. Capt. John Smith wrote of the Bay’s bounty when he explored it in 1608, but he did not bring with him a comprehensive monitoring program that described what the Bay’s varied ecological communities looked like in “pristine” conditions.

Two years ago, the Bay Program’s Ecologically Valuable Species strategy noted that most people would idealize the pristine Bay as “teeming with game fish, blue crabs, oysters, and waterfowl, with clear water and a minimum of ‘nuisance’ organisms” such as algae, sea nettles and too dense beds of submerged aquatic vegetation.

Such a vision, the report noted, was “pleasant, if perhaps unrealistic.” In reality, each of those “nuisance” species have “a vital role to play in a balanced and healthy system.”

Many scientists believe that the Bay before European settlement was probably dominated by oysters and other bottom dwelling, or “benthic,” species. That, said Steve Jordan, a Maryland Department of Natural Resources biologist and director of the Oxford Cooperative Laboratory, would be similar to the communities found in the less-impacted coastal bays along the mid-Atlantic Coast.

But over the centuries, the bottom of the Bay is where sediment, toxics, dead algae and other debris piles up, and where oxygen in the water is most depleted because of excess nutrients.

“One of the things that we look for as a real strong indicator [of a healthy system] is the diversity of bottom-feeding fish,” Jordan said. “It’s one of the best indicators that we’ve been able to find for biological conditions.”

And there is historical evidence to suggest that biodiversity among the Bay’s benthic communities has been greatly altered since Colonial times.

Grace Brush of Johns Hopkins University and Sherrie Cooper of the University of Maryland’s Sea Grant College Program, examined core samples from the Bay bottom and found that after European colonization, the diversity of diatoms decreased even as diatom abundance increased.

Diatoms are nutrition-rich algae cells that are a major part of the diet for many aquatic species. In particular, the scientists found, benthic diatoms — those found on the bottom of the Bay or on underwater plants — were replaced with planktonic species found floating higher in the water column.

The shift happened at a time when the land was cleared, and increased amounts of sediment were washing into the Bay, blocking the light and covering large areas of the bottom.

But algae and worms were not the only species to decline. Archaeologists working at St. Mary’s City, the one-time capitol of Maryland, have found that during the 1600s and early 1700s, settlers heavily relied on bottom-dwelling fish such as sturgeon, sheepshead, red drum, black drum and perch.

Some of those, especially sheepshead and sturgeon, are almost gone from the Bay today.

“By the early 1800s, the agricultural system was such that plowing had exposed so much ground to erosion that the smaller tributaries, like the St. Mary’s River, were being heavily silted,” said Henry Miller, director of research for the museum at St. Mary’s City. “What that did was have a serious negative effect on all the bottom-dwelling creatures.”

So if managers were able to restore the biodiversity to something like what John Smith found, what would it look like? It might be a Bay much different than many might think.

The most direct beneficiaries might not be things like striped bass, Jordan said, but rather the depleted populations of bottom dwellers, “which is not what a lot of people want to hear.”

If that is the case, Jordan asked, “what is it about biodiversity that anyone would want?”

The answer, he said, is a system that is more balanced and stable. A Bay with greater biodiversity would have a healthier benthic community that would help consume excess algae which, in turn, would help clear the water and improve water quality.

Instead, unconsumed algae forms blooms that cloud the water and block light needed by Bay grasses which, in turn, are needed to provide important habitat for blue crabs, young striped bass and other species. And when that algae dies, it sinks to the bottom where — absent the algae-consuming bottom-dwellers — it is broken down by bacteria in a process that depletes the water of oxygen.

Some scientists believe that the role once performed by those organisms has been taken over by bacteria. The result: Instead of turning the algae biomass into food that works its way back up the food chain — ultimately supporting everything from eagles to striped bass — it just decays at the bottom.

The Ecologically Valuable Species Strategy outlined a monitoring and research plan to help better understand the role that many of these species, and their communities, play in the Bay. Until managers understand and promote healthy communities, the strategy warns, the Bay may never truly be “restored.”

“No matter what is done to control nutrients and improve habitat conditions, there must be an adequate base of zooplankton, forage fish and macrobenthos to support healthy and productive populations of recreational and commercial finfish,” the strategy states. “Many ecologically valuable species, although most people would recognize neither their names nor their appearances, are the ‘species in the middle’ — balancing elements in the Bay ecosystem.”

That balance, Jordan said, “is real biodiversity … We certainly can’t manage for biodiversity simply by managing striped bass or blue crabs or oysters.”

“It requires a large complement of species; if you go out and count them, you would expect a larger number than you would have in a degraded system. The system depends on the components as much as the components depend on the system.”

Or, put another way, as Jordan explained, in a balanced, biodiverse system there may not be as big of an increase in the number of striped bass as people might like to see, “but on the other hand, we might get sturgeon back.”