Once legendary for its production of fish and shellfish, the Chesapeake Bay today is churning out huge quantities of something most people can’t even see: bacteria.

In fact, the Bay appears to produce more bacteria than any other estuary. Overabundance of the tiny microbes, which is the primary cause of oxygen depletion of in the water, could make the job of cleaning the Chesapeake much harder than anyone presently thinks.

“The thing that is most out of whack in the Chesapeake Bay is this bacterial component,” said Robert Jonas, a microbiologist with George Mason University.

Scientists have known for years that the Bay was filled with bacteria, which deplete oxygen as they decompose excess algae and other dead material.

But recent studies by Jonas indicate that bacteria levels in the Bay aren’t just high for an estuary — they’re unprecedented. Work by Jonas and his colleagues have found that bacteria abundances in the Bay are at least double — and sometimes 10 times greater — than what would normally be expected in an estuary.

In the Bay, bacteria often number 15 million to 20 million per milliliter of water. In other estuaries, Jonas said, high concentrations typically only reach 5 million to 8 million per milliliter, and are often lower — in the 1 million to 2 million per milliliter range.

Even in other nutrient-enriched estuaries such as the Columbia River and those in North Carolina, “you don’t see any numbers like this,” Jonas said. The Hudson River only on occasion approaches concentrations routinely seen in the Bay.

Some of the Bay’s tributaries are even worse. In recent summers, Jonas has found sustained bacteria abundances of 40 million to 50 million per milliliter in several parts of the Potomac River.

Such overabundance of bacteria could have serious implications for cleanup efforts, which are aimed at reducing nutrients to improve dissolved oxygen levels in the water. Nutrients fuel algae growth and, when there is more algae than can be consumed by fish and other species, the excess dies and is decomposed by bacteria.

Bacteria, relative to their size, have rapid metabolisms and consume disproportionately large amounts of oxygen. In deep areas of the Bay, where the water isn’t replenished with oxygen from the air, the bacteria cause oxygen-depleted “dead zones” lethal to fish and shellfish.

Even that doesn’t stop the bacteria. When the dissolved oxygen level hits zero in the bottom waters, the bacteria don’t shut off — they just switch to using sulfate in the water. When that happens, they create hydrogen sulfide, which is toxic to other organisms. As other aquatic creatures die, the bacteria get even more to decompose.

Nutrient reduction strategies are aimed at keeping that from happening by limiting the amount of algae produced. But, according to Jonas, the Chesapeake has more bacteria than one would predict based on the amount of algae in the water. “We found the bacteria in the Bay did not correlate with phytoplankton,” he said.

That, he said, could explain why monitoring has shown no improvement in oxygen levels in the Bay or its tributaries despite nutrient control efforts over the past decade.

While algae production can be related to the amount of inorganic nutrients entering the water — chemical forms of nitrogen and phosphorus — bacteria production seems to be related more to dissolved organic nutrients: sugars, amino acids and other substances created as living material breaks down in the water.

Organic nutrients can come from a wide range of sources, everything from wastewater treatment plants to plant debris from tidal marshes or runoff from the watershed.

Cindy Gilmour, a scientist with the Academy of Natural Sciences, said a decade of monitoring on the Patuxent River indicates that bacteria growth is related to how much organic nutrients are washed into the river — an amount that seems to vary based on flow.

And in parts of the Patuxent, researchers have seen bacteria concentrations that rival the highest seen in the Potomac. Jonas and Gilmour say the high bacteria concentrations in the Patuxent could explain why dissolved oxygen levels have not improved in the river despite sharp reductions in inorganic nutrients in the past decade. It’s hard to say for sure, the scientists acknowledge, because bacteria has generally received less attention — and monitoring — than other organisms.

“It may be that managers may want to consider limiting the amount of organics that come into the system to limit the amount of bacteria,” Gilmour said. “But that is kind of a stretch. I wish I had more data to support that.”

While much of the Patuxent’s organic nutrients may come from runoff and tidal marshes, Jonas believes the Potomac is different. In the Potomac, he said, organic nutrients fueling bacteria production seems to be coming from algae.

The lower Potomac, where Jonas has seen some of the highest bacteria concentrations, is far removed from potential runoff sources of organics, but has large algae concentrations.

In research supported in part by the Bay Program, Jonas has found disproportionately high amounts of organic nutrients associated with algae production in the Potomac. In the water, scientists measure algae production by filtering them through glass fiber filters, which catch the algae but let the water trickle through.

Jonas has done the same thing in the lower Potomac, but focused on the amount of organic nutrients that had dissolved in the water and were flowing through the filter. “What we found,” he said, “is that almost all the oxygen-demanding organics [which fuel bacteria production] went through that filter. They didn’t stay on top of it.”

During the summer in the Potomac, he said, as much as 90 percent of the nutrients available to bacteria were dissolved organics missed by normal monitoring efforts. That means, he said, if people assume only nutrients in the algae are leading to oxygen depletion, their estimates can be off by as much as a factor of 10.

He theorizes that the Bay is so nutrient-enriched that phytoplankton don’t have to be efficient at using nutrients; rather than fueling production, the nutrients are passing through, or are being released into the water as the algae are consumed by zooplankton.

Likewise, Jonas sees signs that there are so many organic nutrients in the water that bacteria don’t have to operate efficiently, either.

In a typical estuary, almost all bacteria are attached to solid particles, which allow them to conserve energy as they feed. In the Bay, the reverse is true. Almost all bacteria float freely in the water. “In this case,” Jonas said, “it would appear that these bacteria just don’t care. They are getting everything they need without having to worry about energy.”

Jonas said the uniqueness of the Bay’s bacteria is “a real discovery. This puts the Bay out in a brand new world. This has not ever been seen before in the world. We have an opportunity to understand this kind of system and say is this going to happen in a lot of places in the world, or is the Bay unique?”

And why is the Bay so different? Jonas isn’t sure, but said it could be a byproduct of the Chesapeake being so nutrient-enriched for so many years that “normal” operations have been greatly altered. Also, the lack of oysters to filter algae from the water has probably contributed to the overabundance of algae — and dissolved organic nutrients — to fuel bacteria.

Jonas expects that the Bay Program’s nutrient control efforts should ultimately help return the Bay to a more typical estuarine situation in which algae produce less organic nutrients and bacteria abundances are reduced. But because bacteria production turns out to be so high relative to algae production, Jonas said nutrient reductions beyond those currently under way will likely be needed to improve oxygen conditions. “The system is more complex than we understood,” he said.

Keeping an eye on bacteria could bring some good news, though, by providing the first clue that the system is recovering, Jonas said. If bacteria begin moving back to particulate matter, it will be be a sign that their energy supply is being reduced — a first step in controlling the tiny organisms.

“You would see this estuary turn back to something that you would expect from a more healthy estuary,” he said. “These things are so out of whack, I think we really have a good shot at seeing improvement by tracking them.”