In the cramped deHavilland Beaver, a rugged bush plane designed during World War II and owned by VIMS, Dr. Harding uses advanced sensors to look for signs that the main bay is recovering from its overdose of nutrients.
Poking out of a hole in the bottom of the aircraft, the sensors pick up subtle shadings of color in the murky water below, indicating the presence of chlorophyll, the substance plants use to convert sunlight to energy. That chlorophyll helps him spot algae "blooms," massive growths of microscopic plants that deprive the water of life-giving sunlight and oxygen.
In his office, Dr. Harding uses a computer to translate the sensor readings into splashy color portraits of the bay. Splotches of blue and green indicate relatively good water quality, with only modest algae concentrations, while bright patches of yellow, orange and red show where algae growth has run wild.
For years, scientists have gone out on the bay to monitor its health, collecting water samples from a fleet of research vessels several times a year. That type of monitoring is essential, but boats can miss patchy blooms that die and disappear in a matter of days.
Flying from Newport News, Va., to Baltimore and back, once or twice a week in spring and summer, Dr. Harding has been able to get a more comprehensive, up-to-date picture. "It's given us a whole new view of the variability in the bay," he said.
After five years of aerial scans, it's still too early to tell if the bay is improving, Dr. Harding said.
Later this year, he hopes to get an even better view of the Chesapeake -- from outer space. NASA plans to launch a water-reading satellite that should allow scientists to track chlorophyll almost daily.
Bacteria in nutrient picture
With the Patuxent River as her laboratory, Dr. Gilmour monitors returns from a massive experiment on nitrogen.
This is the first Chesapeake tributary to have its sewage treatment plants upgraded to remove the nutrient, and Dr. Gilmour and her academy colleagues look for signs of improvement in the river.
But water-borne bacteria signal a possible complication in the seemingly simple calculus of the bay cleanup. They are not disease-causing germs, just the natural bacteria that recycle all living things, through the process we know as "decay."
The Patuxent is brimming with billions and billions of bacteria, Dr. Gilmour said, and they help create "dead zones" in the water, just as algae do. Bacteria consume the dissolved oxygen in water as they busily ingest the nutrients in decaying algae and other organic matter, and at very high concentrations actually cloud the water.
"The amount of bacterial growth out there is just phenomenal," she said. At times, the bacteria outnumber the algae.
Actually, bacteria could be a plus or a minus for the river's recovery, Dr. Gilmour explained. They may help by out-competing algae for declining levels of nutrients.
Or bacteria may hurt if, as some scientists believe, they have helped alter the river's "food web," reducing the available food supply for small marine animals and fish. If that theory holds, restoration of the Patuxent may be harder than previously believed.
From water samples collected every two weeks by a state research vessel, she and other scientists use powerful microscopes to manually count and identify the number and types of bacteria. The researchers then use sophisticated computer technology to calculate the "biomass" or volume of those bacteria and relate it to the flow of nutrients into the river.
In two years of study, Dr. Gilmour has found some evidence to support the theory that bacteria may contribute to the bay's ills. While water quality is improving in some lower stretches of the river, there is little recovery so far in upper reaches, where bacteria levels are high.
To clean up the Patuxent -- and possibly the rest of the bay -- it may be necessary to reduce not just nitrogen but other organic matter on which bacteria feed, Dr. Gilmour said. That could require additional upgrades of sewage treatment plants, and extra cost.
But more research on bacteria is needed, and it could take years, she added.
Recalling stress of 1980s
Given the news out of Washington, Chesapeake scientists worry that the tide may be ebbing for their work, and for other government-funded research. "This is the scariest time for environmental scientists since the early days of Reagan," said Dr. Gilmour.
She recalled how during Ronald Reagan's first term (1981-1984), his administration tried to slash federal funding for scientific research. Congress blocked those cuts, but this time is wielding the knife.