THE BOAT IS BOBBING UP AND DOWN on a late spring day on the Chesapeake Bay. The previous day was rainy, and tomorrow will be, too. But this crew is on a mission, and they work through bad weather.

They're aboard the R/V Bay Eagle, the 65-foot-long, main research vessel of the Virginia Institute of Marine Science (VIMS). About four miles east of Chesapeake Beach, they've arrived at the first stop of the day on a planned route in the estuary's Maryland portion.

Captain John Olney Jr. sounds a horn, the signal for VIMS marine scientist Gregg Mears to begin deploying a trawl net wrapped on a big spool mounted above the stern. Commercial trawling isn't allowed in the Chesapeake, which makes this operation an unusual sight. But trawling can be useful to study the estuary's fish populations, which is what this crew is doing today.

The ship motors at a constant three knots for exactly 20 minutes. The scientists winch up the net and steer it onto the deck. A mass of marine life squirms at the bottom of the net. By trawling the same way each time across many locations in the Bay, scientists can turn the wet piles they collect into reliable data about fish populations in the Chesapeake Bay, America's largest estuary.

The net is unloaded and disgorges 13 striped bass, which are among the estuary's top predator fish and are prized by both commercial and recreational fishers. The scientists sort and measure them. They will also examine the fish to find out what's inside their stomachs — what kinds of little fish and other small creatures are they eating? The scientists on this ship are fish detectives, and they're gathering clues.

The clues are helping them and other researchers solve mysteries about the Bay's larger fish and the smaller fish they eat. Knowing more about how they interact could help fisheries managers better manage stripers and other big fish. Among the mysteries still to be solved: why have populations of some important larger species, like Atlantic croaker and summer flounder, declined?

The ChesMMAP survey began in 2002 when scientists Rob Latour (top, left) and Chris Bonzek (top, right) of the Virginia Institute of Marine Science secured funding to launch the project. They have worked with scientists Ed Houde (bottom, left) and Ryan Woodland (bottom, right) of the Chesapeake Biological Laboratory in Maryland to analyze the data collected. Houde and Woodland have examined how environmental factors like springtime temperatures can affect the abundance of prey species eaten by larger predators. Photographs, Jeffrey Brainard (top), Nicole Lehming (bottom)

In 2001 two VIMS fisheries scientists, Rob Latour and Chris Bonzek, attended a meeting at the Chesapeake Biological Laboratory (CBL) in Solomons, Maryland, a part of the University of Maryland Center for Environmental Science. The topic was how to apply a new approach in fisheries management, called ecosystem-based fisheries management, in the Chesapeake Bay. The idea behind this approach is that to set sustainable harvest levels for larger predator fish species, you have to take a broad view. You have to study and consider the many influences within the ecosystem where the fish live that influence their survival. For one, you have to pay attention to what the predator fish eat.

Bonzek had recently attended a meeting in Canada about studying fisheries and ecosystems. An important point, Bonzek recalls from that discussion, was that "if you are going to go down this path towards multispecies or ecosystem-based management, the main thing you need on top of your routine monitoring is the diet data — who is eating who, and how much." Latour adds, "I realized we didn't have a lot of data on this, even though the Chesapeake Bay is a data-rich area."

Bonzek and Latour knew that finding out more about fish diets would require collecting a lot of data in a more comprehensive way than ever before.

An early study in the estuary showed how it might be done here. In the early 1990s, Kyle Hartman was a Ph.D. student at CBL. Working with his adviser, Stephen Brandt, Hartman caught some of the Bay's top predator fish — bluefish, weakfish, and striped bass — off the lab's dock in Solomons. He cut them open and identified their stomach contents. Hartman published some of the first scholarly studies about what these species were eating. But the work had its limitations. It was focused at just one location in the Chesapeake, whose length stretches 200 miles from its mouth at Virginia Beach to its top at Havre de Grace, Maryland.

After Bonzek and Latour's meeting at CBL, as they made the long drive back to VIMS, they tossed around an idea. Could they team up on a survey that would collect these kinds of detailed data about what the big predator fish species were eating over the entire expanse of the Bay?

Latour was a freshly minted Ph.D. looking for a substantial research project. He and Bonzek had lined up some funding that would allow VIMS to piggy-back additional data collection work onto some existing research cruises that Bonzek was overseeing to monitor striped bass and other economically important predator fish in Virginia waters.

In 2002 the new project was born, christened the Chesapeake Bay Multispecies Monitoring and Assessment Program or ChesMMAP. Bonzek and Latour originally figured they could run the project for at least a year and then judge whether to go on. In the end they garnered funding and support to keep it going to this day. Scientists go out on the Bay Eagle and collect samples of predator fish five times a year along nearly the entire length of the Maryland and Virginia portions of the Bay. The project has created one of the largest databases about fish diets in any estuary in the world. And that database has emerged as an important tool for scientists in Maryland and Virginia who are working together to understand more about fish food in the Chesapeake.

Since 2002, the ChesMMAP research project has run five annual cruises, each of which collects fish at 80 randomly selected stations spread around the Bay. That adds up to more than 5,800 stations sampled and a massive trove of data on fish diets. This map shows the locations and frequency of past visits. Each circle represents a square mile; some circles contain more than one monitoring station. Map, Virginia Institute of Marine Science

Aboard the Bay Eagle, VIMS marine scientist Gregg Mears drops the trawl net again. The Bay Eagle is just off Kenwood Beach on the Bay's western shore, its net skimming the bottom 27 feet below.

Mears and the other crew members have the procedures of trawling down well — they traveled to a university in Newfoundland, Canada, to go through a special training program there. During each cruise, the ChesMMAP crew will raise and lower their trawl net many times, collecting samples at approximately 80 locations across the Maryland and Virginia portions. Avoiding underwater obstacles in a shallow waterbody like the Chesapeake Bay is a constant challenge. The network of ChesMMAP monitoring stations omits the estuary's upper section, north of Pooles Island, because it contains so many submerged trees that the researchers call it Sherwood Forest. Lower in the Bay, Captain Olney occasionally has to back up the Bay Eagle to free the net when it snags on something. The crew continually maps these obstacles on GPS so the ship can avoid them on future cruises.

Each cruise takes about eight days to complete. The crew bunks onboard in sleeping bags. That can mean a lot of days away from family. Mears keeps a close eye on whether the cruise dates conflict with his daughter's twice-a-year dance recitals.

Still, he says, "It's the best job I've ever had." The work can contribute to managing Chesapeake Bay fish populations, he notes, both as a food resource and as part of a healthy, balanced ecosystem. "Humans have a tendency to not be good stewards of the environment and to push things out of whack. I'd like to think some of what we do helps to bring things back in balance."

What the scientists catch in the trawl net varies with the season. In the spring, striped bass are plentiful as they migrate from the Atlantic Ocean up the estuary to spawn. In late fall, the stripers migrate back out to the ocean. Atlantic croaker (also called hardheads) turn up in greater numbers in summer months, migrating back to the ocean by around September.

As the Bay Eagle's trawling run off Kenwood Beach ends, the crew members spring into a flurry of coordinated action. They haul up the trawl net, which is again squirming. This time it contains five stripers, two white perch, and one menhaden. For each species caught, the scientists sort each individual by size. Bigger, older fish tend to eat different kinds of prey than smaller, younger ones do, and the scientists want to track those differences to build a detailed picture of consumption patterns.

ChesMMAP crew members haul in a sample using a bottom trawl net (above left). On the Bay Eagle's shipboard lab (above right), Alex Johnson and Rebecca Hailey weigh and process fish for further analysis. Back at the Virginia Institute of Marine Science (VIMS), Gregg Mears (bottom) examines and weighs the contents of predators' stomachs. Photograph, VIMS (top left); Jeffrey Brainard (top right and bottom)

Mears measures the length of each fish. No need to use a tape measure. He simply places each one on a FishMeter, a sensing device that looks like a large ruler. He touches an electronic sensor at the fish's tail, and its length is automatically recorded on a shipboard computer. Then on to the next fish, and the next.

To find out what the fish are eating, the scientists pick out up to five individual fish from each size group within each species. Why only five? Other fisheries research has shown that this sample size is highly representative of the rest of the fish from that species caught in the net as well as others left swimming in the estuary. That's because fish of similar ages tend to gather in the same school and feed together.

The representatives are brought below deck to a shipboard lab. In these cramped quarters, trawling chief Dustin Gregg and research specialists Alex Johnson and Rebecca Hailey have set up a kind of assembly line. They collect additional data about each fish, including its precise age, which they determine by removing its otoliths — bone-like mineral deposits in its head bearing rings that record age, like tree rings do. The scientists remove each fish's stomach and store it in preservative for later analysis. It's one more set of clues relevant to knowing who is eating whom in the Chesapeake.

Once a ChesMMAP cruise ends, Mears returns to a bigger lab at VIMS, in Gloucester Point, Virginia. This is where he will analyze the stomach contents.

Mears sits at a lab table in this white room and carefully unties a cheesecloth bag that contains a fish stomach. Some people call him and his colleagues the "fish medical examiners" because of what they do next. He cuts open a stomach from a striped bass. Inside Mears finds two menhaden, a favorite prey of stripers. He measures them and records the details in a computer database.

On to the next fish stomach. These contents are harder to identify. There's a soft pulp; before the fish was caught, it had partially digested whatever living thing this was. Mears marks down the material as "unidentified." For some species, that mystery category describes a significant portion of the total stomach contents by weight — 15 percent for Atlantic croaker, for example. The ChesMMAP data can only reveal so much about fish diets. "We do the best we can with what's in front of us," Mears says.

The stomachs yield more than fish flesh. Mears displays a tray of objects that he and his colleagues have pulled from fish stomachs over the years. There's a rock the size of your palm. There are also shell pieces from blue crabs and vertebrae from skates.

In a single day, Mears can process as many as 80 fish stomachs from ChesMMAP. During the past 15 years, more than 47,000 ChesMMAP stomachs have passed through this room. That's a lot of fish guts — and data.

The ChesMMAP project had collected more than a decade's worth of data when in 2014 a new effort was launched to sift through and interpret the clues that the fish detectives had so carefully and steadily collected. The Chesapeake Bay Watershed Agreement, a document that guides planning efforts among the federal and state partners working to improve the estuary's water quality, was revised that year. The updated agreement called for evaluating the Chesapeake's "forage fish base," a term scientists use to describe prey eaten by larger predatory fish species.

The Chesapeake Bay Program's Scientific and Technical Advisory Committee (STAC) took up the call. The committee held a workshop of scientists, who pored over the ChesMMAP data and generated a report that offered surprising new insights about which forage species were most important in the diets of the predators.

The workshop report focused on the feeding patterns of five predators deemed representative of all Bay predators because of their variation in body type and behavior: Atlantic croaker, clearnose skate, striped bass, summer flounder, and white perch. The report's authors, among them Chris Bonzek and Tom Ihde, identified which forage species showed up in the stomach contents of each of these five. Forage species were deemed "important" food sources if they represented at least five percent by weight in the stomach contents of at least one predator collected during a single ChesMMAP survey trip. "Key" forage species were those that showed up in more than one predator's stomach.

The Predators
and the Prey

To find out who is eating whom in Chesapeake Bay, scientists looked inside the stomachs of predator fish. There they discovered that these five important predators did much of their dining on these 10 species of prey. A large part of their diet was, surprisingly, small invertebrates, animals like mysids and worms that have no backbones.  more. . . .

Overall, the predators had an extensive dining menu, but only ten Bay species were "key." The leading one was a small but mighty fish, the bay anchovy. This species measures only about four inches long but is the most abundant fish in the Chesapeake.

Another prey fish, Atlantic menhaden, widely known to be a staple of the striped bass diet, didn't make the select list of "key" forage species — the other predators didn't favor it as much — but did make the list of "important" species, of which there were also ten.

Although bigger fish were eating smaller fish, a striking finding was that bigger fish were also eating plenty of invertebrates. These small creatures lacking backbones were six of the ten key prey species, the analysis found — animals such as mysids (shrimp-like crustaceans), marine bristle worms (a class called Polychaetes), and mantis shrimp. That abundance was notable because predators more quickly and completely digest soft-bodied invertebrates like worms than they do bony fish, leaving fewer clues in their stomachs. The soft invertebrates may be even more abundant in fish diets than the analysis suggested.

Unexpectedly the ten key forage species also included juvenile fish from three species of Bay predators: Atlantic croaker, spot, and weakfish. These young fish were small enough that they offered easy pickings for bigger, older predators. Juvenile fish abound in the Chesapeake Bay because it is the most important nursery area on the East Coast for these and other Atlantic Ocean species. But this nursery is also a dining hall.

The STAC workshop raised additional questions beyond what predators were eating. How much fish food does the Bay contain overall? Is it enough for the larger predator species? How does the abundance of food change over time?

Some fresh insights came in a 2016 report by fisheries scientists Andre Buchheister and Ed Houde of the Chesapeake Biological Laboratory. Buchheister, a postdoctoral researcher, expanded on studies of fish diets that he had begun at VIMS as a graduate student of Rob Latour's. Buchheister and Houde merged data from ChesMMAP and other sources to create a set of indices estimating abundances over time for different kinds of forage species and predator fish.

Stable Prey,
Declining Predators

Since 2002, the abundance of many of the most-consumed types of prey in the Chesapeake Bay (worms, for example) has remained stable. But several species of predator fish (such as croaker) have declined.  more. . . .

What they found was striking. The populations of many types of forage fish and invertebrates had remained largely stable since ChesMMAP began collecting data about the bigger fish in 2002. But the top predators themselves were eating less of this food during this period. That was because, other than striped bass, most of the other top predators studied had declined in abundance. There were fewer Atlantic croaker, spot, summer flounder, and weakfish in the estuary.

"We're hearing anecdotal observations of anglers around here saying, 'I can't catch any flounder any more. Where are all the flounder?'" Latour says. "That is a scary sort of prospect." Like striped bass, these species are popular among recreational fishers and important players sitting at the apex of the Bay's food web. "When some species start to decline," he says, "it does have cascading effects, albeit it can be difficult for us to measure sometimes. If it goes too far in one direction, you get things out of sync."

Where have the predators gone? The stability of the forage indices may rule out one possible cause — that there is not enough food in the estuary for the bigger fish to eat, Latour says. Other causes might be at work. Latour says one might be climate change. As waters in the Chesapeake Bay and coastal Atlantic Ocean warm, the ranges of these species may be shifting northward as the fish seek cooler waters.

Fisheries scientists may need to consider other effects of a changing climate on the forage species in the Bay and the predators that eat them. Ryan Woodland, also of the Chesapeake Biological Laboratory, has worked with Buchheister, Houde, and Latour to study how populations of forage species vary under a variety of environmental conditions. One finding is that in years when springtime came early to the Chesapeake — when the estuary warmed up relatively early in the year — forage species were affected in different ways. For invertebrates, like worms, an early spring was associated with higher abundances in Bay tributaries. But for forage fish, like Atlantic silverside, the effect was lower abundances in the Bay's mainstem.

Scientists hope that by identifying and exploring interactions among predators, their prey, and environmental conditions, they can provide natural resource managers with useful new tools for managing both predators and prey at sustainable levels.

"If we can pinpoint conditions that are particularly good or particularly bad for forage, then we can also have an idea of when there is going to be a lot of food available for these predators that we love to catch and eat," Woodland says. "The dream is to have this sort of information available to fisheries managers so when they are making the decisions about harvest limits or size limits, they have the information to say, there's going to be a lot of food available for striped bass this summer, so we don't have to worry about it being a poor year for stripers based on food alone."

But if evidence indicates the populations of forage species have declined that year, fisheries managers might decide to compensate by lowering the allowable harvest of a predator like striped bass. That could avoid what might otherwise be a decline in the striper population that might persist into future years. The fisheries managers could add data about forage availability to the other data they now consider — such as how many young stripers hatched recently — to generate more accurate answers to the key question: how many stripers can be safely and sustainably harvested over time without overfishing the population?

Managers have a limited set of other tools to reverse any decrease in the abundance of forage species that might occur in the future. With little exception, most types of the key prey species are not directly regulated. One management option is to increase the acreage of healthy nursery grounds for forage fish, such as underwater grass beds in tidal marshes and creeks; increasing these is also a leading goal of the Chesapeake Bay Watershed Agreement. Information about where prey species are abundant could help managers target the restoration efforts to protect and increase that abundance. This information might also influence decisions about shoreline development. Studies by the Smithsonian Environmental Research Center found that after property owners installed bulkheads to control shoreline erosion, forage abundance in adjacent Bay waters declined.

The recent research findings about predators and forage are helping to support the development of ecosystem-based fisheries management in the estuary, says Bruce Vogt, a scientist with the National Oceanic and Atmospheric Administration who coordinates a Chesapeake Bay Program committee on sustainable fisheries. "I think we've made significant progress in a short period of time," he says. But more work remains. "Our next step is to figure out how to best serve those findings up to managers in a way that they can utilize them."

Finding ways to manage prey species may require more research to puzzle out some remaining mysteries about them.

An important one is to plug gaps in information about the abundance of forage fish. The ChesMMAP trawl net is designed primarily to catch the larger predator fish; smaller prey fish can slip through. Other monitoring programs run by VIMS and the Maryland Department of Natural Resources use different nets designed to capture smaller, forage fish, but collectively these programs do not cover as wide an expanse of the Bay as ChesMMAP does. VIMS expects to collect more extensive data about forage fish starting in 2018 when it launches a new research vessel to replace the Bay Eagle. Unlike its predecessor, this 93-foot vessel will be large enough to deploy two different kinds of trawl nets at a single location, one designed to catch bigger predator fish and another to snare small prey fish.

Another mystery to be solved is how well the forage species themselves are fed. The 2014 STAC report called for a Bay-wide survey to count zooplankton, the tiny crustaceans and other creatures floating in the estuary. These form the foundation of the Bay's food web and provide food that the forage species eat. Such data have not been collected in the Chesapeake Bay since 2002, when funding for a survey that collected zooplankton ended.

Yet another need, cited in the STAC report, is for better sampling of forage species in the Chesapeake's shallow, near-shore waters, which support the underwater grass beds where many forage species live. Neither the Bay Eagle nor its successor can collect fish in depths shallower than about 12 feet. One consequence is that blue crabs, which make up the Bay's largest commercial fishery by value and which frequent the shallows, may be undercounted as a significant source of prey for predator fish.

Unraveling these mysteries requires scientists and resource managers to take the kind of broad view of the Chesapeake Bay espoused under an ecosystem-based fisheries management approach.

"There has been a lot of work on individual components of the forage" in the Chesapeake, says Woodland. His colleague Ed Houde spent years doing seminal studies of the population dynamics of the bay anchovy and Atlantic menhaden, for example. "What no one has really done," Woodland says, "is to take the whole forage base and look at how predators are consuming that. Putting it all together into a coherent idea of what's going on at the level of the ecosystem is relatively new. I think it's really exciting."