Using Spectral Imaging to Map Vital Mudflat Microbial Life in San Francisco Bay
In newly published research, USGS scientists mapped ecologically vital microbial biofilm communities that thrive on intertidal mudflats—using remote sensing technology to characterize their distribution, composition, and nutritional value.
Though often overlooked, these slimy microbial mats are essential components of estuarine ecosystems. They play a critical role in nutrient cycling and serve as a major food source for migratory shorebirds. Some species, such as the Western sandpiper (which winters along coasts across the Americas and breeds in northern Alaska), may consume up to 20 percent of their body weight in biofilm per hour when fueling up for migration.
Because biofilm communities are thin, patchy, and located on soft, unstable substrate, they are difficult to study directly. To get around this, researchers used spectroscopy—a technique that measures how different materials reflect light across a wide range of wavelengths—to study biofilms from afar. Focusing on the southern San Francisco Bay, California, the team used high-resolution field spectrometers, airborne imaging tools, and satellite data to detect and analyze these biofilms.
The team first developed a new index using field-based HySpex spectrometers capable of detecting changes in pigment signatures at a resolution of five millimeters. These pigments—unique to different types of microorganisms such as diatoms, cyanobacteria, and chlorophytes—act like spectral fingerprints, allowing scientists to distinguish among microbial groups.
Then, using data from NASA’s AVIRIS-NG airborne imaging spectrometer (which scans at a 3.7-meter spatial resolution), the researchers mapped the abundance and nutritional profile of the biofilms, including carbohydrates, lipids, and total organic carbon.
The team was able to map not only where biofilms are present, but what types of microorganisms dominate them and how much nutritional value they contain. They found that diatom-dominated biofilms—a preferred food for Western sandpipers and other small shorebirds during migration—had two to four times higher concentrations of these nutritional markers than biofilms dominated by cyanobacteria or chlorophytes.
“This gives us, for the first time, a landscape-scale picture of the quality and availability of food for migratory birds,” said the researchers. The maps will help managers understand how food resources for wildlife shift across time and space.
Beyond wildlife ecology, the technique offers a window into how intertidal biofilms influence carbon and nutrient cycles in estuaries—key processes in climate regulation and water quality. Biofilm also contributes to the stability of mudflats by holding sediment in place, reducing erosion and turbidity.
This novel remote sensing approach could significantly improve how scientists monitor these biologically rich but difficult-to-access habitats. It also highlights the benefits of combining field-based and remote-sensing data to better characterize coastal ecosystems.
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