Multiscale comparison of hyperspectral reflectance from periphyton in three Oregon rivers used for municipal supply

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By Oregon Water Science Center May 10, 2023

In this study, USGS scientists from multiple centers used advanced hyperspectral imaging techniques to advance monitoring of attached benthic algae (periphyton) in Cascade Range rivers used for municipal water supply. Periphyton are naturally occurring, but excess growth can harm ecosystems and degrade raw and treated drinking water quality. In these rivers, periphyton contain cyanobacteria that produce multiple cyanotoxins including microcystins, anatoxins, cylindrospermopsins, and saxitoxins (Carpenter, 2023). Improved tracking of periphyton helps our understanding of annual and seasonal variations in algal conditions, informs drinking water treatment and fisheries management, and provides a tool for public health officials to track and anticipate algae blooms.

Many Oregonians likely have memories of carefully slipping across algae covered rocks while exploring local rivers. Benthic algae live on hard substrate, coating rocks and making for some tricky footing. They are a natural and important part of aquatic food webs, but excess growths foul water quality, harm aquatic life, and threatens the quality of drinking water.

Algae grows by photosynthesis, making sugars from sunlight energy, water, and carbon dioxide. The decline in carbon dioxide during the day causes pH to rise, and releases oxygen to the water. At sundown, photosynthesis stops and algae respire the stored sugars causing pH to drop back down, and oxygen declines. High biomass of periphyton can result in large fluctuations in pH and dissolved oxygen, from super-saturated to well undersaturated by the early morning hours, after a night of darkness. The daily extremes in pH sometimes exceed 8.5 standard pH units, the state standards set to protect aquatic life.

Black handheld hyperspectral sensor seen from the side as it plunges underwater to get data from the river bed. — ASD handheld hyperspectral sensor plunges underwater to get hyperspectral signature data from algae on the river bed. It's important to get data above and below water to account for the spectral signature of water.

Benthic algae may also harbor cyanobacteria that produce cyanotoxins, which can cause serious health effects in humans, dogs, and other animals. When large volumes of algae die and detach during “sloughing” events, it leads to episodes of poor water quality, reducing water clarity as algae move downstream. Algae is mostly organic carbon, so when it moves downstream in the flow during sloughing events it increases carbon in raw water entering drinking water treatment plants. These events may degrade drinking water through production of chloroform and other disinfection byproducts that are harmful to human health. They form when organic carbon in raw water reacts with chlorine during treatment. Algae may also impart tastes and odors, or cyanotoxins in drinking water supplies. Cyanotoxins are routinely monitored by the State of Oregon Department of Environmental Quality in water supplies affected by harmful algae blooms (HABs).

One scientist holds a river rock, another uses a handheld camera-like spectrometer to get color spectrum data from the rock. — Scientists use an ASD handheld spectrometer to gather color spectrum data from algae on a river cobble above water.

To identify and manage these problem situations, resource managers and scientists need advanced and efficient methods to detect algae as it’s growing and when it becomes entrained into the water column and moves toward drinking water intakes.

To identify and quantify benthic algae requires extensive training and expertise, and collection and analysis of samples can be labor intensive and costly. Also, many large rivers that are drinking water sources are difficult to wade across, creating a challenge for getting representative algae samples. Hyperspectral imagery data is an alternative way to monitor algae using remote sensing, including handheld sensors, drones, airplanes, and satellites.

USGS hydrologist uses a laptop to prep a drone for flight. — USGS hydrologist Paul Diaz preps a DJI M600 drone for flight at Clackamas River, Lazy Bend campground.

Hyperspectral imaging captures a wide range of wavelengths for each pixel, whereas typical cameras only include red, blue, and green bands. Light striking each pixel breaks down into many different wavelengths providing more information on the reflective properties of a material. Spectral images from field surveys may be compared to a library of known spectral reflectance signatures obtained with a microscope to identify the types of algae and cyanobacteria in a sample or on a rock. Recent studies in Oregon and elsewhere show promise for this technology to detect cyanobacteria in lakes and reservoirs using their spectral signatures. This study aims to develop a similar reference library for periphyton in rivers draining Oregon’s Cascade Range including the Clackamas, McKenzie, and North Santiam Rivers, which are critical sources of drinking water for 700,000 Willamette Valley residents.

The spectral data and information gleaned can be used to monitor and track the growth and health of algae and cyanobacteria to better understand and manage risks posed by these organisms.

Objectives:

Identify and differentiate major divisions of periphyton (green algae, diatoms, and cyanobacteria) by their hyperspectral reflectance

signatures.

Compare hyperspectral reflectance signatures from different platforms (field spectrometers, hyperspectral sensors mounted to drones, and satellites) to identify the most promising approach for monitoring periphyton in these rivers. Future data collection will include airplane-based multi-band spectra.

Initial Findings:

Our initial results are promising with different reflectance signatures observed for different types of periphyton. Several species of filamentous green algae (Cladophora, Draparnaldia, Spirogyra, Stigeoclonium, Ulothrix, and Zygnema); diatoms in the Cymbellaceae and Epithemiaceae Families (Cymbella, Gompohoneis, and Epithemia); and multiple genera of cyanobacteria (Nostoc, Oscillatoria, and Phormidium) were imaged over the two seasons.

Click images to view some of the periphyton types observed in local rivers

Underwater photo of bright green, long hairy looking green algae clinging to rounded cobbles in the Clackamas River

Sun sparkles on a thin layer of water running over a matt of green and brown cyanobacteria

underwater photo of brown algae coating a rock.

A slimy snot looking mass of stalked diatoms glistens under the water surface.

Hyperspectral monitoring drones can be quickly deployed at targeted sites with excessive periphyton, aided by fixed-wing aircraft with multi- or hyper-spectral sensors. Blooms can progress rapidly, and the ability to get hyperspectral imagery from satellites can be limited by scheduling and cloud cover, and pixel size. The ability to map long river reaches would provide resource managers with information about the extent and health of a bloom, and assist drinking water treatment plant operators plan for, anticipate, and respond to algal blooms.