Skip Navigation LinksResearch Areas > Bioassessment > Algal Index of Biotic Integrity

Project: Algal Index of Biotic Integrity for Streams

Background and Objective

Nutrients are the fourth most common cause of stream impairment in Southern California coastal watersheds. Excessive nutrient inputs from agriculture, residential development, and atmospheric deposition, along with reduced riparian vegetation and associated increases in light and temperature, are often associated with macroalgal blooms. Such blooms can impair stream beneficial uses by rendering the in-stream environment inhospitable to biota and/or causing unpleasant aesthetics or odors.

Establishing numeric targets for nutrient levels in streams is complicated by the chemical, physical, and biological interactions that influence eutrophication. Previously, no verified tools evaluated the overall effects of nutrients on stream health in Southern California. However, as primary producers, algae are the biotic community most directly responsive to nutrients. Algal bioindicators therefore have potential for measuring the net effect of nutrients on the ecological health of streams more effectively than other traditional methods. Such algal bioassessment methods have been successfully developed in other parts of the country and world.

A previous pilot project conducted in the San Gabriel River watershed in 2006 sought to determine the feasibility of developing an algal Index of Biotic Integrity (IBI) for Southern California streams by analyzing the relationship between algal assemblages and water quality data. Briefly, the pilot project found that 1) diversity of algal taxa in Southern California appeared to be sufficient to support development of an IBI, 2) Southern California algal taxa exhibited trends in sensitivity and tolerance similar to other regions, and 3) diatom and soft algae taxonomic data tell consistent “stories” about physical habitat and water quality. For both assemblages, there was decreasing diversity overall, and a relative increase in nutrient-tolerant taxa, with increased nutrient concentrations. These findings provided the impetus to undertake a project that would provide the foundation for an algal IBI for Southern California’s coastal watersheds.

The objective of this project was to produce tools to support development of numeric targets for managing nutrient impairment. This involved: 1) compiling a reference data set of algal communities and nutrient levels for Southern California coastal streams, and 2) using the reference dataset to develop a draft algal Index of Biotic Integrity (IBI) using benthic soft algae and diatoms. The IBI will provide an additional water-quality monitoring tool that could serve as an indicator of nutrient impairment in streams.

A diatom film coating on a rock (left). Microscope image of soft algae (right).


This project was initiated in 2007 and completed in 2013.


Methods for this project can be grouped under five major activities:

• Review and select protocols for algae sampling and analysis

The multi-habitat protocol used by the US Environmental Protection Agency (USEPA) Environmental Monitoring and Assessment Program (EMAP) and the targeted habitat approach used by the US Geological Survey National Water Quality Assessment (NAWQA) will be reviewed and tested to determine what is most appropriate for data collection and sample analysis for this project, and whether modifications are necessary.  

• Collect algae, water chemistry, and environmental indicator data

Algae and water chemistry samples will be collected from stream reaches across a gradient of disturbance severity and across multiple coastal watersheds within the southern California Bight. In addition, data on physical and habitat characteristics and key stressor variables will be collected. This data will also be used for a pilot study to assess application of an algal IBI in non-perennial streams. 

• Develop a draft algal Index of Biotic Integrity (IBI)

The dataset from this project will be used to develop a draft IBI based on benthic algal community composition. The diatom component of the draft IBI will be evaluated in conjunction with a team on the Central Coast (headed up by CSU Monterey Bay), in order to assess whether there is ecological justification for use of a single diatom-based IBI in the combined southern California and Central Coast regions. 

• Inform development of nutrient numeric targets for streams using algae

The project dataset will be used to create a conceptual model that relates benthic algae to nutrient levels and relevant physical parameters. Project results will be interpreted in light of draft nutrient numeric endpoints proposed by the State Water Resources Control Board.

• Demonstrate the draft IBI in an ambient survey

As a follow-up to this project, the draft IBI will be used as part of an ambient survey in order to demonstrate its utility in monitoring and relationship to other measures of condition.


Researchers developed algae IBIs based on different combinations of algal assemblages, i.e., those comprised of diatom metrics only, soft algae metrics only, and “hybrids” consisting of a combination of diatom metrics and soft algae metrics. Among the hybrid IBIs, some required the full laboratory protocol for soft algae to generate the types of data necessary for IBI calculation, while some required only a subset of the full protocol: (a) identifying specimens to species level, but not measuring their biovolume; or (b) taking biovolume measurements, but identifying only to genus level or above).

Performance of the different of IBI types was compared using a series of evaluation criteria, such as responsiveness to anthropogenic stress, signal:noise ratio, repeatability of IBI scores among replicate samples, redundancy among metrics, and indifferent to natural gradients. Overall, hybrid IBIs performed best; however, there was no apparent advantage to collecting biovolume information for the soft algae. Hybrid IBIs with only species presence/absence information for the soft algae metrics performed as well as hybrids that included relative biovolumes of soft algal taxa. Single-assemblage IBIs, although inferior to hybrids, performed reasonably well in that they were all able to distinguish between “reference” sites with little anthropogenic influence and highly disturbed sites. Single-assemblage IBIs are also less costly to calculate than hybrids and could be considered suitable for certain applications where high-resolution data may not be crucial, such as routine monitoring.


This project was conducted in collaboration with the University of Colorado at Boulder; California State Universities at San Marcos and Monterey Bay; and University of California, Santa Cruz.


How to use stream algae for bioassessment - January 2012 demonstration for SCCWRP member agencies describing the process of bioassessment using algae and resources for implementation.

Development of an Algal Index of Biotic Integrity for southern California streams (Video) - January 2011 presentation to SCCWRP member agencies describing interpretation of algal community data and summarizing preliminary findings.

Building algal bioassessment capacity for California streams (Video) - January 2010 presentation to SCCWRP member agencies describing research to develop an algal IBI.

For more information on Algal Index of Biotic Integrity, contact Betty Fetscher at (714) 755-3237.
This page was last updated on: 6/25/2014