"The Scoop" on What We Do

A story map created by Ecology’s Marine Sediment Monitoring Team

Study Design and Goals

Our Puget Sound sediment monitoring uses a random sampling design that allows us to meet our goals of 1) calculating spatial extent estimates of an area (km²) with given sediment conditions, and 2) comparing changes in sediment and benthos condition over time. 

How we collect and analyze our samples

A van Veen grab is lowered to the sea floor, retrieving a double 0.1-m² sample of  surface sediment  and benthos. We scoop off the top 2-3 cm of surface sediment for physical, chemical, and biogeochemical analyses; and sieve an entire grab for benthic invertebrates. Study details are described in the program’s  Quality Assurance Monitoring Plan  (QAMP). 

Physical Habitat

Puget Sound is a complex system with a wide range of habitat types. During our sediment sampling, we encounter everything from silt and clay to coarse gravel. Our station depths vary from 2 meters in shallow, protected bays to over 200 meters in the open Straits.

Characterizing the physical habitat helps explain the distribution of benthic invertebrates, chemical contaminants, and organic material. Changes in the physical habitat are biologically important and are often reflected in the benthic community structure and ecosystem function.

The parameters we measure at our monitoring locations include:

Biogeochemistry

Biogeochemistry, a recent addition to sediment monitoring

Our  biogeochemistry  measures include total carbon (TC), total organic carbon (TOC), total inorganic carbon (TIC), and total nitrogen (TN). Stable isotopes of carbon (δ¹³C) and nitrogen (δ¹⁵N) were added to the monitoring program in 2017 to quantify and distinguish between types and sources of  organic matter . Biogenic silica and sulfides were added in 2018.

Organic matter is an important food source for many benthic species, but when there is too much, its decomposition can deplete valuable oxygen and release toxic by-products such as sulfide and ammonia (Hyland et al., 2005). This results in a visible and often “rotten egg” smelling anoxic mud layer, which is not a friendly place for most benthos to thrive. Benthic communities in these locations are often dominated by opportunistic species that are adapted to survive in stressful conditions (Pearson and Rosenberg, 1977).

The mud in the right-hand photo shows lighter-colored oxygenated sediment layer over the black anoxic sediment layer. You can also see these layers from the hole left behind in the left-hand photo.

The source of the organic matter making it to sediments can be just as important as the amount. Organic matter from marine algae (phytoplankton) tends to be a better-quality food source for benthos, while terrestrially-derived organic matter delivered to Puget Sound from rivers and streams tends to be a poorer-quality food source.

Carbon and nitrogen relationships point to sources of organic matter

Organic matter can have different carbon and nitrogen characteristics, depending on where it originates. For example, algal-derived organic matter has lower ratios of carbon to nitrogen (C:N); higher C:N ratios are associated with land-based vascular plants ( Krishna et al., 2013 ; Brandenberger et al., 2008;  Goñi et al., 2013 ;  Meyers, 1997 ). Higher values of δ¹³C, ranging from -23 to -21, are generally associated with phytoplankton, and values ranging from -30 to -25 are associated with terrestrial plants ( Jumars et al., 2015 ;  Cloern et al., 2002 ;  Simenstad and Wissmar, 1985 ).

Measuring these biogeochemical parameters gives us only a partial picture of the source and accumulation of the organic matter making it to the sediment. The high variability in factors such as seasonality of primary productivity, sediment transport, water column properties, biological processing, etc., can greatly influence the amount, type, and quality of sedimentary organic matter. However, we can identify some general patterns.

Chemical Contamination

Why we monitor chemical contaminants

Chemical contaminants are considered a key  anthropogenic  (human-caused) pressure on the Puget Sound ecosystem. They can be toxic to biota, including  benthic  (bottom-dwelling) invertebrates. Also, contaminants taken up in benthic tissues may bioaccumulate, that is, be concentrated as they move up the food web.

Our suite of contaminants*, most from EPA’s  Priority Pollutant  list, has been measured in sediments collected for our monitoring program. While the majority of stations in Puget Sound did not have elevated levels of these chemicals, the highest concentrations were found in urban bays ( Weakland et al., 2018 ;  Partridge et al., 2018 ). In many bays, contaminant levels have decreased over time, but it is still important to continue monitoring for these chemicals.

*See the full contaminant list on page 63 of our  QAMP .

Evaluating sediment chemistry

We compare contaminant concentrations in our samples to the Washington State  Sediment Quality Standards  (SQS), established to protect benthic communities, as benchmarks. The SQS are concentrations at the threshold of expected adverse effects ( Ecology, 2013 ).

From the individual ratios of measured contaminant concentrations to their respective SQS, we calculate the average, or  mean SQS quotient  (mSQSq).

The mSQSq is used to calculate our  Sediment Chemistry Index  (SCI), which is on a scale of 0-100 scale, with 0 indicating highly contaminated and 100 indicating no contamination by the SQS chemicals ( Long et al., 2006 ;  Dutch et al., 2018 Appendix B-1 ).

The Puget Sound Partnership (PSP) has adopted the SCI as one of the Vital Signs of Puget Sound health, with a target value of 93.3.

01 / 10

Benthic Community

What are benthos and why are they important?

Invertebrates that live in and on sediments are known as  benthos . They are a vital link in the food web, as they are prey items for fish, birds, and marine mammals. Benthos also play a key role in cycling nutrients and gases as they move through, feed, and respire within the sands and muds of Puget Sound. In addition, many benthic species are commercially and culturally important to humans. 

Benthic invertebrates have been harvested by indigenous peoples for centuries. Patrick Braes, Squaxin Island Tribe, harvests manila clams (left) while Quinault Indian Nation tribal member Jayal Billie, with daughter Shaiola, help with the razor clam harvest (right). Photos courtesy of Debbie Ross-Preston, Northwest Indian Fisheries Commission.

Species such as Dungeness crab (left) and geoduck (right) are restaurant favorites in the Pacific Northwest, and an important part of the regional economy. Photos from Wikimedia Commons.

Benthos as biological indicators

Benthos have limited capacity for movement, which makes them vulnerable to natural and human-caused pressures, including chemical contamination, carbon and nutrient loading, and climate change. Benthic communities change in response to multiple shifting environmental conditions, making them excellent biological indicators. ​

The illustration depicts many of the climate- and human-related activities in the Puget Sound watershed that contribute to these pressures, resulting in changing conditions in both  pelagic  and  benthic  habitats. Both water column and sediment-dwelling organisms are affected by these habitat changes.  

We use our  Benthic Index  to track these changes in the benthos by classifying communities as either  adversely affected  or  unaffected  by these pressures.

For further details, visit our " Conceptual Model " story map in this collection.

How we study the benthos

In our monitoring program, benthos are sieved from the sediments, sorted into five major taxa groups, and identified to the lowest possible taxonomic level.

Click on each group below for Flickr photos of these organisms:

To determine how well Puget Sound sediments support life, we then:

Measures of community structure​

Classifying communities using our Benthic Index

We use these measures of community structure, plus the abundance of tolerant and sensitive taxa, to determine whether benthic communities are adversely affected or unaffected.

Adversely affected: Low diversity and dominance by taxa that are tolerant of disturbed conditions, regardless of abundance.

Unaffected: High diversity and lots of sensitive taxa, regardless of abundance.

Classifying benthic organisms using Ecological Group

An additional tool for assessing the health of the benthic community is the Multivariate AZTI Marine Biotic Index (M-AMBI). M-AMBI is widely used for assessing the ecological quality of marine and estuarine environments based on benthic (bottom-dwelling) macroinvertebrates. It integrates the AZTI Marine Biotic Index (AMBI) with metrics of species richness and diversity. These three metrics are combined using multivariate statistical techniques to produce the M-AMBI score.

Components of M-AMBI

  1. Species Richness: This refers to the number of different species present. Higher species richness typically indicates a healthier ecosystem.
  2. Shannon-Wiener Diversity Index (H'): This index measures the diversity within a community, considering both the number of species and the evenness of their abundances.
  3. AZTI Marine Biotic Index (AMBI): This index classifies species into five ecological groups (EGs) based on their sensitivity to environmental stress (Borja et al., 2000; Borja and Muxika, 2005; Sigovini et al., 2013):
  • EG1: Highly sensitive species: These species are very sensitive to organic enrichment and low oxygen levels. They are typically found in more pristine environments.
  • EG2: Sensitive species: Species in this group are generally tolerant of mild organic pollution but are still sensitive to high levels of disturbance.
  • EG3: Tolerant species: These species can tolerate higher levels of organic enrichment and low oxygen conditions.
  • EG4: Opportunistic species: These species can rapidly colonize environments with high levels of organic pollution and low oxygen levels. They have high reproductive rates and short life cycles and often dominate heavily disturbed environments.
  • EG5: Very tolerant species: These species are very resilient to environmental stressors. They are highly tolerant to organic enrichment and oxygen depletion and are often found in heavily polluted environments.

M-AMBI Score interpretation

  • High M-AMBI Score: Indicates good ecological quality with a diverse and healthy benthic community.
  • Low M-AMBI Score: Suggests poor ecological quality, often due to environmental stressors like pollution or habitat degradation.

M-AMBI Calibration for the Marine Sediment Monitoring Program (MSMP)

The condition categories utilized by the MSMP were determined through the analysis of species richness, AMBI, and H' scores from all available benthic community data dating back to 1989. The M-AMBI condition categories were then compared to the existing Sediment Benthic Index (SBI) categories to ensure they accurately reflect the ecological quality. Of the 1662 samples assessed with both the SBI and M-AMBI, 1610 (96.9%) had consistent classification of benthic community condition.

Measuring biomass: size matters

Biomass and size of benthic organisms can provide valuable information on:

  • Stability of benthic communities over time
  • Size structure not captured by abundance data
  • Effects of stressors on size and development of individual organisms

Organisms are separated into five species-specific size classes based on length: small, medium, large, x-large, and megafauna. They are then assigned wet-weight estimates.  Megafaunal  organisms (those weighing > 2 g) are analyzed separately and excluded from the results shown because their large mass has the potential to skew the dataset.  

Note: Biomass estimates are averages of size-specific weights of reference specimens for each taxon. These averages are continually updated with new weight data for infrequently occurring taxa and more data for common taxa, so the biomass estimates will change slightly over time as more accurate estimates are generated. 

Biomass estimates can help characterize benthic communities

Let's add biomass to our abundance and diversity graphic. We can use abundance and biomass together to see the patterns that characterize a healthy benthic community. Like abundance, the biomass at adversely affected sites is generally driven by just a few stress-tolerant taxa, whereas unaffected sites have diverse communities of many smaller individuals. 

  • Adversely affected: Fewer types of larger, stress-tolerant animals; or high biomass per animal (= larger average body size).
  • Unaffected: Higher numbers of many types of smaller animals; or low biomass per animal (= smaller average body size).

But isn’t high benthic biomass a good thing?

You might think that high biomass would be an indicator of a healthy community, but that is not always the case. The taxa that thrive at adversely affected stations may be better adapted to stressful conditions, giving them the opportunity to grow larger as they out-compete more sensitive taxa for resources.

The graph on the right shows the distribution of average body size and taxa richness of benthos collected throughout Puget Sound. It includes all stations where biomass has been estimated to date (2016-2018) for Puget Sound and its urban bays. A clear inverse relationship exists between average body size (biomass ÷ abundance) and taxa richness, with most adversely affected stations having larger animals and smaller numbers of taxa.

    Functional feeding guilds, another way to look at the benthos

    Functional feeding guilds are  trophic  categories that integrate information on how, where, and what benthos eat. We classify benthos by feeding guilds as defined by  Macdonald et al., 2010  and  2012 . These data, examined along with the other variables we measure, may help us interpret their role in and influence on the sediments they inhabit.

    See our results

    Visit our results story maps for our latest Urban Bays and Puget Sound findings!

     

    The mud in the right-hand photo shows lighter-colored oxygenated sediment layer over the black anoxic sediment layer. You can also see these layers from the hole left behind in the left-hand photo.

    Benthic invertebrates have been harvested by indigenous peoples for centuries. Patrick Braes, Squaxin Island Tribe, harvests manila clams (left) while Quinault Indian Nation tribal member Jayal Billie, with daughter Shaiola, help with the razor clam harvest (right). Photos courtesy of Debbie Ross-Preston, Northwest Indian Fisheries Commission.

    Species such as Dungeness crab (left) and geoduck (right) are restaurant favorites in the Pacific Northwest, and an important part of the regional economy. Photos from Wikimedia Commons.