Coastal Molecular Monitoring

Both wildlife and humans depend on marine coastal habitats and the species that reside there, but these places are experiencing changing environmental conditions and human activity, which could potentially harm coastal resources. In order for state and federal agencies to manage and protect these environments, methods are needed to detect changes in coastal environments over time. The use of indicator species, organisms whose health reflects the condition of the environment they inhabit, is one approach for evaluating the status of nearshore ecosystems.

Dr. Counihan collecting mussels from the inter-tidal zone

Mighty Mussels

Bivalves are useful as indicator species because they concentrate things, such as contaminants, in the water due to their filter feeding method. Mussels and razor clams are also generally sessile, which makes them easy to sample and ensures they are serving as indicators of the environment they were collected from.

Two species were selected for this study in Alaska: bay mussels (Mytilus trossulus) and razor clams (Siliqua patula). Both species inhabit the intertidal zone, but mussels are epifaunal, which means they attach themselves to substrates like rocks, while razor clams are infaunal, which means they live in the sand. Mussels and razor clams are important food resources for terrestrial and marine wildlife, and razor clams are an important economic resource. Razor clams are harvested for commercial and personal use on the west coast of Cook Inlet. A large personal use fishery is also present on the east coast of Cook Inlet, but it has been closed since 2015 due to low population numbers.

A mother bear and her cubs dig for razor clams on the Silver Salmon beach in Lake Clark National Park and Preserve.

Let’s get Molecular!

We chose to use gene transcription and biomarkers to evaluate the health of mussels and razor clams. In a nutshell, an organism is made of cells that produce signals when it encounters something in the environment, whether good or bad. These signals send a message to DNA to make more or less of a particular protein. This results in either an increase or decrease in messenger RNA (mRNA), and gene transcription assays measure these alterations in mRNA levels.

Detecting these early changes in mRNA is an advantage of gene transcription assays, which can provide the earliest evidence an animal is responding to something in their environment. The mRNA is then translated into proteins, and biomarker assays can be used to measure changes in the amount of specific proteins. An advantage of the biomarker assays is that proteins tend to be more stable than mRNA, so they could detect changes that gene transcription assays miss depending on when samples are collected. Figure 1 below provides a visualization of these processes and where gene transcription and biomarker assays play a role.

Figure 1. How a cell responds to a stressor.

What did we learn?

Mussels and clams were collected at three sites each in Lake Clark and Katmai National Parks and Preserves during the summers of 2015 and 2016 (Figure 2). Samples were used in the biomarker and gene transcription assays, and the results provided information on the health of the bivalves and their environments.

Figure 2. Locations of Lake Clark and Katmai National Parks and Preserves in Alaska.

Mussels and razor clams from Lake Clark had a better condition factor, which means they had more soft tissue for their size, had thicker shells, and also produced more calmodulin (CaM) gene transcripts, which is an indicator of growth (Figure 3). These results together indicated Lake Clark mussels and razor clams were in better condition than mussels and razor clams from Katmai, which suggests higher quality or quantity nutrients are available at Lake Clark sites.

Figure 3. Boxplots of condition factor and shell thickness biomarkers and calmodulin (CaM) gene transcription, which are all indicators of growth, in mussels. A lower value for CaM indicates higher levels of gene transcripts.

Bivalves possess immune cells called hemocytes that produce substances, such as hydrogen peroxide, to kill things they engulf, like pathogens. Razor clams from Katmai in 2015 had higher hemocyte counts and hydrogen peroxide production. We also found transcripts of peptidylprolyl isomerase A (PPIA) and ferritin were elevated. Both PPIA and ferritin are transcribed during immune responses (Figure 4). These results suggest something was present in the Katmai environment in 2015 that stimulated immune activity in razor clams.

Figure 4. Boxplot of peptidylprolyl isomerase A (PPIA) gene transcription in razor clams. A lower value for PPIA indicates higher levels of gene transcripts.

Finally, cytochrome P450, a protein that responds to oil and other contaminants, and heat shock proteins (HSP), which respond to stress, were higher at certain sites in Katmai and Lake Clark in 2016. There were no known human sources of contaminants at these sites during that time. However, natural oil seeps are present near these sites and may have caused the elevation of cytochrome P450 and HSPs. The amount of oil released from seeps can vary and is the likely reason an effect was seen in 2016 but not 2015.

Main Takeaways

The results of the gene transcription and biomarker assays provided a lot of information about the health of mussels and razor clams and, subsequently, the environment they inhabit. While results of the gene transcription and biomarker assays were often complementary, there were some differences in results, which were likely the result of varying degradation/stability of proteins and mRNA. This highlights the benefit of using both techniques. The assays were able to detect differences at the local scale (between sites within a park) and at a larger scale (between parks), which is important to determine how widespread an environmental change or influence is.

Most coastal sites in Alaska are remote and logistically difficult to access; therefore, it is valuable that so much information was gained from very small amounts of tissue of these indicator species. Baseline values for gene transcription and biomarkers were established by this project, so that these techniques can be used to continue monitoring the parks for changes. Continued monitoring is important to detect subtle changes that can have major impacts on ecosystems.

Most of the sites, like this one in Lake Clark, can only be accessed by boat or float plane during the summer.

This Paper In A Nutshell post is based on two recently published papers. If you would like to read them for more in-depth information, they are both available for free.

Counihan KL, Bowen L, Ballachey B, Coletti H, Hollmen T, Pister B, Wilson TL. 2019. Physiological and gene transcription assays to assess responses of mussels to environmental changes. PeerJ 7:e7800.

Bowen L, Counihan KL, Ballachey B, Coletti H, Hollmen T, Pister B, Wilson TL. 2020. Monitoring nearshore ecosystem health using Pacific razor clams (Siliqua patula) as an indicator species. PeerJ 8:e8761.

Written by: Dr. Katrina Counihan, ASLC Assistant Research Scientist, COHO Lab Director

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