Cooperative Agreement for CESU-affiliated Partner with Californian Cooperative Ecosystem Studies Unit

The U.S. Geological Survey Western Ecological Research Center (USGS-WERC) is offering a funding opportunity to a CESU Partner of the Californian Cooperative Ecosystems Studies Unit (CESU) program in the continuing development and advancement of a wildlife immunology research program.

Nearshore marine habitats worldwide are facing unprecedented challenges due to expanded commercial and industrial development, resource extraction and environmental changes, which all have the potential to significantly degrade coastal ecosystems and biological resources. Although nearshore areas in Alaska may have had fewer direct effects due to their remote nature and inaccessibility, they nevertheless are subject to impacts associated with a warming climate and potential effects of oil and gas development, tourism and harvest of marine resources. Alterations associated with increased temperatures and other stressors, have already been noted in Alaska marine waters, and continuing alterations, such as acidification, are anticipated. Commercial and industrial developments in the Alaska nearshore, including oil and gas extraction, are increasing, with the potential to contribute contaminants to the environment that can damage coastal resources. A primary lesson from the 1989 Exxon Valdez oil spill is that low levels of hydrocarbons persisting in the environment can have a long-lasting effect on survival of exposed species.
In recent work, have found differences in gene transcription results between parks and among sites in Alaska, which indicate variation in both large-scale and local environmental conditions. Changing environmental conditions in coastal ecosystems necessitate methods to assess the health of intertidal communities and facilitate management decisions to sustain these resources.
Gene transcription assays will be a valuable technique because they provide early evidence of changes in physiologic status. In the conclusions of our recently published paper, monitoring nearshore ecosystem health using Pacific razor clams (Siliqua patula) as an indicator species (Bowen et al. 2020, PeerJ) we determined that further development of gene transcription methods as well as controlled laboratory exposure studies would improve our capacity to monitor for early signs of physiological impacts in razor clams and their ecosystems due to changing environmental conditions.
USGS-WERC is offering this opportunity to a CESU Partner having the capability to complete, and with demonstrated experience conducting and publishing results, transcriptomic analyses of the Pacific Razor Clam. Through this CESU agreement, the federal and state university partners will cooperate fully in development of a research program that will produce decision support tools and other products for use in nearshore marine ecosystem conservation strategies and management worldwide. The cooperation of the USGS and its CESU partner brings a combination of expertise to address this objective that is greater than that possessed by either partner on its own.
Research Objectives

This research has two distinct elements that will each result in a peer-reviewed publication and data release. All work will provide datasets that USGS and the CESU Partner will collaboratively use to produce peer-reviewed scientific publications. These publications and related products (e.g., data sets and models) will be used by agencies (e.g. USFWS, NPS, CA and AK state and local agencies, and NGOs) to inform their priorities, strategies, and objectives for the management of marine nearshore ecosystems. A final product will be a transcriptome panel that can be used to assess the health of nearshore marine ecosystems worldwide.

Here is a brief description of each of the two work elements to be addressed in this research:
1) Alaska’s Pacific razor clams (Siliqua patula) are important for commercial and personal harvest, and as prey for marine animals. Currently, the largest commercial razor clam fishery in Alaska occurs in west Cook Inlet near Polly Creek and annual harvest averages approximately 300,000 pounds while recreational clam harvests provide a boost to local economies. The state’s largest sport and personal use Pacific razor clam fishery historically occurred along a 50-mile area of beach between the Kasilof and Anchor rivers on the east side of Cook Inlet, where almost one million clams per year were harvested from 1977-2006. However, between 2009 and 2012, the annual harvest was 54% below the long-term mean (1977-2008), indicating ECI was showing dramatic declines. These declines resulted in subsequent restrictions of ECI clamming in 2013 with full closure in 2015. Following this closure, razor clam numbers have not recovered to historical abundances. In contrast, the razor clam fisheries in WCI continue to support a commercial and personal use fishery over the same time frame.

2) One of the limitations of this study was the relatively small number (n=5) of genes included in the transcript panel. This stems from the fact that relatively little is known about the genetic makeup of Pacific razor clams in comparison with other commercially harvested invertebrate species (Bowen et al., 2020). Studies have been performed on the Chinese razor clam (Sinonovacula constricta) identifying genes responding to heavy metals, anthropogenic sound, and bacterial challenge, but no transcription-based studies of the Pacific razor clam were found in the literature prior to initiation of our work. In fact, GenBank®, the National Institutes of Health genetic sequence database, an annotated collection of all publicly available DNA sequences, contains only three genetic sequences for Pacific razor clams, all representing one gene. In addition, a relatively recent transcriptomic study of the Chinese razor clam, found only 9.9% of the 147,669 transcribed sequences had significant matches in GenBank. Nevertheless, the 5 genes used in our study have been shown to respond to stressors in other efforts, both of the Chinese razor clam and other bivalves. However, examination of additional genes or the entire Pacific razor clam transcriptome might reveal differences, consequently leading us to refine our conclusions.