Bivalves

How do environmental properties associated with changing land-ocean connections affect bivalve distribution, abundance, physiology, and population connectivity, can eDNA be used to monitor their recruitment?

Hardshell clams and mussels have been a subsistence harvest species for millennia as well as a popular recreational harvest species in the northern Gulf of Alaska region. Dramatic declines of hardshell clams in the region over the past decade have raised concern in Kachemak Bay community members, the Seldovia Village Tribe (SVT), and resource managing agencies, such as Alaska Department of Fish and Game (ADF&G).

Clam success varies across species, size, and life history stages, and depends on past and present environmental exposure. Within the Interface of Change project, researchers will collect data on clam success and environmental conditions. Where available, historical data provided by partners (ADFG and SVT) will supplement our data collection. The goal is to use field and historical data to look for relationships between coastal environmental qualities with the distribution, abundance, biomass, size distribution, and body condition of hardshell clams.

Hypotheses:

1.) Increased turbidity, reduced salinity, and shifts in temperature and nutrient sources will correlate with the distribution, abundance, biomass, size, and body condition of hardshell clams.

2.) Mussels from non-glacierized estuaries will be more resistant and resilient to pulsed, acute shifts to abiotic variables such as salinity, turbidity, temperature, and pH than will cohorts from glacierized watersheds, which will be more tolerant of prolonged, chronic shifts.

3.) Hardshell clam genomes exhibit spatially partitioned selection across the GoA.

4.) Hardshell clam eRNA will reflect transcriptional differences between life-history stages.

Hardshell Clams

Gloved hands hold two clams: a larger one on the left, a smaller, whiter one on the right. — A butter clam, left, and a Pacific littleneck clam, right.

Population Abundance & Physiology

UAF graduate student Hannah Gerrish holds up a butter clam while sampling at the China Poot site in Kachemak Bay.

In effort to better understand why clam populations are declining in Kachemak Bay, a team led by UAF marine biologist Katrin Iken and graduate student Hannah Gerrish is characterizing the physiology, distribution, and abundance of butter clams (Saxidomus gigantea) and Pacific littleneck clams (Leukoma staminea) at beach sites in Kachemak Bay.

They are looking for any correlations between clam physiological data and environmental factors, such as water turbidity and salinity, using aquatic data loggers installed at each site.

In addition, they are consulting historical Alaska Department of Fish & Game records to investigate whether the average clam body size for each species has changed over time, and whether body size can be correlated with any environmental factors.

Female scientists installing equipment on a beach with a boat nearby on the water. — Interface of Change project director Brenda Konar and UAF graduate student Hannah Gerrish install a HOBO data logger at the edge of a beach at their China Poot sampling location in Kachemak Bay. The logger captures a continuous stream of water quality data, which the team compares to clam physiology and population data.

Metabolic Analysis

To examine how environmental properties affect the metabolic health of hardshell clams, UAA environmental chemist Pat Tomco and postdoctoral researcher Monica Brandhuber are comparing the detectable metabolites in harvested clams across sampling sites in Kachemak Bay. In the ASET lab, they are running clam tissue samples through Liquid Chromatography-Mass Spectrometry (LC/MS) equipment.

Clam body parts from samples getting put into foil. — In preparation for metabolomics analysis, each sampled clam is dissected, and its body parts are separated as separate lab samples to be processed through Liquid Chromatography-Mass Spectrometry (LC/MS) lab equipment.

Population Genomic Spatial Variation

Restoring and cultivating clam populations requires a thorough understanding of their population genomic structure. Despite their importance as subsistence species, no studies have previously assembled the genomes of hardshell clam species in Alaska.

UAF fish geneticist Jessica Glass and graduate student Rachel Lekanof hypothesize that hardshell clam genomes vary in accordance with environmental conditions across the Gulf of Alaska.

In partnership with the intertribal Chugach Regional Resources Commission (CRRC) and scientists at the Alutiiq Pride Marine Research Institute, Glass and Lekanof employ high-throughput genomic sequencing to characterize the extent to which gulf populations of butter clams (Saxidomus gigantea) and Pacific littleneck clams (Leukoma staminea) and exhibit genetic connectivity and local adaptation.

Population Life History Stage Detection Using eRNA

Environmental DNA sampling is a technique that allows environmental scientists to detect what species are present in an environment by running tests on a sample of water, or another type of environmental sample. This method offers a powerful approach to characterize biodiversity and distinguish species, even populations of species, across the tree of life.

A student points to a small eDNA vial. — Environmental DNA (eDNA) water samples are processed in a lab setting through several steps: sample filtration, DNA extraction from the sample, PCR amplification, DNA sequencing, data processing and analysis.

Currently, when scientists work with environmental DNA, or eDNA for short, their methods focus primarily on DNA. However, a limitation of eDNA is the inability to differentiate between life history stages of the same species. In the case of fish and shellfish, different life stages include larval, juvenile, adult, and spawning events. Being able to distinguish what life stage is present would provide additional valuable information for science, population management, and cultivation of marine species.

In collaboration with the Alutiiq Pride Marine Research Institute, Jessica Glass and her lab are experimenting with eRNA assays - environmental RNA - to see if we can use eRNA in place of eDNA to distinguish between larval and adult littleneck and butter clams. Because RNA regulates gene expression in organisms which changes over their life history, eRNA may be an effective tool for quantifying juvenile versus adult clams in a population.

Mussels

Mussels are also an important species for harvesting in the Gulf of Alaska, both for subsistence and mariculture. In recent years, mussel populations have become destabilized.

Shelving with plastic totes and a system of PVC piping and wires. — Shelving with 48 replicate experimental plastic totes sitting in plexiglass water baths. Mussels in each experimental tote are exposed to different water conditions, which are controlled independently by Arduino and Raspberry Pi components. The plexiglass baths the totes are contained in are set to different temperatures of water for comparison.

A growing body of research suggests that variable environmental conditions, such as the changing of tides, play an important role in organismal adaptation. UAS marine biologist Julie Schram is leading a team to determine how Pacific blue mussels respond to varying environmental conditions over varying time periods.

To do this, Schram and UAS hydrologists Jason Fellman and Eran Hood are gathering environmental data from intertidal marine and stream water quality sensors deployed in Lynn Canal.

In conjunction with gathering field water quality data, Schram is conducting a series of controlled laboratory experiments that expose mussels to a simulation of natural variation of environmental conditions. The experimental setup will compare mussel response to different combinations of shifts in salinity, pH, turbidity, and temperature over varying periods of time.