Visiting Researchers

 

The River Project is the only marine science field station in New York City, and as such, the facility as well as the living and preserved specimen collections housed there are vital resources for visiting researchers. The River Project frequently partners with other organizations and researchers to study various elements of the estuary, and conduct cutting-edge marine science research that cannot be carried out anywhere else in New York City. See below for descriptions of some research that is being done in the Wetlab right now!

 

Projects in the lab - Summer 2017

 
A Blue Mussel (Mytilus edulis) attached to a heartbeat sensor.

A Blue Mussel (Mytilus edulis) attached to a heartbeat sensor.

 
Gurr attaching his custom heartbeat sensors.

Gurr attaching his custom heartbeat sensors.

Sam Gurr - Blue Mussel Heartbeats in Response to Stressors

Gurr’s current research at TRP is in partnership with Autodesk, a software company, and is based upon the concept of biosensing for water quality of an urban system.  Digital sensors are widely used with chemical, optical, and acoustic systems for pH, DO, depth, currents, temperature, salinity, chlorophyll, etc. Data from these sensors offer a continuous and high resolution view of our coasts - we now are aware of multiple coupled dynamics and co-occuring stressors that oscillate on a seasonal as well as a daily rhythm.  These conditions are captured as a numerical value by these sensors, but digital sensors alone do not provide a full story.  This is especially true in urban coasts such as New York City where the ramifications of waste water discharge include exposure of PCBs, fecal bacteria, trace metals, pharmaceuticals, etc.  

 

Biosensors are not new to science, but technological innovations are allowing novel approaches that can be deployed both in the lab and in-situ. Organism such as blue mussels are semi-sessile filter feeders not only rely upon a set of optimal environmental conditions, but lack effective mobility to escape conditions that may cause harm; this is why they are a great bio-indicators. We measure cardiac activity and valve gape behavior tiny sensors glues on the outside of the shell.  This is a minimally invasive technique that allows us to receive data on their metabolic and behavioral activity.  We aim to demonstrate that biosensors augment digital sensing in a light that can reflect ecosystem health status for restoring and rehabilitating shellfish populations to local marine habitats around NYC.  

 

Sam Gurr received his MS at Stony Brook University (August 2017) studying the in-situ cardiac activity of bay scallops among bays of Long Island - specially focused on their response to hypoxia. You can learn more at his webpage: http://you.stonybrook.edu/samuelgurr/


Dr. Elizabeth Alter - Creating a Genetic Database for Hudson River Species

Our lab is developing the use of environmental DNA (eDNA) as a highly sensitive, minimally invasive technique for surveying fish biodiversity in the Hudson River and its tributaries. Whereas traditional survey methods such as electrofishing, gillnetting, and visual transects rely on direct observation of species to determine presence, the eDNA methods we are working with infer presence by the detection of species specific DNA fragments found in water samples. This enables us to detect species without having to catch or even see them, which is advantageous for studying rare and elusive species, or habitats where other methods become impractical. Since we collect only water from study sites, our impact on the host ecosystems is kept to a minimum, avoiding the potential mortality often posed by capture based sampling methods.

 

This isn’t to say that we never need to catch or handle fish though. In fact, the most important component of an eDNA survey is a good reference library of DNA barcodes for all fish species we want to be able to detect. Since assembling such a library requires encountering each species at least once in order to extract DNA, and we are interested in many species that are hard to catch, local fish collections like that of The River Project are an invaluable resource to us. Though our current project is focused on the Hudson River, all of the barcodes we produce are submitted to public genetic databases so that they can be used by researchers around the world.

 

We recently completed water sampling from sites along the Hudson River and 11 of its tributaries. The data produced from these samples should provide us with a high resolution snapshot of local fish communities, the contributions to biodiversity made by each tributary, and the extent to which invasive species have colonized the watershed. 

 

Read more about the Alter lab at http://www.fishfiles.org/

 
Students in Dr. Alter's taking samples.

Students in Dr. Alter's taking samples.

 
Fin clipping samples taken from The River Project's specimen collection to be turned into genetic barcodes.

Fin clipping samples taken from The River Project's specimen collection to be turned into genetic barcodes.


A student in Baruch College's College Now program collecting biodeposits from oysters for Dr. Gosnell's study.

A student in Baruch College's College Now program collecting biodeposits from oysters for Dr. Gosnell's study.

Students processing samples in the lab.

Students processing samples in the lab.

Dr. Stephen Gosnell - Impact of Predators on Oyster Biodeposition

My lab has been collaborating with The River Project and Billion Oyster Project on a study focused on how the presence of predators impacts biodeposition in oysters. Oysters feed by filtering plankton from the water, which is important to improving water quality.  Biodeposition also connects pelagic (water) and benthic (sediment) systems as oysters produce biodeposits (poop, to put it scientifically).  These biodeposits may act as fertilizer and increase the rates at which sediment microbes contribute to denitrification, or the removal of available nitrogen to the air.   Denitrification is an important ecosystem service provided by coastal habitats, as excess nitrogen in aquatic systems can lead to algal blooms and resulting low oxygen conditions that can harm other living things.  This is especially true in NY due to the high amounts of nitrogen our waters.  

 

We know from past studies that oysters grow less when they are near predators, so we assume predators impact their feeding.  Changes in oyster feeding could include how much they filter from the water or how they use what they filter, and either of these changes might impact biodeposition quantity and quality and eventually influence denitrification rates.  This summer we're exploring this issue by seeing how previous exposure to predators (oyster drills) interacts with immediate exposure to the predators to influence biodeposition by oysters. Preliminary results indicate oysters biodeposit more in the presence of predators. We plan to continue this work to quantify impacts of predators on oyster filtration rates and denitrification in adjacent sediments to better understand how these species interactions might influence ecosystem services.

 

Read more about Dr. Gosnell's research at http://www.jstephengosnell.com/


Dr. Erika Crispo - Oyster Genetics

In order to understand the dynamics of a population, it is fruitful to study its genes. Where did the individuals in the population come from? What part of the genome is functionally important in one population versus another? Addressing these questions is important to fully understand how we can best restore oysters in the Hudson River estuary. Dr. Erika Crispo and her research team at Pace University are collaborating with The River Project and the Billion Oyster Project to understand the genetics of oysters in our neighborhood. Her research has two main foci: (1) using genetic markers to understand how populations are connected by ‘gene flow’, or movement of genes via interbreeding among populations, and (2) understanding which functional genes are impacted by the environment, potentially identifying ‘stress response’ genes that can be used as indicators of stress.

Her first objective is to determine where naturally-spawned oysters are coming from. This work begins by sampling DNA from oysters from restoration stations and various locations in the harbor. When new recruits are identified at these sites, we can sample DNA from these juvenile oysters to determine whether they were spawned from caged oysters, or whether they are coming from some other parental source – and, more importantly, ‘which’ parental source. This information will help inform oyster restoration managers where to source oysters from and where to plant them to maximize recruitment and build a sustainable wild population.

Her second objective is to understand the functional importance of genes in oysters. DNA is essentially a recipe for making proteins. But even if two individuals share the same ‘recipe’, the protein might be produced in one individual but not in the other. Under what environmental conditions is this so? What influences the control of the DNA recipe (i.e., gene expression) under different environmental conditions? Knowing the answers to these questions is important for understanding how oysters respond to environmental stressors such as elevated temperatures, increased acidity, hypoxia, disease, and predation.

Read more about Dr. Crispo's work at https://www.pace.edu/dyson/sections/meet-the-faculty/faculty-profile?username=ecrispo