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Predicting the Impact of Billion Oysters on Microbially-Driven Biogeochemical Cycling in New York City Waterways

$306
Pledged
4%
Funded
$10,000
Goal
14
Days Left
  • $306
    pledged
  • 4%
    funded
  • 14
    days left

About This Project

This pilot project by Genspace, Billion Oyster Project, and the mGAMUT lab applies metagenomic and metatranscriptomic profiling to study microbial communities along our local oyster reef at Bush Terminal Park. The goal is to observe changes in these communities' functional capacity and taxonomic profiles due to oyster presence, and establish infrastructure for community-led environmental DNA analysis of local waterways.

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What is the context of this research?

The Billion Oyster Project is a combined habitat restoration effort, water quality monitoring program, community engagement partnership, and climate resiliency infrastructure project that aims to rebuild the once-flourishing oyster reefs throughout NYC’s waterways. Efforts are already well underway to achieve their goal of restoring one billion oysters in New York Harbor by 2035, with 18 active community-supported and community-built oyster reefs. One goal of the Billion Oyster Project is to understand how oysters impact water quality, with the possibility that they may reduce the population of microbial species that are harmful to humans (e.g., those causing harmful algae blooms). Yet, we do not know how the addition of so many oysters might impact local microbial communities.

What is the significance of this project?

The addition of one billion filter feeders to the ecosystem is sure to restructure the local microbial community in more ways than the removal of harmful organisms. Bivalve populations exert strong top-down control on microbial communities via predation and simultaneously redirect nutrients back to these communities through their excretions which are in-turn consumed by microbes. Understanding these processes is critical to assessing how oysters might shape local greenhouse gas production and carbon storage rates, because microbial communities drive aquatic carbon cycles. In short, it is difficult to predict how the oyster reef restoration around New York Harbor will impact regional biogeochemical cycling and carbon storage.

What are the goals of the project?

The goal is to observe changes in the aquatic microbial communities' functional capacity and taxonomic profiles due to oyster presence then incorporate these insights directly into microbially-aware biogeochemical modeling frameworks. This will allow us to estimate the impacts of future oyster reef-building efforts on local biogeochemical cycles, greenhouse gas production, and carbon storage. As a pilot project, our goal is to run this experiment using water samples from the Bush Terminal Park oyster reefs and establish the infrastructure workflows for future community-led environmental DNA analysis of local waterways.

Budget

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The waders and personal flotation device would be used by project members for entering the oyster reefs and its vicinity for the sample collection. The membrane filter, sampling bottles and cooler will be used for collecting and transporting the samples from the Bush Terminal Park reef to Genspace which are both located in Sunset Park, New York.

The DNeasy PowerWater Kit, Filter Tower, RNA Prep Kit, and cDNA Reverse Transcription Kit will be used for extracting DNA and cDNA from the 150 collected water samples over three months.

For sequencing costs, we plan to use the Illumina Mini-seq at Genspace for sequencing a subset of the samples as part of a test run, but we also plan to apply for grants like the Department of Energy's Community Science Program: https://jgi.doe.gov/user-progr... for more comprehensive shotgun metagenomics and transcriptomics sequencing.

Endorsed by

This is a much needed study to understand the effect of reintroduced oysters on the microbial community, the key to our waterways' health. I am excited about this team of researchers which has a valuable breadth of metagenomic, oyster, and NYC water ecosystem knowledge through their combined expertise. I also want to highlight the importance of the genetic analyses conducted at a community biology lab which can serve as a model for similar research of this caliber to be done in a molecular science space dedicated to being accessible to all.
The study of metagenomics and metatranscriptomics would be tremendously helpful in advancing our understanding of local waterways and their microbial communities. Bringing this research forward as part of a community biology lab can show that it is possible (and desirable) to democratize the infrastructure for this kind of important research

Project Timeline

First, we will conduct monthly water sampling and DNA extraction at Bush Terminal Park and Genspace. Our reef has a unique feature where during a low tide, the reef is isolated as a separate lagoon from the river. Hence, we will prioritize spatial resolution over time resolution which would also give us scheduling flexibility.

Next, we will focus on sequencing, data analysis, and modeling with support from the mGamut Lab.

May 27, 2024

Project Launched

Jun 30, 2024

Complete a trial of Water Sampling, RNA and DNA Extraction

Nov 30, 2024

Collect and extract DNA and RNA, and produce cDNA from RNA, from 150 water samples

Dec 31, 2024

Acquire additional funding and sequence collected DNA

Mar 31, 2025

Data Analysis and Modeling

Meet the Team

Sally Kong
Sally Kong

Affiliates

Genspace
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Jackie Lee Weissman
Jackie Lee Weissman
Assistant Professor

Affiliates

Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
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Casey Lardner
Casey Lardner
Lab & Operations Manager

Affiliates

Genspace
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Tanasia Swift
Tanasia Swift
Field Station Program Manager

Affiliates

Billion Oyster Project
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Team Bio

Our interdisciplinary team from the Billion Oyster Project, Genspace, and the mGAMUT lab at Stony Brook University combines a wealth of expertise in environmental science, genomics, and software engineering. We are united by our deep commitment to engaging and educating local communities, fostering a greater understanding of ecosystem dynamics, and making scientific research accessible.

Sally Kong

Sally is a software engineer, artist, and educator based in Brooklyn, NY. After studying computer science and robotics, she has built automation pipelines and artist tools for 3D animated feature films and games at Disney’s Blue Sky Studios, Netflix, and Rockstar Games. She has been an active member of Genspace since 2022 as part of the Engineered Matter Labs team, and is also a global teaching assistant for MIT Media Lab’s synthetic biology course, "How To Grow Almost Anything."

Jackie Lee Weissman

Jackie Lee “JL” Weissman (they/she) leads the Microbial Genomes And Metagenomes to Unravel Traits (mGAMUT) at Stony Brook University. Her research examines how microbes survive and thrive across diverse environments. She develops new tools to infer what microbes are doing and can do from DNA sequences captured directly from the environment (“metagenomes”), aiming to improve the representation of microbially-mediated biogeochemical cycles in global climate models. She believes everyone, with supportive mentorship, can become a highly-capable computational biologist, and loves to show students how a little coding can go a long way.

Previously, JL served as the inaugural Director for Proposal Development at the City College of New York, where they managed large, interdisciplinary efforts to bring center-level funding to the college and trained early-career researchers in grantmaking. They maintain research affiliations in biology at CCNY and the University of Southern California and have taught at The Cooper Union School of Art. Before returning to New York, they were faculty at Chapman University, where they ran a computational biology research lab, taught, and developed initiatives to improve mentorship at the college level.

Casey Lardner

Casey Lardner (she/her) is the Lab & Operations Manager at Genspace, the world's first community biology lab. She holds a Ph.D. in Neuroscience from the Icahn School of Medicine at Mount Sinai and completed postdoctoral research at Columbia University. Building on a background in ecology and evolutionary biology, much of her research used next-generation sequencing in mice and wild, urban rats to model and understand the human brain. As a graduate student, she co-directed an outreach group called “MINDS” and produced a science storytelling show called Studying the Brain. After her postdoc, she pursued full-time science communication and informal science education as a program coordinator in the Neuroscience Institute at NYU Langone. She is the president of BraiNY, a regional organization of the Society for Neuroscience in NYC and is enamored with all brains and minds – whether they belong to mice, pizza rats, people, or other living things.

Tanasia Swift

Tanasia Swift, Field Stations Program Manager, oversees the Field Station Program which includes 9 active sites around New York City. Tanasia holds a B.A. in Environmental Studies and is a Waterfront Edge Design Guidelines (WEDG) professional. Tanasia joined Billion Oyster Project in 2017 after 4 years of working as a program manager for non-profit youth programs in Brooklyn, NY. She manages community connections, leads in the development of field stations, and supervises the development of outdoor programming at each Field Station. Her commitment to NYC communities and climate justice is a driving force in her role. In addition to her work at Billion Oyster Project, Tanasia a member of Meridian Institute’s Diversity Equity and Inclusion Aquaculture Community of Practice, a Core Member at Superhero Clubhouse, a New York-based environmental theater organization, and a former Ambassador for Girls That Scuba, the largest community of women divers. Her work has been featured in the local press.

Lab Notes

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