A new way to understand the Chesapeake Bay’s role in releasing and capturing greenhouse gases
In July 2019 and August 2021, a team of scientists from the University of Maryland Center for Environmental Science (UMCES) spent several days aboard the Chesapeake Bay research vessel Rachel Carson collecting DNA from the Chesapeake Bay, from particles of varying sizes in the water and from sediment on the seafloor. Their goal was to understand how much the Chesapeake Bay is a source of greenhouse gases to atmosphere versus a sink, or container, and how it impacts the Earth’s changing climate.
“This project will give us the most detailed picture yet of who the major microbial groups are in the Chesapeake Bay, where they live in the Bay, and how they are driving important nutrient and carbon cycles in the Bay,” said Assistant Professor Clara Fuchsman.
There is an incomplete understanding of how changing environmental conditions affect the rates of greenhouse gases being captured and released by the Chesapeake Bay, and scientists want to know more. Greenhouse gases in aquatic systems like the Chesapeake Bay are primarily produced and consumed by microbes— bacteria and archaea—but fundamental knowledge about their ecology is lacking. UMCES scientists, together with collaborators from Johns Hopkins University, are examining these microbial communities, from particles in the water column and from the sediments below in the Chesapeake Bay, in a project supported by the Department of Energy’s Joint Genome Institute (DOE-JGI).
DNA samples collected also collected in 2019 and 2021 will be used for a metagenomic sequencing at The Joint Genome to study the key genes and metabolic pathways that are involved in greenhouse gas transformations in the Chesapeake Bay and to map their distribution. The data will become publicly available for other scientists interested in collaborating on this research.
Tiny but mighty
Any organism that requires a microscope to be seen is named a microbe or a microorganism. The key microorganisms in Chesapeake Bay are phytoplankton, bacteria, and archaea. These are the key players in aquatic ecosystems that drive the cycling of nutrients and carbon.
When thinking about bacteria in Chesapeake Bay, we might first think about harmful pathogens, such as a bacterium called Vibrio, which can cause illness in humans and fish. Yet, the vast majority of bacteria in the environment are not harmful and simply make their living by consuming carbon and nutrients.
Archaea are also simple single cells and superficially resemble bacteria, but evolved independently and are metabolically unique. Archaea were first discovered from hot springs and were originally thought to only exist in similarly extreme environments. However, we now know they are plentiful throughout the environment, including the Chesapeake Bay.
Bacteria and archaea together play a dominant role in where and when key greenhouse gases are produced and removed from ecosystems. Methane and nitrous oxide are important and potent greenhouse gases that are produced and consumed in aquatic systems. They become greenhouse gases when they leave the water and enter the atmosphere. Understanding where and when they are produced and consumed is critical for understanding how the Chesapeake functions as a source or sink for greenhouse gases to the atmosphere.
Early environmental microbiology approaches attempted to quantify and identify the activity of bacteria in an ecosystem by culturing all bacteria living in a collected sample. However, it is now known that bacteria and almost all archaea cannot grow under normal laboratory conditions—they resist growing alone isolated in the lab— and these early studies missed the vast majority of microbes from the environment.
Modern techniques to study microbes in the environment include sequencing their DNA. Metagenomics involves sequencing all the DNA collected from a particular sample, as opposed to sequencing a single specific gene. This not only which microbes are present at a particular time and place, but also, based on what genes they carry, helps to identify what these microbes are likely doing in the environment.
“Our understanding of where and when greenhouse gases are produced and consumed in the Chesapeake is poorly understood,” said Sairah Malkin. “We know that specialized archaea and bacteria are the main producers and consumers of the greenhouse gases methane and nitrous oxide, but many fundamental questions remain”
Which bacteria and archaea are the most important for producing and consuming greenhouse gases? Where are these microbes found? How do they interact with each other and with the environment? What else are these microbes capable of doing in the environment?”
Answering these questions will provide a much deeper understanding of greenhouse gas production and consumption in Chesapeake Bay, widely considered a model system for understanding how estuaries around the world function and respond to human-induced influences.