Mini Exploration of a Salt Marsh

Impacts of sea-level rise on sediment microbial community structure and function in two New England salt marshes, USA

Matt R. Simon, Gregory P. Zogg & Steven E. Travis

DOI 10.1007/s11368-017-1710-8.

Upon Further Investigation

Sitting before me is a computer, keyboard and a mouse. But that’s not all. There is an invisible world here, invisible to the naked eye. Without this invisible world, our world wouldn’t exist. Behold the world of microorganisms.

Microorganisms, or microbes, are lifeforms that can only be seen with the aid of a microscope and include bacteria and archaea. Without life at this level, much of what we know would be in disarray: there would be no oxygen, we’d be incapable of digesting food, and pollution would be more of a nightmare than it already is. Due to the minuscule size of these critters, we have had to develop a fair degree of technological advancements in order to study them. As a result, microbial ecology is relatively young as a field. To date, most ecological studies focus on the literal “big picture” flora and fauna like how bees aid in the pollination of plants; but to get the real story, we must look much more closely, literally.  

Spartina alterniflora confronted by sea water. Source: Wikimedia

Ecosystems & Sea Level Rise

Take salt marshes. With almost daily flooding and draining by tides, they are considered to be a fairly “stressful” environment. Microbes direct the ecosystem by creating habitats suitable for vegetation to grow. Salt marshes must stay above sea-level, which will become increasingly more difficult with climate change. In this study, Simon, Zogg & Travis quantify how soil respiration, a natural microbial activity related to plant decomposition, is influenced by rising sea-levels. Scientists use microbial respiration as indicator for bacterial population size and activity. More activity means greater or faster breakdown of organic matter or dead plants. This activity ultimately lowers a plant’s relative elevation above sea level while photosynthesis and growth increases a plant’s elevation relative to sea level.

How salt marshes and other habitats associated with marine-terrestrial boundaries will be impacted by rising sea level remains an important question. What happens to a salt marsh when active microbial populations decrease? Salt marshes play crucial roles for our coastlines: they provide an extensive habitat for fish and migratory birds, as well as provide flood control and absorb greenhouse gasses. Understanding the impacts of these effects will help land managers take proper precautions to mitigate future effects from natural disturbances, such as sea-level rise.

Salt marsh at high tide. Source:

The Intergovernmental Panel on Climate Change predicts that we might see as much as a 98 cm increase in sea level by 2100. To investigate how microbial communities may react to a gain in sea-level rise, Simon et al collected soil beneath a low-lying grass, Spartina alterniflora, from two salt marshes in New England. In the lab, they created a “pseudo-marsh” with an indoor flow-through seawater system mimicking the tidal range of both present day and future heights. They then compared microbial communities and respiration rates.


Researchers identify bacterial species by extracting soil, but of particular interest is not just the mud: it’s the DNA of the microorganisms they care about and want to extract. DNA, found in every living organism, has pieces that are specific to each organism. Researchers commonly use a piece called 16S ribosomal RNA. This stretch of information is almost like a fingerprint for every species of bacteria and archaea; each species’ sequence is unique. Researchers are putting microbial puzzle pieces together to characterize microbial communities individual soils of salt marshes, relating local natural processes to their microbial communities in order to make future inferences about the conditions of habitats.

With an elevated sea-level of 40 cm, the activity of the microbial community in the soil was reduced by 24%: the microbes are breaking down less organic material. This pattern has also been seen in other salt marsh systems along the East Coast (Miller et al 2001; Nyman and Delaune 1991).  As conditions shift from well-aerated to inundated, the soil environment becomes more stressful for aerobic microbes, possibly explaining these trends in microbial activity.

The two sites in New England also displayed some interesting differences. The site located in Massachusetts had a less diverse microbial community compared to the site in New Hampshire. A consistent pattern was observed: as the level of water was increased, the microbial population decreased and the respiration rates were reduced. The Massachusetts site’s microbial community was less diverse and had lower activity than New Hampshire. This suggests that as water level increased, the breakdown of dead and decaying vegetation slowed down. The data may therefore indicate that less diverse microbial communities may have a harder time responding to change.

Swampscott River, Newfields, NH. Source: Wikimedia.


As water levels increase in salt marshes, their breakdown of plant matter slows. This may initially benefit salt marshes because less decomposition means a higher elevation above the water for plants. However, the consequences in the long-run are uncertain. As more research is conducted on microbial species in relation to plants and sea-level rise, we can better characterize shifts in ecosystems and provide critical understanding for preserving important and dynamic habitats like the salt marsh from the effects climate change.


Miller WD, Neubauer SC, Anderson IC (2001) Effects of sea level induced disturbances on high salt marsh metabolism. Estuaries 24:357–367.

Nyman JA, DeLaune RD (1991) CO2 emission and soil Eh responses to different hydrological conditions in fresh, brackish, and saline marsh soils. Limnol Oceanogr 36:1406–1414.


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Aidan Barry

I am truly fascinated by our ever-changing world, from ecosystems to the interstitial cracks. I'm currently earning my Master's in Natural Resources from the University of Connecticut. My research is focused on how sea-level rise and restoration strategies alter carbon cycling and microbial communities in salt marshes. When I'm not in the lab or covered in marsh muck, there's a good chance I'm down at the beach surfing, up in the mountains backpacking, or performing music somewhere in between. Instagram: aidanbarry94

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