What can 100 years of mud tell us?

REFERENCE: Capo, E., Debroas, D., Arnaud, F., Perga, M.-E., Chardon, C. and Domaizon, I. (2017), Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming. Environ Microbiol, 19: 2873–2892. doi:10.1111/1462-2920.13815

Background ~ Studying mud

It turns out mud can tell us a whole lot about environmental change. The field of paleolimnology is dedicated to retrieving cores of mud from lakes to study the history of environmental change. Why do we look at lakes? They are depressions on the landscape that collect all sorts of useful information from atmospheric deposition to watershed inputs.

One significant archive that lakes contain is the remains of the biota that existed throughout the history of the lake. How do we access this archive of chemical and biological material stored at the bottom of lakes? Scientists core these sediments using a variety of methods and use the contents of the mud to answer questions about the lake and the environment surrounding the lake. These questions are usually addressed using data from proxy sources. A proxy is a chemical or biological material that reconstructs a past process like productivity or a physical parameter like temperature. These proxies can also be explored to determine trends and patterns in the biota’s response to change. In this article, scientists used sedimentary DNA from core materials to determine how microorganisms respond to rising temperatures and changes in levels of phosphorus, a nutrient that can lead to eutrophication.

Sediment Core
Cores of mud like this were obtained by Capo and others to analyze the DNA remains of microbial communities. Source: NOAA Public Domain Library. Credit: Courtesy of Officers and Crew of NOAA Ship PISCES; Collection of Commander Jeremy Adams, NOAA Corps. Licensing: Attribution 2.0 Generic
Research ~ The DNA of dead microscopic organisms

The scientists spearheading this study, Capo and others, looked at two different lakes in the French Alps – Lake Annecy and Lake Bourget. Phosphorus pollution in the mid-20th century from industrial and domestic sources impacted each of these lakes. However, the lakes were impacted differently – Lake Annecy experienced moderate increases in phosphorus, while Lake Bourget had more dramatic increases in phosphorus. Since that time, both lakes have recovered and now have low levels of nutrients in their water. In addition, these lakes have also experienced rising temperatures from climate change. These environmental changes made both lakes compelling sites to test how eukaryotic microorganisms respond to change.

The only issue is that some microorganisms do not leave behind any discernible morphological remains, which makes them difficult to study using paleolimnology. However, DNA – the building blocks of life – can often persist in sedimentary material and reveal the identity of the organisms buried in the mud. In this study, Capo and colleagues used this sedimentary DNA to get genetic information on thousands of types of microorganisms.

Impact ~ Two drivers of change

What did they find? Both phosphorus and the warming climate affected the composition of microbial eukaryotes in the studied lakes. The investigators found that phosphorus increased richness (the number of species) to a point, but if phosphorus kept increasing past a certain point (more than fifteen micrograms per liter), that trend reversed. In addition, Capo and the research team found that a certain type of microorganism, the ciliates, increased in number as phosphorus increases, which suggests that they might be a good indicator of past eutrophication.

The ciliate Paramecium. The authors found that ciliate increased (% of reads) with higher levels of phosphorus, possibly as a result of having more prey during eutrophic periods. Source: Originally uploaded to the English Wikipedia, where it was made by Barfooz. Licensing: Creative Commons Attribution-Share Alike 3.0 Unported

The results of this study also show that after disturbance (increased phosphorus and eutrophication) the lakes did not have the same microbial community as they did before the disturbance. This is an interesting finding because it shows that even if a system has recovered from a previous disturbance, the microbial community may have a different structure and composition. The authors theorize that this may be due to climate warming, which also affects the composition of microbial communities. From the early 80s to the present (i.e., the period of climate warming), the authors found an increased presence, both in type and number, of Dinophyceae (a class of dinoflagellates) in both lakes and Chrysophyceae (golden algae) in Lake Bourget. Further, they found that the lakes had different responses to warming, indicating that different levels of phosphorus inputs in the past may have led to different responses to climate change. This is an interesting finding considering that many lakes are currently, or have previously, been impacted by eutrophication, and rising temperatures are affecting lakes globally.

Research in paleolimnology and paleoecology has been fundamental in unlocking the history of past environmental change, and this research shows how recently developed tools like sedimentary DNA analysis will aid in these efforts. Ultimately, understanding how microorganisms respond to past environmental change is essential in forecasting how ecosystems will respond to current changes, such as warming climate.

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Trisha Spanbauer

I am an NSF postdoctoral fellow in the Department of Integrative Biology at the University of Texas at Austin. My research interests are primarily on how the environment shapes communities and populations of microorganisms over a variety of timescales. I take an interdisciplinary approach, fusing paleoecological methods with molecular ecology.

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