Deep Baltic Microbes Have a Taste for Alcohol and Cannibalism

In the carbon-rich sediments of the Baltic Sea, microbes use a variety of strategies to make a living from different types of organic material that have settled there, including making and consuming alcohol and breaking down proteins from dead cells.

In the last 16,000 years, the bottom of the Baltic Sea experienced good times and bad times. Shifting inputs from rivers and seawater, and advancing and receding glaciers, have affected the quantity and quality of organic matter drifting down to the seafloor. All of these changes are recorded in sediments, creating a “natural laboratory” for studying how microbial communities survive in sediments created during both rich and lean times.

In a new paper in Applied and Environmental Microbiology [1], DCO members report that the carbon cycling in Baltic Sea sediments is more complex and cannibalistic than they had imagined. Deep Life Community members Laura Zinke (University of California Davis, USA), Clemens Glombitza (NASA Ames Research Center, USA), Jordan Bird (Indiana University, Bloomington, USA), Bo Barker Jørgensen (Aarhus University, Denmark), Karen Lloyd (University of Tennessee, Knoxville, USA), Jan Amend (University of Southern California, USA), and Brandi Kiel Reese (Texas A&M University, USA) analyzed DNA and geochemical data from Baltic Sea sediments to see how microbial communities varied, depending on whether they had received organic carbon from marine or terrestrial sources. Regardless of the food source, all communities had a complicated carbon cycle, with microbes fermenting organic compounds to make alcohol and degrading proteins from dead microbes.

“Once carbon is buried in sediments, it doesn’t just stay there,” said Zinke. “There is a really rich diversity of ways that microorganisms can obtain energy.” 

Baltic Map
DNA in sediments from three sites in the Baltic Sea and one in Kattegat reveal complex communities of microbes that are all especially active producers and consumers of alcohol. Credit: Image courtesy of Zinke et al.

The researchers performed sequencing on sediment samples from different depths at three sites in the Baltic Sea and one in Kattegat, a strait that connects the Baltic to the North Sea. Colleagues at Aarhus University previously sequenced DNA from specific sediment layers in cores collected from these locations. Using funding from the DCO Census of Deep Life the researchers performed additional sequencing to cover a wider range of sediment age and salinity. They sequenced metagenomes (all the DNA) to indicate which organisms live in each sediment layer and metatranscriptomes (all the RNA) to investigate how the microbes are behaving. 

As expected, the researchers saw that sediments that formed when the Baltic Sea received inputs from marine sources had more genes for protein metabolism compared to sediments that formed when the sea received inputs from rivers. Ocean water often supports high concentrations of algae in the water column, which leads to sediment layers rich in their proteins. In contrast, sediment layers with terrestrial inputs have lower total organic carbon levels. Microbes in all of these layers carry genes to metabolize carbohydrates, but they have more of them in the marine-influenced layers. 

In all of the sediments, however, the researchers identified numerous genes for breaking down organic matter through multiple types of fermentation. “There are a lot of genes being expressed for alcohol production and consumption,” said Kiel Reese. “That was a surprise for me.” Data from the metatranscriptome, which are all of the genes that microbes have “turned on” in the sample, suggest that these pathways are active, signifying that alcohol could be an underrated component of carbon cycling in deep sediments.

“Another interesting finding,” said Kiel Reese, “was the microbes were able to use necromass,” which is the remains of fellow cells. “They were using the peptides from other microbes as a food source, so they were ‘recycling’ their own in a cannibalistic way.” Taken all together, the findings suggest that there are a variety of ways for microbes to use the organic compounds in the sediments. 

The study also highlights a need for more focused research on fermentation, said Zinke. “We’ve known about fermentation in sediments pretty much as long as we’ve known about microbes in sediments, but it doesn’t get a lot of attention,” said Zinke. “Fermentation is a complex and dynamic process and something that deserves more study in the future as is demonstrated by our findings.” 

IODP Expedition 347
Aboard IODP Expedition 347, researchers pull up sediment cores from the Baltic Sea. Credit: Laura Zinke

 

Sediment Cores
Researchers collected sediment samples from multiple depths within the cores to investigate the microbial communities living in the different layers. Credit: Laura Zinke

Main image: Brandi Kiel Reese records the depth of sediment cores collected from the floor of the Baltic Sea. Credit: Laura Zinke

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