BU team unveils Nebraska Salt Marsh microbiome

You may not realize that, over 100 million years ago, Nebraska was covered by a large sea. This covered an estimated 20,000 acres, but now all that is left is salt marshes that are widespread around the state.

Sampling sites at the Eastern NE Salt Marshes.

These salt marshes are part of a rare wetland type that occurs in the Sandhills, the North Platte Valley and the valley of the Salt Creek and Little Salt creek. These saline wetlands are in danger of disappearing and several conservation efforts are ongoing to preserve this unique ecosystem.

Restoration and conservation efforts of native ecosystems for the most part focus on the insect and plant community, however the underlying microbial community is crucial to any preservation of marsh vegetation. Little is known about the bacteria and nutrient metabolism that occurs in these inland salt marshes, that are thousands of miles away from any coast, and have not been part of a larger saline body of water for apparently millions of years.

Microbes are responsible for cycling and balancing the nutrients in any environmental ecosystem. So if we try to study and preserve these unique wetlands, we should start at the core, and look at what microorganisms are present and how they metabolize nutrients” says Dr. John Kyndt, who led the current research effort.

The BU team set out to investigate the algal and bacterial composition (the so-called ‘microbiome’) of these Salt Marshes. Samples were taken from the Salt Creek marshes near Lincoln last fall and analyzed in the BU labs. Biology undergraduate student Sierra Athen extracted DNA and used Illumina sequencing to produce the bacterial signatures. Together with BU employee Shivanghi Dubey, they used bioinformatic analyses to identify and compare the algae and bacteria in these samples. The results were recently published in the journal Life:


“These marshes are one of the only places in the United States where the naturally occurring water is saline. Realizing that this study could help in conservation of these endangered salt marches was not only motivating but also quite intriguing”, says Shivangi Dubey.

The team found that all these bacteria are well adapted to the high saline and alkaline conditions of the marshes, but some rare bacteria are present as well. For example, Rubribacterium was previously only isolated from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present in the Nebraska Salt Marsh samples.

Microbial sulfur metabolism at the NE Salt Marsh ecosystem.

The microbial ecosystem appears to be well-balanced as far as sulfur and other nutrients, nevertheless, urban development, agricultural runoff, and the growth of invasive plant species are some of the current threats to maintaining these vital ecosystems. This current study establishes a good baseline for further studies on microbiological diversity, nutrient cycling, and ecological impacts in this locally important watershed.

These land-locked saltmarshes are a relic of ancient oceans and, in some way, studying these salty microbes that live there, takes you back to the last ages of dinosaurs, which can be quite fascinating”, says Dr. Kyndt.


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