Seasonal Variations of the Nebraska Salt Marsh Microbiome: Environmental Impact, Antibiotic Resistance, and Unique Species

The Nebraska Salt Marshes are unique inland saltwater ecosystems, and this exploratory study is aimed at understanding the microbial composition and diversity that is providing the underlying support for these ecosystems. The microbiome shows both temporal and spatial variations that are concurrent with seasonal variations in salinity, temperature, and vegetation growth. Whole genome metagenomics analysis showed the predominance of purple non-sulfur bacteria in each season, indicating their importance in the marsh ecosystem. The fall season showed the highest microbial diversity and coincided with the highest levels of antimicrobial resistance markers to a variety of natural and synthetic antibiotics. In addition to the metagenomics approach, we also isolated and sequenced several unique species, most of them belonging to what appear to be new species of purple non-sulfur or purple sulfur bacteria. Both the metagenomics analysis and isolated species indicate that the nitrogen and sulfur cycling is well balanced in these marshes by a high relative abundance of purple bacteria. Noteworthy is the isolation of a new strain of <i>Vibrio cholerae</i>, which is a known human intestinal pathogen, that was predominantly present in the fall samples carrying several antibiotic resistance markers. Overall, the Nebraska salt marsh microbiome showcases both seasonal variations in microbial composition, a concerning prevalence of multiple antibiotic resistance, and the presence of unique bacterial species well-adapted to its distinctive alkaline and saline environment.