Tropical lacustrine sediment microbial community response to an extreme El Niño event

Authors: CHEN, MINGFEI - University Of Illinois; CONROY, JESSICA - University Of Illinois; SANFORD, ROBERT - University Of Illinois; WYMAN-FERAVICH, D - Pennsylvania State University; Chee Sanford, Joanne; Connor, Lynn

Submitted to: Nature Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/10/2023
Publication Date: 4/27/2023
Citation: Chen, M., Conroy, J.L., Sanford, R.A., Wyman-Feravich, D.A., Chee Sanford, J.C., Connor, L.M. 2023. Tropical lacustrine sediment microbial community response to an extreme El Niño event. Nature Scientific Reports. 13. Article 6868. https://doi.org/10.1038/s41598-023-33280-2.
DOI: https://doi.org/10.1038/s41598-023-33280-2

Interpretive Summary: Microbial communities perform important ecosystem services like nutrient cycling through key processes that support complex systems of biological life in virtually all types of environments. With the burgeoning information now attainable through technologies such as high throughput genetic sequencing, we can begin to understand not only how resident microbes cause changes to their physical and chemical environments, but also the underlying principles that govern their response to current conditions of climate change. To apply molecular methods developed in our ARS lab, along with collaborators, we used samples taken in years before and after documented El Niño effects (i.e. higher precipitation events) from lakes in Kiritimati, Kiribati. We show changes in the microbial communities corresponded to the salinity changes resulting from documented rainfall influx and found accordingly, evidence for changes in microbial functional activities known to be impacted by salinity levels. We further show successful application of a bioinformatics tool FAPROTAX that allows microbial metabolic predictions based on the taxa found in the community. The impact of this study is a better understanding of how to integrate contemporary biological data to study the modern impacts of factors such as changing rainfall patterns on nutrient (carbon and nitrogen) cycling, particularly leading to improved analyses within more complex systems like agricultural soils whereby increasing our understanding of the critical relationships between soil microbes and plant productivity.

Technical Abstract: Salinity can influence microbial community and related functional groups in lacustrine sediments, but few studies have examined temporal variability in salinity and associated temporal microbial community and functional group changes. To better understand how microbial communities and functional groups respond to salinity, we examined geochemistry and functional gene amplicon sequence data collected from 13 lakes located in Kiritimati, Republic of Kiribati (2°N, 157°W) in July 2014 and June 2019, dates which bracket the very large El Niño event of 2015-2016 and a period of extremely high precipitation rates. Lake water salinity values in 2019 were significantly reduced and strongly correlate with alpha and beta diversity of the microbial community. Specifically, phylum- and family-level results indicate that more halophilic microorganisms occurred in 2014 samples, whereas more mesohaline, marine, or halotolerant microorganisms were detected in 2019 samples. Functional Annotation of Prokaryotic Taxa (FAPROTAX) and functional gene results (nifH, nrfA, aprA) suggest that salinity influences the relative abundance of key functional groups (chemoheterotrophs, phototrophs, nitrogen fixers, denitrifiers, sulfate reducers), as well as the microbial diversity within functional groups. Accordingly, we conclude that the observed decrease in salinity caused substantial changes in the microbial community and functional gene groups in the lacustrine sediments of Kiritimati.