Metagenomes from the Loxahatchee wildlife refuge in the Florida Everglades

Benskin, J. B.; Alvarez, D. A.; Cadavid, N. A.; Childs, C. A.; Cupelli, M. F.; De, L. A.; Diaz, A. M.; Eldridge, S. A.; Elhabashy, Y. B.; Fleming, A. E.; Fox, N. A.; Franco, M.; Gaspari, J. C.; Gerstin, I. M.; Gibson, K. A.; Huott, A. L.; Johnson, A. O.; Majhess, E. G.; Mantilla, G.; Perez, G. S.; Prieto, J. J.; Reutter, B. C.; Rivera, E. I.; Rootes, T. R.; Sellers, J.; Streibig, A. M.; Wilkinson, J. S.; Zayas-Bazan, S.; Bhadha, J. H.; Clum, A.; Daum, C.; Glavina del Rio, T.; Lail, K.; Roux, S.; Eloe-Fadrosh, E.

doi:10.1101/2021.02.16.430518

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bioRxiv · 10.1101/2021.02.16.430518

Metagenomes from the Loxahatchee wildlife refuge in the Florida Everglades

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Abstract

The Florida Everglades ecosystem represents a significant wetlands area and serves as a terrestrial carbon reservoir mediated in large part by microorganisms. Shotgun metagenome sequencing provides a snapshot of microbial diversity and the frequency of metabolic and functional gene content. Here, we present an analysis of 20 sediment samples collected from the Arthur R. Marshall Loxahatchee National Wildlife Refuge to characterize the taxonomic and functional potential of the microbial and viral communities, and reconstructed metagenome-assembled genomes. A total of 122 medium-quality and 6 high-quality MAGs are reported, three of which likely represent a novel species within the class Dehalococcoidia. The most abundant phyla of bacteria and archaea were Proteobacteria and Euryarchaeota, respectively. Caudovirales was the most abundant viral order. Significant differences in taxonomic composition and diversity were observed among collection sites. Additionally, water samples were analyzed for pH, total nitrogen, total organic carbon, elements (P, K, Mg, Fe, Mn, Pb, Ca, S), chloride, electric conductivity, orthophosphate, nitrate, and ammonia, while the sediment samples were analyzed for carbon, nitrogen, and pH. Differences in measured aquatic and sediment analytes revealed significant correlations with numerous phyla. Significant correlations were observed between estimated gene frequencies of both aquatic and sediment analytes, most notably between kup/kdpB and dsrA/cysC with potassium and sulfur, respectively, as well as phoD/phnX and cysC with pH. Together, these data provide an important view into the functional and metabolic potential encoded within the sediment microbial communities in the Florida Everglades.

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Benskin, J. B., Alvarez, D. A., Cadavid, N. A., Childs, C. A., Cupelli, M. F., De, L. A., Diaz, A. M., Eldridge, S. A., Elhabashy, Y. B., Fleming, A. E., Fox, N. A., Franco, M., Gaspari, J. C., Gerstin, I. M., Gibson, K. A., Huott, A. L., Johnson, A. O., Majhess, E. G., Mantilla, G., Perez, G. S., Prieto, J. J., Reutter, B. C., Rivera, E. I., Rootes, T. R., Sellers, J., Streibig, A. M., Wilkinson, J. S., Zayas-Bazan, S., Bhadha, J. H., Clum, A., Daum, C., Glavina del Rio, T., Lail, K., Roux, S., Eloe-Fadrosh, E.. 2021-02-17. Metagenomes from the Loxahatchee wildlife refuge in the Florida Everglades. https://doi.org/10.1101/2021.02.16.430518

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