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Article

Developing Indicators of Nutrient Pollution in Streams Using 16S rRNA Gene Metabarcoding of Periphyton-Associated Bacteria

1
United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
2
School of Public Health & Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
3
United States Environmental Protection Agency, Office of Research and Development, Research Triangle Park, NC 27711, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Constantinos V. Chrysikopoulos
Water 2022, 14(15), 2361; https://doi.org/10.3390/w14152361
Received: 6 June 2022 / Revised: 22 July 2022 / Accepted: 27 July 2022 / Published: 30 July 2022
(This article belongs to the Special Issue Applied Ecology Research for Water Quality Management)
Indicators based on nutrient-biota relationships in streams can inform water quality restoration and protection programs. Bacterial assemblages could be particularly useful indicators of nutrient effects because they are species-rich, important contributors to ecosystem processes in streams, and responsive to rapidly changing conditions. Here, we sampled 25 streams weekly (12–14 times each) and used 16S rRNA gene metabarcoding of periphyton-associated bacteria to quantify the effects of total phosphorus (TP) and total nitrogen (TN). Threshold indicator taxa analysis identified assemblage-level changes and amplicon sequence variants (ASVs) that increased or decreased with increasing TP and TN concentrations (i.e., low P, high P, low N, and high N ASVs). Boosted regression trees confirmed that relative abundances of gene sequence reads for these four indicator groups were associated with nutrient concentrations. Gradient forest analysis complemented these results by using multiple predictors and random forest models for each ASV to identify portions of TP and TN gradients at which the greatest changes in assemblage structure occurred. Synthesized statistical results showed bacterial assemblage structure began changing at 24 µg TP/L with the greatest changes occurring from 110 to 195 µg/L. Changes in the bacterial assemblages associated with TN gradually occurred from 275 to 855 µg/L. Taxonomic and phylogenetic analyses showed that low nutrient ASVs were commonly Firmicutes, Verrucomicrobiota, Flavobacteriales, and Caulobacterales, Pseudomonadales, and Rhodobacterales of Proteobacteria, whereas other groups, such as Chitinophagales of Bacteroidota, and Burkholderiales, Rhizobiales, Sphingomonadales, and Steroidobacterales of Proteobacteria comprised the high nutrient ASVs. Overall, the responses of bacterial ASV indicators in this study highlight the utility of metabarcoding periphyton-associated bacteria for quantifying biotic responses to nutrient inputs in streams. View Full-Text
Keywords: phosphorus; nitrogen; agriculture; periphyton; biomonitoring; bioassessment; 16S; gradient forest; boosted regression trees; threshold indicator taxa analysis; TITAN phosphorus; nitrogen; agriculture; periphyton; biomonitoring; bioassessment; 16S; gradient forest; boosted regression trees; threshold indicator taxa analysis; TITAN
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MDPI and ACS Style

Pilgrim, E.M.; Smucker, N.J.; Wu, H.; Martinson, J.; Nietch, C.T.; Molina, M.; Darling, J.A.; Johnson, B.R. Developing Indicators of Nutrient Pollution in Streams Using 16S rRNA Gene Metabarcoding of Periphyton-Associated Bacteria. Water 2022, 14, 2361. https://doi.org/10.3390/w14152361

AMA Style

Pilgrim EM, Smucker NJ, Wu H, Martinson J, Nietch CT, Molina M, Darling JA, Johnson BR. Developing Indicators of Nutrient Pollution in Streams Using 16S rRNA Gene Metabarcoding of Periphyton-Associated Bacteria. Water. 2022; 14(15):2361. https://doi.org/10.3390/w14152361

Chicago/Turabian Style

Pilgrim, Erik M., Nathan J. Smucker, Huiyun Wu, John Martinson, Christopher T. Nietch, Marirosa Molina, John A. Darling, and Brent R. Johnson. 2022. "Developing Indicators of Nutrient Pollution in Streams Using 16S rRNA Gene Metabarcoding of Periphyton-Associated Bacteria" Water 14, no. 15: 2361. https://doi.org/10.3390/w14152361

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