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Environmental DNA reveals the structure of phytoplankton assemblages along a 2900-km transect in the Mississippi River

View ORCID ProfileJoseph M. Craine, Michael W. Henson, J. Cameron Thrash, Jordan Hanssen, Greg Spooner, Patrick Fleming, Markus Pukonen, Frederick Stahr, Sarah Spaulding, Noah Fierer
doi: https://doi.org/10.1101/261727
Joseph M. Craine
1Jonah Ventures, 1600 Range St. #201, Boulder, CO, 80301 USA.
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  • ORCID record for Joseph M. Craine
  • For correspondence: josephmcraine@gmail.com
Michael W. Henson
2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
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J. Cameron Thrash
2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
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Jordan Hanssen
3O.A.R. Northwest, Seattle, WA 98103, U.S.A.
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Greg Spooner
3O.A.R. Northwest, Seattle, WA 98103, U.S.A.
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Patrick Fleming
3O.A.R. Northwest, Seattle, WA 98103, U.S.A.
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Markus Pukonen
3O.A.R. Northwest, Seattle, WA 98103, U.S.A.
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Frederick Stahr
4School of Oceanography, University of Washington, Seattle, WA 98195, USA.
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Sarah Spaulding
5Institute of Arctic and Alpine Research, University of Colorado, Boulder, 80309 USA
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Noah Fierer
1Jonah Ventures, 1600 Range St. #201, Boulder, CO, 80301 USA.
6Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO80309, USA
7Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, CO 80309
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Abstract

The environmental health of aquatic ecosystems is critical to society, yet traditional assessments of water quality have limited utility for some bodies of water such as large rivers. Sequencing of environmental DNA (eDNA) has the potential to complement if not replace traditional sampling of biotic assemblages for the purposes of reconstructing aquatic assemblages and, by proxy, assessing water quality. Despite this potential, there has been little testing of the ability of eDNA to reconstruct assemblages and their absolute and relative utility to infer water quality metrics. Here, we reconstruct phytoplankton communities by amplifying and sequencing DNA from a portion of the 23S rRNA region from filtered water samples along a 2900-km transect in the Mississippi River. Across the entire length, diatoms dominated the assemblage (72.6%) followed by cryptophytes (8.7%) and cyanobacteria (7.0%). There were no general trends in the abundances of these major taxa along the length of the river, but individual taxon abundance peaked in different regions. For example, the abundance of taxa genetically similar to Melosira tropica peaked at approximately 60% of all reads 2750 km upstream from the Gulf of Mexico, while taxa similar to Skeletonema marinoi began to increase below the confluence with the Missouri River until it reached approximately 30% of the reads at the Gulf of Mexico. There were four main clusters of samples based on phytoplankton abundance, two above the confluence with the Missouri and two below. Phytoplankton abundance was a poor predictor of NH4 + concentrations in the water, but predicted 61% and 80% of the variation in observed NO3 -and PO4 3-concentrations, respectively. Phytoplankton richness increased with increasing distance along the river, but was best explained by phosphate concentrations and water clarity. Along the Mississippi transect, there was similar structure to phytoplankton and bacterial assemblages, indicating that the two sets of organisms are responding to similar environmental factors. In all, the research here demonstrates the potential utility of metabarcoding for reconstructing aquatic assemblages, which might aid in conducting water quality assessments.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 08, 2018.
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Environmental DNA reveals the structure of phytoplankton assemblages along a 2900-km transect in the Mississippi River
Joseph M. Craine, Michael W. Henson, J. Cameron Thrash, Jordan Hanssen, Greg Spooner, Patrick Fleming, Markus Pukonen, Frederick Stahr, Sarah Spaulding, Noah Fierer
bioRxiv 261727; doi: https://doi.org/10.1101/261727
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Environmental DNA reveals the structure of phytoplankton assemblages along a 2900-km transect in the Mississippi River
Joseph M. Craine, Michael W. Henson, J. Cameron Thrash, Jordan Hanssen, Greg Spooner, Patrick Fleming, Markus Pukonen, Frederick Stahr, Sarah Spaulding, Noah Fierer
bioRxiv 261727; doi: https://doi.org/10.1101/261727

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