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Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

View ORCID ProfilePaula B. Matheus Carnevali, Adi Lavy, Alex D. Thomas, Alexander Crits-Christoph, Spencer Diamond, Raphaeël Meéheust, Matthew R. Olm, Allison Sharrar, Shufei Lei, Wenming Dong, Nicola Falco, Nicholas Bouskill, Michelle Newcomer, Peter Nico, Haruko Wainwright, Dipankar Dwivedi, Kenneth H. Williams, Susan Hubbard, Jillian F. Banfield
doi: https://doi.org/10.1101/2020.05.14.086363
Paula B. Matheus Carnevali
1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
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  • ORCID record for Paula B. Matheus Carnevali
Adi Lavy
1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
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Alex D. Thomas
2Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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Alexander Crits-Christoph
3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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Spencer Diamond
1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
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Raphaeël Meéheust
1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
4Innovative Genomics Institute, Berkley, CA, USA
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Matthew R. Olm
3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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Allison Sharrar
1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
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Shufei Lei
1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
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Wenming Dong
5Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Nicola Falco
5Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Nicholas Bouskill
5Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Michelle Newcomer
5Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Peter Nico
5Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Haruko Wainwright
5Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Dipankar Dwivedi
5Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Kenneth H. Williams
5Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Susan Hubbard
5Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Jillian F. Banfield
1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
2Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
4Innovative Genomics Institute, Berkley, CA, USA
5Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
6Chan Zuckerberg Biohub, San Francisco, CA, USA
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  • For correspondence: jbanfield@berkeley.edu
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Abstract

Biogeochemical exports of C, N, S and H2 from watersheds are modulated by the activity of microorganisms that function over micron scales. This disparity of scales presents a substantial challenge for development of predictive models describing watershed function. Here, we tested the hypothesis that meander-bound regions exhibit patterns of microbial metabolic potential that are broadly predictive of biogeochemical processes in floodplain soils along a river corridor. We intensively sampled floodplain soils located in the upper, middle, and lower reaches of the East River in Colorado and reconstructed 248 draft quality genomes representative at a sub-species level. Approximately one third of the representative genomes were detected across all three locations with similar levels of abundance, and despite the very high microbial diversity and complexity of the soils, ~15% of species were detected in two consecutive years. A core floodplain microbiome was enriched in bacterial capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. We did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, at the watershed scale meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations in floodplain soils. Given this, we conducted a transcriptomic analysis of the middle site. Overall, the most highly transcribed genes were amoCAB and nxrAB (for nitrification) followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Thus, widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.

Competing Interest Statement

The authors have declared no competing interest.

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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 May 15, 2020.
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Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale
Paula B. Matheus Carnevali, Adi Lavy, Alex D. Thomas, Alexander Crits-Christoph, Spencer Diamond, Raphaeël Meéheust, Matthew R. Olm, Allison Sharrar, Shufei Lei, Wenming Dong, Nicola Falco, Nicholas Bouskill, Michelle Newcomer, Peter Nico, Haruko Wainwright, Dipankar Dwivedi, Kenneth H. Williams, Susan Hubbard, Jillian F. Banfield
bioRxiv 2020.05.14.086363; doi: https://doi.org/10.1101/2020.05.14.086363
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Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale
Paula B. Matheus Carnevali, Adi Lavy, Alex D. Thomas, Alexander Crits-Christoph, Spencer Diamond, Raphaeël Meéheust, Matthew R. Olm, Allison Sharrar, Shufei Lei, Wenming Dong, Nicola Falco, Nicholas Bouskill, Michelle Newcomer, Peter Nico, Haruko Wainwright, Dipankar Dwivedi, Kenneth H. Williams, Susan Hubbard, Jillian F. Banfield
bioRxiv 2020.05.14.086363; doi: https://doi.org/10.1101/2020.05.14.086363

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