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Selective carbon sources influence the end-products of microbial nitrate respiration

Hans K. Carlson, Lauren M. Lui, Morgan N. Price, Alexey E. Kazakov, Alex V. Carr, Jennifer V. Kuehl, Trenton K. Owens, Torben Nielsen, Adam P. Arkin, Adam M. Deutschbauer
doi: https://doi.org/10.1101/829143
Hans K. Carlson
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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  • For correspondence: HKCarlson@lbl.gov AMDeutschbauer@lbl.gov
Lauren M. Lui
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Morgan N. Price
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Alexey E. Kazakov
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Alex V. Carr
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Jennifer V. Kuehl
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Trenton K. Owens
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Torben Nielsen
2Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Adam P. Arkin
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
3Department of Bioengineering, University of California, Berkeley, CA 94720, USA
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Adam M. Deutschbauer
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
4Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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  • For correspondence: HKCarlson@lbl.gov AMDeutschbauer@lbl.gov
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Abstract

Respiratory and catabolic pathways are differentially distributed in microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end-products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end-products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content and function.

Footnotes

  • Conflict of interest: The authors declare no conflict of interest.

  • Grant information: This work was funded by ENIGMA, a Scientific Focus Area Program supported by the U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics: GTL Foundational Science through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U. S. Department of Energy.

  • https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA576510

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Posted November 04, 2019.
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Selective carbon sources influence the end-products of microbial nitrate respiration
Hans K. Carlson, Lauren M. Lui, Morgan N. Price, Alexey E. Kazakov, Alex V. Carr, Jennifer V. Kuehl, Trenton K. Owens, Torben Nielsen, Adam P. Arkin, Adam M. Deutschbauer
bioRxiv 829143; doi: https://doi.org/10.1101/829143
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Selective carbon sources influence the end-products of microbial nitrate respiration
Hans K. Carlson, Lauren M. Lui, Morgan N. Price, Alexey E. Kazakov, Alex V. Carr, Jennifer V. Kuehl, Trenton K. Owens, Torben Nielsen, Adam P. Arkin, Adam M. Deutschbauer
bioRxiv 829143; doi: https://doi.org/10.1101/829143

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