Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment
- Arizona State University, United States
- USDA, United States
- J Craig Venter Institute, United States
- Universidad Nacional Autónoma de México, Mexico
- Rice University, United States
- University of Montana, United States
Abstract
Several universal genomic traits affect trade-offs in the capacity, cost, and efficiency of biochemical information processing underpinning metabolism and reproduction. We analyzed their role in mediating planktonic microbial community responses to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Ciénegas, Mexico—one of the first whole-ecosystem experiments involving replicated metagenomic assessment. Mean bacterial genome size, GC content, total number of tRNA genes, total number of rRNA genes, and codon usage bias in ribosomal protein sequences were higher in the fertilized treatment, as predicted assuming oligotrophy favors lower information-processing costs while copiotrophy favors higher processing rates. Contrasting changes in trait variances also suggested differences between traits in mediating assembly under copiotrophic versus oligotrophic conditions. Trade-offs in information-processing traits are apparently sufficiently pronounced to play a role in community assembly as the major components of metabolism—information, energy, and nutrient requirements—are fine-tuned to an organism's growth and trophic strategy.
Data availability
Raw sequence data and metadata have been submitted to NCBI Sequence Read Archives, accessible through BioProject PRJEB22811.
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Cuatro Cienegas Lagunita Fertilization ExperiementNCBI Sequence Read Archives, PRJEB22811.
Article and author information
Author details
Funding
National Science Foundation (DEB-0950175)
- James J Elser
National Aeronautics and Space Administration (NAI5-0018)
- James J Elser
National Aeronautics and Space Administration (NNH05ZDA001C)
- Janet L Siefert
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- David Donoso, Escuela Politécnica Nacional, Ecuador
Version history
- Received: July 1, 2019
- Accepted: January 27, 2020
- Accepted Manuscript published: January 28, 2020 (version 1)
- Version of Record published: February 18, 2020 (version 2)
Copyright
© 2020, Okie et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment
eLife 9:e49816.
https://doi.org/10.7554/eLife.49816
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