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.
-
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.
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.
Metrics
-
- 2,640
- views
-
- 307
- downloads
-
- 28
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
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
Further reading
-
- Ecology
For the first time in any animal, we show that nocturnal bull ants use the exceedingly dim polarisation pattern produced by the moon for overnight navigation. The sun or moon can provide directional information via their position; however, they can often be obstructed by clouds, canopy, or the horizon. Despite being hidden, these bodies can still provide compass information through the polarised light pattern they produce/reflect. Sunlight produces polarised light patterns across the overhead sky as it enters the atmosphere, and solar polarised light is a well-known compass cue for navigating animals. Moonlight produces an analogous pattern, albeit a million times dimmer than sunlight. Here, we show evidence that polarised moonlight forms part of the celestial compass of navigating nocturnal ants. Nocturnal bull ants leave their nest at twilight and rely heavily on the overhead solar polarisation pattern to navigate. Yet many foragers return home overnight when the sun cannot guide them. We demonstrate that these bull ants use polarised moonlight to navigate home during the night, by rotating the overhead polarisation pattern above homing ants, who alter their headings in response. Furthermore, these ants can detect this cue throughout the lunar month, even under crescent moons, when polarised light levels are at their lowest. Finally, we show the long-term incorporation of this moonlight pattern into the ants’ path integration system throughout the night for homing, as polarised sunlight is incorporated throughout the day.
-
- Ecology
Climatic warming can shift community composition driven by the colonization-extinction dynamics of species with different thermal preferences; but simultaneously, habitat fragmentation can mediate species’ responses to warming. As this potential interactive effect has proven difficult to test empirically, we collected data on birds over 10 years of climate warming in a reservoir subtropical island system that was formed 65 years ago. We investigated how the mechanisms underlying climate-driven directional change in community composition were mediated by habitat fragmentation. We found thermophilization driven by increasing warm-adapted species and decreasing cold-adapted species in terms of trends in colonization rate, extinction rate, occupancy rate and population size. Critically, colonization rates of warm-adapted species increased faster temporally on smaller or less isolated islands; cold-adapted species generally were lost more quickly temporally on closer islands. This provides support for dispersal limitation and microclimate buffering as primary proxies by which habitat fragmentation mediates species range shift. Overall, this study advances our understanding of biodiversity responses to interacting global change drivers.
