Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment

• Published in: eLife 2020-01, Vol.9
• Main Authors: Okie, Jordan G, Poret-Peterson, Amisha T, Lee, Zarraz Mp, Richter, Alexander, Alcaraz, Luis D, Eguiarte, Luis E, Siefert, Janet L, Souza, Valeria, Dupont, Chris L, Elser, James J
• Format: Article
• Language: English
• Subjects: Adaptation; Bacteria - genetics; Bacteria - metabolism; Bacterial genetics; Base Composition - genetics; Bias; Biochemistry; Biosynthesis; Codon Usage - genetics; codon usage bias; Codons; Deoxyribonucleic acid; DNA; Ecology; Ecosystem; Ecosystems; Efficiency; Energy metabolism; Fertilizers; GC content; Genes; genome size; Genome, Bacterial - genetics; Genomes; Genomics; Hypotheses; Information processing; Metabolism; Metagenome - genetics; Metagenomics; Mexico; Nutrient enrichment; Nutrient requirements; Organisms; phosphorous fertilization; Phosphorus; Physiological aspects; Physiology; Plankton - genetics; Plankton - metabolism; Plankton - microbiology; Ponds - microbiology; Prejudice; Protein Biosynthesis - genetics; Proteins; RNA; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; RNA, Ribosomal - genetics; RNA, Ribosomal - metabolism; RNA, Transfer - genetics; RNA, Transfer - metabolism; rRNA; rRNA operon copy number; Transfer RNA; tRNA
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.49816

Several universal genomic traits affect trade-offs in the capacity, cost, and efficiency of the biochemical information processing that underpins metabolism and reproduction. We analyzed the role of these traits in mediating the responses of a planktonic microbial community to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Ciénegas, Mexico. This is one of the first whole-ecosystem experiments to involve 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 all higher in the fertilized treatment, as predicted on the basis of the assumption that oligotrophy favors lower information-processing costs whereas 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 because the major components of metabolism-information, energy, and nutrient requirements-are fine-tuned to an organism's growth and trophic strategy.