期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 113, 期 40, 页码 E5925-E5933出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1602897113
关键词
metagenomics; metatranscriptomics; metaproteomics; biogeochemical; gene-centric model
资金
- US Department of Energy (DOE) Joint Genome Institute
- US DOE Office of Science [DE-AC02-05CH11231]
- Unger Vetlesen and Ambrose Monell Foundations
- Tula Foundation Centre for Microbial Diversity and Evolution
- Natural Sciences and Engineering Research Council of Canada (NSERC)
- Genome British Columbia
- Canada Foundation for Innovation
- Canadian Institute for Advanced Research
- W. R. Wiley Environmental Molecular Sciences Laboratory (EMSL)
- US DOE Office of Biological and Environmental Research
- Department of Mathematics, University of British Columbia
- Canadian Institute for Advanced Research Global Fellowship in the Integrated Microbial Biodiversity Program
- NSERC
- Max Planck Society
- Pacific Institute for the Mathematical Sciences (International Graduate Training Centre for Mathematical Biology)
Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet-a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite leakage during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as meta-genomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales.
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