Redox-informed models of global biogeochemical cycles - PubMed (original) (raw)

Review

Redox-informed models of global biogeochemical cycles

Emily J Zakem et al. Nat Commun. 2020.

Abstract

Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments."Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things." -Georgia O'Keefe.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1

Fig. 1. Key microbially driven redox transformations that mediate the atmospheric fluxes of climatically relevant gases.

Radiatively active gases are notated with red type. The processes in black type are represented in some way (though not necessarily with electron balancing) in both the marine and terrestrial biospheres in earth system models within the Coupled Model Intercomparison Project (land: NCAR Community Earth System Model; ocean: GFDL COBALTv2), which are used for projections of climate change in reports by the Intergovernmental Panel on Climate Change. Processes in green type are represented in only the terrestrial model. Current models do not yet include other relevant reactions, some of which are represented in gray type, such as anaerobic ammonia oxidation (anammox), the marine production and consumption of methane, the redox cycling of iron, manganese, and other metals, and the methane-relevant redox chemistry of phosphorus. COBALTv2 does account for sulfate reduction in marine sediments, but sulfate is not represented. Image courtesy of NASA.

Fig. 2

Fig. 2. Schematic of a single cell represented as a metabolic functional type carrying out the aerobic oxidation of ammonia.

The redox balance informs the elemental ratios of substrates utilized, biomass synthesized, and waste products excreted (Table 1).

Fig. 3

Fig. 3. Solutions from a global simulation resolving multiple metabolic functional types.

Net primary productivity (NPP), the biomasses of the metabolic functional types, and the sinking particulate organic carbon (POC) flux are resolved along a transect of a global microbial ecosystem model coupled with an estimate of the ocean circulation (Darwin-MITgcm).

Fig. 4

Fig. 4. Model simulation and observations of the marine nitrification system.

Biogeochemistry is driven by microbial metabolic functional types in a vertical water column model. Lines are model solutions, and marked points are observations from two stations in the Pacific Ocean, (see Supplementary Fig. 2 for more detail) (a). Chlorophyll a concentrations and abundances of ammonia-oxidizing organisms (AOO) and nitrite-oxidizing organisms (NOO). Observed abundances are of the 16S rRNA abundances of archaeal Marine Group I and _Nitrospina_-like bacteria,. Model abundances are converted from biomass with 0.1 fmol N cell-1 for AOO, 0.2 fmol N cell-1 for NOO, and one gene copy per cell. (b). Light (solar irradiance) and bulk nitrification rates.

Similar articles

Cited by

References

    1. Falkowski PG, Fenchel T, Delong EF. The microbial engines that drive Earth’s biogeochemical cycles. Science. 2008;320:1034–1039. doi: 10.1126/science.1153213. - DOI - PubMed
    1. Heimann M, Reichstein M. Terrestrial ecosystem carbon dynamics and climate feedbacks. Nature. 2008;451:289–292. doi: 10.1038/nature06591. - DOI - PubMed
    1. Matsumoto K, Hashioka T, Yamanaka Y. Effect of temperature-dependent organic carbon decay on atmospheric pCO2. J. Geophys. Res. 2007;112:G02007.
    1. Volk, T. & Hoffert, M. I. In The carbon cycle and atmospheric CO2: natural variations Archean to present. Chapman conference papers, 1984 (eds. Sundquist, E. T. & Broecker, W. S.) 99–110 (American Geophysical Union, 1985).
    1. Oschlies A, Brandt P, Stramma L, Schmidtko S. Drivers and mechanisms of ocean deoxygenation. Nat. Geosci. 2018;11:467–473. doi: 10.1038/s41561-018-0152-2. - DOI

Publication types

MeSH terms

Substances

LinkOut - more resources