Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities.

Ryan De Montmollin Jennings,Zackary J Jay,William P Inskeep,Helen W Kreuzer,Laura M Whitmore,Jacob P Beam,Mark A Kozubal,James J Moran

doi:10.3389/fmicb.2017.00088

Ryan De Montmollin Jennings, Zackary J Jay + Show 6 more

Open Access

https://doi.org/10.3389/fmicb.2017.00088

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Abstract

Although the biological fixation of CO2 by chemolithoautotrophs provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs as a carbon and energy source, the relative amounts of autotrophic C in chemotrophic microbial communities are not well-established. The extent and mechanisms of CO2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable 13C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous “streamer” communities) were investigated. Genes of the 3-hydroxypropionate/4-hydroxybutyrate, dicarboxylate/4-hydroxybutyrate, and reverse tricarboxylic acid CO2 fixation pathways were identified in assembled genome sequence corresponding to the predominant Crenarchaeota and Aquificales observed across this habitat range. Stable 13C analyses of dissolved inorganic and organic C (DIC, DOC), and possible landscape C sources were used to interpret the 13C content of microbial community samples. Isotope mixing models showed that the minimum fractions of autotrophic C in microbial biomass were >50% in the majority of communities analyzed. The significance of CO2 as a C source in these communities provides a foundation for understanding community assembly and succession, and metabolic linkages among early-branching thermophilic autotrophs and heterotrophs.

Highlights

Despite the significance of microorganisms in most major element cycles, the contribution of microbial inorganic carbon (C) fixation to global C cycling is not yet well-resolved (Shively et al, 2001; Reinthaler et al, 2010)
The 13C contents of dissolved inorganic C (DIC) and dissolved organic C (DOC) measured across 15 geothermal systems averaged −2.7% (± 2.8) and −21.7% (± 2.3), respectively (Figure 1)
Most of the δ13C-DOC values from geothermal sites were close to the average δ13C value obtained for landscape organic C (−23.7%), a few springs exhibited slightly heavier δ13C values near −17 to −18% (Table 1)

Summary

Introduction

Despite the significance of microorganisms in most major element cycles, the contribution of microbial inorganic carbon (C) fixation to global C cycling is not yet well-resolved (Shively et al, 2001; Reinthaler et al, 2010). Resolution of the C cycle is important across multiple scales, ranging from specific microbial communities to regional environments, and to the global Earth. Resolution of C cycling at the microbial community scale requires the integration of metabolic and molecular data (e.g., metagenome sequence) with geochemical studies, such as stable carbon isotope (13C) analysis or isotope probing. Stable isotope probing (SIP) using 13CO2 and subsequent analysis of heavy DNA allows for the identification of organisms responsible for the fixation of CO2 in microbial communities; SIP is technically challenging in situ across a large number of different environments. Direct analysis of stable carbon isotopes (i.e., 13C) has been employed to dissect the trophic structure of numerous different ecosystems, and can provide primary evidence for the sources of C to specific biota (Peterson and Fry, 1987)

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