Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater

Martin Taubert,Nico Jehmlich,Rola Houhou,Martin Von Bergen,Petra Rösch,Georgette Azemtsop Matanfack,Kirsten Küsel,Beatrix M Heinze,Jürgen Popp,Will A Overholt

doi:10.1038/s41396-021-01163-x

Abstract

Current understanding of organic carbon inputs into ecosystems lacking photosynthetic primary production is predicated on data and inferences derived almost entirely from metagenomic analyses. The elevated abundances of putative chemolithoautotrophs in groundwaters suggest that dark CO2 fixation is an integral component of subsurface trophic webs. To understand the impact of autotrophically fixed carbon, the flux of CO2-derived carbon through various populations of subsurface microbiota must first be resolved, both quantitatively and temporally. Here we implement novel Stable Isotope Cluster Analysis to render a time-resolved and quantitative evaluation of 13CO2-derived carbon flow through a groundwater community in microcosms stimulated with reduced sulfur compounds. We demonstrate that mixotrophs, not strict autotrophs, were the most abundant active organisms in groundwater microcosms. Species of Hydrogenophaga, Polaromonas, Dechloromonas, and other metabolically versatile mixotrophs drove the production and remineralization of organic carbon. Their activity facilitated the replacement of 43% and 80% of total microbial carbon stores in the groundwater microcosms with 13C in just 21 and 70 days, respectively. The mixotrophs employed different strategies for satisfying their carbon requirements by balancing CO2 fixation and uptake of available organic compounds. These different strategies might provide fitness under nutrient-limited conditions, explaining the great abundances of mixotrophs in other oligotrophic habitats, such as the upper ocean and boreal lakes.

Highlights

From soils to deep-sea sediments, the vast majority of cells on Earth must find a way to thrive in environments devoid of photosynthesis [1]
Metagenomic-based studies have elucidated a diverse array of microorganisms bearing the metabolic potential for chemolithoautotrophy [4, 13,14,15,16], accounting for 12% to 47% of the microbial community detected in groundwater [17,18,19,20]
The conventional approach of calculating the most probable 13C relative isotope abundance (RIA) of a peptide does not take into account the information contained in 13C isotopologue patterns, which allow a differentiation between direct utilization of a labeled carbon source and cross-feeding, as previously described [39]

Summary

INTRODUCTION

From soils to deep-sea sediments, the vast majority of cells on Earth must find a way to thrive in environments devoid of photosynthesis [1]. Metagenomic-based studies have elucidated a diverse array of microorganisms bearing the metabolic potential for chemolithoautotrophy [4, 13,14,15,16], accounting for 12% to 47% of the microbial community detected in groundwater [17,18,19,20] Discoveries such as these have cast doubt on paradigms portraying modern groundwater as being primarily inhabited by heterotrophic microbes fueled by organic material from the surface. By mapping the quantitative information derived from SIsCA to metagenome-assembled genomes (MAGs), we were able to characterize carbon utilization and trophic interactions between active autotrophs and heterotrophs in the groundwater microbiome over a period of 70 days. Monitoring deuterium incorporation into microbial cells helped gauge metabolic activity, as well as determine optimal time points for sampling

MATERIALS AND METHODS

RESULTS

CONCLUSIONS