Environmental controls of dark CO2 fixation in wetland microbiomes

Abstract

Rising atmospheric concentration of CO2 is a major concern to society due to its global warming potential. In soils, CO2 fixing microorganisms are preventing a part of the CO2 from entering the atmosphere. Yet, the pathways behind dark CO2 fixation are rarely studied in situ. Here we examined the environmental controls on the abundance and expression of key genes involved in microbial CO2 fixation in estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic and metatranscriptomic analyses confirmed that wetland microbiota harbor all six known CO2 fixation pathways and that these pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reductive tricarboxylic acid cycle (rTCA) and the Calvin cycle were favored by low salinity and O2 rich niches high in organic matter, while the transcription of the key genes for the Wood-Ljungdahl pathway (WLP) and dicarboxylate/4-hydroxybutyrate cycle (DC/4-HB cycle) were favored by low O2 niches poor in organic matter. Taxonomic assignment of transcripts implied that dark CO2 fixation was mainly linked to few bacterial phyla, namely, Desulfobacterota, Gemmatimonadota, Methylomirabilota, Nitrospirota and Pseudomonadota.