Environmental controls of dark CO2 fixation in wetland microbiomes

Abstract

ABSTRACTRising atmospheric concentration of CO2is a major concern to society due to its global warming potential. In soils, CO2fixing microorganisms are preventing a part of the CO2from entering the atmosphere. Yet, the pathways behind dark CO2fixation are rarely studiedin situ. Here we examined the environmental controls on the abundance and expression of key genes involved in microbial CO2fixation in estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic and metatranscriptomic analyses confirmed that wetland microbiota harbor all six known CO2fixation 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 O2rich 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 O2niches poor in organic matter. Taxonomic assignment of transcripts implied that dark CO2fixation was mainly linked to few bacterial phyla, namely, Desulfobacterota, Gemmatimonadota, Methylomirabilota, Nitrospirota and Pseudomonadota.