Soil Carbon-Fixation Rates and Associated Bacterial Diversity and Abundance in Three Natural Ecosystems

Abstract

CO assimilation by autotrophic microbes is an important process in soil carbon cycling, and our understanding of the community composition of autotrophs in natural soils and their role in carbon sequestration of these soils is still limited. Here, we investigated the autotrophic C incorporation in soils from three natural ecosystems, i.e., wetland (WL), grassland (GR), and forest (FO) based on the incorporation of labeled C into the microbial biomass. Microbial assimilation of C (C-MBC) differed among the soils from three ecosystems, accounting for 14.2-20.2% of C-labeled soil organic carbon (C-SOC). We observed a positive correlation between the cbbL (ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit gene) abundance, C-SOC level, andC-MBC concentration confirming the role of autotrophic bacteria in soil carbon sequestration. Distinct cbbL-bearing bacterial communities were present in each soil type; form IA and form IC RubisCO-bearing bacteria were most abundant in WL, followed by GR soils, with sequences from FO soils exclusively derived from the form IC clade. Phylogenetically, the diversity of CO-fixing autotrophs and CO oxidizers differed significantly with soil type, whereas cbbL-bearing bacterial communities were similar when assessed using coxL. We demonstrate that local edaphic factors such as pH and salinity affect the C-fixation rate as well as cbbL and coxL gene abundance and diversity. Such insights into the effect of soil type on the autotrophic bacterial capacity and subsequent carbon cycling of natural ecosystems will provide information to enhance the sustainable management of these important natural ecosystems.

Isotope discrimination by form IC RubisCO from Ralstonia eutropha and Rhodobacter sphaeroides, metabolically versatile members of ‘Proteobacteria’ from aquatic and soil habitats

“…ε values for form IC RubisCOs have yet to be determined. Form IC RubisCO gene sequences are commonly detected in samples collected from soil, lakes, rivers and estuaries (Selesi et al ., ; Tolli and King, ; Nigro and King, ; Brauer et al ., ; ; Yuan et al ., ; Wu et al ., ; Alfreider et al ., ; Lynn et al ., ) as well as the open ocean (Caspi et al ., ; Pichard et al ., ). Facultative autotrophs with form IC RubisCOs are commonly cultivated from soil, lake and river samples; these Alpha ‐ proteobacteria and Beta‐proteobacteria may be responsible for the molecular detection of form IC enzymes from these habitats (e.g., Brauer et al ., ).…”

Insights into the microbial autotrophic potential of a shallow oligotrophic alpine pond

“…An exact calculation of the proportion of CO2-fixing bacteria on the total bacterial community is not achievable based on functional gene abundance data. Nevertheless, supposing that (i) the average copy number of 16S rRNA copies per genome in the bacterial cells is four to six and (ii) the average number of cbb operons in bacteria is two (Yuan et al 2013;Lynn et al 2017), then we can estimate that 2-3% of the bacteria in the pond sediments may have the potential to fix CO2 through the CBB cycle.…”

Enhancement of soil carbon and nitrogen stocks by abiotic and microbial pathways in three rubber‐based agroforestry systems in Southwest China

“…In addition to affecting plant physiology and growth, soil pH affects soil biogeochemistry and microbial communities (Wu et al, 2013). SEM analysis revealed that the effect of intercropping treatments on the abundance of cbbL and nosZ genes was mediated by the increase in soil pH (Lynn et al, 2017). This is in line with previous findings that plant diversity increases soil pH and microbial biomass as well as bacterial and fungal abundance (Latz et al, 2016; Wang et al, 2008; Wu et al, 2017).…”