A phototrophy-driven microbial food web in a rice soil

Light is a major driver of primary productivity in most ecosystems on Earth. Phototrophic microorganisms harvest light to synthesize organic biomass for sustaining the global energy and carbon flow. However, the bottom-up model of phototrophic microorganisms as primary production and food source for higher trophic levels remains unclear in the terrestrial environment. Rice soil microcosms treated with different carbon sources (C-13-formate, C-12-formate, or a control without formate) were incubated for 21 days under illumination. For each microcosm, genomic DNA were extracted and fractionated by isopycnic ultracentrifugation. Subsequently, the analyses were conducted on these samples with real-time quantitative PCR, PCR-denaturant gradient gel electrophoresis fingerprinting, and sequencing analysis of bacterial 16S rRNA, eukaryotic 18S rRNA, and photosynthetic functional genes. Our analysis indicated that formate carbon was assimilated by a subset of bacteria and eukaryotes. Based on molecular fingerprinting and sequencing analysis, the primary producers were determined to be the microorganisms affiliated with purple phototrophic bacteria, cyanobacteria, and algae. The detection of protozoa and fungi-like 18S rRNA gene sequences in the C-13-enriched DNA fractions suggested that these organisms acted as consumers. They fed on nutrients derived from labeled phototrophic microorganisms. Molecular evidence suggests that in the light-driven microbial food web, the carbon flow from formate is initiated by phototrophic primary and secondary producers. Their biomasses subsequently sustain the growth of consumers in the rice soil.