Metatranscriptomic evidence for classical and RuBisCO-mediated CO2 reduction to methane facilitated by direct interspecies electron transfer in a methanogenic system

Abstract

In a staged anaerobic fluidized-bed ceramic membrane bioreactor, metagenomic and metatranscriptomic analyses were performed to decipher the microbial interactions on the granular activated carbon. Metagenome bins, representing the predominating microbes in the bioreactor: syntrophic propionate-oxidizing bacteria (SPOB), acetoclastic Methanothrix concilii, and exoelectrogenic Geobacter lovleyi, were successfully recovered for the reconstruction and analysis of metabolic pathways involved in the transformation of fatty acids to methane. In particular, SPOB degraded propionate into acetate, which was further converted into methane and CO2 by M. concilii via the acetoclastic methanogenesis. Concurrently, G. lovleyi oxidized acetate into CO2, releasing electrons into the extracellular environment. By accepting these electrons through direct interspecies electron transfer (DIET), M. concilii was capable of performing CO2 reduction for further methane formation. Most notably, an alternative RuBisCO-mediated CO2 reduction (the reductive hexulose-phosphate (RHP) pathway) is transcriptionally-active in M. concilii. This RHP pathway enables M. concilii dominance and energy gain by carbon fixation and methanogenesis, respectively via a methyl-H4MPT intermediate, constituting the third methanogenesis route. The complete acetate reduction (2 mole methane formation/1 mole acetate consumption), coupling of acetoclastic methanogenesis and two CO2 reduction pathways, are thermodynamically favorable even under very low substrate condition (down to to 10−5 M level). Such tight interactions via both mediated and direct interspecies electron transfer (MIET and DIET), induced by the conductive GAC promote the overall efficiency of bioenergy processes.

Metatranscriptomic Evidence for Magnetite Nanoparticle-Stimulated Acetoclastic Methanogenesis under Continuous Agitation

“…4), indicate that the acetoclastic pathway mainly works for methanogenesis in the presence of MNPs under continuous agitation. In previous studies, metatranscriptomic analyses have demonstrated that genes coding for hydrogenotrophic methanogenesis pathways are upregulated in methanogens in association with the occurrence of Geobacter, and these data are considered to support the idea that DIET is involved in methanogenesis (17,18). In contrast, the metatranscriptomic data reported here suggest that MNPs stimulate acetoclastic methanogenesis, and we therefore conclude that MNPs did not promote DIET in agitated cultures.…”

Combined Effect of Activated Carbon Particles and Non-Adsorptive Spherical Beads as Fluidized Media on Fouling, Organic Removal and Microbial Communities in Anaerobic Membrane Bioreactor

“…Methanofastidiosales was absent in both bulk liquid and GAC, but was present on ABS (4.4%). These observations collectively suggest that biofilm and bulk communities in AFMBR are distinct from each other, corroborating with previous studies [ 59 , 60 ]. Collectively, biocarrier material is also a determining factor in how the microbial community is shaped.…”

“…Moreover, Geobacter can consume acetate and extracellularly release electrons that are used by Methanothrix via direct interspecies electron transfer (DIET) [ 62 ]. Under such circumstances, Methanothrix could utilize CO 2 as the carbon source for methanogenesis, which would otherwise be impossible without its exoelectrongenic partner [ 60 ]. Although bulk liquid also contains Geobacter (1.3%), the currently known mechanisms of DIET requires proximity to function and is unlikely to occur in the suspension of liquid [ 62 ].…”

Genome sequencing as a new window into the microbial community of membrane bioreactors – A critical review

“…Metatranscriptomics have recently been used in combination with metagenomics to analysis MBR microbial community dynamics and interactions (Yang et al, 2019). However, these methods are still in their infancy and only a few studies have applied them in the context of MBR, making it hard to source sufficient literature for a thorough review.…”