Metagenomic and Metatranscriptomic Analysis of an Electromethanogenic Microbial Community
Authors: Babanova Sofia , Carpenter Kayla , Ishii Shunichi , Ishii Shino , Flynn Michael , Hogan John , Bretschger Orianna 
Published: February 2020

Researchers have described the mechanisms of extracellular electron uptake in model electrogens like Shewanella oneidensis MR-11 and Geobacter sulfurreducens2
 as well as providing evidence for direct electron uptake for some methanogenic strains in BESs3. However, practical applications of BESs will require the use of mixed microbial populations to ensure performance stability by taking advantage of microbial adaptation and symbioses that can reduce the impact of environmental or operational perturbations.  However, little is known about the taxonomic composition of mixed microbial biofilms that successfully drive electromethanogenesis. Even less is known about the functional association of specific genes and pathways expressed by microbial community members that enable cooperation/competition in an electromethanogenic system. Here we utilized a novel stimulus-induced metatranscriptomic approach in combination with metagenomics to identify the microbial taxa in an electromethanogenic biofilm and quantify the dynamic responses of key genes associated with electron uptake, hydrogen production/utilization and carbon dioxide fixation.

Two dual-compartment bioelectrochemical systems (BES1 and BES2) were inoculated with rice paddy soil, a minimal media without additional soluble carbon sources or chemical mediators, and a 20% CO2 headspace (balance N2).  The systems were operated as described in Bretschger et al.4 using a subpassage technique to accelerate the enrichment of highly active electromethanogenic communities. 

The stimulus-induced metatranscriptomic experiments and metagenomic analyses were executed according to methods described in Ishii et al.5
,
6. Both systems were exposed to an open circuit condition for 45 minutes and biofilms were sampled before and after the operational change (Fig. 1a, main). At the time of sampling both systems were consuming electricity and producing methane (Fig. 1a, inset). However, BES2 was consuming more electrons per unit biomass than BES2, even though both systems had roughly equivalent methane production activity. The results from the metagenomic analyses show that the same strains of methanogens, sulfate reducers and fermenters were present in BES1 and BES2; however, they were present in different relative abundances, which may explain the performance differences (Fig. 1b and c).  Further, the stimuli applied to both reactors induced different functional responses from the respective communities, which also indicates that the relative abundance of species impacts how they functionally respond in BESs. Future work will address the specific interactions that correlate with these performance differences. These data yield new perspectives on the functional and taxonomic dynamics of electromethanogenic microbial communities and how they may be controlled in BESs.

1                Ross, D. E., Flynn, J. M., Baron, D. B., Gralnick, J. A. & Bond, D. R. Towards electrosynthesis in Shewanella: energetics of reversing the Mtr pathway for reductive metabolism. PloS one 6, e16649 (2011).

2                Gregory, K. B., Bond, D. R. & Lovley, D. R. Graphite electrodes as electron donors for anaerobic respiration. Environmental Microbiology 6, 596-604 (2004).

3                Lohner, S. T., Deutzmann, J. S., Logan, B. E., Leigh, J. & Spormann, A. M. Hydrogenase-independent uptake and metabolism of electrons by the archaeon Methanococcus maripaludis. The ISME journal 8, 1673-1681 (2014).

4                Bretschger, O. et al. Functional and taxonomic dynamics of an electricity-consuming methane-producing microbial community. Bioresource technology 195, 254-264 (2015).

5                Ishii, S. i. et al. A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer. Nature Communications, doi:doi:10.1038/ncomms2615 (2013).

6                Ishii, S. i. et al. Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach. Scientific reports 5 (2015).

Figure 1