In situ Electrochemical Studies of the Terrestrial Deep Subsurface Biosphere at the Sanford Underground Research Facility, South Dakota, USA

Yamini Jangir,Laura A Zinke,Jan P Amend,Brandi Kiel Reese,Mohamed Y El-Naggar,Cynthia M Anderson,Nicole M Beedle,Amruta A Karbelkar,Greg Wanger

doi:10.3389/fenrg.2019.00121

Abstract

The terrestrial deep subsurface is host to significant and diverse microbial populations. However, these microbial populations remain poorly characterized, partially due to the inherent difficulty of sampling, in situ studies, and isolating of the in situ microbes. Motivated by the ability of microbes to gain energy from redox reactions at mineral interfaces, we here present in situ electrochemical colonization (ISEC) reactor as a method to directly study microbial electron transfer activity and to enable the capture and isolation of electrochemically active microbes. We installed a potentiostatically controlled ISEC reactor containing four working electrodes 1500 m below the surface at the Sanford Underground Research Facility. The working electrodes were poised at different redox potentials to mimic energy-yielding mineral reducing and oxidizing reactions predicted to occur at this site. We present a 16S rRNA analysis of the in situ electrode-associated microbial communities, revealing the dominance of novel bacterial lineages under cathodic conditions. We also demonstrate that the in situ electrodes can be further used for downstream electrochemical laboratory enrichment and isolation of novel strains. Using this workflow, we isolated Bacillus, Anaerospora, Comamonas, Cupriavidus, and Azonexus strains from the electrode-attached biomass. Finally, the extracellular electron transfer activity of Comamonas strain (isolated at -0.19 V vs. SHE and designated WE1-1D1) and Bacillus strain (isolated at +0.53 V vs. SHE and designated WE4-1A1-BC) from and to a poised electrode, respectively, were confirmed in electrochemical reactors. Our study highlights the utility of in situ electrodes and electrochemical enrichment workflows to shed light on microbial activity in the deep terrestrial subsurface.

Highlights

It is important to note that the currents observed in the in situ electrochemical colonization (ISEC) reactor are a combination of both biotic and abiotic redox reactions occurring on electrode surfaces
Our results highlight the potential for poised electrodes to serve as in situ observatories to capture for further downstream studies electrochemically active microbes in the deep terrestrial subsurface
The in situ electrodes deployed at the Sanford Underground Research Facility (SURF) captured many families represented in the borehole fluid, while showing potential-dependent clear shifts in the relative abundance of specific lineages

Summary

Introduction

Minerals that contain redox active elements (e.g., S, Fe, Mn) are abundant in subsurface environments, and can support the growth of microorganisms by acting as electron acceptors for heterotrophic respiration or electron donors for lithotrophic, and often autotrophic, metabolism (Nealson et al, 2002; Bach and Edwards, 2003; Edwards et al, 2005; Fredrickson and Zachara, 2008; Orcutt et al, 2011; Southam, 2012; Shi et al, 2016) This process of extracellular electron transfer (EET) to or from minerals is best characterized in a handful of Fe-reducing bacteria, especially Geobacter and Shewanella species (Lovley and Phillips, 1988; Myers and Nealson, 1988; Shi et al, 2016). While our mechanistic understanding of the molecular pathways that underlie inward EET (i.e., electron transfer from rather than to surfaces) lags behind metal reduction pathways, electrode-based techniques have highlighted the diversity of microbes capable of electron uptake from cathodes: acetogens, methanogens, as well as ironand sulfur-oxidizers (Nevin et al, 2011; Summers et al, 2013; Bose et al, 2014; Beese-Vasbender et al, 2015; Deutzmann et al, 2015; Ishii et al, 2015; Rowe et al, 2015, 2017b)

Methods

Results

Conclusion