Genetic engineering for enhanced productivity in bioelectrochemical systems

Abstract

A shift from petrochemical processes toward a bio-based economy is one of the most advocated developments for a sustainable future. To achieve this will require the biotechnological production of platform chemicals that can be further processed by chemical engineering. Bioelectrochemical systems (BESs) are a novel tool within the biotechnology field. In BESs, microbes serve as biocatalysts for the production of biofuels and value-added compounds, as well as for the production of electricity. Although the general feasibility of bioelectrochemical processes has been demonstrated in recent years, much research has been conducted to develop biocatalysts better suited to meet industrial demands. Initially, mainly natural exoelectrogenic organisms were investigated for their performance in BESs. Driven by possibilities of recent developments in genetic engineering and synthetic biology, the spectrum of microbial catalysts and their versatility (substrate and product range) have expanded significantly. Despite these developments, there is still a tremendous gap between currently achievable space-time yields and current densities on the one hand and the theoretical limits of BESs on the other. It will be necessary to move the performance of the biocatalysts closer to the theoretical possibilities in order to establish viable production routines. This review summarizes the status quo of engineering microbial biocatalysts for anode-applications with high space-time yields. Furthermore, we will address some of the theoretical limitations of these processes exemplarily and discuss which of the present strategies might be combined to achieve highly synergistic effects and, thus, meet industrial demands.

Introduction

Bioelectrochemical systems can be applied for the production of value-added chemicals, the generation of bio-electricity, wastewater treatment, and bio-sensing, among others (Bajracharya et al., 2016; ElMekawy et al., 2015; Mohan, Mohanakrishna, Velvizhi, Babu, & Sarma, 2010; Rosenbaum & Franks, 2014; Simonte, Sturm, Gescher, & Sturm-Richter, 2017). Exoelectrogens that can perform extracellular electron transfer (EET) with electrodes function as electrochemically active biocatalysts in these systems due to their ability to couple intracellular redox-reactions to extracellular electron transfer (Logan, 2009). These organisms can catalyze oxidative reactions on the anode site and reductive reactions on the cathode site, respectively. Here, we will focus on the anode performance of BESs biocatalysts and their improvement via synthetic biology approaches. We will summarize recent advances in broadening the substrate and product spectrum, as well as the overall productivity and current densities in microbial fuel cells (MFCs) and electrode-assisted fermentation approaches. Since synthetic biology raises the opportunity to tailor microbial biocatalysts for BESs, we will describe how various approaches could be synergistically linked in order to meet industrial demands.

Microorganisms that can conduct EET have developed strategies to transport respiratory electrons onto soluble or insoluble extracellular electron acceptors (Lovley & Phillips, 1988; Richter, Schicklberger, & Gescher, 2012). The electron transfer typically occurs via multiple c-type cytochromes that are localized to the inner membrane, the periplasm, and the outer membrane of gram-negative organisms (Richter et al., 2012).

Natural exoelectrogenic microorganisms have developed multiple mechanisms to transfer electrons from the cell-envelope to insoluble electron acceptors, such as anodes. In principle, bacterial electron transfer mechanisms can be divided into three groups. Some microorganisms are able to transfer electrons directly to the anode (Fig. 1 (1)) (Clarke et al., 2011). Therefore, the distance between the active site of the terminal reductase and the insoluble electron acceptor has to be less than 15 Å (Kerisit, Rosso, Dupuis, & Valiev, 2007). In addition, some microorganisms are capable of forming several cell layer thick conductive biofilms. In these biofilms, the electron transfer takes place with the help of so-called nanowires, extracellular matrix embedded soluble cytochromes or other electron shuttling molecules (Fig. 1 (2)) (Lovley & Walker, 2019; Reguera et al., 2005; Sure, Ackland, Torriero, Adholeya, & Kochar, 2016). A third possibility is the synthesis and secretion of soluble redox shuttles or the use of exogenous shuttle molecules that can undergo several redox cycles (Fig. 1 (3)) (Gralnick & Newman, 2007; Marsili et al., 2008; Velasquez-Orta et al., 2010). These redox shuttles, such as riboflavin (in the case of S. oneidensis) or phenazines (in the case of P. aeruginosa), can also transfer electrons from planktonic cells to the anode (Kotloski & Gralnick, 2013; Wang, Kern, & Newman, 2010). In addition, metals can be solubilized via the secretion of metal chelators. The chelated, dissolved acceptor can be reduced at the cell-surface (Kouzuma, Hashimoto, & Watanabe, 2012).

To date, at least nine different bacterial species were used for the production of value-added chemicals in BESs. These microorganisms are either natively capable of using insoluble electron acceptors or have been enabled by genetic modifications or the addition of electron shuttles. Nevertheless, the best-understood organisms belong to the genera Shewanella and Geobacter. Both S. oneidensis and G. sulfurreducens rely on a network of c-type cytochromes spanning the periplasm and the outer membrane (Fig. 2). The genome of S. oneidensis encodes 41 c-type cytochromes with partially overlapping functions, while the genome of G. sulfurreducens encodes 111 putative c-type cytochromes in total (Methé et al., 2003; Romine, Carlson, Norbeck, McCue, & Lipton, 2008). S. oneidensis transfers electrons from the menaquinone pool into the periplasm via the tetraheme c-type cytochrome CymA (McMillan, Marritt, Butt, & Jeuken, 2012). Thereby, CymA is not only involved in electron transfer to ferric iron or anodes but, moreover, is the main gate that delivers electrons to the electron transport chains, reducing, for example, fumarate, DMSO, nitrate, or nitrite (Myers & Myers, 2000; Schwalb et al., 2002a, Schwalb et al., 2002b, Schwalb et al., 2003). Similar to S. oneidensis, in G. sulfurreducens, the nonaheme c-type cytochromes ImcH and CbcL are gating electrons from the quinone pool onto cytochromes in the periplasm. When growing on anodes, the CbcL-dependent pathway operates at or below redox potentials of − 0.10 V vs. the standard hydrogen electrode (SHE), whereas the ImcH-dependent pathway operates only above this value (Zacharoff, Chan, & Bond, 2016). Both organisms use soluble periplasmic c-type cytochromes, such as STC and PpcA, as electron shuttles to bridge the gap of the periplasm, which is too wide to allow direct electron hopping between the two membranes (Fonseca et al., 2013; Lloyd et al., 2003). To transfer through the outer membrane, a trimeric/tetrameric porin-cytochrome complex spans the outer membrane and guides electrons received from periplasmic cytochromes onto terminal electron acceptors. In S. oneidensis, this complex is called the MtrABC-OmcA complex and consists of the β-barrel protein MtrB that, most likely facilitates the interaction between MtrA on the periplasmic site and MtrC on the cell-envelope. Loosely attached to MtrC is the second terminal reductase OmcA (Shi et al., 2006). Both cytochromes contain flavin cofactors that seem to accelerate the terminal electron transfer step, facilitating one electron transport via the formation of semiquinones (Okamoto, Hashimoto, Nealson, & Nakamura, 2013; Okamoto, Nakamura, et al., 2014; Okamoto, Saito, et al., 2014; Xu, Jangir, & El-Naggar, 2016). Similar to the situation in the cytoplasmic membrane, G. sulfurreducens can express several different outer membrane electron conduits. Nevertheless, ExtABCD seems to be the most important complex for ferric iron and electrode reduction (Otero, Chan, & Bond, 2018). In S. oneidensis, the electron transport chain ends almost directly on the surface of the outer membrane, while G. sulfurreducens can extend the electron transfer chain beyond the cell surface. To date, three strategies are thought to play a role. First, the octaheme c-type cytochrome OmcZ was shown to be dispersed throughout the extracellular matrix of G. sulfurreducens (Inoue et al., 2011, Inoue et al., 2010; Rollefson, Stephen, Tien, & Bond, 2011). Moreover, the deletion of key genes for the synthesis of an extracellular polysaccharide led to strains that could not thrive using insoluble ferric iron or an anode as an electron acceptor. It was recently elucidated that the c-type cytochrome OmcS forms long protein filaments that can extend several microns away from the cell. In fact, there is evidence that these OmcS filaments are the nanowires that were long discussed for G. sulfurreducens. Still, the competing opinion is that nanowires are composed of type IV pilus subunits and that aromatic amino acids of these subunits are arranged in a way that leads to conductivity via overlapping π-orbitals (Filman et al., 2019; Lovley & Walker, 2019; Wang et al., 2019). Nevertheless, even if these type IV pili might not be conductive per se, they were shown to be coated by OmcS proteins, which could render them at least partially conductive (Leang, Qian, Mester, & Lovley, 2010). Irrespective of the conductivity mechanisms of these nanowires it is clear that these extensions of G. sulfurreducens can facilitate electron transfer beyond the dimensions of individual cells.

The efficiency of a biotechnological production routine can be viewed from several perspectives as for instance (I) how much of the substrate is converted into the desired product, (II) what is the space-time-yield of the production process or (III) how many byproducts will be present in the reactor broth at the end of the production process. A low energy gain for the organisms and consequently a high catabolic production rate accompanied with low anabolic substrate conversion is favorable for efficient processes. This can be achieved under anoxic conditions. However, anoxic fermentations as for instance the conversion of glucose to lactic acid or ethanol and carbon dioxide come with the boundary condition that the products have to have on average the same oxidation state as the substrate. A more oxidized end-product demands the addition of an electron acceptor as for instance oxygen. Still, the addition of a respiratory electron acceptor like oxygen has the disadvantage that the energy yield for the biocatalysts will become tremendously higher. Hence, the ratio of catabolic over anabolic substrate conversion will decrease.

A solution highlighted in this review is to couple a respiratory process with an infinitely available anoxic electron acceptor. This is the concept of electrode-assisted fermentations (Flynn, Ross, Hunt, Bond, & Gralnick, 2010). Here, a solid-state anode of a bioelectrochemical system is the electron acceptor for the microorganisms. This electron acceptor can be poised to a certain potential which will determine the kinetics of the fermentation process. Moreover, the lower the potential at which the electrons are transferred to the anode, the more energy they carry. This energy can for instance be used via the concept of a microbial electrolysis cell in which the electrons are used to produce hydrogen on the cathode side. Although this requires the intake of a certain amount of additional energy, it was proposed that microbial electrolysis cells can lead to a hydrogen production with up to 75% less energy demand compared to conventional water electrolysis. Moreover, an electrode-assisted fermentation can be conducted in a biofilm reactor which offers the benefit of continuous production processes using a natural retentostat, which makes it easy to separate the end-product from the substrate and the biocatalyst.

Today, there are many bulk chemicals of great industrial interest. In fact, Werpy and colleagues ranked the 30 most promising bio-based building block precursors for a petro-independent economy (Werpy, Holladay, & White, 2004). At least 16 of them cannot be produced as sole end-products in anaerobic fermentations since they are more oxidized than for instance glucose (Fig. 3). Hence, they provide a potential target group for future strain developments and we will review in later parts of this review how far we are on the journey to develop processes for the electrode-assisted production of at least some of these compounds.