also strategies to transport Fe3+ ions from the mineral to the cell, using chelators (i.e. siderophores). In any case, the communities have to be highly organized, as otherwise the energetic costs of manufacturing such structures would not be compensated by the energy gain of reducing the extracellular electron acceptor.
All known Shewanella strains have been shown to secrete flavin mononucleotide (FMN), a molecule that can shuttle one or two electrons from its alloxazine ring structure to the extracellular electron acceptors (Marsili et al. 2008; von Canstein et al. 2008; Coursolle et al. 2010). Three out of the 10 hemes of the multiheme cytochrome MtrF, an MtrC homolog, have been shown to directly reduce FMN (–150 mV). En route to reduce FMN, electrons move from MtrF hemes with a low redox potential to MtrF hemes with a higher redox potential (Watanabe et al. 2017).
Another way in which MR‐1 can reduce solid phase electron acceptors is via nanowires. Nanowires in MR‐1 extend out of its outer‐membrane and include the periplasm (Gorby et al. 2006; Pirbadian et al. 2014). These outer‐membrane extensions bud out of the cell and form into vesicles. Thus, a nanowire is not a smooth filament, it is in fact a chain of outer membrane vesicles connected to each other with a periplasmic interior and can be differentiated from flagella and pili by electron cryotomography (see Figures 3, 4, and 7 in Subramanian et al. 2018). The outside of the vesicle is coated with outer membrane cytochromes (e.g. MtrC) and the inside (periplasm) is coated with periplasmic cytochromes (e.g. MtrA; Subramanian et al. 2018). These vesicles along the nanowire in turn are divided by gap junctions, which keep vesicles apart (Subramanian et al. 2018). These vesicles are also dynamic and can grow and shrink in size or transition from multiple vesicles into a single giant vesicle and vice versa (see Figure 5 in Subramanian et al. 2018). When multiple vesicles are connected to each other, it is hypothesized that electrons hop between the vesicles from cytochrome complex to cytochrome complex when heme groups are in close range. When these complexes are not in close range, it is hypothesized that cytochrome complexes or electron shuttles physically diffuse between vesicles until reaching another cytochrome complex thereby passing on the electrons (Subramanian et al. 2018).
It is known that G. sulfurreducens has two different types of filaments, which are implicated to participate in iron oxide reduction. Their three‐nanometer‐wide pili (termed e‐pili) are mostly composed of the PilA protein with the hexaheme cytochrome OmcS distributed along the pili (Costa et al. 2018). In Geobacter, the e‐pili are extensions of the cytoplasmic membrane (Reguera et al. 2005) that protrudes out of a channel protein embedded in the outer membrane (Shi et al. 2007). Studies by Malvankar et al. (2011, 2015) showed that the Geobacter e‐pili are essential for reducing iron oxide. These e‐pili have also been shown to transfer electrons between Geobacter and other species (Lovley, 2017). It is hypothesized that electrons could travel along the e‐pili, from pili protein to pili protein, until reaching the solid phase electron acceptor (Feliciano et al. 2012; Lampa‐Pastirk et al. 2016). Vargas et al. (2013) showed that overlapping π–π orbitals of aromatic moieties and aromatic amino acids that make up the pili protein PilA give the pili their conductive property. Recently, Filman et al. (2018) showed through cryo‐electron microscopy (cryo‐EM) and biochemical modeling that a second type of conductive filament is produced by G. sulfurreducens (termed OmcS‐filaments), which could be involved in long‐range electron transfer to iron minerals and other microorganisms. Unlike the outer membrane cytochrome vesicles of the MR‐1 nanowire, the OmcS cytochromes are packed close enough along the length of the filament to allow for direct electron transfer between the heme groups of these cytochromes (Filman et al. 2018). A recent publication by Walker et al. (2019) shows that the archaellum of the archaeon Methanospirillum is conductively similar to the e‐pili of Geobacter, demonstrating that these structures are not limited to bacteria.
Furthermore, siderophores, which are low molecular weight chelators (400–1000 kDa; Saha et al. 2012), are produced by organisms under iron‐limited conditions in order to acquire and take up iron that would otherwise be bound to iron oxides or organic matter. There are various types of siderophores, which are classified based on the type of ligand that binds the iron. The ligands include moieties, such as catecholates, phenolates, hydroxamates, carboxylates, and mixed types (Saha et al. 2012), where the oxygen groups of the ligands form a bond to the iron center. Siderophores are excreted out of a bacterial cell by a transport protein or a pump (e.g. ATPase) and form a bond with Fe3+ ions (Saha et al. 2012). Once captured, either the Fe3+ ion enters the cell after being released from the siderophore, or the entire siderophore‐iron complex enters the cell (Saha et al. 2012). While siderophores have a high affinity for iron, most siderophores also chelate other metals albeit with a lower affinity (Kraemer 2004). For example, Pseudomonas aeruginosa secretes the siderophore pyochelin, which in addition to Fe3+ also chelates other cations (Braud et al. 2009). While the chelation is thus not precisely specific for iron, specificity arises at the stage where pyochelin bound to iron(III) is taken into the cell by a specific transporter at a higher rate than three other pyochelin metal complexes, implying that siderophore‐iron uptake by its transporter is selective in this organism.
A further strategy that is employed by uncultivated members of the Desulfobulbaceae family (filament‐forming cable bacteria; Nielsen et al. 2010; Pfeffer et al. 2012; Schauer et al. 2014, pp.1314–1322) is cell‐to‐cell conductive electron transport, possibly via c‐type cytochromes which are present in the envelope of single cable bacterial filaments (Figure S5, Kjeldsen et al. 2019) and show a redox gradient along the filament (Kjeldsen et al. 2019). However, this has yet to be experimentally verified. Cells attach to one another in a long chain to form a bacterial “cable”. The outer membrane of cable bacteria is rigid and has tubular channels that connect the periplasm of neighboring cable bacteria to each other (Reguera 2018). The periplasm of these cells appears to be packed with c‐type cytochromes (Bjerg et al. 2018).
Using minicores of shallow marine sediment from Aarhus Bay, Risgaard‐Petersen et al. (2012) observed that sulfate can be oxidized 2 cm away from the reduction of oxygen, and that an electron gradient was present in the pore fluid. This was interpreted as indicative of microbial communities performing long‐distance electron transport. Pfeffer et al. (2012) observed that sulfate could be reduced by cable bacteria at the bottom of long filaments within the top 2 cm of marine sediments. Subsequent in‐situ studies of cable bacteria, have also observed them within the top few millimeters of coastal marine sediments (Otte et al. 2018).
While more details about the molecular pathways of electron transport are being discovered, it is still poorly understood how the different strategies of accessing solid electron acceptors affect the rates of dissolution of different iron mineral phases. Future studies using nondestructive in vivo techniques, such as interferometry (Waters et al. 2009) may provide possible routes to better understand and quantify mineral surface reactions in the presence of living microbes.
3.3.3. Uptake of Iron as a Nutrient
In addition to acting as an electron acceptor, iron is an important nutrient for all living organisms. Most importantly, iron plays a major role as reactive centers in electron shuttling enzymes, e.g. cytochrome, ferredoxin, and iron‐sulfur proteins. Hence, it is critical that a sufficient level of iron is always available in order to drive the essential catabolic functions in the cell. Even under strongly sulfidic conditions, apparently there is still enough iron available despite the low solubility of iron sulfides (cf. Figure 3.1).
MR‐1 in particular requires a large number of heme‐containing cytochromes for its respiratory versatility. In a hypothesized model, one way iron could enter MR‐1, is via undefined porins on the cell surface (Bennett et al. 2018). Under iron‐deficient conditions MR‐1 can secrete siderophores, such as putrebactin, to acquire Fe3+ and transport the Fe3+‐siderophore complex via a TonB protein complex on the outer membrane (Bennett et al. 2018). Once inside the periplasm, the protein FeoB could transport Fe2+ into the cytoplasm (Bennett et al. 2018). MR‐1 could
