Talk:Shewanella oneidensis MR-1: Background and Applications

Introduction

Figure 1. Shewanella onedensis MR-1 growing on hematite. Shewanella are gram-negative, proteobacteria that are facultative anaerobes and can respire on a tremendous variety of inorganic and organic electron acceptors. One such electron acceptor is Fe₂O₃, which is commonly found in the clay hematite. (Photo from Oak Ridge National Laboratory; http://www.ornl.gov/info/ornlreview/v37_3_04/article02.shtml).

The genus Shewanella consists of gram-negative proteobacteria that are typically rod shaped, 2-3 μm in length and 0.4-0.7 μm in diameter (Fig 1). These facultative anaerobes are often found in marine sediments, and can swim with the aid of a single polar flagellum (Venkateswaran et al., 1999). Since the modern characterization Shewanella in 1988, DNA:DNA hybridization and 16S rRNA sequencing has been used to identify more than 40 distinct species. The features that characterize this genus include psychrotolerance, mild halophilicity, and the capacity to reduce an unparalleled array of inorganic and organic compounds for respiration (Gralnick et al., 2007). Their capacity to respire on various metals as well as their production of endogenous hydrocarobons has ignited tremendous interest in the characterization and potential applications of these microorganisms.

Brief History

Shewanella was originally identified in 1931 as one of multiple species of bacteria growing on putrid butter (Hammer, 1931). It was first classified as part of the genus Achromobacter and was reclassified multiple times on the basis of its polar flagella, its status as a non-fermentive marine bacteria, and the guanine/ cystine content (% GC) of its DNA (Gralnick et al., 2007). In 1985, 5S rRNA sequencing was used support an entirely new name for the genus, Shewanella. The name was given as a tribute to Dr. James M. Shewan for his work in fisheries microbiology (MacDonell et al., 1985).

Model Species of the Genus Shewanella: Shewanella oneidensis MR-1

In 1988, a group of scientists became curious about the unexplained levels of reduced manganese (Mn²⁺) present in New York’s largest freshwater lake, Lake Oneida (Fig 2). In nature, manganese generally exists in its oxidized form (Mn⁴⁺), and thus the scientists hypothesized that some biological process was reducing the manganese. Upon experimentation, they discovered a species of Shewanella that respires by transferring electrons to Mn⁴⁺. Interestingly, oxidized manganese is insoluble, which indicated that the bacteria have a way to transfer electrons to metal outside of their cells for respiration. After rRNA sequencing, the bacteria was characterized as a Shewanella , and the species was named Shewanella oneidensis MR-1 (“manganese reducer”) after the lake in which it was discovered (Slonczewski et al, 2011). This MR-1 species was the first shewanella to genome to be sequenced, and thus it has become a model system for the study of the genus (Gralnick et al., 2007).

Mechanism of Action for Metal Reduction: Biofilm Formation

The ability to respire on insoluble substances is a true biological feat that scientists have begun to deeply investigate. The first step to successful reduction of extracellular metals is the formation of biofilms by shewanella on the metal oxide. Biofilms facilitate close contact between the bacteria and the oxidized metal (Thormann et al., 2004). A study by Thormann et al. (2004) investigated mechanism of biofilm formation by Shewanella oneidensis MR-1 on glass surfaces. They reported that the microbes first attach and grow laterally until they cover the majority of the surface available to them. The Shewanella then begin to develop the biofilm vertically creating towering structures (Fig 3). Using mutagenesis experiments, the scientists discovered that the microbes do not need to swim in order to attach to the surface. The swimming motility is actually critical to formation of the three dimensional structures. Instead, the biosynthesis of a type IV pilus (Fig 4A) is crucial to microbe to surface adhesion and the ability to retract pili (Fig 4B) is required for lateral coverage by the biofilm. The scientists also reported that the Shewanella grow more robust biofilms, with greater microbe to surface interactions, when nutrient levels are poor (Fig 5). This probably happens because when nutrient levels are high in the media and oxygen is available (as was the case in this experiment), the organisms can simply catabolize the nutrients aerobically rather than investing energy in the formation of a biofilm for low energy-yielding respiration. However, the typically anaerobic natural environments of Shewanella encourage biofilm formation, which allows them to thrive on nutrients that most other organisms cannot use.

Transfer of Electrons: Cytochromes and Riboflavins

Once the biofilm adhering the microbe to the metal is formed, molecules are required to transfer electrons from the microbial cell to the metal for respiration. Some of the most important molecules for this transfer are called cytochromes, which are electron transport proteins that associate small, reversible energy transitions with electron transfer. Cytochrome proteins consist of the protein structure containing a heme cofactor (Fig 6). The heme cofactor is composed of a ring of conjugated double bonds surrounding an iron atom. Double bonds and iron atoms can acquire and transfer electrons because they have narrowly spaced energy levels that facilitate small energy transitions. These small energy transitions prevent the loss of energy as heat, and instead, energy can be converted to small process such as the pumping of protons across a membrane or the reduction of metals (Slonczewski et al, 2011).

In nature, there are various types of cytochromes, and Shewanella oneidensis MR-1 has been reported to contain at least 42 putative cytochrome c molecules (Meyer et al., 2004). The cytochrome c molecules of Shewanella have multiple heme groups and exist in the inner membrane (CymA), the periplasm (MtrA), and the outer membrane (MtrC and OmcA). The outer membrane cytochromes, MtrC and OmcA, are lipoproteins associated to the outer membrane and the outer membrane proten MtrB (Fig 7). They are fixed in the outermembrane by the type II protein secretion pathway (Fig 8). In this position MtrC and OmcA cytochromes are exposed to the extracellular environment where they can contact with metals to which they transfer electrons. These outer membrane cytochromes are so crucial to metal reduction that Shewanella putrefaciens MR-1 species that are missing OmcA and MtrC are 45% and 75% slower respectively at reducing MnO₂ than non-mutated strains (Myers et al., 2001). While the function of most of the other cytochrome c variants have yet to be elucidated, some have been implicated in fumurate, nitrate, and DMSO reduction (Fredrickson, et al., 2008).

Riboflavins

In Figure 7, the reduction on the left depicts intermediate flavins as part of the metal reduction pathway because they have been shown to shuttle electrons to metals that do not contact extracellular cytochromes. Riboflavins, otherwise known as vitamin B2 (Figure 9), have conjugated double bonds that allow the small energy transitions useful for the carrying electrons. Further, its largely polar tale increases the solubility of riboflavin such that it can shuttle electrons from cell surface to external metals. Marsili et al. (2007) discovered the use of riboflavins as soluble electron shuttles when the media surrounding biofilms of Shewanella oneidensis MR-1 was removed and electron transfer dropped by > 70%. In organisms that use strictly outer membrane cytochromes, such as Geobacter, the removal of the media surrounding the biofilm has a minimal affect on rates of electron transfer (> 5%). This finding suggested that Shewanella produce a molecule that completely dissociates from the membrane and moves freely in the media. When the components of the media were characterized using reverse phase liquid chromatography coupled with secondary mass spectroscopy (LC-MS), the soluble, electron carrier riboflavin was identified. The study also demonstrated that riboflavins quickly adhere to Fe³⁺ and Mn⁴⁺, which are commonly reduced by Shewanella further supporting the hypothesis that riboflavins act as electron shuttles for the microbes. The production of riboflavins helps explain the ability of Shewanella to transport electrons to metals that are > 50 μm away from the cell surface (Lies et al., 2005).

Transfer of Electrons: Nanowire Synthesis

Along with cytochromes and riboflavins, Shewanella oneidensis MR-1 have also been shown to synthesize pilus-like, electrically conducive appendages known as bacterial nanowires. Gorby et al. (2005) viewed these nanowires using scanning electron microscopy in Shewanella that had been exposed to very low oxygen conditions or anaerobic conditions with low concentrations of electron acceptors such as Fe^{3+ or fumurate. By contrast, Shewanella that were exposed to high oxygen conditions (O2 > 2% air saturation) did not produce confluent biofilms or extensive nanowires (Fig. 10). The nanowires were 50-150 nm in diameter and extended tens of microns or longer connecting the bacteria to each other as well as to the surface on which the biofilm is growing. Further, while Geobacter produces long thin filaments as nanowires, Shewanella seem to package multiple filaments together into a type of conductive cable.}

The group demonstrated that these extracellular appendages transmit current by incubating Shewanella with an aqueous suspension of the poorly crystalline silica hydrous ferric oxide (Si-HFO). When they viewed the cultures with transmission electron microscopy, they discovered that the Si-HFO had been transformed to the reduced form of nanocrystalline magnetite along the extracellular features, which were consistent with the dimensions of nanowires. Further, when they visualized samples from the top of the medium, they also found crystalline solid-phase iron oxide (Fig 11). Since there were no cells present at the top of the media, this finding suggests that the nanowires could stretch a significant distance from the cells in order to reduce the aqueous iron oxide, transforming it into crystalline structures (Gorby et al., 2005). In a later study, Gorby et al. (2010) directly measured the conductivity of the nanowires by putting nanofabricated electrodes at the top of the nanowires. They also tested whether nanowires could bridge a metallic electrode and the conductive tip of an atomic force microscope. Using these methods, they discovered that the nanowires are conductive along a micrometer length scale and can transport electrons at rates up to 109/s at 100 mV of applied bias and 1 Ω*cm of resistivity.

Finally, mutagenesis experiments indicated that mutants missing the MtrC and OmaC cytochromes produce filaments that are not electrically conducive. Specifically, filaments produced by mutants did not solidify aqueous iron-oxide, nor did they transmit a current when contacted with the nanofabricated electrodes (Gorby et al., 2010). Thus, these outer membrane cytochromes may act as “intermediate” electron carriers for the nanowires or have some other role in the conductivity of these filaments (Gorby et al., 2005).

Section 3

Include some current research in each topic, with at least one figure showing data.

Conclusion

Overall paper length should be 3,000 words, with at least 3 figures.

References

[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.

Edited by student of Joan Slonczewski for BIOL 238 Microbiology, 2009, Kenyon College.