Nanowires in the oceans can conduct electricity and combat climate change

Using a model bacteria to study nanowires

In a new paper published in Nature Microbiology, a Yale team led by Yangqi Gu and Nikhil Malvankar at the university's Microbial Sciences Institute analyzed how the common soil bacteria Geobacter employs tiny protein filaments called “nanowires” to produce electricity and survive without oxygen. The scientists chose Geobacter as a model system to study since its filaments are similar to those used by methane-eating microbes. This bacteria uses nanowires made from the cytochrome OmcZ protein and contains a core of metal-containing molecules. The protein filaments are projected into the soil to dispose of excess electrons resulting from the conversion of nutrients to energy and allow the bacteria to "breath" without oxygen.

For the first time, the scientists were able to explain how the bacteria makes the nanowires and how they achieve high electron conductivity. The OmcZ is the highest conductive protein filament known to date, according to the scientists, who also carried out an earlier study of the bacteria. Additionally, the team was able to produce synthetic nanowires, allowing for the possibility of creating them on demand. 

For the study, Yangqi and the team utilized cryo-electron microscopy, which allowed them to examine the atomic structure of the bacteria. They discovered that a special arrangement of metal-containing molecules called hemes line up close to each other in a straight line to allow the nanowires to move electrons with great speed and extremely high stability. The researchers deduced that this mechanism allows the bacteria to survive without using oxygen or oxygen-like molecules.

The paper also explains that the structure of the nanowires helps explain bacterial survival in extreme environments by allowing bacteria to move electrons over 100 times their size. It also explains how the nanowires play a role in the formation of microbial communities in biofilms. 

How did the scientists achieve their results?

To delve deeper into the team’s findings, Interesting Engineering spoke to Nikhil Malvankar, associate professor of Molecular Biophysics and Biochemistry at Yale's Microbial Sciences Institute, where he heads the Malvankar Protein Nanowire Lab.

The following has been edited slightly for flow and clarity.

Interesting Engineering: Can you elaborate on the processes of high-resolution cryo-electron microscopy and purifying nanowires that allowed you to discover the previously-unseen heme structure? What was significant about this approach?  

Nikhil Mavankar: Deep in the ocean or underground, where there is no oxygen, Geobacter “breathe” by projecting tiny protein filaments called "nanowires" into the soil, to dispose of excess electrons resulting from the conversion of nutrients to energy.  These nanowires enable the bacteria to perform environmentally important functions such as cleaning up radioactive sites and generating electricity. Scientists have long known that Geobacter make conductive nanowires – 100,000 times smaller than the width of a human hair – but no one had discovered what they are made of and why they are conductive. In 2020, my lab, led by Sibel Ebru Yalcin, discovered nanowires made up of another cytochrome, and my student Yangqi Gu recently solved its structure. Previously, nobody suspected such structures because cytochromes were not known to form conductive filaments. Our lab is the first to purify nanowires from bacteria without any contamination. This high purity allowed us to obtain a significantly higher resolution structure than other labs. Furthermore, our functional studies established how bacteria use these nanowires for growth, communication, and biofilm formation.

IE: Are there advantages to creating the nanowires synthetically? Would using them to combat climate change, for instance, require synthetic or organic nanowires? 

One of the biggest challenges with nanowires is how to produce them at a large scale with high purity. Using the E-coli strain genetically engineered by Yuri Londer in my lab, Yangqi and Fadel built nanowires synthetically to explain how bacteria make nanowires on demand. They found that bacteria attach a sugar-binding domain to OmcZ to keep it in the monomeric form and use a protease to remove this domain that assembles OmcZ into nanowires as needed (see video – OmcZ (yellow), protease (pink), sugar-binding domain (blue)). Prof. Kallol Gupta’s mass spectrometry ensured that the synthetic OmcZ is similar to that made by Geobacter. This allowed nanowire synthesis at high yield and purity.

IE: What is next for your research? What kind of technology and knowledge would we need to achieve to start the application of nanowires to fight climate change?  

Discovery of nanowires is helping to solve a longstanding mystery of how microbes export electrons outside their body, to minerals, to partner with other bacteria to share energy, and to generate electricity. This discovery of highly conductive nanowires might mean that a variety of other globally-important reactions in environments are also mediated by rapid electron flow. Therefore, rather than relying on diffusion of small molecules as electron carriers, this, in turn, would implicate a new model of direct electron flow via nanowires in processes such as bioremediation, corrosion, and carbon sequestration.

Indeed, Yangqi’s bioinformatic analysis suggests that nanowire machinery could be widespread in diverse bacteria and archaea, including those that regulate climate by consuming 80% of the methane in oceans, which protects the Earth from warming up. Both these methane-consuming and methane-producing microbes need partners to drive an otherwise slow or thermodynamically unfavorable reaction performed by another.

In addition to methane-eating microbes that produce proteins similar to Geobacter nanowires, methane-producing microbes also partner up with Geobacter and share electricity via nanowires. Although many such processes are thought to use such a mechanism, the components, and pathways involved have not yet been identified.

Microbial electron transfer via nanowires could accomplish the same catalytic feat, perhaps faster and more specifically (so that electrons are transferred directly between only the right kinds of organisms) than via rapid diffusion of small molecules. Therefore identifying how electrons move in these nanowires could be the key to understanding how microbes serve as both the biggest producers as well as consumers of methane, to combat climate change by controlling electricity flowing in these nanowires.

The strength and conductivity of these nanowires, coupled with the ability of bacteria to repair broken nanowires, could help create durable, self-healing electronics using living cells. Microbial nanowires offer promise for achieving a new class of electronic materials that could exhibit the electrical and optical properties of metals and semiconductors but retain mechanical properties and diverse functionalities of proteins to bring together synthetic biology with semiconducting technology.

Read the new paper Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity in Nature Microbiology.

Abstract:

OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm−1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome essential for the formation of high-current-density biofilms that require long-distance (>10 µm) extracellular electron transport. However, the mechanisms underlying OmcZ nanowire assembly and high conductivity are unknown. Here we report a 3.5-Å-resolution cryogenic electron microscopy structure for OmcZ nanowires. Our structure reveals linear and closely stacked haems that may account for conductivity. Surface-exposed haems and charge interactions explain how OmcZ nanowires bind to diverse extracellular electron acceptors and how organization of nanowire network re-arranges in different biochemical environments. In vitro studies explain how G. sulfurreducens employ a serine protease to control the assembly of OmcZ monomers into nanowires. We find that both OmcZ and serine protease are widespread in environmentally important bacteria and archaea, thus establishing a prevalence of nanowire biogenesis across diverse species and environments.