Bondism...

6/14/2016

A few months ago, a fellow researcher and friend of mine, Jeff Gralnick (@bacteriality), came to ASU to give a seminar on Shewanella. After the seminar, I invited him out for a beer at a local joint called Taste of Tops. Jeff, being Jeff, could never turn down a beer so off to Tops we went. While at Tops, I discussed with him the idea of #ScienceTheEarth before it even had a name. At the time, it was still this idea I had rolling around in my head. When I told him of my plans, over beer, he was very supportive and suggested I come visit Minnesota. Why yes, I’d love to!

The first lab tour and presentation of #ScienceTheEarth outside of Arizona is in the labs of Daniel Bond (@WanderingBond)and Jeff Gralnick at the University of Minnesota in the Biotechnology Institute. I am picked up from the airport by Jon Badalamenti (@jbadomics ), (Jon’s the guy that isolated and sequenced Geoalkalibacter ferrihydriticus Z-0531T and Geoalkalibacter subterraneus Red1T among other things) a former ASU colleague and advocate of all things beer. Then again, most everyone in the Bond and Glalnick labs are advocates of all things beer.

There are a few things that strike me as I’m driving from the airport to the lab.

The weather here is a lot like Portland. Wet, a little sticky, not Phoenix.
The campus on the St. Paul side of the river is a bit smaller. By a bit smaller I mean located next to a barn on the Minnesota state fair grounds.
The parking lot smells really ‘fresh’ (see the barn from number 2)

Walking into the Bond lab, where Daniel presides, I am greeted to a study room full of beer and sausage. Caleb Levar is in the lab today- a local brew master for Fair State Cooperative and he has supplied the lab with plentiful amounts of sausage. Discussions range from a diversity of topics, from watermelon, to e-pili, to beer, to wall caulking. During our brainstorming session, I tried at least ten different beers- I cannot even remember the names of all of them, but I did manage to capture an image of a Wisconsin Belgian Red from New Glarus Brewery. This beer tasted more like a fruit juice than beer- absolutely fantastic!
Rumor has it that Daniel is known to talk- a lot. Get the guy talking about cells, electrochemistry, beer, cows, and you could easily spend an entire afternoon. Of course, with great conversation comes great quotable moments. To commemorate Daniel’s quotable moments, the lab has made him a custom shirt full of what have been labelled “Bondisms.”
A few examples:

It’s wonky
Is it glowing yet?
Let’s all work at the state fair during the summer – selling fried squid on a stick.

During my seminar, we gained a new Bondism, “"Is this just Fick's Law telling us to 'suck it'?" #shitbondsays. This one occurred during my lecture titled: “pH Shifts in the Anode Potential Response from Thermincola ferriacetica Suggest Rate Limiting Proton Coupled Electron Transfer Protein.” What he’s getting at is the fact that, despite our best efforts, we cannot seem to get biofilms in microbial electrochemical cells (MXCs) to produce current densities higher than 10-15 A m-2. With T. ferriacetica one would assume that this would be possible given the thermodynamic and kinetic benefits of operating a reactor at twice the temperature (60C vs 30C) of a mesophilic reactor. A major limitation to current production in MXCs is the accumulation of protons in the biofilm. More protons means lower pH, lower pH means a more acidified biofilm, a more acidified biofilm means all of our bacteria eventually turn into pickled gew! At high temperatures, we suspect that protons will be able to move out of the biofilm at a greater rate and thus enable higher current production. This is the case at lower buffer concentrations, but not at high buffer concentrations. Something else is limiting these biofilms once they achieve a certain current density and increasing cell numbers doesn’t seem to help. I have a paper about this under review and will divulge more information once it’s published in the Science section of the blog.

I also got a little tour of the lab. People in the Bond lab are primarily working on mutants of an anode respiring bacterium called G. sulfurreducens. The purpose of using these mutants is to gain insights into which genes are important for biofilm formation, metal reduction, and anode respiration. Most of the mutants in this lab are deletions of some sort.

The first research project I am shown is conducted by Fernanda Jimenez Otero (@fer_jimotero), a graduate student in the lab. Her work involves deleting pathways from Geobacter sulfurreducens, an anode respiring bacteria, to see how these deletions affect biofilm development and current density. Her research shows that certain deletions cause biofilms to pack more tightly and thus produce about 40% more current per unit area. She is also using radioactively labelled carbon and nitrogen to probe into where new growth and substrate turn-over occurs in biofilms. She is presenting at ASM 2016 in Boston at the same session as I am, just 15 minutes prior to my talk. The name of the session is “Microbial Electric Grids: Electromicrobiology, Fuel Cells, Nanowires, and Cable Bacteria” in room 252A on Friday, June 17 at 2:45PM. Her abstract is located on page 479.

The next research project is led by Eric Kees (@lostmykees) and involves using MXCs to determine if evolution can be halted using an anode. To run this experiment, anode respiring bacteria that are mutated and have less functionality than their wild type (non-mutated) counterparts are introduced to an MXC and allowed to occupy the anode. After they develop a biofilm on the anode, wild type are added. Theoretically, the wild type bacteria should be able to grown more efficiently on the anode and thus select away the mutants. However, since the anode is already occupied by the mutant strain, the physical constrains of accessing an anode that is already occupied prevent the wild type bacteria from overtaking the anode.

Before I am to depart the University for my last lab tour, I am informed by the local weather agency that a tornado warning has been issued for most of the Minneapolis- St. Paul area. As Jon and I are driving through the rain on our way to the brewery, the radio informs us that the tornado warning has been lifted.

For my last ‘lab tour’, I am told that I am going to a brewery called the Fair State Brewing Cooperative. (I also went to Surly Brewing, another local staple, and it was quite good.) At Fair State, Caleb Levar (@celevar1) took Jon and me into the basement where there is a room with about 50 barrels of beer brewing. To my recollection, all of them contained sour beers- most around pH 3-4. He snuck over to a barrel he was particularly fond of and, after working a nail for about a minute, opened a little hole to remove some of the beer. It smelled like a campfire and tasted like a sweet wine, almost like a sour moscato. Before departing, we had a little time of a bar chat. For scientists, this usually means writing down Greek symbols next to some cassettes and talking about mutations, rates, and the probability that anything we’re writing down will ever produce publishable data. I swear, I need to convince Bill Gates to make a ‘beer talk’ grant through the Bill and Melinda Gates Foundation so that we can start funding these things! I’ll have to make that my goal at American Society for Microbiology conference this week.