465 - Partners Produce Predator Prevention

Fungus cells with 
bacterial symbionts
By Büttner et al. 2021
PNAS 118:e2110669118
CC BY-NC-ND 4.0

This episode: Bacteria living inside soil fungus produce toxins that can protect their host from tiny predators!

Download Episode (7.7 MB, 11.2 minutes)

Show notes:
Microbe of the episode: Mycobacterium virus DLane

Takeaways

Soils have many different organisms cooperating and competing for resources. Some little worms called nematodes prey on fungi in the soil, while fungi may effectively defend themselves or strike back with toxins or traps that catch and kill the worms. On top of these interactions are other organisms that interact in various ways. In this study, bacteria living inside a kind of soil fungus produce toxins that defend the fungus against predatory nematodes.

Journal Paper:
Büttner H, Niehs SP, Vandelannoote K, Cseresnyés Z, Dose B, Richter I, Gerst R, Figge MT, Stinear TP, Pidot SJ, Hertweck C. 2021. Bacterial endosymbionts protect beneficial soil fungus from nematode attack. Proc Natl Acad Sci 118:e2110669118.

Other interesting stories:

• Sequencing stomach bacteria to find out how prehistoric populations migrated

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, Google Podcasts, Android, or RSS. Support the show at Patreon, or check out the show at Twitter or Facebook.

Interview of me on the podcast Curioscity

Another good podcast you should check out is Curioscity, in which the host, Calvin Yeager, interviews other scientists about various aspects of science, their research, and other aspects of how science gets done!

He recently interviewed me about my experience getting a job as a scientist outside academia, and what that's like, so if you'd like to hear about that, here's the link:

Curioscity 53 - What Is Industry?

Special episode, hurricanes, and more

Hey all, I've been working on a somewhat special episode that is taking me longer than usual, so I don't have anything for this week. It may be up next week, but it is unlikely due to Hurricane Dorian and/or family events. Look forward to it!

No episode this week

Sorry, no episode this week, possibly next week too, but I am working on some good ones.

Skipping a week

Sorry, no episode this week, due to vacations and busy-ness.

State Fair

Last interruption for a while: I was participating in the NC State Fair all weekend. It was fun and there were even microbe exhibits there! Though mostly ones encouraging hand-washing.

No episode this week

Family event this weekend, so I didn't have time to get an episode up. See you next week!

Hurricane Florence

No episode this week, thanks to Hurricane Florence. I'm ok though and will be back next week! Everyone stay safe.

No episode this week

No episode this week. I am working on getting some papers published! Stay tuned.

Hurricane Preparedness

No episode this week. Busy preparing for the edge of Hurricane Irma. To all my listeners in a hurricane's path, stay safe!

BacterioFiles Special - ASM2015

Here's my summary of ASM2015, an exciting weekend full of science.

Download Episode (11.5 MB, 12.5 minutes)

The convention center in NOLA

Bird in a bayou

Not solid ground

Your host

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe at iTunes, check out the show at Twitter, MicrobeWorld, or Facebook

ASM2015 General Meeting Next Week

No full episode next week; BacterioFiles will be at ASM2015! But I will try to have some conference content to share nevertheless.

Scientists for Science

My interests here mostly are not focused on research directly relating to infectious diseases and pathogens, but I do think this research is worth doing, worth funding, and worth talking about. Pathogens can be just as fascinating as any other microbe, if not sometimes more so.

However, in light of certain recent research that has had a high potential for shock value (such as modifying bird flu to be transmitted easily between ferrets), there has some talk of restricting the kinds of research that should be done on potentially dangerous emerging pathogens (or, in the case of smallpox, almost obsolete ones).

The hosts of This Week in Virology have discussed this issue a great deal recently, and I agree with them that great care must be taken when putting in place these sorts of restrictions. The risks of such research are generally known and minimized by the regulations we already have in place (only working in BSL-3 and -4 conditions, for example), whereas the benefits are unknown and could be very great, even beyond the question of how to treat or prevent the disease being studied. The results of basic science are unpredictable.

So what is needed is not gut reactions to the issue, but careful, serious, considered conversation. If you feel the same way, whether you're a scientist or not, you can show your support by visiting www.scientistsforscience.org (founded by the TWiV team, I believe) and by spreading the word.

New podcast about plant pathology

Plants are very important for people (and bacteria!), and I talk a lot about soil ecology on this show, but microbes can cause disease in plants too, as much or more as in animals, especially fungi. So I'd like to introduce this newly minted podcast about plant pathology, the study of plant diseases, hosted by a graduate student in that field of study. If it sounds interesting, check out The Plant Pathology Podcast!

New Domain Name

In case you hadn't noticed, the show's website is now bacteriofiles.com. Thanks to listener Andrew Billo for his donation!

What I've been doing in my lab

...for those who are curious.

I took this picture a while ago so I don't remember exactly what was growing, but it definitely included some strain of a soil bacterium.

The point of the complicated setup is to be able to keep these bacteria in a constant state of healthy proliferation; that is, about every 5-10 hours (depending on the strain), every cell in the tank in the center will have divided into two new cells, effectively doubling the population.

This is called exponential growth, because when this takes place in a flask of a given amount of broth, nothing added or removed, the size of the population doubles every 5-10 hours, so the number of cells in the population, if you start with 2, is 2 to the nth power, where n is the number of 5-to-10-hour periods (depending on the strain) that have passed. So after 5-10 hours, there will be 4 cells, then after 10-15 hours, 8 cells, then 16, then 32, then 64, and it goes up exponentially.

However, this is not the case in this picture, because rather than having a given amount of broth, there's a bottle of fresh broth outside the frame up above, and new broth is being added to tank where the bacteria are growing, so their food is being constantly replenished at a certain rate. At the same time, the volume in the tank is being kept constant by removing excess material, including the cells in it, thus reducing the size of the population. So the size of the population of bacteria effectively remains constant over time.

The point of this is to study the behavior of the bacteria. There are some good reasons to maintain a population of bacteria this way; for one thing, you can repeatedly make changes to the broth you're feeding them, or other environmental factors, to see how the behavior changes, without having to repeatedly clean out and sterilize the tank, add fresh medium, and inoculate it again.

In my case, what I'm currently doing, is trying to figure out how much hydrogen gas my bacteria produce when I feed them a certain amount of sugar. As long as they have everything else that they need, it should be the case that the more sugar I give them, the more hydrogen they produce, and I'm trying to quantify the relationship between those two factors.

In order to do that, I make a tank of broth with a known amount of sugar, feed it to the bacteria until the population size stabilizes, and measure the amount of hydrogen they produce with that white box to the left. I'm also measuring the size of the population using other methods. Then, I increase the concentration of sugar in the broth, keeping everything else the same, let the population stabilize, and measure the new values of hydrogen and population size. Once I've done this a few times, I can make a graph of hydrogen produced per gram of sugar added or something.

The other cool thing about the setup in this picture is that it allows me to control many environmental factors and take measurements in real time: the unit on the right is a unit that controls and takes measurements, and it can measure the amount of oxygen in the tank, the pH, the temperature, and how much broth is left in the tank, and it uploads these values to a computer on the other side of the bench. It feeds in air (for oxygen) at a certain rate, controls the stirring (to help the oxygen dissolve), and pumps water through a jacket around the tank to control the temperature. There are also sensors on the other side that measure the concentrations of certain gases that come out of the tank, and the computer records those too. So it's a lot of control and information.

That's about it for this kind of experiment. In case I've kept your attention this long and you're interested in more, I started a new blog here to help myself review papers for my own research, so feel free to check it out.

BacterioFiles Special Edition - ASM2013 General Meeting Day 2

Here's my summary of the second day of ASM2013, an exciting day full of science.

Session 1: Pumping at the Microbial Well
Section 1: Advanced Plant to Advanced Fuel
Presented by Jay D. Keasling,
In order to produce long-chain carbon compounds for diesel and jet fuels, it is possible to engineer bacteria like E. coli to produce them the way they produce long fatty acids for their membranes, but in a better form for extraction. Also, plants produce many terpene compounds for defense, such as bisabolene, that can also be good for fuel, and bacteria can be engineered to produce these too, but it can be tricky due to these compounds' toxicity.
Paper on good efflux pumps for biofuel production: Dunlop et al, 2011, Mol. Sys. Biol. 7:487 doi: 10.1038/msb.2011.21

Section 2: Is There a Path to Cellulosic Biofuels?
Presented by Thomas W. Jeffries
His main point was that the use of fossil fuels should be a transitional state between the pre-industrial era and a sustainable system of renewable energy. Fossil fuels should be an investment in the future, not something we should build our whole infrastructure around. They are going to run out someday, after all.

Poster: 280 - Comparisons of CRISPR Content Between Saliva and Skin: Viral Exposures May Not Be Body Site Specific
R. Robles-Sikisaka, M. Naidu, M. Ly, J. Saizman, S.R. Abeles, T. Boehm, D.T. Pride

Session 2: Uncovering the Function of Unknown Proteins
Section 1: Evolution and the Proteome: Insights into Protein Function from Deeply Conserved Gene Modules
Presented by Edward Marcotte
How should one go about figuring out the function of unknown proteins? Possibly by comparing homologs in other, even distantly related organisms. Even homologous genes in yeast and humans can have similar functions. And of the ~500 essential proteins in yeast that have human homologues, 60% of them can be replaced with the human version and the yeast will still be viable.

Section 2: Small Proteins Can No Longer Be Ignored
Presented by Gisela Storz
Her group has discovered some bacterial proteins smaller than 50 amino acids long, that seem to be related to metal metabolism.

Download Episode (7.36 MB, 8 minutes)

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe at iTunes, check out the show at Twitter, MicrobeWorld, or Facebook

BacterioFiles Special Edition - ASM2013 General Meeting Day 1

I went to the General Meeting of the American Society for Microbiology, in Denver, Colorado, and I wanted to share some of the fascinating science that I experienced. So here's my summary of the first day!

Section 1: I missed it because Denver is confusing and it took me so long to find parking. Apparently it was interesting, though, discussing how a certain bacterium, Caulobacter crescentus, divides into two daughter cells, one that holds onto a surface and the other that swims away.

Section 2: The Killers, the Cures, and the Limits of Life: Frontiers of Science in the Unseen World
Presented by Nathan D. Wolfe
I missed some of this section, but what I heard was interesting, about how endogenous retroviruses may have made mammalian development possible, and how significant portions of the microbial world may still be unknown.

Section 3: Engineering by Evolution
Presented by Frances Arnold
This was quite interesting. As an engineer, Dr. Arnold is interested in making cells and their enzymes do stuff, so she works on improving their abilities. There is tremendous diversity of amino acid sequences (i.e. proteins) in nature, but it represents only a small amount of the possible combinations of amino acids. Most such combinations are useless as enzymes, but a few are even more effective than anything (yet found) in nature. Dr. Arnold discussed how to find these combinations.
Here is the paper published about the heat-stable cellulases that I discussed: Wu and Arnold, 2013, Biotechnol. Bioeng. 110:1874 doi: 10.1002/bit.24864.

Download Episode (6.45 MB, 7 minutes)

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe at iTunes, check out the show at Twitter, MicrobeWorld, or Facebook

I Passed!

Preliminary exams complete. Full speed ahead toward PhD!

Announcement

I regret to announce this, but I am about to embark on one of the major trials of being a grad student: the preliminary examination. What this amounts to, for me, is writing a 15+ page grant proposal in six weeks on a topic I haven't been studying all this time, while carrying on all my previous research responsibilities. So BacterioFiles will be on hiatus for now, at least until I feel reasonably confident in my progress, possibly for the whole six weeks. We'll see.

One positive thing from this is that I will be able to refill my cache of awesome research to talk about, so look forward to more good stuff coming out before too long.