Monday, September 7, 2020

432 - Moses Microbes Maintain Moisture

Gypsum
This episode: Bacteria living in the driest place on earth have ways to extract water from the mineral structures of rocks!

Download Episode (3.7 MB, 5.4 minutes)

Show notes:
Microbe of the episode: Irkut lyssavirus

News item

Takeaways
Microbes living in extremely dry conditions have it tough. Water is important both for the chemistry and structure of all cells. Desert microbes are very good at acquiring and holding on to the water they can find, but in places such as the Atacama Desert in Chile, there's almost none available.

However, microbes can be very resourceful. In this study, phototrophs were discovered that can actually extract water molecules bound up in the crystalline structure of the mineral gypsum, and this allows them to survive in hyperarid regions. They do this by secreting organic acid molecules to etch the rock and release the water, converting gypsum to anhydrite, which is a mineral with the same chemical structure except without the water.

Journal Paper:
Huang W, Ertekin E, Wang T, Cruz L, Dailey M, DiRuggiero J, Kisailus D. 2020. Mechanism of water extraction from gypsum rock by desert colonizing microorganisms. Proc Natl Acad Sci 117:10681–10687.

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Monday, August 31, 2020

431 - Conductive Cables Control Carbon

Cable bacteria around
plant roots
From Scholz et al. 2020
Nat Commun 11:1878

This episode: Cable bacteria around rice roots transport electrons and help prevent formation of methane!

Thanks to Vincent Scholz for his contribution!  
Download Episode (5.7 MB, 8.3 minutes)

Show notes:
Microbe of the episode: Vibrio alginolyticus

News item

Takeaways
Transforming other things into methane is a great way to make a living for some kinds of microbes. These tend to live under still water, like in rice fields or wetlands, or in the guts of cattle. And while this methane could be useful as natural gas if collected, it's a much more potent greenhouse gas than carbon dioxide when released into the atmosphere.

In this study, cable bacteria were inoculated into rice pots in the lab. Cable bacteria transfer electrons from deeper down in the ground up to the surface to generate energy, and in the process generate sulfate. This sulfate allows other microbes to outcompete the methane producers, reducing the amount of methane produced from rice cultivation in the lab. This may be helpful to reduce greenhouse gas emissions from rice agriculture.

Journal Paper:
Scholz VV, Meckenstock RU, Nielsen LP, Risgaard-Petersen N. 2020. Cable bacteria reduce methane emissions from rice-vegetated soils. 1. Nat Commun 11:1878.

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Monday, August 24, 2020

430 - Dextrose Deposits Delay Dormancy

E. coli
This episode: Bacteria that can store sugar as glycogen have multiple advantages when food is only available sporadically!
Download Episode (7.2 MB, 10.4 minutes)

Show notes:
Microbe of the episode: Carnivore bocaparvovirus 3

Takeaways
Almost all habitats experience some sort of change and fluctuation; very few are totally stable, depending on the timeframe. So strategies to change and adapt with changing conditions can greatly help an organism thrive. For example, methods of storing energy are helpful when food is only available sporadically.

Some bacteria, like humans, can store sugar in a polymer called glycogen, which can be quickly produced when food is abundant and quickly broken down to ease a transition to fasting. In this study, bacteria that could produce and use glycogen were able to stay active longer and grow better in the face of intermittent starvation. They were even better able to acquire new food when more became available.

Journal Paper:
Sekar K, Linker SM, Nguyen J, Grünhagen A, Stocker R, Sauer U. 2020. Bacterial Glycogen Provides Short-Term Benefits in Changing Environments. Appl Environ Microbiol 86.

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Monday, August 17, 2020

429 - Springtails Smell, Spread Streptomyces

Springtail Folsomia candida
By Andy Murray
CC BY-SA 2.0

This episode: Bacteria in soil produce smells to attract arthropods that eat them but also spread their spores!

Download Episode (6.2 MB, 9.0 minutes)

Show notes:
Microbe of the episode: Blotched snakehead virus

News item

Takeaways
Soil, especially after a rain, often has a characteristic "earthy" smell. This soil smell is actually the result of certain bacteria producing a volatile chemical called geosmin. Many geosmin producers are in the Streptomyces genus, which produces a large variety of interesting chemicals, but geosmin is one of the few that is nearly universal in the genus.

This study found that insect-like arthropods called springtails are attracted to geosmin. These animals usually feed on fungi, but they will also eat bacteria when available. Despite this result, the bacteria continue to produce the chemical, which is linked to their sporulation cycle. The study found that springtails carry intact bacterial spores to new places stuck to the insides and outsides of the animal, and this enhances the dispersal ability of the bacteria.

Journal Paper:
Becher PG, Verschut V, Bibb MJ, Bush MJ, Molnár BP, Barane E, Al-Bassam MM, Chandra G, Song L, Challis GL, Buttner MJ, Flärdh K. 2020. Developmentally regulated volatiles geosmin and 2-methylisoborneol attract a soil arthropod to Streptomyces bacteria promoting spore dispersal. 6. Nat Microbiol 5:821–829.

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Monday, August 10, 2020

428 - Microbes May Manage Mysteries


This episode: The skin microbes that people leave behind may be used to identify them, even after other people have touched the same surface!


Download Episode (5.4 MB, 7.9 minutes)

Show notes:
Microbe of the episode: Actinobacillus lignieresii

Takeaways
The microbial communities in and on our bodies are highly complex and highly varied between people; this complexity has raised the question of whether the microbes that people transfer onto things they touch could be used in forensics, to track their movement and activity, like fingerprints or DNA evidence. One difficulty with this approach is that microbe communities are constantly changing as conditions change or other microbes are introduced.

This study simulated such microbial tracking in a couple of scenarios, such as touching door handles in an office building and touching various surfaces in a home in a mock burglary. Tracking a person on door handles worked fairly well for up to an hour after the contact, even if other people had also touched the same door handles. However, the accuracy of identifying the "burglar" in a home was not very high, but modifying the analysis from looking at the community as a whole to only rare microbes relatively unique to an individual improved the results.

Journal Paper:
Hampton-Marcell JT, Larsen P, Anton T, Cralle L, Sangwan N, Lax S, Gottel N, Salas-Garcia M, Young C, Duncan G, Lopez JV, Gilbert JA. 2020. Detecting personal microbiota signatures at artificial crime scenes. Forensic Sci Int 313:110351.

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Monday, August 3, 2020

427 - Simple Cells Stay Strong

Fluorescent SimCells
By Fan et al. 2020,
PNAS 117(12):6752
CC BY 4.0
This episode: Bacterial cells with their genomes removed can still be active and useful!


Download Episode (10.2 MB, 14.9 minutes)

Show notes:
Microbe of the episode: Rosavirus A

Takeaways
Microbes have amazing biochemical transformation abilities, creating and breaking down many compounds and proteins. This makes them great candidates for many purposes, in medicine, industry, and environmental remediation. In some of these purposes, though, there are risks associated with adding foreign microbes, especially engineered ones, that can replicate themselves and possibly persist, into new places.

To avoid this risk, this study turns intact bacteria into SimCells, simplified entities with most of their genetic material removed, leaving only the proteins and other components and just enough DNA to accomplish desired tasks. These SimCells were able to continue performing tasks for around 10 days before running out of the cellular resources needed to keep going. One of these tasks was producing a compound that damaged cancer cells in a dish but left non-cancerous cells unharmed.

Journal Paper:
Fan C, Davison PA, Habgood R, Zeng H, Decker CM, Salazar MG, Lueangwattanapong K, Townley HE, Yang A, Thompson IP, Ye H, Cui Z, Schmidt F, Hunter CN, Huang WE. 2020. Chromosome-free bacterial cells are safe and programmable platforms for synthetic biology. Proc Natl Acad Sci 117:6752–6761.

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Monday, July 27, 2020

426 - Sensory Cilia Supply Susceptibility

C. elegans roundworm
By Bob Goldstein, UNC Chapel Hill
CC BY-SA 3.0
This episode: A fungus paralyzes its tiny worm prey by acting on the worm's own sensory hairs!


Download Episode (6.0 MB, 8.7 minutes)

Show notes:
Microbe of the episode: Bat associated cyclovirus 9

Takeaways
Not all predators are fast or agile; some are sneaky, or good trap builders, or just good chemists. The predator club includes animals but also plants and even fungi. For example, the oyster mushroom fungus can paralyze roundworms in the soil that touch its filaments, then degrade their bodies and consume their nutrients.

The mechanism of this paralysis has been a mystery, but it's one step closer to being solved. This study found that intact sensory cilia, little hairs on the worm's head that help it sense its surroundings, are required for the paralysis to work. Worms with mutations in the structure of their cilia were protected from paralysis. How exactly the fungus acts on these cilia and the neurons they connect to, though, is still unknown.

Journal Paper:
Lee C-H, Chang H-W, Yang C-T, Wali N, Shie J-J, Hsueh Y-P. 2020. Sensory cilia as the Achilles heel of nematodes when attacked by carnivorous mushrooms. Proc Natl Acad Sci 117:6014–6022.

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Monday, June 22, 2020

425 - Paired Predators Prevent Pathogen Persistence

Haloed plaques, Bdellovibrio,
and bacteriophage
By Hobley et al. 2020,
J Bacteriol 202(6), CC BY 4.0
This episode: A bacteriophage and bacterial predator can wipe out a population of bacteria that could develop resistance to each individually!

Thanks to Laura Hobley, J. Kimberley Summers, and Jan-Ulrich Kreft for their contributions!

Also a note: I will be taking a short break from podcasts while I rebuild my collection of awesome microbiology stories to talk about.


Download Episode (6.8 MB, 9.9 minutes)

Show notes:
Microbe of the episode: Blackbird associated gemycircularvirus 1

Takeaways
Bacteriophages and bacterial predators that prey on other bacteria are both very good at killing large numbers of bacteria. But bacteria as a whole are also very good at surviving being killed in large numbers; there are almost always a few that have the right genes to overcome whatever is doing the killing. This is what makes the threat of antibiotic resistance so scary, and why phage therapy is both very promising and very limited.

In this study, however, a combination of phages and the bacterial predator Bdellovibrio bacteriovorans is able to completely eradicate a population of bacteria, or at least reduce their numbers below a detectable level. A mathematical model based on these data predicts that despite the two killers working independently, they can effectively eliminate all the individual prey organisms that would otherwise be able to resist killing by either one alone.

Journal Paper:
Hobley L, Summers JK, Till R, Milner DS, Atterbury RJ, Stroud A, Capeness MJ, Gray S, Leidenroth A, Lambert C, Connerton I, Twycross J, Baker M, Tyson J, Kreft J-U, Sockett RE. 2020. Dual Predation by Bacteriophage and Bdellovibrio bacteriovorus Can Eradicate Escherichia coli Prey in Situations where Single Predation Cannot. J Bacteriol 202.

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Monday, June 15, 2020

424 - Stranger Cells Switch Stable States

Lactobacillus bacteria

Pelzer et al. 2012, PLOS One e49965

This episode: Certain bacteria can greatly affect the makeup of a microbial community, even if they quickly disappear!

Thanks to Dr. Daniel Amor for his contribution!


Download Episode (6.3 MB, 9.2 minutes)

Show notes:
Microbe of the episode: Gadgets Gully virus

News item

Takeaways
Microbial communities show more than just competition between species. Stable assemblies of many species can exist for long periods in places like the human gut, despite constant minor shifts in conditions. More major shifts, or invaders like pathogens coming in and taking over, can cause big disruptions in the community and lead to long-term gut dysbiosis, which can be, interestingly, also a stable community. 

This study shows that invaders into a community, even if they don't persist for very long, can cause a shift from one stable state to another, by favoring the dominance of a species or group that was not dominant before, for example by changing the pH of the environment. So competition is always present. This could be helpful to know for efforts to intentionally shift community structures.

Journal Paper:
Amor DR, Ratzke C, Gore J. 2020. Transient invaders can induce shifts between alternative stable states of microbial communities. Sci Adv 6:eaay8676.

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Monday, June 8, 2020

423 - Roundworm Riders Route Rootworm Resistance

Western corn rootworm adult

By Siga, CC BY-SA 4.0

This episode: Helping insect-killing bacterial symbionts of nematodes evolve resistance to chemicals that major corn pests use to defend themselves!


Download Episode (10.0 MB, 14.0 minutes)

Show notes:
Microbe of the episode: Listeria virus PSA

Takeaways
Interactions between species and even kingdoms in nature can be complex and multilayered. This means that when we want to intervene to cause a particular outcome, there may be multiple points at which we can act, but the consequences may be hard to predict.

In this study, action was taken to counteract the damage the Western corn rootworm causes to corn crops, using a tiny roundworm that attacks the insect pest with deadly bacteria. The rootworm defends itself by accumulating plant-produced toxins that inhibit the bacteria. Directed evolution was used to make the bacteria more resistant, and this led to more effective killing of the pest.

Journal Paper:
Machado RAR, Thönen L, Arce CCM, Theepan V, Prada F, Wüthrich D, Robert CAM, Vogiatzaki E, Shi Y-M, Schaeren OP, Notter M, Bruggmann R, Hapfelmeier S, Bode HB, Erb M. 2020. Engineering bacterial symbionts of nematodes improves their biocontrol potential to counter the western corn rootworm. 5. Nat Biotechnol 38:600–608.

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Monday, June 1, 2020

422 - Frigid Phototrophs Fuel Fords

Algae growing in 20-liter bioreactor

Kim et. al, 2020. CC BY 4.0

This episode: Producing both biodiesel and bioethanol fuels from cold-loving Arctic algae!


Download Episode (8.7 MB, 12.6 minutes)

Show notes:
Microbe of the episode: Royal Farm virus

Takeaways
Renewable fuels such as biofuels can allow existing infrastructure and vehicles to continue to operate in a more sustainable manner, which could reduce the cost and impact of switching to new/different systems of transportation like electricity. Economically competitive methods of producing biofuels are still being explored and developed.

In this study, Arctic algae are grown in cold temperatures using only light, carbon dioxide, and a few minerals, and then broken down to produce biodiesel and bioethanol, which can be used as fuel in many different internal combustion engines. The amounts produced are comparable to other algae-based systems being researched, and use of the cold-loving organisms could reduce the cost of production in colder latitudes and seasons.

Journal Paper:
Kim EJ, Kim S, Choi H-G, Han SJ. 2020. Co-production of biodiesel and bioethanol using psychrophilic microalga Chlamydomonas sp. KNM0029C isolated from Arctic sea ice. Biotechnol Biofuel 13:20.

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Monday, May 25, 2020

421 - Nucleocapsids Navigate Nano Nuggets

Gold nanorods bound to phage
Used with permission
This episode: Using phages to target gold nanoparticles to infecting bacteria, then using light to heat the nanoparticles just enough to kill the bacteria!

Thanks to Huan Peng and Raymond Borg for contributing!


Download Episode (10.6 MB, 15.4 minutes)

Show notes:
Microbe of the episode: Pantoea agglomerans

News item

Takeaways
Viruses that infect bacteria, bacteriophages, are often very good at overcoming bacterial defenses and killing them. This raises the possibility, and many times actuality, of using phages to treat bacterial infections that are no longer treatable with antibiotics. But bacteria can evolve resistances to viruses as well as drugs, and using multiplying, evolving entities as treatments in people raises questions about the safety and consistency of the treatment.

This study circumvents these questions by using phages for delivery and targeting of bacteria rather than the therapeutic agent itself. The actual treatment is done with tiny rods of gold, gold nanorods, bound to the phage surface. When a certain wavelength of light hits these nanorods, they vibrate enough to generate enough heat in their immediate surroundings to render nearby bacteria nonviable. Thus the infection is treated in a very localized, targeted way that doesn't leave any active bacteria or phages behind. The authors have plans to study this approach as a topical treatment of wounds.

Journal Paper:
Peng H, Borg RE, Dow LP, Pruitt BL, Chen IA. 2020. Controlled phage therapy by photothermal ablation of specific bacterial species using gold nanorods targeted by chimeric phages. Proc Natl Acad Sci 117:1951–1961.

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Monday, May 18, 2020

BacterioFiles 420 - Cell Societies Stay Stable

Bacteroides species
This episode: Simplified gut communities growing in bioreactors grow and metabolize reproducibly, with only moderate variations, even when individual members of the community are absent!


Download Episode (8.2 MB, 11.9 minutes)

Show notes:
Microbe of the episode: Citrobacter virus Merlin

Takeaways
The community of microbes in our guts is highly complex, with thousands of species all interacting with each other, with our own cells, and with the contents of our diet. Each region of the gut has a different collection of microbes as well. Many questions remain to be answered about the functions and fluctuations of these communities. How can we study such a complex system? Which species, if any, are most important for its continued function?

In this study, a simplified community of only 14 species is grown repeatedly in bioreactors, and one species at a time is left out of the community to see what will change in its absence. This reveals effects different species have on the overall growth, carbon source consumption, and production of various metabolites relevant to gut health. Some microbes have large effects, but none of them appears to be crucial for the overall function and stability of the community.

Journal Paper:
Gutiérrez N, Garrido D. 2019. Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes. mSystems 4:e00185-19.

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Monday, May 11, 2020

BacterioFiles 419 - Marine Methane Microbe Multiplication

Anaerobic methanotrophs
BacterioFiles is back! This episode: Measuring how quickly marine methane-consuming microbes become active when new methane enters an area!


Download Episode (9.0 MB, 13.0 minutes)

Show notes:
Microbe of the episode: Torque teno midi virus 6

Takeaways
Oceans and the organisms living in them have a large effect on the planet, in terms of climate and gases they absorb from or release into the atmosphere. They are a source of much of a potent greenhouse gas, methane, but microbes living in ocean sediments also consume large amounts of methane. These anaerobic methanotrophic archaea generate energy for themselves by transforming methane and sulfate into carbonate and sulfide.

In this study, however, methane-consuming microbes were only found active at sites of methane seepage. Even in sites where methane had previously been present, only few of these microbes were present and active. After enriching samples of these sediments for up to 8 months, still the only activity that was seen was from actively methane-consuming communities. So once dispersed, such communities seem slow to regenerate as the locations of methane seepage shift.

Journal Paper:
Klasek S, Torres ME, Bartlett DH, Tyler M, Hong W-L, Colwell F. 2020. Microbial communities from Arctic marine sediments respond slowly to methane addition during ex situ enrichments. Environ Microbiol 22:1829–1846.

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Monday, March 16, 2020

BacterioFiles 418 - Special Sea Species Swallows Cells

New microbe engulfing prey
By Shiratori et al. 2019
Nat Commun 10(1):1-11, CC BY 4.0
This episode: A newly discovered species of bacteria consumes other bacteria as prey by engulfing them!

Also a note to listeners: Because things are hectic at work right now (unless that changes due to current events), I'm planning to put the show on hold for a few weeks. So if you don't see new episodes, that's why.


Download Episode (8.7 MB, 12.6 minutes)

Show notes:
Microbe of the episode: SARS-CoV-2! This is the coronavirus responsible for COVID-19, the current pandemic. For more up-to-date information, please refer to the American Society for Microbiology, This Week in Virology, and other reputable sources. Stay healthy!

Takeaways
There are bacteria living almost every different lifestyle you can think of, including predatory, preying on other bacteria. Since bacterial cells are usually quite rigid, bacterial predators usually consume others either by burrowing inside them or digesting them from outside, rather than engulfing prey like eukaryotes often do.

The study here discovers a new kind of bacteria, in the group called Planctomycetes, known for having unusually flexible cells and internal compartments like eukaryotes. This new species does engulf its prey, including bacteria and even tiny algae, and digests them inside itself. It possesses multiple adaptations that suit it for this lifestyle.

Journal Paper:
Shiratori T, Suzuki S, Kakizawa Y, Ishida K. 2019. Phagocytosis-like cell engulfment by a planctomycete bacterium. Nat Commun 10:1–11.

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Monday, March 9, 2020

BacterioFiles 417 - Bacteriophage Blocks Bacterial Bouncers

Pseudomonas aeruginosa
By Y_tambe, CC BY-SA 3.0
This episode: A phage defends its genome against bacterial host defenses by building a wall to keep them out!


Download Episode (7.0 MB, 10.2 minutes)

Show notes:
Microbe of the episode: Myroides odoratus and M. odoratimimus

News item

Takeaways
Parasites and their hosts are constantly in arms races with each other, each thriving best when it acquires new and more effective methods of attack, defenses, defenses against defenses, and so on. Bacterial defenses against viruses that infect them mostly involve cutting up viral genomes, either by the indiscriminate specific-cutting restriction enzymes, or by adaptive, sequence-sensing CRISPR/Cas systems.

Bacteriophages have proteins that can defend against the CRISPR/Cas system, but they mostly require the sacrifice of multiple failed infections before the proteins build up enough to defeat the defense. In this study, a phage is discovered that can immediately defend against all DNA-cutting systems, by constructing a nucleus-like protective compartment inside the host.

Journal Paper:
Mendoza SD, Nieweglowska ES, Govindarajan S, Leon LM, Berry JD, Tiwari A, Chaikeeratisak V, Pogliano J, Agard DA, Bondy-Denomy J. 2020. A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases. Nature 577:244–248.

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Monday, March 2, 2020

BacterioFiles 416 - Oxygen Or Other Oxidizes Iron?

Chlorobium phaeoferrooxidans
By Thompson et al, 2019.
Sci Adv 5:eaav2869.
CC BY-NC 4.0
This episode: Earth's iron deposits could have been created by anaerobic light-harvesting microbes instead of those that make oxygen!


Download Episode (9.3 MB, 13.5 minutes)

Show notes:
Microbe of the episode: Streptomyces avidinii

News item

Takeaways
In the ancient earth, the sun was dimmer, the world was colder, and oxygen was rare because photosynthesis had not yet evolved. Without oxygen to oxidize it, iron remained in its soluble, more accessible form, and many organisms took advantage of it for anaerobic metabolism.

But was it photosynthesis and the oxygen it created that transformed most of the planet's iron into its insoluble form, creating large iron deposits in the ground? This study explores the possibility that it was another form of light-harvesting metabolism, called photoferrotrophy, that uses light and the transformation of iron to generate energy. This hypothesis is found to be consistent with the evidence we have about what the early earth was like.

Journal Paper:
Thompson KJ, Kenward PA, Bauer KW, Warchola T, Gauger T, Martinez R, Simister RL, Michiels CC, Llirós M, Reinhard CT, Kappler A, Konhauser KO, Crowe SA. 2019. Photoferrotrophy, deposition of banded iron formations, and methane production in Archean oceans. Sci Adv 5:eaav2869.

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Monday, February 24, 2020

BacterioFiles 415 - Global Glomus Growth Guesses

How mycorrhizal fungi work
By Nefronus, CC BY-SA 4.0
This episode: A global estimate of plants and their root fungi shows how agriculture may have greatly affected soil carbon storage over time!


Download Episode (5.7 MB, 8.3 minutes)

Show notes:
Microbe of the episode: Rhizobium virus RHEph4

News item

Takeaways
Even small organisms can have a big effect on the climate of the planet if there are enough of them. This includes trees, which are small relative to the planet, and also includes the fungi that attach to the roots of trees and other plants. These mycorrhizal fungi thread subtly through the soil, some occasionally popping up mushrooms, and transfer valuable nutrients they gather to the trees in exchange for carbon fixed from the air.

Knowing how big an effect a given kind of organism has requires knowing how much of it is around. This study collates data from various surveys of global plant populations and the fungi that interact with their roots, to estimate a global picture of the fungi below our feet. It estimates that a kind of fungus that stores more carbon in the soil may have been replaced in many areas with fungi that store less, or no fungi at all, due to the transformation of land from wild areas to farmland.

Journal Paper:
Soudzilovskaia NA, van Bodegom PM, Terrer C, Zelfde M van’t, McCallum I, Luke McCormack M, Fisher JB, Brundrett MC, de Sá NC, Tedersoo L. 2019. Global mycorrhizal plant distribution linked to terrestrial carbon stocks. Nat Commun 10:1–10.

Other interesting stories:

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Monday, February 17, 2020

BacterioFiles 414 - Producing Proton Power Perpetually

Microalgae Chlamydomonas reinhardtii
This episode: Microalgae can produce hydrogen, but other metabolic pathways take priority, except when special engineered hydrogenase enzymes can overcome this limitation!


Download Episode (8.4 MB, 12.2 minutes)

Show notes:
Microbe of the episode: Alphapapillomavirus 11

Takeaways
There are many options being explored as ways to replace fossil fuels. Electricity and batteries are good, but they have their limitations, especially for long-distance high-energy travel such as airplanes. Hydrogen is one good option: high energy density, clean-burning, simple to produce. Microbes can produce hydrogen through various metabolic pathways, including fermentation, nitrogen fixation byproduct, and photosynthesis. However, competing metabolic pathways make microbial hydrogen production less efficient.

In this study, scientists engineer a hydrogenase enzyme for hydrogen production in microalgae that can compete better with carbon fixation as a destination for the electrons and protons that hydrogen production requires. This engineered enzyme allowed the algae to produce hydrogen continuously, even during photosynthesis.

Journal Paper:
Ben-Zvi O, Dafni E, Feldman Y, Yacoby I. 2019. Re-routing photosynthetic energy for continuous hydrogen production in vivo. Biotechnol Biofuels 12:266.

Other interesting stories:

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Monday, February 10, 2020

BacterioFiles 413 - Finding Fire Fungi Footholds

Pyrophilous fungus
Pholiota highlandensis
This episode: Some fungi only form fruiting bodies after forest fires; where do they hide the rest of the time? At least for some of them, the answer is: inside mosses!

Thanks to Daniel Raudabaugh for his contribution!

Download Episode (6.2 MB, 9.0 minutes)

Show notes:
Microbe of the episode: Nocardia brevicatena

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Takeaways
Forest fires can do a lot of damage, but life grows back quickly. Certain kinds of plant seed actually only germinate after a fire, and a similar thing is true of certain kinds of fungi: they only form fruiting bodies (like mushrooms, for spreading spores) after a fire. For plants, the advantage may come from increased access to light with some or all of the canopy burned away, and fungi may benefit from less competition on the ground. But in between burn events, these fire-loving (pyrophilous) fungi seem to disappear. Where do they go?

The study here sought an answer, suspecting an association with some mosses that reappeared soon after a forest fire in North Carolina in 2016. They looked for fungi lurking as endophytes inside moss and other samples, both by growing them on agar and by DNA sequencing, and they found a number of different known pyrophilous fungi. Some of these were in soil, or samples from outside the burned area, but the majority were inside mosses growing in the recently burned zone.

Journal Paper:
Raudabaugh DB, Matheny PB, Hughes KW, Iturriaga T, Sargent M, Miller AN. 2020. Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi. Fungal Ecol 43:100870.

Other interesting stories:

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

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Monday, February 3, 2020

BacterioFiles 412 - Carbon Concentration Complicates Crop Cooperation

Wheat plants
By Bluemoose, CC BY-SA 3.0
This episode: Looking at the effects of almost doubling CO2 concentrations on the interaction between wheat varieties and beneficial fungi!

Download Episode (8.1 MB, 11.8 minutes)

Show notes:
Microbe of the episode: Lato River virus

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Takeaways
As the world's population grows, feeding everyone will grow more challenging. Advances in technology in the past have made today's population possible, but future advances may be needed, especially in the face of an increasing concentration of carbon dioxide in the atmosphere.

Soil microbes that partner with crop plants for the benefit of each may be part of the solution. One option to explore is a group called mycorrhizal fungi, which associate with plant roots to extend their nutrient-gathering ability, in exchange for carbon compounds produced by photosynthesis. This study examined the influence of increased carbon dioxide in the atmosphere on the interaction of several varieties of wheat with these fungi.

Journal Paper:
Thirkell TJ, Pastok D, Field KJ. Carbon for nutrient exchange between arbuscular mycorrhizal fungi and wheat varies according to cultivar and changes in atmospheric carbon dioxide concentration. Glob Change Biol.

Other interesting stories:

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

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Monday, January 27, 2020

BacterioFiles 411 - Parasite Produces Partial Plant-like Predator

A choanoflagellate
By Daniel Stoupin
CC BY-SA 3.0
This episode: Giant virus in newly discovered microscopic marine predator encodes several light-harvesting proteins!

Download Episode (7.8 MB, 11.4 minutes)

Show notes:
Microbe of the episode: Dolphin mastadenovirus A

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Takeaways
Giant viruses are distinct in many ways from other viruses, even aside from their size. One way is the large number and variety of genes they carry in their genome. Though many of their genes are unknown in origin and function, many others appear to take the place of essential reproductive functions, such as translation and protein synthesis. This allows them to assume more control of their host's metabolism and control its resources more optimally.

In this study, the sequence of a giant virus was discovered seemingly infecting a newly discovered microscopic marine predator. The eukaryotic cell feeds on smaller microbes such as bacteria, but strangely, the virus carries genes for several light-harvesting proteins, possibly converting a heterotrophic predator into a partial phototroph.

Journal Paper:
Needham DM, Yoshizawa S, Hosaka T, Poirier C, Choi CJ, Hehenberger E, Irwin NAT, Wilken S, Yung C-M, Bachy C, Kurihara R, Nakajima Y, Kojima K, Kimura-Someya T, Leonard G, Malmstrom RR, Mende DR, Olson DK, Sudo Y, Sudek S, Richards TA, DeLong EF, Keeling PJ, Santoro AE, Shirouzu M, Iwasaki W, Worden AZ. 2019. A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proc Natl Acad Sci 116:20574–20583.

Other interesting stories:

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

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Monday, January 20, 2020

BacterioFiles 410 - Microbes Modify Muscle Measurement

A laboratory mouse
This episode: Mice that got a microbe transplant from humans with higher physical function performed better in certain ways than mice receiving microbes from humans with lower physical function!

Download Episode (6.7 MB, 9.8 minutes)

Show notes:
Microbe of the episode: Stenotrophomonas maltophila

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Takeaways
Our bodies and our microbe communities are closely interconnected, with effects going both ways. Studies had previously shown that making changes to the microbe communities of mice could even affect the physical function and body composition of the mice.

This study aimed at addressing the same question in humans. There were certain consistent differences in microbial communities between elderly people with high ability to function physically, compared with low functioning people. These differences carried over in transplants of microbes from people to mice, and mice receiving microbes from high-functioning humans did better in tests of grip strength than mice receiving microbes from low-functioning people.

Journal Paper:
Fielding RA, Reeves AR, Jasuja R, Liu C, Barrett BB, Lustgarten MS. 2019. Muscle strength is increased in mice that are colonized with microbiota from high-functioning older adults. Exp Gerontol 127:110722.

Other interesting stories:

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

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Sunday, January 19, 2020

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?

Monday, January 13, 2020

BacterioFiles 409 - Marine Methane Mostly Munched

Methanococcus species
By Anne Fjellbirkeland,
from PLoS Biol 2004:e358
CC BY 2.5
This episode: Microbes in low-oxygen zones in the ocean consume significant amounts of methane anaerobically!

Download Episode (5.2 MB, 7.6 minutes)

Show notes:
Microbe of the episode: Mojiang henipavirus

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Takeaways
Methane is a much more potent greenhouse gas than carbon dioxide. Fortunately there's not as much of it in the atmosphere, but even smaller amounts can have significant effects on the climate.

One source of methane is low-oxygen zones in the ocean, where certain kinds of archaea make methane as part of their energy metabolism. This study found that other anaerobic microbes in the same areas consume much of this methane, preventing it from reaching the atmosphere.

Journal Paper:
Thamdrup B, Steinsdóttir HGR, Bertagnolli AD, Padilla CC, Patin NV, Garcia‐Robledo E, Bristow LA, Stewart FJ. 2019. Anaerobic methane oxidation is an important sink for methane in the ocean’s largest oxygen minimum zone. Limnol Oceanogr 64:2569–2585.

Other interesting stories:

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.