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!


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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.

Other interesting stories:

• Certain foods could activate or inhibit bacteriophages and modulate the gut microbiota
• Some antibiotic-producing bacterial colonies have specialized members that do all the antibiotic production

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

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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.

Other interesting stories:

• Two bacteria growing together on agar make pretty patterns
• Marine bacteria kill and digest other bacteria (paper)

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

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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!


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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.

Other interesting stories:

• Some archaea can survive for a while trapped inside salt crystals (paper)
• Bacteria degrade BPA in soil (paper)

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

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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!


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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.

Other interesting stories:

• Bird and bat microbiomes have some similarities
• Twins often share certain gut microbes, even if they've been living apart for decades

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

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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.

Other interesting stories:

• Engineering a common industrial yeast strain to fix carbon dioxide (paper)
• Lake microbes convert microplastics into essential fatty acids

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

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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!


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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.

Other interesting stories:

• Helpful vaginal microbes inhibit HIV infection (paper)
• Engineering bacteria to fix nitrogen that grain plants can use (paper)

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.

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.

Other interesting stories:

• Gut microbes help whales digest tricky fats in their diet
• Bacteria deliver antibiotic to competitors using capsules made of its own membrane (paper)

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.