447 - Big Bacteria Bank Behaviors

Achromatium
By Ionescu et al. Mol Biol Evol
DOI: 10.1093/molbev/msaa273
CC BY-NC 4.0

This episode: Giant bacteria with many chromosomes in each cell carry extra genes to help them live in many different environments!

Thanks to Dr. Danny Ionescu for his contribution!

Download Episode (8.7 MB, 12.7 minutes)

Show notes:
Microbe of the episode: Propionibacterium virus SKKY

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Takeaways

We think of bacteria a certain way: too small to see and having mostly just a single large chromosome with all the genes they need for their lifestyle and not much more. And most bacteria are like that. But not all! Giant bacteria exist, some of which can be so large that individual cells can be seen without a microscope.

Achromatium species are one such kind of bacteria. They form clumps of minerals that take up most of their internal volume, but their cells are big enough to see and handle. In order to supply all parts of their vast innards with proteins, they have many copies of their chromosome distributed throughout their cytoplasm.

In this study, a survey of Achromatium genomes from all different kinds of ecosystem revealed that even different species in very different environments all seem to share one set of genetic functions, but only use the ones they need for their particular lifestyle while archiving the rest.

Journal Paper:
Ionescu D, Zoccarato L, Zaduryan A, Schorn S, Bizic M, Pinnow S, Cypionka H, Grossart H-P. Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems. Mol Biol Evol https://doi.org/10.1093/molbev/msaa273.

Other interesting stories:

• As with other infections, gut microbiota correlates with severity of COVID-19
• Fungi help plants defend against aphids

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

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446 - Biofilm Benefits Bone Braces

Biofilm-coated implant
By Tan et al. 2020,
Sci Adv 6:eaba5723
CC BY-NC 4.0

This episode: The biofilm that probiotic bacteria can leave behind on a titanium implant seems to help it integrate better with the existing skeleton, with less inflammation and risk of infection!

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Show notes:
Microbe of the episode: Methylobacterium organophilum

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Takeaways

Skeletal implants make it a lot easier for many people to stay mobile as they age, but the surgical procedure of implanting is risky. Its invasive nature puts stress on the immune system, which puts stress on other systems, and the spread of antibiotic resistance is increasing the risk of a hard-to-treat infection.

In this study, probiotic bacteria grow in a biofilm on titanium implants before being inactivated, leaving only the biofilm behind on the implant. This biofilm-coated implant showed improved bone integration, antimicrobial resistance that was not toxic to the body's own tissues, and reduced inflammation when implanted into rats.

Journal Paper:
Tan L, Fu J, Feng F, Liu X, Cui Z, Li B, Han Y, Zheng Y, Yeung KWK, Li Z, Zhu S, Liang Y, Feng X, Wang X, Wu S. 2020. Engineered probiotics biofilm enhances osseointegration via immunoregulation and anti-infection. Sci Adv 6:eaba5723.

Other interesting stories:

• Certain gut microbes correlate with lower risk from norovirus (paper)
• Mixture of microbes similar to kombucha engineered to produce living functional materials

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

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445 - Living Lurking Landmine Locators

Bioluminescence over landmine
By Shemer et al. 2020,
Microb Biotechnol
CC BY-NC

This episode: Engineered bacteria encapsulated in little beads sense chemicals from landmines and give off light!

Download Episode (6.4 MB, 9.3 minutes)

Show notes:
Microbe of the episode: Bifidobacterium pullorum

Takeaways

Landmines are a good way to take an enemy by surprise and do some damage. They're so good that some places in the world still aren't safe to go decades after a conflict, due to intact landmines hidden in the area. In order to detect them from a distance to aid in disarming efforts, we need something very good at detecting the faint odor they give off—something like bacteria!

In this study, bacteria are engineered to detect breakdown products of TNT in landmines and produce light—bioluminescence. These bacteria are encapsulated in polymer beads and are stable for months in the freezer, and could accurately pinpoint a landmine buried in sand for a year and a half.

Journal Paper:
Shemer B, Shpigel E, Hazan C, Kabessa Y, Agranat AJ, Belkin S. Detection of buried explosives with immobilized bacterial bioreporters. Microb Biotechnol https://doi.org/10.1111/1751-7915.13683.

Other interesting stories:

• Wastewater treatment plant could power itself from electricity produced by microbes
• Microbial exposures correlate with presence or lack of allergies in both people and their dogs

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

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444 - Strange Sequence Stops Cell Subjugation

T4 Bacteriophage
By Victoramuse,
CC BY-SA 4.0

This episode: An interesting bacterial genetic element protects against viruses in a unique way!

Download Episode (7.1 MB, 10.3 minutes)

Show notes:
Microbe of the episode: Mongoose associated gemykibivirus 1

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Takeaways

Even single-celled, microscopic organisms such as bacteria have to deal with deadly viruses infecting them. And while they don't have an immune system with antibodies and macrophages like we do, they still have defenses against infection, mostly based on sensing and destroying viral genomes. Restriction enzymes cut viral genomes at specific places, and CRISPR/Cas targets and destroys specific viral sequences. Knowing this, when microbiologists contemplate a strange genetic element of unknown function in bacteria, it's worth considering that it may be relevant to defense against phages.

The strange element in this case is retrons: a special reverse transcriptase enzyme takes a short non-coding RNA transcript and transcribes it into DNA, then links the RNA and DNA sequences together. These retrons are found in a variety of forms in a variety of microbes, and their function has been unknown up till now. In this study, one specific retron was found to defend bacteria against a number of phages. By comparing viruses, they discovered that this retron functions by sensing viruses' attempts to defeat another bacterial defense, a sort of second level of defenses. How common such a system is, what variants may exist, and how we may be able to use it for research or biotech purposes remain to be determined.

Journal Paper:
>Millman A, Bernheim A, Stokar-Avihail A, Fedorenko T, Voichek M, Leavitt A, Oppenheimer-Shaanan Y, Sorek R. 2020. Bacterial Retrons Function In Anti-Phage Defense. Cell 183:1551-1561.e12.

Other interesting stories:

• Bacteria can make biodegradable plastics from waste sludge

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

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443 - Gut Group Gives Gamma Guard

Lachnospiraceae
By Public Health Image Library
Attribution

This episode: Certain gut microbes protect mice from harmful effects of high-energy radiation!

Download Episode (7.3 MB, 10.6 minutes)

Show notes:
Microbe of the episode: Solenopsis invicta virus-1

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Takeaways

High-energy radiation can be very dangerous. Besides a long-term increased risk of cancer due to DNA damage, a high enough dose of radiation can cause lethal damage to multiple systems in the body, especially the gastrointestinal tract and the immune system. Finding new ways to treat or prevent damage from radiation would be very helpful for improving the safety of space travel, nuclear energy, and radiotherapy for cancer.

In this study, some mice exposed to a typically lethal dose of radiation survived without ill effects, thanks to certain microbes in their gut. Transferring these microbes to other mice helped those mice survive radiation as well, and even just the metabolites that the bacteria produced were helpful for protecting the cells in the body most affected by radiation.

Journal Paper:
Guo H, Chou W-C, Lai Y, Liang K, Tam JW, Brickey WJ, Chen L, Montgomery ND, Li X, Bohannon LM, Sung AD, Chao NJ, Peled JU, Gomes ALC, van den Brink MRM, French MJ, Macintyre AN, Sempowski GD, Tan X, Sartor RB, Lu K, Ting JPY. 2020. Multi-omics analyses of radiation survivors identify radioprotective microbes and metabolites. Science 370:eaay9097.

Other interesting stories:

• Algae incorporated into 3D-printed human tissues for research can provide oxygen for cells
• Bacteria in sea squirts produce potentially useful antifungal compound

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

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442 - Fossil Phototroph Phagocytosis

Fossilized coccolithophores
By Gibbs et al. 2020
Sci Adv 6:eabc9123
CC BY-NC 4.0

This episode: Algae surviving impact that killed the dinosaurs seem to have consumed other organisms to make it through the dark times!

Download Episode (7.1 MB, 10.3 minutes)

Show notes:
Microbe of the episode: Chaetoceros tenuissimus RNA virus 01

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Takeaways

Being able to look through time and learn about what might have happened to creatures throughout Earth's history is what makes paleontology great. Everyone knows about dinosaurs and what happened to them at the end of the Cretaceous period thanks to science. But what we can learn is not limited just to large organisms; there are ways to learn about microorganisms of the past as well, including by looking at fossils!

In this study, fossils of hard-shelled algae from around the end of the dinosaurs show that many of these microbes in the oceans went extinct at the same time due to the massive space impact. Debris blocked out sunlight for years, making it difficult for photosynthetic organisms to survive. So some of these algae appear to have survived by preying on smaller organisms, pulling them in through a hole in their shell.

Journal Paper:
Gibbs SJ, Bown PR, Ward BA, Alvarez SA, Kim H, Archontikis OA, Sauterey B, Poulton AJ, Wilson J, Ridgwell A. 2020. Algal plankton turn to hunting to survive and recover from end-Cretaceous impact darkness. Sci Adv 6:eabc9123.
Other interesting stories:

• Phages could help treat diabetic wound infections without harming microbiota (paper)

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

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441 - Hyphal Hijacker Helps Harvests

Fungus growing in root
By Zhang et al. 2020
Molec Plant 13:1420-1433
CC BY-NC-ND 4.0

This episode: A fungus-infecting virus transforms the fungal foe into a friend of its host plant!

Download Episode (6.1 MB, 8.9 minutes)

Show notes:
Microbe of the episode: Hepacivirus J

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Takeaways

Viruses can be useful for treating various diseases, especially bacterial infections and cancer. Their ability to target certain cell types specifically makes them great at hunting down and killing disease-causing cells without harming the body's healthy tissue. And just as bacteriophages can work to treat bacterial disease in us, fungal viruses could help to treat serious fungal infections in crop plants.

In this study, a fungus-infecting virus goes beyond treating a deadly fungal disease in rapeseed plants. Fungus infected with this virus no longer causes disease, but lives in harmony with the host plant, protects it from other fungal diseases, and even helps it to grow better.

Journal Paper:
Zhang H, Xie J, Fu Y, Cheng J, Qu Z, Zhao Z, Cheng S, Chen T, Li B, Wang Q, Liu X, Tian B, Collinge DB, Jiang D. 2020. A 2-kb Mycovirus Converts a Pathogenic Fungus into a Beneficial Endophyte for Brassica Protection and Yield Enhancement. Mol Plant 13:1420–1433.

Other interesting stories:

• Engineering E. coli to turn carbon dioxide into biomass
• Radiation super-resistant bacteria survive 1 year exposed to low Earth orbit

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.