Monday, April 19, 2021

451 - Phototrophs Fancy Floating Feasts

Prasinophyte algae
By Bock et al. 2021, ISME J
CC BY 4.0
This episode: Despite being photosynthetic, some kinds of algae engage in predatory behavior, hunting and consuming live bacteria!

Thanks to Nicholas Bock for his contribution!

Download Episode (4.9 MB, 7.1 minutes)

Show notes:
Microbe of the episode: Paramecium bursaria Chlorella virus 1

News item

Takeaways
Although most of them are microscopic, algae perform a significant portion of the photosynthesis on the planet, because there are so many of them. But even though photosynthesis seems like a reliable way of acquiring energy, there are conditions under which even algae benefit from gathering energy and nutrients from other organisms. This is called phagomixotrophy, when algae hunt and consume bacteria.

In this study, scientists developed fluorescence methods for detecting and studying this predation in a group of algal phytoplankton that's not well-studied, prasinophytes. They found that all five species they looked at engaged in bacterivory under nutrient-depleted conditions, and that they preferred live bacteria to killed ones.

Journal Paper:
Bock NA, Charvet S, Burns J, Gyaltshen Y, Rozenberg A, Duhamel S, Kim E. 2021. Experimental identification and in silico prediction of bacterivory in green algae. ISME J.

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Monday, April 5, 2021

450 - Subterranean Spotlights Support Cyanobacteria

Carlsbad Caverns
By Eric Guinther, Marshman
CC BY-SA 3.0
This episode: Lighting in caves open to tourists supports the growth of unwanted photosynthetic bacteria!

Thanks to Zoƫ Havlena for her contribution!

Download Episode (6.6 MB, 9.5 minutes)

Show notes:
Microbe of the episode: Dill cryptic virus 2

Takeaways
Caves can contain amazing beauty, intricate geological formations formed by minerals, water, and time. Some, such as Carlsbad Caverns in New Mexico, have been fitted with instruments to allow tourists to pass through and see the wonders within; definitely a worthwhile experience.

Caves also have their own natural microbiota that can live within them, in the dark, somewhat cold, and nutrient-poor conditions. But with the lighting installed to allow tourism, photosynthetic microbes have been able to take hold in the communities of these show caves. These microbes can outcompete the natural microbes, and can cause discoloration and unwanted growths on cave formations. They are difficult to remove without much effort and the risk of damaging the cave formations themselves. 

This study looked at the effects of the color of lighting in the caves, as well as other factors, on the growth of these so-called "lampenflora." It supports new efforts and methods to control the issue.

Journal Paper:
Havlena Z, Kieft TL, Veni G, Horrocks RD, Jones DS. 2021. Lighting Effects on the Development and Diversity of Photosynthetic Biofilm Communities in Carlsbad Cavern, New Mexico. Appl Environ Microbiol 87.

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Monday, March 29, 2021

449 - Paralyzed Poisons Push Power

Hydrothermal vent
This episode: Deep-sea bacteria can detoxify cadmium and convert it to light-capturing particles!

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Show notes:
Microbe of the episode: Arthrobacter virus Sonny

Takeaways
Hydrothermal vents can have thriving communities, despite being too deep for much light to penetrate. Microbes can derive energy from chemicals coming out of the vent, and form the foundation of the food chain. But toxic heavy metals also come out of the vent, including lead, mercury, and cadmium.

The microbes in this study were found to be resistant to cadmium, which they can detoxify by combining it with the sulfur found in the amino acid cysteine. This forms cadmium-sulfur nanoparticles, which can function as light-absorbing semiconductors, allowing the bacteria to harvest light energy.

Journal Paper:
Ma N, Sha Z, Sun C. 2021. Formation of cadmium sulfide nanoparticles mediates cadmium resistance and light utilization of the deep-sea bacterium Idiomarina sp. OT37-5b. Environ Microbiol 23:934–948.

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Monday, March 22, 2021

448 - Myxomycete Makes Mycelial Memories

Slime mold on a log
By frankenstoen, CC BY 2.5
Finally found some good stories, so we're back! This episode: How slime molds encode and use memories built into their own bodies!

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Show notes:
Microbe of the episode: Aeromonas salmoncida

Takeaways
Despite being single-celled organisms, slime molds have fairly complex behavior, including a basic form of memory. They often grow as a network of tubes of cytoplasm branching out from one place to find and exploit new sources of food in their environment. When these tubes connect to new food, other less productive branches of its body shrink away.

As it turns out, this body form serves a role in memory also. This study determined that the slime mold's tubes undergo constant squeezing, which moves cell contents around and also shrinks them. When tubes are connecting to a food source though, they secrete a softening agent that allows the pressure to expand the tubes instead of shrinking them. These larger tubes consequently are capable of transporting more softening agent farther away to newer food sources, so the history of food discoveries is recorded in the slime mold's own body, which also influences its responses to new discoveries.

Journal Paper:
Kramar M, Alim K. 2021. Encoding memory in tube diameter hierarchy of living flow network. Proc Natl Acad Sci 118.
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Monday, February 8, 2021

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

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.

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Monday, February 1, 2021

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!

Download Episode (5.5 MB, 7.9 minutes)

Show notes:
Microbe of the episode: Methylobacterium organophilum

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.

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Monday, January 25, 2021

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.

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Monday, January 18, 2021

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


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.

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Monday, January 11, 2021

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


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.

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