488 - Social Slimes Synchronize Sorties

Fonticula alba
By Toret et al. 2022
Curr Biol 32:1962
CC BY 4.0

This episode: Slime mold amoebas Fonticula alba have interesting and unique foraging and reproductive behaviors!
Download Episode (7.3 MB, 10.6 minutes)

Show notes:
Microbe of the episode: Cajanus cajan Panzee virus

News item

 

Takeaways

How did life develop from single-celled organisms acting independently into the complex, multicellular organisms we see and are today? Although it is difficult to look back through time to study how ancient organisms may have developed along this path, it is possible to investigate modern organisms that occupy a zone in between single-celled and multicellular, to see if we can get some hints to our own development, and also learn about some interesting microbes along the way!

This study into the social amoeba, or slime mold, Fonticula alba, finds that the individual amoebal cells in a population join together into collectives and break apart into individuals at different stages of their complex life cycle, depending on the status of the bacteria around them that they forage as prey. The investigators tease out the various pathways taken by these amoebas.

Journal Paper:

Toret C, Picco A, Boiero-Sanders M, Michelot A, Kaksonen M. 2022. The cellular slime mold Fonticula alba forms a dynamic, multicellular collective while feeding on bacteria. Curr Biol 32:1961-1973.e4.

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485 - Small Cell Sculpts Sticky Snot Sphere

Mucosphere with captured prey
Larsson et al. 2022.
Nat Commun 13:1301
CC BY 4.0

This episode: A marine protist predator traps prey microbes in an attractive bubble of mucus, eats what it wants, and lets the rest sink, possibly sequestering significant amounts of carbon!
Download Episode (7.8 MB, 11.4 minutes)

Show notes:
Microbe of the episode: Bat associated cyclovirus 1

News item

Takeaways

The oceans have a lot of unique, unexplored life in them. This is true on a macro level but even more on a microscopic level, with many different kinds of microbes of various groups with fascinating life strategies. And despite being microscopic, with enough of them around, they can affect the whole planet's climate in significant ways.

In this study, one protist species gets most of its nutrients from photosynthesis, but what it can't get from the sun, it takes from prey microbes by force. To catch its prey, it creates an intricate bubble of mucus called a mucosphere, and waits for other microbes to swim into it, thinking it is food, and get stuck. Then the predator chooses the prey cell it wants and abandons the rest, letting them sink to the ocean floor and locking away the carbon they contain in the process.

Journal Paper:
Larsson ME, Bramucci AR, Collins S, Hallegraeff G, Kahlke T, Raina J-B, Seymour JR, Doblin MA. 2022. Mucospheres produced by a mixotrophic protist impact ocean carbon cycling. Nat Commun 13:1301.

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462 - Super Ciliate Symbiont Set

Pseudoblepharisma tenue
By Muñoz-Gómez et al, 2021,
Sci Adv 7:eabg4102, CC BY 4.0

This episode: A eukaryote has symbionts living in it: green algae and also purple bacteria, a combo never seen before!

Download Episode (6.1 MB, 8.8 minutes)

Show notes:
Microbe of the episode: Staphylococcus virus phiETA

News item

Takeaways

Having bacteria as endosymbionts is fairly common in life on Earth: almost all eukaryotes have them in the form of mitochondria and sometimes chloroplasts. These former bacteria somehow got inside the ancestral eukaryote, either as parasites or as prey, and ended up as integral parts of their host's metabolic functions. Some organisms, especially insects, obtained bacterial endosymbionts more recently, that help them balance their metabolic needs when living on limited diets.

Algae have been known to be endosymbionts also, performing photosynthesis for their host. But in this study, a ciliate with both algae and purple photosynthetic bacteria as endosymbionts was discovered. Purple bacteria as symbionts is rare, and this combination has not been observed before. Interestingly, though algae produce oxygen through their photosynthesis, the ciliate prefers living in low-oxygen sediment at the bottom of a pond. The symbionts and their host seem to adjust their metabolisms as needed depending on the needs at the time; they may each perform photosynthesis, fermentation, or respiration if light, organic carbon, or oxygen are available.

Journal Paper:
Muñoz-Gómez SA, Kreutz M, Hess S. 2021. A microbial eukaryote with a unique combination of purple bacteria and green algae as endosymbionts. Sci Adv 7:eabg4102.

Other interesting stories:

• Oxygen-producing microbes could help treat acute strokes

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452 - Prokaryotic Partner Powers Protist

Anaerobic ciliate
By Graf et al. 2021
Nature, CC BY 4.0

This episode: Single-celled eukaryotes can thrive without oxygen with the help of bacterial endosymbionts that respire nitrate the way our mitochondria respire oxygen!

Thanks to Jon Graf for his contribution!

Download Episode (12.4 MB, 18.1 minutes)

Show notes:
Microbe of the episode: Brenneria salicis

News item 1 / News item 2

Takeaways

The combination of a bacterium and other microbe into the first eukaryote was a big advance in evolutionary history; it made possible the huge variety of different body shapes and sizes we see today. This is thanks to the bacterial endosymbiont, the mitochondrion, taking on specialized metabolic tasks for the cell.

We already knew about endosymbionts that help with oxygen respiration, with photosynthesis (chloroplasts), and with amino acid synthesis (certain endosymbionts in insects). But bacteria have other metabolic abilities that are very useful in certain conditions; do these bacteria ever team up with other organisms? The answer is yes! In this study, ciliates were discovered at the bottom of a lake in oxygen-free waters. These protists have an bacterial endosymbiont that helps them respire, not oxygen, but nitrate instead, generating more energy than most anaerobic ciliates.

Journal Paper:
Graf JS, Schorn S, Kitzinger K, Ahmerkamp S, Woehle C, Huettel B, Schubert CJ, Kuypers MMM, Milucka J. 2021. Anaerobic endosymbiont generates energy for ciliate host by denitrification. Nature.

Other interesting stories:

• Bacterial cellulose film is very good at separating oil and water

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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.

Other interesting stories:

• Fecal microbe transplant seems to help mice recover from spinal cord injury (paper)

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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!

Download Episode (4.6 MB, 6.7 minutes)

Show notes:
Microbe of the episode: Aeromonas salmoncida

News item

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.
Other interesting stories:

• Bacteria-derived gene editing tool TALEN better than CRISPR in some cases
• Live microbes in oceans produce more hydrocarbons than oil seeps introduce, priming microbes to break down oil (paper)

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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

News item

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)

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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

News item

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:

• Deep-sea mussels collect multiple symbiont microbes to use best one for current environment
• Microscopic water droplets help bacteria survive on dry leaves

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BacterioFiles 398 - Marathon Microbes Maximize Mileage

Veillonella parvula

From Gronow et al. 2009

Stand Genomic Sci 2(1): 57-65

This episode: Bacteria found in the guts of serious athletes help mice exercise longer by transforming their metabolic waste!

Download Episode (7.3 MB, 10.6 minutes)

Show notes:
Microbe of the episode: Aggregatibacter (Actinobacillus) actinomycetemcomitans

News item

Takeaways
Our gut microbes affect many aspects of health, and many aspects of how we live affect our microbes. One such aspect is physical exertion, which has been associated with enrichment of various microbes in the guts of athletes. This observation led to the question: are these microbes just benefiting from the high levels of exertion, or are they able to contribute also?

This study found that certain such bacteria, when given to mice, enabled the mice to run for a longer period on a treadmill. These microbes break down lactic acid, which is generated in our bodies when we push our physical limits, but the study provided evidence that the longer run times were due not to removal of this waste product, but to the propionate compound produced by its degradation.

Journal Paper:
Scheiman J, Luber JM, Chavkin TA, MacDonald T, Tung A, Pham L-D, Wibowo MC, Wurth RC, Punthambaker S, Tierney BT, Yang Z, Hattab MW, Avila-Pacheco J, Clish CB, Lessard S, Church GM, Kostic AD. 2019. Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism. Nat Med 25:1104–1109.

Other interesting stories:

• Aphids hijacked viral gene to determine whether they grow wings
• Phage therapy could help treat green sea turtles

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BacterioFiles 357 - Colossal Contagion Codes Catabolism

Tetraselmis alga
By: David Patterson and
Bob Andersen, CC BY-NC 3.0

This episode: A new giant virus infecting marine algae brings its own genes related to fermentation, generating energy in the absence of oxygen!

Thanks to Drs. Chris Schvarcz and Grieg Steward for their contributions!

Download Episode (14 MB, 15.25 minutes)

Show notes:
Microbe of the episode: Borrelia anserina

News item

Journal Paper:
Schvarcz CR, Steward GF. 2018. A giant virus infecting green algae encodes key fermentation genes. Virology 518:423–433.

Other interesting stories:

• Plant virus influences aphid nutrition and population growth
• Hosts can benefit from E. coli iron-gathering proteins
• Fog can sustain and transport microbes long distances
• Using bacteriophages to form useful nanostructures out of gold

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Episode outline:

BacterioFiles 351 - Tupanvirus Transports Translation Tools

Tupanvirus pictures
From: Abrahão et al,
2018, Nat Commun 9:749

This episode: A new giant virus has genes for a surprisingly complete system of protein synthesis!

Download Episode (10.1 MB, 11.1 minutes)

Show notes:
Microbe of the episode: Phocid alphaherpesvirus 1

Video of tupanvirus intracellular factory

Journal Paper:
Abrahão J, Silva L, Silva LS, Khalil JYB, Rodrigues R, Arantes T, Assis F, Boratto P, Andrade M, Kroon EG, Ribeiro B, Bergier I, Seligmann H, Ghigo E, Colson P, Levasseur A, Kroemer G, Raoult D, La Scola B. 2018. Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere. Nat Commun 9:749.

Other interesting stories:

• Gut microbes can help with the healthy effects of berries (paper)
• Leaf microbes can protect plants from pathogens, at least when plants aren't fertilized
• Exploring the microbes living on an 18th century mummy (paper)

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

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Episode outline:

BacterioFiles 346 - Prokaryote Prey Plug Picoalgae

Alga (C) with bacterial prey (P)
By: Kamennaya et al,
PLOS Biol 2018

This episode: Very small ocean algae consume bacterial prey of a similar size to themselves by engulfing them only partially!

Download Episode (8.9 MB, 9.7 minutes)

Show notes:
Microbe of the episode: Bradyrhizobium japonicum

Journal Paper:
Kamennaya NA, Kennaway G, Fuchs BM, Zubkov MV. 2018. “Pomacytosis”—Semi-extracellular phagocytosis of cyanobacteria by the smallest marine algae. PLOS Biol 16:e2003502.

Other interesting stories:

Using nanomagnets to control quorum sensing by pulling bacteria together (paper)

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Episode outline:

BacterioFiles 326 - Ciliate Symbionts Selected Separately

Euplotes ciliates

This episode: Learning about endosymbionts by comparing bacteria living inside eukaryotes to their free-living cousins!

Thanks to Dr. Vittorio Boscaro for his contribution!
Download Episode (9.7 MB, 10.6 minutes)

Show notes:
Microbe of the episode: Ancalochloris perfilievii

Journal Paper:
Boscaro V, Kolisko M, Felletti M, Vannini C, Lynn DH, Keeling PJ. 2017. Parallel genome reduction in symbionts descended from closely related free-living bacteria. Nat Ecol Evol 1:1160.

Other interesting stories:

Wolbachia naturally found in mosquitoes inhibits malaria transmission (paper)

Group of 5 microbes help regulate Hydra's body contractions

In mice, fungi can function somewhat in place of gut bacteria (paper)

Bacteriophages get carried all over the body

Bacteria engineered to make boron-carbon bonds

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

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Episode outline:

BacterioFiles 296 - Predator Permits Pathogen Penetration

Cyclopoid copepod

This episode: Tiny crustaceans eat paramecia, allowing viruses to infect algae inside them!

Download Episode (9.1 MB, 9.9 minutes)

Show notes:
Follow-up to episode 259: mass-producing worm spit healing protein

News item

Journal Paper:
DeLong JP, Al-Ameeli Z, Duncan G, Etten JLV, Dunigan DD. 2016. Predators catalyze an increase in chloroviruses by foraging on the symbiotic hosts of zoochlorellae. Proc Natl Acad Sci 113:13780–13784.

Other interesting stories:

Microbes are important for protecting bees

Ant bacteria produce potential new antibiotics

Old microbes discovered living in mine crystals

Skin bacteria could protect against pathogens

Author is writing poems in a bacterial genome so they survive the apocalypse (paywall)

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

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BacterioFiles 271 - Dictyostelium Delivers DNA Deathtraps

Sentinel cells fluorescing green
Credit: Xuezhi Zhang

This episode: Slime molds have special cells that capture and kill bacteria using traps made of DNA!
Download Episode (11.2 MB, 12.25 minutes)

Show notes:
Follow-up study from ep 255 group related to this study

Link to Audiommunity episode about Neutrophil Extracellular Traps

Journal Paper:
Zhang X, Zhuchenko O, Kuspa A, Soldati T. 2016. Social amoebae trap and kill bacteria by casting DNA nets. Nat Commun 7:10938.

Other interesting stories:

Making E. coli produce propane fuel (paper)

Bacteria can convert algae directly into ethanol (paper)

Certain chronic virus infections could indicate your family history

Viruses can transfer pigment production ability between bacteria

Different sizes of bacteria impose different limitations

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

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BacterioFiles 246 - Prowling Protist Predator Packs

This episode: Amoebas in soil gang up on and eat much larger roundworms!

Download Episode (10.5 MB, 11.3 minutes)

Show notes:
Journal Paper
Video of amoebas eating worm
Discussion on This Week in Microbiology

Other interesting stories:

Fungi living inside plants produce potential anticancer compound (paper)

Local bacteria help protect and nurture crops in Nigeria (paper)

Squished bacteria grow as pancake-shaped cells (paper)

Bacteria living in fungi that help plants have many genes taken from their hosts (paper)

Engineering yeast that produce opiates cheaply

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

BacterioFiles 237 - Proving Protist Predation Parentage

This episode: Vampirovibrio chlorellavorus, a predatory bacterium that feeds on Chlorella algae, is currently lost from science, but its genome has been sequenced and interpreted anyway, to reveal a surprising family history!


Download Episode (9.4 MB, 10.25 minutes)

Show notes:
Journal Paper

Other interesting stories:

Appetite-suppressing bacteria could treat obesity

Skin bacteria could save frogs from deadly fungus

Developing yeast that produce lots of biofuel lipids

Vineyard soil microbiome affects vine microbes (and thus, wine)

Microbes could make super-sensitive bioelectromechanical sensors

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BacterioFiles Micro Edition 143 - Parasites Prevent Paired Pestilences

This episode: Gut parasites may fight each other to infect!

Download Episode (9.7 MB, 10.6 minutes)

Show notes:
News item/Journal Paper

Other interesting stories:

**Fungus-bacterium community does well producing biofuel from cellulose (paper)
**Improving microbes' ability to generate electricity
**Cyanobacterium can produce 5 different biofuels
**Sequencing-based community sampling may overestimate microbial diversity (paper)
**Bacteria could help harvest biofuel algae by clumping them together (paper)

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BacterioFiles Micro Edition 125 - Phototroph Fusion Fights Fevers

This episode: Green algae could help create new cheaper, more stable vaccines for developing countries!

Download Episode (4.5 MB, 5 minutes)
Transcript

Show notes:
News item/Journal Paper

Other interesting stories:

**Some dirt in the diet could be very healthy
**Gut bacteria seem to kill Salmonella directly
**Bacteria may influence biological clocks, at least in squid
**Protein in mountain bacteria similar enough to brain protein to allow comparison
**Soil bacterium could reduce contamination of crops with deadly fungal toxin (paper)

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BacterioFiles Micro Edition 118 - Fungi Found in Seafloor Sediments

This episode: Fungi are found living deep under the sea!

Download Episode (3.15 MB, 3.5 minutes)
Transcript

Show notes:
News Item/Journal Paper

Other interesting stories:

**Scientists test artificial feces transplants to treat C. difficile infections
**Exposure to bacteria from adult male mice seems to protect young female mice against type 1 diabetes
**Bacteria that take electrons from iron can take them directly from electricity too and fix carbon dioxide
**Sea creatures often team up with bacteria that produce potential new drugs
**Engineered herpes virus could inhibit metastasis of certain cancers

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