483 - Recycling Resources Raises Robustness

E. coli

This episode: Adding tags to proteins to increase their degradation can help engineered bacteria grow and survive better under various conditions!
Download Episode (7.3 MB, 10.4 minutes)

Show notes:
Microbe of the episode: Lactococcus virus sk1

News item

Takeaways

Engineering bacteria with new genetic pathways allows us to use them in many new and promising applications. Some of these are industrial fermentations, growing large quantities of bacteria to use as catalysts for production of chemicals of interest, such as biofuels. But in other cases, engineered microbes can be most useful in less controlled environments, such as the soil. In these situations, the engineering can throw off their natural metabolic balance, making them less tolerant of the stresses of such environments.

In this study, a solution to this issue was tested using protein tags that signal the bacterial enzymes to degrade the engineered proteins. A variety of tags allowed for a variety of rates of degradation, allowing engineers to tune in the ideal rate. Bacteria with these engineered tags grew better in nutrient limited conditions than those without.

Journal Paper:
Szydlo K, Ignatova Z, Gorochowski TE. 2022. Improving the Robustness of Engineered Bacteria to Nutrient Stress Using Programmed Proteolysis. ACS Synth Biol 11:1049–1059.

Other interesting stories:

• Microbes found in tap water could influence composition of the gut microbiome (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.

482 - Colony Concentric Clock Construction

Bacillus subtilis
By Y tambe,
CC BY-SA 3.0

This episode: Single-celled bacteria can act independently to create patterns and structure in their biofilm communities!
Download Episode (9.6 MB, 14.0 minutes)

Show notes:
Microbe of the episode: Dictyostelium discoideum Skipper virus

News item

Takeaways

Large multicellular organisms like us have interesting mechanisms for using one set of genetic instructions present in all cells to form a large, complex community of many different types of cells with different structures and functions, all working together. Single-celled microbes do not have the same requirements for genetic or structural complexity, but they do often display interesting communal patterns and behaviors.

In this study, bacteria growing in colonies on agar displayed a particular mechanism of pattern formation previously seen only in eukaryotes, called segmentation clock or clock and wavefront process. In this process, the cells in the colony are all acting individually without communication with each other, but nevertheless form a repeating ring structure in the colony as it grows, possibly allowing some measure of differentiation of cells that could help the community survive various challenges.

Journal Paper:
Chou K-T, Lee DD, Chiou J, Galera-Laporta L, Ly S, Garcia-Ojalvo J, Süel GM. 2022. A segmentation clock patterns cellular differentiation in a bacterial biofilm. Cell 185:145-157.e13.

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.

472 - Caulobacter Condensates Compartmentalize Kinase

Caulobacter crescentus

This episode: Bacteria can use blobs of disordered proteins to quickly adapt to new conditions!

Thanks to Dr. Saumya Saurabh for his contribution!
Download Episode (10.9 MB, 15.9 minutes)

Show notes:
Microbe of the episode: Drosophila melanogaster Micropia virus

 

Takeaways

Bacteria can adapt to environmental fluctuations via mechanisms operating at the various levels of the central dogma, or metabolism (stringent response). Recently, researchers at Stanford University discovered a mechanism that allows bacteria to sense and rapidly adapt to nutrient fluctuations by simply tuning protein self-assembly as a function of nutrient availability. Termed membraneless organelles or condensates, these proteinaceous assemblies can dynamically sequester key signaling enzymes within them in response to environmental cues. Biophysical adaptation mediated by organelles is fast, reversible, and facile; thereby representing a crucial step in the mechanistic understanding of microbial adaptation.

Journal Paper:
Saurabh S, Chong TN, Bayas C, Dahlberg PD, Cartwright HN, Moerner WE, Shapiro L. 2022. ATP-responsive biomolecular condensates tune bacterial kinase signaling. Sci Adv 8:eabm6570.

Other interesting stories:

• Bacteria produce biofuel from carbon dioxide, light, and solar power-generated electricity
• Vine that can mimic leaves of different trees may get info from bacteria (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.

470 - Super Small Symbionts Soothe Symptoms

Tiny symbiont Saccharibacteria (yellow-green)
on host bacteria (red)
By Utter et al.,
CC BY-SA 4.0

This episode: Tiny bacteria that live on larger bacteria reduce the inflammation and gum disease the bigger microbes cause in the mouths of mice!

Download Episode (6.3 MB, 9.2 minutes)

Show notes:
Microbe of the episode: Actinomadura viridilutea

Takeaways

Even bacteria can be hosts to smaller symbionts living on them. Some kinds of these extremely tiny bacteria live in various parts of our bodies, and are sometimes associated with inflammation and the resulting disease. But being associated with something isn't necessarily the same as causing that thing.

In this study, tiny bacteria living on other bacteria in the mouths of mice were found to reduce the inflammation caused by their bacterial hosts, resulting in less gum disease and bone loss in the jaw. Even when the tiny bacteria were no longer present, their former bacterial hosts were still less disruptive to the mouse mouth.

Journal Paper:
Chipashvili O, Utter DR, Bedree JK, Ma Y, Schulte F, Mascarin G, Alayyoubi Y, Chouhan D, Hardt M, Bidlack F, Hasturk H, He X, McLean JS, Bor B. 2021. Episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss in mice through host bacterial modulation. Cell Host Microbe 29:1649-1662.e7.

Other interesting stories:

• Anti-tumor bacteria: engineered E. coli colonizes tumors and attracts immune response
• Cats have skin bacteria that could inhibit drug resistant pathogens

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.

469 - Prophage Provides Partial Protection

Salmonella invading cells

This episode: A virus lurking in a bacterial genome protects its host population from infection with other phages, by killing off infected cells!

Download Episode (7.6 MB, 11.0 minutes)

Show notes:
Microbe of the episode: Olive latent ringspot virus

Takeaways

Many bacteriophages just go in and gobble up all their host's resources to make a bunch of new viruses right away. Others play a longer game, splicing into and lurking in the host's genome across multiple generations until conditions are right to multiply more rapidly. It is beneficial to these latter kind when their host is resistant to the fast-killing variety, but how can bacteria be resistant to some phages but not others?

In this study, one prophage (the phage genome integrated into the bacterial genome) carries a gene that does this in an interesting way. It prevents invading phages from replicating and kills the host cell so the infection can't spread, protecting the population (and all the other cells containing the prophage). It also contains an immunity element that allows the prophage to replicate itself without interference.

Journal Paper:
Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. 2021. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe 29:1620-1633.e8.

Other interesting stories:

• Migration affects birds' gut microbiota
• Sometimes E. coli can keep Salmonella from causing problems in the gut

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.

467 - Prion Pivots Productive Pathways

Saccharomyces yeast
By Mogana Das Murtey and
Patchamuthu Ramasamy
CC BY-SA 3.0

This episode: Prions in yeast can allow better adaptation to changing conditions!

Thanks to David Garcia for his contribution!

Download Episode (9.5 MB, 13.9 minutes)

Show notes:
Microbe of the episode: Hepatovirus F

News item

Takeaways

Prions can be deadly. They're misshapen proteins that cause a cascade of misfolding of similar proteins if they get into the nervous system, resulting in neurodegeneration in mammals. But in other organisms, they are not always so scary; some fungi use prions to regulate their behavior in varying conditions.

In this study, a prion allows yeast to switch between a fast-growing lifestyle with shorter reproductive lifespan that can be beneficial in conditions where nutrients are often plentiful, and a slower-growing but more enduring lifestyle that helps in more scarce conditions.

Journal Paper:
Garcia DM, Campbell EA, Jakobson CM, Tsuchiya M, Shaw EA, DiNardo AL, Kaeberlein M, Jarosz DF. 2021. A prion accelerates proliferation at the expense of lifespan. eLife 10:e60917.

Other interesting stories:

• Modified yeast probiotic could tune its effects as needed by sensing bowel inflammation

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.

463 - Selectively Stimulating Cell Squatters

Bacteriophages
By Jancheva and Böttcher
2021, JACS 143:8344-8351
CC BY 4.0

This episode: Bacteria produce a compound that causes a phage lurking in the genome of a competing species to wake up and start killing that competitor!

Download Episode (8.2 MB, 12.0 minutes)

Show notes:
Microbe of the episode: Zaire ebolavirus

News item

Takeaways

Some bacteriophages infect and immediately destroy their hosts in a burst of new viruses, while others can be stealthier, integrating their genome into the genome of the host and remaining there quietly even over multiple generations of the bacteria. When something stresses the host, such as DNA damage, these integrated phages (prophages) become active and start producing new viruses, killing their host like the other kind does.

In this study, one kind of bacteria release a chemical that wakes up phages in a competitor species of bacteria. This is helpful for competition, but even more interesting is that out of the six prophages in the competitor species, the chemical wakes up only one of them. Such selective phage induction could be interesting to study.

Journal Paper:
Jancheva M, Böttcher T. 2021. A Metabolite of Pseudomonas Triggers Prophage-Selective Lysogenic to Lytic Conversion in Staphylococcus aureus. J Am Chem Soc 143:8344–8351.

Other interesting stories:

• Lab-evolved fungus strain could protect honeybees from mites

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.

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

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.

460 - Prokaryote Publicity Prevents Protist Processes

Emiliania huxleyi
By Alison R. Taylor
UNC Wilmington Microscopy
PLoS Biology, June 2011 Cover
CC BY 2.5

This episode: A bacterial communication signal makes algae stop growing, which helps them survive virus attacks!

Download Episode (5.3 MB, 7.7 minutes)

Show notes:
Microbe of the episode: Veillonella parvula

Takeaways

Many interesting interactions between microbes take place in the ocean. As single-celled organisms lacking complex sensory organs, many such interactions and communications are mediated by chemical signals. Some bacteria, for example, each produce small amounts of certain chemicals and release them into the environment. When the concentration of the chemical signal builds up to a certain point, the bacteria change their behavior to take advantage of their high numbers that must be present to produce so much of the signal. This process is called quorum sensing.

Some of these chemical signals can affect the behavior of organisms other than bacteria also. In this study, a common marine algal species was found to stop growing in response to a certain bacterial signal. This chemical inhibits an enzyme required for the algae to produce nucleotides to replicate their genomes. As a result, the algae are able to resist destruction by a virus that would otherwise decimate their populations.

Journal Paper:
Pollara SB, Becker JW, Nunn BL, Boiteau R, Repeta D, Mudge MC, Downing G, Chase D, Harvey EL, Whalen KE. 2021. Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality. mSphere 6:e00009-21.

Other interesting stories:

• Comparing ancient gut microbes from fecal fossils to modern gut communities / also this one

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.

458 - Slimy Cells Stop Sinking

Colonies of strains with
different floating strengths
By Kessler et al. 2021,
J Bacteriol 203(11):e00023-21
CC BY 4.0

This episode: Bacteria can resist the force of gravity in liquid culture by covering themselves with goopy sugar polymers like parachutes!

Download Episode (10.4 MB, 15.2 minutes)

Show notes:
Microbe of the episode: Brevicoryne brassicae virus

Takeaways

Put bacteria in a centrifuge, and most of the time you end up with a compact pellet of cells at the bottom of the tube, and mostly cell-free liquid above it. Bacteria do have ways to remain suspended in liquid, even without constant stirring or shaking of the container, but swimming, for example, consumes energy.

In this study, artificial selection allowed the discovery of bacteria that could resist centrifuging speeds up to 15000 times the force of gravity, remaining suspended in liquid instead of forming a pellet. Production of polysaccharide was important, but not sufficient; for the most resistance to sinking, bacteria had to attach the polysaccharide to their cell surface, to act as a sort of parachute.

Journal Paper:
Kessler NG, Caraballo Delgado DM, Shah NK, Dickinson JA, Moore SD. 2021. Exopolysaccharide Anchoring Creates an Extreme Resistance to Sedimentation. J Bacteriol 203(11):e00023-21.

Other interesting stories:

• Engineered probiotic yeast could help prevent vitamin A deficiency

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.

456 - Invader Induces Increased Immensity

Sulfolobus infected
with STSV1
By Xiangyux
From Wikipedia

This episode: A virus of archaea stops cells from dividing, so they just keep getting bigger and releasing more viruses!

Download Episode (6.9 MB, 10.1 minutes)

Show notes:
Microbe of the episode: Streptomyces caelestis

Takeaways

Viruses affect their hosts many different ways: instant hostile takeover of cellular machinery, lurking unseen in the genome for generations, inducing reduced cell division or excessive cell division, and more. Archaeal viruses are relatively unknown in their genetic abilities and lifestyles, but we do know that they tend not to destroy their hosts through explosive viral reproduction, and that some archaea have eukaryote-like cell cycle phases.

In this study, some viruses infecting a thermophilic archaeon interrupt its cycle in the growth phase, so hosts expand in size up to around 17 times normal, continuously releasing new viruses over time. Eventually some archaea in the population gain resistance to the viruses via their CRISPR/Cas systems, and normal-sized cells dominate the population again.

Journal Paper:
Liu J, Cvirkaite-Krupovic V, Baquero DP, Yang Y, Zhang Q, Shen Y, Krupovic M. 2021. Virus-induced cell gigantism and asymmetric cell division in archaea. Proc Natl Acad Sci 118:e2022578118.

Other interesting stories:

• Chocolate is a fermented food

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.

453 - Phenazine Faciliates Phosphorus Feeding

Pseudomonas aeruginosa
By Y_tambe, CC BY-SA 3.0

This episode: Some bacteria produce antibiotics that can also help them gather more nutrients!

Download Episode (5.0 MB, 7.3 minutes)

Show notes:
Microbe of the episode: Diadromus pulchellus toursvirus

News item 1

Takeaways

Antibiotics have saved a lot of lives since they were discovered and used to treat many previously untreatable bacterial infections. But bacteria themselves have been making antibiotics much longer than we have, to help compete in their environment. However, sometimes these compounds are not produced in large enough concentrations to act as antibiotics, killing or inhibiting rival bacteria. Why waste energy on this sublethal production? Are there other functions these molecules can perform?

In this study, bacteria produce an antibiotic called phenazine that can damage cell components by redox reactions, transferring electrons. But it can also help liberate the essential nutrient phosphorus from being bound to insoluble particles, allowing the bacteria to grow better even in the absence of competitors.

Journal Paper:
McRose DL, Newman DK. 2021. Redox-active antibiotics enhance phosphorus bioavailability. Science 371:1033–1037.
Other interesting stories:

• Bacterial proteins stuck to tumor cells could be targeted

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.

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)

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.

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

News item

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!

Subscribe: Apple Podcasts, Google Podcasts, Android, or RSS. Support the show at Patreon, or check out the show at Twitter or Facebook.

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!

Subscribe: Apple Podcasts, Google Podcasts, Android, or RSS. Support the show at Patreon, or check out the show at Twitter or Facebook.

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

News item

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!

Subscribe: Apple Podcasts, Google Podcasts, Android, or RSS. Support the show at Patreon, or check out the show at Twitter or Facebook.

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.

Other interesting stories:

• Bacteria can grow so well in spent nuclear fuel ponds, they make the water cloudy
• Certain probiotic bacteria might be able to degrade gluten and protect people with celiac

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 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.

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!

Subscribe: Apple Podcasts, Google Podcasts, Android, or RSS. Support the show at Patreon, or check out the show at Twitter or Facebook.

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:

• Plants use arsenic-dumping genes from bacteria to get essential nutrients
• Another study engineering better viruses for phage therapy

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 404 - Phages Force Food Finding

Synechococcus cyanobacteria

This episode: Another climate-related story: Cyanobacteria infected by viruses continue taking up nutrients from their environment, using it to make more viruses than would otherwise be possible!

Download Episode (6.3 MB, 9.2 minutes)

Show notes:
Microbe of the episode: Microcystis virus Ma-LMM01

News item

Takeaways
Though global warming is a global problem, accurate models for predicting where things are headed need to incorporate the activity of even the smallest organisms, if they're numerous enough. Photosynthesis and other activities of microbes in the oceans are a big sink for carbon, but cycles of other nutrients and also viruses can affect the carbon cycle.

In this study, phages infecting photosynthetic ocean bacteria were able to continue their host's uptake of nitrogen from the environment even after mostly shutting down the host's own protein production and growth. This has implications for how viruses affect carbon cycling by cyanobacteria and how quickly populations of these bacteria may grow or die off.

Journal Paper:
Waldbauer JR, Coleman ML, Rizzo AI, Campbell KL, Lotus J, Zhang L. 2019. Nitrogen sourcing during viral infection of marine cyanobacteria. Proc Natl Acad Sci 116:15590–15595.

Other interesting stories:

• Transplants of gut microbes help koalas eat wider range of food
• Skin bacteria can help attract (or repulse) mosquitoes (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.