This episode: Trends of declining lichen populations and biocrust cover overall match trends of increasing temperatures in Colorado dryland!

Download Episode (6.4 MB, 9.3 minutes)

Show notes:
Microbe of the episode: Cherry chlorotic rusty spot associated partitivirus

Takeaways:

Global climate change is affecting almost every natural system on the planet, in predictable and also sometimes unexpected, complex ways. Microbes perform key roles in many different ecosystems, providing and recycling important nutrients and even macroscopic structure. One example of this is biocrusts in dryland environments, such as areas in the western US with low annual rainfall. Microbes other organisms form a stable surface binding soil and sand particles together, helping to retain moisture and prevent erosion and transformation of land into desert.

In this study of a Colorado park over more than 20 years, important species of symbiotic fungi and photosynthetic microbes in the form of lichens have declined significantly. The land is mostly untroubled by grazing or human activity, but changes in climate and moisture and the presence of invasive plants could affect lichens. However, the temperature increase over the decades showed the best correlation with the lichen decline. The loss of these species could lead to nutrient shortages in the long term for these communities.

Journal Paper:

Finger-Higgens R, Duniway MC, Fick S, Geiger EL, Hoover DL, Pfennigwerth AA, Van Scoyoc MW, Belnap J. 2022. Decline in biological soil crust N-fixing lichens linked to increasing summertime temperatures. Proc Natl Acad Sci USA 119:e2120975119.

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This episode: A virus partners with a parasitoid wasp to help exploit fruit fly victims!

Download Episode (7.7 MB, 11.2 minutes)

Show notes:
Microbe of the episode: Actinomadura livida

Takeaways Parasitoid wasps have an interesting lifestyle: they inject their eggs into the larvae of other insects, and their young hatch and grow up by consuming the host from the inside. Some of these wasps also inject a virus along with the egg, which supports the wasp offspring by suppressing the host immune system.

Most of these parasitoid helper viruses are integrated into the host wasp genome and are translated and produced as needed, but in this study, an independently replicating entomopoxvirus serves as an example of a virus-wasp mutualism. The study explores how the virus can infect the wasp prey, and how it gets passed on to wasp offspring.

Journal Paper:
Coffman KA, Hankinson QM, Burke GR. 2022. A viral mutualist employs posthatch transmission for vertical and horizontal spread among parasitoid wasps. Proc Natl Acad Sci 119:e2120048119.

 

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This episode: Gene transfers between viruses and eukaryotes have happened many times throughout evolutionary history!

Download Episode (7.5 MB, 10.9 minutes)

Show notes:
Microbe of the episode: Mycoplasma subdolum

News item

Takeaways As we've all seen recently, viruses can cause a lot of trouble. Their biology requires them to be parasites inside the cells of their hosts, and they can cause devastating disease, so it's hard to think of them as having played important roles in the development of life on Earth, including our own evolution.

However, this study found thousands of apparent historical transfers of genes from virus to host or from host to virus in the cells of all kinds of different eukaryotes. Some of these genes play important roles in the cell, helping to make them what they are.   Journal Paper:
Irwin NAT, Pittis AA, Richards TA, Keeling PJ. 2022. Systematic evaluation of horizontal gene transfer between eukaryotes and viruses. Nat Microbiol 7:327–336.

 

Other interesting stories:

• Building a device that translates signals from one microbe to communicate with another
• Cloaking antitumor bacteria to fight cancer without immune system interference

 

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This episode: Human-based food used as bait by hunters can reduce bears' gut microbe diversity!

Download Episode (5.9 MB, 8.6 minutes)

Show notes:
Microbe of the episode: Actinomadura verrucosospora

News item

Takeaways Gut microbes are important for the health of most animals. In humans, many things can affect our gut microbe community, including diet, medications, and lifestyle. Eating a varied diet with diverse kinds of plant-based foods can maintain a healthy, functional community of many different kinds of microbe. However, eating mostly highly processed grain-based foods can reduce the diversity and functionality of the gut community.

This is also true in bears. In this study, when bears consumed more processed, grain-based human foods via hunters leaving such foods out as bait, the gut communities in these bears had reduced diversity of microbes. The effects of this reduced diversity were not determined, but it is reasonable to assume it was not good for the bears' overall health.   Journal Paper:
Gillman SJ, McKenney EA, Lafferty DJR. 2022. Human-provisioned foods reduce gut microbiome diversity in American black bears (Ursus americanus). J Mammal 103:339–346.

 

Other interesting stories:

• 3D-printed electrode structures harvest electricity from bacterial photosynthesis
• Gut microbes are important for helping tadpoles survive in warmer conditions

 

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This episode: Simple microscopic animals can survive extreme radiation by ejecting damaged cells that might otherwise become cancer!

Download Episode (7.3 MB, 9.2 minutes)

Show notes:
Microbe of the episode: Helleborus net necrosis virus

News item

Takeaways Any multicellular organism with different types of cells needs some sort of cell regulation, to keep each cell type doing what it's supposed to do for the good of the organism as a whole. We know what happens when this regulation fails and one type of cells starts multiplying out of control: cancer.

However, cancer has never yet been observed in certain organisms, including the simple microscopic animal Trichoplax adhaerens. In this study, these animals are exposed to large amounts of radiation and then observed over years to see if they can develop cancer or have interesting mechanisms of resisting it.   Journal Paper:
Fortunato A, Fleming A, Aktipis A, Maley CC. 2021. Upregulation of DNA repair genes and cell extrusion underpin the remarkable radiation resistance of Trichoplax adhaerens. PLOS Biol 19:e3001471.

 

Other interesting stories:

• Genes transferred from bacteria to algae helped land plants evolve

 

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This episode: How family members share gut microbes across multiple generations!

Download Episode (7.3 MB, 10.7 minutes)

Show notes:
Microbe of the episode: Dyozetapapillomavirus 1

Takeaways Our gut's microbial communities can greatly influence our health, for good or bad. The makeup of these communities can be influenced by many factors, including genetics, health status, diet, and other aspects of the environment we live in. We've learned a lot about this topic recently, but there's a lot more we still don't understand.

In this study, gut microbe samples from individuals spanning multiple generations in the same families were compared, to see how much influence family relationships and cohabitation could have on the gut communities. Both genetic relationship and living together had influences on which gut microbes different people shared.   Journal Paper:
Valles-Colomer M, Bacigalupe R, Vieira-Silva S, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J, Falony G. 2022. Variation and transmission of the human gut microbiota across multiple familial generations. 1. Nat Microbiol 7:87–96.

 

Other interesting stories:

• Simple modification to interesting bacteria make them excrete nitrogen fertilizer
• Making carbon dioxide into useful chemicals with bacteria

 

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This episode: Bacteriophages can hitch a ride on bacteria they don't infect to travel through soil on fungal filaments, potentially helping their carriers by infecting and killing their competitors!

Download Episode (7.1 MB, 10.3 minutes)

Show notes:
Microbe of the episode: Epinotia aporema granulovirus

News item

Takeaways For tiny bacteria, partially dry soil can be like a vast system of caverns, with particles of soil separated by air-filled spaces much bigger than individual bacteria. Not all bacteria can swim through liquid, and those that can't simply try to thrive as best they can wherever they may be. But for those that can swim, fungi and other filamentous organisms can form bridges between soil particles that motile bacteria can swim across, reaching new places.

In this study, phages were found to hitch a ride on bacteria they don't normally infect, crossing fungus-like filaments to new places and infecting the bacteria they find there. The bacteria carrying them can also benefit from this interaction, since the phages help the carrier bacteria compete and establish a colony in the new location.   Journal Paper:
You X, Kallies R, Kühn I, Schmidt M, Harms H, Chatzinotas A, Wick LY. 2022. Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system. 5. ISME J 16:1275–1283.

 

Other interesting stories:

• Fungus species discovered in spacecraft assembly facility
• Oral microbes uniquely influence immune system interaction with mouth bones

 

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This episode: Beetles inoculate bamboo with a fungus that consumes the bamboo sugars to feed the beetle larvae!

Download Episode (7.7 MB, 11.2 minutes)

Show notes:
Microbe of the episode: Saccharomyces cerevisiae virus L-BC (La)

News item

Video: Lizard beetle laying its egg

Takeaways The structural polymers that make up plants, such as cellulose, can be difficult for many organisms to digest. Some kinds of bacteria and fungi can do it, and some animals (cows, pandas, termites) partner with these microbes to be able to eat otherwise indigestible plant material. This includes insects such as leaf-cutter ants that farm external gardens of microbes, providing them plant material and then eating the resulting microbial growth.

In this study, the lizard beetle lays its eggs in bamboo and inoculates the walls of the bamboo with a fungus that provides food to the larvae. Chemical analyses suggest that the fungus only consumes the simple sugars in the bamboo rather than breaking down the tougher polymers, which raises questions about the evolution of this interaction.   Journal Paper:
Toki W, Aoki D. 2021. Nutritional resources of the yeast symbiont cultivated by the lizard beetle Doubledaya bucculenta in bamboos. Sci Rep 11:19208.

 

Other interesting stories:

• Using bacteria to detect and target colon cancer for imaging (paper)
• Filters made from kombucha cultures could work better than synthetic types

 

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This episode: New techniques allow specific modifications in certain members of a complex community of microbes, without isolating them in pure culture first!

Download Episode (11.5 MB, 16.7 minutes)

Show notes:
Microbe of the episode: Tomato golden mosaic virus

News item

Takeaways The technology for understanding and manipulating microbial genetics has come a long way in a short time. It used to take years even to sequence a small genome, and now thousands can be sequenced in just a few days. The technology to change and even create genetic sequences is also much further advanced now than just a few decades ago. But still, many analyses and modifications require a pure culture of a microbe to carry out.

This study tested a method for modification of single or multiple species in a community of many. The method allows for identification of which species were successfully modified in targeted ways, and can allow the modified species to be extracted and studied individually.   Journal Paper:
Rubin BE, Diamond S, Cress BF, Crits-Christoph A, Lou YC, Borges AL, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Rovinsky R, Smock DCJ, Tang K, Owens TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM, Banfield JF, Doudna JA. 2022. Species- and site-specific genome editing in complex bacterial communities. 1. Nat Microbiol 7:34–47.

 

Other interesting stories:

• Microbes that degrade plastic may be increasing in response to plastic pollution
• Algae in ocean communicate with each other using fluorescence

 

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This episode: Predatory bacteria could protect lobster farms from disease-causing bacteria!

Download Episode (4.8 MB, 7 minutes)

Show notes:
Microbe of the episode: Gordonia rubripertincta

    Takeaways Antibiotics have done wonders for controlling bacterial pathogens. Many people have lived that would otherwise have died, and some industries have produced much more than they would have, particularly those involved in animal farming. However, more and more targeted pathogens are developing resistance to the antibiotics we have, and new ones are harder to discover, so alternative approaches are needed.

Here, predatory bacteria take the place of antibiotics in a study on farmed spiny lobsters. These predators swim after and attach to prey bacteria, hollowing out their contents to use as nutrients to make more predators. They do not hurt the lobsters, but the study finds they do reduce the number of pathogenic prey organisms injected into the lobsters at the same time.   Journal Paper:
Ooi MC, Goulden EF, Smith GG, Bridle ARY 2021. 2021. Predatory bacteria in the haemolymph of the cultured spiny lobster Panulirus ornatus. Microbiology 167:001113.

Other interesting stories:

• 3D-printing bacterial biofilms
• Review of latest in oncolytic (cancer-killing) viruses

 

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This episode: A bacteriophage that overcomes the bacterial CRISPR/Cas immune system by interrupting the CRISPR DNA with its own genome!

Download Episode (6.8 MB, 10 minutes)

Show notes:
Microbe of the episode: Wenzhou mammarenavirus

Takeaways Bacteria have many ways to resist being exploited by bacteriophage viruses, including the adaptable CRISPR/Cas system that uses a piece of viral nucleic acid sequence to target and destroy incoming phages. But phages also have many ways to evade and disrupt bacterial defenses.

In this study, a phage is discovered that inserts its own genome into the CRISPR/Cas sequence in the bacterial genome, disrupting the bacterial defenses. To escape the defenses while it is doing this insertion, it carries genes for previously-unknown anti-CRISPR proteins. But inserting and removing a viral sequence from the bacterial genome is not always a clean procedure.   Journal Paper:
Varble A, Campisi E, Euler CW, Maguin P, Kozlova A, Fyodorova J, Rostøl JT, Fischetti VA, Marraffini LA. 2021. Prophage integration into CRISPR loci enables evasion of antiviral immunity in Streptococcus pyogenes. 12. Nat Microbiol 6:1516–1525.

Other interesting stories:

• Great article on the history of phage therapy

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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)

 

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This episode: Many organisms produce the smell of earth, geosmin, and many others can sense it–but why?

Download Episode (6.0 MB, 8.7 minutes)

Show notes:
Microbe of the episode: Acidianus spindle-shaped virus 1

  News item  
Takeaways The smell of soil or earth is one of the most recognizable smells, and comes largely from a chemical called geosmin, produced by many different kinds of bacteria. Many animal species are sensitive to geosmin, some attracted by it and others repelled. But it is still not entirely understood what is the evolutionary benefit to the microbes that produce it, or the reason why different animals are sensitive to it in different ways.

In this study, different geosmin-producing bacteria were paired with tiny bacteria-eating roundworms, nematodes, to see how the chemical affected their interactions. Production of geosmin affected the worms' movement, apparently inducing them to avoid colonies of the producing microbes in some cases, though the worms still sometimes fed on the bacteria. Adding geosmin to colonies of different bacteria did not affect the worms' behavior though, so other factors seem to be involved.

Journal Paper:

Zaroubi L, Ozugergin I, Mastronardi K, Imfeld A, Law C, Gélinas Y, Piekny A, Findlay BL. 2022. The Ubiquitous Soil Terpene Geosmin Acts as a Warning Chemical. Appl Environ Microbiol 88:e00093-22.

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This episode: A phage both kills bacterial pathogens and selects for reduced virulence!

Download Episode (6.3 MB, 9.9 minutes)

Show notes:
Microbe of the episode: Helminthosporium victoriae 145S virus

  News item
  Takeaways Using bacteria-killing viruses to treat bacterial infections, or phage therapy, can be a good alternative to antibiotics in some situations when there are no effective antibiotics for a particular infection. But bacteria can evolve resistance to phages as well as antibiotics, often with little cost to their fitness.

In this study, a phage not only could treat an infection by attacking the bacteria, but the bacterial hosts that do evolve resistance to the phage do so by getting rid of certain structures that help them to cause more serious infection. Thus, therapy with this phage may both reduce the bacterial load and also make those remaining less virulent.   Journal Paper:
Kortright KE, Done RE, Chan BK, Souza V, Turner PE. 2022. Selection for Phage Resistance Reduces Virulence of Shigella flexneri. Appl Environ Microbiol 88:e01514-21.

Other interesting stories:

• Plastic-eating bacteria could produce biodegradable plastic
• Harmless variant of acne bacteria could help prevent more serious skin infection

 

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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

 

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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

 

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This episode: Harmless gut microbes resist cholera with good defense or better offense!

Download Episode (5.8 MB, 8.4 minutes)

Show notes:
Microbe of the episode: Streptomyces corchorusii

  News item
  Takeaways The community of microbes in our guts is highly diverse, yet generally they all coexist relatively peacefully. Some pathogens can invade this community and cause massive disruptions. Cholera is a disease caused by a pathogen that injects its competing bacteria with toxins and disrupts the health of the gut, leading to very watery diarrhea that can quickly dehydrate victims.   This study found that some microbes commonly found harmlessly existing in the gut can resist destruction by the cholera pathogen. One of these resists by striking back with its own toxin injection system; the other creates a barrier of slime around itself that keeps the invader's toxins from reaching it. Such resistant gut microbes could help to reduce the threat of diseases such as cholera.   Journal Paper:
Flaugnatti N, Isaac S, Lemos Rocha LF, Stutzmann S, Rendueles O, Stoudmann C, Vesel N, Garcia-Garcera M, Buffet A, Sana TG, Rocha EPC, Blokesch M. 2021. Human commensal gut Proteobacteria withstand type VI secretion attacks through immunity protein-independent mechanisms. Nat Commun 12:5751.

Other interesting stories:

• Producing super-strong fibers with engineered microbes
• Some gut bacteria store some drugs inside their cells

 

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

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

 

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This episode: Bacteria are able to extract metals from rocks for industrial use, even in microgravity!

Download Episode (6.2 MB, 9.0 minutes)

Show notes:
Microbe of the episode: Decapod ambidensovirus 1

  News item
  Takeaways As humanity makes progress toward becoming an interplanetary species, consideration is needed on how travelers can survive and thrive in distant places. These methods may look very different from what works well on Earth, with differences in gravity, atmosphere, and access to resources. For example, mining for materials for construction may not be feasible using methods common on Earth. An alternative may be biomining, using microbes that can selectively extract and purify specific metals from minerals.   In this study, the European Space Agency tested the ability of several microbes to extract vanadium from rocks in different gravity conditions, on the International Space Station. Two out of three microbes were able to extract twice as much vanadium as was extracted in the absence of microbes, both on a planet and up in space.   Journal Paper:
Cockell CS, Santomartino R, Finster K, Waajen AC, Nicholson N, Loudon C-M, Eades LJ, Moeller R, Rettberg P, Fuchs FM, Van Houdt R, Leys N, Coninx I, Hatton J, Parmitano L, Krause J, Koehler A, Caplin N, Zuijderduijn L, Mariani A, Pellari S, Carubia F, Luciani G, Balsamo M, Zolesi V, Ochoa J, Sen P, Watt JAJ, Doswald-Winkler J, Herová M, Rattenbacher B, Wadsworth J, Everroad RC, Demets R. 2021. Microbially-Enhanced Vanadium Mining and Bioremediation Under Micro- and Mars Gravity on the International Space Station. Front Microbiol 12:663.

Other interesting stories:

• A prokaryote with internal metabolic compartments (paper)

 

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This episode: Bacteria living inside soil fungus produce toxins that can protect their host from tiny predators!

Download Episode (7.7 MB, 11.2 minutes)

Show notes:
Microbe of the episode: Mycobacterium virus DLane

Takeaways Soils have many different organisms cooperating and competing for resources. Some little worms called nematodes prey on fungi in the soil, while fungi may effectively defend themselves or strike back with toxins or traps that catch and kill the worms. On top of these interactions are other organisms that interact in various ways. In this study, bacteria living inside a kind of soil fungus produce toxins that defend the fungus against predatory nematodes.   Journal Paper:
Büttner H, Niehs SP, Vandelannoote K, Cseresnyés Z, Dose B, Richter I, Gerst R, Figge MT, Stinear TP, Pidot SJ, Hertweck C. 2021. Bacterial endosymbionts protect beneficial soil fungus from nematode attack. Proc Natl Acad Sci 118:e2110669118.

Other interesting stories:

• Sequencing stomach bacteria to find out how prehistoric populations migrated

 

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This episode: Certain nectar-dwelling bacteria can induce pollen to germinate to access their tasty proteins!

Download Episode (6.0 MB, 8.8 minutes)

Show notes:
Microbe of the episode: Clostridium oceanicum

  News item
  Takeaways Nectar in flowers seems like it would be a great place for microbes to live, since it has so much sugar, but it's actually somewhat difficult to thrive solely in and on nectar. The carbon in sugar is only one essential element for life, and there's enough of it that it can be overwhelming to the osmotic balance of many microbes. Pollen could provide more nutrients in the form of protein and the nitrogen that comes with it, but it is difficult to penetrate its hard shell.   In this study, certain kinds of bacteria that live in nectar were able to access more pollen protein than other microbes by inducing pollen to germinate, growing out of its shell, or burst and release the protein directly. These microbes only benefited from pollen that were still alive and able to germinate, and not from those that had been disabled.   Journal Paper:
Christensen SM, Munkres I, Vannette RL. 2021. Nectar bacteria stimulate pollen germination and bursting to enhance microbial fitness. Curr Biol 31:4373-4380.e6.

Other interesting stories:

• Bacteria recycling plastic into vanilla flavor

 

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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

 

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

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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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This episode: Slime mold amoebas Fonticula alba have interesting and unique foraging and reproductive behaviors!

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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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This episode: Training a phage strain on bacteria can increase its ability to control those bacteria for much longer than an untrained phage!

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Show notes:
Microbe of the episode: Pepper yellow leaf curl Indonesia virus

  News item
  Takeaways With resistance to antibiotics spreading more and more among deadly bacteria, finding alternatives to treat infections is becoming more important. One option is phage therapy, using viruses that infect bacteria to weaken or wipe out pathogens, but this can be tricky. Sometimes it takes too long to prepare an effective population of phage for treatment, and sometimes the target pathogen evolves resistance to the phage too quickly   In this study, a phage that was trained, or pre-evolved, to infect specific bacteria more effectively, was able to dominate the population consistently and prevent it from becoming fully resistant. For comparison, against an untrained strain of the same phage, the bacteria developed almost complete resistance after several days.   Journal Paper:
Borin JM, Avrani S, Barrick JE, Petrie KL, Meyer JR. 2021. Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance. Proc Natl Acad Sci 118.

Other interesting stories:

• Engineered gut bacteria could sense and indicate bowel inflammation

 

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

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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

 

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This episode: Transplanting microbes from some corals to others could help the corals survive high temperatures!

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Show notes:
Microbe of the episode: Streptomyces olivaceoviridis

  News item
  Takeaways The ever-rising temperatures of our modern world are putting more and more stress on various ecosystems. This is true even on the ocean floor: record-high temperatures damage reefs by causing coral bleaching, in which corals lose their photosynthetic endosymbionts. If conditions do not improve, these corals eventually die.   Corals have microbial symbionts other than the phototrophs, also. We know from ourselves and from plants that microbes can have big effects on their hosts, so it seemed worth testing whether symbionts from more heat-resistant corals could transfer heat resistance to more vulnerable individuals. Recipients of this treatment did show enhanced heat resistance, but the microbial community composition did not always change after the treatment.   Journal Paper:
Doering T, Wall M, Putchim L, Rattanawongwan T, Schroeder R, Hentschel U, Roik A. 2021. Towards enhancing coral heat tolerance: a "microbiome transplantation" treatment using inoculations of homogenized coral tissues. Microbiome 9:102.

Other interesting stories:

• Tiny bacterium kills larger bacterium that makes troublesome foam

 

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

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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

 

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This episode: Newspapers report on scientific studies about microbiomes a fair amount, but certain kinds of studies are more likely than others to show up in the news!

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Show notes:
Microbe of the episode: Cafeteriavirus-dependent mavirus

  Takeaways Research into the human microbiome has generated a lot of interest, even among non-scientists. This is especially true since the beginning of the Human Microbiome Project in 2007. But sometimes things are lost in translation from published studies into general news.   This study is a survey of microbiome studies reported in six different news sources from three different countries, either general news or business news. General news did a better job reporting on different kinds of microbiome studies proportionally, but certain kinds of studies were reported on proportionally more or less frequently than they were published.   Journal Paper:
Prados-Bo A, Casino G. 2021. Microbiome research in general and business newspapers: How many microbiome articles are published and which study designs make the news the most? PLOS ONE 16:e0249835.

Other interesting stories:

• Gut microbes in C-section babies can be similar to non-surgical births after several years

 

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

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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

 

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This episode, in honor of World Ocean Day: Bacteria that may move between high and low pressure areas in the ocean use a particular molecule to protect their cells from being crushed!

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Show notes:
Microbe of the episode: Rickettsia rickettsii

  News item
  Takeaways Life in the ocean can have many challenges, depending on the organism and where it lives. Microbes can be found in almost every region, from the warmest to coldest, brightest to darkest, and shallowest to deepest. Sometimes microbes are carried from shallow to deep regions, where the weight of so much water causes immense pressure, which can inhibit cellular structural integrity and function. So life in the deep sea must have ways to deal with this pressure to survive. In this study, bacteria transform a fairly common chemical into a molecule that cushions and protects their cellular structures from the effects of high pressure, allowing them to survive lower down than they would otherwise.   Journal Paper:
Qin Q-L, Wang Z-B, Su H-N, Chen X-L, Miao J, Wang X-J, Li C-Y, Zhang X-Y, Li P-Y, Wang M, Fang J, Lidbury I, Zhang W, Zhang X-H, Yang G-P, Chen Y, Zhang Y-Z. 2021. Oxidation of trimethylamine to trimethylamine N -oxide facilitates high hydrostatic pressure tolerance in a generalist bacterial lineage. Sci Adv 7:eabf9941.

Other interesting stories:

• Engineering microbes to produce petroleum product precursor isoprene

 

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This episode: Spores of some bacteria latch onto the tails of other bacteria and ride along as they move around in the soil!

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Show notes:
Microbe of the episode: Bohle iridovirus

  News item
  Takeaways The soil is a complex environment, and microbes that live in soil need complex lifestyles to thrive. There are many examples of cooperation, competition, and other adaptations to highly varied situations.   In this study, bacteria that grow like filamentous fungi don't have the mechanisms to move autonomously, but their spores can hitch rides on other kinds of bacteria that swarm through the soil using their propeller-like tails called flagella to push themselves toward the plant roots they prefer to grow near.   Journal Paper:
Muok AR, Claessen D, Briegel A. 2021. Microbial hitchhiking: how Streptomyces spores are transported by motile soil bacteria. ISME J.

Other interesting stories:

• "How microbes in permafrost could trigger a massive carbon bomb"

 

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

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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

 

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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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This episode: A probiotic strain of E. coli can target and destroy pathogens that survive a treatment of antibiotics!

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Show notes:
Microbe of the episode: Streptomyces griseoruber

  Takeaways Antibiotic resistance is becoming more and more of a problem as bacterial pathogens develop resistance to more and more drugs. For some people who develop an infection that is resistant to everything, it's as if they were living back in the days before antibiotics were discovered, when all they could do was pray for survival. New antibiotics are needed, but even more needed are new ways of approaching treatment of infections, using innovative approaches and combinations of therapeutics.

In this study, a probiotic strain of Escherichia coli was used to target potentially pathogenic E. coli bacteria that can survive treatment with a particularly effective type of antibiotic, fluoroquinolones. This probiotic strain, called Nissle, delivers toxins directly to the survivors, preventing resistant pathogens from proliferating.

 

Journal Paper:
Hare PJ, Englander HE, Mok WWK. 2022. Probiotic Escherichia coli Nissle 1917 inhibits bacterial persisters that survive fluoroquinolone treatment. J Appl Microbiol 132:4020–4032.

 

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This episode: Despite being photosynthetic, some kinds of algae engage in predatory behavior, hunting and consuming live bacteria!

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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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This episode: Lighting in caves open to tourists supports the growth of unwanted photosynthetic bacteria!

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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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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.

Other interesting stories:

• Different fungi behave differently in growing through a tiny maze
• Bacteriophages could be used as disinfectants in some situations (paper)

 

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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

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

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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

 

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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

News item   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

 

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

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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

 

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

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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

 

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

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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

 

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

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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)

 

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This episode: Incorporating light-absorbing molecules into bacterial membranes can allow bacteria to use solar energy to transform nitrogen gas into fertilizer!

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Show notes:
Microbe of the episode: Wheat dwarf virus

  Takeaways Turning nitrogen gas into biologically useful compounds, such as protein or ammonia for fertilizer, is an essential part of the global nitrogen cycle and therefore, for agriculture. Today much fertilizer is produced from nitrogen gas by a chemical process that requires large amounts of energy, contributing to global warming. But certain bacteria can perform the same process using special enzymes much more efficiently.

In this study, a light-absorbing molecule was inserted into the cell membrane of some of these bacteria, allowing them to use light energy directly to power the nitrogen converting enzymes. These "biohybrids" were able to produce convert significantly more nitrogen gas and produce additional bacterial biomass from it, showing promise for using such an approach for more sustainable microbial fertilizer production.  

Journal Paper:
Chen Z, Quek G, Zhu J, Chan SJW, Cox‐Vázquez SJ, Lopez‐Garcia F, Bazan GC. 2023. A Broad Light‐Harvesting Conjugated Oligoelectrolyte Enables Photocatalytic Nitrogen Fixation in a Bacterial Biohybrid. Angew Chem Int Ed 62:e202307101.

 

Other interesting stories:

• Update on using mosquito bacteria to block mosquito-borne viruses

 

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

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Show notes:
Microbe of the episode: Hepacivirus J

  News item
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

 

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This episode: Bacteria pay for the privilege of cruising around soil on fungus filaments!

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Show notes:
Microbe of the episode: Clostridium acetobutylicum

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Takeaways In the complex environment of soil, many different kinds of organisms coexist. Some compete with each other, while others cooperate in fascinating interactions. One example is how bacteria can swim through a film of water surrounding the filaments of fungi, allowing them to traverse more quickly and reach new locations.   In this study, an interaction between fungus and bacterium is discovered in which the bacteria benefit from the fungus in enhanced ability to travel, and the fungus benefits by absorbing vitamins that the bacteria produce.   Journal Paper:
Abeysinghe G, Kuchira M, Kudo G, Masuo S, Ninomiya A, Takahashi K, Utada AS, Hagiwara D, Nomura N, Takaya N, Obana N, Takeshita N. 2020. Fungal mycelia and bacterial thiamine establish a mutualistic growth mechanism. Life Sci Alliance 3(12):202000878.

Other interesting stories:

• Honeybee gut microbes help them define their social groupings
• Smells that cheese fungi make help cheese microbe community develop

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This episode: Bacteria protect farmed mushrooms from damage by other bacteria by breaking down their toxins!

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Show notes:
Microbe of the episode: Tomato mosaic virus

Takeaways

Almost all organisms are vulnerable to pathogenic microbes that make them sick or cause damage. Most also have other microbes that help them grow better or protect them from pathogens. This includes animals, plants, and also fungi.

In this study, bacterial pathogens produce a toxin that causes button mushrooms to turn brown and rot. However, other bacteria can degrade this toxin and protect the fungus, and can also degrade molecules the pathogens produce to help them swarm to new places, restricting their movement.

Journal Paper:
Hermenau R, Kugel S, Komor AJ, Hertweck C. 2020. Helper bacteria halt and disarm mushroom pathogens by linearizing structurally diverse cyclolipopeptides. Proc Natl Acad Sci 117:23802–23806.

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This episode: Actinomycete bacteria are often helpful to insects, but some can be deadly yet still attractive!

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Show notes:
Microbe of the episode: Streptomyces corchorusii

  News item
Takeaways
Actinomycete bacteria do a lot of interesting things. They grow like fungi, with mycelia and spores, and produce many interesting compounds, including antibiotics and other useful pharmaceuticals. They often team up with insects, producing such compounds to assist them in competing with other organisms or resisting disease.   But such amazingly helpful powers of chemistry can also be amazingly harmful. In this study, multiple strains of these bacteria were able to kill fruit fly larvae that ingested their spores. The toxin the bacteria produced was a chemical that interferes with cells' DNA-protein interactions. The bacteria also produced an odor that, in certain concentrations, lured the larvae to their doom.
Journal Paper:
Ho LK, Daniel-Ivad M, Jeedigunta SP, Li J, Iliadi KG, Boulianne GL, Hurd TR, Smibert CA, Nodwell JR. 2020. Chemical entrapment and killing of insects by bacteria. Nat Commun 11:4608.

Other interesting stories:

• Eukaryotes borrowed viperin genes for proteins that prokaryotes use to fight viruses (paper)
• Bacteria can break down plastic even faster with newly discovered enzyme

Also news, Feedspot ranked BacterioFiles in the top 5 virology podcasts! Check out the list for other good shows about viruses.

 

Email questions or comments to bacteriofiles at gmail dot 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.