487: Probiotic Pulverizes Pathogen Persisters

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. 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.

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.   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.

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. 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.

This episode: Slime mold amoebas Fonticula alba have interesting and unique foraging and reproductive behaviors! Download Episode (7.3 MB, 10.6 minutes) Show notes: Microbe of the episode: Cajanus cajan Panzee virus News item   Takeaways How did life develop from single-celled organisms acting independently into the complex, multicellular organisms we see and are today? Although it is difficult to look back through time to study how ancient organisms may have developed along this path, it is possible to investigate modern organisms that occupy a zone in between single-celled and multicellular, to see if we can get some hints to our own development, and also learn about some interesting microbes along the way! This study into the social amoeba, or slime mold, Fonticula alba, finds that the individual amoebal cells in a population join together into collectives and break apart into individuals at different stages of their complex life cycle, depending on the status of the bacteria around them that they forage as prey. The investigators tease out the various pathways taken by these amoebas.   Journal Paper: Toret C, Picco A, Boiero-Sanders M, Michelot A, Kaksonen M. 2022. The cellular slime mold Fonticula alba forms a dynamic, multicellular collective while feeding on bacteria. Curr Biol 32:1961-1973.e4. 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.

This episode: A probiotic strain of E. coli can target and destroy pathogens that survive a treatment of antibiotics! Download Episode (8.2 MB, 12 minutes) 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.   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.

This episode: Incorporating light-absorbing molecules into bacterial membranes can allow bacteria to use solar energy to transform nitrogen gas into fertilizer! Download Episode (6.5 MB, 9.9 minutes) 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   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.

This episode: A marine protist predator traps prey microbes in an attractive bubble of mucus, eats what it wants, and lets the rest sink, possibly sequestering significant amounts of carbon! Download Episode (7.8 MB, 11.4 minutes) Show notes: Microbe of the episode: Bat associated cyclovirus 1 News item Takeaways The oceans have a lot of unique, unexplored life in them. This is true on a macro level but even more on a microscopic level, with many different kinds of microbes of various groups with fascinating life strategies. And despite being microscopic, with enough of them around, they can affect the whole planet's climate in significant ways. In this study, one protist species gets most of its nutrients from photosynthesis, but what it can't get from the sun, it takes from prey microbes by force. To catch its prey, it creates an intricate bubble of mucus called a mucosphere, and waits for other microbes to swim into it, thinking it is food, and get stuck. Then the predator chooses the prey cell it wants and abandons the rest, letting them sink to the ocean floor and locking away the carbon they contain in the process.   Journal Paper: Larsson ME, Bramucci AR, Collins S, Hallegraeff G, Kahlke T, Raina J-B, Seymour JR, Doblin MA. 2022. Mucospheres produced by a mixotrophic protist impact ocean carbon cycling. Nat Commun 13:1301. 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.

This episode: Certain phages in the gut are linked with increases in performance on some cognitive tests! Download Episode (7.5 MB, 10.9 minutes) Show notes: Microbe of the episode: Streptomyces bikiniensis News item Takeaways Our gut microbiota includes a large number of viruses, mostly bacteriophages. These fall into two groups, the lytic kind that infects and reproduces itself immediately in a host, and the lysogenic kind that can integrate its genome into the host bacterial genome and remain dormant for long periods. In this study, a higher proportion of lysogenic phages was correlated with increased performance on cognitive tests in multiple species. In humans, men showed a small increase in some tests and women in others. In mice and fruit flies, transplant or ingestion of phages was linked to increased memory performance.   Journal Paper: Mayneris-Perxachs J, Castells-Nobau A, Arnoriaga-Rodríguez M, Garre-Olmo J, Puig J, Ramos R, Martínez-Hernández F, Burokas A, Coll C, Moreno-Navarrete JM, Zapata-Tona C, Pedraza S, Pérez-Brocal V, Ramió-Torrentà L, Ricart W, Moya A, Martínez-García M, Maldonado R, Fernández-Real J-M. 2022. Caudovirales bacteriophages are associated with improved executive function and memory in flies, mice, and humans. Cell Host Microbe 30:340-356.e8. 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.

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)   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.

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. 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.