BacterioFiles

This episode: Using phages to target gold nanoparticles to infecting bacteria, then using light to heat the nanoparticles just enough to kill the bacteria! Thanks to Raymond Borg and Huan Peng for contributing!

Download Episode (10.6 MB, 15.4 minutes) Show notes: Microbe of the episode: Pantoea agglomerans News item Takeaways Viruses that infect bacteria, bacteriophages, are often very good at overcoming bacterial defenses and killing them. This raises the possibility, and many times actuality, of using phages to treat bacterial infections that are no longer treatable with antibiotics. But bacteria can evolve resistances to viruses as well as drugs, and using multiplying, evolving entities as treatments in people raises questions about the safety and consistency of the treatment. This study circumvents these questions by using phages for delivery and targeting of bacteria rather than the therapeutic agent itself. The actual treatment is done with tiny rods of gold, gold nanorods, bound to the phage surface. When a certain wavelength of light hits these nanorods, they vibrate enough to generate enough heat in their immediate surroundings to render nearby bacteria nonviable. Thus the infection is treated in a very localized, targeted way that doesn't leave any active bacteria or phages behind. The authors have plans to study this approach as a topical treatment of wounds. Journal Paper: Peng H, Borg RE, Dow LP, Pruitt BL, Chen IA. 2020. Controlled phage therapy by photothermal ablation of specific bacterial species using gold nanorods targeted by chimeric phages. Proc Natl Acad Sci 117:1951–1961.

Other interesting stories:

• Two bacteria growing together on agar make pretty patterns
• Marine bacteria kill and digest other bacteria (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: Simplified gut communities growing in bioreactors grow and metabolize reproducibly, with only moderate variations, even when individual members of the community are absent!

Download Episode (8.2 MB, 11.9 minutes) Show notes: Microbe of the episode: Citrobacter virus Merlin Takeaways The community of microbes in our guts is highly complex, with thousands of species all interacting with each other, with our own cells, and with the contents of our diet. Each region of the gut has a different collection of microbes as well. Many questions remain to be answered about the functions and fluctuations of these communities. How can we study such a complex system? Which species, if any, are most important for its continued function? In this study, a simplified community of only 14 species is grown repeatedly in bioreactors, and one species at a time is left out of the community to see what will change in its absence. This reveals effects different species have on the overall growth, carbon source consumption, and production of various metabolites relevant to gut health. Some microbes have large effects, but none of them appears to be crucial for the overall function and stability of the community. Journal Paper: Gutiérrez N, Garrido D. 2019. Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes. mSystems 4:e00185-19.

Other interesting stories:

• Some archaea can survive for a while trapped inside salt crystals (paper)
• Bacteria degrade BPA in soil (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.

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

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 newly discovered species of bacteria consumes other bacteria as prey by engulfing them!

Download Episode (8.7 MB, 12.6 minutes) Show notes: Microbe of the episode: SARS-CoV-2! This is the coronavirus responsible for COVID-19, the current pandemic. For more up-to-date information, please refer to the American Society for Microbiology, This Week in Virology, and other reputable sources. Stay healthy! Takeaways There are bacteria living almost every different lifestyle you can think of, including predatory, preying on other bacteria. Since bacterial cells are usually quite rigid, bacterial predators usually consume others either by burrowing inside them or digesting them from outside, rather than engulfing prey like eukaryotes often do. The study here discovers a new kind of bacteria, in the group called Planctomycetes, known for having unusually flexible cells and internal compartments like eukaryotes. This new species does engulf its prey, including bacteria and even tiny algae, and digests them inside itself. It possesses multiple adaptations that suit it for this lifestyle. Journal Paper: Shiratori T, Suzuki S, Kakizawa Y, Ishida K. 2019. Phagocytosis-like cell engulfment by a planctomycete bacterium. Nat Commun 10:1–11.

Other interesting stories:

• Engineering a common industrial yeast strain to fix carbon dioxide (paper)
• Lake microbes convert microplastics into essential fatty acids

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 phage defends its genome against bacterial host defenses by building a wall to keep them out!

Download Episode (7.0 MB, 10.2 minutes) Show notes: Microbe of the episode: Myroides odoratus and M. odoratimimus News item Takeaways Parasites and their hosts are constantly in arms races with each other, each thriving best when it acquires new and more effective methods of attack, defenses, defenses against defenses, and so on. Bacterial defenses against viruses that infect them mostly involve cutting up viral genomes, either by the indiscriminate specific-cutting restriction enzymes, or by adaptive, sequence-sensing CRISPR/Cas systems. Bacteriophages have proteins that can defend against the CRISPR/Cas system, but they mostly require the sacrifice of multiple failed infections before the proteins build up enough to defeat the defense. In this study, a phage is discovered that can immediately defend against all DNA-cutting systems, by constructing a nucleus-like protective compartment inside the host. Journal Paper: Mendoza SD, Nieweglowska ES, Govindarajan S, Leon LM, Berry JD, Tiwari A, Chaikeeratisak V, Pogliano J, Agard DA, Bondy-Denomy J. 2020. A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases. Nature 577:244–248.

Other interesting stories:

• Helpful vaginal microbes inhibit HIV infection (paper)
• Engineering bacteria to fix nitrogen that grain plants can use (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: Earth's iron deposits could have been created by anaerobic light-harvesting microbes instead of those that make oxygen!

Download Episode (9.3 MB, 13.5 minutes) Show notes: Microbe of the episode: Streptomyces avidinii News item Takeaways In the ancient earth, the sun was dimmer, the world was colder, and oxygen was rare because photosynthesis had not yet evolved. Without oxygen to oxidize it, iron remained in its soluble, more accessible form, and many organisms took advantage of it for anaerobic metabolism. But was it photosynthesis and the oxygen it created that transformed most of the planet's iron into its insoluble form, creating large iron deposits in the ground? This study explores the possibility that it was another form of light-harvesting metabolism, called photoferrotrophy, that uses light and the transformation of iron to generate energy. This hypothesis is found to be consistent with the evidence we have about what the early earth was like. Journal Paper: Thompson KJ, Kenward PA, Bauer KW, Warchola T, Gauger T, Martinez R, Simister RL, Michiels CC, Llirós M, Reinhard CT, Kappler A, Konhauser KO, Crowe SA. 2019. Photoferrotrophy, deposition of banded iron formations, and methane production in Archean oceans. Sci Adv 5:eaav2869.

Other interesting stories:

• Gut microbes help whales digest tricky fats in their diet
• Bacteria deliver antibiotic to competitors using capsules made of its own membrane (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: A global estimate of plants and their root fungi shows how agriculture may have greatly affected soil carbon storage over time!

Download Episode (5.7 MB, 8.3 minutes) Show notes: Microbe of the episode: Rhizobium virus RHEph4 News item Takeaways Even small organisms can have a big effect on the climate of the planet if there are enough of them. This includes trees, which are small relative to the planet, and also includes the fungi that attach to the roots of trees and other plants. These mycorrhizal fungi thread subtly through the soil, some occasionally popping up mushrooms, and transfer valuable nutrients they gather to the trees in exchange for carbon fixed from the air. Knowing how big an effect a given kind of organism has requires knowing how much of it is around. This study collates data from various surveys of global plant populations and the fungi that interact with their roots, to estimate a global picture of the fungi below our feet. It estimates that a kind of fungus that stores more carbon in the soil may have been replaced in many areas with fungi that store less, or no fungi at all, due to the transformation of land from wild areas to farmland. Journal Paper: Soudzilovskaia NA, van Bodegom PM, Terrer C, Zelfde M van't, McCallum I, Luke McCormack M, Fisher JB, Brundrett MC, de Sá NC, Tedersoo L. 2019. Global mycorrhizal plant distribution linked to terrestrial carbon stocks. Nat Commun 10:1–10.

Other interesting stories:

• Phages bind to fish mucosal surfaces and protect from infection
• Examining how archaea affect meteorites

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: 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

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: Some fungi only form fruiting bodies after forest fires; where do they hide the rest of the time? At least for some of them, the answer is: inside mosses! Thanks to Daniel Raudabaugh for his contribution!

Download Episode (6.2 MB, 9.0 minutes) Show notes: Microbe of the episode: Nocardia brevicatena News item Takeaways Forest fires can do a lot of damage, but life grows back quickly. Certain kinds of plant seed actually only germinate after a fire, and a similar thing is true of certain kinds of fungi: they only form fruiting bodies (like mushrooms, for spreading spores) after a fire. For plants, the advantage may come from increased access to light with some or all of the canopy burned away, and fungi may benefit from less competition on the ground. But in between burn events, these fire-loving (pyrophilous) fungi seem to disappear. Where do they go? The study here sought an answer, suspecting an association with some mosses that reappeared soon after a forest fire in North Carolina in 2016. They looked for fungi lurking as endophytes inside moss and other samples, both by growing them on agar and by DNA sequencing, and they found a number of different known pyrophilous fungi. Some of these were in soil, or samples from outside the burned area, but the majority were inside mosses growing in the recently burned zone. Journal Paper: Raudabaugh DB, Matheny PB, Hughes KW, Iturriaga T, Sargent M, Miller AN. 2020. Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi. Fungal Ecol 43:100870.

Other interesting stories:

• Probiotic yeast species could inhibit pathogenic yeasts (paper)
• Plant passes on nitrogen fixing symbionts to offspring

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: Looking at the effects of almost doubling CO2 concentrations on the interaction between wheat varieties and beneficial fungi!

Download Episode (8.1 MB, 11.8 minutes) Show notes: Microbe of the episode: Lato River virus News item Takeaways As the world's population grows, feeding everyone will grow more challenging. Advances in technology in the past have made today's population possible, but future advances may be needed, especially in the face of an increasing concentration of carbon dioxide in the atmosphere. Soil microbes that partner with crop plants for the benefit of each may be part of the solution. One option to explore is a group called mycorrhizal fungi, which associate with plant roots to extend their nutrient-gathering ability, in exchange for carbon compounds produced by photosynthesis. This study examined the influence of increased carbon dioxide in the atmosphere on the interaction of several varieties of wheat with these fungi. Journal Paper: Thirkell TJ, Pastok D, Field KJ. Carbon for nutrient exchange between arbuscular mycorrhizal fungi and wheat varies according to cultivar and changes in atmospheric carbon dioxide concentration. Glob Change Biol.

Other interesting stories:

• Microbes could make paper whitening more environmentally friendly (paper)
• Compound from rotifers could prevent transmission of eukaryotic parasite

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.