Bacteriofiles

This episode: Cable bacteria around rice roots transport electrons and help prevent formation of methane!   Thanks to Vincent Scholz for his contribution! Download Episode (5.7 MB, 8.3 minutes) Show notes: Microbe of the episode: Vibrio alginolyticus   News item Takeaways Transforming other things into methane is a great way to make a living for some kinds of microbes. These tend to live under still water, like in rice fields or wetlands, or in the guts of cattle. And while this methane could be useful as natural gas if collected, it's a much more potent greenhouse gas than carbon dioxide when released into the atmosphere.   In this study, cable bacteria were inoculated into rice pots in the lab. Cable bacteria transfer electrons from deeper down in the ground up to the surface to generate energy, and in the process generate sulfate. This sulfate allows other microbes to outcompete the methane producers, reducing the amount of methane produced from rice cultivation in the lab. This may be helpful to reduce

This episode: Bacteria that can store sugar as glycogen have multiple advantages when food is only available sporadically! Download Episode (7.2 MB, 10.4 minutes) Show notes: Microbe of the episode: Carnivore bocaparvovirus 3 Takeaways Almost all habitats experience some sort of change and fluctuation; very few are totally stable, depending on the timeframe. So strategies to change and adapt with changing conditions can greatly help an organism thrive. For example, methods of storing energy are helpful when food is only available sporadically.   Some bacteria, like humans, can store sugar in a polymer called glycogen, which can be quickly produced when food is abundant and quickly broken down to ease a transition to fasting. In this study, bacteria that could produce and use glycogen were able to stay active longer and grow better in the face of intermittent starvation. They were even better able to acquire new food when more became available. Journal Paper: Sekar K, Linker SM, Nguyen J, Grünhagen A, St

This episode: Bacteria in soil produce smells to attract arthropods that eat them but also spread their spores! Download Episode (6.2 MB, 9.0 minutes) Show notes: Microbe of the episode: Blotched snakehead virus   News item Takeaways Soil, especially after a rain, often has a characteristic "earthy" smell. This soil smell is actually the result of certain bacteria producing a volatile chemical called geosmin. Many geosmin producers are in the Streptomyces genus, which produces a large variety of interesting chemicals, but geosmin is one of the few that is nearly universal in the genus.   This study found that insect-like arthropods called springtails are attracted to geosmin. These animals usually feed on fungi, but they will also eat bacteria when available. Despite this result, the bacteria continue to produce the chemical, which is linked to their sporulation cycle. The study found that springtails carry intact bacterial spores to new places stuck to the insides and outsides of the animal, and this enha

This episode: The skin microbes that people leave behind may be used to identify them, even after other people have touched the same surface! Download Episode (5.4 MB, 7.9 minutes) Show notes: Microbe of the episode: Actinobacillus lignieresii Takeaways The microbial communities in and on our bodies are highly complex and highly varied between people; this complexity has raised the question of whether the microbes that people transfer onto things they touch could be used in forensics, to track their movement and activity, like fingerprints or DNA evidence. One difficulty with this approach is that microbe communities are constantly changing as conditions change or other microbes are introduced.   This study simulated such microbial tracking in a couple of scenarios, such as touching door handles in an office building and touching various surfaces in a home in a mock burglary. Tracking a person on door handles worked fairly well for up to an hour after the contact, even if other people had also touched the

This episode: Bacterial cells with their genomes removed can still be active and useful! Download Episode (10.2 MB, 14.9 minutes) Show notes: Microbe of the episode: Rosavirus A Takeaways Microbes have amazing biochemical transformation abilities, creating and breaking down many compounds and proteins. This makes them great candidates for many purposes, in medicine, industry, and environmental remediation. In some of these purposes, though, there are risks associated with adding foreign microbes, especially engineered ones, that can replicate themselves and possibly persist, into new places.   To avoid this risk, this study turns intact bacteria into SimCells, simplified entities with most of their genetic material removed, leaving only the proteins and other components and just enough DNA to accomplish desired tasks. These SimCells were able to continue performing tasks for around 10 days before running out of the cellular resources needed to keep going. One of these tasks was producing a compound that da

This episode: A fungus paralyzes its tiny worm prey by acting on the worm's own sensory hairs! Download Episode (6.0 MB, 8.7 minutes) Show notes: Microbe of the episode: Bat associated cyclovirus 9 Takeaways Not all predators are fast or agile; some are sneaky, or good trap builders, or just good chemists. The predator club includes animals but also plants and even fungi. For example, the oyster mushroom fungus can paralyze roundworms in the soil that touch its filaments, then degrade their bodies and consume their nutrients.   The mechanism of this paralysis has been a mystery, but it's one step closer to being solved. This study found that intact sensory cilia, little hairs on the worm's head that help it sense its surroundings, are required for the paralysis to work. Worms with mutations in the structure of their cilia were protected from paralysis. How exactly the fungus acts on these cilia and the neurons they connect to, though, is still unknown. Journal Paper: Lee C-H, Chang H-W, Yang C-T, Wali N,

This episode: This episode: A bacteriophage and bacterial predator can wipe out a population of bacteria that could develop resistance to each individually! Thanks to Laura Hobley, J. Kimberley Summers, and Jan-Ulrich Kreft for their contributions!   Also a note: I will be taking a short break from podcasts while I rebuild my collection of awesome microbiology stories to talk about. Download Episode (6.8 MB, 9.9 minutes) Show notes: Microbe of the episode: Blackbird associated gemycircularvirus 1 Takeaways Bacteriophages and bacterial predators that prey on other bacteria are both very good at killing large numbers of bacteria. But bacteria as a whole are also very good at surviving being killed in large numbers; there are almost always a few that have the right genes to overcome whatever is doing the killing. This is what makes the threat of antibiotic resistance so scary, and why phage therapy is both very promising and very limited.   In this study, however, a combination of phages and the bacterial pre

This episode: Certain bacteria can greatly affect the makeup of a microbial community, even if they quickly disappear!   Thanks to Dr. Daniel Amor for his contribution! Download Episode (6.3 MB, 9.2 minutes) Show notes: Microbe of the episode: Gadgets Gully virus News item Takeaways Microbial communities show more than just competition between species. Stable assemblies of many species can exist for long periods in places like the human gut, despite constant minor shifts in conditions. More major shifts, or invaders like pathogens coming in and taking over, can cause big disruptions in the community and lead to long-term gut dysbiosis, which can be, interestingly, also a stable community.    This study shows that invaders into a community, even if they don't persist for very long, can cause a shift from one stable state to another, by favoring the dominance of a species or group that was not dominant before, for example by changing the pH of the environment. So competition is always present. This could be

This episode: Helping insect-killing bacterial symbionts of nematodes evolve resistance to chemicals that major corn pests use to defend themselves! Download Episode (10.0 MB, 14.0 minutes) Show notes: Microbe of the episode: Listeria virus PSA Takeaways Interactions between species and even kingdoms in nature can be complex and multilayered. This means that when we want to intervene to cause a particular outcome, there may be multiple points at which we can act, but the consequences may be hard to predict.   In this study, action was taken to counteract the damage the Western corn rootworm causes to corn crops, using a tiny roundworm that attacks the insect pest with deadly bacteria. The rootworm defends itself by accumulating plant-produced toxins that inhibit the bacteria. Directed evolution was used to make the bacteria more resistant, and this led to more effective killing of the pest. Journal Paper: Machado RAR, Thönen L, Arce CCM, Theepan V, Prada F, Wüthrich D, Robert CAM, Vogiatzaki E, Shi Y-M,

This episode: Producing both biodiesel and bioethanol fuels from cold-loving Arctic algae! Download Episode (8.7 MB, 12.6 minutes) Show notes: Microbe of the episode: Royal Farm virus Takeaways Renewable fuels such as biofuels can allow existing infrastructure and vehicles to continue to operate in a more sustainable manner, which could reduce the cost and impact of switching to new/different systems of transportation like electricity. Economically competitive methods of producing biofuels are still being explored and developed.   In this study, Arctic algae are grown in cold temperatures using only light, carbon dioxide, and a few minerals, and then broken down to produce biodiesel and bioethanol, which can be used as fuel in many different internal combustion engines. The amounts produced are comparable to other algae-based systems being researched, and use of the cold-loving organisms could reduce the cost of production in colder latitudes and seasons. Journal Paper: Kim EJ, Kim S, Choi H-G, Han SJ. 202

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 surfa

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 consum

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-co

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

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

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 P

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

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 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 201

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.