Bacteriofiles

This episode: Giant virus in newly discovered microscopic marine predator encodes several light-harvesting proteins! Download Episode (7.8 MB, 11.4 minutes) Show notes: Microbe of the episode: Dolphin mastadenovirus A News item Takeaways Giant viruses are distinct in many ways from other viruses, even aside from their size. One way is the large number and variety of genes they carry in their genome. Though many of their genes are unknown in origin and function, many others appear to take the place of essential reproductive functions, such as translation and protein synthesis. This allows them to assume more control of their host's metabolism and control its resources more optimally. In this study, the sequence of a giant virus was discovered seemingly infecting a newly discovered microscopic marine predator. The eukaryotic cell feeds on smaller microbes such as bacteria, but strangely, the virus carries genes for several light-harvesting proteins, possibly converting a heterotrophic predator into a partia

This episode: Mice that got a microbe transplant from humans with higher physical function performed better in certain ways than mice receiving microbes from humans with lower physical function! Download Episode (6.7 MB, 9.8 minutes) Show notes: Microbe of the episode: Stenotrophomonas maltophila News item Takeaways Our bodies and our microbe communities are closely interconnected, with effects going both ways. Studies had previously shown that making changes to the microbe communities of mice could even affect the physical function and body composition of the mice. This study aimed at addressing the same question in humans. There were certain consistent differences in microbial communities between elderly people with high ability to function physically, compared with low functioning people. These differences carried over in transplants of microbes from people to mice, and mice receiving microbes from high-functioning humans did better in tests of grip strength than mice receiving microbes from low-functi

This episode: Microbes in low-oxygen zones in the ocean consume significant amounts of methane anaerobically! Download Episode (5.2 MB, 7.6 minutes) Show notes: Microbe of the episode: Mojiang henipavirus News item Takeaways Methane is a much more potent greenhouse gas than carbon dioxide. Fortunately there's not as much of it in the atmosphere, but even smaller amounts can have significant effects on the climate. One source of methane is low-oxygen zones in the ocean, where certain kinds of archaea make methane as part of their energy metabolism. This study found that other anaerobic microbes in the same areas consume much of this methane, preventing it from reaching the atmosphere. Journal Paper: Thamdrup B, Steinsdóttir HGR, Bertagnolli AD, Padilla CC, Patin NV, Garcia‐Robledo E, Bristow LA, Stewart FJ. 2019. Anaerobic methane oxidation is an important sink for methane in the ocean’s largest oxygen minimum zone. Limnol Oceanogr 64:2569–2585. Other interesting stories: Correlated microbiome metabolit

This episode: Ocean bacteria brought up from the sea floor into the air can help create clouds! Download Episode (6.1 MB, 8.9 minutes) Show notes: Microbe of the episode: Streptomyces thermodiastaticus News item Takeaways The ocean is an important player affecting the climate of the planet, in many ways. Its effects on clouds influence the amount of solar radiation reflected back into space or trapped as heat, and microbes play a role in this effect. Certain microbes make particles that form the nucleus of water droplets or ice crystals that make up clouds, and other microbes can perform this nucleation themselves. In this study, an unusual combination of a phytoplankton bloom and strong winds and currents, all in the right places, led to a large number of ice-nucleating bacteria being fed and then brought up from the sea floor and launched into the air, possibly affecting weather patterns in the Arctic. Journal Paper: Creamean JM, Cross JN, Pickart R, McRaven L, Lin P, Pacini A, Hanlon R, Schmale DG, Ce

Probably the last episode of the year. See you in the next! This episode: Fungus living inside plants helps them form partnerships with nitrogen-fixing bacteria! Download Episode (5.9 MB, 8.5 minutes) Show notes: Microbe of the episode: Prevotella intermedia Takeaways Plants are very good at acquiring carbon, but they can often use some help with other nutrients. Many form partnerships with microbes such as nitrogen-fixing bacteria or mycorrhizal fungi that can help gather nutrients from the soil better than the plants' own roots. In this study, legume plants could form a partnership with nitrogen-fixing bacteria in its roots, but a fungus living inside the plant could enhance this partnership even more, increasing the amount of nitrogen acquired and influencing the community of microbes around the plant roots in ways favorable to all partners. Journal Paper: Xie X-G, Zhang F-M, Yang T, Chen Y, Li X-G, Dai C-C. 2019. Endophytic Fungus Drives Nodulation and N2 Fixation Attributable to Specific Root Exudat

This episode: DNA from related species can kill certain pathogens when they incorporate it into their genome! Download Episode (7.9 MB, 11.5 minutes) Show notes: Microbe of the episode: Ungulate tetraparvovirus 3 Paper summary (paywall) Takeaways Neisseria gonorrhoeae, the bacteria that cause gonorrhea, have the unusual ability of taking up DNA from their surroundings at any time and making use of it in their own genome. This helps them acquire useful traits that help them survive better, such as antibiotic resistance. But it turns out that the ability is also a secret weakness! This study showed that when N. gonorrhoeae takes up DNA from harmless, commensal species of Neisseria in the body, the DNA is similar enough to be incorporated into the genome but different enough that it kills the pathogen. This effect also occurs with a serious pathogen in the same genus, N. meningitidis. Journal Paper: Kim WJ, Higashi D, Goytia M, Rendón MA, Pilligua-Lucas M, Bronnimann M, McLean JA, Duncan J, Trees D, Jerse A

This episode: Coating metal surfaces with artificial biofilms could help keep the surfaces corrosion-free even in the ocean! Download Episode (6.3 MB, 9.1 minutes) Show notes: Microbe of the episode: Hymenopteran ambidensovirus 1 Takeaways The ocean can be a harsh place for metal surfaces. Between the water, the salt, and oxygen (near the surface), corrosion is a common reality. Microbes in the ocean can contribute to this too, degrading metal structures to obtain energy for their metabolism. They colonize surfaces in biofilms that can be difficult to remove, a process called biofouling. In this study, instead of trying to remove or prevent biofilms on surfaces, artificial biofilms were created by coating the surfaces and specially selected bacterial cells with polymers. This approach did not prevent colonization by other organisms in the sea, but preliminary results suggested that the community that did take up residence was not as corrosive as the communities found on uncoated steel. Journal Paper: Rija

This episode: Another climate-related story: Cyanobacteria infected by viruses continue taking up nutrients from their environment, using it to make more viruses than would otherwise be possible! Download Episode (6.3 MB, 9.2 minutes) Show notes: Microbe of the episode: Microcystis virus Ma-LMM01 News item Takeaways Though global warming is a global problem, accurate models for predicting where things are headed need to incorporate the activity of even the smallest organisms, if they're numerous enough. Photosynthesis and other activities of microbes in the oceans are a big sink for carbon, but cycles of other nutrients and also viruses can affect the carbon cycle. In this study, phages infecting photosynthetic ocean bacteria were able to continue their host's uptake of nitrogen from the environment even after mostly shutting down the host's own protein production and growth. This has implications for how viruses affect carbon cycling by cyanobacteria and how quickly populations of these bacteria may grow

This episode: First episode of a climate-related arc! Considering microorganisms is important when predicting the amount of carbon coming from soil as temperature increases! Download Episode (4.7 MB, 6.75 minutes) Show notes: Microbe of the episode: Streptomyces virus Zemlya News item Takeaways Soil as a whole has a big influence on the climate of the planet, by enabling the communities of organisms that live in it to interact and grow, taking up gases from the atmosphere and putting others back in. Even aside from plants that grow in it, the other organisms in soil can respire and break down compounds to produce CO2, adding to what's in the atmosphere already. There has long been observed a relationship between ambient temperatures and this respiration in soil, such that more heat means more activity and more gases released from the soil, but today's study found that the microbial biomass in a given piece of land can have a big effect on the temperature/respiration relationship. Journal Paper: Čapek P,

This episode: Gut microbes can stimulate immune cells in mouse brains to fight off viral infections! Download Episode (9.0 MB, 13.0 minutes) Show notes: Microbe of the episode: Streptoverticillium mobaraense News item Takeaways The central nervous system, including the brain, is a protected area of the body. Pathogens that get in can do a lot of damage, including memory loss, paralysis, and death, so there's a strict barrier in healthy people that keeps most things out of this area: the blood-brain barrier. The immune system is also kept separate, so special cells called microglia do the patrolling and protection of the brain. Nevertheless, microbes in the gut can influence the function of the immune system in the brain, even from a distance. In this study, mice lacking gut microbes did not have as effective an immune response to a virus infecting the brain, and it was found that molecules from bacterial outer membranes were sensed by microglia to activate their defensive response. Journal Paper: Brown D

This episode: In this partnership between fungus and algae, the algae eventually take up residence inside their partner! Download Episode (8.4 MB, 12.1 minutes) Show notes: Microbe of the episode: Erwinia tracheiphila News item/Summary article Takeaways Partnerships and cooperation between otherwise free-living organisms is common in the natural world. Partnering with a photosynthetic organism is a smart approach, allowing the partner to get its energy from the sun and making gathering nutrients easier for the phototroph, and possibly offering protection as well. But in most partnerships, each partner stays separated by its own cell membrane. In this study, a fungus and an alga grow well together, exchanging carbon for nitrogen, similar to how lichens operate. But after a month or so of co-culture, the algae apparently enter the cells of the fungus somehow and live inside it, happily growing and dividing, turning the fungus green. Journal Paper: Du Z-Y, Zienkiewicz K, Vande Pol N, Ostrom NE, Benning C, B

This episode: Figuring out how gut communities change with changes in diet! Download Episode (6.1 MB, 8.8 minutes) Show notes: Microbe of the episode: Hepacivirus A News item Takeaways Diet can play a big role in our health. It's not a magic pill that can cure or prevent anything, but a good diet can significantly reduce many health risks for the average person, compared with a bad diet. Diet also has a big effect on the community of microbes in our gut, and this may play a role in the health effects we see from diet, so understanding how food and microbes interact is important. This study looked at the diet quality of participants in several food categories, and correlated this with various kinds of microbes found inside them. Journal Paper: Liu Y, Ajami NJ, El-Serag HB, Hair C, Graham DY, White DL, Chen L, Wang Z, Plew S, Kramer J, Cole R, Hernaez R, Hou J, Husain N, Jarbrink-Sehgal ME, Kanwal F, Ketwaroo G, Natarajan Y, Shah R, Velez M, Mallepally N, Petrosino JF, Jiao L. 2019. Dietary quality and the

This episode: Bacteria can aide the production of the useful material graphene, using their ability to add electrons to external surfaces! Download Episode (7.7 MB, 11.3 minutes) Show notes: Microbe of the episode: Brevibacterium frigoritolerans News item Takeaways Advanced materials often take advanced techniques to create, but they offer numerous benefits: increased strength and flexibility, smaller size, more options. One such material is graphene, which is basically a sheet of carbon atoms linked together like chainmail. It is only a single atom thick but is amazingly strong, mostly transparent, and good at conducting heat and electricity. The trick is, it's hard to make in large quantities cheaply and easily. Sheets of carbons can be obtained from blocks of graphite, but these sheets are graphene oxide, which lack the desirable properties of graphene. Chemical methods can be used to remove the oxidation, but they are harsh and difficult. Luckily, bacteria are great at microscopic remodeling. In this

This episode: Bacteria found in the guts of serious athletes help mice exercise longer by transforming their metabolic waste! Download Episode (7.3 MB, 10.6 minutes) Show notes: Microbe of the episode: Aggregatibacter (Actinobacillus) actinomycetemcomitans News item Takeaways Our gut microbes affect many aspects of health, and many aspects of how we live affect our microbes. One such aspect is physical exertion, which has been associated with enrichment of various microbes in the guts of athletes. This observation led to the question: are these microbes just benefiting from the high levels of exertion, or are they able to contribute also? This study found that certain such bacteria, when given to mice, enabled the mice to run for a longer period on a treadmill. These microbes break down lactic acid, which is generated in our bodies when we push our physical limits, but the study provided evidence that the longer run times were due not to removal of this waste product, but to the propionate compound produc

This episode: Plants stimulate their root bacteria to compete better, and these bacteria help the plants resist disease! Download Episode (7.3 MB, 10.6 minutes) Show notes: Microbe of the episode: Bacillus circulans Takeaways In some ways, plants' roots are like our gut. They both absorb nutrients, and they both have complex communities of microbes living alongside the host cells. These microbes can assist their hosts in various ways, and get fed in return. In this study, one species of root bacterium is able to compete against others by producing an antimicrobial compound. The plant stimulates this production with chemical signals, and benefits from its symbionts' increased competitiveness because the bacterium helps the plant resist infection. Journal Paper: Ogran A, Yardeni EH, Keren-Paz A, Bucher T, Jain R, Gilhar O, Kolodkin-Gal I. 2019. The Plant Host Induces Antibiotic Production To Select the Most-Beneficial Colonizers. Appl Environ Microbiol 85:e00512-19. Other interesting stories: Plant virus

This episode: Bacterial enzymes could convert donated blood to be compatible with more people in need! Download Episode (8.0 MB, 11.7 minutes) Show notes: Microbe of the episode: Cucumber leaf spot virus News item Takeaways Blood transfusions using donated blood save many lives. Unfortunately, most donations can't be given to just anyone that needs blood; there must be a match in blood type between donor and recipient, or else a life-threatening reaction could occur in the recipient's body. So type A can't donate to type B, or vice versa, but type O is compatible with the other types. In this study, bacterial enzymes found in human gut microbes have the ability to cleave off the unique type A and B sugars on the surface of red blood cells. This could allow the conversion of all donated blood to type O, greatly increasing the blood bank supply, but more testing is needed to develop the process. Journal Paper: Rahfeld P, Sim L, Moon H, Constantinescu I, Morgan-Lang C, Hallam SJ, Kizhakkedathu JN, Withers S

This episode: Five different ways of thinking about our relationship with our microbes! Download Episode (20.4 MB, 29.8 minutes) Show notes: Microbe of the episode: Tuhoko rubulavirus 3 News item Takeaways The microbiome by itself is an amazingly complicated community of many different species, with different lifestyles and metabolisms, all living together in competition and cooperation. On top of that, interactions between the microbiome and our body and our lifestyle multiply the complexity even more. This article explores five different views of the microbiome and how it fits into our body (or how the body fits in with the microbiome). From the organ view to the ecosystem view, each is a different way of looking at the different functions, dynamic patterns, and integration of the microbiome in its host, and each provides guidance for how to approach treatment of disease and maintenance of health. Journal Paper: Morar N, Bohannan BJM. 2019. The Conceptual Ecology of the Human Microbiome. The Quarterly

This episode: Not as simple as it sounds—how rod-shaped bacteria maintain their shape! Thanks to Dr. Ethan Garner for his contribution! Download Episode (6.3 MB, 9.2 minutes) Show notes: Microbe of the episode: Erwinia virus M7 News item Takeaways Microbes seem like they should be a lot simpler than large multicellular organisms, but even what seems like it should be a simple system in microbes can be surprisingly complex. In this case, the system bacteria maintaining their particular cell shape. Spherical cells have it easier: just add more cell material at every point. But for rods, they must make the cell longer without making it wider. How do they accomplish this? Two groups of proteins work together to help rod-shaped species grow, but how they work wasn't specifically known. In this study, it was found that one group of proteins adds more cell material as it moves around the circumference, while the other adds structure to the cell that allows it to maintain shape. The more of these structural pro

This episode: Bacterial symbionts of amoebas help them survive bacterial infection, and prevent pathogens from spreading to others as much! Download Episode (7.5 MB, 8.1 minutes) Show notes: Microbe of the episode: Eubacterium dolichum News item Takeaways Amoebas are free-living, single-celled organisms, but they have some things in common with some cells of our immune system (macrophages). For example, certain bacterial pathogens can infect both in similar ways. So it can be useful to study the interactions of amoebas and bacteria to learn about our own immune defenses. In this study, the amoeba Acanthamoeba castellanii has another bacterial symbiont that helps it resist killing by the bacterial pathogen Legionella pneumophila. Once the amoebas recovered from the infection, they were more resistant to future challenges. Even better, the symbiont prevented the pathogen from transforming into a more spreadable form like it does when infecting amoebas alone. Journal Paper: König L, Wentrup C, Schulz F, Was

This episode: A marine protist can orient itself along magnetic fields thanks to bacterial symbionts on its surface that make magnetic nanoparticles! Download Episode (7.2 MB, 7.9 minutes) Show notes: Microbe of the episode: Chlorocebus pygerythrus polyomavirus 3 Takeaways Various kinds of bacteria can orient their movement along a magnetic field. These are called magnetotactic, and they use this ability to swim toward or away from the surface of their aquatic habitat, to adjust their oxygen exposure according to their preference. No eukaryotic microbes have yet been discovered that can sense and react to magnetic fields like these prokaryotes. In this study, however, a protist was discovered that can do it via its partnership with ectosymbionts, or bacteria attached to its surface, that sense magnetism and orient their host's movement. In return, factors of the host's metabolism may feed its symbionts. Journal Paper: Monteil CL, Vallenet D, Menguy N, Benzerara K, Barbe V, Fouteau S, Cruaud C, Floriani M,