Monday, March 16, 2020

BacterioFiles 418 - Special Sea Species Swallows Cells

New microbe engulfing prey
By Shiratori et al. 2019
Nat Commun 10(1):1-11, CC BY 4.0
This episode: A newly discovered species of bacteria consumes other bacteria as prey by engulfing them!

Also a note to listeners: Because things are hectic at work right now (unless that changes due to current events), I'm planning to put the show on hold for a few weeks. So if you don't see new episodes, that's why.


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:

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Monday, March 9, 2020

BacterioFiles 417 - Bacteriophage Blocks Bacterial Bouncers

Pseudomonas aeruginosa
By Y_tambe, CC BY-SA 3.0
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:

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Monday, March 2, 2020

BacterioFiles 416 - Oxygen Or Other Oxidizes Iron?

Chlorobium phaeoferrooxidans
By Thompson et al, 2019.
Sci Adv 5:eaav2869.
CC BY-NC 4.0
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:

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Monday, February 24, 2020

BacterioFiles 415 - Global Glomus Growth Guesses

How mycorrhizal fungi work
By Nefronus, CC BY-SA 4.0
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:

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Monday, February 17, 2020

BacterioFiles 414 - Producing Proton Power Perpetually

Microalgae Chlamydomonas reinhardtii
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:

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Monday, February 10, 2020

BacterioFiles 413 - Finding Fire Fungi Footholds

Pyrophilous fungus
Pholiota highlandensis
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:

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Monday, February 3, 2020

BacterioFiles 412 - Carbon Concentration Complicates Crop Cooperation

Wheat plants
By Bluemoose, CC BY-SA 3.0
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:

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Monday, January 27, 2020

BacterioFiles 411 - Parasite Produces Partial Plant-like Predator

A choanoflagellate
By Daniel Stoupin
CC BY-SA 3.0
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 partial phototroph.

Journal Paper:
Needham DM, Yoshizawa S, Hosaka T, Poirier C, Choi CJ, Hehenberger E, Irwin NAT, Wilken S, Yung C-M, Bachy C, Kurihara R, Nakajima Y, Kojima K, Kimura-Someya T, Leonard G, Malmstrom RR, Mende DR, Olson DK, Sudo Y, Sudek S, Richards TA, DeLong EF, Keeling PJ, Santoro AE, Shirouzu M, Iwasaki W, Worden AZ. 2019. A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proc Natl Acad Sci 116:20574–20583.

Other interesting stories:

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Monday, January 20, 2020

BacterioFiles 410 - Microbes Modify Muscle Measurement

A laboratory mouse
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-functioning people.

Journal Paper:
Fielding RA, Reeves AR, Jasuja R, Liu C, Barrett BB, Lustgarten MS. 2019. Muscle strength is increased in mice that are colonized with microbiota from high-functioning older adults. Exp Gerontol 127:110722.

Other interesting stories:

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Sunday, January 19, 2020

Interview of me on the podcast Curioscity

Another good podcast you should check out is Curioscity, in which the host, Calvin Yeager, interviews other scientists about various aspects of science, their research, and other aspects of how science gets done!

He recently interviewed me about my experience getting a job as a scientist outside academia, and what that's like, so if you'd like to hear about that, here's the link:

Curioscity 53 - What Is Industry?

Monday, January 13, 2020

BacterioFiles 409 - Marine Methane Mostly Munched

Methanococcus species
By Anne Fjellbirkeland,
from PLoS Biol 2004:e358
CC BY 2.5
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:

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Monday, January 6, 2020

BacterioFiles 408 - Currents Carry Cloud Creators

Snowflake
By Alexey Kljatov, CC BY-SA 4.0
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, Ceniceros J, Aydell T, Colombi N, Bolger E, DeMott PJ. 2019. Ice Nucleating Particles Carried From Below a Phytoplankton Bloom to the Arctic Atmosphere. Geophys Res Lett 46:8572–8581.

Other interesting stories:

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