462 - Super Ciliate Symbiont Set

Pseudoblepharisma tenue
By Muñoz-Gómez et al, 2021,
Sci Adv 7:eabg4102, CC BY 4.0

This episode: A eukaryote has symbionts living in it: green algae and also purple bacteria, a combo never seen before!

Download Episode (6.1 MB, 8.8 minutes)

Show notes:
Microbe of the episode: Staphylococcus virus phiETA

News item

Takeaways

Having bacteria as endosymbionts is fairly common in life on Earth: almost all eukaryotes have them in the form of mitochondria and sometimes chloroplasts. These former bacteria somehow got inside the ancestral eukaryote, either as parasites or as prey, and ended up as integral parts of their host's metabolic functions. Some organisms, especially insects, obtained bacterial endosymbionts more recently, that help them balance their metabolic needs when living on limited diets.

Algae have been known to be endosymbionts also, performing photosynthesis for their host. But in this study, a ciliate with both algae and purple photosynthetic bacteria as endosymbionts was discovered. Purple bacteria as symbionts is rare, and this combination has not been observed before. Interestingly, though algae produce oxygen through their photosynthesis, the ciliate prefers living in low-oxygen sediment at the bottom of a pond. The symbionts and their host seem to adjust their metabolisms as needed depending on the needs at the time; they may each perform photosynthesis, fermentation, or respiration if light, organic carbon, or oxygen are available.

Journal Paper:
Muñoz-Gómez SA, Kreutz M, Hess S. 2021. A microbial eukaryote with a unique combination of purple bacteria and green algae as endosymbionts. Sci Adv 7:eabg4102.

Other interesting stories:

• Oxygen-producing microbes could help treat acute strokes

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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452 - Prokaryotic Partner Powers Protist

Anaerobic ciliate
By Graf et al. 2021
Nature, CC BY 4.0

This episode: Single-celled eukaryotes can thrive without oxygen with the help of bacterial endosymbionts that respire nitrate the way our mitochondria respire oxygen!

Thanks to Jon Graf for his contribution!

Download Episode (12.4 MB, 18.1 minutes)

Show notes:
Microbe of the episode: Brenneria salicis

News item 1 / News item 2

Takeaways

The combination of a bacterium and other microbe into the first eukaryote was a big advance in evolutionary history; it made possible the huge variety of different body shapes and sizes we see today. This is thanks to the bacterial endosymbiont, the mitochondrion, taking on specialized metabolic tasks for the cell.

We already knew about endosymbionts that help with oxygen respiration, with photosynthesis (chloroplasts), and with amino acid synthesis (certain endosymbionts in insects). But bacteria have other metabolic abilities that are very useful in certain conditions; do these bacteria ever team up with other organisms? The answer is yes! In this study, ciliates were discovered at the bottom of a lake in oxygen-free waters. These protists have an bacterial endosymbiont that helps them respire, not oxygen, but nitrate instead, generating more energy than most anaerobic ciliates.

Journal Paper:
Graf JS, Schorn S, Kitzinger K, Ahmerkamp S, Woehle C, Huettel B, Schubert CJ, Kuypers MMM, Milucka J. 2021. Anaerobic endosymbiont generates energy for ciliate host by denitrification. Nature.

Other interesting stories:

• Bacterial cellulose film is very good at separating oil and water

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436 - Copper Concentrates Culture Current

Geobacter sulferreducens
By Mantapia11147,
CC BY-SA 4.0

This episode: Copper electrodes, rather than killing bacteria in microbial fuel cells, allow them to generate higher densities of electric current!

Download Episode (5.0 MB, 7.2 minutes)

Show notes:
Microbe of the episode: Xipapillomavirus 2

News item

Takeaways

Copper is widely used as a way to make surfaces and materials antimicrobial, to cut down on the spread of pathogens in hospitals and other environments. Among other mechanisms, it reacts with oxygen to form reactive oxygen species that are very harsh on microbial proteins. But copper is also a good electrical conductor, which would be useful to use in microbial fuel cells, which exploit bacterial metabolism to generate electricity. Microbes form biofilms on an electrode and transfer electrons to it as a way for them to generate energy. Most such fuel cells have used graphite electrodes to avoid toxicity.

In this study, fuel cell bacteria grew well on a copper electrode in an oxygen-free environment. The copper actually allowed them to increase the amount of current they produced per unit of area, as ionic copper diffused through the biofilm and allowed electrons to flow through the biofilm to the electrode from layers farther from the electrode that otherwise would not have access. Even graphite electrodes could be improved by adding these copper ions to the biofilm directly.

Journal Paper:
Beuth L, Pfeiffer CP, Schröder U. 2020. Copper-bottomed: electrochemically active bacteria exploit conductive sulphide networks for enhanced electrogeneity. Energy Environ Sci 13:3102–3109.

Other interesting stories:

• Lizard gut microbes are affected by temperature, and may affect lizard heat tolerance (paper)
• Phages in ice show evidence of trading genes easily to adapt to new environments

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431 - Conductive Cables Control Carbon

Cable bacteria around
plant roots
From Scholz et al. 2020
Nat Commun 11:1878

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 greenhouse gas emissions from rice agriculture.

Journal Paper:
Scholz VV, Meckenstock RU, Nielsen LP, Risgaard-Petersen N. 2020. Cable bacteria reduce methane emissions from rice-vegetated soils. 1. Nat Commun 11:1878.

Other interesting stories:

• Viruses in fecal transplants, not just bacteria, may be useful for health
• Superworms and their symbiont bacteria can degrade styrofoam

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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:

• Gut microbes help whales digest tricky fats in their diet
• Bacteria deliver antibiotic to competitors using capsules made of its own membrane (paper)

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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:

• Correlated microbiome metabolites with compounds in blood of twins (paper)
• Bacteria inhibit soil fungi via airborne chemicals (paper)

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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BacterioFiles 403 - Mercury Modifies Microbe Metabolism

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, Starke R, Hofmockel KS, Bond-Lamberty B, Hess N. 2019. Apparent temperature sensitivity of soil respiration can result from temperature driven changes in microbial biomass. Soil Biol Biochem 135:286–293.

Other interesting stories:

• Phosphate-solubilizing bacteria could help replace fertilizer for plants (paper)
• Ciliate protists have bacterial microbiomes too

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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BacterioFiles 399 - Conductor Creating Carbon Canvases

Scanning probe microscope
image of graphene
By U.S. Army Material Command
CC BY 2.0

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 study, electron-transferring bacteria are able to reduce the graphene oxide to graphene with properties almost as good as are achieved by chemical reduction.

Journal Paper:
Lehner BAE, Janssen VAEC, Spiesz EM, Benz D, Brouns SJJ, Meyer AS, van der Zant HSJ. 2019. Creation of Conductive Graphene Materials by Bacterial Reduction Using Shewanella oneidensis. ChemistryOpen 8:888–895.

Other interesting stories:

• Frog skin gut bacteria correlate with resistance to deadly virus
• Skin microbiota could be transplanted to treat skin conditions (paper)

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BacterioFiles 398 - Marathon Microbes Maximize Mileage

Veillonella parvula

From Gronow et al. 2009

Stand Genomic Sci 2(1): 57-65

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 produced by its degradation.

Journal Paper:
Scheiman J, Luber JM, Chavkin TA, MacDonald T, Tung A, Pham L-D, Wibowo MC, Wurth RC, Punthambaker S, Tierney BT, Yang Z, Hattab MW, Avila-Pacheco J, Clish CB, Lessard S, Church GM, Kostic AD. 2019. Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism. Nat Med 25:1104–1109.

Other interesting stories:

• Aphids hijacked viral gene to determine whether they grow wings
• Phage therapy could help treat green sea turtles

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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BacterioFiles 376 - Pressurized Pollutant Pulls Products

Bacillus megaterium
By Osmoregulator, CCBY-SA 3.0

This episode: Supercritical carbon dioxide and bacteria that can grow in it make a great combination for biofuel production!

Download Episode (9.4 MB, 10.2 minutes)

Show notes:
Microbe of the episode: Flexibacter aggregans

Takeaways
Biofuels are an important part of humanity's move away from non-renewable resources. They have a higher energy density than batteries are yet able to achieve, giving them significant advantages for transportation purposes in which tapping into an electric grid isn't possible. Depending on the biofuel, they also have the advantage of existing infrastructure: we don't need to build a whole new system of charging or refueling stations, but can use the systems already in place.

However, biofuels as a collection of technologies still need some refinements. Yields for the more potentially sustainable approaches are low, and the lower the concentration of a soluble fuel, the more difficult it is to separate it from the non-fuel components of a fermentation. Microbial products also face the risk of contamination of a fermentation by unwanted organisms that use up the substrate without producing desirable products.

In this study, supercritical carbon dioxide is considered as a fix for both of these problems. The gas is pressurized to a point at which it is indistinguishable from liquid. A strain of Bacillus megaterium is specially selected as capable of growing and fermenting in this environment, while contaminants are inhibited. The solvent potential of supercritical carbon dioxide also serves as a way to extract the biofuel product—in this case, isobutanol—from the aqueous part of the culture medium. While it needs some development, this approach yields promising results.

Journal Paper:
Boock JT, Freedman AJE, Tompsett GA, Muse SK, Allen AJ, Jackson LA, Castro-Dominguez B, Timko MT, Prather KLJ, Thompson JR. 2019. Engineered microbial biofuel production and recovery under supercritical carbon dioxide. Nat Commun 10:587.

Other interesting stories:

• Yeast adopted useful iron-capturing bacterial protein

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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BacterioFiles 342 - Cyanide Stops Cell Suckers

Chromobacterium growing on agar

This episode: Some bacteria can defend themselves from bacterial predators by producing cyanide!

Thanks to Dr. Robert Mitchell for his contribution!

Download Episode (7.7 MB, 8.4 minutes)

Show notes:
Microbe of the episode: Dyoepsilonpapillomavirus 1

News item

Journal Paper:
Mun W, Kwon H, Im H, Choi SY, Monnappa AK, Mitchell RJ. 2017. Cyanide Production by Chromobacterium piscinae Shields It from Bdellovibrio bacteriovorus HD100 Predation. mBio 8:e01370-17.

Other interesting stories:

Using bacterial DNA to estimate movement of river water

Making bacteria produce biologic drugs that last longer in the body

Fungal pigment could be a useful semiconductor

Parasitic microbe uses chemical defense against defenses of fungus-growing ants

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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Episode outline:

BacterioFiles 324 - Prokaryote Prefers Poorer Power

Green Dragon Spring, Yellowstone
Credit: National Park Service

This episode: Hot spring archaea prefer to use elements that give them less energy even when more energetic options are available!

Download Episode (8.1 MB, 8.8 minutes)

Show notes:
Microbe of the episode: Vitreoscilla beggiatoides

News item

Journal Paper:
Amenabar MJ, Shock EL, Roden EE, Peters JW, Boyd ES. 2017. Microbial substrate preference dictated by energy demand rather than supply. Nat Geosci 10:577–581.

Other interesting stories:

Developing good methods for using skin microbiome for forensics (paper)

Microbe discovered that consumes groundwater contaminant dioxane

Mucus-eating gut microbes can produce beneficial nutrients and vitamins (paper)

Making new beer and wine flavors with different yeast

Providing leaf microbiota to help endangered plants survive in wild

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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Episode outline:

BacterioFiles 313 - Colonies Correct Chloride Corrosion

Ancient Roman nails
By Takkk - Own work,CC BY-SA 3.0

This episode: Bacteria could help treat corrosion to preserve ancient iron artifacts!

Thanks to Drs. Pilar Junier and Edith Joseph for their contributions!

Download Episode (13.4 MB, 14.7 minutes)

Show notes:
Journal Paper:
Comensoli L, Maillard J, Albini M, Sandoz F, Junier P, Joseph E. 2017. Use of Bacteria To Stabilize Archaeological Iron. Appl Environ Microbiol 83:e03478-16.

Other interesting stories:

Archaeal communities on skin change with age

Using viruses to deliver useful stuff to the nervous system

Polymer-coating bacteria to improve their electricity-generating ability

61% of yeast essential genes can be replaced by E. coli versions (paper)

Breast milk and skin are important sources of microbes for infants (paper)

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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Episode outline:

BacterioFiles 301 - Cells Simulate City Structures

This episode: Ancient microbes built underwater structures that look like sunken, ancient cities!

Download Episode (10.6 MB, 11.7 minutes)

Show notes:
Microbe of the episode: Actinomadura luteofluorescens

News item 1/News item 2

Journal Paper:
Andrews JE, Stamatakis MG, Marca-Bell A, Stewart C, Millar IL. 2016. Exhumed hydrocarbon-seep authigenic carbonates from Zakynthos Island (Greece): Concretions not archaeological remains. Marine and Petroleum Geology 76:16–25.

Other interesting stories:

Insecticide-resistant insects have insecticide-degrading gut bacteria (paper)

Microbe spores that can survive in space

Fungus-gardening ants are choosy about how much CO₂ they want in their gardens (paper)

Biochar helps microbes transfer electrons around in soil

Exposure of infants to furry pets affects microbiota

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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BacterioFiles 275 - Building Bacterial Batteries

This episode: Scientists build a battery out of microbes and electrodes that can store and release electricity repeatedly!
Download Episode (7.5 MB, 8.1 minutes)

Show notes:
News item

Interesting articles about anaerobic digesters
Journal Paper:
Molenaar SD, Mol AR, Sleutels THJA, ter Heijne A, Buisman CJN. 2016. Microbial Rechargeable Battery: Energy Storage and Recovery through Acetate. Environ Sci Technol Lett 3:144–149.

Other interesting stories:

Viruses are transferred with fecal transplant, but only ones that attack bacteria (paper)

Communities of microbes on skin don't change much

Antibodies from mother in milk help babies tolerate good microbes

Bacteria could help control insects by killing males

More associations between childhood bacteria and asthma

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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BacterioFiles 240 - Water Worms Make (carbon) Monoxide Meals

This episode: Marine worms and their microbial symbionts can live on the toxic gas carbon monoxide!

Reminder: this is the last episode for at least a few weeks while I am wrapping up my PhD. See you again when I'm done!


Download Episode (11.1 MB, 12.1 minutes)

Show notes:
Journal Paper

Other interesting stories:

Salt-loving extremophiles eat carbon monoxide at Mars-level concentrations (paper)

Better biotech processes by microbial cooperation (paper)

Different ways to engineer microbes to produce propane

Not all organisms share exactly the same genetic code

Queen bees have different microbes than other bees (paper)

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This show features music from Mevio's podsafe Music Alley.

BacterioFiles 232 - Exploring Enzymes' Element Effects

This episode: Bacteria can convert soluble uranium to an insoluble form, and distinguish between different isotopes!

Download Episode (8.2 MB, 8.9 minutes)

Show notes:
News item/Journal Paper

Other interesting stories:

Bacteria could help degrade environmental chemical contaminant (paper)

Phage could treat dental infections

Bacteria and grass together clean up soil

Mutant E. coli keeps getting longer without dividing

Algae could produce malaria vaccine

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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BacterioFiles 222 - Cells Store Solar Sparks

The setup. Torella et al. 2015

This episode: Bacteria engineered to produce liquid fuel can eat carbon dioxide and hydrogen from solar-powered water-splitting!

Download Episode (11.2 MB, 12.25 minutes)

Show notes:
Journal Paper

Other interesting stories:

Some bugs need their vitamin-producing microbes, but kill them to harvest the vitamins

How specific gut microbes influence immune system (paper)

Bacteria used to produce various food ingredients

Bacteria could produce polyester beads that bind specific proteins (paper)

Rainforest bacteria could help plants grow better in poorer soil (paper)

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BacterioFiles 221 - Co-culture Close Contact, Cats, and Cockerels

More related than some bacteria

This episode: More distantly related bacteria can help each other grow (and produce lots of hydrogen) by temporarily fusing with each other!

Download Episode (12.7 MB, 13.9 minutes)

Show notes:
News item/Journal Paper

Bacterial close contact

Note: I said C. acetobutylicum was used in WWII to make acetone for bombs, but it was actually World War I, used to make cordite, a replacement for gunpowder.

Other interesting stories:

Gut microbes can affect brain's defensive barrier in mice

Getting E. coli to produce higher amounts of nice-smelling biofuel compounds

Using fungi to control avocado-damaging pests

Bacterial proteins used to modify human cells' immune signaling (paper)

Worm gut bacteria could help degrade plastic waste

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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BacterioFiles 214 - Cable-Chlorophyte Coop Conducts Current

Cable bacteria
Malkin and Meysman, 2015

This episode: Cable bacteria and algae set up electric grid in sediments!

Download Episode (6 MB, 6.5 minutes)

Show notes:
Journal Paper

Other interesting stories:

Daily rhythms are important for gut microbes and their hosts

Wild yeasts are very diverse in the smells they produce (paper)

Gut microbiome may be involved in alcoholism (paper)

Tiny tiny viruses can have very big effect on ocean carbon

Mouse lupus correlates with certain gut bacteria

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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This show features music from Mevio's podsafe Music Alley.