476 - Bamboo Breakdown Benefits Beetle Babies

Bamboo
By I Kenpei,
CC BY-SA 3.0

This episode: Beetles inoculate bamboo with a fungus that consumes the bamboo sugars to feed the beetle larvae!
Download Episode (7.7 MB, 11.2 minutes)

Show notes:
Microbe of the episode: Saccharomyces cerevisiae virus L-BC (La)

News item

Video: Lizard beetle laying its egg

Takeaways

The structural polymers that make up plants, such as cellulose, can be difficult for many organisms to digest. Some kinds of bacteria and fungi can do it, and some animals (cows, pandas, termites) partner with these microbes to be able to eat otherwise indigestible plant material. This includes insects such as leaf-cutter ants that farm external gardens of microbes, providing them plant material and then eating the resulting microbial growth.

In this study, the lizard beetle lays its eggs in bamboo and inoculates the walls of the bamboo with a fungus that provides food to the larvae. Chemical analyses suggest that the fungus only consumes the simple sugars in the bamboo rather than breaking down the tougher polymers, which raises questions about the evolution of this interaction.

Journal Paper:
Toki W, Aoki D. 2021. Nutritional resources of the yeast symbiont cultivated by the lizard beetle Doubledaya bucculenta in bamboos. Sci Rep 11:19208.

Other interesting stories:

• Using bacteria to detect and target colon cancer for imaging (paper)
• Filters made from kombucha cultures could work better than synthetic types

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

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466 - Microbes Mining Mars Minerals

Basalt close up
By Helgi, CC BY-SA 4.0

This episode: Bacteria are able to extract metals from rocks for industrial use, even in microgravity!

Download Episode (6.2 MB, 9.0 minutes)

Show notes:
Microbe of the episode: Decapod ambidensovirus 1

News item

Takeaways

As humanity makes progress toward becoming an interplanetary species, consideration is needed on how travelers can survive and thrive in distant places. These methods may look very different from what works well on Earth, with differences in gravity, atmosphere, and access to resources. For example, mining for materials for construction may not be feasible using methods common on Earth. An alternative may be biomining, using microbes that can selectively extract and purify specific metals from minerals.

In this study, the European Space Agency tested the ability of several microbes to extract vanadium from rocks in different gravity conditions, on the International Space Station. Two out of three microbes were able to extract twice as much vanadium as was extracted in the absence of microbes, both on a planet and up in space.

Journal Paper:
Cockell CS, Santomartino R, Finster K, Waajen AC, Nicholson N, Loudon C-M, Eades LJ, Moeller R, Rettberg P, Fuchs FM, Van Houdt R, Leys N, Coninx I, Hatton J, Parmitano L, Krause J, Koehler A, Caplin N, Zuijderduijn L, Mariani A, Pellari S, Carubia F, Luciani G, Balsamo M, Zolesi V, Ochoa J, Sen P, Watt JAJ, Doswald-Winkler J, Herová M, Rattenbacher B, Wadsworth J, Everroad RC, Demets R. 2021. Microbially-Enhanced Vanadium Mining and Bioremediation Under Micro- and Mars Gravity on the International Space Station. Front Microbiol 12:663.

Other interesting stories:

• A prokaryote with internal metabolic compartments (paper)

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427 - Simple Cells Stay Strong

Fluorescent SimCells
By Fan et al. 2020,
PNAS 117(12):6752
CC BY 4.0

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 damaged cancer cells in a dish but left non-cancerous cells unharmed.

Journal Paper:
Fan C, Davison PA, Habgood R, Zeng H, Decker CM, Salazar MG, Lueangwattanapong K, Townley HE, Yang A, Thompson IP, Ye H, Cui Z, Schmidt F, Hunter CN, Huang WE. 2020. Chromosome-free bacterial cells are safe and programmable platforms for synthetic biology. Proc Natl Acad Sci 117:6752–6761.

Other interesting stories:

• Biofuel-producing bacteria can generate electricity at the same time (paper)
• Using dried microbial biomass as fertilizer works pretty well (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)

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BacterioFiles 405 - Coated Colonizers Counteract Corrosion

Coated bacteria on a coated surface
Rijavec et al. 2019, Adv Sci 1901408

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:
Rijavec T, Zrimec J, Spanning R van, Lapanje A. 2019. Natural Microbial Communities Can Be Manipulated by Artificially Constructed Biofilms. Adv Sci 6:1901408.

Other interesting stories:

• Some microbe biofilms can protect outdoor metal sheets from corrosion
• How bacteria can be helpful for growing edible mushrooms (review)

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BacterioFiles 389 - Prokaryotes Pacify Protein Problem

E. coli bacteria

This episode: Engineered bacteria could help people digest an essential nutrient when they can't digest it themselves!

Download Episode (8.5 MB, 9.3 minutes)

Show notes:
Microbe of the episode: Kadipiro virus

News item (paywall)

Science-Based Medicine blog article about phenylketonuria, Synlogic, and engineering bacteria to treat this disorder, with lots of good detail

Takeaways
Treating genetic disorders can be very difficult. Sometimes they can be managed, with lifestyle, diet, or medication, but cure has almost always been out of the picture. With a disorder such as phenylketonuria (PKU), for example, in which the body is unable to fully metabolize the amino acid phenylalanine, diet and medication may work to some extent.

In an effort to provide better options for PKU, scientists at Synlogic, Inc have created a strain of Escherichia coli that produces phenylalanine-degrading enzymes in the gut. The hope is that ingesting this bacterium could allow PKU patients to be less restrictive with their diet.

Journal Paper:
Isabella VM, Ha BN, Castillo MJ, Lubkowicz DJ, Rowe SE, Millet YA, Anderson CL, Li N, Fisher AB, West KA, Reeder PJ, Momin MM, Bergeron CG, Guilmain SE, Miller PF, Kurtz CB, Falb D. 2018. Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria. Nat Biotechnol 36:857–864.

Other interesting stories:

• Probiotic molecule induces protection in mice against viral brain infection
• E. coli growing with artificially synthesized genome (Extra information)

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BacterioFiles 388 - Floor Fungi Fracture Phthalates

This episode: Microbes in household dust help degrade potentially harmful plasticizer chemicals!

Thanks to Ashleigh Bope for her contribution!

Download Episode (6.7 MB, 7.3 minutes)

Show notes:
Microbe of the episode: Rosa rugosa leaf distortion virus

News item

Takeaways
Modern life and technology comes with modern challenges, including exposure to chemicals in building materials and such that humans didn't encounter much before the last few generations. Phthalate esters, found in PVC and other materials, can accumulate in homes and cause some problems, especially in children.

Modern life is also new to microbes, but they are very adaptable and versatile. In this study, microbes in household dust show some ability to break down the phthalates over time. Whether this activity is significant and beneficial to residents remains to be discovered.

Journal Paper:
Bope A, Haines SR, Hegarty B, Weschler CJ, Peccia J, Dannemiller KC. Degradation of phthalate esters in floor dust at elevated relative humidity. Environ Sci: Processes Impacts.

Other interesting stories:

• Native fungi tag team to kill invasive insect pest (paper)

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

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BacterioFiles 386 - Cupola Contaminant Cleaners

Pisa cupola painting
By JoJan, CC BY-SA 3.0

This episode: Bacteria help gently clean residue off artworks painted on stone!

Download Episode (5.6 MB, 6.1 minutes)

Show notes:
Microbe of the episode: Cellulophaga virus Cba171

Takeaways
More and more cleaning products these days contain an ingredient called "enzymes." These are proteins that break down contaminants biologically instead of just removing them chemically, in a targeted manner.

In a similar approach, this study explores applying bacteria directly to classic artwork painted directly on stone, to clean up residues on the surface. These bacteria can produce enzymes on site and degrade the contaminants while leaving the underlying paint intact.

Journal Paper:
Ranalli G, Zanardini E, Rampazzi L, Corti C, Andreotti A, Colombini MP, Bosch‐Roig P, Lustrato G, Giantomassi C, Zari D, Virilli P. 2019. Onsite advanced biocleaning system on historical wall paintings using new agar-gauze bacteria gel. J Appl Microbiol 126:1785–1796.

Other interesting stories:

• Mouth bacteria prevent gum disease by interfering with activity of other bacteria (paper)
• Despite identical genetics, individual bacteria can behave differently through random variation

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

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BacterioFiles 385 - Prokaryotes Protect Paper

Lysobacter enzymogenes 

attacking a fungal hypha

GFDL

This episode: Bacteria produce antifungal compounds that can protect paper from fungal deterioration!

Download Episode (6.8 MB, 7.4 minutes)

Show notes:
Microbe of the episode: Acetobacter aceti

Takeaways
Paper is a very useful information storage medium, but it is also somewhat delicious for microbes that can break it down as food, degrade the quality, and cause indelible stains and discoloration under the right conditions. Preventing this usually requires careful control, such as keeping humidity low, for storing paper for long periods.

In this study, scientists tested the ability of the bacterium Lysobacter enzymogenes to protect paper via the antifungal compounds it produces. This first required filtering out the pigments that the bacteria produced, to prevent them from discoloring the paper. Once a method for this filtering was in place, they found the bacterial culture supernatant could significantly reduce fungal growth on various kinds of paper, and protect the paper from staining and degradation.

Journal Paper:
Chen Z, Zou J, Chen B, Du L, Wang M. 2019. Protecting books from mold damage by decreasing paper bioreceptivity to fungal attack using de-coloured cell-free supernatant of Lysobacter enzymogenes C3. J Appl Microbiol 126:1772–1784.

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

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BacterioFiles 363 - Tiny Treasure Tunnels

Tunnels in garnet
By: Ivarsson et al. 2018,
PLoS ONE 13(8):e0200351
CC BY 4.0

This episode: Intricate networks of tunnels in garnet gemstones seem to have come from tunneling microorganisms!

Thanks to Magnus Ivarsson for his contribution!

Download Episode (5.4 MB, 5.9 minutes)

Show notes:
Microbe of the episode: Streptomyces griseosporeus

News item

Journal Papers:
Ivarsson M, Skogby H, Phichaikamjornwut B, Bengtson S, Siljeström S, Ounchanum P, Boonsoong A, Kruachanta M, Marone F, Belivanova V, Holmström S. 2018. Intricate tunnels in garnets from soils and river sediments in Thailand – Possible endolithic microborings. PLOS ONE 13:e0200351.

Other interesting stories:

• Swimming algae can move through bloodstream to deliver drugs
• Mosquito microbes engineered to inhibit spread of malaria (paper)
• A probiotic inhibits a pathogen by interfering with its signaling between cells
• Healthy microbiota seems important for mice recovering from heart attack

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

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Episode outline:

BacterioFiles 300 - Hyphae Help Horizontal (Gene Transfer)

Oyster mushroom mycelium
By Tobi Kellner, CC BY-SA 3.0

This episode: Filament-forming organisms help bacteria swim through soil and exchange genes with each other! Also, new feature: microbe of the episode!

Download Episode (13.2 MB, 14.4 minutes)

Show notes:
Microbe of the episode: Azotobacter vinelandii

News item

Video of bacteria swimming along mycelium:

Full statement from Tom Berthold

Journal Paper:
Berthold T, Centler F, Hübschmann T, Remer R, Thullner M, Harms H, Wick LY. 2016. Mycelia as a focal point for horizontal gene transfer among soil bacteria. Sci Rep 6:36390.

Other interesting stories:

Bacterial DNA reduces mouse airway allergies

Changes in microbiomes of people in 500-day space simulation (paper)

Using advanced electron microscopy to visualize giant virus

Bacterial predators find prey by both being trapped by their own whirlpools

Many unusual viruses are moving around in the fluids of the rocky ocean floor

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

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BacterioFiles 280 - Saccharomyces Smash Small Spaces

This episode: Microbes in tight spaces grow so much they can build up pressure and burst out!
Download Episode (5.5 MB, 6 minutes)

Show notes:
News item

Video: cells expanding walls of chamber
Video: cells squished together
Video: cells bursting out of chamber

Journal Paper:
Delarue M, Hartung J, Schreck C, Gniewek P, Hu L, Herminghaus S, Hallatschek O. 2016. Self-driven jamming in growing microbial populations. Nat Phys 12:762–766.

Other interesting stories:

Fungi can infect and kill mosquito larvae

Buildings could enhance our encountering beneficial microbes

Bacteria could generate micro amounts of power

Microbes could help improve food supply (paper)

Modified E. coli can produce more useful fuels, chemicals

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

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BacterioFiles 274 - Proteobacteria Purify Piscine Pee

Adult female zebrafish

By Azul - Own work, Copyrighted free use

This episode: Bacteria in the gills of fish help break down their metabolic wastes before they reach toxic levels!
Download Episode (7.4 MB, 8.1 minutes)

Show notes:
News item

Journal Paper:
van Kessel MAHJ, Mesman RJ, Arshad A, Metz JR, Spanings FAT, van Dalen SCM, van Niftrik L, Flik G, Wendelaar Bonga SE, Jetten MSM, Klaren PHM, Op den Camp HJM. 2016. Branchial nitrogen cycle symbionts can remove ammonia in fish gills. Environ Microbiol Rep 8:590–594.

Other interesting stories:

How do microbes live in the harsh conditions of salt-secreting tree leaves? (paper)

Bacteria inside fungi affect how they interact with plants (paper)

Wolbachia may prevent dengue transmission by affecting mosquito lipids (paper)

Effects from fungi in soil can be detected from space

Bacterial mosquito symbionts block Zika transmission

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

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BacterioFiles 273 - Bottle-Biting Bacteria

Ideonella azotifigens cells

This episode: Newly discovered bacteria can break down especially long-lived type of plastic!
Download Episode (6.4 MB, 7 minutes)

Show notes:
News item 1/News item 2 (loginwall)

Journal Paper:
Yoshida S, Hiraga K, Takehana T, Taniguchi I, Yamaji H, Maeda Y, Toyohara K, Miyamoto K, Kimura Y, Oda K. 2016. A bacterium that degrades and assimilates poly(ethylene terephthalate). Science 351:1196–1199.

Other interesting stories:

Worms may help gut health by modifying microbe community

Figuring out how breastmilk helps babies' microbes

Gut bacteria can affect fruit fly reproduction (paper)

Bacteria can crawl along and kill fungal filaments (paper)

Feeding mice fiber for bacteria increases their anti-inflammatory effect (paper)

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

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BacterioFiles 254 - Clostridium Consolidates Combustibles Conversion

This episode: Engineering bacteria to convert cellulose directly into useful biofuels and chemicals can be tricky!
Download Episode (13.9 MB, 15.2 minutes)

Show notes:
News item

Journal Paper:
Lin PP, Mi L, Morioka AH, Yoshino KM, Konishi S, Xu SC, Papanek BA, Riley LA, Guss AM, Liao JC. 2015. Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum. Metab Eng 31:44–52.

Other interesting stories:

Cute photosynthetic protist could do interesting metabolic processes

Using advanced technique to link antibiotic production to specific beewolf microbes

Termite gut protist has bacterial symbiont that fixes carbon and nitrogen (paper)

Geography and household members influence fungi and bacteria of home dust

Probiotic ineffective at preventing colonization by drug-resistant pathogens

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BacterioFiles 250 - Bacteria Boost Berry Borer Beetle Babies

This episode: Gut bacteria make it possible for coffee berry borer beetles to live entirely on caffeine-rich food!

Download Episode (6.9 MB, 7.5 minutes)

Show notes:
Journal Paper

Other interesting stories:

Molecule from plague bacteria could be helpful removing rust and such (paper)

Bacteria can clean up toxic chromium pollution (paper)

Chemical from a yeast could save bats from deadly fungus

Cocktail of phages works better than single kind to prevent food poisoning

Fungi help trees survive drought conditions

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BacterioFiles 248 - Tiny Travelers Transport Toxin Trashers

Swarming P. vortex (red)
carrying cargo (green).
Finkelshtein et al. 2015

This episode: Bacteria that swarm around in groups carry other bacteria with them that can be helpful for degrading toxins!

Download Episode (14.2 MB, 15.5 minutes)

Show notes:
Journal Paper/Explanatory video

Other interesting stories:

Bacterium can help biofuel-producing algae grow better (paper)

Super-tolerant yeasts found in high volcanic place in super-dry desert (paper)

Bacteria living in even non-legume plants (like rice) could fix nitrogen for their host

Algae are becoming more popular as alternative protein in food

Microbiome resistance to C. difficile infection depends on many bacteria together

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BacterioFiles 206 - Mollusc Maneuvers Microbe Machines to Macerate Maples

Shipworm, in or out of wood.
O'Connor et al, 2014.

This episode: When digesting wood, shipworms outsource their microbial symbionts from gut to gills!

Download Episode (9.7 MB, 10.6 minutes)

Show notes:
Journal Paper

Other interesting stories:

Swimming alga Euglena could help treat iron overdose (paper)

Bacteria in bees could produce useful antimicrobials

Tough bacteria could help make nuclear waste storage safer

Learning about ancient cultures from their fossilized feces (paper)

Using phages to make wastewater treatment better

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BacterioFiles 203 - P. putida Promotes Plant Pollutant Purification

This episode: Bacteria living in plants could help plants clean up cancer-causing pollutants!

Download Episode (6.9 MB, 7.5 minutes)

Show notes:
News item/Journal Paper

NCSU Master's of Microbial Biotechnology Website
Paul Hamilton: website/email

Other interesting stories:

Amphibian skin bacteria can fight deadly infectious fungus (paper)

Human skin fungus surprisingly found in harsh ocean environments

Using bacteria to remove stinky compounds from wastewater

Making painkillers from microbes instead of plants

Fungal parasites only influence behavior of their specific ant host species

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BacterioFiles 201 - Plastic-Producing Prokaryote Process

PHB granules in cells

This episode: Bacteria from wastewater treatment sludge can produce lots of biodegradable plastic!

Download Episode (7.1 MB, 7.75 minutes)

Show notes:
Journal Paper

Other interesting stories:

Soil bacterium spores could treat tumors when injected

In mice, antibiotics early in life disrupt metabolism

Figuring out what our microbiome does in the body after we die (paper)

Microbes affect geological formations in caves

Insect gut microbes may be good source of new antibiotics

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.