491 - Less Liquid Lands Losing Lichens

Lichens on rock By Jesse Noar CC BY 4.0

This episode: Trends of declining lichen populations and biocrust cover overall match trends of increasing temperatures in Colorado dryland!
Download Episode (6.4 MB, 9.3 minutes)

Show notes:

Microbe of the episode: Cherry chlorotic rusty spot associated partitivirus

Takeaways:

Global climate change is affecting almost every natural system on the planet, in predictable and also sometimes unexpected, complex ways. Microbes perform key roles in many different ecosystems, providing and recycling important nutrients and even macroscopic structure. One example of this is biocrusts in dryland environments, such as areas in the western US with low annual rainfall. Microbes other organisms form a stable surface binding soil and sand particles together, helping to retain moisture and prevent erosion and transformation of land into desert.

In this study of a Colorado park over more than 20 years, important species of symbiotic fungi and photosynthetic microbes in the form of lichens have declined significantly. The land is mostly untroubled by grazing or human activity, but changes in climate and moisture and the presence of invasive plants could affect lichens. However, the temperature increase over the decades showed the best correlation with the lichen decline. The loss of these species could lead to nutrient shortages in the long term for these communities.

Journal Paper:

Finger-Higgens R, Duniway MC, Fick S, Geiger EL, Hoover DL, Pfennigwerth AA, Van Scoyoc MW, Belnap J. 2022. Decline in biological soil crust N-fixing lichens linked to increasing summertime temperatures. Proc Natl Acad Sci USA 119:e2120975119.

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486 - Biohybrid Bacteria Build Biomass

Azotobacter vinelandii

This episode: Incorporating light-absorbing molecules into bacterial membranes can allow bacteria to use solar energy to transform nitrogen gas into fertilizer!
Download Episode (6.5 MB, 9.9 minutes)

Show notes:
Microbe of the episode: Wheat dwarf virus

 

Takeaways

Turning nitrogen gas into biologically useful compounds, such as protein or ammonia for fertilizer, is an essential part of the global nitrogen cycle and therefore, for agriculture. Today much fertilizer is produced from nitrogen gas by a chemical process that requires large amounts of energy, contributing to global warming. But certain bacteria can perform the same process using special enzymes much more efficiently.

In this study, a light-absorbing molecule was inserted into the cell membrane of some of these bacteria, allowing them to use light energy directly to power the nitrogen converting enzymes. These "biohybrids" were able to produce convert significantly more nitrogen gas and produce additional bacterial biomass from it, showing promise for using such an approach for more sustainable microbial fertilizer production.

Journal Paper:
Chen Z, Quek G, Zhu J, Chan SJW, Cox‐Vázquez SJ, Lopez‐Garcia F, Bazan GC. 2023. A Broad Light‐Harvesting Conjugated Oligoelectrolyte Enables Photocatalytic Nitrogen Fixation in a Bacterial Biohybrid. Angew Chem Int Ed 62:e202307101.

Other interesting stories:

• Update on using mosquito bacteria to block mosquito-borne viruses

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460 - Prokaryote Publicity Prevents Protist Processes

Emiliania huxleyi
By Alison R. Taylor
UNC Wilmington Microscopy
PLoS Biology, June 2011 Cover
CC BY 2.5

This episode: A bacterial communication signal makes algae stop growing, which helps them survive virus attacks!

Download Episode (5.3 MB, 7.7 minutes)

Show notes:
Microbe of the episode: Veillonella parvula

Takeaways

Many interesting interactions between microbes take place in the ocean. As single-celled organisms lacking complex sensory organs, many such interactions and communications are mediated by chemical signals. Some bacteria, for example, each produce small amounts of certain chemicals and release them into the environment. When the concentration of the chemical signal builds up to a certain point, the bacteria change their behavior to take advantage of their high numbers that must be present to produce so much of the signal. This process is called quorum sensing.

Some of these chemical signals can affect the behavior of organisms other than bacteria also. In this study, a common marine algal species was found to stop growing in response to a certain bacterial signal. This chemical inhibits an enzyme required for the algae to produce nucleotides to replicate their genomes. As a result, the algae are able to resist destruction by a virus that would otherwise decimate their populations.

Journal Paper:
Pollara SB, Becker JW, Nunn BL, Boiteau R, Repeta D, Mudge MC, Downing G, Chase D, Harvey EL, Whalen KE. 2021. Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality. mSphere 6:e00009-21.

Other interesting stories:

• Comparing ancient gut microbes from fecal fossils to modern gut communities / also this one

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459 - Prokaryotes Provide Polyp Perserverance

Coral
By Brocken Inaglory
CC BY-SA 4.0

This episode: Transplanting microbes from some corals to others could help the corals survive high temperatures!

Download Episode (5.7 MB, 8.3 minutes)

Show notes:
Microbe of the episode: Streptomyces olivaceoviridis

News item

Takeaways

The ever-rising temperatures of our modern world are putting more and more stress on various ecosystems. This is true even on the ocean floor: record-high temperatures damage reefs by causing coral bleaching, in which corals lose their photosynthetic endosymbionts. If conditions do not improve, these corals eventually die.

Corals have microbial symbionts other than the phototrophs, also. We know from ourselves and from plants that microbes can have big effects on their hosts, so it seemed worth testing whether symbionts from more heat-resistant corals could transfer heat resistance to more vulnerable individuals. Recipients of this treatment did show enhanced heat resistance, but the microbial community composition did not always change after the treatment.

Journal Paper:
Doering T, Wall M, Putchim L, Rattanawongwan T, Schroeder R, Hentschel U, Roik A. 2021. Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues. Microbiome 9:102.

Other interesting stories:

• Tiny bacterium kills larger bacterium that makes troublesome foam

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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 419 - Marine Methane Microbe Multiplication

Anaerobic methanotrophs

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-consuming communities. So once dispersed, such communities seem slow to regenerate as the locations of methane seepage shift.

Journal Paper:
Klasek S, Torres ME, Bartlett DH, Tyler M, Hong W-L, Colwell F. 2020. Microbial communities from Arctic marine sediments respond slowly to methane addition during ex situ enrichments. Environ Microbiol 22:1829–1846.

Other interesting stories:

• Bird and bat microbiomes have some similarities
• Twins often share certain gut microbes, even if they've been living apart for decades

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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 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:

• Phages bind to fish mucosal surfaces and protect from infection
• Examining how archaea affect meteorites

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

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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:

• Microbes could make paper whitening more environmentally friendly (paper)
• Compound from rotifers could prevent transmission of eukaryotic parasite

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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 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:

• Bacterial immune system (CRISPR/Cas) could save bananas from fungus that wipes them out
• Potentially useful antibiotic produced by gut microbe (paper)

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

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BacterioFiles 404 - Phages Force Food Finding

Synechococcus cyanobacteria

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 or die off.

Journal Paper:
Waldbauer JR, Coleman ML, Rizzo AI, Campbell KL, Lotus J, Zhang L. 2019. Nitrogen sourcing during viral infection of marine cyanobacteria. Proc Natl Acad Sci 116:15590–15595.

Other interesting stories:

• Transplants of gut microbes help koalas eat wider range of food
• Skin bacteria can help attract (or repulse) mosquitoes (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 350 - Microbes Mysteriously Make Methane

Nitrogenase protein structure
By Jjsjjsjjs - Own work
CC BY-SA 3.0

This episode: A version of the microbial enzyme that fixes nitrogen can also convert carbon dioxide to methane!

Download Episode (11.8 MB, 12.9 minutes)

Show notes:
Microbe of the episode: Human mastadenovirus D

Journal Paper:
Zheng Y, Harris DF, Yu Z, Fu Y, Poudel S, Ledbetter RN, Fixen KR, Yang Z-Y, Boyd ES, Lidstrom ME, Seefeldt LC, Harwood CS. 2018. A pathway for biological methane production using bacterial iron-only nitrogenase. Nat Microbiol 3:281–286.

Other interesting stories:

• Gut bacterial metabolite helps protect mice against gut pathogen

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

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Episode outline:

BacterioFiles 285 - Sultry Snow Cell Sun Screen

Red snow
By Will Beback, CC BY-SA 3.0

This episode: Algae growing in Arctic snow make red pigments that heat up their surroundings!

Download Episode (6.8 MB, 7.5 minutes)

Show notes:
News item

Journal Paper:
Lutz S, Anesio AM, Raiswell R, Edwards A, Newton RJ, Gill F, Benning LG. 2016. The biogeography of red snow microbiomes and their role in melting arctic glaciers. Nat Commun 7:11968.

Other interesting stories:

Bacterial species benefit from losing genes they don't need

Soil fungi help plants grow better in salty conditions (paper)

Bacterial predators actually help treat infection in rats

Some bacteria produce methane while harvesting phosphorus (paper)

Probiotics could help treat skin problems (paper)

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

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BacterioFiles 267 - Crust Color Cooks Communities

Biocrusts in Moab, Utah
Credit: Estelle Couradeau

This episode: Cyanobacteria in biocrusts produce pigments that heat their surroundings up to 10 degrees hotter!
Download Episode (7 MB, 7.6 minutes)

Show notes:
News item

Journal Paper:
Couradeau E, Karaoz U, Lim HC, Nunes da Rocha U, Northen T, Brodie E, Garcia-Pichel F. 2016. Bacteria increase arid-land soil surface temperature through the production of sunscreens. Nat Commun 7:10373.

Other interesting stories:

Engineering better bioplastic production from bacteria

Groups of bacteria can show a kind of memory

Bacteria in gut are competing and killing each other a lot

Exercise helps mice gut health, regardless of weight (paper)

Bacteria help insects tolerate cabbage toxin

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

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BacterioFiles 266 - Solar Cyborg Cells Capture Carbon

Cells of Moorella thermoacetica
forming spores in culture

This episode: Adding exotic elements to convert spore-forming bacteria into light-capturing cyborgs that convert carbon dioxide into useful chemicals!
Download Episode (9.7 MB, 10.5 minutes)

Show notes:
News item 1/News item 2

Journal Paper:
Sakimoto KK, Wong AB, Yang P. 2016. Self-photosensitization of nonphotosynthetic bacteria for solar-to-chemical production. Science 351:74–77.

Other interesting stories:

Unusual archaeal virus sorta looks like Ebola (paper)

Understanding how probiotics could prevent cancer in mice (paper)

Giant viruses have immune system against virophages

Using evolution to help yeast produce more ethanol from biomass (paper)

Remnants of viruses in our DNA helps us fight off infections

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

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

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

BacterioFiles 200 - Converted Clostridium Consumes Carbon monoxide

This episode: Carbon monoxide-eating bacteria get modified to produce more useful products!

Download Episode (16 MB, 17.5 minutes)

Show notes:
Journal Paper

Other interesting stories:

Other mosquito microbes compete with and inhibit Wolbachia

Helicobacter extract seems to help prevent asthma (paper)

Lots of microbes living in water drops suspended in tar

Spores could be good for vaccines delivered to mucosal surfaces (review)

Various archaea are floating around in the air (paper)

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

Subscribe at iTunes, check out the show at Twitter, MicrobeWorld, or Facebook

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