Today Dr. Estelle Couradeau, Assistant Professor in the Department of Ecosystem Science and Management and the Huck Institutes of the Life Sciences at the Pennsylvania State University, joins the quality quorum today to discuss the role that the soil microbiome can play in terms of agriculture, moderating temperature, and protecting specific environments.

Host: Mark O. Martin

Guest: Estelle Couradeau

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• The Erskine Foundation fellowship website.
• An overview of Paenibacillus.
• An article discussing the fascinating colonial morphology often found with Paenbacillus.
• A blog post that demonstrates that the odd appearance of Paenibacillus can be used by other microbes for dispersal!
• Dr. Jo Handelsman's essential book, "A World Without Soil."
• A fine video describing the soil microbiome.
• The complexity of soil with regard to where and how microbes can live.
• Science journalist Carl Zimmer's indispensable essay likening the microbial ecology of lakes to the human body: "The Human Lake."
• An overview of dormancy in microbes.
• The "BonCat" (bio-orthogonal non-canonical amino acid tagging) technique for detecting living microbes in a sample without cultivation.
• An overview of flow cytometry in microbiology.
• An essay suggesting that marine bacteria are involved in the production of clouds.
• An article about climate change and microbes.
• An article about cyanobacteria and "sunscreen."
• A review article about the "biocrust" concept.
• A video overview of beautiful and fascinating microbial fossils: stromatolites.
• A video by Dr. Couradeau describing her research.
• Articles by Dr. Couradeau and colleagues asking which microbes are active in soil: here, here, and here.
• Articles by Dr. Couradeau and colleagues asking if microbes can change the temperature of a desert: here and here.
• Articles by Dr. Couradeau and colleagues that explore the hidden microbiomes of Andean páramo wetlands: here and here.
• Dr. Couradeau's faculty website.
• Dr. Couradeau's research website.

Intro music is by Reber Clark

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Today Dr. Michael D.L. Johnson, Associate Professor of Immunobiology at the University of Arizona, joins the quality quorum today to discuss copper, microbiology, and a possible new strategy to fight bacteria that cause disease.

Host: Mark O. Martin

Guest: Michael D. L. Johnson

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• A link to Hartiful, the Etsy artist who custom creates glow in the dark (and many other kinds) pins.
• A link to the essential science artist Beatrice the Biologist.
• A link to World Microbiome Day.
• A link to Micropia, the microbiology museum in Amsterdam.
• A recent article on the growing threat of antibiotic resistance among disease causing bacteria.
• A video demonstrating the Kirby Bauer procedure, which shows antimicrobial effects and zones of inhibition.
• A link to an earlier #MattersMicrobial episode with Dr. Michael Schmidt describing copper and microbes.
• A review article describing the impact that copper can have on microbes.
• A review article on Streptococcus pneumoniae, the organism with which Dr. Johnson works.
• An video celebrating the role that S. pneumoniae had in determining that DNA was the genetic material prior to World War 2.
• An overview of siderophores that help microbes obtain needed iron.
• An article about redox activity and copper and microbes.
• The relationship between metal toxicity and antimicrobial activity.
• The role that copper plays in agriculture.
• The differences between Gram positive and Gram negative bacteria.
• An article on efflux pumps and metal toxicity in microbes.
• An article describing how iron binding proteins also bind copper.
• An article describing how zinc interacts with microbes.
• A wonderful description of Dr. Johnson's "Trojan Horse" approach to battle disease causing microbes.
• A relevant review article by Dr. Johnson and his colleagues discussing copper and microbes.
• An overview of the "Hypothesis Fund," which supports unusual ideas in science.
• A video of Dr. Johnson describing his research.
• Dr. Johnson's faculty website.
• Dr. Johnson's research laboratory website.

Intro music is by Reber Clark

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Host: Mark O. Martin

Guest: Jo Handelsmann, Shruthi Magesh

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• Here is a link to the Etsy shop where one can buy the wonderful "THIS IS WHAT A MICROBIOLOGIST LOOKS LIKE" enamel pins.
• Here is a link to the World Microbiome Day website.
• Here is a link to the interesting work of Contamination Club.
• The story of Alexander Fleming's famous contaminant that led to the discovery of penicillin.
• Here is a link to Dr. Handelsman's recent book, "A World Without Soil." Highly recommended.
• The website for Dr. Handelsman's wonderful "Tiny Earth" program, helping students worldwide to screen soil for antimicrobial production (and learning about microbial diversity).
• An overview of the microbial complexity of soil.
• A video overview of biofilms.
• A video overview of types of bacterial motility.
• A video overview of "gliding motility" among bacteria.
• Some bacteria can "hitchhike" or are carried by other bacteria, such as Paenibacillus.
• Learning about an odd sport involving "zorbs."
• An introductory essay on "zorbing" and motility.
• Another introductory essay on "co-zorbing," the topic of today's discussion.
• A description of Flavobacterium johnsoniae, which carries out "zorbing."
• The original article on THOR ("The Hitchhikers of the Rhizosphere") by Dr. Handelsman and colleagues.
• The original "zorb" paper by Dr. Handelsman and colleagues that was discussed during today's podcast.
• The "co-zorb" paper by Dr. Handelsman, Dr. Magesh, and colleagues that was discussed during today's podcast.
• A fascinating video by Dr. Handelsman and her path to becoming a microbial scientist. Highly recommended..
• Dr. Handelsman's faculty website.
• The website for the Wisconsin Institute for Discovery.
• Dr. Handelsman's research laboratory website.

Intro music is by Reber Clark

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Today Dr. Morgan Sobol, Assistant Professor in the Department of Biology at Texas State University, joins the Quality Quorum today to discuss how microbes on early earth began interacting with elements like nitrogen, making life possible here and perhaps elsewhere in the universe! You will learn about the fundamental and amazing enzyme nitrogenase!

Host: Mark O. Martin

Guest: Morgan Sobol

Download MM134 (37 MB MP3, 62 mins)

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• The website for ASM Microbe, the annual meeting of microbiologists.
• The "live" #MattersMicrobial session recorded at ASM Microbe, with Dr. Hannah Reich.
• An essential article about "A World Without Microbes."
• A video version of "A World Without Microbes."
• An introduction to microbial ecology.
• An overview of the enzyme that fixes carbon dioxide into organic matter, Rubisco.
• An overview of the enzyme that converts practically inert dinitrogen gas into bioavailable ammonia, nitrogenase.
• A short essay on metalloenzymes, including nitrogenase.
• An overview of nitrogen fixing microbes, and the strategies they use.
• A review editorial describing the burgeoning field of astrobiology.
• A link to a NASA program exploring early evolution of microbial life.
• An article on the microbially caused Great Oxidation Event that changed our atmosphere eons ago, making life like forms like ours possible.
• An article exploring the evolution of microbial nitrogen fixation.
• An abstract by Dr. Sobol and colleagues, discussing the evolution of nitrogen fixation in an ancient ecological context.
• A lovely article about the microbiology of Yellowstone National Park.
• Dr. Sobol's faculty website.
• Dr. Sobol's interesting research group website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

Dr. Hannah Reich of the Department of Environmental Biology at the State University of New York's College of Environmental Science and Forestry joins the #QualityQuorum to discuss how microalgal interactions (including with bacteria) are fundamental contributors to large scale ecosystem processes including the ocean carbon pump, the duration of algal blooms, and the evolutionary success of coral reefs.

Host: Mark O. Martin

Guest: Hannah Reich

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• An essay on the coral holobiont.
• A discussion of the phycosphere.
• A discussion of the rhizosphere.
• A review of the roles of iron in microbial biology.
• An overview of siderophores in the microbial world.
• An article about iron, the warming oceans, and coral.
• A VERY recent article by Dr. Reich and colleagues regarding siderophores in the coral holobiont.
• A very nice short video by Dr. Reich explaining her work at ESF.
• Dr. Reich's faculty website.
• Dr. Reich's fascinating laboratory group website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

Today Dr. Jeffrey Barrick, John A. Hannah Distinguished Professor of the Department of Microbiology, Genetics, & Immunology and the Department of Entomology at Michigan State University, joins the quality quorum today to discuss how microbes can be used to study evolution itself. He will also discuss the impressive and ongoing LTEE program, the experiments that originate from it, and what they tell us about evolution.

Host: Mark O. Martin

Guest: Jeffrey Barrick

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• Here is a link to an article about the late great Abigail Salyers.
• Here is what I wrote about Dr. Salyers. I learned so much from her.
• An article about the contributions of Dr. Theodosius Dobzhansky to the study of evolution.
• The concept of contingency during evolution.
• An overview of microbial evolution.
• A link to "Microbes and Evolution," a book discussed during this podcast.
• A link to "A Primer for Experimental Evolution," a book discussed during this podcast.
• The concept of Growth Advantage in Stationary Phase (GASP).
• A video about the MEGA plate experiment by Dr. Michael Baym and colleagues. This is a "must watch."
• An video about Dr. Richard Lenski, originator of the LTEE.
• Dr. Lenski's website.
• The LTEE (long term evolutionary experiment) website. There is so much here to explore.
• An excellent introduction to the LTEE.
• An article about the amazing " climbing citrate mountain" innovation during LTEE described in the podcast.
• A video by Dr. Lenski about LTEE.
• A video by Dr. Barrick that is worth your time.
• Dr. Barrick's faculty website at Michigan State University.
• Dr. Barrick's research laboratory website.

Intro music is by Reber Clark

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Today Dr. Sam Brown, Professor of Biological Sciences at Georgia Tech University, joins the quality quorum today to discuss the social lives of bacterial pathogens. He will also discuss VERY recent research from his lab group exploring the specialist/generalist problem in Pseudomonas aeruginosa, and thoughts on cryptic convergent specialization!

Host: Mark O. Martin

Guest: Sam Brown

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• An overview of behavioral ecology.
• An article describing evolutionary trade offs and game theory.
• A video describing Tinbergen's "Four Whys" involving behavioral ecology.
• A wonderful essay by Carl Zimmer relating lake ecology and microbial ecology in humans.
• A Pseudomonas plush toy from Giant Microbes.
• The Pseudomonas contaminated eyedrops story told by Dr. Brown, as summarized by the CDC.
• An essay about sociomicrobiology.
• An overview of quorum sensing.
• An overview of biofilms.
• An article describing specialization versus generalism in ecology.
• A description of a "confusion matrix" in data analysis.
• A somewhat dated overview of PCA (principle component analysis).
• The article about convergent cryptic specialization under discussion today on this podcast from Dr. Brown's research group (first author Mehlferber).
• A VERY interesting article from Dr. Brown's research team describing eco-evolutionary aspects of polymicrobial infections.
• Dr. Brown's faculty website.
• Dr. Brown's laboratory group website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

Today Dr. Kevin Kohl, Associate Professor of Biological Sciences at the University of Pittsburgh, joins the #QualityQuorum to discuss how he and his colleagues study the interplay between animals, their resident gut microbes, and the overarching concept of the holobiont.

Host: Mark O. Martin

Guest: Kevin Kohl

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• The One Health Microbiome Center at Pennsylvania State University.
• A very fine essay on the holobiont concept for non-microbiologists.
• A general introductory overview of the holobiont concept.
• The holobiont concept and the coral symbiosis.
• A partial history of the development of the holobiont concept.
• Dr. Casadevall suggests that context and thus outcomes describes the term "pathogen," and a similar analysis applies to the holobiont.
• A very short description of the holobiont concept.
• Another overview of the holobiont concept in general, coauthored by Dr. Kohl.
• Some basic rules for thinking about the holobiont concept.
• A video introduction to the holobiont concept, by Dr. Seth Bordenstein.
• I highly recommend this essay by the science writer Carl Zimmer, "The Human Lake," to think of the connections between lake ecology and microbial interactions with humans.
• Another wonderful article recommended by Dr. Kohl, by Dr. Margaret McFall-Ngai and coauthors, detailing the impact microbes have on animals over evolution and development.
• The wood rat – creosote – microbiome connection to the holobiont concept, discussed on this podcast (coauthored by Dr. Kohl).
• The fascinating work by Dr. Kohl and colleagues showing the relationship between tadpole development and pond microbes discussed in this podcast.
• A must read article by Dr. Kohl and colleagues, "Through the microbial looking glass: our shifting understanding of the holobiont and microbes as mediators of organismal biology," illustrates the development and influence of the holobiont concept.
• Dr. Richard Prum's book, "Performance All the Way Down," was discussed during this podcast. There is also a video where Dr. Prum discusses the ideas in this book, describing gene regulation as a performance.
• Dr. Kohl's faculty website.
• Dr. Kohl's (very interesting) research website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

Today Dr. Michael Travisano, Distinguished McKnight University Professor in the College of Biological Sciences of the University of Minnesota, joins the #QualityQuorum to discuss fascinating work from his lab group exploring evolutionary questions from a microbial perspective.

Host: Mark O. Martin

Guest: Michael Travisano

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• Here is the link to the article we discussed during the podcast, authored by Dr. Travisano and Dr. Rainey.
• An overview of the concept of adaptive radiation.
• The ecological/evolutionary concept of "cheating" which applies to the mat forming bacteria discussed in this podcast.
• A link to an article by Dr. Jo Handelsman and colleagues about THOR, a simple microbial community that has shows great functional diversity.
• A wonderful essay about Dr. Rich Lenski's role in the LTEE.
• An essay from "Small Things Considered" describing "rewinding" evolution using microbial systems.
• A wonderful book by Stephen Jay Gould, "Wonderful Life" about evolution.
• Another book well worth your attention: "Chance and Necessity" by Jacques Monod.
• An article about the challenges of multicellularity in bacteria.
• The wonderful short video example of "snowflake yeast" evolving within days.
• A link to another #MattersMicrobial podcast by Dr Will Ratcliff, about "snowflake yeast."
• An article by Dr. Travisano and colleagues describing conflict and cooperation in microbial societies discussed on this podcast.
• An article by Dr. Travisano and colleagues about the evolution of "snowflake yeast," discussed on this podcast.
• An article by Dr. Travisano and colleagues discussing the role of other microbes in the development of multicellularity, discussed on this podcast.
• An article by Dr. Travisano and colleagues, on the repeatability of microbial adaptive evolution discussed on this podcast.
• A list of references authored by Dr. Travisano and colleagues.
• Dr. Travisano's faculty website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

Today Dr. Joseph Zackular, Assistant Professor of Pathology and Laboratory Medicine at the Perelman School of Medicine at the University of Pennsylvania, joins the #QualityQuorum to discuss some fascinating microbiology involving the bacterium Clostridiodes difficile (also known as C. diff), which can cause disease in infants, the elderly, and the immunocompromised.

Host: Mark O. Martin

Guest: Joseph Zackular

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Become a patron of Matters Microbial!

• An essay about siderophores in bacteria.
• The Giant Microbes "Cdiff" toy.
• The website of Dr. Patrick Schloss.
• A link to the #MattersMicrobial podcast with Dr. Schloss.
• An overview of Clostridioides difficile from a patient / physician perspective.
• A review article of research involving Clostridioides difficile.
• An overview on polymicrobial diseases.
• A wonderful opinion piece by Dr. Arturo Casadevall regarding the term "pathogen."
• An overview of Enterococcus in the gut microbiome.
• The technology of imaging mass spectrometry.
• An article on Stickland fermentation of amino acids among gut bacteria.
• Work by Dr. Zackular and colleagues discussed in this podcast, describing how FMT can be used as a treatment.
• Work by Dr. Zackular and colleagues discussed in this podcast, describing how different members of the host microbiome interact, and how that relates to disease.
• Work by Dr. Zackular and colleagues discussed in this podcast, describing the role of amino acid metabolism to changes in microbiome structure.
• Work by Dr. Zackular and colleagues discussed in this podcast, describing how Enterococcus can modulate the disease causing characteristics of C. difficile.
• An interesting paper showing that polymicrobial effects are more common than expected.
• An article arguing that there is no single "healthy" microbiome.
• A lovely primer on this topic for most nonmicrobiologists.
• An overview on fecal microbiome transplants and the treatment of human disease.
• The website for the Center for Microbial Medicine at the University of Pennsylvania.
• A great video by Dr. Zackular and colleagues, well worth your time.
• Dr. Zackular's academic website.
• Dr. Zackular's laboratory website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]