The Lettuce, the Phage and the Microbe


Rod-shaped E. coli bacteria nestle inside a minute pore in the leaf called a stoma. E. coli bacteria on lettuce by AgriLife Today (2010) CC BY-NC-ND 2.0, on Flickr

In the days before the Thanksgiving, the Centers for Disease Control in Atlanta released a stark warning: Don’t eat the Romaine Lettuce. The agency was investigating a a multi-state outbreak of a strain of bacteria called
Escherichia coli
, which in addition to causing diarrhea and other unpleasant gastrointestinal symptoms, can also cause acute kidney failure and death.

The suspected carrier of this virulent microbe: Romaine Lettuce.

The Suspect! Romaine Lettuce by Rainer Zenz (2006) CC-BY-SA-3.0 from Wikimedia Commons

The internet has been awash in memes highlighting the lethality of poor Romaine lettuce, which is normally lauded for its tastiness in salads and nutrition content. But don’t just blame it on Romaine!

This is actually a interesting ecological saga of microbial romance, ruminant guts, and watershed management intersecting with our salad plates.

Let’s start with E. coli.

Colorized scanning electron micrograph of Escherichia coli, by NIAID (2013) CC By-2.0 on Flickr

E. coli is a type of bacteria that normally lives in the intestines of humans and animals. Most E. coli strains are harmless, and actually provide a protective role in the intestine by preventing disease-causing bacteria from moving in. They also help make Vitamin K. Scientists love using E. coli an a model bacteria in the lab. It is easy to feed and grow!

On an environmental scale, E. coli can get transferred from its home in the intestines to the larger world via … poop.

So how do the bacteria make it from poop into another intestinal home? Water! Humans came up with this ingenious idea of making our poop go away by sending it into flowing water.

Bye! Wolfmann (2018) CC BY-SA 4.0, from Wikimedia Commons

We have mitigated the E. coli transfer somewhat by treating our sewage (which I realize is just a fancy word for poop-water) before dumping it out into rivers and lakes. However, leaky septic systems and intense storm overflow events may cause sewage to bypass the treatment process and end up in the water anyway. Animal poop lying around on the ground (or in big lagoons on a cattle feedlot) may get washed into waterways by rain.

Belleville Lake beach closed due to high bacteria levels (E. coli) in the water. Local sources of E. coli bacteria include leaky septic systems and storm runoff containing animal poop. by PPJ (2018) CC BY SA 2.0.

Some of this E. coli-laden water makes it to a farm irrigation system, where it waters the the lettuce. And leaves behind a nice film of E. coli bacteria in search of a new intestine to live in.

Most E. coli versions aren’t dangerous. This water-borne bacteria becomes a problem when the kinds of E. coli venturing forth into the water include less-benign, disease-causing versions. These pathogenic strains secrete toxins that can damage tissue cells in the human body. Scientist can track these variants by their serotype designations (i.e. O157:H7) that refer to the arrangement of sugar molecules in the E. coli bacterium cell wall.

So where do the toxins come from? For example, E. coli O157:H7 produces a Shiga toxin that damages intestinal cells to cause bloody diarrhea, and potentially even kidney failure by damaging the tiny kidney capillaries with the debris of broken cells. Shiga toxin was first identified in the bacterium Shigella dysenteriae, a pathogen that causes dysentery (severe diarrhea.) Producing bacterial toxins may confer evolutionary advantages over non-toxin mediated infection by increasing the virulence of the bacteria, as well as increasing transmissibility of bacterial particles via diarrhea output.

“You have died of dysentery.” Screenshot from classic Apple II educational computer game, Oregon Trail.

But how did the genes for making Shiga toxin make it from the genome of Shigella into its cousin E. coli?  Through bacteria sharing genes via bacteriophage, or its less sexy name, Transduction.

Bacteriophages (virues that infect bacteria) are often floating around places like intestines where lots of different kinds of bacteria are hanging out.

Just going through a phage.  Bacteriophage exterior by Adenosine  (2009) CC BY-SA 3.0  from Wikimedia Commons

In this case, a phage may have transferred a snippet of genetic material containing the toxin-coding region from a Shigella spp. bacterium into an E. coli bacterium, granting a previously benign microbe an infectious advantage. (Tangent: Bacteria can also use this process to transfer genes for antibiotic resistance.

Okay, so now that we have a Shiga-toxin producing strain of E. coli, how did it end up on the Romaine lettuce? Are sick humans just pooping indiscriminately all over our lettuce fields (or within the watersheds that flow into irrigation systems?)

Possibly,  however a more likely culprit has a ruminant digestive system and hooves:

Serious, serious cattle by J.C. Burns (2017) CC BY-NC-ND 2.0, on Flickr

Turns out that cattle (and other ruminants such as deer, goats and sheep) are asymptomatic carriers of the Shiga-toxin producing strains of E. coli. The bacteria do not make the cattle sick, possibly because they lack specific cell receptors the bacteria use to attack blood vessels.  The cattle are a living reservoirs for these E. coli strains, as well as contributing to literal reservoirs for the bacteria in the form of waste retaining ponds full of cattle poop. That poop-carrying water is just a rainstorm and a watershed away from making its way to the lettuce fields.  Voila, you’ve got an epidemic of foodborne illness!

While it’s tempting to reduce the media narrative to “Romaine Lettuce is now deadly,” I think it’s much more interesting to look at the interconnections between all of the players in this story (The Cattle, the Poop, the watersheds, the E. Coli and the bacteriophage). The science is much weirder than you might imagine.


World Soil Day – Dec. 5th

harvesting sweet potatoes in field
Harvesting Sweet Potatoes in Mechanicsville, VA. Lance Cheung, U.S. Department of Agriculture (2013) CC BY 2.0, on Flickr

In case you missed it, this past Monday, December 5th, was World Soil Day! Yay!

In this Onion piece, Scientists Make Discovery About World’s Silt Deposits But Understand If You Aren’t Interested In That. Similarly, you might gaze glassy-eyed at my exclamatory proclamation about soils, and move on to celebrity gossip or waffle recipes.

However, here at the Protopian Pickle Jar, I’m offering some reasons for blog-reading, clothes-wearing, oxygen-breathing, food-eating humans to get excited about soils!

Everything We Eat and Everything We Wear!
In TEVA, we taught the kids a chant: “Sun, Soil, Water, Air! Everything we eat and everything we wear!” Then, we challenged them to come up with an item that did not derive its existence from any of those things. (It’s rhyming version of the adage I learned in my undergrad earth science classes, “If it’s not grown, it’s mined.”) No matter what they came up with (plastic dinosaurs, fuzzy socks, water bottles) we were able to trace back its origin to a natural resource.

Every piece of clothing I’m wearing (including dyes, zippers, elastics and snaps)from my cotton underwear to my wool socks to my poly-blend shirt ultimately began with the soil. (Synthetics made from petroleum-based chemicals are mined from oil, which develops from long-dead marine algae, a kind of deposit of ancient solar energy.) Every item of food I eat – fruit, veggies, grains, meat, dairy, mineral supplements- began with the soil.* (Even food that comes from marine ecosystems is still linked to and dependent upon terrestrial soils.)

Ecosystem Services
While I was busy playing with the internet, earth’s soil bacteria are running the planet’s biogeochemical cycles. These soil-dwelling microbes are quietly moving the Earth’s carbon, nitrogen, oxygen, sulfur (and other elements!) through the biosphere using a series of metabolic handoffs. The bacteria may just be trying to get some energy (we might say, “Eat!”) by moving a few electrons around. Collectively, these reactions produce the atmosphere we breathe, the greenhouse gases and feedbacks that drive our habitable global climate, and fix the soil nutrients required for plants to photosynthesize.

One example of how microbes affect our environment : During the Biosphere 2 experiment, scientists sealed inside the closed environment faced incredibly low oxygen levels (dropping from ambient 21% to 14%). Barely able to breathe, the scientists could not sustain the daily activity required to continue the project. Biosphere 2 designers did not account for high levels of microbial respiration of the organic material in the Bio2 soils that were pulling oxygen out of the enclosed environment.

The Final Frontier
Not only do we rely on these soil microorganisms for the air we breathe and the food we eat, we don’t know very much about them. From the UN FAO Soil Portal: “Soil biology plays a vital role in determining many soil characteristics, yet, being a relatively new science, much remains unknown about soil biology and about how the nature of soil is affected.” We’re still learning how human activities affect soil microbes, often in unintended ways.

For more information, check out the Soil Science Society of America’s blog Soil Matters, Get the Scoop!

Beneath the Surface

Abstract by Andy Maguire (2016) CC By 2.0, on Flickr]
Abstract by Andy Maguire (2016) CC By 2.0, on Flickr

While I was watching the surface-bound shenanigans of other humans via Facebook, soil microbes have been steadily plugging away,  keeping the bio-geochemical cycles of the planet going.   A team led by scientists at the Lawrence Berkeley National Labs & UC Berkeley has reconstructed the genomes of 2500+ microbes that live in soil and groundwater of a Colorado aquifer. In addition to identifying (and naming) new phyla of bacteria, the researchers found new insights into how bacteria work together to power the carbon, nitrogen and other chemical cycles of the entire planet!

The paper appears online in Nature Communications. The soil microbiome census, using genomic techniques (“terabase-scale shotgun DNA sequencing”) to identify new taxa of bacteria in the samples, is especially important because while 1/5th of the Earth’s biomass exists underground, we still don’t know very much about about these organisms.

Once the genomes of the different bacteria were sequenced, scientists combed the data looking for genes related to microbial energy metabolism (gaining/losing electrons, carbon and nitrogen fixation, etc). By looking at which microbes with specific abilities were present in the samples, the researchers could infer what reactions (and combination of reactions) are taking place community-wide.

These combination of reactions are called “the metabolic handoffs.” Organisms may only have one or two metabolic tricks up their own sleeves (okay, I know microbes have neither hands nor sleeves, but bear with me here.) However, in the community of subterranean microbes, there are *a lot* of metabolic abilities across the different species. The waste products of one organism are food for another one that has the ability to extract energy from it. Or, as we liked to say as Teva Educators, “Waste equals food! Waste equals food! Waste equals food!”

TL;DR From the Press Release:

The scientists found the carbon, hydrogen, nitrogen, and sulfur cycles are all driven by metabolic handoffs that require an unexpectedly high degree of interdependence among microbes. The vast majority of microorganisms can’t fully reduce a compound on their own. It takes a team. There are also backup microbes ready to perform a handoff if first-string microbes are unavailable.

Previously unnoticed by humans, soil microbes are hard at work shuffling electrons as a team to keep the carbon, nitrogen, sulfur and hydrogen cycling around our biosphere. They deserve a shoutout from this grateful macro-organism.

Tangents for this Post:
Okay, I wasn’t just watching humans on FB. Other organisms include:
Glockenspiel-playing chickens
Rescued Cows
Pigeons (here and here)
Left-handed snail romance
Ticklish Rats

Building biofilms

B0008256 Confocal micrograph of Bacillus subtilis
Confocal micrograph of Bacillus subtilis Credit: Fernan Federici & Jim Haseloff. Wellcome Images. CC BY-NC-ND 4.0, via Flickr.

I’m pretty amazed by microorganisms. They’re tiny, invisible to our eyes, but are hugely influential in the state of our bodies, our food and in making the Earth around us a habitable place for us to to live. I’ve recently been reading up on structures microorganism such as bacteria and fungi create. One that’s getting a lot of my attention is the humble biofilm.

Bacteria (and other microorganisms)that might be otherwise free-floating, form biofilms by sticking to a surface. New members join in, sticking to the already adhering cells. The cells of a biofilm often embed themselves in goo they secrete called the extracellular polymeric substance (EPS). The newly formed biofilm is more resistant to being moved away or to attack by antibiotics.

Biofilms are everywhere! The slimy stuff that you brush off your teeth in the morning. Biofilm. The scummy goo that clings to pebbles in streams. The nitrogen fixing film that clings to the roots of plants in soil. Also, scientists are just starting to understand how biofilms play a role in human diseases such as  sinus infections and how beneficial bacterial biofilms in the appendix may protect the intestines.

For example, researchers at Case Western University recently discovered how three different microbes- bacteria E. coli and S. marcescens, and the fungus C. tropicalis – work together to form a symbiotic biofilm in the intestines that play a role in Crohn’s disease. The biofilm adheres to the tissue of the intestines and triggers the inflammation associated with Crohn’s disease.

Understanding how different microbes work together under specific environmental triggers may lead to ways to better ways of healing infections and protecting our bodies from pathogens. Additionally, we may gain more insight into how microbial ecosystems work in our soil, water and air.

A post about pickles

Pickles in jars
Pickles!! by M Prince Photography (2014) CC-BY-NC-ND 2.0 via Flickr.

For a blog that calls itself “Protopian Pickle Jar,” it occurs to me that I rarely post about fermented vegetables.

However, last week, I got a real hankering for pickles. Not just any pickles from the grocery store, mind you, but an authentic deli-style, non-vinegar based lacto-fermented pickles. Like the kind that used to come from a pickle barrel on the Lower East Side. Or that we would make in the Picklearium (aka Center for Cultural Proliferation) at Isabella Freedman and devour off the IF salad bar. Surprisingly, these are kind of hard to find. They do sell them in the “refrigerated kosher section” at the grocery store. I bought 2 jars and started eating them almost immediately upon returning home.

Maybe it was all the salt-loss from our 105 deg F heat index weather. Maybe my gut microbes were calling out for replenishment. Maybe, as my grandma would said, I was in search of a “cheap drunk,” that the biting taste of fermented pickles provides.

Internet-provided potential pickle-hankering insights:

In her Tablet Magazine article, “A Barrel Full of Jewish Flavor,” Marjorie Ingall provides some context for the yearnings of her pickle-fiend children.

But not everyone viewed pickles as a benign and tasty foodstuff. …WASPier Americans saw the pickle as morally suspect. [Jane Zigelman] quotes physician and author Dr. Susanna Way Dodds, who wrote in 1883: “The spices in it are bad, the vinegar is a seething mass of rottenness … and the poor little innocent cucumber … if it had very little ‘character’ in the beginning, must now fall into the ranks of the ‘totally depraved.’ ”

Jews did not get this memo. When Lower East Side public schools let children out at lunchtime, kids ran en masse to the nearest pushcarts. Social service workers were horrified. “Pickles were seen—by a nation on its way to Prohibition—as a compulsion for those too young to drink alcohol,” noted Ziegelman. They were often classified as a “stimulant,” along with coffee, tobacco, and whiskey. … The City’s Board of Education established school lunch in large part to wean immigrant children away from their degenerate pickle lust.

Mmmm, degenerate pickle lust.

But there may also be a serious psychological component to my yen for fermented veggies.

Peter Andrey Smith, in the New York Times Magazine, examines how bacteria in your gut can affect your mood. In the study of “psychobiotics,” scientists recognized that communities of microbes living in our not only do things like create vitamins, but they also secrete neurotransmitters that can affect our moods. Nurturing the bacteria that release these chemicals may help alleviate depression and anxiety in their human hosts.

In addition, researchers at William and Mary found an association between increased consumption of fermented foods and reduction of social anxiety in genetically-prone young adults.
While there is much research to be done in this intersection of psychology and delicious, delicious fermented foods, I can testify that I was a pretty happy human when consuming vast quantities of fermented vegetables from the Isabella Freedman salad bar. (I see a potential sociological/microbiological study to be conducted by generations of future Adamahniks…)

Finally, the New York Times Video profiles Sandorkraut: A Pickle Maker, a short documentary (~12 min) by Ann Husaini and Emily Lobsenz about legendary (in Adamahnik-circles) pickling enthusiast and writer Sandor Katz.
I first became aware of Katz’s work at Adamah (his book, “Wild Fermentation” is recommended reading for incoming cohorts.) The filmmakers explain, ” While empowering his followers to try their own hand at fermenting, he is not only reinvigorating an ancient cultural practice, but also reminding us what it means to be in a symbiotic relationship with microorganisms that have evolved alongside us throughout history.”

Invisible You – the Human Microbiome

Interesting exhibit at intersection of art and science at the Eden Project, a conservatory/science museum in the UK.

Wellcome Trust Blog

This month the Eden Project launches a new permanent exhibition dedicated to the entire world that exists within us – Invisible You. The Human Microbiome. Science project manager from Eden, Gabriella Gilkes, tells us about many happy hours spent marvelling down the lens at that fantastical world, and how it is a dream come true.

Microbiological Portrait - Mellissa Fisher Microbiological Portrait – Mellissa Fisher

 ‘I am afraid that the experiments you quote, M. Pasteur, will turn against you. The world into which you wish to take us is really too fantastic.’  – La Presse, 1860

Louis Pasteur’s discovery of ‘tiny animalcules’ down the lens of his microscope changed the world of biomedical science. That same world is changing again today through the scientific discoveries of the human microbiome. The advent of genomics, with cheaper and easier methods of DNA sequencing have allowed the study of that microbial ecosystem – the invisible…

View original post 611 more words

Microbes of the Earth!

Wrinkled landscape along mountain
Hues of the Earth by Dru! (2014) CC BY-NC 2.0 via Flickr.

As a humans, we tend to focus on microbes that live in and on human bodies. I wanted to write about some of the amazing things we are discovering about the microbes that live on the skin of the Planet Earth.

Rhodococcus rhodochrous
Forest Service scientists in Missouri have used a common soil bacterium, Rhodococcus rhodochrous, to develop a treatment for White-Nose Syndome in bats.

Lori Cuthbert reports for Discovery News, “the researchers grew the bacterium on cobalt, which produced so-called volatile organic compounds (VOCs) that stop the fungus [that causes White Nose Syndrome], Pseudogymnoascus destructans, from growing. “The amazing part about this is that these compounds diffuse through the air and act at very low concentrations, so the bats are treated by exposing them to air containing the VOCs (the compounds do not need to be ‘directly’ applied to the bats),” according to a USFS press release.”

White Nose Syndrome has been a threat to hibernating bat populations in North America since 2006, when it was discovered in the Northeastern U.S.. About 6 million bats have died from WNS.

Mycobacterium vaccae
I’ve always wondered why playing in the dirt made me feel so happy and relaxed. Researchers think that ingestion of soil microbe Mycobacterium vaccae may boost gardeners levels serotonin and norepinephrine, neurotransmitters responsible for improving mood. When I first saw this posted on Facebook, I thought, “This has to be one of those weird hippie hoaxes that float around the internet.” But then I found the paper detailing the mouse studies showing that mice who ingest live M. vaccae have less anxiety and are more effective at solving a maze. I will continue to dose myself with soil at my summer job with a community garden.

Chemoautotrophic Brine-dwelling bacteria
For a detour into some truly Lovecraftian microbial performance art, brings us the Origins of Antarctica’s Blood Falls. The red color of the water is due to the microbial inhabitants of the very salty water that wells up from under the glacier, who metabolize iron and sulfur compounds.

Scientists think that Blood Falls may just be a small outlet of a much larger sub-glacial super-salty ecosystem. Studying extremophile microbial communities like the one at Blood Falls could offer insights into what kind of life might exist in harsh environments on other planets.