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…

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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.

Ticks & Their Mysterious Microbes

Borrelia burgdorferi by NIAID (2011) CC BY 2.0 via Flickr.
Borrelia burgdorferi by NIAID (2011) CC BY 2.0 via Flickr.

While I’m browsing Facebook, I sometimes glance at the topics in the “Trending” column in the upper right hand corner of the homepage. While they are usually related to celebrity gossip or disasters of some kind, today I was intrigued a geographically relevant piece of click-bait: “Powassan virus: Rare Virus Spread by Ticks Found in Southern Connecticut.”

As an environmental educator in the woods of Connecticut, I have encountered my share of ticks – those shameless, blood-sucking arthropods that are carriers for a veritable zoo of exotic microbes. Our usual practice to avoid ticks was to wear long sleeves and long pants, tuck pants into socks (aka “cool pants” or “forest pants”), and do nightly tick checks before going to sleep. If we did locate a tick (or one of our students did), there was often a panicked rush to the medic to remove the critter in an appropriate and safe manner.

Our primary concern with tick bites was the transmission of Lyme disease (caused by the spirochete Borrelia burgdorferi). When I was an Adamahnik farmer in the Spring of 2013, I was pretty sick with symptoms that presented as extreme fatigue, fever and joint pain. When I went to the local ER, they ran a test for Lyme, which came back as negative. However, the doctor explained, due to the high prevalence of Lyme in the area and high rate of false negatives for the lab test, they were still going to put me on a 2 week course of antibiotics (doxycycline).

At the time, I think the side effects from the doxy made me feel sicker than I did initially! I was still sick a week later (when antibiotics should have started to have some effect), so I went back for additional testing. Those blood tests also came back negative, and the doctor discontinued antibiotics. I was still pretty tired, but eventually started feeling better.

I can’t say if I had Lyme or one its tick-bite-transmitted fellow travelers (also treated with doxycycline) or an even more mundane human-transmitted bug. I am really, really glad I eventually got over it.

The presence of emerging tick-borne viral infections such as Powassan virus strikes fear into the hearts of campers, educators and parents (not to mention the “ick” factor associated with being bitten by creepy-crawly critters.) You can’t treat them with doxy – medical treatment for this potentially fatal virus is limited to supportive therapy such as IV fluids and respiratory ventilators. There are also potential neurological side-effects of the virus.

Before panic sets in, it is helpful for me to remember a few things: “Emerging” doesn’t mean that the viruses are particularly new – they’re just new to being detected by science. Lyme Disease was described as a distinct disease in 1976 when doctors identified a cluster of kids with arthritis symptoms around Old Lyme, Connecticut. Borrelia burgdorferi, a spirochete shaped kind of bacteria, was identified as the infectious agent in 1981. Modern DNA analysis on ticks gathered in the 19th and 20th indicated infection with B. burgdorferi, and it is likely that the bacteria has been around in ticks and their bitees for thousands of years (Steere, Coburn & Glickstein (2004)).

The oldest known human infection with Lyme is Otzi the Iceman, a 5300 year old mummy discovered in the Alps. Scientists have detected bacteria of Borrelia sp. in a 15 million year old tick fossilized in amber.

Emerging tick-borne infections are not limited to the Northeast US. Back home in KS, a Bourbon County farmer came down with a mysterious virus, which later turned out to be an exotic-sounding Thogoto virus new to science, which researchers linked to ticks.

The Cary Insitute of Ecosystem Studies in Millbrook, NY studies the ecology of emerging infectious disease. Climate change and human land use changes all impact ticks, their microbes and other hosts, than can affect the spread of these diseases to humans. Check out their resource section for fascinating information on the ecology of tick-borne diseases!

For now, I’m tucking my pants into my socks.

Tangents for this post:

The History of Arthropod-borne Human Diseases in South Carolina (I know it’s not CT, but it’s still fascinating.)

The Outdoors Hates You (Wired Magazine, 2012)