Author Archives: Mykl Nelson

Streptomyces: what’s not to love?

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© Jones et al/eLife under CC BY 4.0

We live in a world where we’re recognizing and discovering an ever-more complex and interwoven web of life—this vast ecology of our planet. We can see that life has taken many different routes to find success, and we call these paths ‘kingdoms’: animal, plant, fungui, protist, archaea, and bacteria. While we belong to and often focus on the first kingdom—that of animals—we are at what is only the beginning of discovery of the benefits we can reap from those in the last kingdom; we can harness the potential of bacteria to our good.

I want to tell you all about the bacterial genus Streptomyces. The genus is noted for the scent of their spores. You know that smell after a rain? That’s ‘petrichor’, ancient Greek for ‘rock’ and ‘ethereal blood of the gods.’ This smell is from a mix of compounds, but a significant contributor is geosmin, itself a by-product of the hydrophobic spores atop the aerial growth of this filamentous bacteria are launched from the earth with the force of raindrops striking the ground. The average human nose is incredibly sensitive to this chemical; we’re able to notice it as faintly as three parts-per-trillion—like a single drop in 40 Olympic swimming pools! Geosmin is also the reason we like the smell of freshly-dug earth, and it’s responsible if there’s a ‘muddy’ taste in your fish.

But there’s plenty more to love than just a pleasant smell. Most of its many, varied species are found living in soils the world over. They are commonly aerobic and produce exudates which resemble mycelium-like networks throughout the substrate in which they live. These exudates and the volatile organic compounds they off-gas are created in a category called secondary metabolites.

By Anne van der Meij, Joost Willemse, Martinus A. Schneijderberg, René Geurts, Jos M. Raaijmakers & Gilles P. van Wezel - [1]doi:10.1007/s10482-018-1014-z, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=94443322

Living organisms create secondary metabolites as interactions with their environment. These compounds are not strictly required for survival. Sometimes called ‘relational’ or ‘ecological’ interactions, because it’s facilitating the meeting of the lifeform with the greater world. Contrast this to primary metabolites, which are required for growth, development, and reproduction.

How Streptomyces offers such tremendous potential

  • The great genetic variety it holds as the most populous genus in its phylum, with more than 700 species cataloged thus far. There are even species which rank among the longest genomic strands in all the bacterial kingdom: S. violaceoruber with 8.7 million base-pairs (Mbp) and S. scabiei at a whopping 10.1 Mbp.
  • Add to this the knowledge that Bacteria have more protein-coding genes from Eukaryotes, and that that gulf widens as genomes lengthen, and we find a very complex and active set of organisms.
  • A final point to the activity of the Streptomyces genome: it averages 12% of its protein-encoding genes dedicated to secondary metabolite production, a “high proportion” when compared to the rest of the kingdom (Nikolaidis et al., 2023). This all paints a picture of Streptomyces having a strong ability to affect the world around it.

Global focus on the genus

The discovery which launched Streptomyces into global focus was the creation of streptomycin, an antibiotic which helped treat tuberculosis. This compound was isolated from S. griseus in 1943 and won the Nobel Prize for Medicine in 1952. Various extracts and synthetizations from this genus have focused on the antimicrobial properties and their application both for human health as well as pesticidal controls for use in agricultural production.

However, the global zeitgeist of our time is beginning to focus our attention inwards, to examine what we might do to change our bodies from within to better fit their environment without. Of notable interest is what’s been termed our ‘microbiome,’ all the various microscopic life inhabiting our very bodies. We’ve already scoured the genetic potential of Streptomyces for over 100,000 applications of reducing harmful microbial activity in humans and for agricultural chemicals (Alam et al., 2022). What if there is still more to be gained from this genus, and what if the methods might be different than laboratories and synthesized extracts?

Environmental interactions between microbes & humans

Exposure to different environments and inputs can change the various microbiomes in our bodies. We know the gut microbiome is tremendously affected by both temporary and long-term dietary options (Leeming et al., 2019).

Scientific experiments continue to investigate what effects various environmental exposures have on human health. In particular, investigations into affecting the microbiome on human skin are still ongoing. Our skin interacts with the world before and one behalf of all our other organs, and so might hold great potential for affecting reactions or purposeful changes to each of our skin’s microbiomes.

One recent study (Mhuireach et al., 2022) hypothesized that the hands of gardeners would be a likely place for soil-to-skin transfer of microbial populations. Complications, including hand-washing, confound the issue. But they did find Streptomyces among the top ten most abundant genera found in urban garden sample soils! The authors go on to emphasize the importance of soil/skin contact, citing Roslund et al. (2020) who found that biodiverse playgrounds improved children’s health and immune-function. Such findings reinforce efforts— at to get children outside and interacting with curated, natural play environments.

Further reading

Read more about this research on human health and garden soil contact, fresh from Oregon State University’s Garden Ecology Lab.

And now, you can carry on with your day knowing you’ve got about as much breadth of knowledge of Streptomyces as possible without beginning to delve into specific species. Thanks for reading!

Astroculture 101

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#SpaceFlower, a zinnia grown on the International Space Station (ISS). Image courtesy of Wikipedia Commons.

Read this article to learn:

  1. The diversity of crops grown in space
  2. First food crop grown in space (onion)
  3. What ‘lightsicles’ are
  4. NASA and air purification
  5. Space Seeds™
  6. The primary problem facing astroculture (irrigation) and why (microgravity)
  7. First space-grown vegetable eaten in space (lettuce)
  8. Expansion of production area in astrocultural trials (1000x increase)

Why astroculture?

Astroculture: growing food in space! ‘Sure, cool concept,’ you might be thinking, ‘but what does this have to do with garden ecology?’ Well, the tight confines onboard spacecraft are more constraining than most any compact, dense city on Earth could claim. Perhaps only those in capsule-style housing can begin to appreciate the cramped living quarters of astronauts.

The effort to grow food in space is about more than creating a system which can reduce the need for supply shuttles from Earth. Astroculture is the proving ground for compact, synthetic production environments. Any experiments are as isolated as possible. This has resulted in NASA (or the National Aeronautics Space Administration) and other space agencies playing a central role in the development of new technologies to support the growth of plants in artificial conditions.

From 1970 to the present there have been:

  • 21 plant growth chamber design systems
  • 50 different cultivation experiments
    • across ~40 species

The first food crop grown in space were onions in July, 1975, by cosmonauts Klimuk and Sevastianov during the Salyut space program of the Soviet Union. They aimed a few bulbs from the crew’s on-board lighting system at the seeded trays, but nothing more. Some plants did germinate, and for the first plants humans have put in space, that’s a significant enough accomplishment on its own. One of the limitations to this and all the other experiments at this time were the short flight durations. Only two years previous, the record time in space was set at just eight weeks—by the United States.

NASA pioneered research into intra-canopy lighting with a technique they called ‘lightsicles’—poles of lights which lit ever-higher as the plants grew taller. This idea itself isn’t new. Experiments ‘on the ground’ had shown that shading out lower leaves will lead to senescence or the decay and loss of those leaves.

See, the problem wasn’t in supplying the right spectrum of light—controlled conditions in space quickly produced plants with lush growth in their upper canopy. The problem they quickly realized was a shading out and subsequent decay and loss of leaves below the plant canopy. Lights like high-pressure sodium or metal halide were simply too hot to be placed within the plant canopy itself. This heat also meant there was significant distance between light source and plant. This empty space between light and plant was the most the aeronautic agencies were willing to sacrifice to carry out these agricultural experiments. They definitely were not going to now account for empty space between lights on multiple sides of a plant’s growing area!

The scientists at NASA were ready and waiting for something better. They quickly embraced emerging technologies like LEDs for all the same reasons Earth-bound producers have: they’re energetically efficient with little waste heat all in a compact design. This lighting design and strict need for density meant NASA also found itself on the frontier of vertical farming innovations.

Experiments in astroculture, of growing plants in space, mostly boil down to understanding plant function in microgravity. Be this on a shuttle, station, Luna, or Mars, all locations exert less gravitational force than the Earth.

Steve Swanson tending Romaine lettuce aboard the ISS. Image courtesy of Wikipedia Commons.

In 1982 Arabidopsis was successfully grown seed-to-seed in space then germinated back on Earth. This was proof of concept, plant life off-planet was possible. But the success rate was only about half, and all with a simple, model plant. This is like sending mice into space before chimps or humans. Subsequent experiments of greater scope found microgravity seriously impedes and sometimes even alters plant physiology.

Now, let’s talk about carbon dioxide for a second. Plants breathe the air, just like us, but they’ve got a use for CO2: it plays a key role in photosynthesis. Atmospheric enrichment of CO2 within closed production environments has been practiced since the 1970s. A limited set of experiments in 1989 found CO2 supplementation also improved a great number of factors in microgravity. But this might not be so groundbreaking or critical to astroculture. This is still well before the current field of controlled environment agriculture had developed. We now see carbon dioxide as key to increasing plant growth but also recognize a number of other inherently limiting factors within artificial environments. Put shortly: most plants, on terra firma or in outer space, do better with CO2 supplementation.

What has emerged as uniquely problematic in microgravity is irrigation. Maintaining a reliable range of moisture in the root zone has become the critical adaptation of astrocultural production. I’m sure we’re all familiar with water adhesion and its surface tension. On the planet’s surface, adhesion and tension are frequently dwarfed by the force of gravity itself. This pulls water into the soil, pulls water through the soil, and actually plays a large part in the water cycle itself. In microgravity, adhesion and tension begin to exert their dominance. It’s difficult to direct and instead will cling to most surfaces it touches. So when water is applied to the root zone, it clings to the roots. Many plants end up anoxic: they’ve drowned in their flooded conditions.

The latest developments are using porous tubes and/or plates to slow the delivery of water and nutrients. It seems like, if we can’t stop water from coating everything it touches, the plan is to greatly restrict its flow and access to non-target areas. A slow osmosis via a clay pipe works as a bottleneck to prevent drowning.

In the early 2000s on board the International Space Station, astronauts successfully completed two generations–that’s seed-to-seed,-to-seed—of soy: Space Seeds™. Ok, they’re not really trademarked, but it’s fun to call them ‘space seeds.’

Astronauts Scott Kelly and Kjell Lindgren eating the first leaves of space-grown lettuce. Image courtesy of NASA Johnson on flickr.

On August 10, 2015, NASA astronauts were officially allowed to eat space-grown produce for the first time: some leaves of lettuce.

In addition to innovative irrigation control techniques, the latest astrocultural experiments have just recently begun to increase in scale. The first growing area, in 1971, was a mere 10cm2. Little gains were made until 2014 when they achieved 1700cm2 of production area by using an ‘inflatable’ model which astronauts assembled once in outer space. The latest plans utilize a vertical racking system and aim for a full square meter (10,000 cm2).

Well, that’s a lengthy enough primer on growing plants in space. There’s plenty more to be told and a wealth of discoveries yet to be made. If you’re interested in some further reading, perhaps try some of these options.

A grand summary of astroculture is nicely reported in Zabel et al. (2016) http://dx.doi.org/10.1016/j.lssr.2016.06.004

Read a report from NASA (2010):  https://www.nasa.gov/mission_pages/station/research/10-074.html

Space Gardening with NASA: https://science.nasa.gov/science-news/news-articles/space-gardening

There are some visually pleasing, incredibly informative graphics here: https://ntrs.nasa.gov/archive/nasa/casi.ntrs.nasa.gov/20160013269.pdf

ISS: from NASA to Napa  https://www.nasa.gov/mission_pages/station/research/news/ADVASC

What’s next in urban agriculture?

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What’s next in urban agriculture is going to take place in the cityscape we’ve all heard described before: two-thirds of the world’s 10 billion people will be living in urban areas—mostly across 40 or more mega-cities around the globe—by the year 2050. You’re probably bracing yourselves, waiting for either a list of depressing facts or some ‘hail Mary, technology can save us all’ kind of talk.

Not today. Today we think of green pastures amid concrete jungles.

Urban agriculture is the production, processing, and marketing of produce based on living systems from the land or water located throughout urban and peri-urban areas. Anyone cropping food, flowers, fiber, feed, or herbs from their corner of their city is engaging in a small-lot, local agriculture with an utterly minimized transport chain from grower to eater. These green, vegetative, productive spaces within city landscapes can provide valuable ecosystem services: floral habitat for pollinators, stormwater management, and even mediating the temperature extremes of urban heat islands. People often find urban gardens foster cross-cultural and multi-generational spaces for social interaction. These disparate green spaces, however small each might be, aggregate to large areas across metropolitan regions. A conservative 20 acres of urban gardens in Portland, Oregon, fifty-one acres in Chicago, Illinois, and a whopping 120 acres in Madison, Wisconsin!

More good news: these growing plots don’t stop at the hobby level. Across the United States, counties with significant urban encroachment also produce the lion’s share of fruits, nuts, berries, and vegetables, as well as accounting for most of the farm-gate value of these goods.

But now we come to a bit of bad news, unfortunately. Because while these urban-adjacent farmlands produce the most food in the most high-value agricultural markets, their days are numbered. While not as romantic as the Amazonian forests, some of the most fertile land across this country is being consumed and paved over by sprawling cityscapes. This plight is common due to a mismatch between those who own deeds to land and those who seek the land’s productive agricultural use. Countless urban spaces have seen their productive days ended when the land became valuable enough for someone to decide to sell it off for development.

This is relevant to us today because growing food within the cities themselves is one of the easiest ways to increase our resilience against disruptions to our modern, industrialized food supply chain. Just as victory gardens stabilized many citizens through global wars, we too can use our land and our labor to renovate vacant land in shrinking cities like Baltimore, Cincinnati, Philadelphia, Detroit, and the others which are sure to follow the implosion of the last economic boom.

New American farmers—entrepreneurs all—are literally working overtime to access the new niche markets which are springing up across modern urban centers. They’ve surveyed the future and invested in becoming extremely specialized producers of fine agricultural goods. To me, that sounds like taking quite chance: betting it all on a small market with few, discerning clients.

But we might gain some of their confidence if we examine some of their assumptions. Barring extreme, world-altering scenarios like an extinction-event asteroid impact, human population in 2050 is pretty well guaranteed at this point. It’s only thirty years away and average birthrate is not quickly changing. This also means we can be pretty secure in the assumption of continued urbanization. The current population density alone is enough to birth enough humans to further compound the growth of urban centers. This makes the relevance of things like tele-commuting more a question of degree of urban density and sprawl growth. Lastly, many farmers are seeing their emotional investment in the quality of food finally reflected in public policy.

A proposed “new food equation” predicts the end of ‘cheap food’ as global calorie production has been secured. The focus is now changing to include quality, or the nutritional content of foodstuffs. Nations recognize that food production remains a matter of national security in a number of ways. First as a matter of imports and exports. Self-sufficiency means not relying upon another nation to feed your populace. Excessive production enables exports which not only enrich a nation but can operate as the same leverage which is being avoided in the previous example. Lastly, public officials and private people are beginning to attribute more health complications and costs to dietary factors like obesity or malnutrition.

New urban farmers are exploring many novel approaches to urban agricultural production. Controlled Environment Agriculture (CEA) is taking protected cultural growing techniques and implementing them using modern technology. Managers can adjust a whole palette of environment controls: light, temperature, precipitation, atmospheric composition, hormonal regulation, and genetic alteration.

This is made possible largely due to advances in microelectronic technology. Light-emitting diodes (LEDs) have drastically slashed the cost AND increased the efficiency of artificial lighting. Cost-effective LEDs have revolutionized indoor production like plastic sheeting did for field production. And with the decreased cost of indoor production comes increased innovation as more minds are able to devise feasible plans to grow something worthwhile in artificial conditions. Some of these ideas look to the world’s growing demand for protein and consider growing plant-protein for lab-burgers whiles others simply aim to minimize their livestock and grow insect-protein.

How can someone possibly stay abreast of all these developments? I feel like I’ve listed too many, and yet for each example in this text there are a dozen which could not be included. Well, the first way is to get directly involved! Find and become a part of something in urban agriculture. If you’re in relevant circumstances you’ll need to expend less energy trying to stay informed as this will simply become a common topic of your conversations. You could also set up some phrases to trigger a news-aggregator to your inbox. Look for topics relevant to new urban farming. I reiterate my point about protein production: it’s going to be big at some point and the innovation is going to be discovered by a small operation facing unconventional challenges. While it’s cliché and tastes like papier-mâché to say: apps! Seriously, be on the lookout for apps which facilitate the work of small farmers. If there’s ever going to be a mass mobilization of people into agriculture, then we need to simplify and systematize as much as we can. Trust me, most of them will feel fine if they’re no longer forced to wear so many hats.

If you’re still interested, you might benefit from investigation into various topics which have been extensively researched and greatly overlap with many facets of urban agriculture. Cuba’s organopónicos system demonstrates the practical success of urban food production when actively pursued by many people and policies. The Netherlands  have led global greenhouse production for years, and they continue to innovate and push the boundaries of protected and synthetic production environments.

Space! The final frontier. It’s exciting, isn’t it? I’m excited even just to say the word. I really did shout it out just then. I’m dreaming of going to space one day, how about you? Anyway, astronauts are experimenting with plant growth and crop production in space. It’s all quite enthralling, but too much for this post. If you’d like to know more, keep an eye out for my next post in a couple months!

Further research options:

An article from National Geographic about how The Netherlands ‘feed the world.’ Especially interesting is the third picture showing vertical production of chickens.

An all-encompassing chapter regarding urban soils, from my most favored author on the subject: Pouyat et al., 2010.

A podcast episode about urban growers in early New England who are called “The Diggers.” I suggest starting at either 40 seconds in or at 3:20, then listening through to at least 12:15.

Meet Mykl Nelson; Urban Agriculture Instructor at OSU

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My name is Mykl Nelson, a world citizen intent on feeding the globe.

 

 

 

 

 

 

 

 

 

The first distinct connection to food I remember was in the late 90s while living in İzmir, Turkey. We had a large mulberry tree in our yard which bore delicious fruit. I also remember the bazaar in the Buca province. Cart after cart of people selling mounds of all manner of produce. After leaving Turkey, and for maybe half of my childhood summers, I lived on the farm of my paternal grandparents’ in Worland, Wyoming. I saw many aspects of high, dry farming of row crops: sugar beets, alfalfa, barley, and dent corn. I could only catch fleeting glimpses into the life of my grandfather, a commodity farmer. But in my recent years I’ve been openly told that these American farmers vehemently hoped their children were “too smart to get into farming.” Their wish came true. Of four children and nine grandchildren, I’m the only one in agriculture.

I turned on to agriculture when a friend and I built a 400 square-foot poly-tunnel in our backyard in Colorado. We didn’t know anything more than that we wanted to grow our own food. I remember feeling so incredibly accomplished, fulfilled, and validated picking personal salads straight into dinner bowls. I took that inspiration to fuel my travel to the Pacific Northwest, a place I knew I could immerse myself in the world of tending plants. I pushed every aspect of my network to get more involved in farming and to gain space to garden. I’ve worked on three organic urban farms since moving to Oregon. I went back to school and retrained from political science to agricultural science. I continued my education with a graduate project which firmly oriented my interests to the world of urban agriculture.

I am now an instructor of urban agriculture here at Oregon State University. My current duties are to develop new online courses to train and empower new urban growers to produce food within the confines of their modern environment. This work is challenging, as urban agriculture suffers from a distinct lack of focused research. One of the most relevant discoveries from my graduate research project is that nearly all advice extended to urban growers is simply copied from traditional agriculture. Even if suggestions are altered with respect to the scale and local environment of urban growers, the research supporting these suggestions is still wholly based upon traditional agricultural methods of food production. I am developing my courses with this mismatch in mind. I have changed my approach from seeking to broadly support food production and instead specifically analyze and adapt traditional recommendations to work in an urban environment.

I use scientific research to inform my course development on many levels. At the macro-level, articles like one by Oberholtzer, Dimitri, and Pressman (2014) have reported that most farmers, and new farmers especially, struggle with complications in managing the farm’s business much more than the challenge of growing their crops. I used these findings to inform the outline of a new course that I am developing: Introduction to Urban Agriculture. Rather than spending time covering the how or why of plant growth in much detail, I’ve instead focused on how urban growers can adapt agricultural principles to their unique environment. I strive to keep students aware of how these factors should influence their management activities and always keep the concept of ‘value’ in their mind. On a more micro-level, I have built the lectures regarding soil and plant growth with adaptations of my own previous graduate research.

My method of teaching is heavily influenced by a new wave of teaching research which is well represented by James Lang’s book: Small Teaching. Broadly, this approach suggests frequent review of material as well as a more piecemeal and cyclical approach to teaching topics rather than large chunks of lecture punctuated by intermittent exams. Further, I refuse to accept that an online classroom is limiting. Modern students are demanding more than just lectures laid over powerpoint slides. I am exploring numerous avenues to increase engagement and foster social connection, all facilitated by digital platforms. I expect my courses to provide foundational pillars of knowledge for new urban growers as they pursue OSU’s new and entirely online certificate in urban agriculture. I hope to see every student embark on their own path to grow food within their urban environments. I look forward to reports of former pupils starting and operating successful urban farming businesses.