Welcome to the MicroBiome

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Nanotechnology is uncovering the hidden world and the millions of microbial species living in one gram of soil. These micro-kingdoms of new species could change the face of farming forever.


There’s more going on in your soil than you think. In soil, plants, livestock, humans — everywhere, in fact — communities of microorganisms, more complex and well-organized than the biggest, busiest cities on the planet, are thriving.

Scientists have been probing these largely invisible worlds for new antibiotics and enzymes for generations, but it has taken powerful computing technology to finally expose what’s really going on in these microscopic ecosystems.
Nanotechnology allows scientists to uncover the secrets of these hidden worlds revealing the millions of single-celled organisms and microbial species living in a gram of soil.
Many remain unnamed and some lifeforms discovered are neither plant, animal nor fungi.
Now with the help of nanotechnology, scientists are beginning to understand these microbiomes and, more importantly, how to leverage these new insights to help farmers grow better crops.
Our tour guide into this new world is Eoin Brodie, the Irish-born University of California, Berkeley molecular microbiologist who pioneered advances in nanotechnology that measure microbiome community dynamics.
Brodie is a staff scientist in the Earth Sciences Division at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory and adjunct assistant professor in the Department of Environmental Science, Policy and Management, University of California, Berkeley.
According to Brodie, understanding how soil microbiomes affects crop fertility and nutrition changes the face of farming forever.

How did you become interested in microorganisms?
I grew up in Dublin, surrounded by farmland, cattle pastures and sheep grazing. My PhD work was on the impact of agricultural intensification on soil microbes. We now do a lot of work trying to understand and model how microbes transform soil organic matter and mobilize nutrients, and how they can be harnessed to improve plant yields. For instance, we know they produce proteins, enzymes and chemicals that can be extremely valuable. They may give us insights into nitrogen and phosphorus availability in soil, and they also could be extremely useful for biotechnology. Many antibiotics and enzymes in animal feeds already come from soil microbes. If we can even expand our knowledge base by a few percent, the potential types of enzymes, antibiotics and new chemicals we could make is mind-boggling.
Can you give us a sense of how much we know — or don’t know — in this new realm?
We’ve only been looking at a very small portion of the microbes on earth, maybe one percent that we can cultivate.
Of those, we’ve only identified about half of the DNA for what it actually does. When you can’t ‘read’ half the parts list, it’s very difficult to predict how a microbe is going to respond or function. We know these genes exist but we don’t know what they do, or what enzymes or proteins they make.

Is this where nanotechnology comes in?
Yes. Nano units are a thousand times smaller than micrometers, and we have a thousand micrometers in one millimetre. A human hair is about 100 micrometers across. Big bacteria are one or two micrometers in size. Nanotechnology is the building, construction and understanding of elements, structures and compounds at that scale — one million to the millimetre.
Nanoscience has a fundamental role in understanding how microbes talk to plants, how they share metabolites. If we can determine what regulates nitrogen fixation, for instance, we might improve crop productivity and reduce or eliminate fertilizer use. 
People working in nanotechnology today are just at the beginning, trying to scale up our understanding in the same way we scaled up understanding of the human genome. There, one of the great advances in DNA sequencing was the ability to parallelize biological assays. Instead of sequencing a few DNA strands at a time, we now sequence millions at a time.
Already, nanotechnology is replacing micro-technology for making computer chips. Amazing work is going on in developing miniaturized sensors based on radio frequency identification (RFID) technology. RFID tags both transmit and acquire energy from radio waves, so they don’t need batteries or wires.
We could make tens of thousands of RFID sensors from a single silicon wafer, mix them with seed and plant them in soil. As roots grow and pass the sensors, we would get readouts of things like pH, oxygen concentration and the presence of specific chemicals. We also could track how readings change over time. Then, we could build three-dimensional models of how microbes influence the area around the root and soil.
Imagine millimetre-size, autonomous sensors without batteries distributed in a field, giving a high density of information about moisture, pH, nitrate concentration, temperature and other things. They could feed near real-time data to a server to inform me, as a producer, where the most productive areas of my field are located and occurring. Then, you have the potential for really customized agriculture within fields at whatever management scale is practical.

How long before something like this could actually be implemented at farm level?
Scientists are already starting to build devices the size of semiconductor chips, with nanoscale channels, to capture tiny samples of DNA and test their products with tiny amounts of reagents, all in parallel.
Similarly, we could use nanoscale imaging sensors to detect reactions and use semiconductor technologies to make tens of thousands of sensors from a single silicon wafer, which massively reduces the cost of those assays. 
And consider this: Perhaps we could apply this to optimize irrigation or fertility. Imagine having these sensors deployed across a field, at different locations and at different depths reporting to a central receiver: where your ammonia is going, when it’s being turned into nitrate, how much of it is leaving or leaching, the response of plant roots to that nitrate, how the plant roots are growing, what the living underground health of the 
plant looks like, etc.
At some point, nano-sensors will be used to measure functions throughout the microbiome. That’s many years away, but once we develop this platform then many types of tests could be deployed on those sensors. Right now, people are developing this for mapping networks in the human brain. Once you develop these technologies, you start to find all sorts of uses for them that you never considered.

What does a normal microbiome look like?
Think of a forest. You’ve got different types of trees, animals and insects. These have evolved to work together to form a stable ecosystem.
A microbiome is the microbial version of a forest. Individually, each species has different functions. Together, they are essential for the stability and activity of the system. Resources flow between members, roles are shared or divided. Supply chains move resources around efficiently. If something happens to the system, organisms performing a function will be lost but others step in to perform the role, like nitrogen mineralization or cellulose decomposition.
This sounds amazing, as if we’ve just discovered a new field of science for a new world.
That’s right. Technological innovations and computing innovations coming together right now are allowing us to really appreciate the functions of microbes individually. The next chapter is to learn to manipulate them in a way that sustainably increases crop yield without releasing too much nutrient, without making a crop susceptible to pests or pathogens. That’s extremely challenging, but many extremely smart people are working on it in many locations around the world.

Where will we see convergence between this science and the needs of farmers?
With an incremental approach, we could see an application in crop fertility. Our production systems don’t always interact in predictable ways. If you had the information during the planning phase, you could design a fertility program that incorporates the responses of the microbiome to nutrients as they are delivered during the growing season. We would incorporate this into a model that runs in the background with relatively few inputs, like location, climate and key features of the microbiome. Some agricultural companies are starting to provide these services now.

How else could this be used in farming?
Another approach is disruptive technology. Specific bacteria can increase yield through hard regulation of plant growth hormones. They affect only one thing in the plant, like production of shoots or roots. We’re starting to understand how those bacteria work and live within plants.
Certain bacteria and fungi can solubilize phosphorus in the soil. That’s a big deal, particularly for plants like soybeans. When plants already have bacteria that can supply nitrogen, then phosphorus becomes the limiting nutrient. Phosphorus can be present but inaccessible. Some microbes can mine that phosphorus, in excess of their own needs, and supply it to plants.
Several major companies are moving into this area with so-called ‘biologicals,’ bacteria and fungi that promote plant growth. Monsanto and Syngenta have a biological now, called JumpStart, a phosphorus-solubilizing fungus that was found in a lab in Canada.
Until recently, biologicals were only developed ad hoc. A microbe seemed to have an effect; you’d inoculate a plant and it worked. But, in another soil, it didn’t work because that microbe had to compete with bacteria and fungi already in that soil, or because the plant responded differently and kicked it out.
We’ve seen this in plant and human nutrition. The field of probiotics has been as unsuccessful as plant nutrition, and for the same reason. Humans have varying diets and varying genetics, so we’re all slightly different. We have our own microbiomes, we eat varying foods, and yet we expect one probiotic microbe to colonize every microbiome. That’s unlikely to happen in our stomachs, and in our fields, until we understand the factors controlling the survival of that microbe.
The potential is huge. There is a lot of room for doing this research in a more scientific and logical way. When we do understand these interactions of specific microbes, plants and soils, we could build a cocktail of microbes to perform the functions we want under a range of conditions.

Does this imply a need for much more complex soil testing?
There is a potential for that. Existing tests measure extractable nutrients, and do a reasonably good job at understanding what the crop plants can extract. That’s not necessarily what the microbes can extract. When we understand what the microbes need and do, we can start to optimize them for specific plants and soils.

And does that imply more efficient fertilizer use or smaller fertilizer bills?
Maybe. Nitrification begins when you apply ammonium fertilizer. It was believed that a very narrow group of soil bacteria performed this function. DNA sequencing revealed a whole new domain of life that does this, the Archaea domain. In fact, in many soils, Archaea happen to be more prevalent than the bacteria. We didn’t know this before, but the Archaea were contributing to the conversion of ammonia to nitrate, and to the loss of that ammonia as nitrous oxide.
To a great degree, microbes control nutrient availability in the soil, especially for nitrogen and phosphorus. Pulses and legumes need inoculation with nitrogen-fixing bacteria. Other plants attract microbes that supply nitrogen but that live outside, near the roots. We are identifying what types of microbes these are by using DNA sequencing. As we come to understand them, maybe we can modify the plant or the soil environment to make them work better.
In sugar cane, scientists have recently discovered nitrogen-fixing bacteria living within the plant tissue. They don’t even interact with soil. They take nitrogen from the atmosphere and give it directly to the plant. We’re working to understand how this happens, how we can optimize this for the plant or for the microbe. These bacteria were isolated from sugar cane and now are being used in things like bio-energy crops, like switchgrass, to provide nitrogen without the addition of mineral fertilizer. Once these microbes take hold, there is potential for them to be self-sustaining in the crop over long periods.

Is there a link between organic matter and the microbiome?
This actually touches a paradigm shift in understanding soil organic matter. It was thought that soil organic matter was partially decomposed plant material. In fact, the stable organic matter in soil actually is the end product of microbes. In many cases, microbes eat the plant material. What the microbes excrete or leave behind after the microbe dies sticks to the minerals and makes the stable organic matter in soil.
The proteins and enzymes that microbes make end up being stuck to soil minerals for a very long time — and also tie up the minerals. Effectively, they’re not available to other microbes. That type of information is going to be very important for understanding how long organic matter stays in the soil.

What about other soil components?
Soil animals are important in that they physically transform soil by burrowing and mixing, but the chemical transformations they make, in large part, are due to the microbes that live in their gut. That’s how nutrients — NPK and energy — flow through a soil ecosystem. Large plant material needs to be processed by soil animals before microbes can accelerate the decomposition. Soil animals have a gut microbiome, just like we do. It’s essential for worms to have these microbes to make humus (dark organic material in soil), just like it’s essential for us to have microbes for our health.

What’s still needed?
There’s a whole new set of high-throughput technologies that sort-of exist, but no one lab or initiative is pulling them together. There are technologies to help us understand how the other 50 percent of the microbe genes work, for example, by producing and folding enzymes, screening enzyme functions, and for finding enzyme structures without laborious crystallization. To really understand microbiomes, we need those technologies to be integrated.
We also need to keep talking about the potential of the microbiome to improve the health of our planet, the health of humanity, the production of food and the fundamental understanding of our world.

About the Author
John Dietz

Freelancer John Dietz and wife Angie left the city in 1980 to live in the country at Arden, the Crocus Capital of Manitoba. Dietz became a farm writer while a communications specialist for Manitoba Agriculture (1975-1980). His news releases introduced zero tillage in Western Canada, the Manitoba Weed Fair, Manitoba Agricultural Hall of Fame and much more. He regularly contributes to a major American farm magazine, Successful Farming, and is author of three tractor books.

Dietz enjoys news, sciences, photography, wild saskatoons and garden-grown raspberries.


His website is: www.prairie-stock.smugmug.com.

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