Tag Archives: microbiology

Don’t treat soil like dirt!

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Soil is a precious resource, yet most of us pay little attention to the stuff under our feet.  It is the medium in which we grow our food and the foundation on which we build our cities. Soils filter our water, detoxify our pollutants, decompose our waste and hold vast reserves of the nutrients required for life. Soils are also fragile, taking thousands to million of years to develop but destroyed in minutes by human development.

For the past three years, myself and my fellow soil enthusiast Aurora have spent our Saturdays in December showing kids how awesome soil and the microbes that inhabit it actually are. We’ve developed a number of soil and microbiology activities to teach kids of all ages what soil actually is, who lives in it, and why we should value it. The take-home message? Don’t treat soil like dirt! Human beings (and nearly ever other species on earth) depend on soil for our very survival.

Here are some highlights from the last two weeks of the workshop:

Checking out some protozoa under the microscope!
Making a hypothesis before conducting an experiment!
Making a hypothesis before conducting an experiment!
MAKING SOIL! This is always a favorite. Want to make soil at home with your kids? Check out my homebrew recipe below...
MAKING SOIL! This is always a favorite. Want to make soil at home with your kids? Check out my homebrew recipe below…
Probably the coolest thing I've ever made in photoshop.
Probably the coolest thing I’ve ever made in photoshop.

We are even participating in an international, crowd-sourced science experiment known as the Tea Bag Index experiment to measure rates of decomposition in different soil types! This is a fun and easy experiment you can do in your backyard. All you need is a few teabags and a scale.  Decomposition, the breakdown of once-living organic matter and conversion into soil organic matter, is an important step in the global carbon cycle that is driven primarily by soil microorganisms. Ultimately, decomposed carbon is respired back to the atmosphere as carbon dioxide. Scientists are currently trying to understand how global climate change will affect decomposition and the microbial “respiration” of CO2 from soils. Projects such as the Tea Bag Index experiment provide scientists with valuable data that can be used to inform predictions about changes to the global carbon cycle. For more information on the Tea Bag Index experiment check out the website:


Or click here to access the protocol and get involved directly!


Most importantly, our workshop strives to underscore the importance of soils in our everyday lives.  Kids (and parents) often come unsure of what exactly soil is or why it should matter to them, and often enjoy the experience so much that they return week after week.

Live in the Philly area and got kids? Check us out, every Saturday for the rest of the month!

And since I can’t seem to stop geeking out about this stuff, here are some more cool resources to check out on soil science education:

USDA NRCS Healthy Soil Fact Sheets

The microbial loop theory: 30 years of cross-Atlantic communication barriers

The more forest ecologists learn about plant nutrients, the more evidence accumulates that plants are not simply passive organisms whose chances of survival are based on environmental factors outside of their control.  In acquiring basic nutrients from the soil, one may well imagine that a plant’s success is dependent on chemical properties of the soil alone. By simple “luck of the draw”, plants that seed in nutrient-rich spots will grow faster and larger than plants seeding in nutrient poor regions.

In several of my previous posts, I’ve addressed this issue one way or another, talking about plant-mychorrizhal associations and root-grafting as strategies that allow less fortunately placed plants to acquire sufficient nutrients to survive. I’d like to now address an entirely different theory concerning plant nutrient acquisition, one which, despite thirty years of European research, remains hotly contested and represents one of the major theoretical divides between European and American soil/plant ecologists.

The microbial-loop theory is a paradigm developed several decades ago and has become a cornerstone of European thinking about how plants interact with other soil organisms. In essence a relatively simple idea, the microbial loop would, if proved, require the reevaluation of a huge body of North American literature about plant nutrient acquisition, which generally argues that that basic nutrient demands and stoichiometric constraints- most notably nitrogen limitation in temperate forests and phosphorous limitation in the tropics, exert a fundamental control over forest productivity.

It is well known that plants exert significant control over the processes that occur in the rhizosphere, a narrow zone of soil and pore space that surrounds their roots. Here, plants dump simple sugars such as glucose in order to nourish an active microbial community. They apparently do so because microbes exhibit a diverse array of metabolic capabilities that plants themselves do not have. Microbial processes release essential nutrients, such as nitrogen, from complex organic matter in a plant-soluble form. This much about plant-microbe symbioses- trading carbon for nitrogen or another plant-limiting nutrient- is agreed upon by American and European scientists.

We start entering hot water when we look more closely at the actual microbial players in this game- who are they and what exactly are they doing? “Microbe” is really a very generic term that can refer to pretty much any organism that is invisible to the unaided eye. Within this umbrella grouping, two slightly more specific classess of organisms seem to be important in the rhizosphere: protozoa and bacteria. Bacteria are the tiny prokaryotic organisms that are largely responsible for decomposition and the release of plant-available nutrients. Protozoa, however, are single celled eukaryotes. They are larger, have more complex cellular organization, and importantly, feed on their smaller bacterial neighbors. Any soil sample that contains bacteria almost certainly contains protozoa as well. The relationship between these two groups of microorganisms represents a classic and well-studied predatory-prey model.

So, given that plants are feeding microbes by dumping sugar into the soil, who is the sugar intended for? The bacteria, or the protozoa? The classic paradigm would argue that the bacteria, as the important nutrient-acquiring organisms, are the intended recipients of plant carbon exudates.

But what does this make the protozoa? Are they just thieves, stealing a farmer’s corn that was intended to feed his cattle? Numerous studies have shown that protozoan populations increase dramatically in the presence of plant carbon exudates because they are using the carbon themselves. A high-energy, readily available food source is just as appealing to protozoa as it is to bacteria.  Why would plants, that have perfected so many survival strategies over evolutionary time, allow this to happen?

The microbial loop theory argues that it is the protozoa that plants are “cultivating”. Why? Protozoa prey on bacteria, and bacteria, remember, are full of the nutrients that plants need. After eating a bacteria filled meal, a protozoa will likely excrete those same nutrients, making them available for plants. The protozoa are a conduit, passing nutrients to plants that would otherwise be locked up in the bacterial community.

There is mounting evidence from various lines of research in support of the microbial loop theory. Experiments have shown that early in development, plant root architecture is dramatically altered in the presence of protozoa. Increased root branching increases surface area, or “real estate” that protozoa can inhabit. “Tracer” studies, using a labeled isotope of a nutrient, are now providing evidence for a flow of soil nutrients from bacteria to protozoa before becoming plant-available. Finally, molecular studies of bacterial communities reveal an increased abundance of less-palatable bacterial species in the presence of protozoa, and an increased frequency of genes involved with bacterial defense. This genetic evidence underscores the importance of protozoan predation in structuring bacterial communities. Soon, perhaps, nano-cameras will be available to visualize what is actually happening in the rhizosphere between plants, bacteria and protozoa.

The importance of understanding this interaction is not trivial.  The means by which plants get their nutrients has ramifications for ecosystem productivity, ecosystem nutrient cycling, and responses to environmental change. Should we progress forward in the field of ecosystem science, a critical reexamination (and open discussion!) of what exactly is going on in the rhizosphere between plants and they critters they cultivate is necessary.

A detailed review of microbial loop theory and a paper that addresses some of the important counter-arguments:

1.    Bonkowski, M. Protozoa and plant growth: the microbial loop in soil revisited. NEW PHYTOLOGIST 162, 617-631 (2004).
2.    Ekelund, F., Saj, S., Vestergard, M., Bertaux, J. & Mikola, J. The “soil microbial loop” is not always needed to explain protozoan stimulation of plants. SOIL BIOLOGY & BIOCHEMISTRY 41, 2336-2342 (2009).

Bacteria using “silicate sunscreen” provide a glimpse into Archean Earth

If you had the misfortune of becoming stranded for any length of time in the Atacama desert, you’d probably like nothing better than to see a clear blue pools of water stretching out across the landscape. Upon closer examination, however, these pools may begin to look a bit funny, perhaps a tad too crystalline. Known as el Tatio, this strange geyser field used to be a popular site for guides to stop and allow sweltering groups of tourists to get a refreshing drink of clean, clear Chilean water. It was only recently discovered that el Tatio contains the highest natural concentrations of arsenic on Earth- hundreds of times higher than the World Health Organization’s “recommended maximum limit” of ten micrograms/liter.

el Tatio geyserfield, Atacama desert, Chile

An abundance of arsenic is not the only strange thing about el Tatio- high concentrations of silicate minerals give the geyser an unusually glassy look (another good reason that the water is really not fit for human consumption!) Strange environments produce strange biology. Scientists studying el Tatio are now discovering some of the strangest- and perhaps oldest- microbial adaptations on Earth to cope with the stress on a dessicatingly dry, blazingly sunny environment awash in arsenic.

The microbes that have chosen to reside in this harsh environment are primarily arsenic reducers- they use energy from redox reactions involving arsenic to synthesize organic compounds. If this sounds at all familiar to you, it should. Plants do something very similar when they allow sunlight to stimulate their photosystems, releasing electrons that are later used to reduce carbon dioxide into organic carbon sugars. These bugs belong to a rare collection of microbes known as chemolithautotrophs- organisms that produce their own food, much like plants, using an alternate electron acceptors to eventually fix carbon dioxide.

Taking advantage of an abundance of arsenic to produce their own organic food source solves one of the problems associated with living in el Tatio- a scarcity of bioavailable carbon in the environment. It doesn’t, however, solve the problem of the intense sunlight that literally bombards the Atacama desert with powerful UV radiation all day. If the microbes in el Tatio didn’t have some way to protect themselves, their photoreceptors would quickly bleach and their DNA would be destroyed.

It turns out that this problem is solved by taking advantage of the peculiarly high levels of silica in el Tatio’s water. For most microorganisms, silicate mineral concentrations at these levels would be fatal- the precipitation of sharp silicious minerals would literally puncture any soft, free floating cell that tried to make a living. (Imagine living suspended in water, with giant, jagged pieces of glass floating around everywhere). These hardy microbes, however, precipitate a tough polysaccharide on their outer cell membranes that is actually able to capture silica particles and assemble them into a protective coating. Rather then let shards of silicate minerals destroy them, they assemble a house. This protective silicate coating serves two essential defensive purposes. Building silica shells protects the microbes from the silica itself, but it also deflects damaging UV radiation, preventing UV rays from damaging their cellular machinery.

Sounds creative, right? Actually, it may just be one of the oldest tricks in the book. Dr. Philip Bennett and colleagues at the University of Texas, Austin, are now  suggesting that sunscreening oneself up with silica may be  an ancient adaptation to survive in a world with a very thin atmosphere. Remember, when microbes first appeared some 3.5 billion years ago, the world was a very different place. There was very little oxygen in the atmosphere to absorb and deflect harmful UV radiation. Anyone alive today would have suffered acute radiation poisoning. Before the oxygenation of the atmosphere, some strange defenses must have been in place to allow early life to survive. The isolated bugs of the Atcama desert may be giving us clues as to how autotrophy originated on Archean Earth.

Credit: Dr. Philip Bennett, University of Texas at Austin. “Microbial Geochemistry: Coupling microbial ecology and mineral chemistry” . Oral presentation.

gaming with microbes

Bioengineer Ingmar Riedel-Kruse has two lifelong passions: microbes and video games.  Determined to find a way to bring these disparate interests together, he was struck by a strange idea- creating a gaming experience that operates based on biological processes by using live microbes.

Riedel-Kruse and several other scientists at Stanford University  have developed a basic game console that uses electric fields or chemical gradients to nudge tiny paramecia around a microfluid chamber. The motion of microbes causes computer animated paramecium to wriggle around on a player’s laptop screen. They have used this technology to create a variety of simple games, including “Ciliaball”, a soccer game, and “Pond Pong” a two player game that throttles microbes back and forth across a ping-pong interface by releasing chemical stimulants from a needle. Other prototype games, including “Biotic pinball”, “PAC-mecium” and “PolymerRace” all put a biotic spin on familiar video game motifs.


Since their inception, video games have had utility beyond simple entertainment- they have defined cultural trends, transmitted information, and explored new ways of imagining the world. Despite the importance of biotechnology in many aspects of modern life, the field has had little impact on gaming.There is hope that this new gaming technology will provide scientists a way to crowdsource biology experiments and information to players- if they can make a game that keeps people’s attention.

New games involving live yeast and DNA are also under development. If you’re interested in learning more about this peculiar form of microbe-torture, check out this month’s issue of Lab on a Chip for a full description of new games.

“Petri Arcade”. 2011. Science: News of the Week. 331: 385.
Riedel-Kruse et al. 2011. Design, engineering and utility of biotic games. Lab on a Chip 11: 14-22.

GeoChip: linking genetics with environmental processes

Over the past decade, environmental scientists have been casting a wider net in their attempts to understand complex environmental processes on a molecular scale. Once fascinating new line of research involves co-opting techniques developed by geneticists, largely for the biomedical industry, in order to understand how genes are important regulators of earth-scale processes as carbon and nitrogen cycling.

The GeoChip is a clear example of this search for new methods to answer old questions. Microbiologists  are working on remote Antarctic islands to understand some of the simplest nutrient cycling pathways in the world. The ecosystems they study are often composed of only a handful of fungal and microbial species. These simple food chains allow resarchers to contruct basic models of how energy and nutrients (such as carbon and nitrogen) are transferred.

This is where GeoChip comes in. GeoChip is a gene microarray chip designed to identify “functional genes” involved in important nutrient cycles. It allows the identification of genes in an environmental sample that regulate carbon fixation, decomposition, and atmospheric nitrogen fixation, to name a few.  Understanding what functional genes are available in a system allows scientists to both understand the potential of that system for cycling nutrients and better predict how that system will respond to environmental change.

Imagine a glass floor divided into hundreds of indentical squares. Each of these squares contains a different fragment of DNA, reconstructed by geneticists from known DNA sequences. When scientists want to probe an environmental sample for specific DNA sequences, they “wash” their sample over the floor. Fragments of DNA will stick to their complementary sequence on the floor, causing a square to light up. Scientists can “read” a GeoChip by identifying fluroescently lit spots where environmental DNA has attached. They use this information to develop a picture of the functional genes present in that system.

In Antarctica, GeoChip is already been used to answer important ecological questions. For example, scientists are finding that genes for nitrogen fixation, the crucial ecosystem process that produces plant-useable nitrogen in the soil, occur in lichen-rich areas. Lichens are believed to be among the earliest land colonizers, and the ability of lichen-dominated systems to add nitrogen to the soil may be an important finding in reconstructing the early colonization of terrestrial systems. Other findings include carbon-fixation genes in plots that lack vegetation, indicating microbial communities that are able to perform some sort of photosythesis in the absence of plants.


Yergeau et al. 2007. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. The ISME Journal 1: 163–179