Tag Archives: bacteria

American Gut

American Gut

Most of us have heard at some point or another that we have entire ecosystems of microbes living in our gut. Mostly of these microbes are happy symbionts that help us digest our food, but some can occasionally becoming pathogenic and cause health problems. Have you ever wondered what your gut microbial community looks like? Now you can find out! The Earth Microbiome Project (http://www.earthmicrobiome.org/), founded several years ago with the ambitious goal of “sequencing the microbiome of planet earth”, (or, in other words, characterizing basically all of the genetic diversity that exists on our planet), has begun a smaller, more targeted project with the aim of characterizing the gut communities of human populations.

Some of the key science questions driving this project : to what extent do gut microbial communities vary among people? At what scales can we discern patterns in microbial community composition? Are similar microbial communities found among people from similar geographic regions, with shared genetic history, or with a shared diet? And, perhaps more interestingly to most of us, to what extent does the composition of our gut community impact our own health? Once we have enough data to start answering some of these basic questions, perhaps we can even start making predictions about what sorts of lifestyles will lead to what sorts of gut flora, and how these communities, in turn, will impact our overall health.

It costs just $100 to join and get your microbiome sequenced. And the information could change your life!

Protozoa drive growth enhancing hormone release in the rhizosphere: where biochemistry meets ecology

Though numbering far fewer in the soil than the bacteria they prey on, protozoa are an indispensible link in the transfer of nutrients through the food web that drives forest productivity. These single celled, eukaryotic “bactivores” concentrate themselves in regions of high bacterial activity, notably in the vicinity of plant roots. I’ve previously discussed the “microbial loop theory”, a paradigm for understanding plant nutrient acquisition in terms of the interactions between root exudates, protozoan predators and bacterial prey. To summarize briefly, plant roots exude sugary compounds to “prime” the surrounding soil, making it a highly suitable habitat for bacterial populations. Protozoans naturally move in, too. As quickly as bacteria decompose organic matter to recycle nutrients for their own growth and metabolism, protozoans eat bacteria and excrete those very same nutrients in a form readily available for plants. This “microbial loop” of nutrients is essentially an ecological fertilization system built on a very simple predator-prey model.
Given the advantage plant obtain by maintaining a large and healthy microbial (bacterial + protozoan) community, what strategies can plants employ to ensure that they are supporting the largest and best community possible? (Note that best, from the plants perspective, means the community that mineralizes the most plant-available nutrients in the rhizosphere.) A first obvious strategy for a growing plant would be to release more food- to exude more sugary carbon from its fine root tips. But another, possibly more important step precedes this, and it has to do with root architecture.
Most plants begin their foray into the earth as a seedling, by sending a long, primary taproot straight down like a sledgehammer. Lateral roots begin branching off this main taproot slightly later, and from these lateral roots networks of fine roots, or root hairs, spread out like tiny fingers to penetrate the smallest nooks and crannies in the soil matrix. It is these root hairs which become the site of almost all nutrient and water acquisition and can end up covering an enormous surface area in a mature plant. And it is in the narrow band around these root hairs known as the rhizosphere that a microbial food web has evolved to provide those nutrients.
But plants don’t just grow root hairs everywhere. That would be a waste of energy. Root growth is highly plastic and sensitive to environmental parameters such as soil moisture and nutrient availability. If, for instance, a calcium deposit exists several inches from a primary lateral root, root hairs will likely develop in the direction of that deposit to access as many nutrients as possible. How can plants regulate their growth so precisely in order to ensure themselves the best chance of survival?
It turns out that a complex set of biochemical pathways drive plant growth, and that these pathways can be switched “on” or “off” according to the presence or absence of growth hormones. Auxins are a class of hormones that are particularly important in mediating the growth of plastic stem cells in response to the environment. They are largely responsible for phototropism, the phenomenom that anyone with a windowsill plant has observed, that plants tend to concentrate their above-ground growth in the direction of the most sunlight. Belowground, auxins are largely responsible for root branching and the selective production of root hairs.
At this point you might be wondering why I’ve diverged from my original topic (the microbial loop) to discussing the biochemistry of plant growth. Well, recent research suggests that these two subjects may be even more intricately linked than previously imagined. Growth hormones such as auxins are responsible for the production of fine roots, and by the same token responsible for the maintenance of a rhizosphere in which microbial communities thrive. Though they are hardly aware of it, microbes desperately need auxins to ensure the continued maintenance of the roots they depend upon as a primary food source. A recent study conducted by rhizosphere ecologists (there aren’t very many of them, in case you were wondering) in Germany has found that protozoa selectively “graze” on certain bacteria in the rhizosphere while largely ignoring others. Which bacteria do they choose to ignore? The ones that produce auxins that promote root growth. By selectively removing amoebae, a key bacterial predator, from experimental plant roots, the researchers found a marked decrease in plant auxin concentrations compared to treatments that contained amoebae. Soils with amoebae predators maintained plants with higher auxin concentrations and increased root branching.
It is becoming clear that the interspecies interactions that plants, protozoa and bacteria all depend on may be far more nuanced than we previously understood. Future research to characterize the specific players in this complex web would allow scientists to develop a more holistic picture of exactly who and what is driving plant growth and ecosystem nutrient cycling.
Krome et al. 2010. Soil bacteria and protozoa affect root branching via effects on the auxin and cytokinin balance in plants. Plant Soil: 328, 191-201.

In the turbulent phyllosphere, bacteria associate tightly with host plants

Large populations of bacteria  reside on leaf surfaces, in a zone known as the phyllosphere. Dr. Noah Fierer and colleagues at the University of Colorado, Boulder used high resolution DNA barcoding techniques to create a profile of the bacterial communities on 56 different tree species. They were interested in measuring 1) intraspecific variation, or the changes in phyllosphere communities across  different species and 2) interspecific variation, the changes in community composition within a species from tree to tree. Looking at the community variation within a single tree species allowed the researchers to isolate specific environmental variables that may be influencing community structure. To understand interspecific changes in diversity along environmental gradients, Fierer and colleagues barcoded Pinus ponderosa trees taken from several locations across the world.

Dr. Fierer found that phyllosphere communities are not randomly distributed, but organized in patterns that could be predicted given the relatedness of the tree species. In other words, related bacteria inhabit related tree leaves. Moreover, they found that the interspecific bacterial diversity- the difference between Pine and Oak tree phyllosphere communities, for instance- is greater than the intraspecific variability between distant individuals of the same species. Certain bacterial taxa were more common on gymnosperms (plants that reproduce by seed) than angiosperms (flowering plants). However, within a single species such as P. Pondersoa, bacterial communities could be highly similar across thousands of miles. Given that the bacterial communities in two handfuls of soil taken 10 meters apart are likely to look nothing alike, this result suggests a strong selection for particular bacterial species inhabiting particular leaves, regardless of environmental gradients.

Terrestrial leaf surface area is estimated to exceed 10^8 km^2, making the phyllosphere one of the largest microbial habitats on earth. Phyllosphere communities face the distinct challenge of extreme and unpredictable environmental variability. Imagine if your world could go from brilliantly sunny to dark in a manner of seconds, and that such events occurred randomly throughout the day. Rainstorms are not trivial events, but epic floods that pose imminent threat to all but the most resilient individuals. Temperature change is rapid and often extreme, and gusts of wind threaten to blow you upside down or off into oblivion. One may imagine that in such a turbulent world, bacteria with very specific properties would not only inhabit, but become expert dwellers on, very particular types of leaves. Dr. Fierer’s research supports this hypothesis by demonstrating a tight coupling between bacterial species and leaf properties associated with different tree species.