Tag Archives: microbial ecology

microbes improve carbon cycle models

Microorganisms are key drivers of the global carbon cycle both on the land and in the ocean. Through a diverse array of metabolic strategies, microbes decompose organic and recycle organic carbon. Just as we respire a fraction of the carbon we consume as CO2, so do microbes. Globally, vast quantities of organic carbon are funneled through many billions of microbes every year: to be decomposed, recycled, and respired into the atmosphere. In spite of this, microbial activity has historically been ignored in attempts to model the global carbon cycle and predict climate change-related feedbacks. Instead, our models rely on untested assumptions that microbes and their carbon cycle activities will respond in uniform, predictable manners to increases in temperature, and as such, can essentially be ignored.

A recent paper in Nature Geoscience paper challenges this assumption by explicitly integrating microbial physiology into a new model of the soil carbon cycle. Compared with traditional models, the new model more accurately matches current observations of carbon stocks and fluxes across ecosystems. Regarding future carbon cycling in a warming world, the model produces several widely different scenarios that vary due to the potential response of microbes to rising temperatures. In short, if microbes respond negatively to warming by decreasing their “growth efficiency”; that is, if warming slows down their growth rates, no additional carbon is released to the atmosphere as the soil warms. But if microbes are able to adapt to higher temperatures and maintain their current growth efficiencies, higher temperatures will accelerate carbon decomposition rates and lead to potentially huge additional losses of carbon dioxide from soils.

The integration of biological mechanisms into earth system models is an important step forward in our ability to forecast future climates. Future research that empirically measures microbial community responses to long-term warming is desperately needed in order to accurately model and predict this potentially huge feedback to the global carbon cycle.



The history beneath your feet

I think about dirt a lot more than most people. Probably this is the result of my background in ecosystem science, the study of how nutrients and energy flow throughout the biosphere. The soil represents a huge sink for all major nutrients that sustain life on earth, and an important source of nutrients such as carbon and nitrogen that are naturally recycled to the atmosphere.

But it’s not economic, or really even environmental value that makes soil so fascinating to me. It’s history. In the forests of northeastern Puerto Rico where I’m currently conducting research, the historic record deposited in soil is up to 8, 10 or 15 meters thick and stretches back 300,000 years into the past, to a time when the island itself was shooting up out of the Gulf of Mexico due to rising magmatic rock deep beneath the ocean floor.

If you start looking closely at the composition of soil, you will quickly discover a wealth of information recorded within it. Tiny grains of minerals, produced from thousands to millions of years of water dissolving rock, form the physical matrix on which life has developed. As these clean, crystalline minerals slowly rot, they are chemically transformed into new compounds such as clays. Clays and other secondary minerals add stickiness to the soil, allowing decomposing organic materials to adhere. Slowly, a strange collection of organic materials that were once living and the inorganic ingredients that supported their existence begins to accumulate. As this assortment of the dead and rotting grows, so does the living biomass that it sustains. Most of the soil microfauna is involved in feeding off dead (or other living) organic materials and ultimately recycling nutrients that would otherwise be locked away forever. Embracing death is a way of life in the world’s most biologically diverse ecosystem.

But wait- I was talking about history. Yes, living organisms, dead organic materials, clays and minerals are all important components of the soil, but how do we piece together a history (and of what? The geology that the soil formed over? The forest that once stood atop it? The long-dead animals whose traces still linger within it?) from such a complex and dynamic system?

The answer is not entirely clear. But I am convinced that history is sitting in the dirt, rotting away, waiting patiently for someone to find a way to unwrap the stories contained within.


Back to the future- ecosystem memory in environmental metagenomes

Over the past two decades, the study of ecology has been revolutionized by the advent of molecular genetics techniques. Originally developed with only biomedical applications in mind, some forward thinking ecologists quickly realized the possibilities that these technologies could offer. One of the fastsest growing areas of environmental research is metagenomics, the study of pooled genetic material from an environmental sample. In a gram of soil or a droplet of seawater, millions of unique species of bacteria exist with their own unique genetic make-up. Combine an enormous number of bacteria with even more abundant viruses- naked fragments of DNA encased in a protein coat that serve no other purpose than to infect living cells and hijack their DNA replication machinery- and you have a metagenome.

Thanks to a handful of pioneering scientists, scientists can now take a sample from practically any environment- soil, ocean water, subsurface rocks, or cloud water, to name a few, and sequence its “genome”. The genes obtained from an environmental sample indicate the total potential that the sample is biologically capable of.

What sorts of information is metagenomics providing us? Genes present in environmental samples encode proteins that perform numerous ecosystem functions- enzymes that decompose organic matter and release carbon, nitrogen and phosphorus, as well as numerous important micronutrients. Proteins that detoxify organic wastes, or convert inorganic gases such as carbon dioxide into sugar.

A major challenge moving forward from genomic information to understanding, at the most fundamental level, how an environmental system functions, relates to the fact that a genome is not a reflection of every process going on in a system, but rather an indication of what that system is capable of. Only a fraction of your body’s genes are being translated into proteins at any given time- some are turned on or off at certain points in your life, and some are only activated under the proper environmental conditions.

The mechanisms underlying gene expression in humans are still  largely unknown, but it is becoming increasingly clear that in microbial metagenomics, gene expression is highly sensitive  to external stimuli. The emerging framework for microbial gene expression is actually strikingly similar to economic resource allocation theory. Why waste time and energy producing a protein to degrade cellulose if there is no cellulose in your vicinity? Why produce nitrogenase, the protein responsible for taking inert atmospheric nitrogen and converting it into a form useable by plants, if there is already abundant organic nitrogen in the soil? Proteins represent an energetic cost, and microbes exist in a competitive, resource limited environment where any misallocation of resources almost certainly compromises your chances of survival.

Given that microbes will only express those genes that provide the maximum return on investment, what does a metagenome really tell us? Memory. As ecologists begin to push forward from examining metagenomes to studying gene expression and protein expression in environmental samples, Mary Firestone, one of the pioneers of the field of molecular microbial ecology, encourages her colleagues to look “back to the future”. All the genes present in a sample, she argues, provide a written history of what the environment has been like in the past. Resource allocation theory and evolutionary theory tell us this. Why would a gene be present, if there wasn’t a selective advantage to it at some point? Much as paleontologists can study changes in dinosaur morphology over time and infer changing environmental conditions, microbial ecologists can use metagenomics to infer what must have been the conditions at some point in the past. And if something occurred in the past to select for a bacteria carrying a particular gene, it may well happen in the future. Carbonic anhydrase is a protein commonly found in surface seawaters that is responsible for converting dissolved CO2 into bicarbonate, and in doing so acidifies the environment. The presence of carbonic anhydrase encoding genes in a seawater sample may indicate a past in which CO2 concentrations were much higher. Forward thinking about how to deal with new genomic information may in fact be a history lesson.

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.