By: Bertrand D. Eardly, Professor of Biology
Most of us don’t realize that our planet is dominated by microbes. Recent studies have shown that for every one of our own cells, we carry at least ten bacterial cells. This unseen bacterial community, both on and in our bodies, consists of hundreds of species who are nearly as different from each other as they are from us. Perhaps more amazing is the fact that there appears to be millions more bacterial species elsewhere on our planet, such as in soils and in our oceans. How do we know this, and perhaps more importantly, why should we care?
We know this because all life forms on the planet, from bacteria to humans, rely on a simple programming language that consists of a four-letter code in a molecule we call DNA. Studies on the commonalities and differences in this code have not only allowed us to confirm the common ancestry of all life, but they have also revealed that the bacteria, which have resided on the planet the longest, also contain the most genetic diversity. This can be explained by the fact that the number of mutational differences in self-replicating molecules such as DNA accumulates as organisms diverge from a common ancestor. The use of these differences to build a conceptual “tree of life” is called molecular systematics. An awareness of these genetic relationships has not only helped us to appreciate the massive diversity of life on our planet, but it has also provided insight on how species and communities develop and change over time.
With regard to the second question above, concerning why we should care about bacterial diversity; obviously certain bacteria are of more immediate importance than others because of their medical significance. However few realize that the bacteria in our soils and in our oceans are the primary drivers of the most fundamental processes in our global ecosystems. For example, their metabolic processes are responsible for the maintenance of the composition of our atmosphere. Furthermore these bacteria are pivotal in harnessing the different forms of energy needed for the production of the building blocks of life–upon which we all depend.
In my research at Penn State Berks, I have used the principles of molecular systematics to study the evolution of a mutualistic relationship between a group of soil bacteria known as “rhizobia,” and a group of plants known as legumes. Collectively, the legumes are valued being a source of high quality dietary protein for humans, livestock, and other animals. In order to build proteins, all plants require large amounts of “fixed” or non-atmospheric nitrogen, as it is a primary component of all proteins. Fixed nitrogen is limited in soils however, and plants must compete with one another for the scarce quantities available. Indeed, nitrogen is second only to water among the nutrients that limit plant growth worldwide. Legumes are unusual, in that they have evolved a cooperative arrangement with rhizobia, which have the ability to fix atmospheric nitrogen into ammonium. The rhizobia then supply the ammonium to legumes for protein synthesis. This process is called symbiotic nitrogen fixation.
Rhizobia are uniquely adapted for this because they produce an enzyme called nitrogenase, which binds atmospheric nitrogen and converts it to ammonium. This conversion requires large amounts of energy, and in symbiotic nitrogen fixation, the energy is supplied by sugars from photosynthesis in the legume. When legumes encounter rhizobia in the soil, they selectively allow the bacteria to invade their root systems, where they form tumor-like nodules. Here the bacteria thrive on the sugars produced by the plant and carry out the process of symbiotic nitrogen fixation. The fixed nitrogen that they produce not only enhances the growth of the host legume, but it can also enrich the soil with the protein nitrogen after the plant returns to the soil and is decomposed. This is how soils are created.
Nitrogen can also enter the ecosystem in other ways. For example, we can chemically synthesize ammonium to make mineral nitrogen fertilizers. However this strategy is fraught with negative environmental consequences. For instance, if nitrogen fertilizers are over-applied, then they can pollute our lakes and oceans. Also, the industrial production of ammonium is expensive because the process requires the burning of large quantities of fossil fuels, and this contributes to the global greenhouse gas problem.
Over the past twenty-five years at Penn State Berks, I have used the principles of molecular systematics to critically evaluate the classification of the different types of rhizobia. When I began my work, rhizobial species were defined on the basis of the range of legumes that they could infect. Through the use of molecular systematics, I realized that this does not accurately reflect the degree of genetic relatedness between the rhizobia, because their genetic determinants of host range are carried on laterally transferable genetic elements. Consequently, collaborators and I developed a new taxonomic framework for rhizobia that is based on more stable genetic differences within the bacteria. Through our studies, we identified a new photosynthetic species of rhizobia and we also reclassified several others. We also conducted surveys of native rhizobial populations around the globe and demonstrated that rhizobia, like their legume hosts, have distinct centers of genetic diversity from which they have migrated to different parts of the world.
More recently, I have initiated a collaborative study with Dr. Tami Mysliwiec, Associate Professor of Biology, in a senior-level biology course at Penn State Berks where our students are studying soil microbial populations in an industrial barren in Palmerton, Pennsylvania. From the late 1800s through 1980, a large zinc smelting plant there produced tons of toxic atmospheric pollutants that virtually eliminated native forests over several hundred acres on Blue Mountain, which is downwind of the plant. In 1983, the area was designated an EPA Superfund site. Since then efforts have been undertaken by the EPA to remediate the soils with fertilizers, seed, and sewage sludge. Unfortunately regrowth of the forests have been extremely slow because of the sensitivity of most plants to the heavy metals that have accumulated in the soils.
The central goals of our project, which were initiated in consultation with the EPA, are to use molecular systematics methods to determine how the microbial populations in the contaminated soils have been influenced by the high metal concentrations, and also to study how the populations are responding to the ongoing remediation activities. Our initial results have shown that even though the soils are largely infertile, they still contain viable populations of rhizobia. This observation is encouraging, because it suggests that the introduction of compatible legumes back into these ecosystems could be a part of a sustainable strategy for restoring the native fertility of these contaminated soils.
Although I appreciate the fact that many may find the idea that we share a common ancestor with a microbe to be difficult to accept, I think it is important that these individuals realize that if this were not the case, then the study of the diversity of life on our planet would be impossibly complicated, and the science of biology would be nothing more than a collection of disconnected observations. It is precisely because of these universal commonalities of life that someone like me who is studying microbes on a hilltop in eastern Pennsylvania, can apply the same principles and techniques as a medical researcher or a plant breeder. To me, the fact that all life relies on the same language is, and will continue to be–truly amazing.