Huge Potential in Earth’s Smallest Organisms

Dr. Konstantinidis and a student review microbial research data.

It is well recognized that the smallest organisms, the bacteria and archaea, constitute the largest biomass on Earth and are also the most diverse among all living organisms. Whether in soils, waters, deep subsurface environments, or in the atmosphere, the bacteria are affecting, if not controlling, all the biogeochemical cycles that sustain life. Yet, little informatin is know about how microbes perform their activities. For instance, we know that bacteria are often the basis for disease, but we know little about pathogen ecology. We know that each gram of soil or liter of seawater carries more than 3,000 distinct bacterial species, each carrying up to 5,000 genes, but we understand too little about what this immense genetic diversity means or how useful it may be. One of the primary reasons for this is attributed, in part, to the fact that the great majority of microorganisms resists cultivation in the laboratory and thus, cannot be studied efficiently. However, Dr. Kostas Konstantinidis, assistant professor of environmental engineering, is leading a program to develop novel culture-independent, or metagenomics, and bioinformatics approaches to study microbial communities in-situ, both engineered (e.g., bioremediation and wastewater treatment reactors) and natural (e.g., terrestrial or marine) systems. He also works with biotechnological applications of microbial biodiversity.

Dr. Konstantinidis has already made important contributions in these areas of
research. In 2007, he launched the Environmental Microbial Genomics Laboratory, known as Enve-omics Lab: a state-of-the-art computational and wet laboratory that focuses on the smallest organisms on the planet. His scientific interests are at the interface of microbial ecology, engineering, and computational biology.

Dr. Konstantinidis’ research group has developed pioneering culture-independent approaches (metagenomics) to study natural microbial communities. In metagenomics, genomics techniques such as DNA cloning and sequencing are applied directly to environmental samples, bypassing the need for isolation and cultivation of individual species.

Using culture-independent techniques, the researchers have provided new insights into how life adapts to the deep and cold oceans, the largest biome on the planet. Their work revealed, for instance, that the deep-sea microbial communities at 4,000m depth are enriched in genes conferring rapid evolution and metabolic versatility to cope with the scarce but diverse food resources available in-situ. The discoveries have also opened up new biotechnological opportunities, including designing enzymes that are functional under high-pressure and low temperature (the temperature of the deep sea is invariably ~40 C). With support from the U.S. Department of Energy, Dr. Konstantinidis’s team is also extending the metagenomic approaches to study underground microbial communities in Alaskan soils and other temperate regions. This investigation focuses on how these communities respond to the predicted effects of climate change such as increased atmospheric CO2 and temperature, especially with respect to whether the communities release or sequestrate soil carbon.

Dr. Konstantinidis and his team are also applying cutting-edge “omics” technologies to evaluate microorganisms isolated in the laboratory. The goal is to provide a system-level understanding of bacterial species. In a recent example of this work, researchers applied these technologies to a study of 10 closely related strains of Shewanella, an important family of bacteria. The Shewanella are key players not only in cleaning up toxic heavy metal contaminants in the environment, but also in the emerging field of microbial fuel cells for electricity generation. The group has been able to link the phenotype of each Shewanella organism to specific genes in the genome (genotype) using a series of physiological, transcriptomic and proteomic experiments. They have also identified the genes responsible for metal reduction. Insights currently emerging from this work will enable the identification of the most effective Shewanella strain for cleaning up specific contaminants within a given environment. The group also found that the Shewanella genus is more genomically and phenotypically diverse than previously anticipated and that the Shewanella organisms frequently exchange large parts of their genome in order to cope with fluctuating environmental conditions, such as sexual adaptation. These findings are, in fact, revolutionary as bacteria have been viewed as being primarily asexual organisms by the scientific community. The findings will also have important implications for microbial source tracking and indentifying bacterial species concepts: an unsettled issue with major practical consequences for reliable diagnosis of infectious disease agents, intellectual property rights, bioterrorism agent oversight, and quarantine.

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