Geomicrobiology

Geomicrobiology is the study of the influence of microbes—bacteria and similar microscopic organisms that cause fermentation and disease—on geological processes. As the field is relatively new, scientists are becoming increasingly aware of the effects of fungi, yeasts, and algae on rocks, the soil, and the ocean floor. Geomicrobiology has implications for many scientific foci, including rock weathering, geochemical recycling, and the breakdown of certain minerals. The growth of this scientific field is aided by improved technologies such as electron microscopy, three-dimensional computer modeling software, and state-of-the-art laboratories.

Basic Principles

Geomicrobiology involves the study of microbes' effects on Earth's geological processes. Microbes play an important role in changing the chemical composition of soil. They also contribute to the deformation and breakdown of igneous rocks (stones formed when molten magma cools) and metamorphic rocks (whose composition changes under different environmental conditions). Furthermore, bacteria and other forms of microbial organisms can provide clues about the different chemical compounds that existed in certain prehistoric environments.

Geomicrobiologists focus on bacteria that grow on sediments, usually in underwater environments. When these microscopic organisms coalesce, they form microbial mats, which are rubbery sheets comprising layers of different species of bacteria. The mats become an ecosystem, as microbes at the higher layers emit waste that is consumed by those on the lower levels. This transfer causes the formation of different types of minerals and can contribute to chemical and mineralogical changes in the sediment in which they are buried. In time, microbial mats are buried in sediment, forming rocks known as stromatolites. These fossils serve as some of the only evidence of the role microbes played in the Earth's earliest stages of development.

Background and History

Geomicrobiology owes its origins largely to the scientific contributions of two seventeenth-century scientists: Englishman Robert Hooke and Dutchman Antoni van Leeuwenhoek. Hooke built one of the first compound microscopes, a device that could increase magnification to a much greater degree than earlier devices, which he used to study insects, bird feathers, and other small organic subjects and specimens. Hooke's work with the microscope was recorded in his seminal book Micrographia.

Inspired by the work, Leeuwenhoek built an even more powerful microscope, which enabled him to study even smaller organisms. As the microscopes he built during his career evolved, Leeuwenhoek began to move beyond multicellular organisms and studied algae and even the film on his teeth. The strange images he observed were submitted to the Royal Society of London, and Leeuwenhoek entered into history as one of the first scientists to observe living bacteria.

In the centuries that followed, microbiology's applications were generally limited to medicine and biology. However, in the late nineteenth century, Russian geographer Vasily Dokuchaev became convinced that the Earth's soil contained microscopic organisms like the world above ground did. Dokuchaev initiated the first study of the genetic composition of the Earth, identifying and studying microorganisms in the soil and their influence on the environment. In light of his groundbreaking work, Dokuchaev has been dubbed the founder of modern genetic soil science, a field from which geomicrobiology has evolved.

Microbes and Microbial Mats

Microbes, bacteria, and similar microscopic organisms play many roles in the Earth's geological processes. One such role is in the immobilization and, ultimately, the chemical alteration of minerals. Microbes and various species of bacteria grow on the sediment at the floor of oceans, lakes, rivers, and other bodies of water. In time, these growths become layered microbial mats, with each lower layer feeding on the waste material of the higher level.

The mats impact minerals and rocks beneath them, in some cases removing nutrients necessary for the formation and maintenance of certain sedimentary rocks. For example, the presence of aggressive species of microorganisms in a groundwater environment with a limited supply of phosphorus can lead to the destruction of the sedimentary rock feldspar. Similarly, sediment that has been colonized by microbes at the bottom of a deep ocean basin, where oxygen is scarce, has been found to immobilize certain metal ions, causing a change in the chemical composition of the basin.

The chemical by-products of microbes and bacteria can lead to the breakdown of nearby rocks. For example, the waste products of the bacterium Bacillus mucilaginosus are acidic; as the presence of this bacterium increases, so, too, does the acidity of the immediate vicinity. The acids cause the weathering of silicate minerals (weathering itself being a process by which rock is broken down into smaller particles), which leads to a change in the chemical and mineralogical composition of the immediate environment.

The Contributions of Microorganisms

The weathering effects of microorganisms on minerals have important implications, some positive and some negative, for the structure of Earth's crust and Earth's climate. In some cases, microbes consume nutrients and deposit materials that benefit the development of certain crystals and minerals. Microbes frequently absorb pollutants and return water and other valuable elements to the soil in a process called bioremediation. However, minerals are not very stable; if microbes absorb too much of the pollutants, they also may withhold carbon dioxide from the minerals and make it difficult for those minerals to undergo weathering. In time, it is possible that a disruption in mineral weathering caused by microbial consumption of high amounts of pollutants can lead to an increase in Earth's overall temperature.

Microbes play an important role in the cycling of certain elements. Elemental cycling, the process by which elements move in various forms through the planet's subterranean, ground-level, and above-ground environments, is critical to life on Earth, as it brings such vital elements as carbon, nitrogen, and oxygen (and water, a compound) to each level. As scientists use improved technologies, such as mass spectrometers and chromatography, they are increasingly seeing a more widespread involvement of microbes in this geochemical process.

For example, scientists launched a study of the presence of iron hydroxide in a creek in California. Existing evidence had indicated that the cause of the presence of the iron-based compound was primarily inorganic (especially given that the studied stream had flowed from groundwater that was lacking sufficient amounts of oxygen). However, researchers noticed that a microbial mat formed at a point where the anoxic groundwater met with oxygen-rich water (anoxic meaning a state in which oxygen is severely low). This new evidence led researchers to conclude that the cycling of iron in this area was likely caused by microorganisms in the system.

Microorganisms and Prehistory

The evolving field of geomicrobiology is also uncovering evidence of the role that microbes played in Earth's prehistoric eras. Scientists have increasingly been studying such periods to better understand changes in geological processes. In one study, scientists focused on an area off the southeast coast of India. Using electron microscopes and spectrometers, the researchers revealed the presence of fossilized bacteria from the early Holocene era (about 10,000 years ago). These bacteria were closely linked to fossilized microscopic plant fragments. The scientists concluded the bacteria had likely consumed toxic compounds, such as arsenic, from nearby pyrite crystals. The bacteria enabled the crystals to fertilize the soil and retain toxic substances that could stymie plant life. Such information is highly useful for persons looking to understand how toxic substances are absorbed and stored in the soil.

Computer Modeling

Because the processes associated with geomicrobiology commonly transpire over longer periods, it is necessary to compile long-term data to illustrate the process in question clearly. To that end, using two three-dimensional computer models proves highly effective. Some models may focus on long-term concepts, such as fossilization or element cycling. Others focus on a specific region, such as the Antarctic ice shelf. An essential benefit of using computer models is that, once completed, such programs may serve collectively as a skeletal framework for any region or trend, enabling scientists to compare different processes and variables.

An example of this utility of computer modeling can be found in studies of the proposal to store nuclear waste at Yucca Mountain in Nevada. To gauge the effects that microbes would have on this area in light of the waste materials that would be introduced, scientists created a computer code, Microbial Impacts to the Near-Field Environment Geochemistry (MING), which allows researchers to study different species of microbes along with specific temperatures, mineral deposits, and time periods of as long as one million years. By allowing for such a diversity of variables, MING is helping researchers to map and study potential geomicrobiological changes at the site over time.

Evolving Microscopy

The microscope has long been a staple of biology, and geomicrobiology continues to advance because of improvements made to microscopy. One of the most invaluable microscopes is the electron microscope, which can view objects at a magnification hundreds of thousands of times greater than a standard microscope. Electron microscopes can now show geomicrobiological study subjects in three dimensions and with greater clarity than previous incarnations; this allows scientists to study such trends as microbial colonization and element cycling, among other phenomena. Some electron microscopes can examine the internal structure of microbes. This technology uses X-rays to look inside these microorganisms with extraordinary clarity.

In addition to using microscopy, geomicrobiologists frequently use chromatographers and spectrometers. This technology is designed to capture special affinities of microbes, such as gaseous or liquid by-products in the case of chromatographs, and the release of energy in the case of spectrometry. For example, spectrometers have been used to study isotope excursions. Similarly, chromatographs study the release of energy in the metabolic processes of microbes during elemental cycling. These technologies add a new dimension to geomicrobiology.

Relevant Organizations and Networks

Geomicrobiology presents a wide range of implications for the scientific community and for others concerned with global climate change especially. Many interested organizations take geomicrobiology as a starting point for their involvement in scientific research into climate change.

Several government agencies in the United States have departments dedicated to geomicrobiology. The U.S. Geological Survey (USGS), for example, runs a special project focused on geomicrobiology and the broader field of geobiology. This project includes a study of the genetic composition of microbial mats and the role microorganisms play in their respective environments. Also, the National Science Foundation provides funding for geomicrobiology research.

Universities and colleges play key roles in studying geomicrobiology. Princeton University's Department of Geosciences, for example, has a geomicrobiology group dedicated to the study and public dissemination of information in this field. Manchester University in England and Aarhus University in Denmark also have strong programs in this interdisciplinary arena. It is at many of these universities that the leading theories and research on active and historical volcanic sites, for example, are developed and investigated.

Because information can be shared globally instantly using the Internet, geomicrobiology research continues to gain importance. Princeton's geomicrobiology and similar groups collaborate on projects and share data with their colleagues worldwide. Other networks, such as the Geological Society of America, have divisions and programs in geobiology and geomicrobiology.

Implications and Future Prospects

The field of geomicrobiology is relatively new and ever-evolving. Twenty-first-century technology has further enabled scientists to track the relationship between microorganisms and their geological environment. Modern scientists better understand the complex processes that shaped the Earth throughout its history. Computer systems capable of compiling large volumes of data and using this data to develop models are helping researchers analyze trends that occur over thousands, if not millions, of years. These technologies are also helping geomicrobiologists study such pressing issues as pollution and climate change.

Principal Terms

anoxic: a physical state in which oxygen is low

bioremediation: a geomicrobiological process whereby bacteria, microbes, and other microorganisms consume pollutants and deposit water, nutrients, and other by-products

elemental cycling: the process by which elements move in various forms through the planet's subterranean, ground-level, and above-ground environments

microbe: a microscopic organism capable of causing fermentation or disease

microbial mat: a rubbery sheet comprising layers of different species of bacteria and microbes

stromatolite: a fossilized microbial mat

weathering: a geological process whereby igneous, metamorphic, or sedimentary rock is broken down into smaller particles

Bibliography

Archana, G. “Geomicrobiology: An Indian Perspective.” Current Science, vol. 100, no. 4, 2011, pp. 451-52.

Brown, David J., and Martin Lee. “From Microscopic Minerals to Global Climate Change?” Geology Today, vol. 23, no. 5, 2007, pp. 172-77.

Canfield, Don, et al. Aquatic Geomicrobiology. Academic Press/Elsevier, 2005.

Ehrlic, Henry Lutz, and Dianne K. Newman. Geomicrobiology. 6th ed., CRC Press, 2016.

Konhauser, Kurt. Introduction to Geomicrobiology. 2nd ed., Wiley-Blackwell, 2020.

Lopez-Fernandez, Margarita, et al. "Bentonite Geomicrobiology." The Microbiology of Nuclear Waste Disposal, 2021, pp. 137-55. doi.org/10.1016/B978-0-12-818695-4.00007-1.

Michael, Greenwood. "What is Geomicrobiology?" News-Medical, 2021, www.news-medical.net/life-sciences/What-is-Geomicrobiology.aspx. Accessed 20 July 2024.

O’Brien, Rachel, and Jennifer A. Roberts. “Teaching the Principles of Geomicrobiology and the Process of Experimental Research to Undergraduate and First-Year Graduate Students.” Journal of College Science Teaching, vol. 38, no. 2, 2008, pp. 30-38.

Staicu, Lucian C., and Larry Barton. Geomicrobiology: Natural and Anthropogenic Settings. Springer, 2024.

Suzuki, et al. "Deep Microbial Proliferation at the Basalt Interface in 33.5–104 Million-year-old Oceanic Crust." Communications Microbiology, vol. 3, no. 136, 2020 www.nature.com/articles/s42003-020-0860-1.