Environmental Microbiology

Summary

The majority of Earth's biomass consists of microorganisms, and everything consumed and created by microorganisms significantly impacts the surrounding environment and all other living organisms. Environmental microbiology focuses on the role of these microorganisms in both causing environmental deterioration and rectifying ecological degradation while also considering microbial ecology in both natural and polluted environments. Environmental microbiology technology harnesses the natural ability of microorganisms to remove pollutants, such as crude oil and industrial waste, from the environment.

Definition and Basic Principles

Environmental microbiology is the study of microbial community structure and physiology within the environment, whether soil, water, or air. At a fundamental level, environmental microbiology is the study of the role of microorganisms as both the cause and the remediation of environmental pollution and ecological degradation.

Environmental microbiology is a multidisciplinary science, blending environmental science and the biology of microscopic organisms. It involves the development, application, adaptation, and management of biological systems and microorganisms to repair and prevent environmental damage caused by pollution. This discipline investigates how microorganisms can be both detrimental and beneficial to the environment and human society, particularly in relation to the restoration and remediation of the world's natural environment (air, water, and soil). The field has benefited from advancements in genetic engineering and modern microbiological concepts, which have encouraged the development of traditional and innovative solutions to environmental contamination.

Background and History

Any discussion of environmental microbiology must touch on the history of microbial discovery. Although the technology involved in environmental microbiology is evolving and expanding, the first steps toward the establishment of this field began hundreds of years ago with the discovery of microorganisms. In the mid-seventeenth century, both Antoni van Leeuwenhoek and Robert Hooke observed nonliving and living microorganisms under self-made microscopes, thereby discovering the reason behind one of nature's conundrums—the decomposition of plants and animals. Although the identification of microbes (living things not visible to the naked eye) in 1675 was instrumental in advancing biological science, the true significance of the role of microbes in disease was not understood until some two hundred years later.

By the late nineteenth century, research conducted by Dutch microbiologist Martinus W. Beijerinck and Russian microbiologist Sergei Winogradsky had greatly advanced the understanding of microorganisms and their possible role in ecological processes. Beijerinck developed a method for isolating microorganisms called the enrichment culture technique, and Winogradsky enhanced scientific awareness of microbial diversity and discovered the autotrophic (self-feeding) ability of bacteria. He went on to develop the Winogradsky column culture technique, which showed that water in a lake contains a number of organisms performing various processes at different levels. The discipline of environmental microbiology was made possible by the work of these early scientists. Although traditional microbe research focused on the role of microbes in causing disease, Beijerinck and Winogradsky began to examine their role in disease prevention.

The roots of environmental microbiology also lie in urban waste management and treatment. The field originally focused on monitoring the movement of pathogens and treating them within natural and urban environments to protect municipal water quality and public health. As the world became more urbanized in the late nineteenth century, the incidence of communicable diseases such as typhoid fever and cholera increased. To combat the spread of diseases, cities and communities began to treat water with various filtration and disinfectant methods. For the most part, such approaches to water treatment were instrumental in the elimination of waterborne bacterial diseases in developed countries, and disinfection processes continue to be widely used.

As research continued into the 1960s, however, it became apparent that the viruses and protozoa parasites that caused waterborne diseases were much more resistant to the process of disinfection than were bacteria. Already treated urban water supplies were still plagued by uncontrolled outbreaks of giardia (which causes giardiasis), cryptosporidium (which causes cryptosporidiosis), and norovirus (which causes gastroenteritis). Although serious outbreaks within the developed world are rare, the continued occurrence of water pathogens has meant that the field of environmental microbiology still has a very strong focus on water quality and the treatment and control of water pathogens. Perhaps of most concern is the fact that some 10 to 50 percent of diarrheal illnesses are caused by waterborne microbial organisms not yet identified by science.

Before long, the effects of water quality on human health were not the only area of concern for environmental microbiology. By the 1960s, concern over the effects of chemicals in the natural environment had increased, and it became obvious that poor human health was not the only issue. Chemicals in the soil and water found their way into the human food chain through groundwater use and consumption, affecting not only human health but also animal and plant species using those same soil and water supplies. Significant chemical contamination, such as the massive Exxon Valdez oil spill in 1989, highlighted the need to investigate the potential for microorganisms in bioremediation. In the twenty-first century, the use of microorganisms in the treatment and control of pathogens and bioremediation processes is a key feature of environmental microbiology.

How It Works

Microorganisms are found in all areas of the biosphere, even environments of extreme temperatures, acidity, salinity, and darkness that are inhospitable to most other organisms. They account for the vast majority of Earth's biomass. The entire number of microorganisms living on Earth is almost immeasurable, but it is estimated that more than 1 billion microorganisms live in just 1 gram of soil. Microorganisms are vital to the health and function of the planet and are responsible for a vast number of natural life processes. They are the most significant players involved in the synthesis and degradation of important molecules. They provide energy to other organisms, are responsible for most of the planet's photosynthesis, are able to fix nitrogen and recycle nutrients in ecosystems, and are also capable of causing lethal diseases for humans, flora, and fauna.

Fundamentally, environmental microbiology is about harnessing the natural ability of microbes and their relationships with other microbes to address environmental issues and solve environmental problems. The main focus of environmental microbiology remains the use of microorganisms in the treatment and control of pathogens and in bioremediation processes. Modern-day technological advancements in genetic engineering and biotechnology have, however, greatly increased the applications of this scientific field. The increased applications for environmental microbiology are important in view of the ability of pathogens such as bacteria and viruses to evolve and emerge rapidly in an environment under increasing stress from the human population.

Applications and Products

The application of genomics and molecular biology to environmental microbiology has allowed scientists to discover the vast diversity and complexity that exists in natural microorganism communities. Despite advanced human-developed technology, however, it is estimated that only a small number of microorganisms have actually been described by science or have been grown in laboratory conditions. This means that scientists not only are unsure of all the possible effects of such organisms on human health and the environment but also have not even begun to understand or determine the many potential applications and products of such organisms.

New discoveries and principles of environmental microbiology can have vast potential in other areas of science, such as biotechnology, pharmaceutics, biomedical research and engineering, the chemical and textile industries, bioremediation and wastewater treatment, pathogen control, mineral recovery, sustainable agriculture, and resource conservation. However, the majority of research is in the applications for bioremediation, water quality, and the biotreatment of waste material and wastewater.

Bioremediation. Human society is increasingly exploiting the flexible appetite of microbes (particularly bacteria) to remediate environments containing contaminants such as industrial waste, crude oil, and polychlorinated biphenyls (PCBs). Bioremediation is usually classified as either in situ or ex situ and is defined as the use of microorganisms, such as fungi and bacteria, and their enzymes to return a contaminated environment to its original condition. In situ, bioremediation entails treating the contamination in place and relies on the ability of the microorganisms to metabolize or remove the contaminants inside a naturally occurring system. Ex situ remediation involves removing the polluted material from the site and treating it elsewhere, and it relies on some form of artificial engineering and input. Although the process of bioremediation can occur naturally, it can be promoted through artificial human stimulus through the use of environmental microbiology technology.

For example, environmental microbiology technology is used to remediate crude oil spills in coastal areas. Although oil is a naturally occurring fossil fuel, it can cause significant ecological damage when accidentally introduced into marine (and terrestrial) environments during oil spills. Large spills can be difficult to contain and collect. The longer a spill remains in the environment, the greater the potential damage. Environmental microbiology techniques, specifically hydrocarbonoclastic bacteria (HCB), can be used to clean up oil spills. These bacteria can degrade hydrocarbons (in this case, oil) and are, therefore, beneficial as bioremediators.

Waste Biotreatment and Water Quality Treatment. Biotreatment processes involve the environmentally friendly treatment of waste material, including wastewater, using living microorganisms. Scientific research has demonstrated that while wastewater processes are one of the most important functions of environmental microbiology and use a significant diversity of microorganisms, many of these microorganisms are yet to be classified or cultured. This indicates that the potential of microbes in biotreatment is not yet fully understood. Research on metagenome technology (metagenomics), however, is highlighting the diversity, structure, and functions of microorganisms. This research has looked at the role of microbes in processes such as nitrogen cycling, anaerobic ammonium oxidation, and methane fermentation in the treatment of wastewater, with a particular focus on the use of bacterial biofilms and bioreactors.

One of the most important applications of environmental microbiology is in controlling waterborne pathogens and diseases. The treatment of drinking water is, of course, not new. Water disinfection processes were key in the fight against bacterial waterborne pathogens. The introduction of environmental microbiology techniques, however, has assisted in controlling pathogens and contaminants other than bacteria. In particular, microorganisms are used to decompose contaminants such as organic matter, nitrates, and phosphate in wastewater and to improve water quality. The removal of organic material is done through both bacterial aerobic and anaerobic decomposition, but the removal of ammonium and nitrates is much more complex. It requires both aerobic and anaerobic conversion to remove the pollutants and involves the bacterial conversion of ammonia to nitrite and nitrate to nitrogen gas, which can be safely released into the atmosphere.

Bioassessment and Bioindicators. In environmental microbiology, bioindicators are bacteria that detect and respond to surrounding environmental conditions. Bioindicators can be any organism and are used in numerous industries and fields of science, including environmental microbiology. Bacteria, however, are considered superior precursors of human-caused environmental degradation, as they possess the highest surface-area-to-volume ratio of all organisms.

Careers and Course Work

Students who wish to pursue a career in environmental microbiology can come from diverse fields but must have a strong grounding in basic microbiology, molecular biology, and environmental science. A solid grasp of genetically modified organisms is also helpful.

Many universities provide undergraduate and postgraduate degrees in environmental microbiology. Upon course completion, students should understand the interactions between microorganisms in natural and artificial environments, particularly contaminated aquatic and terrestrial ecosystems. Most courses focus on teaching and researching fundamental and applied features of biodegradation, bioremediation strategies, and biosensors for toxicity assessment.

Graduates with environmental microbiology degrees who have done postgraduate research can enter careers in environmental and microbiology consulting, water treatment and resource management, bioremediation and bioassessment in the private sector, specialized government organizations and agencies, and universities and institutions undertaking teaching and research.

Social Context and Future Prospects

The growing global population and its impact on the environment, particularly the fresh water supply, make water treatment and bioremediation increasingly important. Future research will continue to focus on these aspects and applications of environmental microbiology. It is estimated that only a small percentage of the world's microbial species have been classified and cultured, which means there is significant unrealized potential for human uses of microorganisms. Many believe, however, that the emergence of metagenome technology holds the key to rapid advancement in microbiology and human understanding of life. Heralded as the most important advancement since the invention of the microscope, metagenomics applies genomic analysis (the examination of an organism's complete DNA) to entire microorganism communities, thereby avoiding the need to isolate and culture individual microbes.

The COVID-19 pandemic demonstrated the need for new technologies to control the spread of airborne pathogens. This became a priority in the 2020s as environmental microbiologists researched technologies such as filters to prevent the spread of bacteria and viruses. They also studied how animals can harbor several microorganisms without developing symptoms of illness. These microorganisms exist in biofilms, which are multispecies associations. Environmental microbiologists hope that developing a better understanding of biofilms might explain the existence and transmission of viruses.

Twenty-first-century research focuses on applying environmental microbiology to remove heavy metal pollution, destroy specific xenobiotics (foreign chemicals found in a living organism), treat water and air pollution caused by carbon dioxide and sulfur dioxide, and develop biodegradable plastics and other useful materials. To prevent bacteria transmission, metals with antimicrobial properties like copper, silver, and gold became increasingly popular for use in frequently touched surfaces. Silver nanoparticles were also increasingly used in building materials and fabrics.

Bibliography

Cummings, Stephen, editor. Bioremediation: Methods and Protocols. Humana, 2010.

Greig, Anissa, et al. "A Pipeline for Targeted Metagenomics of Environmental Bacteria." Microbiome, 15 Feb. 2020, microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-0790-7. Accessed 12 March 2022.

Hurst, Christon J., et al., editors. Manual of Environmental Microbiology. 3rd ed., ASM, 2007.

Illman, Walter, and Pedro Alvarez. “Performance Assessment of Bioremediation and Natural Attenuation.” Critical Reviews in Environmental Science and Technology, vol. 39, no. 4, 2009, pp. 209–70.

Karnwal, Arun. Environmental Microbiology: Advanced Research and Multidisciplinary Applications. Bentham Books, 2022.

Karnwal, Arun, and Abdel Rahman Mohammad. Environmental Microbiology. Bentham Science, 2022. 

Liu, Wen-Tso, and Janet K. Jansson, editors. Environmental Molecular Microbiology. Caister, 2010.

Reineke, Walter, and Michael Schlömann. Environmental Microbiology. 3rd ed., Springer Spektrum, 2023.

Watson, Rowan, et al. "Efficacy of Antimicrobial and Anti-Viral Coated Air Filters to Prevent the Spread of Airborne Pathogens." Scientific Report, vol. 12, doi.org/10.1038/s41598-022-06579-9. Accessed 12 March 2022.