Part of Our World: Microbial Biodiversity Drives Innovation

Microbes make considerable contributions to, and are greatly affected by, the environment in which they exist and function. When that environment is altered by climate change, the microbial population changes too. For example, drastic increase or decrease in temperature or moisture levels or higher concentrations of toxic substances like heavy metals, plastics or agrochemicals force microbes to evolve in order to survive. These uniquely evolved traits can help rid the environment of those substances, which might be toxic to most, if not all, other life forms.

A flooded farm in Berrigan, New South Wales, 2 months after the flood.
A flooded farm in Berrigan, New South Wales, 2 months after the initial flood event.
Source: Wikimedia Commons

Bioremediation Applications for Microbes Abound

The ASM Microbe 2023 Applied and Environmental Science (AES) track highlighted how microbes work (and can be put to good use) in diverse environments. For example, the AES session, “Environmental Biotechnology for and Biodegradation of Forever Chemicals: PFAS and Plastics,” explored new discoveries about microbial communities that possess the unique ability to degrade polyfluoroalkyl substances (PFAS), plastics and other soil and environmental contaminants. PFAS, which are present in industrial processes and household items, like cleaning products, personal care products or nonstick cookware, can move through soil and contaminate sources of drinking water, as well as accumulate in fish and other marine life.

Microbes are uniquely positioned with the potential for degradation of emerging contaminants that could negatively affect animal and human health. The session examined "the process of how microbes act on those contaminants in the environment [and seek to] understand the process of that bioremediation, as well as ways to try to stimulate or control that process,” said Erica Majumder, Ph.D., Assistant Professor of Bacteriology at the University of Wisconsin-Madison and Track Leader for AES.

Another way microbiologists are using microbes to address environmental problems is by inoculating plant seeds with engineered microbes that can help promote disease suppression, provide a buffer from stress and reduce the need for agrochemical treatments. “The emphasis here is on understanding the microbiome associated with plants and how you might inoculate seeds to promote certain plant traits,” said Ariane Peralta Ph.D., Associate Professor in the Department of Biology at East Carolina University. “Helping to reduce the incidence of plant or fungal pathogens down the road can help sustain nutrient management and increase yield.” The role of microbes in agriculture extends far and wide, ranging from the role of microbes in crop production to exploring and understanding how the relationships between microbes and livestock can be used to promote safety and sustainability.

Microbes in a Changing Environment

Microbes can subsist and even thrive in diverse environments, providing they find ways to adapt when they encounter change. The microbial environment is continuously shifting—the sudden absence or overabundance of resources, the introduction of new microbes to a community and the effects of human behavior or intervention on a given ecosystem all play a role. “Ecology, Evolution and Biodiversity (EEB) is now becoming centralized and integrated across other tracks,” said Britt Koskella, Ph.D., Associate Professor in the Department of Integrative Biology at the University of California, Berkeley and Track Leader for EEB at ASM Microbe 2023. “There’s clearly a great deal of overlapping interest between EEB and Climate Change & Microbes (CMM) (the newly incorporated ASM Microbe guest track), so I’m excited to explore the topic integration across both tracks.”

At the crux of that interface was the EEB track session, “Microbiome Management in a Changing World,” which examined applications in microbial ecology and evolution when developing or implementing solutions to environmental problems. “Microbes adapt far more quickly than plants and animals,” Koskella said. “We’re looking at how we might actually leverage that rapid adaptation to stay ahead of change.”

Research in both EEB and AES are also relevant to the emerging subfield of disaster microbiology, which examines the effects of severe storms and natural disasters on microbes. Severe upheaval of microbial populations, due to tornadoes, floods, fires, heat waves, hurricanes and other natural or human-made disasters, can force microbes to further adapt to new environmental stressors. These microbial adaptions can have major impacts on human health—some microbes might become pathogenic or increase in pathogenicity, while others develop new potential for beneficial applications like bioremediation.

For example, soil salinity is a major agricultural issue because it inhibits or prevents crop growth. The Tohoku earthquake triggered a massive tsunami in Japan in 2011, which significantly increased salt content in the soil. Not long after, scientists demonstrated that application of halophilic microorganisms and recycled waste glass to tsunami-affected ground could reduce the hypersalinity of the soil. Understanding microbial adaptation and evolution becomes increasingly crucial as the occurrence of natural disasters grows more common with rising global surface temperatures.

Disaster Microbiology,” an EEB session at ASM Microbe 2023, illustrated the variety of research that applies to the emerging area of study, explored the effect of natural or human-made disasters on microbes and examined the potential impact that an increasing frequency of such disasters could have on microbes and their evolution.

Microbes as Indicators and Predictors for Protecting Human Health

After a natural disaster, contaminated wastewater and runoff can quickly spread disease. Wastewater surveillance is a valuable tool that can be used to identify and respond to outbreaks. “Before the start of the COVID-19 pandemic, far fewer people were aware of wastewater epidemiology,” AES Track Leader Majumder said. “But many microbiologists working within AES have been focused on that their entire careers.”

Utility workers access sewer pipes to obtain wastewater test samples.
COVID-19 Wastewater testing at Oregon State University.
Source: Oregon State University, 2021

Scientists used wastewater surveillance as a tool to observe and respond to outbreaks long before the emergence of SARS-CoV-2—in the 1930s, infectious poliovirus was found in the sewage of cities experiencing outbreaks. Human pathogens excreted in bodily fluids, or present on skin or hair during the period of active infection, pass into sewage systems during bathing, cleaning and waste elimination. Now, monitoring pathogen presence through wastewater surveillance can provide earlier detection of an outbreak and inform scientists of newly developed variants, including those of SARS-CoV-2, influenza, Norovirus and mpox.

This year at ASM Microbe 2023, the AES track session, “Ethics, Policy and Methods in Wastewater-based Surveillance,” reviewed new and emerging technologies within wastewater surveillance, as well as the direction of the field and ethical implications to keep in mind as those technologies and methods are developed.

Evolution Can Generate Stronger Pathogens

Ecology and evolution constantly drive new variation in pathogens, and examining these variations can provide clues as to how we might better respond to emerging pathogens that threaten human health. “Having recently gone through the COVID-19 pandemic and seeing how a virus can shift, [this topic] is particularly relevant,” EEB Track Leader Koskella said. The ASM Microbe 2023 session, "Switching It Up: Viral Recombination as a Driver of Diversity," covered the mechanisms of recombination in RNA viruses and detailed the best laboratory and analytical practices to detect the exchange of genetic material between microorganisms. A key concern, according to Koskella, is “how rapidly viruses can reassort their genes, pick up new genes or develop new host range.” This session looked at examples from the emergence and spread of SARS-CoV-2 variants to facilitate better understanding of the ways in which recombination can drive viral evolution and cause changes in virulence.

Evolution of parasites genes is another area of interest. Parasitic genes give no known benefit to the host but are still maintained in genomes—the question remains, what, if any, purpose do these genes serve to the organism, or is the moniker of parasite accurately bestowed? In pursuit of answers, the ASM Microbe 2023 session "Parasitic Genes as Drivers of Microbial Ecology and Evolution" examined different classes and examples of parasitic genes and how they evolve. “These 2 sessions are really going to highlight how important microbial evolutionary change is and how rapidly it can occur,” Koskella said.

The Math of Microbes 

The foundation of existing knowledge within microbiology increases scientists’ ability to make more accurate predictions in commensal ecological systems, as well novel pathogens. “With the information about metabolic use and overlap, we can begin to predict and describe species coexistence, which is critical to future predictability and microbiome engineering,” Koskella said. "Math of Microbes: Computation and Mathematical Modeling of Microbial Interactions,” highlighted how data sets can be leveraged to identify what functional capabilities microbial communities have, how to distill that data into parts and how to model it to be able to make predictions.

“To me, where ecology and evolution is critical at this moment in the microbiome field, is that we can use these molecular approaches to understand what microbes are present, what they are doing and how,” Koskella said. “Identifying why they are there and how we might predict who might be present in the future is a question completely rooted in ecology and evolution.”

Listen as Dr. Jessica Lee, scientist for the Space Biosciences Research Branch at NASA's AIMS Research Center in Silicon Valley, discusses microbial food production in space and the impacts of microgravity and extreme radiation when sending Saccharomyces cerevisiae to the moon.

As Above, So Below

Apollo 11 astronaut Buzz Aldrin on the Moon.Apollo 11 astronaut Buzz Aldrin on the moon.
Source: NASA
AES even extends beyond Earth’s atmosphere to examine microbes in outer space. The ASM Microbe 2023 session “The Microbiology of Human Spaceflight: Astronaut Health and Habitat Sustainability,” provided an overview of key research topics and issues that must be resolved to successfully conduct human space exploration. “Even for those who may not be specifically working in the field of space microbiology, it touches a wide variety of areas of microbial research and several AES subtracks,” Majumder said. “It combines so many different aspects of health and sustainability and even agriculture.” Though there are marked differences between how microbes function in space and how they function on Earth, exploring microbial resolutions for the unique challenges of space travel can support and translate into solution development in agriculture and human health—for example, identifying ways that microbes can perform processes usually performed by plants, like vitamin production, water recycling, air decontamination and waste management.

Still, how microbes behave in synthetic communities is not necessarily how they behave in natural communities. As best as the conditions of space can be replicated in a lab on Earth, environmental factors and members of Earth-bound microbial consortia that cannot be accounted for or incorporated in a synthetic community may mean microbes behave differently than expected outside that community. 

ASM Microbe 2023’s panel discussion, "The Opportunities and Pitfalls of Synthetic Community Research,” addressed the perks and limitations of synthetic community research in developing solutions. “We can use these simplified synthetic communities to understand how microbes interact, how they work together—or don’t,” Koskella explained. “As you expand ecological reality, those interactions may not always be applicable.” Peralta also noted the opportunity to recognize and leverage generalizable patterns, while acknowledging the variation microbes provide in ecological systems. “There’s a point where oversimplifying or overengineering a system can actually make it more likely to fail more quickly in response to new stressors,” Peralta said. “We’re looking at how to manage microbes and microbial functions in a way that’s more accurate.”

Author: Emily Ready

Emily Ready
Emily Ready is the Communications Program Officer at ASM. She earned her Bachelor of Arts degree in Public Relations from the University of South Carolina.