Environmental Microbiology, Ecology, & Evolution

FAQ: Microbiology of Built Environments, May 2016

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Built environments are the structures that humans create to shelter from the outdoors and provide spaces for living, working, playing, and getting places. Along with humans, pets, pests, and house plants, built environments house a range of microbes. Preliminary studies indicate that indoor spaces have distinct microbial communities, influenced by building materials, ventilation and airflow, moisture, and human and animal activity. The Academy convened a colloquium in September 2015 to examine the role of complex microbial ecosystems found in built environments, including their effects on building chemistry and human health. Studying the microbiology of built environments can change the ways we design, build, operate, occupy, and clean our indoor spaces.



FAQ: Interactions Between Climate Change and Microbial Ecosystems, March 2016

The Academy convened a colloquium on March 3, 2016 to discuss interactions between the earth’s changing climate and microbial function. This colloquium was a collaborative effort between the ASM and the American Geophysical Union (AGU), whose mission is to galvanize a community of Earth and space scientists that collaboratively advance and communicate science and its power to ensure a sustainable future. This colloquium was aimed at addressing the significance of microbes in the expanding biogeochemistry field. The report is currently being written and will be released in fall 2016.

Viruses Throughout Life & Time: Friends, Foes, Change Agents








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Executive Summary
In contrast to their negative reputation as disease causing agents, some viruses can perform crucial biological and evolutionary functions that help to shape the world we live in today, according to Viruses Throughout Life & Time: Friends, Foes, Change AgentsViruses Throughout Life & Time: Friends, Foes, Change Agents is based on the deliberation of a group of scientific experts who gathered for two days in San Francisco, CA in July 2013 to answer a series of questions regarding the variety of roles that viruses play in the natural world.

FAQ: Human Microbiome, January 2014



The human microbiome, the collection of trillions of microbes living in and on the human body, is not random, and scientists believe that it plays a role in many basic life processes.  As science continues to explore and better understand the identities and activities of the microbial species comprising the human microbiome, microbiologists hope to draw connections between microbiome composition, host genetics, and human health.  FAQ: Human Microbiome addresses this growing area of research.







Teaching Materials:

Human Microbiome Infographic
Human Microbiome Trifold

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How Microbes Can Help Feed the World, August 2013


 Feed the World

"How Microbes can Help Feed the World" looks in depth at the intimate relationship between microbes and agriculture including why plants need microbes, what types of microbes they need, how they interact and the scientific challenges posed by the current state of knowledge.  It then makes a series of recommendations, including greater investment in research, the taking on of one or more grand challenges such as characterization of the complete microbiome of one important crop plant, and the establishment of a formal process for moving scientific discoveries from the lab to the field.





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FAQ: West Nile Virus, July 2013

west nile  

Where does the virus come from? How is it spread? Can we predict when and where outbreaks will occur? What factors determine how sick a person will become if they are infected with West Nile virus?

To help answer the many questions people have about this multi-faceted virus, the American Academy of Microbiology has issued a new report entitled FAQ: West Nile Virus. The Academy convened twenty-two of the world’s leading experts on West Nile virus in March, 2013 to consider and answer some of the most frequently asked questions about West Nile virus. The resultant report provides non-technical, science-based answers to questions that people may have about the virus.



FAQ: Influenza, April 2013


Where do new influenza viruses come from? How are they different from the influenza viruses that circulate every year? Why is vaccination so important? To help answer the many questions people have about this multi-faceted virus, the American Academy of Microbiology has issued a new report entitled FAQ: Influenza. The Academy convened twelve of the world’s leading experts on influenza in October, 2012 to consider and answer some of the most frequently asked questions about influenza. The resultant report provides non-technical, science-based answers to questions that people may have about the virus.




Moving Targets: Fighting the Evolution of Resistance in Infections, Pests, and Cancer, March 2013



Concerned about antibiotic resistance? What if an insect pest becomes desensitized to the protective chemicals applied to crops? All kinds of living organisms have evolved mechanisms of resistance against the chemicals designed to control them – from bacteria, viruses, cancer cells to weeds. In the Academy of Microbiology’s newest, free report, explore the Darwinian principles underlying the evolution of resistance in these different biological communities and learn how experts in these fields have developed potentially discipline-spanning strategies of combatting them. 





Microbes in Pipes: The Microbiology of the Water Distribution System, January 2013



Non-microbiologists may assume that the goal of water utilities should be the elimination of all microbes from our drinking water. But the water we drink has never been sterile; perfectly safe water contains millions of non-pathogenic microbes in every glassful. Like every other human built environment, the entire water distribution system — every reservoir, every well, every pipe, and every faucet — is home to hundreds or thousands of species of bacteria, algae, invertebrates, and viruses, most of which are completely harmless to humans. In April, 2012, the American Academy of Microbiology convened a colloquium to assess what is known about the microbial inhabitants of the water distribution system and to propose goals for advancing our understanding of these communities in order to enhance the safety of our drinking water and the resilience of our water infrastructure.

Incorporating Microbial Processes into Climate Models, February 2012

Microbes are critical players in every geochemical cycle relevant to climate including carbon, nitrogen, sulfur, and others. The sum total of microbial activity is enormous, but the net effect of microbial activities on the concentration of carbon dioxide and other climate-relevant gases is currently not known. In February of 2011, the American Academy of Microbiology convened a colloquium to discuss how to integrate microbiological processes and climate models. Based on that colloquium, this report examines our current understanding of how microbes influence climate and identifies key biogeochemical processes, heavily influenced by microbes, which offer attractive starting points to begin collaborations between the two fields. The report also recommends changes to data collection and accessibility, improved incentives for interdisciplinary collaborations, and the development of new technologies as important steps. While the challenge of integrating microbes into climate models is great, one thing is certain, microbes are a force in climate change that cannot be ignored.

Microbial Evolution, August 2011



It has been over 150 years since the publication of On the Origin of Species, Charles Darwin’s landmark book based on his observations of animals in the Galapagos Islands. The two core principles he described in his work, descent with modification and natural selection, have helped us understand life’s tremendous diversity. But how do these same principles pertain to the microbial world that Darwin could not see? In 2009 the American Academy of Microbiology convened a colloquium in the Galapagos Islands to address this question. Based on that colloquium, this report summarizes the unique challenges posed by microbes, like vast evolutionary time scale, genetic promiscuity and rapid division, which complicate understanding microbial evolution. It also identifies areas of research and education where more information is needed to overcome these challenges. The report concludes that due to the power of microbes as model systems, tools in biotechnology, and drivers in biogeochemical and climate cycles, understanding microbial evolution may give us more than just the ability to understand microbial diversity; it will help understand the world around us.

The Rare Biosphere, August 2011



The microbial world represents the last truly unexplored frontier in the diversity of life on Earth. New environmental sampling technologies have revealed a wealth of rare microbial species in the soil, ocean, even our own bodies that were effectively cloaked from previous sampling methods by more abundant species. Dubbed the rare biosphere, these microbial species, while individually rare, collectively account for more than 75% of the biomass of some microbial communities, yet little is known about them. This rare biosphere represents a treasure trove of genetic novelty that may possess numerous unique bioprocesses and biomaterials. These rare species may play keystone roles in microbial communities and act as a reservoir of genetic diversity. But how can scientists effectively study the rare biosphere? In April 2009 the American Academy of Microbiology convened a colloquium to explore this question. Based on that colloquium, this report analyzes the current state of study of the rare biosphere and identifies where gaps in knowledge exist. The report concludes that the Herculean task of studying the rare biosphere requires an international collaborative effort and additional environmental sampling, coupled with a focus on advancing sequencing and data analysis technologies. With less than 1% of microbial species able to be grown in the laboratory, the prospects of new discoveries in the rare biosphere seem as vast as microbial diversity itself.

FAQ: Microbes and Oil Spills, February 2011



Is it true that microbes cleaned up the oil spill in the Gulf of Mexico? Can bacteria really “eat” oil, and if so, how? To help clear up the confusion the American Academy of Microbiology has brought together the nation’s leading experts to consider and answer some of the most frequently asked questions regarding microbes and oil spills. This mini-colloquium, the first in a new series of reports designed to provide a rapid response to emerging issues, took place at ASM Headquarters in Washington, DC on October 28, 2010.




Teaching Materials

ASM Curriculum Guidelines Description

Large-Scale Sequencing: The Future of Genomic Sciences? December 2009



Scientists can gain insights into new ways to use microorganisms in medicine and manufacturing through a coordinated large-scale effort to sequence the genomes of not just individual microorganisms but entire ecosystems, according to a new report from the American Academy of Microbiology that outlines recommendations for this massive effort. The report, “Large-Scale Sequencing: The Future of Genomic Sciences?” is based on a colloquium convened by the Academy in September 2008. The report outlines recommendations for large-scale microbial sequencing efforts directed toward cultivated isolates and single cells, as well as a community-scale approach to characterize a set of defined ecosystems of varying complexity.

Antibiotic Resistance: An Ecological Perspective on an Old Problem, September 2009



According to the report, it is possible to co-exist with resistance by- developing new strategies to prevent resistance from spreading and, where it already exists, identify the strains we need to protect against; find new ways to treat resistance infections effectively in patients; and manage reservoirs of antibiotic strains in the environment. The report summarizes the current scientific understanding of antibiotic resistance, the scope of the problem, and methods at our disposal for detecting emergence and preventing spread. The knowledge gaps about the prevalence of resistant strains and resistant infections are highlighted as are the unique problems and challenges in developing countries.

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The Fungal Kingdom: Diverse and Essential Roles in Earth's Ecosystem, 2008

Prepared by Arturo Casadevall, Joe Heitman, and Merry Buckley.

Fungi can cause a number of life-threatening diseases but they also are becoming increasingly useful to science and manufacturing every year. However, many people, scientists among them, are largely unaware of the roles fungi play in the world around us. Research on fungi and fungal diseases are seriously neglected as a result – a situation with grave negative repercussions for human health, agriculture, and the environment. The Fungal Kingdom explores the roles fungi play in the world around us.

ABC Radio Broadcast Transcript

Dr. Casadevall is interviewed by ABC Radio National, Australia

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Uncharted Microbial World: Microbes and Their Activities in the Environment, 2008



Prepared by Caroline Harwood and Merry Buckley.

Humans live in the midst of a seething, breathing microbial world. Microorganisms populate every conceivable habitat, both familiar and exotic, from the surface of the human skin, to rainforest floors, to hydrothermal vents in the ocean floors. Despite the powerful and pervasive role of microbes in sustaining life, most of the microbial world remains a mystery. This is the subject of The Uncharted Microbial World: Microbes and Their Activities in the Environment.

Mycobacterium avium paratuberculosis: Infrequent Human Pathogen or Public Health Threat? August 2008


Prepared by Carol Nacy and Merry Buckley.

People with Crohn’s disease (CD) are seven-fold more likely to have in their gut tissues the bacterium that causes a digestive-tract disease in cattle called Johne’s disease. The role this bacterium may or may not play in causing CD is a top research priority. This report points out that the cause of Crohn’s disease is unknown, and the possible role of this bacterium, which could conceivably be passed up the food chain to people, has received too little attention from the research community.

Microbial Energy Conversion, 2006


Prepared by Merry Buckley and Judy Wall.

The report details one of the world’s largest problems – the need for clean, renewable sources of energy.

Marine Microbial Diversity: The Key to Earth's Habitability, December 2005



Prepared by Jennie Hunter-Cevera, David Karl, and Merry Buckley.

The report outlines how life on Earth may owe its existence to tiny microorganisms living in oceans, but the effect of human-induced change on the vital services these microbes perform for the planet remains largely unstudied.

From Outside to Inside: Environmental Microorganisms as Human Pathogens, 2005



Prepared by Gerard A. Cangelosi, Nancy E. Freitag, and Merry R. Buckley.

While many infectious diseases are caused by human-to-human transmission, others are caused by microorganisms that exist in the outside environment. The difference between the two is the ability for environmental pathogens to survive and thrive outside the host. The report recommends that scientists from different fields work together to address the challenges presented by these environmental pathogens.

The Global Genome Question: Microbes as the Key to Understanding Evolution and Ecology, 2004


Prepared by Merry R. Buckley.

Examines the current state of knowledge of microbial genomics, the technical challenges of using genomics in microbial systems, and the achievements that may now be possible by applying genomics to the study of microbiology. Makes recommendations for future directions in education and research.

100 Years of Bacillus thuringiensis: A Critical Scientific Assessment, 2002



Prepared by Eugene Nester, Ph.D., Linda S. Thomashow, Ph.D., Matthew Metz, Ph.D., and Milton Gordon, Ph.D.

Presents the case of Bacillus thuringiensis (Bt) and its use in agriculture. Compares genetic modification of crops to alternatives and addresses the current controversy, positive outcomes, and potential risks associated with transgenic plants. Makes specific recommendations for future research, evaluation and environmental monitoring, scientific coordination, and public education.

Microbial Communities: From Life Apart to Life Together, 2002

Prepared by Merry Buckley.

Discusses issues surrounding microbial communities and their role in human health, industrial processes, and ecological functions, with recommendations for future research, education, and collaboration.

Microbial Ecology and Genomics: A Crossroads of Opportunity, 2002



Prepared by David A. Stahl and James Tiedje.

Examines the explosion of new information in microbial biology made available by recent advances in molecular technology--and looks at the important questions that remain. Recommends next steps for the integration of genomics with microbial systematics, evolution, and ecology.

Antimicrobial Resistance: An Ecological Perspective, 2002



Synthesizes conclusions reached by working groups at 1999 colloquium. Takes a broad view of the problem of increasing resistance to antimicrobials and its consequences for human, animal, and environmental health. Provides an overview of the current situation and offers specific recommendations for scientific research, surveillance programs, and education efforts.

Geobiology: Exploring the Interface Between the Biosphere and the Geosphere, 2001

Prepared by Kenneth Nealson, William A. Ghiorse, and Evelyn Strauss.

This report identifies possibilities and challenges facing the developing, interdisciplinary science of geobiology.

Health, Climate and Infectious Disease: A Global Perspective, 2001



Prepared by Joan B. Rose, Anwar Huq, and Erin K. Lipp.

Takes a look at the combined advances in microbiology, meteorology, climatology, epidemiology, oceanography, ecology, medicine, and space science that are shedding light on the intricate connections between weather, oceans, and emerging and re-emerging diseases. Makes specific recommendations for future data collection, research collaboration, risk assessment, and the use of technology and molecular techniques.

Climate, Infectious Disease and Health: An Interdisciplinary Perspective, 1998



Prepared by Rita R. Colwell, and Jonathan A. Patz.

Discusses research issues relating to the effects of climate on the incidence and distribution of infectious disease. Addresses specific infectious diseases and offers recommendations for future research.

A Global Decline in Microbiological Safety of Water: A Call for Action, 1995



Prepared by Timothy E. Ford, Ph.D., and Rita R. Colwell, Ph.D., D.Sc.

Discusses issues in identification of the current extent of waterborne disease outbreaks, the future threat of waterborne outbreaks, and epidemics (and potential pandemics) within both developed and developing countries. Provides a framework for addressing these water quality issues globally.