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USGS Microbiology Featured Topics

U.S. Geological Survey microbiology efforts span the disciplines and cover many broad research areas, including fish and wildlife health and disease, climate change, microbial ecology, public health and water quality, geomicrobiology, and ecosystem function.

USGS Microbiology Featured Topics 2010

Searching for New Forms of Life on Earth

Photo: Researchers Ronald Oremland and Felisa Wolfe-Simon examine a mud sample from Mono Lake. Credit: Henry Bortman, Science/AAAS
Photo: Researchers Ronald Oremland and Felisa Wolfe-Simon examine a mud sample from Mono Lake. Credit: Henry Bortman, Science/AAAS.

Researchers in Dr. Ron Oremland’s USGS laboratory in Menlo, Park, California have just discovered a new way to look at and for possible extraterrestrial life. Oremland had previously discovered bacteria in the hypersaline, alkaline,  arsenic-rich Mono Lake in eastern California, that use the usually toxic element in photosynthesis, chemo-autotrophy,  or anaerobic respiratory reactions,  However, it had not been demonstrated that an organism could take up arsenic for internal use to drive cell metabolism. Last year, Dr. Felisa Wolfe-Simon joined Oremland’s lab, supported by a NASA Astrobiology fellowship. She proposed to determine whether arsenic, in the form of the arsenate ion, could be substituted for phosphate ions inside the bacterial cell.  To achieve this, the researchers inoculated sediments from Mono Lake into a growth medium, which contained arsenic but not phosphorus.  They were able to isolate a strain of bacteria (GFAJ-1) that grows in arsenate-rich or phosphate-rich conditions but does not grow when deprived of both arsenate and phosphate.  

tufa towers in Mono Lake
Tufa towers in Mono Lake. Photo credit: USGS.

This is a real breakthrough as previously we have recognized six elements that sustain life (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) to which we now, in some cases, may add arsenic.  Once these initial results were obtained at the USGS, they engaged collaborating colleagues at other institutions (ASU, LLNL, SLAC, Duquesne University) who employed a diversity of analytical tools (e.g., x-ray spectroscopy, nano-SIMS, ICP-mass spectroscopy, electron microscopy) in addition to radioisotope tracers work conducted at USGS to confirm that arsenate was incorporated into internal biomolecules, including the backbone of DNA, a slot usually occupied by phosphate. For further information contact: Dr. Ron Oremland.

Additional Links:

Posted: December 7, 2010

Fecal Bacteria, The

Cover image of publication This book offers an integrated discussion of fecal bacteria and their presence and ecology in the intestinal tract of mammals, the environment, and the food supply. Fecal bacteria are used in examining and assessing water quality in order to offer protection from illnesses related to swimming in or ingesting contaminated water and as indicators of contamination of ready-to-eat foods and fresh produce.

Author: Editors: Michael J. Sadowsky (University of Minnesota) and Richard L. Whitman (US Geological Survey)
Book ISBN or Item Number: 978-1-55581-608-7


USGS Authors/co-authors:

  • Chapter 5. Environmental Sources of Fecal Bacteria, Muruleedhara N. Byappanahalli and Satoshi Ishii
  • Chapter 6. Physical and Biological Factors Influencing Environmental Sources of Fecal Indicator Bacteria in Surface Water, Richard L. Whitman, Meredith B. Nevers, Katarzyna Przybyla-Kelly, and Muruleedhara N. Byappanahalli
  • Chapter 8. Modeling Fate and Transport of Fecal Bacteria in Surface Water, Meredith B. Nevers and Alexandria B. Boehm
  • Chapter 13. Conclusions and Future Use of Fecal Indicator Bacteria for Monitoring Water Quality and Protecting Human Health, Michael J. Sadowsky and Richard L. Whitman

Posted: September 17, 2010

USGS Microbiology Web site Wins 2010 Communication Award

Gloeotrichia sp. with Sytox Green. Photo credit: Barry H. Rosen, USGSThe USGS Interdisciplinary Microbiology Web site facilitates collaboration between scientists and increases the understanding of USGS microbiology to the public. The site is a central place to find the centers, scientists, and research involved in USGS microbiology. In recognition of its valuable information, layout, and design, the Web site won the 2010 Shoemaker Communication Award--an annual communications excellence competition for USGS employees--in the Internet Product category.

USGS scientists from across the disciplines have provided the research summaries, publication announcements, and other information that has made the site a valuable source of news and science in USGS microbiology. The feedback of scientists and the public has been instrumental to the success of the site. If you have questions or comments, please visit the Contact Us page.

Posted: August 10, 2010

A double-crested cormorant with only one functional wing, a typical sign of infection with Newcastle disease (Salton Sea, CA).
Wildlife Health Bulletin: Virulent Newcastle Disease Virus Found in Double-Crested Cormorants
Abnormal puffer fish from Shark’s Cove, Oahu, with cloudy eye and sediment on the back.  Photo credit: (T.M. Work, USGS)
Wildlife Health Bulletin: Puffer Fish Die-off in Hawaii (PDF)
Viruses in Deep Gulf of Mexico Sediments and Cold-Seep Chemosynthetic Communities

Tubeworms and soft corals at a seep site off the west coast of Florida. Photo credit: NOAA/OERMarine viruses, mainly bacteriophages (viruses that specifically infect bacteria) are the most abundant organisms in the ocean and underwater sediments. These viruses affect bacterial diversity and population succession, productivity, and the flow of carbon. Little is known about the distribution and abundance of viruses in deep-sea, cold-seep environments. This paper is the first to present data on viral dynamics from cold-seep environments and sediments below 1000 meters water depth in the Gulf of Mexico. It is part of an upcoming special issue of Deep-Sea Research II that highlights recent work on chemosynthetic communities in the deep Gulf of Mexico.

Read the journal article:

Christina A. Kellogg. Enumeration of viruses and prokaryotes in deep-sea sediments and cold seeps of the Gulf of Mexico. Deep-Sea Research II. 2010. doi: 10.1016/j.dsr2.2010.05.006 (online abstract)

Posted: June 21, 2010

Searching for New Life Forms on Earth

Satellite image of Mono LakeMono Lake, California may host organisms fundamentally different from all other known forms of life. Felisa Wolfe-Simon, in collaboration with Ronald S. Oremland, is studying the biochemical makeup of the microorganims that thrive in the lake's high concentration of arsenic. While Dr. Wolfe-Simon and partners are revealing novel modes of microbial metabolism, the scientists are also testing for microbes with genetic structures based on arsenic, rather than phosphorus. If found, such organisms could lead to new hypotheses about the origin of life on Earth, as well as potential life on other planets.

The following give opinions about Dr. Wolfe-Simon's research:

  • Bortman, Henry. "Searching for Alien Life, on Earth." October 29, 2009. Astrobiology Magazine.
  • Davies, Paul. "The Aliens Among Us." May 13, 2010. The New York Times.
  • Davies, Paul. "The Eerie Silence: Renewing our search for alien intelligence." Houghton Mifflin Harcourt Publishing Co, New York (2010).

For more information, read research summaries about arsenic bioremediation, biogeochemical cycling, and energy sources

Posted: May 17, 2010

Gloeotrichia with Sytox Green.  Photo credit: Barry H. Rosen, USGS USGS Open File Report 2010–1289: Microphotographs of Cyanobacteria Documenting the Effects of Various Cell-lysis Techniques.
White-nose bat syndrome. Al Hicks, New York Department of Environmental Conservation Wildlife Health Bulletin: Geomyces destructans detected in Oklahoma Cave Myotis and Listed Missouri Gray Bats

Policies and Practices of Beach Monitoring in the Great Lakes

East Harbor State Park Port Clinton Ohio - EPAFrom the article: Beaches throughout the Great Lakes are monitored for fecal indicator bacteria (typically Escherichia coli) in order to protect the public from potential sewage contamination. Currently, there is no universal standard for sample collection and analysis or results interpretation. In this review, we highlight the variety of sampling routines used across the Great Lakes and the extensive body of research that challenges comparisons among beaches. We also assess the future of Great Lakes monitoring and the advantages and disadvantages of establishing standards that are evenly applied across all beaches.

Read the journal article:

Meredith B. Nevers and Richard L. Whitman. Policies and practices of beach monitoring in the Great Lakes, USA: a critical review. J. Environ. Monit., 2010, 12, 581 - 590, DOI: 10.1039/b917590c (online abstract)

Posted: April 26, 2010

Marine Microbiology in the Twilight Zone: Mesophotic Coral Ecosystems

Technical divers at Pulley Ridge, a mesophotic coral environment at about 60 meters depth. Photo credit: USGSMesophotic coral ecosystems that occur at depths from 30 to 200 m have historically been understudied and yet appear to support a diverse biological community. The microbiology of these systems is particularly poorly understood, especially with regard to the communities associated with corals, sponges, and algae. Many shallow-water organisms have ranges that extend to mesophotic depths, making these deep reefs critical environments for research as shallow coral reefs deteriorate. Mesophotic environments may serve as "safe havens" or refugia for reef species since their depth makes them less susceptible to both natural and anthropogenic impacts.

Read the journal article:

Julie B. Olson & Christina A. Kellogg. Microbial ecology of corals, sponges, and algae in mesophotic coral environments. FEMS Microbiology Ecology; 2010. Volume 73, issue 1, pages 17-30. doi: 10.1111/j.1574-6941.2010.00862.x (online abstract)

Read also about USGS research at the Pulley Ridge mesophotic coral ecosystem.

Posted: April 19, 2010

Biogeochemistry: NO Connection with Methane

Titan. Image Credit: NASA/JPL/Space Science InstituteMicroorganisms that grow by oxidizing methane come in two basic types, aerobic and anaerobic. Now we have something in between that generates its own supply of molecular oxygen by metabolizing nitric oxide.

Read USGS scientist Dr. Ronald Oremland's commentary about the new discovery in Nature magazine: Biogeochemistry: NO Connection with Methane

Oremland, R.S. Biogeochemistry: NO connection with methane. Nature. 2010 Mar 25;464(7288):500-1.

White-nose bat syndrome. Al Hicks, New York Department of Environmental Conservation Wildlife Health Bulletin: White-Nose Syndrome: New Locations in Canada, Maryland and Tennessee Confirmed (.pdf, 30 KB)
Akiapolaau Honeycreeper Climate Change Fact Sheet: Climate Change and Wildlife Health: Direct and Indirect Effects (.pdf, 1.05 MB)

To read .pdf, download Acrobat Reader

Posted: March 26, 2010

Microbes that Cycle Arsenic in Nature: History, Toxicity, and Potential for Energy

Arsenic. Photo credit: National Museum of American History, Behring Center, Smithsonian InstitutionArsenic, well known as a poison, is found in natural systems such as weathered volcanic rocks and alkaline soils, and in man-made sources like mine drainage and irrigation runoff with arsenic-containing pesticides and herbicides. Microbes have used arsenic to survive since early in Earth's history, and are known to detoxify or increase the toxicity of arsenic in water supplies and the environment. USGS scientists and partners are revealing how microbes cycle arsenic in nature, discovering novel modes of microbial metabolism, and are even finding how these microbes exploit arsenic so as to provide themselves with new sources of energy.

Read about the discoveries in the American Society for Microbiology article: Microbial Arsenic Metabolism: New Twists on an Old Poison

Read also research summaries about arsenic bioremediation, biogeochemical cycling, and energy sources.

Posted: February 23, 2010

Virulent Fish Virus Identified for First Time in Lake Superior
Viral hemorrhagic septicemia virus poses threats to fisheries and aquaculture

Lake Superior. Photo credit: NASA USGS news release: For the first time, the presence of an exceptionally virulent fish virus (viral hemorrhagic septicemia virus or VHSV) has been identified in fish from Lake Superior by researchers at the Cornell University’s College of Veterinary Medicine and confirmed by scientists at the USGS Western Fisheries Research Center in Seattle.

The disease (VHS) caused by the virus can result in significant losses in populations of wild fish as well as in stocks of fish reared by aquaculture. It is of sufficient global concern to be one of only nine fish diseases that must be reported to the World Organization for Animal Health.

Read the full story at the USGS Newsroom >>

Posted: February 1, 2010

Complexities of Thiamine Deficiency in Aquatic Organisms

Yellow color shows thiamine degradation on an agar plate of Paenibacillus thiaminolyticus strain 8120. Photo credit: Catherine A. Richter, USGS Columbia Environmental Research CenterThe underlying causes of thiamine deficiency that lead to early mortality syndrome (EMS) in salmonines have yet to be fully understood. Currently, only one agent—Paenibacillus thiaminolyticus isolated from alewives—has been linked to thiamine deficiency in EMS. Scientists have recently developed new quantitative polymerase chain reaction (Q-PCR) assays to detect the bacteria P. thiaminolyticus. The low numbers of P. thiaminolyticus detected in samples with high thiaminase activity reveal that there may be additional, undefined sources of thiaminase activity in alewives.

The complexity of thiamine deficiency in aquatic organisms is the topic of the December 2009 issue of the Journal of Aquatic Animal Health. USGS scientists are co-authors in eight articles of this issue, including the article below:

Catherine A. Richter, Maureen K. Wright-Osment, James L. Zajicek, Dale C. Honeyfield, and Donald E. Tillitt. December 2009. Quantitative Polymerase Chain Reaction (PCR) Assays for a Bacterial Thiaminase I Gene and the Thiaminase-Producing Bacterium Paenibacillus thiaminolyticus. Journal of Aquatic Animal Health, vol 21, issue 4, pp 229-238. DOI: 10.1577/H07-054.1 (online abstract of journal article)

Posted: January 14, 2010

Editor's Choice: Surveillance of Avian Influenza Viruses using Genetic Analysis

Anas acuta. Photo credit: George Gentry, courtesy USFWS Digital LibrarySome migratory birds can carry foreign origin highly pathogenic avian influenza (HPAI) as they fly into North America. How can surveillance activities prioritize which species to track, and which locations? USGS scientists reveal a new approach to optimize surveillance activities. Using viral genomes from northern pintails (Anas acuta), scientists found that genomic analyses of low pathogenic avian influenza (LPAI) viruses can identify the species and regions where the relative risk of HPAI introduction is highest.

Read the article that made Editor’s Choice in the journal Evolutionary Applications:

John M. Pearce, Andrew M. Ramey, Paul L. Flint, Anson V. Koehler, Joseph P. Fleskes, J. Christian Franson, Jeffrey S. Hall, Dirk V. Derksen, and Hon S. Ip. 2009. Avian influenza at both ends of a migratory flyway: characterizing viral genomic diversity to optimize surveillance plans for North America. Evolutionary Applications, vol 2, issue 4, pp 457-468. (online abstract of journal article)

Posted: Januray 7, 2010

Award Winners: Best Paper in the Journal of Aquatic Animal Health

Dr. Maureen K. Purcell (right) accepting the Journal of Aquatic Animal Health Best Paper Award from American Fisheries Society president Bill Franzin (left). Photo credit: Todd Maszaros, Tennessee Wildlife Resources Agency, used with permission.How do species introduced into new environments adapt to disease? A recent study compared Bacterial Kidney disease resistance of introduced Chinook salmon from Lake Michigan to its progenitor stock from Washington State.  The journal article that studied these questions was recently awarded Best Paper in the Journal of Aquatic Animal Health by the American Fisheries Society (AFS).

Read the announcement in ASF’s December 2009 Fisheries publication (PDF, 4.36MB), and the award-winning journal article:

Maureen K. Purcell, Anthony L. Murray, Anna Elz, Linda K. Park, Susan V. Marcquenski, James R. Winton, Stewart W. Alcorn, Ronald J. Pascho, and Diane G. Elliott. Decreased Mortality of Lake Michigan Chinook Salmon after Bacterial Kidney Disease Challenge: Evidence for Pathogen-Driven Selection? Journal of Aquatic Animal Health 2008; 20:225-235. (online abstract of journal article)

Image caption: Dr. Maureen K. Purcell (right) accepting the Journal of Aquatic Animal Health Best Paper Award from American Fisheries Society president Bill Franzin (left). Photo credit: Todd Maszaros, Tennessee Wildlife Resources Agency, used with permission.

Posted: December 28, 2009

USGS Microbiology Featured Topics Archive