USGS - science for a changing world

U.S. Geological Survey - Microbiology

Maps, Imagery, and Publications Hazards Newsroom Education Jobs Partnerships Library About USGS Podcasts/RSS

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.

Microbiology

USGS Microbiology Featured Topics 2011

USGS Tracks Fish Virus
Geographic distribution of collection sites for VHS virus in the Great Lakes region. Photo credit: Tarin M.Thompson, USGS Western Fisheries Research Center.

(Larger view) Geographic distribution of collection sites for VHS virus in the Great Lakes region. Different colored dots show the two dominant genetic types of virus in red and blue, and minor variants are in yellow. The focus of the red genotype in the eastern portions of the region is the first evidence of differences developing between the virus genotypes.
Photo credit: Tarin M.Thompson, USGS Western Fisheries Research Center.

In the latest issue of Diseases of Aquatic Organisms, researchers from the USGS Western Fisheries Research Center, along with collaborators from Cornell University, Michigan State University, US Fish and Wildlife Service, and Fisheries and Oceans Canada report their results from a genetic survey of Viral hemorrhagic septicemia virus (VHSV) genotype IVb isolates collected between 2003 and 2009. The deadly fish virus has now been reported from all five Great Lakes, as well as inland waters surrounding the Great Lakes. Genetic diversity was extremely low among virus isolates, which was consistent with the hypothesis that this virus was newly introduced into previously naïve host populations. (https://www.ncbi.nlm.nih.gov/pubmed/21991663)

For more information, contact Gael Kurath, USGS Western Fisheries Research Center.

 

 

 

 

Posted: November 1, 2011

Preventing Pandemic The Wildlife Forensics of New and Emerging Diseases
(Photo credit: N. Batbayar, Mongolia WSC
The USGS works with international partners to mark and track whooper swans with GPS transmitters. Photo credit: N. Batbayar, Mongolia Wildlife Science and Conservation Center

Studying diseases in wildlife is obviously important work for the health and welfare of wildlife, but it is also very important for the health of humans and domestic animals — 7 out of 10 emerging human diseases originate in wildlife or domestic animals. For nearly 40 years, wildlife disease researchers (including wildlife veterinarians, microbiologists, epidemiologists, and others) have come to the USGS National Wildlife Health Center, a specialized biological containment facility in Madison, WI, where they work to identify known as well as new and emerging diseases — and sometimes develop treatments for them.

Together with partners from around the world, the USGS National Wildlife Health Center provides information to help detect, identify, and manage wildlife disease events when they occur.

Read the full USGS Science Feature by Carol Meteyer with Gail Moede, Catherine Puckett, and Tania Larson: Preventing Pandemic The Wildlife Forensics of New and Emerging Diseases, and USGS Corecast, Disease Detectives: Investigating the Mysteries of Zoonotic Diseases

 

Posted: September 14, 2011

Pathogen Fitness and Virulence of a Fish Virus
Photo: Fulbright Scholar Michele Penaranda. Credit: Gael Kurath/USGS.
Photo: Rainbow Trout. Credit: Gael Kurath/USGS.

In a latest issue of The Journal of Virology, researchers from the USGS Western Fisheries Research Center and the University of Washington examined the relationship between pathogen fitness and virulence using an important fish virus, Infectious hematopoietic necrosis virus (IHNV). Pathogen fitness and virulence are typically quantified by measuring only one or two pathogen fitness traits. In this study, the researchers independently quantified four viral infection cycle traits, namely, host entry, within-host replication, within-host coinfection fitness, and shedding. The researchers report that viral fitness was independently regulated by each of the traits examined, with the largest impact on fitness being provided by within-host replication. The results are thus congruent with the assumption that virulence and within-host replication are correlated but suggest that infection cycle fitness is complex and that replication is not the only trait associated with virulence. For more information, visit https://www.ncbi.nlm.nih.gov/pubmed/21307204.

For more information, contact Gael Kurath, USGS Western Fisheries Research Center.

Additional link:

In Vivo Fitness Associated with High Virulence in a Vertebrate Virus Is a Complex Trait Regulated by Host Entry, Replication, and Shedding (pdf)

 

Posted: September 7, 2011

Genetic Control of Pathogenicity in the Great Lakes Strain of Viral Hemorrhagic Septicemia Virus (VHSV)
Infection tests in juvenile yellow perch confirmed that recombinant VHSV IVb virus produced by reverse genetics mimics the wild type virus by causing classic disease signs such as external hemorrhages as well as mortality. Photo credit: Gael Kurath/USGS.
Photo: Infection tests in juvenile yellow perch confirmed that recombinant VHSV IVb virus produced by reverse genetics mimics the wild type virus by causing classic disease signs such as external hemorrhages as well as mortality. Photo credit: Gael Kurath/USGS.

Researchers from the Western Fisheries Research Center (USGS) and the University of Maryland Biotechnology Institute have developed reverse genetic capabilities for the Great Lakes strain of Viral hemorrhagic septicemia virus (VHSV IVb). This new tool was used to knock-out the VHSV IVb non-viron (NV) gene and demonstrate that the NV is essential for pathogenicity in yellow perch. The VHSV IVb reverse genetic system will be a valuable tool to investigate all aspects of the viral life cycle. In 2005, the VHSV IVb strain emerged in the Great Lakes and was associated with wild fish kills in a wide range of species. The results are reported in the latest issue of Marine Biotechnology (https://www.ncbi.nlm.nih.gov/pubmed/20936318). For more information, contact Gael Kurath, USGS Western Fisheries Research Center.

 

Additional resources:

Western Fisheries Research Center
Viral Hemorrhagic Septicemia Virus in the Great Lakes
University of Maryland Center of Marine Biotechnology Institute (UMBI)

 

Posted: August 9, 2011

Efficacy of DNA Vaccines for an Important Fish Virus
Photo: Fulbright Scholar Michele Penaranda. Credit: Gael Kurath/USGS.
Photo: Fulbright Scholar Michele Penaranda. Credit: Gael Kurath/USGS.

Researchers from the USGS Western Fisheries Research Center, University of Washington and Clear Springs Food Inc. have reported their findings on cross-protective efficacy of DNA vaccines for the fish virus Infectious hematopoietic necrosis virus (IHNV). This study demonstrated that rainbow trout mount a broad immune response following vaccination that can cross-protect against different IHNV strains. IHNV causes significant mortality in both wild and cultured salmon and trout in North America, Asia and Europe. The abstract can be found at https://www.ncbi.nlm.nih.gov/pubmed/21385613.

For more information, contact Gael Kurath, USGS Western Fisheries Research Center.

 

 

 

 

 

Posted: August 9, 2011

Geology and Meteorology of Sites Infected with White-Nose Syndrome before July 2010 in the Southeastern United States
Map showing the locations of cave-bearing carbonate strata and sites infected with white-nose syndrome (WNS) before July 2010 in the southeastern United States. Sites are numbered in the approximate order in which WNS infection was detected.
Map showing the locations of cave-bearing carbonate strata and sites infected with white-nose syndrome (WNS) before July 2010 in the southeastern United States. Sites are numbered in the approximate order in which WNS infection was detected. See map for additional details.

Since 2006, numerous bat colonies in North America have experienced dramatic and unusual incidences of mortality. In these colonies, bats are infected by a white fungus named Geomyces destructans, which has been observed on bat muzzles, noses, ears, and (or) wings. Although it is not exactly certain how and why these bats are dying, this condition has been named white-nose syndrome (WNS). WNS has spread from an initial infection site at a cave in New York, and was first identified south of Pennsylvania during January 2009. By the end of June 2010, 41 infected sites had identified in the States of West Virginia, Maryland, Delaware, Virginia, and Tennessee. Most of these sites are natural caves in limestone of either Cambrian-Ordovician age or Silurian-Devonian age. Published air temperature values in these WNS-infected caves range from -3.3 to 15.6 °C, and humidity measurements range from 68 to 100 %. Publication Citation: Swezey, C.S., and Garrity, C.P. (2011), Notes on the geology and meteorology of sites infected with white-nose syndrome before July 2010 in the southeastern United States: National Speleological Society (NSS) News, v. 69 (2), p. 16-25.

 

For more information, contact Christopher S. Swezey or Christopher P. Garrity (U.S. Geological Survey, Reston, Virginia).

back to top

 

 

 

 

Posted: July 12, 2011

Environmental Persistence of Chronic Wasting Disease Exacerbates Deer Population Declines

 
Photo: Deer in Wildlife Habitat Management Area. Photo credit: Bryan J. Richards (USGS).

Chronic wasting disease (CWD) is a fatal disease of deer, elk, and moose transmitted through direct, animal-to-animal contact, and indirectly, via environmental contamination. Researchers used simulation models to demonstrate how indirect transmission and duration of environmental prion persistence may affect epidemics of CWD and populations of North American deer. These models suggest disease prevalence and severity of population decline is driven by the duration prions remain infectious in the environment. High prion persistence is expected to lead to an increasing environmental pool of prions during the early phases (i.e. approximately during the first 50 years) of the epidemic. Contacts: Contacts: Paul C. Cross, Northern Rocky Mountain Science Center (NOROCK), Emily Almberg, Penn State University.

Additional links:

 

 

 

 

Posted: May 26, 2011

Image of Lophelia. Photo credit: Christina Kellogg, USGS.New Website Features USGS Microbiology Research on Deep-sea Coral Ecosystems

 

Sampling Lophelia in the Gulf of Mexico. © USGS/Christina Kellogg
Photo: Sampling Lophelia in the Gulf of Mexico. Photo credit: Christina Kellogg, USGS.

Think of coral reefs and you imagine warm, shallow tropical seas, not the cold, dark waters of the deep ocean. Now the deep ocean's best-kept secrets are being revealed – ancient coral ecosystems hidden from view at great depths. Lophelia.org is an information resource on the cold-water coral ecosystems of the deep ocean. An exciting new section on the microbiology of these corals has been added to the web site featuring content, photos, and video from USGS St. Petersburg Coastal and Marine Science Center scientist and coral microbiology expert, Christina Kellogg.
View the site here.

Posted: March 17, 2011

E. coli populations associated with Cladophora mats in Lake Michigan represent a mixture of stable and transient strains

Photo: Floating Cladophora mats in nearshore water at a southern Lake Michigan beach. . Photo credit:USGS
Photo: Floating Cladophora mats in nearshore water at a southern Lake Michigan beach. . Photo credit:USGS

In the Great Lakes, massive accumulations of Cladophora mats are common along shorelines.   The high densities of E. coli and enterococci in the algal mats have been attributed to bacterial growth, as Cladophora provides an environment that is rich in nutrients and that offers protection from harmful sunlight.  In this study, using genetic techniques and statistical analyses, scientists from the Universities of Minnesota and Wisconsin – Oshkosh and the U.S. Geological Survey (Great Lakes Science Center, Lake Michigan Ecological Research Station) characterized the population structure of E. coli associated with Cladophora mats collected over multiple 3-day intervals from Lake Michigan during 2007-2009.  E. coli populations were highly diverse, consisting of unique strains and large clusters of identical strains; further, E. coli genotypes changed rapidly, even on a daily basis.  The current and related findings by these investigators are consistent with the hypothesis that Cladophora mats serve as an environmental source of indicator bacteria, such as E. coli, to Great Lakes beaches. 


For more information contact: Muruleedhara N. Byappanahali and Richard L. Whitman, Great Lakes Science Center, Dr. Brian Badgley and Dr. Michael Sadowsky, University of Minnessota.


Related Publication: Badgley, B. D., J. Ferguson, G. T. Kleinheinz, C. M. McDermott, T. R. Sandrin, J. Kinzelman, E. A. Junion, M. N. Byappanahalli, R. L. Whitman, and M. J. Sadowsky. 2010. Multi-scale temporal and spatial variation in genotypic composition of Cladophora-borne Escherichia coli populations in Lake Michigan. Water Research 45:721-731.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/20851450

References:

Posted: February 15, 2011

Increasing Swimming Access and Decreasing Public Health Risk from Waterborne Illnesses

Collecting sand samples at an Indiana beach for analysis. Photo credit: USGS
Visitors at Chicago’s 63rd Street Beach. Photo credit: Meredith Nevers, USGS
Swimming access is limited when E. coli concentrations in beach water are high. Photo credit: Meredith Nevers, USGS
Swimming access is limited when E. coli concentrations in beach water are high. Photo credit: Meredith Nevers, USGS

Recent efforts to improve beach monitoring accuracy and timeliness have included the use of empirical predictive models. These models rely on fluctuations in ambient water and weather conditions to predict real-time estimates of water quality indicators (e.g., E. coli, enterococci), rather than the traditional, time-intensive culturing approach currently used in most monitoring programs.   While predictive models are being widely tested, assessments of their accuracy tend to focus on variation in E. coli (the biological indicator used in this study) explained by the model.  In the current study, USGS researchers examined whether predictive models could decrease the level of risk associated with swimming at 14 Chicago beaches.  Results indicated that individual beach predictive models were not necessarily more accurate than a comprehensive model that incorporated multiple beaches, but the use of an individual beach model, along with permissible relaxed standard criteria—per U.S. EPA recommendation—resulted in the most swimming access without any increase in presumed health risk. With upcoming changes in recreational water quality standards, monitoring alternatives will need to focus on improving public health protection through improved strategies.

References:

For more information contact Meredith B. Nevers, and Richard L. Whitman, Great Lakes Science Center.

Posted: February 15, 2011

Abnormal puffer fish from Shark’s Cove, Oahu, with cloudy eye and sediment on the back.  Photo credit: (T.M. Work, USGS) USGS Wildlife Health Bulletin: 2011-01, Revised Case Definitions for White-Nose Syndrome and Winter 2010/2011 Bat Submission Guidelines Date

First Microbiological Characterization of Several Gorgonian Coral Species in the Aleutian Islands

Christina Kellogg collects samples of deep-sea corals for microbiological analysis as soon as they are brought to the surface. Photo credit: Anne Simpson, University of Maine.
Photo: Christina Kellogg collects samples of deep-sea corals for microbiological analysis as soon as they are brought to the surface. Photo credit: Anne Simpson, University of Maine.
Working in the high northern latitudes in the summer means it stays light all day and almost all night. This photo of the research ship Velero IV was taken at 10pm! Photo credit: Christina Kellogg, USGS.
Photo: Working in the high northern latitudes in the summer means it stays light all day and almost all night. This photo of the research ship Velero IV was taken at 10pm! Photo credit: Christina Kellogg, USGS.

USGS and National Marine Fisheries Service (NMFS) researchers have just published the first microbiological characterization of three gorgonian (soft coral) species that inhabit the cold waters of the Aleutian Islands.  In a paper titled ‘Microbial consortia of gorgonian corals from the Aleutian Islands’ St. Petersburg Coastal and Marine Science Center (SPCMSC) scientists Mike Gray, Molly McLaughlin and Christina Kellogg and NMFS scientist Robert Stone used culture-based and 16S rRNA gene-based techniques to characterize the microbial ecology of the deep-sea gorgonian corals Paragorgia arborea, Plumarella superba, and Cryogorgia koolsae.  These corals are among a host of diverse and unique cold-water coral communities in the Aleutians.

 There are more than 50 coral species found nowhere else in the world in the waters of the Aleutians, which lie between Alaska and Russia and divide the North Pacific from the Bering Sea.  As much as 85% of the commercially important fish species in the area are associated with such deep-sea corals.  By understanding the microbial consortia associated with these corals, scientists gain a better understanding of their relationship with their environment and the ecosystem services they provide.  The article was published in the Federation of European Microbiological Societies Microbial Ecology.  You can read the study here: https://onlinelibrary.wiley.com/doi/10.1111/j.1574-6941.2010.01033.x/abstract  

For more information, contact: Christina Kellogg, 727-803-8747 x. 3128.

 

Posted: January 18, 2011

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)

USGS Microbiology Featured Topics Archive


Accessibility FOIA Privacy Policies and Notices
Take Pride in America logo USAGov logo U.S. Department of the Interior | U.S. Geological Survey
URL: contribute.nbii.gov/sites/microbiology/spotlight_2010.html
Page Contact Information: GS-B Biology Web@usgs.gov
Page Last Modified: Monday, 07-Feb-2011 11:43:39 MST
Get Adobe Reader