Proceedings of the U.S. Geological Survey
�

Interdisciplinary Microbiology Workshop,
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Estes Park, Colorado, October 15–17, 2008
�

Scientific Investigations Report 2010–5146 

U.S. Department of the Interior 

U.S. Geological Survey 
Front cover. Gloeotrichia sp. stained with SYTOX® Green; this cyanobacterium was found in 

Klamath Lake, Oregon. Photomicrograph by Barry H. Rosen (U.S. Geological Survey). Scale in 

micrometers (μm). 

Back cover. Several filaments of Lyngbya spp., a cyanotoxin-producing cyanobacterium. These 

filaments were examined and photographed under epifluorescent microscopy, with excitation 

between 450 and 80 nanometers (nm) and emission above 515 nm. With this configuration, 

chlorophyll a appears as a bright red color. These filaments were stained with a nucleic acid stain, 

SYTOX® Green, which is excluded from healthy cells (leaving them red), while damaged cells appear 

yellow. This staining thus provides an indication of the health of these cyanobacterial filaments. 

In this image obtained from a laboratory culture, some of the filaments are exclusively red, some 

filaments alternate between living cells (red) and those that lost cell membrane integrity (yellow), and 

some filaments are completely yellow. Photomicrograph by Barry H. Rosen (U.S. Geological Survey). 
 

 

 

 

 

 

Proceedings of the U.S. Geological Survey 

Interdisciplinary Microbiology Workshop, 

Estes Park, Colorado, October 15–17, 2008 

Edited by Kay Marano Briggs 

Scientific Investigations Report 2010–5146 

U.S. Department of the Interior 

U.S. Geological Survey 
 

U.S. Department of the Interior 

KEN SALAZAR, Secretary 

U.S. Geological Survey 

Marcia K. McNutt, Director 

U.S. Geological Survey, Reston, Virginia: 2010 

For more information on the USGS—the Federal source for science about the Earth, its natural and living resources, 

natural hazards, and the environment, visit http://www.usgs.gov or call 1–888–ASK–USGS 

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Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the 

U.S. Government. 

Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report. 

Suggested citation: 

Briggs, K.M., ed., 2010, Proceedings of the U.S. Geological Survey Interdisciplinary Microbiology Workshop, Estes 

Park, Colorado, October 15–17, 2008: U.S. Geological Survey Scientific Investigations Report 2010–5146, 49 p. (Also 

available online.) 

ISBN 978–1–4113–2963–8 
iii 

Preface 

A U.S. Geological Survey Interdisciplinary Microbiology Workshop was held in Estes Park, 

Colorado, on October 15–17, 2008. Participants came from all USGS regions and disciplines. 

This report contains abstracts from 36 presentations and 35 poster sessions and notes from 5 

breakout sessions. The seven presentation topics follow: 

• Ecology of wildlife and fish disease 

• Mechanisms of fish and wildlife disease 

• Microbial ecology 

• Geographic patterns/visualization 

• Public health and water quality 

• Geomicrobiology 

• Ecosystem function 

The six poster session topics follow: 

• Wildlife disease 

• Disease detection methods 

• Water quality 

• Microbial ecology 

• Metabolic processes 

• Tools and techniques 

Five working groups met in breakout sessions on October 16, 2008. The highlights for each 

working group are summarized in this report, and their goals are listed below: 

• Working Group I: to plan a Fact Sheet on interdisciplinary microbiology in the USGS 

• Working Group II: to plan a USGS interdisciplinary microbiology Web site 

• Working Group III: to suggest ways to broadcast and publicize the types of microbiology 

conducted at the USGS 

• Working Group IV: to identify emerging issues in USGS interdisciplinary microbiology 

research 

• Working Group V: to identify potential opportunities for interdisciplinary microbiology 

work at the USGS 

After the workshop, the USGS interdisciplinary microbiology Web site was activated in June 

2009 at http://microbiology.usgs.gov/. 
iv
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v 

Contents 

Preface ...........................................................................................................................................................iii
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Agenda.............................................................................................................................................................x
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Presentation Abstracts.................................................................................................................................1
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Keynote Speech at Plenary Session .................................................................................................1
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The Ecology of Arsenic: A Lurid Tale of Murder, Mayhem, Microbes, 

Malodorous Mono Muds, and Mars ...........................................................................1
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Section I: Ecology of Wildlife and Fish Disease ..............................................................................1
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Bat White-Nose Syndrome: An Emerging Fungal Pathogen?..............................................1
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Epidemiology and Evolution of Rhabdoviruses in Fish ..........................................................2
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The United States Department of the Interior’s Avian Influenza Surveillance 

Program in North America: Laboratory Results........................................................2
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Ecology of Vector-Borne Diseases in Pacific Island Birds: Hawaii to 

New Caledonia ...............................................................................................................3
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Section II: Mechanisms of Fish and Wildlife Disease ....................................................................3
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Disease Impacts on Populations of Wild Marine Fish...........................................................3
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Mycobacteriosis in Chesapeake Bay.......................................................................................3
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Studies on Plague Pathogenesis in Rodents Using in vivo Imaging ...................................4
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Role of Wild Rodents in Environmental Transport of Prions.................................................4
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Microbial Diseases in Marine Ecosystems: Challenges and Opportunities......................5
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Section III: Microbial Ecology ............................................................................................................5
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Microbiology of Deep-Sea Corals.............................................................................................5
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Development and Application of Denaturing High-Performance Liquid 

Chromatography (DHPLC) Methods for the Analysis of Microbial 

Community Composition................................................................................................6
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The Role of Biological Soil Crusts in Preventing Desertification of Dryland 

Soil Community Dynamics in Sagebrush Steppe and Cheatgrass-Invaded 

Ecosystems .....................................................................................................................6
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Endosymbiotic Fungi in Plants: Ecology and Implications for Climate Change.................7
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Areas of the Northern Great Basin .............................................................................7
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Section IV: Geographic Patterns/Visualization................................................................................8
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Microbial Mapping: Stimulating Hypothesis and Informing the Public..............................8
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A Multiscale Approach to the Concept of Regional Health..................................................8
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Public Health and Geospatial Distribution...............................................................................9
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Critical Habitat Diversity Parameters for Assessing the Geographical 

Distribution of Plague: A Geographic Information System (GIS)-Based 

Case-Control Study and Risk Model of Human Plague Cases in the 

Southwestern United States, 1963–2007 ....................................................................9
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Section V: Public Health and Water Quality...................................................................................10
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Integrating Quantitative Polymerase Chain Reaction (qPCR) and Predictive 

Models To Monitor Beach Water Quality.................................................................10
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Harmful Algal Blooms ...............................................................................................................10
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Pathogens and Antibiotic-Resistant Bacteria in the Environment....................................11
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Microbial Source Tracking, Using Quantitative Polymerase Chain Reaction 

(qPCR), for Enhanced Sanitary Water-Quality Management................................11
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vi 

Transport of Microbes in the Subsurface/Physical Interactions of 

Microbes and Particles...............................................................................................12
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Using Natural Abundance δ13C and ∆14C Values of Phospholipid Fatty Acids 

Geochemical Controls on Microbial Methylation of Mercury in the Florida 

An Overview of Bacterial Controls and Influences on Sulfide Mineral 

Defining “Reactive” Inorganic Mercury and Its Relationship to Microbial 

Natural and Enhanced Bioremediation of Nitrate Contamination in 

Quantifying Microbial Denitrification Rates Using Expressed Functional Gene 

Evaluating Ecosystem Function with Integrated Approaches in Environmental 

Experimental Infection of a North American Raptor with Highly Pathogenic 

Viral Fitness Assays Used in vivo To Investigate Virulence Tradeoffs in an 

Detection of Batrachochytrium dendrobatidis (Chytrid Fungus) in Water 

Quality Control of Quantitative Polymerase Chain Reaction (qPCR) for 

Response of Groundwater Bacteria from Cape Cod, Mass., to Low 

Antibiotic Resistance in an Urban Watershed with Combined 

Flow Cytometry in Microbiology..............................................................................................12
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Section VI: Geomicrobiology ............................................................................................................13
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Geomicrobiology/Nanoscience of Toxic Elements Se and Te............................................13
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Soil Microbial Indices Across Different Geographic Scales .............................................13
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to Characterize Bacterial Carbon Cycling Pathways in Deep Aquifers..............14
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Everglades.....................................................................................................................15
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Weathering....................................................................................................................15
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Methylmercury Formation in Aquatic Ecosystem Studies ....................................16
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Section VII: Ecosystem Function......................................................................................................16
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Groundwater .................................................................................................................16
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Microbial Communities and Carbon Cycling in Response to Global Change ..................17
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Biogeochemistry of Mountain Watersheds: Through the Microbial Window ................17
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Abundance ....................................................................................................................18
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Microbiology .................................................................................................................18
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Poster Session Abstracts...........................................................................................................................19
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Wildlife Disease ..................................................................................................................................19
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Temporal Dynamics of Mixed Avian Influenza Infections in Waterfowl...........................19
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Avian Influenza H5N1...................................................................................................19
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Forecasting the Space/Time Spread of West Nile Virus.....................................................19
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Acute Rhabdovirus of Rainbow Trout .......................................................................20
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Diversity and Pathogenicity of Avipoxvirus from Hawaiian Forest Birds.........................20
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Disease Detection Methods .............................................................................................................21
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and Amphibian Swabs Using PCR: Towards a Life History Assessment............21
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Water Quality.......................................................................................................................................21
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Microbial Quality of Water in Selected Principal Aquifers of the United States............21
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Environmental Water Samples...................................................................................22
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Concentrations of Antimicrobials..............................................................................22
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Sewer Overflows..........................................................................................................23
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Use of Carboxylated Microbial-Sized Microspheres for Estimating 

Cryptosporidium parvum Oocyst Transport within Russian River 

(Sonoma County, Calif.) Bank Filtration Sediments ................................................23
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Examination of the Watershedwide Distribution of Escherichia coli along 

Southern Lake Michigan: An Integrated Approach ...............................................24
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vii 

Seasonal Stability of Cladophora-Associated Salmonella in Lake Michigan 

Watersheds ...................................................................................................................24
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Real-Time Estimation of Taste-and-Odor Occurrences in Cheney Reservoir, 

The South San Francisco Bay Baylands Mercury Project: Mercury Status of 

Enumeration of Viruses and Prokaryotes in Deep-Sea Sediments and 

Microbial Decomposer Communities in Alaskan Permafrost Soils and 

Kansas............................................................................................................................25
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Cyanotoxins in Midwestern Lakes and Reservoirs..............................................................25
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Pond A8, Alviso Slough, and Alviso Marsh, Based on Sediment.........................26
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Microbial Ecology...............................................................................................................................26
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Cold Seeps of the Gulf of Mexico ..............................................................................26
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Their Response to Thaw .............................................................................................27
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Fungal and Methanogen Functional Groups in Boreal Forests and Wetlands 

in Interior Alaska: Abundance, Diversity, and Process in the Face of 

Environmental Change ................................................................................................27
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Fire and Ice: Examining Fungal Mechanisms of Recalcitrant Carbon 

Decomposition in Response to Fire in the Boreal Forest Landscape..................28
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In situ Measurement of Microbially Catalyzed Nitrification and Denitrification 

Rates in Stream Sediments Receiving Coalbed-Methane Discharge, 

Powder River Basin, Wyoming...................................................................................28
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Microbial Methanogenesis in Laboratory Incubations of Coal: Implications for 

a Sustainable Energy Resource in Subsurface Coal Beds ...................................29
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Chemical Character and Lability of Carbon Across a Chronosequence of 

Climate-Induced Changes in Nitrogen Dynamics in Loch Vale Watershed, 

Laboratory Studies of Biogenic Methane Production from Coal by Microbial 

Denitrification-Coupled Iron Oxidation in Cultures from Aquifer Sediments 

Cycling of Methylmercury in the Sediments of the Penobscot River Estuary, 

Role of Microbes in Attenuation and Mobilization of Arsenic at the Lava 

Cr(III) Oxidation by Soluble Mn(III) Chelates: A Potential Biogeochemical 

A Proteomic Profile of a Novel Arsenite-Oxidizing Bacterium 

USGS Interdisciplinary Microbiology Web Site: Marketing USGS 

Application of Phospholipid Fatty Acids in the Evaluation of Post-Katrina 

Drained Sediments of a Drying Arctic Lake, Interior Alaska ................................29
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Indicators of Ecosystem Health and the Impact of Mineralized Terrane.........................30
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Rocky Mountain National Park ..................................................................................30
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Metabolic Processes .........................................................................................................................31
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Consortia: Identifying Organisms, Reactions, and Intermediate Products ........31
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Microbially Induced Temperature Changes in a Petroleum Hydrocarbon Plume..........31
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from Cape Cod, Massachusetts.................................................................................31
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Maine..............................................................................................................................32
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Cap Mine Superfund Site, Nevada County, California ...........................................32
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Pathway for the Enhanced Mobilization of Cr from Spinels .................................33
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Alkalilimnicola ehrlichii strain MLHE-1T ..................................................................33
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Tools and Techniques.........................................................................................................................34
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Flow Cytometry: An Essential Tool in Biomarker Research................................................34
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Microbiology Expertise and Capabilities..................................................................35
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Wetland Soils ................................................................................................................35
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viii 

Breakout Session Outcomes, October 16, 2008......................................................................................36
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Working Group I: To Plan a Fact Sheet on Interdisciplinary Microbiology in 

the USGS.................................................................................................................................36
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Wildlife and Fish Disease .........................................................................................................36
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Microbial Ecology......................................................................................................................36
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Geographic Patterns/Visualization .........................................................................................38
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Public Health and Water Quality .............................................................................................38
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Geomicrobiology........................................................................................................................38
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Ecosystem Function ..................................................................................................................38
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Reference Cited .........................................................................................................................39
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Working Group II: To Plan a USGS Interdisciplinary Microbiology Web Site...........................39
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Moderator’s Notes on Focus Group To Discover Attitudes, Beliefs, and Desires for 

an Interdisciplinary Microbiology Web Site and Reactions to a Prototype.......39
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Introduction .......................................................................................................................39
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Outline of the Discussion.................................................................................................39
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Materials ............................................................................................................................40
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Part I: General Goals for a USGS Microbiology Web Site .........................................40
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Introduction ..............................................................................................................40
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Information Needs...................................................................................................41
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Expectations, Requirements, and Preferences ..................................................41
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Survey Identifying Web Site Goals .......................................................................42
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Part II: Responses to the Mockup Version 1 ................................................................44
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Working Group III: To Suggest Ways To Broadcast and Publicize the Types 

Working Group IV: To Identify Emerging Issues in USGS Interdisciplinary 

Working Group V: To Identify Potential Opportunities for Interdisciplinary 

of Microbiology Conducted at the USGS ..........................................................................44
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Microbiology Research........................................................................................................46
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Microbiology Work at the USGS.........................................................................................48
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Figures 

1.	� Photograph of moderator and members of Working Group II ............................................39
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2.	� Mockup (version 1) of USGS interdisciplinary microbiology Web site—Home page.....40
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3.	� Mockup (version 1) of USGS interdisciplinary microbiology Web site—Research 

activities page .............................................................................................................................41
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4.	� Mockup (version 1) of USGS interdisciplinary microbiology Web site—Page of 

microbiology scientist profiles .................................................................................................42
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Tables 

1.	� Summary of breakout session outcomes from Working Groups I–V. ................................37
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2.	� Results of a survey about the proposed USGS interdisciplinary microbiology 

Web site........................................................................................................................................43
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ix 

Conversion Factors 

Multiply By To obtain 

Length 

foot (ft) 0.3048 meter (m)

nautical mile (nmi) 1.852 kilometer (km)

nanometer (nm) 0.00000003937 inch (in.)

micrometer (μm) 0.00003937 inch (in.)

millimeter (mm) 0.03937 inch (in.)

centimeter (cm) 0.3937 inch (in.)

meter (m) 3.281 foot (ft)

megameter (Mm) 621.37 mile (mi)

Area 

square centimeter (cm2

) 0.1550 square inch (in2

)

square kilometer (km2) 0.3861 square mile (mi2

)

Volume 

microliter (μL) 0.00003381 ounce, fluid (fl. oz)

milliliter (mL) 0.03381 ounce, fluid (fl. oz)

liter (L) 1.057 quart (qt)

Mass 

nanogram (ng) 0.00000000003527 ounce, avoirdupois (oz)

microgram (μg) 0.00000003527 ounce, avoirdupois (oz)

milligram (mg) 0.00003527 ounce, avoirdupois (oz)

gram (g) 0.03527 ounce, avoirdupois (oz)

kilogram (kg) 2.205 pound, avoirdupois (lb)

gigaton (Gt) 1.102 × 109 short ton (2,000 lb)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows: 

°F=(1.8×°C)+32 

Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius (°C) as follows: 

°C=(°F–32)/1.8 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

x 

Agenda for U.S. Geological Survey 

Interdisciplinary Microbiology Workshop, 

Estes Park, Colorado, October 15–17, 2008 

October 15 

8:30 a.m. Opening: Welcome, housekeeping announcements, short explanation of how 

the workshop came to be, and introductions of committee members 

8:45 a.m. Keynote Speech at Plenary Session: Ronald S. Oremland: The Ecology of 

Arsenic: A Lurid Tale of Murder, Mayhem, Microbes, Malodorous Mono 

Muds, and Mars

9:25 a.m. BREAK (15 minutes) 

Section I. Ecology of Wildlife and Fish Disease 

9:40 a.m. David S. Blehert: Bat White-Nose Syndrome: An Emerging Fungal Pathogen?

10:10 a.m. Gael Kurath: Epidemiology and Evolution of Rhabdoviruses in Fish

10:40 a.m. Hon S. Ip: The United States Department of the Interior’s Avian Influenza 

Surveillance Program in North America: Laboratory Results

11:10 a.m. Carter T. Atkinson: Ecology of Vector-Borne Diseases in Pacific Island Birds: 

Hawaii to New Caledonia

11:40 a.m. LUNCH (on site) 

Section II. Mechanisms of Fish and Wildlife Disease 

12:30 p.m. Paul K. Hershberger: Disease Impacts on Populations of Wild Marine Fish

1:00 p.m. Christopher A. Ottinger: Mycobacteriosis in Chesapeake Bay

1:30 p.m. Toni E. Rocke: Studies on Plague Pathogenesis in Rodents Using in vivo 

Imaging

2:00 p.m. Chad J. Johnson: Role of Wild Rodents in Environmental Transport of Prions

2:30 p.m. Thierry M. Work: Microbial Diseases in Marine Ecosystems: Challenges and 

Opportunities

3:00 p.m. BREAK (30 minutes) 

Section III. Microbial Ecology 

3:30 p.m. Christina A. Kellogg: Microbiology of Deep-Sea Corals

4:00 p.m. Andrea L. Foster: Development and Application of Denaturing HighPerformance Liquid Chromatography (DHPLC) Methods for the Analysis 

of Microbial Community Composition

4:30 p.m. Jayne Belnap: The Role of Biological Soil Crusts in Preventing Desertification 

of Dryland Ecosystems

5:30 p.m. DINNER (on site) 

7:00 p.m. Poster Session and Reception 
 

 

 

 

 

 

 

 

 

 

 

 

xi 

October 16 

Section III. Microbial Ecology (continued) 

8:30 a.m. Russell J. “Rusty” Rodriguez: Endosymbiotic Fungi in Plants: Ecology and 

Implications for Climate Change

9:00 a.m. Nicole M. DeCrappeo: Soil Community Dynamics in Sagebrush Steppe and 

Cheatgrass-Invaded Areas of the Northern Great Basin

Section IV. Geographic Patterns/Visualization 

9:30 a.m. Steve C. Guptill: Microbial Mapping: Stimulating Hypothesis and Informing 

the Public

10:00 a.m. Lee De Cola: A Multiscale Approach to the Concept of Regional Health

10:30 a.m. BREAK (30 minutes) 

11:00 a.m. Joseph E. Bunnell: Public Health and Geospatial Distribution

11:30 a.m. Steve Helterbrand: Critical Habitat Diversity Parameters for Assessing the 

Geographical Distribution of Plague: A Geographic Information System 

(GIS)-Based Case-Control Study and Risk Model of Human Plague Cases 

in the Southwestern United States, 1963–2007

12:00 p.m. LUNCH (on site) 

Section V. Public Health and Water Quality 

1:00 p.m. Muruleedhara Byappanahalli: Integrating Quantitative Polymerase Chain 

Reaction (qPCR) and Predictive Models to Monitor Beach Water Quality

1:30 p.m. Jennifer L. Graham: Harmful Algal Blooms

2:00 p.m. Lisa R. Fogarty: Pathogens and Antibiotic-Resistant Bacteria in the Environment

2:30 p.m. Donald M. Stoeckel: Microbial Source Tracking, Using Quantitative Polymerase 

Chain Reaction (qPCR), for Enhanced Sanitary Water-Quality Management

3:00 p.m. BREAK (30 minutes) 

3:30 p.m. Ronald W. Harvey: Transport of Microbes in the Subsurface/Physical 

Interactions of Microbes and Particles

4:00 p.m. W. Bane Schill: Flow Cytometry in Microbiology

5:00 p.m. DINNER (on site) 

7:00 p.m. Breakout Working Groups: There will be several topics the groups will be 

divided into to address. The notebook you receive upon registration will have 

your working group assignment. 
 

 

 

 

 

 

 

 

 

 

xii 

October 17 

Section VI. 

8:30 a.m.

9:00 a.m.

9:30 a.m.

10:00 a.m.

Geomicrobiology 

Ronald S. Oremland: Geomicrobiology/Nanoscience of Toxic Elements Se and 

Te

JoAnn M. Holloway: Soil Microbial Indices Across Different Geographic Scales

Christopher T. Mills: Using Natural Abundance δ13C and Δ14C Values of 

Phospholipid Fatty Acids to Characterize Bacterial Carbon Cycling Pathways 

in Deep Aquifers

William H. Orem: Geochemical Controls on Microbial Methylation of Mercury 

in the Florida Everglades

10:30 a.m. BREAK (15 minutes) 

10:45 a.m.

11:15 a.m.

Mark Stanton: An Overview of Bacterial Controls and Influences on Sulfide 

Mineral Weathering

Mark Marvin-DiPasquale: Defining “Reactive” Inorganic Mercury and its 

Relationship to Microbial Methylmercury Formation in Aquatic Ecosystem 

Studies

11:45 a.m. LUNCH (on site) 

Section VII. 

12:45 p.m.

Ecosystem Function 

Special guest Dr. Erin Muths: A Tale of Disappearing Toads: The Amphibian 

Chytrid Fungus in the Rocky Mountains: 15-minute presentation followed by 

a field walk on site highlighting the habitats and life history of the boreal toad 

and its interactions with the chytrid fungus

2:00 p.m. BREAK (30 minutes) 

2:30 p.m.

3:00 p.m.

3:30 p.m.

4:00 p.m.

4:30 p.m.

Richard L. Smith: Natural and Enhanced Bioremediation of Nitrate 

Contamination in Groundwater

Mark P. Waldrop: Microbial Communities and Carbon Cycling in Response to 

Global Change

Jill S. Baron: Biogeochemistry of Mountain Watersheds: Through the Microbial 

Window

Matthew P. Bachmann: Quantifying Microbial Denitrification Rates Using 

Expressed Functional Gene Abundance

Julie D. Kirshtein: Evaluating Ecosystem Function with Integrated Approaches 

in Environmental Microbiology

5:00 p.m. Closing: Final comments, next steps
 

 

 

 

 

 

 

 

 

 

 

Proceedings of the U.S. Geological Survey 

Interdisciplinary Microbiology Workshop, 

Estes Park, Colorado, October 15–17, 2008 

Edited by Kay Marano Briggs* 

Presentation Abstracts 

Keynote Speech at Plenary Session 

The Ecology of Arsenic: A Lurid Tale of Murder, 

Mayhem, Microbes, Malodorous Mono Muds, 

and Mars 

By Ronald S. Oremland1 

1

U.S. Geological Survey, Water Resources Discipline, 345 Middlefield 

Road, Mail Stop 480, Menlo Park, CA 94205–3561.

Arsenic is a metalloid whose name conjures up images 

of murder. Nonetheless, certain prokaryotes use arsenic 

oxyanions for energy generation, either by oxidizing arsenite 

or by respiring arsenate. These microbes are phylogenetically 

diverse and occur in a wide range of habitats. Arsenic cycling 

may take place in the absence of oxygen and can contribute to 

organic matter oxidation. In aquifers, these microbial reactions 

may mobilize arsenic from the solid to the aqueous phase, 

resulting in contaminated drinking water. Future research will 

build on what is known about arsenic-metabolizing bacteria 

and their potential impact on speciation and mobilization of 

arsenic in nature.

Section I: Ecology of Wildlife and Fish 

Disease 

Bat White-Nose Syndrome: An Emerging Fungal 

Pathogen? 

By David S. Blehert1 

1

U.S. Geological Survey, National Wildlife Health Center, 6006 Schroeder 

Road, Madison, WI 53711–6223.

White-nose syndrome (WNS) is a condition associated 

with an unprecedented bat mortality event in the northeastern 

United States. Since the winter of 2006–2007, bat declines 

ranging from 80 to 97 percent have been observed at surveyed 

hibernacula. Affected hibernating bats often present with 

visually striking white fungal growths on their muzzles, 

ears, and (or) wing membranes. Histopathological analyses 

confirmed that 90 percent (105 of 117) of necropsied bats 

submitted from WNS-positive sites exhibited an associated 

cutaneous fungal infection. Direct microscopy and culture 

analyses demonstrated that the skin of WNS-affected bats 

is colonized by a psychrophilic (cold-loving) fungus with 

a unique conidial morphology. The isolates were initially 

cultured at 3°C and grew optimally between 5°C and 10°C, 

temperatures consistent with the core temperatures of 

hibernating cave bat species within the WNS-affected region. 

There is a growing body of circumstantial evidence supporting 

an association between WNS and cutaneous fungal infection. 

Given the hundreds of thousands of hibernating bats found 

throughout the WNS-affected region, this condition represents 

an unprecedented threat to bats of the northeastern United 

States and potentially beyond.

*

U.S. Geological Survey, 12201 Sunrise Valley Drive, Mail Stop 301, 

Reston, VA 20192–0002.
 

 

 

 

 

 

 

 

 

 

 

 

 

 

2 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Epidemiology and Evolution of Rhabdoviruses in 

Fish 

By Gael Kurath,1,2 Evi Emmenegger,1 Bill Batts,1 and 

Jim Winton1,2 

1

U.S. Geological Survey, Western Fisheries Research Center, 6505 NE 65th 

Street, Seattle, WA 98115.

2

University of Washington, School of Aquatic and Fisheries Sciences, 

Seattle, WA 98195.

Viral species from the family Rhabdoviridae include 

some of the most important pathogens that cause epidemic 

diseases in wild and cultured fish populations. The rhabdovirus 

species infectious hematopoietic necrosis virus (IHNV) is the 

most significant viral pathogen of salmon and trout in North 

America. Genetic typing and phylogenetic analyses of over 

650 field isolates of IHNV have revealed that there are three 

major genogroups of IHNV. These are designated the U, M, 

and L groups because they occur in the upper, middle, and 

lower portions of the geographic range of the virus along the 

Pacific coast. These genogroups vary in genetic diversity, 

rate of evolution, and virulence in different host species. For 

example, virus isolates in the U genogroup are homogeneous, 

with high virulence in sockeye salmon but not in trout. 

Conversely, M type viruses are genetically diverse, with high 

virulence in trout but not in sockeye. We suggest that IHNV

evolution has occurred from an ancestral sockeye virus by host 

jumps into trout and Chinook salmon, likely influenced by 

development of hatchery programs and aquaculture industries. 

Investigations into the mechanistic basis of U and M host 

specificity indicate that rapid viral replication early after 

infection allows the viruses to avoid host immune responses. 

Epidemiological studies based on genetic typing indicate 

that a new genotype of IHNV is emerging along the Pacific 

coast, creating a new threat to steelhead stocks. More recently, 

another fish rhabdovirus, viral hemorrhagic septicemia virus 

(VHSV), has emerged as a major pathogen in the Great Lakes 

region. Since the first outbreak of VHSV in 2005, there have 

been numerous fish kills, and the virus has been isolated from 

25 host species, several of which were not previously known 

to be susceptible to the VHS virus. Historically VHSV was 

thought to be a widespread marine fish virus that adapted 

to cultured rainbow trout in Europe, causing epidemics in 

European fish farms for several decades. The outbreaks in 

the Great Lakes are the first time VHSV has caused major 

disease epidemics in wild freshwater fish. Genetic typing 

suggests that the Great Lakes VHSV is most similar to marine 

VHSV isolates from the coasts of North America and that 

the introduction into the Great Lakes was relatively recent. 

Current studies of virulence of this new VHSV type are 

underway to support decisions needed to manage disease 

caused by VHSV in Great Lakes fisheries.

The United States Department of the Interior’s 

Avian Influenza Surveillance Program in North 

America: Laboratory Results 

By Hon S. Ip,1 Dirk Derksen,2 Tina Egstad,1 Katy Griffin,1 

Alexandria Hauser,1 Mellisa Houfe,1 Keynttisha Jefferson,1 

Melissa Kanter,1 Lucky Karwal,1 Anson Koehler,2 Kim Kooiman,1 

Peter Ladell,1 Renee Long,1 Kim Miller,1 Amy Miyamoto,1 

Jessica Montez,1 Melanie Mossing,1 Rachel Raddington,1 

Adam Ray,1 Stephanie Rieger,1 Hiram Sanchez,1 

Samantha Scott,1 Evan Sorley,1 Josh TeSlaa,1 Jennifer Tuscher,1 

and Thierry Work3 

1

U.S. Geological Survey, National Wildlife Health Center, 6006 Schroeder 

Road, Madison, WI 53711–6223.

2

U.S. Geological Survey, Alaska Science Center, 4210 University Drive, 

Anchorage, AK 99508.

3

U.S. Geological Survey, National Wildlife Health Center, 800 Ala Moana 

Boulevard, Room 5231, Honolulu, HI 96850.

The global expansion of the distribution of highly 

pathogenic avian influenza H5N1 virus has raised concern 

about the role of migratory birds in the long-distance 

dissemination of the virus. In the United States, the 

Department of the Interior, in cooperation with many other 

partners, has developed a risk-based surveillance program 

for the early detection of the possible introduction of H5N1 

by migratory birds. The program identifies target migratory 

bird species and sampling locations based on their migratory 

patterns, population size, habitat, potential contact with 

HPAI-infected birds, and ease of sample collection. Since 

April 2006, a total of 48,325 birds have been tested. Results 

show that 1,201 birds may contain an avian influenza virus as 

identified by matrix real-time reverse-transcription polymerase 

chain reaction (rRT–PCR) and, of these, 45 samples were 

positive according to the H5 rRT–PCR test. Twenty-eight H5 

viruses were isolated following inoculation in embryonating 

chicken eggs. The following subtypes were found: 21 H5N2, 5 

H5N3, and 2 H5N9 subtypes; however, no H5N1 viruses were 

found in the birds collected by the Department of the Interior 

surveillance program. Other avian influenza viruses identified 

include representatives containing combinations of 14 

hemagglutinin and 9 neuraminidase subtypes. Several isolates 

represent new species records. Genetic sequence analysis of 

some of the recovered viruses provides support that migratory 

birds in Alaska are involved in the intercontinental exchange 

of avian influenza viruses between Asia and North America 

and hence could be a mechanism for the introduction of H5N1 

into North America.
 

 

 

 

 

 

 

 

 

 

Section II: Mechanisms of Fish and Wildlife Disease 3 

Ecology of Vector-Borne Diseases in Pacific 

Island Birds: Hawaii to New Caledonia 

By Carter T. Atkinson,1 Dennis A. LaPointe,1 Michael D. Samuel,2 

Susan I. Jarvi,3 Ruth C. Utzurrum,4 and Joshua O. Seamon4 

1

U.S. Geological Survey, Pacific Island Ecosystems Research Center, 

Kilauea Field Station, P.O. Box 44, Hawaii National Park, HI 96718.

2

U.S. Geological Survey, Wisconsin Cooperative Wildlife Research Unit, 

University of Wisconsin, Department of Wildlife Ecology, Room 204, Russell 

Laboratories, Madison, WI 53706.

3

University of Hawaii, Department of Biology, 200 West Kawili Street, 

Hilo, HI 96720.

4

American Samoa Government, Department of Marine and Wildlife 

Resources, P.O. Box 3730, Pago Pago, American Samoa 96799.

Because of their isolation and often unique evolutionary 

history, insular species are particularly vulnerable to the 

introduction of new diseases and disease vectors. The 

introduction of mosquitoes, avian malaria (Plasmodium 

relictum), and avian pox virus (Avipoxvirus spp.) to the 

Hawaiian Islands has become a classic example of the 

potential destructive power of introduced diseases and vectors 

on a vulnerable endemic avifauna. Significant demographic 

impacts and dramatic changes in the distribution of native 

Hawaiian forest birds are tied closely to steep altitudinal 

gradients of disease transmission on the main Hawaiian 

islands. Transmission of pox and malaria is influenced by a 

variety of biotic and abiotic factors, including seasonal and 

altitudinal changes in vector populations that are related to 

temperature and rainfall, availability of larval habitat for 

mosquito vectors, presence of suitable disease reservoirs, and 

potential interactions between pox virus and chronic malarial 

infections. Keys to maintaining diversity of the endemic 

Hawaiian avifauna lie at the extremes of altitudinal gradients 

of disease transmission, both in the lowlands where high 

transmission rates are fostering natural selection of disease 

resistance and in remaining high-elevation refugia where 

restoration efforts are seeking to improve and expand habitat.

In contrast to Hawaii, island archipelagoes of American 

Samoa, Western Samoa, Fiji, and New Caledonia have a 

high diversity of indigenous hematozoan parasites, including 

several distinct lineages of Plasmodium and Haemoproteus, 

Trypanosoma avium, and at least two species of filarial 

worms. Diversity of this parasite fauna increases from east to 

west across the Pacific as distances to Australasia decrease. 

Endemic forest birds of eastern Polynesia probably face the 

greatest risk from introduced vector-borne diseases such as 

West Nile virus both because of their isolation and because 

some of these remote island groups have indigenous vectors 

for transmitting avian pathogens. None of these archipelagos, 

however, are comparable to Hawaii in terms of remoteness, 

historical absence of vectors, and diversity of endemic birds.

Section II: Mechanisms of Fish and 

Wildlife Disease 

Disease Impacts on Populations of Wild Marine 

Fish 

By Paul K. Hershberger1 

1

U.S. Geological Survey, Marrowstone Marine Field Station, Western 

Fisheries Research Center, 616 Marrowstone Point Road, Nordland, WA

98358.

Pacific herring (Clupea pallasii) populations throughout 

the nearshore and coastal regions of the eastern North 

Pacific are routinely impacted by infectious and parasitic 

diseases, including viral hemorrhagic septicemia (VHS), viral 

erythrocytic necrosis (VEN), and ichthyophoniasis. In an 

effort to understand, predict, and mitigate the impacts of these 

diseases on populations of wild marine fishes, we combine 

a holistic approach consisting of disease surveillances in 

wild populations with a reductionistic approach consisting 

of controlled, laboratory-based empirical studies. A major 

impediment to performing well-controlled laboratory studies 

was recently overcome with the development of colonies of 

specific-pathogen-free, immunologically naive Pacific herring. 

These animals are utilized to understand cause-and-effect 

relationships involving disease kinetics, acute and chronic 

impacts of disease, and immunological responses to the 

pathogens. These relationships can help us to understand the 

impacts of disease on wild populations in the context of the 

collapse and failed recovery of adult herring in Prince William 

Sound, age truncation of adult herring in Puget Sound, and 

acute and chronic mortalities that occur among juvenile 

herring throughout the eastern North Pacific.

Mycobacteriosis in Chesapeake Bay 

By Christopher A. Ottinger1 

1

U.S. Geological Survey, Leetown Science Center, National Fish Health 

Research Laboratory, 11649 Leetown Road, Kearneysville, WV 25430.

Mycobacteriosis has been present in Chesapeake Bay 

striped bass since at least the 1980s, as indicated by archived 

tissue samples. It was not until the summer and fall of 1996–

97, however, when large numbers of fish with skin lesions 

were reported in the Pocomoke River and other tributaries 

of Chesapeake Bay, that a great deal of public and scientific 

interest was stimulated about this disease. Mycobacteriaassociated infection and disease in Chesapeake Bay striped 

bass are age dependent. Disease prevalence also appears to 

have temporal and possibly spatial components, although the 

latter is difficult to analyze due to the highly migratory nature 

of this fish. The disease appears to be most severe during the 
 

 

 

 

 

4 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

late summer and fall. Modes of transmission remain poorly 

understood, although limited data indicate that infections can 

be transmitted via the water column. Additional data indicate 

the occurrence of gonadal infection, suggesting the possibility 

of adults transferring the infection to their progeny. Multiple 

species of fishes within the Chesapeake Bay have been found 

to be infected with mycobacteria, suggesting the possibility of 

trophic transfers of infection. Trophic interactions may also 

impact striped bass nutrition directly through reductions in 

prey species numbers. Within the past decade, large numbers 

of emaciated striped bass have been observed in Chesapeake 

Bay, and it is thought that this loss in condition may be largely 

attributed to mycobacteriosis. Laboratory studies indicate that 

inadequate nutrition can predispose fish, thus enhancing the 

severity and progression of mycobacteriosis in striped bass. 

The degree to which poor nutrition contributes to the disease 

process in the wild striped bass population will likely be 

difficult to elucidate. Chesapeake Bay population data indicate 

that the natural mortality rate in the spawning component of 

the striped bass stock increased beginning in the late 1990s. A

cause-effect correlation between increased natural mortality 

and the mycobacteriosis epizootic is surmised but has yet to be 

established. The simultaneous occurrences of increased natural 

mortality along with elevated prevalence of mycobacterial 

infection have, however, raised concerns about the potential 

impact of mycobacteriosis on the striped bass population. 

Studies are currently underway to examine relative return rates 

of externally diseased and healthy striped bass. This work will 

provide information on disease-associated mortality in striped 

bass on a population scale. Additional information on diseaseassociated mortality in striped bass is being collected through 

large-scale cross-sectional surveys of mycobacteriosis in 

mainstem Chesapeake Bay. Modeling of these data with newly 

developed techniques suggests that mycobacteriosis-associated 

mortality may be affecting the species at the population level.

Studies on Plague Pathogenesis in Rodents 

Using in vivo Imaging 

By Tonie E. Rocke,1 Sandra Dawe,2 and Jorge E. Osorio3 

1

U.S. Geological Survey, National Wildlife Health Center, 6006 Schroeder 

Road, Madison, WI 53711–6223.

2

Wisconsin State Lab of Hygiene, 465 Henry Mall, Madison, WI 53706.

3

University of Wisconsin-Madison, School of Veterinary Medicine, 

Department of Pathobiological Sciences, 1655 Linden Drive, Madison, WI 

53706.

Plague, caused by the bacterium Yersinia pestis, is a 

flea-transmitted disease of wild rodents that occasionally 

spills over into humans and other mammals. In the past 

century, plague caused severe epidemics in many parts of 

the world, resulting in human deaths and severe economic 

losses. Fears of a new resurgence of plague have been raised 

by recent plague outbreaks in regions (India and Madagascar) 

where the disease had been dormant for decades; these 

fears were compounded by the isolation of multidrugresistant strains of Y. pestis during the plague epidemic in 

Madagascar. Furthermore, because of its pathogenicity in 

humans (particularly the pneumonic form of the disease) 

and its potential for human-to-human transmission, Y. 

pestis is considered a potential candidate for biowarfare 

and bioterrorism. These factors have renewed interest in the 

pathogenesis of Y. pestis and host response to infection. In 

animals, particularly natural rodent hosts like ground squirrels 

and prairie dogs, the pathogenesis of plague is not well 

characterized. Traditionally, charting the course of plague 

entailed sequential euthanasia of infected animals over time, 

requiring large numbers of animals and the time-consuming 

tasks associated with determining bacterial load in various 

tissues and organs ex vivo. As an alternative technique, we 

are using bioluminescent imaging (BLI) to determine the 

kinetics of disease progression in vivo in real time, reducing 

the number of animals required and the animal-to-animal 

variability. Recombinant, fully virulent, bioluminescent Y. 

pestis C092 was generated using the mini Tn7-transposon 

to introduce the complete lux operon (luxCDABE) into the 

bacterial genome at a unique site. Using a photon-counting, 

intensified charge-coupled device camera, the dissemination 

and tissue localization of bioluminescent Y. pestis was 

monitored and quantified in vivo in mice. Differences in the 

distribution pattern of bacteria were discerned over the course 

of infection in mice inoculated via different routes of exposure 

(intradermal, subcutaneous, and intranasal), demonstrating that 

BLI is capable of distinguishing between different forms of 

plague disease (bubonic, primary septicemic, and pneumonic). 

We also monitored plague infection in animals that received 

different vaccines, demonstrating that BLI can be used 

quantitatively to measure treatment effects. Bioluminescent 

imaging offers several advantages for the study of plague 

pathogenesis, allowing the dissemination of Y. pestis to be 

tracked from the site of exposure through host tissues in real 

time.

Role of Wild Rodents in Environmental Transport 

of Prions 

By Chad J. Johnson1 and Dennis M. Heisey2 

1

University of Wisconsin-Madison, School of Veterinary Medicine, 

Department of Comparative Biosciences, 1656 Linden Drive, Madison, WI 

53706.

2

U.S. Geological Survey, National Wildlife Health Center, 6006 Schroeder 

Road, Madison, WI 53711–6223.

Prion diseases, or transmissible spongiform encephalopathies (TSE), are a group of progressive fatal neurological 

diseases. The infectious agent is novel in that it consists 

of a misfolded form of a normal cellular protein, the prion 

protein (PrPC). The disease form of the prion protein (PrPD) 
 

 

 

 

 

 

 

5 

is highly resistant to inactivation by methods that inactivate 

other pathogens. Chronic wasting disease (CWD) is the first 

documented prion disease of a wild mammalian population. 

CWD agent is maintained in the wild population through 

lateral transmission. There is growing evidence for animalto-animal contact and environmental reservoirs contributing 

to the transmission of the disease agent. The presence of 

environmental sources of the disease agent indicates a 

certain background level of exposure of the disease agent 

to other species in the environment. We are exploring the 

transmission of CWD to various rodent species, including 

meadow voles (Microtus pennsylvanicus), southern redbacked voles (Clethrionomys gapperi), deer mice (Peromyscus 

maniculatus), and white-footed mice (Peromyscus leucopus). 

These rodents scavenge carrion and are an important food 

source for many predator species. Furthermore, these rodents 

enter human and domestic livestock food chains by accidental 

inclusion in grain and forage. All of the rodent species 

except the white-footed mouse have proven susceptible 

to interspecies transmission of CWD via the intracerebral 

route. Meadow voles proved to be most susceptible, with the 

earliest presentation of disease signs after about 7 months 

and with 100 percent mortality by 374 days. This high level 

of penetration indicates a low species barrier in this species 

to interspecies transmission of CWD. Our main objectives 

with this study are determining the following: the risk of 

natural transmission of CWD into rodents, the potential for 

adaptation and maintenance of a TSE in rodent populations, 

the properties of any adapted infectious agent, and the effect 

of prion protein allelic variation on all of the above-listed 

processes.

Microbial Diseases in Marine Ecosystems: 

Challenges and Opportunities 

By Thierry M. Work1 

1

U.S. Geological Survey, National Wildlife Health Center, Honolulu Field 

Station, 800 Ala Moana Boulevard, Room 5231, Honolulu, HI 96850.

Diseases in marine ecosystems are becoming increasingly 

visible, particularly for certain organisms like marine 

mammals, sea turtles, and corals. In the Caribbean, diseases 

of corals and echinoderms have led to severe degradation 

of coral reef ecosystems. Yet our understanding or potential 

management of many diseases in marine ecosystems is limited 

by what we don’t know. For example, the life cycles of many 

marine organisms that are hosts to disease are unknown, 

complicating our understanding of the epizootiology of 

diseases. The life cycles of many marine parasites are 

unknown, making their management a problematic issue. 

Furthermore, many microbial agents present in marine 

ecosystems cannot be cultured by using conventional 

techniques, and thus reagents commonly used to identify 

microorganisms are not suitable or are lacking for marine 

Section III: Microbial Ecology 

microorganisms. Genomic techniques provide a partial answer 

to some of these quandaries; however, detecting the genome 

of an organism and determining the role this organism plays 

in actual disease causation are two very different propositions. 

Some of these quandaries have affected studies of sea turtles, 

fish, and corals. On the other hand, devising creative solutions 

to these problems may provide opportunities to form new 

paradigms about our understanding of wildlife diseases.

Section III: Microbial Ecology 

Microbiology of Deep-Sea Corals 

By Christina A. Kellogg1 

1

U.S. Geological Survey, Florida Integrated Science Center-St. Petersburg, 

Coastal and Watershed Studies Team, 600 4th Street, St. Petersburg, FL

33701.

Coral-associated bacteria and Archaea are beginning 

to be recognized as an important part of the total biology of 

the shallow-water coral holobiont (the entity composed of 

the coral animal, zooxanthellae, and mucus/tissue/skeletaldwelling microbes). Known activities include cycling 

carbon, producing antibiotics, and fixing nitrogen, while 

other metabolic roles remain to be discovered. Deep-sea 

corals have a fundamentally different ecology due to their 

adaptation to cold, dark, high-pressure environments, and, 

thus, they have novel microbiota. Submersibles were used 

to collect samples of both soft corals (gorgonians from 

waters off the Aleutian Islands) and stony coral (Lophelia 

pertusa from the Gulf of Mexico). The corals were brought 

to the surface in specially designed containers to prevent 

contamination from the water column and thermal shock. 

Additionally, a subset of each sample was preserved at depth, 

to control for changes in the microbial community that might 

have resulted from the differences in light, temperature, 

and pressure experienced as the sample was brought to the 

surface. Microbes were analyzed by both cultivation and 

culture-independent methods, making this the first study to 

include both culture-based and molecular data on deep-sea 

coral-associated bacterial communities. There are a few 

similarities between the bacterial symbionts of deep-sea corals 

and those of shallow-water corals, but both cultured isolates 

and 16S rDNA clone libraries reveal novel bacteria. Many 

of these bacteria are similar to prokaryotic symbionts of fish, 

squid, and methane-seep clams. Others are most similar to 

psychrophiles from polar waters. The clone libraries also 

contain a surprising number of mollicute sequences, mainly 

from the family Mycoplasmataceae. Molecular analysis of 

bacterial community diversity in Lophelia pertusa revealed 

a marked difference between communities at two study sites 

that were less than 20 nautical miles apart. This unexpected 

dissimilarity between the dominant members of these bacterial 
 

 

 

 

 

 

 

 

6 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

communities may be evidence of disease or stress at one 

site or may indicate biogeographical differences. This work 

contributes to our understanding of microbial diversity and 

coral holobiont community structure. Characterizing the 

microbial communities of deep-sea corals is fundamental to 

understanding the biology and ecology of deep reefs.

Development and Application of Denaturing 

High-Performance Liquid Chromatography 

(DHPLC) Methods for the Analysis of Microbial 

Community Composition 

By Andrea L. Foster1 

1

U.S. Geological Survey, Mineral Resources Program, 345 Middlefield 

Road, Mail Stop 901, Menlo Park, CA 94025–3561.

Analysis of sequence variation among polymerase 

chain reaction (PCR) amplicons derived from16S rDNA

is currently the standard technique for assessing microbial 

community composition and diversity in environmental 

samples. The pooled amplicons are commonly separated for 

individual sequence analysis by clone library construction 

or by vertical electrophoresis through a polyacrylamide gel 

containing an increasing amount of chemical denaturant 

down the gel (denaturing gradient gel electrophoresis, or 

“DGGE”). Both techniques have significant drawbacks in 

terms of expense, labor costs, quantifiability, and ease of 

downstream processing. Denaturing high-performance liquid 

chromatography (DHPLC) is a relatively new technique 

for separating DNA or RNA fragments on the basis of 

size or sequence variation using reverse phase ion-pairing 

liquid chromatography. Pooled PCR amplicons are passed 

through a separation column containing 18C-alkylated 

polystyrene-divinylbenzene copolymer beads. The beads 

are electrostatically neutral and hydrophobic. The stationary 

phase, triethylammonium acetate (TEAA), has both 

hydrophobic and positively charged ends. It can therefore bind 

to both the beads and the negatively charged phosphate groups 

on DNA or RNA fragments, allowing indirect adsorption of 

the DNA to the separation column beads. Increasing amounts 

of the mobile phase (25 percent acetonitrile in 0.1 molar (M) 

TEAA) decreases the hydrophobic interaction between TEAA

and the separation column beads, so that the DNA-TEAA ion 

pair is released to solution. Both ultraviolet (UV) absorption 

and fluorescence detection of eluted DNA are available, with 

the latter affording increased sensitivity. DHPLC is more 

quantitative, reproducible, and automated than gel-based 

or cloning methods, and it can be coupled to downstream 

fraction collection, decreasing the preparative procedures 

required to obtain sequences of PCR amplicons. Case studies 

have been made of the development and application of 

DHPLC methods for analysis of 16S rDNA or functional 

gene fragments for several microbial groups, including all 

Eubacteria, the sulfate-reducing bacteria, the Archaea, and the 

Fungi. DHPLC as a method of culture-independent analysis 

of microbial communities has unique benefits and limitations 

relative to other methods available or soon to be online at 

the U.S. Geological Survey (USGS), such as quantitative 

PCR and methods using phospholipid fatty acids (PLFAs). 

The technology has potential new applications in the areas of 

microbial ecology and population biology relevant to the types 

of investigations the USGS conducts.

The Role of Biological Soil Crusts in Preventing 

Desertification of Dryland Ecosystems 

By Jayne Belnap1 

1

U.S. Geological Survey, Southwest Biological Science Center, 

Canyonlands Research Station, 2290 SW Resource Boulevard, Moab, UT

84532.

Biological soil crusts (BSCs) are a critical component of 

most dryland ecosystems. The phototropic organisms in these 

soil surface communities are dominated by cyanobacteria, 

mosses, and lichens, and, as they often completely cover 

the large soil interspaces found between plants, they can be 

the dominant living cover in these ecosystems. Biological 

soil crusts influence many aspects of dryland function. 

Cyanobacteria, lichens, and mosses all fix carbon (C) and 

can be an essential source of C for subsurface soil biota. 

Most cyanobacteria and cyanolichens that occur in these 

communities fix nitrogen (N) and can be the dominant source 

of this often-limiting nutrient for plant and soil communities. 

The BSC organisms are sticky and help retain wind-deposited 

nutrients, which can provide up to 75 percent of plant-essential 

nutrients (for example, N, P, K, Mg, Na, Mn, Cu, and Fe). 

Crust organisms also contribute to keeping nutrients available 

to vascular plants by secreting powerful metal chelators. 

Biological soil crusts can also increase water infiltration and 

the retention of nutrient-rich dust, seeds, and organic matter. 

Plant productivity and concentrations of most plant-essential 

nutrients are often higher in plants when they are growing 

in soils covered by BSCs relative to adjacent uncrusted 

soils. Soil food webs are more complex and organisms more 

abundant under well-developed soil crusts than those under 

less developed crusts, and thus nutrient cycling is faster when 

mosses and lichens are present. Biological crusts are also 

vital in reducing wind and water erosion. Most soil surfaces 

in drylands lack protection by rocks or plants and depend on 

BSCs for their stability. Thus, where plant cover is sparse, 

BSCs reduce erosion from otherwise unprotected soil surfaces. 

Unfortunately, these communities are highly susceptible to 

soil surface disturbance, as they are easily crushed and (or) 

buried when disturbed. Experimental disturbances show 

that disruptions of soil surfaces result in decreased N and C 

inputs from soil biota by up to 100 percent. The ability to glue 

aeolian deposits in place is compromised. While sediment 

production from BSC-covered surfaces is minimal, production 
 

 

 

 

 

 

 

 

7 

after disturbance increases by up to 36 times, with soil 

movement initiated at wind velocities well below commonly 

occurring wind speeds. Because the disturbance of desert 

soil surfaces can both reduce fertility inputs and accelerate 

fertility losses, preservation of these organisms could be a 

management goal in dryland ecosystems.

Endosymbiotic Fungi in Plants: Ecology and 

Implications for Climate Change 

By Russell J. “Rusty” Rodriguez1 

1

U.S. Geological Survey, Western Fisheries Research Center, 6505 N.E. 

65th Street, Seattle, WA 98115.

Climate change is predicted to negatively impact aquatic 

and terrestrial ecosystems due to increased frequency and 

severity of drought, disease, salinization, and biological 

invasions. This possible increase in droughts will result in 

difficult decisions concerning water allocations for supporting 

agriculture, supplying public utilities, generating electricity, 

and sustaining ecosystems. While significant research effort 

has been invested in climate predictions and decreasing CO2, 

comparatively little effort has gone into mitigating the impacts 

of climate change. We have developed an Adaptive Symbiotic 

strategy to mitigate impacts of climate change on plants in 

natural and managed ecosystems. This strategy is based on 

the fact that fungal endophytes adapt to environmental stress 

(drought, salinity, disease, temperature) and confer stress 

tolerance to host plants. Plants appear unable to adequately 

adapt to stress, thus making fungal symbionts significant 

adaptive components of plant communities. Symbiotically 

conferred stress tolerance occurs in a habitat-specific manner, 

and both plants and fungi switch partners across microhabitats 

in order to maximize fitness. The mechanism(s) responsible 

for symbiotically conferred stress tolerance involves 

diminishing the amount of reactive oxygen generated under 

stress. In addition, drought tolerance is based on increased 

water efficiency in symbiotic plants, which require less water 

for normal growth and development. Therefore, decreased 

water needs in symbiotic plants can translate into decreased 

irrigation demands, allowing more water to be allocated for 

sustaining aquatic ecosystems. I have studied the mechanisms 

responsible for stress tolerance, the ecological significance of 

symbiosis, and the use of symbionts to mitigate the impacts of 

climate change.

Section III: Microbial Ecology 

Soil Community Dynamics in Sagebrush Steppe 

and Cheatgrass-Invaded Areas of the Northern 

Great Basin 

By Nicole M. DeCrappeo,1,2 David A. Pyke,1 and 

Peter J. Bottomley2 

1

U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, 

3200 S.W. Jefferson Way, Corvallis, OR 97331.

2

Oregon State University, Department of Crop and Soil Science, 3017 

Agricultural and Life Science Building, Corvallis, OR 97331.

Sagebrush steppe ecosystems in the northern Great 

Basin have been dramatically altered by the invasion of the 

exotic annual grass Bromus tectorum (cheatgrass). We have 

extensively studied the effects of this shrub-to-grassland 

conversion on soil biota in eastern Oregon, southern Idaho, 

Utah, and Nevada. Surveys of biological soil crust, microbial, 

and nematode communities using a variety of techniques 

(line-point intercept, community-level physiological profiling 

[CLPP], phospholipid fatty acid [PLFA] analysis, terminal 

restriction fragment length polymorphism [T-RFLP], and 

sugar-centrifugation and microscopy) have revealed clear 

differences in biotic community structure and dominance 

under sagebrush, bunchgrass, cheatgrass, and interspace areas. 

Preliminary data suggest that sagebrush soils have higher 

saprophytic fungal diversity and abundance and biological 

soil crust cover (cyanobacteria, mosses, and lichens), 

while cheatgrass soils have higher amounts of arbuscular 

mycorrhizal fungi and little to no crust development. We 

are in the process of elucidating the consequences of these 

differences for ecosystem processes by using isotope pool 

dilution techniques in conjunction with bacterial and fungal 

antibiotic treatments. Our specific objective is to determine 

how bacteria and fungi contribute to nitrogen production and 

consumption in sagebrush and cheatgrass rhizosphere soils. 

At larger spatial scales, we have discovered soil community 

patterns related to edaphic factors at cheatgrass-invaded sites 

across the Great Basin. Initial findings show that sites with 

high pH values (>8.0) can be characterized as having little to 

no biological soil crust development and tend to be dominated 

by bacteria and bacterial-feeding nematodes. Finally, we have 

quantified how restoration and management treatments, such 

as prescribed fire and nutrient additions, temporarily increase 

or decrease certain groups of soil organisms. Ultimately, we 

hope to use this knowledge to increase native plant restoration 

success in the sagebrush steppe.
 

 

 

 

 

 

 

8 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Section IV: Geographic Patterns/ 

Visualization 

Microbial Mapping: Stimulating Hypothesis and 

Informing the Public 

By Stephen C. Guptill1 

1

U.S. Geological Survey (retired), 12201 Sunrise Valley Drive, Reston, VA

20192–0002.

John Snow’s 1855 map of the cholera outbreak in 

London is well known to epidemiologists, biologists, and 

cartographers. While it is unlikely that Snow, upon studying 

the map, had an “ah hah” reaction and rushed to remove the 

handle of the Broad Street pump, the map remains an iconic 

example of the power of being able to geographically visualize 

microbial activity. Microbial activity (from genetic mutations 

to outbreaks of disease) does not occur on a homogeneous 

plane, but rather varies by geographic location. By attaching 

spatial and temporal tags to our observations of microbial 

occurrences, we can use these data in a wide variety of 

visualization and analysis methods. These techniques can be 

used to inform the public by displaying the results of disease 

surveillance and outbreak investigations. The mapping of 

arboviral diseases conducted by the U.S. Geological Survey 

(USGS) under a collaborative agreement with the Centers 

for Disease Control and Prevention (CDC) is an example 

(see http://diseasemaps.usgs.gov). The spatial and temporal 

juxtaposition of disease events in wildlife and human cases 

can trigger insights into methods that allow for the prediction 

of human outbreaks. For example, West Nile virus (WNV) 

cases in wild birds can be used as a predictor of human 

cases on a county-by-county basis. Along similar lines, 

environmental conditions that promote the growth of host, 

vector, or microbe populations can be monitored by using 

remote sensing and field observations. Areas at greater risk of 

malaria or Rift Valley fever outbreaks have been identified by 

using such techniques.

A Multiscale Approach to the Concept of 

Regional Health 

By Lee De Cola1 

1

U.S. Geological Survey, Eastern Geographic Science Center, 12201 

Sunrise Valley Drive, Mail Stop 521, Reston, VA 20192–0002.

Health certainly implies the ability of an organism 

to restore physiological equilibrium when disturbed, but 

is it meaningful to speak of regional health? A region is a 

bounded unit of space, and for some purposes, the human 

body (approximate size 1 square meter) can be considered 

a small region, whose health is in part determined by 

processes at the cellular and microbial level of 1 micrometer 

(10-6 meter). Let us reflect on this size range and ask if the 

concept of health applies at the megameter (106 meter) level. 

Some islands and lakes are clearly bounded regions of this 

size, as are some watersheds. The demography, landscape, 

hydrology, and wildlife of the 160,000-square-kilometer (km2) 

Chesapeake Bay watershed (CBW) region are being modeled, 

and questions of its health arise, but in what sense? We can 

ask if the region’s constituent organisms are healthy, but 

because the members of this ill-defined set form an impossibly 

complicated trophic web, the health of the region cannot 

be any kind of sum of the health ratings of its organisms. 

More narrowly, we can investigate the health of the set of 

human inhabitants: compared to a 1:1,000 random sample 

of global humans, the 15 million inhabitants of the CBW

are probably taller, heavier, and likely to have a longer life 

expectancy. Although we might investigate whether regional 

environmental conditions threaten public welfare, aggregate 

human health can only be one among many indicators of 

regional health. Still at the macro level, CBW scientists are 

modeling and measuring the status, variation, and trends of 

such regional systems as atmospheric and water chemistry, 

land cover and the remotely sensed greenness cycle, and 

wildlife health and biodiversity; they are finding that many 

of these indicators are outside of the ranges typical of the 

region’s 10,000-year history. We may build on this notion of 

regional “physiology” by asking whether regional processes 

are resilient enough to reestablish some kind of equilibrium 

within the next few human generations. Although it is quite 

likely that the chemistry, landscape, and biodiversity of the 

CBW will attain a new equilibrium, many indices will be 

very different from preindustrial ranges, and in this sense, the 

region currently cannot “pass its physical.”

To return to the micro scale, the modern theory 

of infection and immunity suggests a tradeoff between 

endemicity and virulence: impaired host functioning restricts 

highly destructive pathogens from infecting large numbers 

from a population. Because the disequilibrium of the CBW is 

due to human activities, the region’s capacity to host projected 

numbers of humans will be depressed by negative loops that 

will limit the prospects for continued regional exploitation, 

even though some kind of future equilibrium—either managed 

or “natural”—is likely. The evolving concept of regional 

health, although difficult to operationalize, can facilitate 

the development of regional clinical practice allied to the 

broadening field of public health.
 

 

 

 

 

 

 

 

 

 

 

 

 

9 

Public Health and Geospatial Distribution 

By Joseph E. Bunnell1 

1

U.S. Geological Survey, Eastern Energy Resources Team, 12201 Sunrise 

Valley Drive, Mail Stop 956, Reston, VA 20192–0002.

The value in mapping disease occurrence is to illuminate 

the underlying cause of an outbreak, which may then enable 

mitigation measures to be taken to prevent further spread of a 

similar future disease. The earliest example of using a spatioanalytical approach to solving an epidemiological riddle 

is generally credited to John Snow, who mapped a major 

outbreak of cholera in 19th century London, during a time 

before germ theory was well accepted, and hypothesized that 

there was a causal association between the putative source of 

the contagion and case locations. He convinced city officials 

to remove the handle of a pump dispensing contaminated 

water—an intervention that promptly quelled the outbreak. 

A more recent example of how understanding geospatial 

distributions of diseases may lead to improved preventive 

measures is provided by geospatial analysis of Lyme disease 

in the Middle Atlantic and northeast regions of the United 

States. Tick abundance is likely a more reliable measure of the 

effect of landscape features on Lyme disease risk than human 

cases. Geographic information system (GIS) techniques were 

used with statistics incorporating spatial autocorrelation 

to tick distribution data, and multiple regression analysis 

was performed. GIS assisted with secondary and tertiary 

calculations based on raw data, and the investigations 

revealed significant associations between tick abundance 

and specific environmental covariates, including, counterintuitively, soil type. Because a digital subset of soil data 

at much higher resolution and with a more extensive set of 

attributes was subsequently made available, a second analysis 

was conducted. When State Soil Geographic (STATSGO) 

data (1:250,000, from the Natural Resources Conservation 

Service [NRCS]) were used, well-drained soils were found 

to be significantly positively associated with tick abundance, 

in keeping with previous literature reports. Upon analysis 

using Soil Survey Geographic (SSURGO) data (1:24,000, 

from the NRCS), however, it was found that poorly drained 

soils, too, could be positively associated with tick abundance. 

This apparent contradiction was resolved by considering 

precipitation factors and soil water-holding capacity. This 

example demonstrates the power of a GIS approach in 

examining environmental influences on factors controlling 

human disease risk. Observation of previously obscured 

patterns has enabled the generation of hypotheses now being 

tested to explain factors responsible for biologically based 

spatio-analytical trends. If researchers can better understand 

the effects of environmental parameters on disease vector 

distribution, then public health officials will likely be able 

to improve intervention strategies. Other examples where 

analytical tools have been used to generate testable public 

health research hypotheses include: fluorosis in China; 

Section IV: Geographic Patterns/Visualization 

African trypanosomiasis (sleeping sickness); Hurricane Mitch; 

cadmium in the Netherlands; and malaria in Mexico and 

Guatemala.

Critical Habitat Diversity Parameters for 

Assessing the Geographical Distribution of 

Plague: A Geographic Information System 

(GIS)-Based Case-Control Study and Risk Model 

of Human Plague Cases in the Southwestern 

United States, 1963–2007 

By Russell E. Enscore,1 W. Steve Helterbrand,2 

Rebecca J. Eisen,1 James E. Cheek,3 John A. Montenieri,1 

Pamela J. Reynolds,4 Ted L. Brown,4 Paul J. Ettestad,4 and 

Kenneth L. Gage1 

1

Centers for Disease Control and Prevention, National Center for Zoonotic, 

Vector-Borne, and Enteric Diseases, Division of Vector-Borne Infectious 

Diseases, Bacterial Diseases Branch, P.O. Box 2087, Fort Collins, CO 80521.

2

U.S. Geological Survey, Mid-Continent Geographic Science Center, 1400 

Independence Road, Mail Stop 509, Rolla, MO 65401–2602.

3

Indian Health Service, Headquarters West, Epidemiology Section, 801 

Vassar Drive NE, Albuquerque, NM 87110.

4

New Mexico Department of Health, Division of Epidemiology, 1190 S. St. 

Francis Drive, Santa Fe, NM 87501.

Remotely sensed geographic parameters including land 

cover, elevation, and slope were used to develop and validate 

models of peridomestically acquired human plague case sites 

using a case-control study design for the two largest case foci 

in the United States. Analysis of 82 cases and 222 control 

sites from the Four Corners Focus, using 30-meter-resolution 

data layers from the U.S. Geological Survey’s National Land 

Cover Database and National Elevation Dataset, shows strong 

correlations of plague incidence with elevation, slope, and 

vegetative land cover diversity. Higher elevations, above 

2,100 meters (m), are strongly correlated with a 2.64 times 

increased incidence, whereas, lower elevations, below 1,825 

m, are correlated with a 3.13 times reduced incidence. Slope 

greater than 3 percent is strongly associated with a 2.4 times 

increased incidence, as is a vegetative land cover composed 

of shrubland, grassland and juniper, within a 500-m buffer 

zone around sites having a 3.35 times increased incidence. 

All three parameters together in a simple correlation model 

produced a 4.81 times increased incidence. A 30-m-resolution 

risk map (model) was constructed and validated using the 163 

North-Central New Mexico Focus case sites and demonstrates 

a 78 percent accuracy rate. A logistic regression model was 

separately constructed and yielded a best-fit model, which 

included elevation, elevation squared, and the same land cover 

diversity measure. Receiver operating characteristic (ROC) 

curves were used to evaluate the regression models, with the 

best model yielding a ROC value of 0.68. Habitat diversity is a 

critical distribution parameter for human plague risk.
 

 

 

 

 

 

 

 

 

 

10 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Section V: Public Health and Water 

Quality 

Integrating Quantitative Polymerase Chain 

Reaction (qPCR) and Predictive Models To 

Monitor Beach Water Quality 

By Muruleedhara N. Byappanahalli,1 Dawn A. Shively,1 and 

Richard L. Whitman1 

1

U.S. Geological Survey, Great Lakes Science Center, Lake Michigan 

Ecological Research Station, 1100 North Mineral Springs Road, Porter, IN 

46304.

Fecal indicator bacteria, such as fecal coliforms, E. coli, 

and enterococci, have historically been used to determine the 

quality of fresh and marine recreational waters. Currently, 

bacterial culturing requires 18–24 hours to complete, causing 

a considerable delay in issuing beach advisories. The need 

for a more rapid test has been emphasized by local and State 

managers and the U.S. Environmental Protection Agency. 

Quantitative polymerase chain reaction (qPCR) has been 

suggested as a potential rapid test for measuring beach water 

quality. Recent research has shown that enterococci counts 

measured by qPCR correlate well with swimming-associated 

illnesses in recreational waters. The objectives of this project 

were to demonstrate if qPCR is a potential tool for managing 

recreational beaches for microbiological water quality and to 

compare qPCR results with results from empirical predictive 

models. During the summer of 2006, water samples were 

collected from three southern Lake Michigan beaches and an 

associated river outfall (Burns Ditch). Culturable enterococci 

counts (log colony-forming units per 100 milliliters, or log 

CFU/100 mL) for the beaches were significantly correlated 

with calibrator cell equivalents (CCE) as determined by qPCR 

(R=0.650, P<0.0001, N=32). Culturable enterococci densities 

at the beaches were significantly correlated with Burns Ditch 

enterococci densities (R=0.565, P=0.001, N=32). Enterococci 

densities in Burns Ditch were significantly higher than those in 

beach water (P<0.0001). However, there were no correlations 

or significant differences observed between CCE values at 

the study sites. Enterococci CCE results for the study beaches 

correlated well with many independent variables tested in the 

development of the Swimming Advisory Forecast Estimate 

(SAFE) predictive model. Regression analysis resulted in 

a model that incorporated Burns Ditch discharge and an 

interactive term: log-transformed lake turbidity × wave 

height. Our results show that analytically, qPCR compares 

well with the traditional membrane-filtration (MF) method for 

measuring beach water quality. Thus, qPCR may be a viable 

alternative approach for determining beach water quality 

if a standard water-quality criterion for enterococci CCE is 

developed.

Harmful Algal Blooms 

By Jennifer L. Graham,1 Keith A. Loftin,1 Michael T. Meyer,1 

Andrew C. Ziegler,1 John R. Jones,2 and Susan B. Jones3 

1

U.S. Geological Survey, 4821 Quail Crest Place, Lawrence, KS 66049–

3839.

2

University of Missouri, 302 Anheuser-Busch Natural Resources Building, 

Columbia, MO 65211.

3

U.S. Geological Survey, Columbia Environmental Research Center, 4200 

New Haven Road, Columbia, MO 65201.

Harmful algal blooms (HABs) in both marine and 

freshwater environments cause ecologic, economic, and 

public health concerns. In freshwater, the majority of HABs 

are caused by cyanobacteria. Cyanobacteria cause a multitude 

of water-quality concerns, including potential production 

of taste-and-odor compounds and toxins. Taste-and-odor 

compounds cause malodorous or unpalatable drinking water 

and fish, resulting in increased treatment costs and loss 

of aquacultural and recreational revenue. Cyanobacteria 

produce a diverse group of toxins, including hepatotoxins, 

neurotoxins, and dermatoxins, that have been implicated in 

human and animal illness and death in at least 35 U.S. States. 

Acute human toxicoses associated with cyanotoxins have 

most commonly occurred after exposure through recreational 

activities; however, many toxins are potent tumor promoters 

and chronic exposure to low levels in drinking water also 

may pose health risks. Because of potential human-health 

risks, several States have recently added cyanobacteria, 

or the easily measured toxin microcystin, to routine beach 

monitoring programs, and cyanotoxins currently are on 

the U.S. Environmental Protection Agency drinking water 

contaminant candidate list. Despite known human health risks, 

few studies have assessed the distribution, co-occurrence, and 

concentration of cyanotoxins in the United States. Federal 

and State agencies, operators of drinking-water treatment 

facilities, and resource managers increasingly are faced 

with decisions about managing cyanobacterial blooms that 

affect local economies and public awareness, exposure, and 

health; therefore, representative scientific data are needed 

to guide management and public health decisions about 

cyanotoxins and taste-and-odor compounds. During 1999–

2007, several studies were conducted to assess occurrence 

of cyanobacterial toxins and taste-and-odor compounds in 

U.S. lakes, particularly in the Midwest. Total microcystin was 

detected in 78 percent of Midwestern lakes (n=359) during the 

summers of 1999–2006 and in 32 percent of lakes nationally 

(n=1,150) during the summer of 2007. Concentrations in 

these studies exceeded the World Health Organization (WHO) 

recreational guideline of 20 micrograms per liter (μg/L) in 1 

percent of lakes. Cyanobacterial blooms in Midwestern lakes 

(n=23) were sampled in August 2006 to assess occurrence 

of several classes of toxins, including microcystin, anatoxin, 

and cylindrospermopsin. Total microcystin was detected 

in all blooms, with 17 percent of concentrations exceeding 
 

 

 

 

 

 

 

 

11 

20 μg/L. The taste-and-odor compounds geosmin and 

2-methylisoborneol (MIB) also were measured. Geosmin 

was more common (83 percent of lakes) than MIB (35 

percent), but concentrations of both compounds when detected 

always equaled or exceeded the human detection limit of 10 

nanograms per liter (ng/L). These data indicate that toxin and 

taste-and-odor compounds are widespread in Midwestern 

lakes and probably nationally, sometimes at levels that cause 

health concerns.

Pathogens and Antibiotic-Resistant Bacteria in 

the Environment 

By Lisa R. Fogarty,1 Joseph W. Duris,1 and Sheridan K. Haack1 

1

U.S. Geological Survey, Michigan Water Science Center, 6520 Mercantile 

Way, Lansing, MI 48911.

Pathogens, antibiotic-resistant bacteria, and their 

impacts on human health have been studied in great detail 

from a clinical perspective. Increases in antibiotic-resistant 

bacteria and recent waterborne and foodborne outbreaks due 

to pathogenic bacteria have highlighted the need to better 

understand the effect the environment has on human health. 

The U.S. Geological Survey (USGS) Michigan Water Science 

Center (MI WSC) is currently conducting several studies to 

better understand the occurrence, distribution, sources, and 

maintenance of pathogens and antibiotic-resistant bacteria 

in the environment. Much of the information that exists on 

the occurrence of pathogens comes only from the clinical 

setting after the public has already become ill. Nevertheless, 

several waterborne outbreaks due to pathogens have occurred 

following exposure to contaminated waters. Shiga toxinproducing Escherichia coli (STEC) have been implicated in 

several waterborne and foodborne outbreaks in the United 

States. The occurrence of STEC in the environment is 

evaluated by using multiple lines of evidence that include 

DNA-based, immunological, and growth-based assays for 

STEC-related genes. Particular emphasis has been placed 

on occurrence of these markers with respect to land use, 

season, and potential fecal sources. Studies have focused 

on occurrence of the eaeA gene that encodes the intimin 

protein, the stx1 and stx2 genes that encode the STEC 

Shiga toxins 1 and 2, and the rfbO157 gene that encodes 

the O157 somatic antigen in E. coli. In addition, studies 

of enterococci have focused on detection of the humanpathogenic Enterococcus surface protein (esp) gene. Although 

the prevalence of antibiotic-resistant bacteria in hospitals 

has been well documented, the presence of these organisms 

in the environment has not. Antibiotic-resistant bacteria in 

the environment may pose a health threat if the organisms 

are pathogenic or can transfer antibiotic-resistance genes 

to pathogens. Researchers of the USGS MI WSC and the 

Toxic Substances Hydrology (Toxics) Program’s Emerging 

Contaminants in the Environment Project are studying the role 

Section V: Public Health and Water Quality 

the environment may play in the development, maintenance, 

and dissemination of antibiotic-resistant bacteria that pose a 

potential human health concern. Antibiotic resistance studies 

use growth assays and molecular methods. The growth assays 

determine the ability of the organisms to tolerate different 

environmentally relevant antibiotic concentrations. The 

molecular methods identify genes or other genetic elements 

responsible for antibiotic resistance, as well as changes in 

microbial communities after exposure to antibiotics.

Microbial Source Tracking, Using Quantitative 

Polymerase Chain Reaction (qPCR), for 

Enhanced Sanitary Water-Quality Management 

By Donald M. Stoeckel,1 Erin A. Stelzer,1 Linda K. Dick,2 and 

David P. Mau3 

1

U.S. Geological Survey, Ohio Water Science Center, 6480 Doubletree 

Avenue, Columbus, OH 43229–1111.

2

The Ohio State University, School of the Environment and Natural 

Resources, 320C Kottman Hall, 2021 Coffey Road, Columbus, OH 43210.

3

U.S. Geological Survey, Colorado Water Science Center, 201 E. 9th Street, 

Pueblo, CO 81003.

Microbial source tracking (MST) is the science—and 

art—of distinguishing the origins of intestinal microbes on 

the basis of host-specific characteristics. MST scientists 

identify these characteristics by use of host-associated 

phylogenetic groups (such as human-associated clades of 

fecal anaerobes in the order Bacteroidales), populations with 

host-related phenotypes (such as E. coli that are resistant 

to the antibiotics commonly used by humans), or markers 

relevant to host-microbe interactions (such as the humanassociated adhesin gene esp in Enterococcus faecium). Many 

MST tools have been proposed and tested, with the most 

recent family of techniques emerging about 1996. None of 

the various approaches to MST is universally applicable 

to water-quality management needs; each has benefits and 

liabilities in different applications. Applications of MST

include traceback analysis to establish epidemiological 

linkages between contamination sources and receiving waters, 

screening for prioritized sources of fecal contamination as a 

basis to select impaired waterways for remediation, and use 

as a management tool to estimate amounts of fecal-indicator 

bacteria (E. coli or enterococci) coming from different hosts. 

The need for the last application of MST tools was enhanced 

with implementation of Total Maximum Daily Load (TMDL) 

programs across the United States because a TMDL plan 

requires apportionment of the contaminant (fecal-indicator 

bacteria, in this case) according to source. Though many MST

tools are able to detect the presence of fecal contamination 

from animal hosts (such as humans, ruminants, dogs, pigs, and 

others), at this time there is no proven procedure to quantify 

E. coli from various hosts (such as 50 percent from humans, 

10 percent from cattle, and 40 percent from wildlife). Despite 
 

 

 

 

 

 

12 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

the lack of quantitative standard methods for MST, research 

methods that apply protocols based on quantitative polymerase 

chain reactions (qPCR) to detect host-associated markers in 

the environment eventually may allow apportionment of fecal 

contamination by host, at least in relative terms and perhaps 

quantitatively. In preliminary research on Fountain Creek, 

near Colorado Springs, Colo., increases in fecal contamination 

in areas where human contamination was suspected could be 

detected by concurrent increases in human-associated MST

markers. Other current research addresses the extent to which 

host-associated MST marker concentrations can be related to 

fecal-indicator bacteria densities from a host. Fecal indicatorto-MST marker ratios may change over time with various 

environmental stressors. Despite these limitations, however, 

quantitative detection of MST markers enhances water-quality 

management and may allow estimation of the proportion of 

fecal indicators from various hosts.

Transport of Microbes in the Subsurface/ 

Physical Interactions of Microbes and Particles 

By Ronald W. Harvey1 

1

U.S. Geological Survey, National Research Program, University of 

Colorado-Boulder, 3215 Marine Street, Suite E–127, Boulder, CO 80303.

Starting in the late 1800s, the use of microbial tracers 

has helped researchers to gain a better understanding of 

groundwater movement in different types of aquifers. 

However, the importance of studying the subsurface transport 

behavior of the microorganisms themselves is now more 

obvious, largely because of our increasing dependence upon 

limited and fragile groundwater resources. In particular, 

widespread contamination of drinking-water aquifers by 

microbial pathogens and chemical wastes has resulted in an 

increased interest in factors controlling subsurface microbial 

transport. The movement of pathogenic bacteria, viruses, and 

protozoa through aquifers is a major public health concern in 

the United States, where microbial contamination of watersupply wells contributes significantly to the total number of 

waterborne disease outbreaks. The intentional injections of 

nonindigenous bacterial populations into aquifer sediments 

are being carried out in order to enhance bioremediation 

of organically contaminated groundwater and to increase 

oil recovery from less transmissive zones by selective 

bacterial plugging of more permeable strata. The success of 

bioaugmentation depends as much upon the ability of the 

introduced microorganisms to reach the contaminants of 

interest as their ability to survive in situ. Transport properties 

of microorganisms introduced into aquifers can have major 

roles in the transmission of some waterborne diseases, in the 

success of microbially enhanced oil recovery processes, in 

the mobility of surface-active or hydrophobic groundwater 

contaminants, in pore clogging, and in the potential 

subsurface dissemination of genetically engineered bacteria 

for biorestoration. However, many of the factors controlling 

subsurface microbial transport are still poorly understood, 

including the reversible interactions between microorganisms 

and solid surfaces. To better study the controls of microbial 

transport, it has been necessary to improve available 

methodology for investigating microbial transport behavior in 

the laboratory and in the field. The multitude of biological and 

physicochemical factors affecting microbial transport through 

aquifer materials necessitates a refinement of methodologies, 

allowing observations under more controlled experimental 

conditions. Improvements in laboratory and field techniques 

for studying microbial transport behavior in aquifer materials 

and new models of porous media are leading to new findings.

Flow Cytometry in Microbiology 

By W. Bane Schill1 

1

U.S. Geological Survey, Leetown Science Center, 11649 Leetown Road, 

Kearneysville, WV 25430.

Bacteria are ubiquitous inhabitants of all sorts of 

environments including freshwaters and saltwaters, thermal 

vents, arctic snow, acidic mine drainage, petroleum deposits, 

soils, and sediments. Recent studies demonstrate that bacteria 

communicate with each other through chemical messaging 

and even communicate with the cells of plant and animal 

hosts to modulate physiology, development, and the immune 

system. Large shifts in microbial populations can be triggered 

by subtle environmental cues, but once begun, these shifts 

may themselves cause dramatic ecosystem changes. These 

changes may result because microbes are responsible for 

many geochemical processes including metal and sulfur 

oxidation and reduction, nitrification and denitrification, 

fermentation, and methane production. Over 2,300 scientific 

studies (PubMed search) have been published about using 

small subunit ribosomal RNA to elucidate shifts in microbial 

assemblages in response to particular environmental stressors. 

The great majority of those have utilized genetic sequencing 

of ribosomal RNA to identify the bacteria present and their 

distribution. While the advent of high throughput automatic 

sequencing has made these studies feasible, bacteria react 

quickly to environmental insults, and the application of the 

sequencing approach to repetitive samples rapidly becomes 

impractical. The computer programs Primrose and Rose 

(available at http://www.bioinformatics-toolkit.org/Primrose/

index.html) were used to scan bacterial nucleic acid sequences 

(16S ribosomal DNA) available in public databases and 

to search for regions that are highly specific to particular 

phylogenetic groupings. Additionally, several computer 

programs were written in the Icon Programming Language 

to further compare these sequences and to modify these 

sequences from strictly hybridization probes to probes suitable 

for use in an allele-specific primer extension (ASPE) format. 

The ASPE format was chosen for further development because 
 

 

 

 

 

 

 

Section VI: Geomicrobiology 13 

it offers high specificity and relative ease of use. Twentysix ASPE probes were designed to target a broad range of 

bacterial phylogenetic groups that are important in numerous 

and varied environmental settings, as well as in human and 

animal health. These include the alpha-, beta-, gamma-, delta-, 

and epsilon Proteobacteria; the Cytophaga-FlavobacteriumBacteroides Complex; the Cyanobacteria; the Mycobacteria; 

the Arthrobacteria; the Clostridia; the Streptomyces; the 

Staphylococci; Frankia; the Bacilli; and Saccharopolyspora. 

This suite of ASPE probes was further modified by 

incorporation of known target sequences (tag) into the 5′ end 

of the molecule to allow capture on fluorescently bar-coded 

latex beads that have the matching anti-tag covalently attached 

to their surface (www.luminexcorp.com). This dedicated flow 

cytometry system allows the simultaneous detection of up to 

100 targets in a sample, and 96 samples can be analyzed in 

a 96-well microplate format in about 40 minutes. Newer and 

alternative instrumentation systems are available.

Section VI: Geomicrobiology 

Geomicrobiology/Nanoscience of Toxic 

Elements Se and Te 

By Ronald S. Oremland1 

1

U.S. Geological Survey, Water Resources Discipline, 345 Middlefield 

Road, Mail Stop 480, Menlo Park, CA 94025–3561.

Certain anaerobic bacteria respire toxic selenium 

oxyanions and in doing so produce extracellular 

accumulations of elemental selenium [Se(0)]. We examined 

three physiologically and phylogenetically diverse species 

of selenate- and selenite-respiring bacteria, Sulfurospirillum 

barnesii, Bacillus selenitireducens, and Selenihalanaerobacter 

shriftii, for the occurrence of this phenomenon. When grown 

with selenium oxyanions as the electron acceptor, all of these 

organisms formed extracellular granules consisting of stable, 

uniform nanospheres (diameter, ~300 nanometers, or nm) of 

Se(0) having monoclinic crystalline structures. Intracellular 

packets of Se(0) were also noted. The number of intracellular 

Se(0) packets could be reduced by first growing cells with 

nitrate as the electron acceptor and then adding selenite 

ions to washed suspensions of the nitrate-grown cells. This 

procedure resulted in the formation of primarily extracellular 

Se nanospheres. After harvesting and cleansing of cellular 

debris, we observed large differences in the optical properties 

(ultraviolet (UV) to visible absorption and Raman spectra) of 

purified extracellular nanospheres produced in this manner by 

the three different bacterial species. The spectral properties 

in turn differed substantially from those of amorphous 

Se(0) formed by chemical oxidation of H2

Se and of black, 

vitreous Se(0) formed chemically by reduction of selenite 

with ascorbate. The microbial synthesis of Se(0) nanospheres 

results in unique, complex, compacted nanostructural 

arrangements of Se atoms. These arrangements probably 

reflect a diversity of enzymes involved in the dissimilatory 

reduction that are subtly different in different microbes. 

Remarkably, these conditions cannot be achieved by current 

methods of chemical synthesis.

Certain toxic elements support the metabolism of diverse 

prokaryotes by serving as respiratory electron acceptors for 

growth. Here, we demonstrate that two anaerobes previously 

shown to be capable of respiring oxyanions of selenium also 

achieve growth by reduction of either tellurate [Te(VI)] or 

tellurite [Te(IV)] to elemental tellurium [Te(0)]. This reduction 

achieves a sizable stable-Te-isotopic fractionation (isotopic 

enrichment factor [epsilon] = –0.4 to –1.0 per milliliter per 

atomic mass unit) and results in the formation of unique 

crystalline Te(0) nanoarchitectures as end products. The 

Te(0) crystals occur internally within but mainly externally 

from the cells, and each microorganism forms a distinctly 

different structure. Those formed by Bacillus selenitireducens 

initially are nanorods (~10-nm diameter by 200-nm length), 

which cluster together, forming larger (~1,000-nm) rosettes 

composed of numerous individual shards (~100-nm width by 

1,000-nm length). In contrast, Sulfurospirillum barnesii forms 

extremely small, irregularly shaped nanospheres (diameter 

<50 nm) that coalesce into larger composite aggregates. 

Energy-dispersive X-ray spectroscopy and selected area 

electron diffraction indicate that both biominerals are 

composed entirely of Te and are crystalline, while Raman 

spectroscopy confirms that they are in the elemental state. 

These Te biominerals have specific spectral signatures (UV

to visible light, Raman) that also provide clues to their 

internal structures. The use of microorganisms to generate Te 

nanomaterials may be an alternative for bench-scale syntheses. 

Additionally, they may also generate products with unique 

properties unattainable by conventional physical and chemical 

methods.

Soil Microbial Indices Across Different 

Geographic Scales 

By JoAnn M. Holloway1 

1

U.S. Geological Survey, Crustal Imaging and Characterization Team, 

Denver Federal Center, Box 25046, Mail Stop 964, Denver, CO 80225–0046.

Soil microbial communities participate in mineral 

weathering through the production of enzymes and organic 

acids that can accelerate dissolution rates. The intertwining of 

soil chemistry and microbial ecology was examined through 

the Geochemical Landscapes pilot study, which addressed 

variations in soil chemistry on both continental and regional 

scales. Mineral soils for the continental study were collected 

along N-S (Manitoba to Texas) and E-W transects (along 

the 38th parallel) for analysis of major and trace chemical 

concentrations and indices of microbial composition, including 
 

 

 

 

 

 

 

14 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

phospholipid fatty acids (PLFA; n=182) and enzyme assays 

(n=251). Continental-scale data revealed distinct patterns of 

microbial biomass and composition that were largely governed 

by climatic variations and related variations in organic 

carbon. PLFA biomass and arylsulfatase activity, which may 

be related to fungal biomass, were low in regions with low 

annual precipitation, including the Great Basin, Colorado 

Plateau, and southwestern Great Plains. A regional-scale 

study examined the influence of parent lithology on microbial 

community structure in soils from the California Coast Range 

and Sierra Nevada Foothills. Upland soils with a bedrock 

parent (serpentinite, mineralized serpentinite, marine siltstone, 

volcanic rock) were collected in the Cache Creek watershed 

in the Coast Range, with alluvial soils collected along a 

transect following the stream into the Sacramento Valley. 

Samples were also collected from the Sierra Nevada Foothills 

to address the influence of the geomorphic setting and climate 

on serpentine soils. Soils from these parent materials have 

distinct PLFA biomass and community structure that may 

be related to Ca/Mg ratios (serpentinite), and toxicity effects 

of Cr (serpentinite), and Hg (mineralized serpentinite). For 

instance, PLFA biomarkers (for example, 18:2ω6c, 18:1ω9c) 

for fungi represent a greater percentage of total PLFA in 

siltstone parent soils than serpentine soils from the Coast 

Range. Coast Range serpentine soils tend to have a greater 

PLFA biomass than siltstone parent soils, possibly due to 

reduced competition for nutrients from the sparser vegetation 

associated with serpentine soil. Organic carbon and total 

PLFA concentrations are greater in serpentine soils from the 

Sierra Nevada Foothills than in those from the Coast Range; 

however, the concentration of the PLFA biomarker for fungi 

is greater in the Coast Range serpentine soils. Mean annual 

precipitation is somewhat greater at the Coast Range sites (860 

millimeters, or mm) than at the Sierra Nevada Foothills sites 

(680 mm), which should enhance fungal growth. Alternatively, 

fungal growth in Sierra Nevada Foothills serpentine soils may 

be inhibited by relatively large concentrations of Cr, which 

appears to be in a more bioavailable form than in the Coast 

Range serpentine soils.

Using Natural Abundance δ13C and ∆14C Values 

of Phospholipid Fatty Acids to Characterize 

Bacterial Carbon Cycling Pathways in Deep 

Aquifers 

By Christopher T. Mills,1,2 Gregory F. Slater,3,4 Yuki Amano,5 

Robert F. Dias,6 Teruki Iwatsuki,5 Christopher M. Reddy,4 and 

Kevin W. Mandernack2,5 

1

U.S. Geological Survey, Crustal Imaging and Characterization Team, 

Denver Federal Center, Box 25046, Denver, CO 80225–0046.

2

Colorado School of Mines, Department of Chemistry & Geochemistry, 

1500 Illinois Street, Golden, CO 80401.

3

McMaster University, School of Geography and Geology, 1280 Main 

Street West, Hamilton, ON, L8S 4K1, Canada.

4

Woods Hole Oceanographic Institution, Department of Marine Chemistry 

& Geochemistry, Fye 107D, Mail Stop 04, Woods Hole, MA 02543.

5

Japan Nuclear Cycle (JNC), Tono Geoscience Center, Toki-shi, Gifu, 

Japan.

6

Old Dominion University, Department of Chemistry and Biochemistry, 

4541 Hampton Boulevard, Norfolk, VA 23529.

Microorganisms in the deep subsurface compose nearly 

half of the global biomass and drive the cycling of carbon 

and other elements. In these nutrient-poor environments, 

microbes may exploit energy and carbon sources using diverse 

metabolic strategies: consumption of dissolved and (or) 

particulate organic matter (OM) by heterotrophic bacteria, 

conversion of dissolved inorganic carbon (DIC) into biomass 

by autotrophic microbes, and oxidation of dissolved CH4

by methanotrophs. Measurements of the natural abundance 

of stable carbon (δ13C) and radiocarbon (Δ14C) content of 

subsurface carbon pools can provide insight into microbially 

mediated carbon transformations. Although challenging 

in low-biomass subsurface environments, carbon isotope 

measurements of microbial membrane phospholipid fatty 

acids (PLFAs) provide important additional information 

about carbon cycling pathways. Previous pure cultures 

studies have shown a general trend towards more negative 

δ13CPLFA values in the order of heterotrophs, autotrophs, and 

methanotrophs. This trend is due both to varied δ13C values 

of carbon sources and isotope fractionation effects associated 

with their assimilation. Because Δ14CPLFA values are inherently 

corrected for such fractionation effects, they should closely 

match those of their carbon source. We extracted PLFAs 

from microorganisms that were filtered from pristine, anoxic 

groundwaters hosted by both sedimentary and granite rocks 

in central Japan. The most abundant PLFA structures in both 

waters were 16:0, 16:1ω7cis, cy17:0, and 18:1ω7cis. A PLFA

biomarker for type II methanotrophs, 18:1ω8cis, composed 

3 and 18 percent of total PLFAs in the sedimentary and 

granite waters, respectively. The presence of this biomarker 

was unexpected, given the traditional definition of type II 
 

 

 

 

 

 

 

 

Section VI: Geomicrobiology 15 

methanotrophs as obligate aerobes. However, a bacterium 

that grows aerobically with CH4 as the sole energy source 

and produces 56 percent of its total PLFAs as 18:1ω8cis was 

isolated from both waters. The Δ14C values determined for 

type II methanotroph PLFAs in the sedimentary (–861 per mil 

(‰)) and granite (–867‰) waters were very similar to the 

Δ14C values of DIC in each water (~–850‰), suggesting that 

type II methanotrophs ultimately derive all of their carbon 

from DIC. In contrast, δ13C values of type II PLFAs in the 

sedimentary (–93‰) and granite (–60‰) waters indicate that 

these organisms use different carbon assimilation schemes in 

each environment. The δ13CPLFA values (–28‰ to –45‰) of 

non-methanotrophic bacteria in the sedimentary water indicate 

that >65 percent of total bacteria are heterotrophs, and dead 

Δ14C values (~–1,000‰) of some PLFAs suggest that many 

heterotrophs utilize ancient OM, perhaps from lignite seams 

within the sedimentary rocks. The more negative range of 

δ13CPLFA values determined for the granite water (–42‰ to 

–66‰) is likely the result of a microbial ecosystem dominated 

by chemolithoautotrophy and (or) CH4 cycling.

Geochemical Controls on Microbial Methylation 

of Mercury in the Florida Everglades 

By William H. Orem,1 David P. Krabbenhoft,2 Cynthia C. Gilmour,3 

and George R. Aiken4 

1

U.S. Geological Survey, 12201 Sunrise Valley Drive, Mail Stop 956, 

Reston, VA 20192–0002.

2

U.S. Geological Survey, Wisconsin Water Science Center, 8505 Research 

Way, Middleton, WI 53562–3581.

3

Smithsonian Environmental Research Station, P.O. Box 28, 647 Contees 

Wharf Road, Edgewater, MD 21037.

4

U.S. Geological Survey, University of Colorado-Boulder, 3215 Marine 

Street, Suite E–127, Boulder, CO 80303.

Mercury (Hg) is a global contaminant emitted from 

industrial sources that exhibits very high levels of deposition 

in south Florida. Mercury deposited on the vast wetland 

ecosystem of the Everglades can increase in toxicity through 

conversion of Hg2+ deposited in rainfall to methylmercury 

(MeHg). The conversion of inorganic mercury to MeHg 

is microbially mediated, primarily by sulfate-reducing 

bacteria. MeHg is a potent neurotoxin that is also highly 

bioaccumulative. It poses a potential health threat to 

wildlife and humans, primarily through fish consumption. 

The Everglades has some of the highest levels of MeHg in 

fish on record. Our studies over the past decade have been 

aimed at understanding the principal controls on microbial 

MeHg production in the freshwater Everglades. Perhaps 

the most surprising outcomes of our research have been 

the documentation of extensive sulfur contamination in the 

Everglades and the elucidation of the role of sulfur as a major 

control on microbial MeHg production. The extensive use 

of sulfur in agriculture to the north of the Everglades and the 

resulting transport of sulfur (as sulfate) to the Everglades 

through canals dissecting the ecosystem result in stimulation 

of microbial sulfate reduction and net increases in the amount 

of MeHg produced in areas that would otherwise be sulfate 

limited. The effect of excess sulfate load on MeHg production 

in the Everglades, however, is complex. Sulfate increases 

MeHg production through stimulation of microbial sulfate 

reduction, but buildup of sulfide in soil porewater inhibits 

MeHg production. The balance between these two effects of 

sulfur influences both the magnitude and location of MeHg 

production in the Everglades. The complex relationship 

between sulfur geochemistry and MeHg production in the 

Everglades was first deduced from field studies at various 

sites in the ecosystem. This hypothesis has been confirmed 

by experimental studies using mesocosms. These mesocosm 

studies show that increasing sulfate concentrations up to 

about 15 milligrams per liter (mg/L) increases microbial 

MeHg production. At sulfate concentrations greater than 15 

mg/L, buildup of sulfide from microbial sulfate reduction 

inhibits MeHg production, probably by inhibiting microbial 

uptake of Hg2+ through changes in the speciation of mercury 

in soil porewater. Dry/rewet cycles also affect MeHg 

production in the Everglades. These cycles were shown to 

temporarily increase surface water sulfate concentrations 

(due to oxidation of reduced sulfur in soil), stimulating 

microbial sulfate reduction and MeHg production. A unique 

combination of conditions in the Everglades, including high 

mercury deposition, sulfate contamination, and favorable 

environmental conditions (extensive wetland area, wet/dry 

cycles, high dissolved organic carbon), results in high levels of 

MeHg in Everglades biota.

An Overview of Bacterial Controls and 

Influences on Sulfide Mineral Weathering 

By Mark Stanton1 

1

U.S. Geological Survey, Crustal Imaging and Characterization Team, 

Denver Federal Center, Box 25046, Mail Stop 964, Denver, CO 80225–0046.

The weathering of sulfide minerals by bacteria is 

a critical geochemical process in the generation of acid 

rock drainage and acid mine drainage (ARD/AMD). The 

dominant bacteria mediating this process are in the genus 

Acidithiobacillus (formerly Thiobacillus). These microbes, 

commonly referred to as thiobacilli, oxidize ferrous iron (Fe2+) 

and sulfide sulfur (S2-) in sulfide minerals. Thiobacilli prefer 

low-pH environments (<5.0), and some are able to grow at pH 

values near 1.0. Generation of ARD or AMD is perhaps the 

most deleterious consequence of sulfide mineral weathering. 

The acidic pH values and high dissolved metal concentrations 
 

 

 

 

 

 

 

 

 

 

 

16 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

can negatively affect water quality and impair the survival 

of aquatic and terrestrial organisms. The role of bacteria in 

enhancing pyrite (FeS2

) dissolution via iron oxidation has been 

well studied. During abiologic pyrite decomposition at acid 

pH (<5), aqueous ferric iron oxidizes pyrite (ferrous) iron:

.

The rate-limiting reaction is formation of aqueous ferric iron. 

Iron-oxidizing thiobacilli can accelerate the oxidation of 

solution ferrous iron from 1,500 to 78,000 times faster than 

the abiologic rate; rate increases up to a millionfold have 

been noted. Higher numbers of bacteria sorbed to the mineral 

surface generally correlate with increases in dissolution 

rates of pyrite and marcasite. The dissolution of other 

sulfides mediated by bacteria is mostly unknown and poorly 

understood. More work is needed to determine the specific 

role of bacteria in the dissolution of monosulfides such as 

sphalerite (ZnS) and mixed-metal sulfides such as arsenopyrite 

(FeAsS), which can be major sources of metals in AMD 

settings. A current U.S. Geological Survey (USGS) laboratory 

study comparing the abiotic and bacterial dissolution of ZnS 

indicates little difference in rates in short-term experiments. 

Previous USGS field and laboratory studies from several 

ARD/AMD sites were done to quantify the numbers of 

thiobacilli and their effect on iron oxidation. In one such study 

in acidic iron fens in the San Juan Mountains of southwestern 

Colorado, the presence of Leptothrix, a filamentous bacterium 

associated with iron oxidation, indicated active iron oxidation. 

Yet numbers of thiobacilli were generally low (102 to 103

cells/milliliter, or cells/mL) compared to numbers in similar 

environments. This bacterial weathering process is currently 

being used for the extraction of metals from sulfide ores using 

heap leach methods. Significant progress has been made in 

studying this important biogeochemical process.

Defining “Reactive” Inorganic Mercury and 

Its Relationship to Microbial Methylmercury 

Formation in Aquatic Ecosystem Studies 

By Mark Marvin-DiPasquale,1 Jennifer Agee,1 

Lisamarie Windham-Myers,1 Pilar Heredia-Middleton,1 

Evangelos Kakouros,1 Marisa Cox,1 and Carolyn Coates1 

1

U.S. Geological Survey, 345 Middlefield Road, Mail Stop 480, Menlo 

Park, CA 94025–3561.

Mercury (Hg) contamination of aquatic ecosystems 

has long been recognized as a persistent environmental 

problem that threatens both wildlife and human health. The 

conversion of inorganic divalent mercury (Hg(II)) to the more 

toxic methylmercury (MeHg) is a process largely facilitated 

by sulfate-reducing bacteria in anoxic sediments. Recent 

advances in the study of Hg biogeochemistry have begun to 

unravel the most relevant environmental factors that ultimately 

control the formation of MeHg, both in terms of those that 

mediate the activity of the Hg(II)-methylating bacteria and 

those that mediate the availability of Hg(II) to those bacteria. 

The current evidence suggests that only a small fraction of 

the total Hg(II) may be available for Hg(II)-methylation; this 

fraction is termed the “reactive” inorganic mercury (Hg(II)R) 

fraction. An operationally defined measure of Hg(II)R has 

been developed and is being used across a wide range of 

mercury ecosystem studies currently being conducted by the 

U.S. Geological Survey (USGS). Results from an international 

study comparing multiple methods used to quantify specific 

mercury fractions indicate that the Hg(II)R method provides 

a good proxy for the pool of Hg(II) truly available for Hg(II)-

methylation. Deep core profiles from San Francisco Bay 

demonstrate that Hg(II)R concentrations are highest in surface 

sediment and decrease with depth. Additional geochemical 

evidence from multiple ongoing studies suggests that the size 

of this pool is controlled by sediment redox conditions and the 

association of Hg(II) with solid-phase reduced-sulfur minerals. 

Laboratory oxic/anoxic slurry experiments simulating 

sediment perturbations (such as dredging or slough scouring) 

demonstrate that the oxidation of deeply buried sediment can 

increase the Hg(II)R pool size up to sixtyfold. This result is 

presumably related to the reoxidation of the reduced-sulfur 

minerals to which nonreactive Hg(II) is strongly bound, 

and the subsequent liberation of Hg(II) (as Hg(II)R). These 

findings have significant implications for dredging operations 

and for the reconstruction of wetland habitat with dredge 

material. A major conclusion of this body of research is 

that defining the Hg(II)R pool, and the factors that control 

it both spatially and temporally, is a critical component of 

environmental studies that aim to understand microbial MeHg 

production dynamics within and across ecosystems.

Section VII: Ecosystem Function 

Natural and Enhanced Bioremediation of Nitrate 

Contamination in Groundwater 

By Richard L. Smith1 

1

U.S. Geological Survey, University of Colorado-Boulder, 3215 Marine 

Street, Suite E–127, Boulder, CO 80303.

Nitrate is a prevalent contaminant in groundwater 

systems, originating from a variety of agricultural, industrial, 

and wastewater-disposal practices. Denitrification is a key 

process that can affect the fate and transport of nitrate in the 

subsurface and the ultimate delivery of nitrogen to surface 

waters. A long-term study of the factors that affect the in situ 

function of subsurface denitrification has been conducted in 

a sand-and-gravel aquifer on Cape Cod, Mass. The aquifer 

has been contaminated by the discharge of dilute, treated 

wastewater, which has resulted in a large contaminant plume 
 

 

 

 

 

 

 

17 

that is characterized by geochemical gradients of fixed carbon 

and nitrogen that provide a suitable redox environment 

for denitrification to occur naturally. This study features 

natural gradient tracer tests (primarily with 15N) as in situ 

activity assays to quantify rates of denitrification within the 

geochemical and hydrologic context of the aquifer. These tests 

can quantify individual steps of the denitrification pathway and 

the overall effect the process has on nitrogen oxide speciation 

and nitrogen loads. In zones in which the process was most 

active, low-level concentrations of nitrite, nitrous oxide, and 

nitric oxide could all be detected, and it was demonstrated that 

turnover of these intermediate pools was a sensitive shortterm approach for quantifying nitrogen and electron flow via 

denitrification. Combined tracer test and laboratory studies 

with aquifer core material suggested that both inorganic 

(hydrogen, Fe(II), and possibly methane) and organic (acetate 

and bulk dissolved organic carbon (DOC)) electron donors 

were fueling denitrification, but that nitrate reduction to 

ammonium or nitrate/nitrite reduction coupled to ammonium 

oxidation (anammox) were apparently insignificant nitrateconsuming processes. Another aspect of the study was 

to determine approaches that could be used to enhance 

denitrification as a nitrate remediation tool, particularly for 

situations where the process was electron donor limited. 

Autotrophic, hydrogen-coupled denitrification was particularly 

effective at nitrate removal, but it was restricted to a pumpand-treat approach due to limited hydrogen solubility in 

water. In situ enhancements with formate or Fe(II) were also 

tested. Both stimulated denitrification. Formate stimulation 

was relatively slow and produced stoichiometric, persistent 

concentrations of nitrite. Adding nitrate to an Fe(II) zone 

very quickly stimulated denitrification, with only transient 

accumulation of nitrous oxide (no nitrite). Delivery of Fe(II) to 

the subsurface could be difficult in many cases, but production 

of insoluble Fe(III) oxides could have additional benefits by 

removing other concurrent contaminants, such as phosphate, 

arsenic, or sorbable organic compounds.

Microbial Communities and Carbon Cycling in 

Response to Global Change 

By Mark P. Waldrop1 

1

U.S. Geological Survey, 345 Middlefield Road, Mail Stop 962, Menlo 

Park, CA 94025–3561.

Global change phenomena such as climate warming, 

permafrost thaw, wildfires, and drought are affecting terrestrial 

ecosystem biogeochemistry, particularly in northern latitudes, 

but also in the continental United States. Soil microbial 

communities are critical to the carbon biogeochemistry of 

ecosystems, for they decompose as much carbon as is annually 

photosynthesized by plants. There is strong evidence that 

variation in the composition of the below-ground microbial 

community affects the way in which ecosystems function 

Section VII: Ecosystem Function 

and can affect regional to global biogeochemistry. Particular 

functional groups of microorganisms, such as decomposer 

fungi, have a disproportionate effect on elemental cycles. 

For example, in northern latitude soils, climate warming is 

accelerating permafrost thaw and wildfire intensity, altering 

the abundance of soil decomposers and, thus, directly 

affecting rates of biogeochemical processes. This and other 

types of microbial community information can be used 

by the next generation of mechanistic microbial-based C 

cycling models. A next step will be to merge bioinformatics 

with geoinformatics that can be used to build a spatially 

explicit map of microbial biogeography that is linked to 

environmental and process data. Such a map has many uses 

beyond understanding ecological principles that structure 

community composition and diversity. Such spatially 

explicit information can potentially be used for assessing 

how global change will affect microbial communities and 

the biogeochemical processes (such as C, N, and S cycling) 

within specific regions. Researchers from the U.S. Geological 

Survey (USGS), U.S. Department of Agriculture Forest 

Service (USFS), U.S. Department of Energy (DOE), and the 

National Science Foundation (NSF) are currently conducting 

several continental-scale inventories, and these inventories can 

be linked to a multi-institution effort to study vulnerabilities 

within the carbon cycle. Microbial communities are central to 

biogeochemical processes, and linking microbial information 

with biogeochemical models and biogeographical data is a 

new frontier for microbiological research within the USGS.

Biogeochemistry of Mountain Watersheds: 

Through the Microbial Window 

By Jill S. Baron,1 Donald H. Campbell,2 and David W. Clow2 

1

U.S. Geological Survey, Fort Collins Science Center and Natural Resource 

Ecology Laboratory, Colorado State University, Fort Collins, CO 80523–1499.

2

U.S. Geological Survey, Colorado Water Science Center, Denver Federal 

Center, Box 25046, Mail Stop 415, Denver, CO 80225–0046.

Nitrogen cycling has been a focus of research for many 

years in Loch Vale Watershed, a long-term ecological research 

and monitoring site in Rocky Mountain National Park. 

Research began in Loch Vale in 1982 and is a joint effort of 

the Biological Resources Discipline and the Water Resources 

Discipline Water, Energy, and Biogeochemical Budgets 

(WEBB) program. Even in this high-elevation catchment, 

which is 82 percent exposed rock or ice, most nitrogen 

measured in surface waters bears an isotopic signature 

indicative of microbial processing. Even the interstitial 

sediments between rocks above the tree line are microbially 

active. Our studies of the microbial role in nitrogen cycling 

have included monitoring, in situ fertilization and laboratory 

experiments of both soils and lake waters, regional surveys, 

ecosystem modeling, and most recently, studies of the origin 

of mass-specific acid, alkane, and chlorin fractions from the 
 

 

 

 

 

 

 

 

18 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

recent past preserved in lake sediments. Our work has helped 

develop insight into the influences of atmospheric nitrogen 

deposition, and more recently, into the effects of changing 

climate on high-elevation terrestrial and aquatic ecosystems.

Quantifying Microbial Denitrification Rates 

Using Expressed Functional Gene Abundance 

By Matthew P. Bachmann1 

1

U.S. Geological Survey, Washington Water Science Center, 934 Broadway, 

Suite 300, Tacoma, WA 98402.

Hydrogeologists interested in certain types of 

contaminant remediation problems have benefited from 

several recent advances in molecular techniques for assessing 

gene expression in subsurface microbial communities. 

One such technique, reverse transcriptase quantitative 

polymerase chain reaction (RT-qPCR), has made possible the 

quantification of functional gene transcripts as a proxy for the 

rate of processes facilitated by microbial enzymes. RNA and 

DNA were extracted from the model organism Paracoccus 

denitrificans grown in batch culture under denitrifying 

conditions; the RNA and DNA were analyzed for gene and 

transcript abundance to determine how the expression of 

functional denitrifying genes varies with measured bulk 

denitrification rates. Measured denitrification rates ranged 

from 1.6 to 57 milligrams per liter per hour (mg/L/hour), and 

relative transcript abundances ranged from 15 to 276 copies 

per milliliter (copies/mL) when normalized to the expression 

of the constitutive RNA polymerase encoding gene rpoB. 

The relationship between nirS transcript abundance and 

denitrification rate is linear (R2

=0.97) at rates above 5 mg/L/

hour, suggesting that RT-qPCR may be an effective tool 

for assessing the rate of denitrification by some common 

denitrifying organisms in nutrient-rich environments. In 

environments where more traditional methods are limited by 

low diffusion rates or poor tracer recovery, this new technique 

can determine a rate from soil or pore-water samples as 

small as 1 milliliter. The determination of an instantaneous 

transformation rate in a single sample makes this method 

well suited to measuring rapidly changing rates and facilitates 

incorporation of microbiological data into groundwater models 

of reactive contaminant transport. Future potential applications 

of this new approach include improved models of subsurface 

nutrient cycling and the fate and transport of a variety of 

common groundwater contaminants with known microbially 

mediated pathways, including arsenic, copper, mercury, and 

several volatile organic compounds.

Evaluating Ecosystem Function with Integrated 

Approaches in Environmental Microbiology 

By Mary A. Voytek,1 Julie D. Kirshtein,1 Michael B. Lowit,1 and 

Bess B. Ward2 

1

U.S. Geological Survey, National Research Program, 12201 Sunrise Valley 

Drive, Mail Stop 430, Reston, VA 20192–0002.

2

Princeton University, Department of Geosciences, 217 Guyot Hall, 

Princeton, NJ 08544–1003.

Microorganisms are involved in the biogeochemical 

cycling of nutrients in the environment. Biotransformations 

of nitrogen for example impact the availability and fate of 

nitrogen in the environment. Microorganisms involved in 

these biotransformations occur with functional redundancy; 

that is, there may be different types of organisms performing 

the same function in a given environment, using either variants 

of the same enzyme or slightly different enzymes to catalyze 

the transformations. The relationship between environmental 

factors and functional gene diversity of ammonia-oxidizing 

bacteria (AOB) was investigated across a transect from the 

freshwater portions of the Chesapeake Bay and Choptank 

River out into the Sargasso Sea. The temporal and spatial 

variation in ammonia oxidizer (bacterial and archaeal) 

diversity of the functional gene, amoA, was assessed by 

clone libraries and (or) functional gene microarray analyses, 

and their total abundance was assessed by quantitative 

polymerase chain reaction (qPCR) analysis. Library constructs 

and hybridization patterns along the transect showed clear 

variations in amoA community composition. Cluster analysis 

of communities along the transect detected three groupings. 

Members of Cluster 1 were most closely related to upper bay 

(freshwater) sediment probes, and Cluster 3 was dominated 

by the marine Nitrosospira-like probe signal. Discriminant 

analysis of the amoA groupings indicated that Clusters 1 and 

2 were positively correlated with temperature and nitrate 

concentration, while Cluster 3 was negatively correlated with 

concentrations of chlorophyll a, dissolved organic carbon, 

and particulate nitrogen and carbon, suggesting that different 

amoA sequences represent organisms that occupy different 

ecological niches within the estuarine/marine environment. 

The lowest diversity in the bacterial AOB was observed in 

samples from the Sargasso Sea and in samples collected 

at most stations during the winter. AO-Archaea were most 

abundant in the Sargasso Sea and in the freshwater sites 

particularly during periods of high flow. Studies such as this 

have begun to elucidate the fundamental ecological question 

of the relationships between the functional complexity and 

genetic diversity of microbial communities, ecosystem 

function, and environmental variables, which until now have 

been virtually unknown.
 

 

 

 

 

 

 

 

 

 

 

 

 

Wildlife Disease 19 

Poster Session Abstracts 

Wildlife Disease 

Temporal Dynamics of Mixed Avian Influenza 

Infections in Waterfowl 

By Jeffrey S. Hall,1 Hon S. Ip,1 J. Christian Franson,1 

Josh TeSlaa,1 Sean Nashold,1 and Christopher Brand1 

1

U.S. Geological Survey, National Wildlife Health Center, 6006 Schroeder 

Road, Madison, WI 53711–6223.

From the National Surveillance Program, up to 20 

percent of wild waterfowl sampled that were positive for 

avian influenza (AI) were infected by more than one isolate. 

Mixed infections are important in the ecology of AI because 

they create the opportunity for reassortment and generation 

of potentially new, more virulent genetic combinations of the 

virus. In this study, we will infect mallards with two isolates 

of low pathogenic AI, sequentially and simultaneously, and 

measure the proportions of each isolate in the infected birds. 

Isolates generated from birds with mixed infections will be 

sequenced and examined for evidence of reassortment. Thus, 

we will be able to determine the reassortment rate in dually 

infected birds.

Experimental Infection of a North American 

Raptor with Highly Pathogenic Avian Influenza 

H5N1 

By Jeffrey S. Hall,1 Hon S. Ip,1 J. Christian Franson,1 

Carol Meteyer,1 Sean Nashold,1 Josh TeSlaa,1 John French,2 

Patrick Redig,3 and Christopher Brand1 

1

U.S. Geological Survey, National Wildlife Health Center, 6006 Schroeder 

Road, Madison, WI 53711–6223.

2

U.S. Geological Survey, 10300 Baltimore Avenue, Beltsville, MD 20705.

3

University of Minnesota, Veterinary Clinical Sciences, 100C Gabbert 

Raptor Center, 1920 Fitch Avenue, St. Paul, MN 55108.

Highly pathogenic avian influenza (HPAI) is primarily a 

disease of poultry and waterfowl. However, several species of 

wild raptors have been found in Eurasia after mortality events 

with HPAI H5N1. Should HPAI H5N1 reach North America 

in migratory birds, several species of raptors are at risk, not 

only from environmental exposure, but also from eating dead 

or infected birds. In this study, we used American kestrels as 

a surrogate species of North American raptor to examine the 

effects of HPAI H5N1 infection in terms of dose response, 

viral shedding, pathology, and survival in this species and 

other more endangered/threatened species. These experimental 

data showed that kestrels are highly susceptible to HPAI 

regardless of dose. All birds succumbed to infection within 

an average of 4–5 days and shed significant amounts of virus 

both orally and cloacally. Examination of tissues revealed 

that the virus was spread throughout the body, but the highest 

levels were found in the brain. This finding corresponded 

to the expression of symptoms, which were predominantly 

neurological. This is the first experimental study of HPAI in 

a North American raptor species and highlights the potential 

risks to other falcon, eagle, and condor species if HPAI comes 

to North America.

Forecasting the Space/Time Spread of West 

Nile Virus 

By Lee De Cola1 

1

U.S. Geological Survey, Eastern Geographic Science Center, 12201 

Sunrise Valley Drive, Mail Stop 521, Reston, VA 20192–0002.

Forecasting depends on autocorrelation; events Z(X, 

T) at a point X and an instant T tend to occur in runs and 

clusters—and diseases can occur in similar organisms. I use 

the 2003 West Nile virus outbreak among humans and birds 

to illustrate these ideas. The map shows that the epidemic was 

concentrated in the New York and upper Rocky Mountain 

region of the United States, but data were reported at the 

county level for three broad taxonomic classes and most of the 

human reports came from counties also reporting bird cases. 

A time series analysis shows that the three kinds of reports all 

occurred around the same time of year, with avian preceding 

human preceding veterinary cases. And when the counties 

are binned by week of first reporting, we see that most of the 

counties reported avian cases several weeks before human 

cases. We can use this conjunction to estimate relative risk: 

the extent to which knowledge of an avian report increases the 

probability of later human reports. This technique is illustrated 

for week 29, showing that later occurrences of human reports 

are more likely in counties reporting avian cases, and the 

forecasts predict about one-quarter of the variance. Finally, 

those counties reporting human cases during the year form 

an induced subgraph of the 3,141 U.S. counties, suggesting 

that spatial autocorrelation is likely to improve forecasting by 

using activities in neighboring regions to predict reports.
 

 

 

 

 

 

 

 

20 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Viral Fitness Assays Used in vivo To Investigate 

Virulence Tradeoffs in an Acute Rhabdovirus of 

Rainbow Trout 

By Gael Kurath,1 Andrew R. Wargo,1 Kyle A. Garver,1,2 and 

Ryan Troyer1,2 

1

U.S. Geological Survey, Western Fisheries Research Center, 6505 NE 65th 

Street, Seattle, WA 98115.

2

University of Washington, Department of Pathobiology, Box 357470, 

Seattle, WA 98195.

We have developed a system to assess viral fitness in 

live juvenile rainbow trout (O. mykiss) using field isolates of 

the rhabdoviral pathogen infectious hematopoietic necrosis 

virus (IHNV). In these assays, juvenile trout are infected with 

selected strains of IHNV that can be distinguished genetically. 

Groups of approximately 25 trout are infected by immersion 

with each strain alone, or with a 1:1 mixture of the two strains. 

Progeny virus populations are characterized after 3 days of 

in-host replication. During development of the assay, we 

showed that IHNV strains of equal virulence that co-circulate 

stably in an aquaculture setting have equal fitness in these 

assays. More recently, we have worked with two strains that 

reproducibly differ in virulence. In assays initiated with a 1:1 

ratio of high-virulence (HV) and intermediate-virulence (IV) 

strains, the progeny virus populations after 3 days of in-host 

replication had a mean HV:IV ratio of 3:1. Thus, these strains 

differ in fitness, with the higher virulence strain being more 

fit. The correlation of higher virulence with higher fitness 

indicates a virulence tradeoff that may explain the persistence 

of high-virulence IHNV in the field. We are using modified 

assays to investigate the contribution of different stages of the 

virus infection cycle to the difference in viral fitness observed 

between HV and IV. Comparative assays using injection of 

virus rather than immersion indicated that ability to enter 

the host was partly responsible for the higher fitness of HV, 

but HV also had higher in-host replication than IV. Analysis 

of virus populations shed into the water indicates that both 

viral strains are shed at equal rates. In all our results, data 

from individual fish provide a high-resolution picture of the 

variability inherent in natural viral infection processes.

Diversity and Pathogenicity of Avipoxvirus from 

Hawaiian Forest Birds 

By Alexis Giannoulis,1 Susan I. Jarvi,1 Carter T. Atkinson,2 

Dennis Triglia,3 Kiara Bianchi,1 Margaret Farias,1 and 

Leayne Patch-Highfill1 

1

University of Hawaii-Hilo, Department of Biology, 200 W. Kawili Street, 

Hilo, HI 96720.

2

U.S. Geological Survey, Pacific Island Ecosystems Research Center, 

Kilauea Field Station, P.O. Box 44, Hawaii National Park, HI 96718.

3

University of Hawaii-Manoa, Department of Botany, Pacific Cooperative 

Studies Unit, Honolulu, HI 96822.

Reports by early naturalists suggest that pox viruses 

(Avipoxvirus spp.) have been affecting native Hawaiian forest 

birds for over 100 years. Clinical signs of the cutaneous form 

of pox in Hawaii include nodular lesions on unfeathered 

areas of the body, especially the feet. Avipoxvirus species 

are exceptional in that they possess genes that can modify 

innate host immunity, and therefore may play a significant 

role, with malaria, in the decline of native forest birds. To 

evaluate diversity and pathogenicity of Avipoxvirus, isolates 

from lesions collected from seven species of birds from four 

Hawaiian islands were cultured in Muscovy duck embryonic 

fibroblasts. We sequenced a fragment of the 4b core protein 

gene. To evaluate within-individual variation, multiple clones 

were sequenced from several individuals. Samples included 

isolates collected from 1993 to 2004. Ancient DNA techniques 

were used to obtain and confirm 4b sequence from a museum 

specimen of an infected `Elepaio (Chasiempis sandwichensis) 

collected in 1900 on Hawaii Island. Phylogenetic analyses 

indicate that at least two variants of pox exist in Hawaii 

that are approximately 6 percent divergent from each other. 

Within-individual variation appears minimal, suggesting 

that individuals are infected by a single pox variant. The 

pox variants we recovered in chickens appear to be fowlpox 

variants and are distinct from the canarypox-like variants 

detected in Hawaiian passerines. Reciprocal experimental 

infections suggest that one variant appears more virulent, 

and that neither long-term immunity nor reciprocal immunity 

was induced. We conclude that the two variants are either 

antigenically distinct or may induce only short-term immunity.
 

 

 

 

 

 

 

 

 

 

Water Quality 21 

Disease Detection Methods 

Detection of Batrachochytrium dendrobatidis 

(Chytrid Fungus) in Water and Amphibian Swabs 

Using PCR: Towards a Life History Assessment 

By Chauncey Anderson,1 Julie Kirshtein,2 Mary Voytek,2 

Christopher Pearl,3 and D. Earl Green4 

1

U.S. Geological Survey, Oregon Water Science Center, 2130 SW 5th 

Avenue, Portland, OR 97201.

2

U.S. Geological Survey, National Research Program, 12201 Sunrise Valley 

Drive, Mail Stop 430, Reston, VA 20192–0002.

3

U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, 

3200 S.W. Jefferson Way, Corvallis, OR 97331.

4

U.S. Geological Survey, National Wildlife Health Center, 6006 Schroeder 

Road, Madison, WI 53711–6223.

The fungal pathogen Batrachochytrium dendrobatidis 

(Bd) causes chytridiomycosis, a disease implicated in 

amphibian declines on five continents. A Bd-specific 

polymerase chain reaction (PCR) assay used to test swabs of 

amphibians for Bd has demonstrated that Bd is widespread in 

the United States and globally. Using the existing laboratory 

assays and primers, we developed a method to test for Bd 

in water by filtration, followed by extraction of DNA from 

particulates retained on the filter. Initial tests confirmed that 

Bd exists in the environment outside its amphibian hosts; 

however, insufficient data were available to indicate the 

range or temporal variability of Bd zoospore densities in 

ponds. Recently, we modified the field method to facilitate 

sample collection and preservation from remote sites, and 

we conducted monthly to bimonthly sampling from ponds 

in Oregon where amphibian populations (primarily Rana 

catesbeiana) have histologically confirmed infections with Bd. 

Seasonal patterns in zoospore densities in water and on frogs 

are shown in relation to water temperature and amphibian 

life cycle. Future testing will help elucidate the most likely 

exposure mechanisms for amphibians by defining the location 

and partitioning of Bd in ponds. Together with swabbing 

of amphibians, these PCR methods are expanding our 

knowledge of the lifecycle of Bd in the environment and its 

interaction with amphibians, and this expansion will foster the 

development of better management strategies for mitigating 

this global threat to amphibians.

Water Quality 

Microbial Quality of Water in Selected Principal 

Aquifers of the United States 

By Sandra S. Embrey1 and Donna L. Runkle2 

1

U.S. Geological Survey, Washington Water Science Center, 934 Broadway, 

Suite 300, Tacoma, WA 98402.

2

U.S. Geological Survey, Ohio Water Science Center, 6480 Doubletree 

Avenue, Columbus, OH 43229–1111.

As part of the National Water-Quality Assessment 

(NAWQA) program, microbiological data were collected 

from more than 1,200 wells in 22 NAWQA study units during 

1993 through 2004. These wells were used for monitoring 

purposes, sources of water for domestic and public supplies, 

and irrigation. The wells constituted 3 major NAWQA

sampling networks representing 16 principal aquifers. Samples 

of untreated groundwater were tested for concentrations of 

fecal-indicator bacteria and the presence of coliphage viruses. 

Summaries of these data showed that nationwide, coliform 

bacteria occur relatively frequently, as nearly 30 percent of 

all wells tested positive. Coliphage viruses, however, were 

rare, as fewer than 4 percent of untreated water samples from 

domestic and public supply wells tested positive. Coliform 

bacteria generally were more prevalent in samples from 

domestic wells than from public supply wells, in fractured or 

porous rock materials than in unconsolidated materials, and 

in principal aquifers with median well depths ranging from 

100 to 200 feet than in aquifers with median depths less than 

100 feet or greater than 200 feet. Of the 16 principal aquifers 

studied, waters most affected by the presence of coliform 

bacteria were those in the Valley and Ridge, Floridan, and 

Piedmont and Blue Ridge aquifers, where more than 50 

percent of sampled wells tested positive. Waters least affected 

were those in the Columbia Plateau, High Plains, Stream 

and River Valley, Coastal Lowlands, Southeastern Coastal 

Plain, Basin and Range, and Snake River aquifers, where 

less than 20 percent of wells tested positive. The Valley and 

Ridge wells had the highest concentrations of total coliform 

bacteria with a median of 2 colony-forming units per 100 

milliliters (CFU/100 mL) and a maximum of 1,600 CFU/100 

mL. High concentrations of Escherichia coli (greater than 300 

CFU/100 mL) were reported for wells completed in the Valley 

and Ridge aquifer in the eastern United States, as well as 

the Mississippian-Pennsylvanian aquifer and the Ordovician 

aquifer in Tennessee. More than 50 percent of wells completed 

in carbonate or crystalline rock types, such as in the Valley 

and Ridge and Floridan aquifers, tested positive for coliform 

bacteria. Conversely, less than 5 percent of wells completed 

in unconsolidated materials, such as those in the Snake River 

aquifer, or in basalt with sand and gravel interbeds, such 

as compose the Basin and Range aquifer, tested positive. 

Although lithologic composition might be one factor in 
 

 

 

 

 

 

 

 

 

 

22 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

the occurrence of fecal-indicator bacteria in the aquifers, 

others, such as geohydrologic characteristics, proximity of 

contaminating sources, interactions with surface water, or 

well-construction features (including age of the well), likely 

control the presence and transport of these bacteria in the 

groundwater.

Quality Control of Quantitative Polymerase 

Chain Reaction (qPCR) for Environmental Water 

Samples 

By Erin A. Stelzer,1 Donald M. Stoeckel,1 and 

Rebecca N. Bushon1 

1

U.S. Geological Survey, Ohio Water Science Center, 6480 Doubletree 

Avenue, Columbus, OH 43229–1111.

Quantitative polymerase chain reaction (qPCR) requires 

routine quality control (QC): mainly, sample replication, a 

serially diluted standard curve, and a no-template control. 

Environmental water samples, however, require additional 

QC because of their more complex matrix. They may contain 

nontarget microorganisms whose DNA/RNA could overload 

the extraction process. Environmental samples also may 

contain PCR-inhibiting compounds that are coextracted with 

the target DNA/RNA. These PCR inhibitors may eventually 

lead to false-negative results or skewed quantitation. 

Therefore, it is important to incorporate controls into various 

steps of the process to guard against sample loss and skewed 

data. Internal controls (IC) are additional QC used to measure 

both DNA/RNA extraction efficiency and qPCR efficiency. 

When extracting a surface-water sample for a microbial 

source tracking (MST) assay, for example, there could be 

so much interference that only a small portion of the DNA

is recovered. This interference-related loss can be estimated 

by coextracting an organism that is similar to the target but 

not found naturally in environmental samples. When running 

an assay for the direct detection of pathogens, larger sample 

volumes are typically used in order to enhance detection 

limits, but the larger the sample volume, the more PCR 

inhibitors are included in the sample. Matrix inhibition can 

be estimated by adding a known amount of the target into a 

separate PCR master mix, which can be run in parallel with 

nonspiked environmental samples. Full detection of the matrix 

spike indicates that the qPCR was not retarded by inhibitors. 

The USGS Ohio Water Microbiology Laboratory (OWML) 

currently uses noncompetitive IC, which means that the target 

and the IC use different primers and probes and the qPCR 

reactions are run separately. However, the OWML is currently 

testing a new competitive IC, which means that the target and 

the IC will share primers but have different probes and can be 

run in the same reaction. Use of competitive IC is an exciting 

new approach that will allow matrix inhibition to be run for 

each target in the same reaction as the test analysis.

Response of Groundwater Bacteria from 

Cape Cod, Mass., to Low Concentrations of 

Antimicrobials 

By Jennifer C. Underwood,1,2 David W. Metge,1 

Ronald W. Harvey,1 Larry B. Barber,1 Michael T. Meyer,3 

Deborah A. Repert,1 and Richard L. Smith1 

1

U.S. Geological Survey, University of Colorado-Boulder, 3215 Marine 

Street, Suite E–127, Boulder, CO 80303.

2

University of Colorado-Denver, 1380 Lawrence Street, Denver, CO 80204.

3

U.S. Geological Survey, Kansas Water District Office, 4821 Quail Crest 

Road, Lawrence, KS 66049–3839.

There is increasing focus on the protection of 

groundwater resources due to the growing reliance on 

groundwater for human consumption. Many antimicrobials 

from anthropogenic sources have been detected in low but 

significant concentrations in groundwater, which may disrupt 

groundwater microbial communities and lead to direct and 

indirect human health consequences. However, it remains 

unclear if the current detected levels of antimicrobials and 

the concomitant presence of antimicrobial resistance alter 

bacterial community structure and, thus, preclude bacteria 

from serving important ecological roles as decomposers, 

nutrient transformers, and contaminant removers. Recently, 

a field-scale test performed in Cape Cod, Mass., assessed 

the effects of sublethal concentrations of sulfamethoxazole 

(SMx) on microbial community viability. Microbial viability 

was compared between groundwater communities with no 

previous exposure to SMx (pristine) and those with previous 

exposure to SMx (contaminant-impacted). After 2 weeks 

of SMx exposure, viability staining with applied stains 

indicated that the ratio of viable to nonviable cells changed 

from 8:1 in both communities to 1:24 in the contaminantimpacted community and 1:762 in the pristine community. 

Thus, the pristine microbial community appeared much more 

sensitive to SMx exposure than the contaminant-impacted 

community. On the basis of these field data, we hypothesized 

that SMx exposure may inhibit some important microbial 

processes, such as denitrification. The removal of nitrate, 

a predominant groundwater contaminant, by microbially 

mediated denitrification was significantly reduced after adding 

100 micrograms per liter (100 μg/L, or 0.39 μM) of SMx 

to a denitrifying groundwater isolate in the laboratory. The 

ecotoxicological impacts of SMx alone and in concert with 

trimethoprim (TMP) and lincomycin (LM) at environmentally 

significant levels on this isolate and on a groundwaterdenitrifying community have been tested. In addition, the 

influence of a sul gene, which codes for resistance to SMx, on 

denitrification inhibition, has been studied.
 

 

 

 

 

 

 

 

 

Water Quality 23 

Antibiotic Resistance in an Urban Watershed 

with Combined Sewer Overflows 

By Jason Vogel,1 Lisa Fogarty,2 and Joseph Duris2 

1

U.S. Geological Survey, Nebraska Water Science Center, 5231 South 19th 

Street, Lincoln, NE 68512–1271.

2

U.S. Geological Survey, Michigan Water Science Center, 6520 Mercantile 

Way, Lansing, MI 48911.

The U.S. Geological Survey (USGS), in cooperation with 

the City of Omaha, conducted a combined sewer overflow 

(CSO) monitoring project to measure the water-quality 

impacts of CSOs on receiving streams in the Papillion Creek 

watershed in Omaha, Nebr., between May and September 

2007. Constituents analyzed in the samples include organic 

wastewater compounds, nutrients, metals, E. coli, chloride, 

biochemical oxygen demand, chemical oxygen demand, 

hardness, and bacterial antibiotic resistance. The monitoring 

network in the watershed consisted of 2 CSOs, 1 stormwater 

outfall, and 12 stream sites. Most stream samples analyzed 

for antibiotic-resistant bacteria were collected during 

scheduled nonstorm times. The scheduled samples were 

generally collected on the third Tuesday of every month. 

Stream samples were also collected during one CSO event. 

Samples were collected from the CSOs and stormwater 

outfall during selected storms during the study period. The 

antibiotic-resistance analysis indicated that up to 95 percent 

of the E. coli from a specific stream site were resistant to 

cephalosporin antibiotics. The cephalosporin-resistant E. coli 

(CRE) could be correlated with wet or dry weather samples 

(as indicated by specific conductance). Vancomycin-resistant 

enterococci were also detected in CSOs and in one stream 

sample. A cluster analysis of CRE concentrations indicated 

that the CSO samples and stream samples collected during 

or immediately after CSO discharges were associated with 

high CRE concentrations. In general, chemical concentrations 

from samples in this group contained higher trace metal 

concentrations and a greater number of wastewater chemical 

detections than the rest of the samples.

Use of Carboxylated Microbial-Sized 

Microspheres for Estimating Cryptosporidium 

parvum Oocyst Transport within Russian 

River (Sonoma County, Calif.) Bank Filtration 

Sediments 

By David W. Metge,1 Ronald W. Harvey,1 and Robert Anders2 

1

U.S. Geological Survey, University of Colorado-Boulder, 3215 Marine 

Street, Suite E–127, Boulder, CO 80303.

2

U.S. Geological Survey, 4165 Spruance Road, Suite 200, San Diego, CA

92101.

Bank filtration, as practiced domestically and 

internationally, involves drawing surface water through 

riverbank and aquifer sediments to nearby collector wells. 

Generally, it is used as a cost-effective pretreatment option to 

reduce many common microbial and chemical contaminants. 

The efficacy of bank filtration systems to remove oocysts of 

the protistan pathogen Cryptosporidium parvum is particularly 

important because of their well-documented episodic high 

abundances in surface waters and high resistance to chemical 

disinfection. This presentation details small-scale laboratory 

studies using carboxylated microspheres and oocysts in 

assessing their transport potential through physically and 

geochemically heterogeneous sediments from a bank-filtration 

site along the Russian River in Sonoma County, Calif. 

Varied methodologies were used to assess how oocyst-sized 

microspheres are affected by passage through poorly sorted 

riverbank sediments between river bottom and horizontal 

collector wells. Initial field experiments suggested that the 

near-surface sediments, which are high in metal oxide content 

(~4 percent), have a high capacity for sorptive filtration 

of oocyst-sized microspheres (2–5 micrometers (μm) in 

diameter). Subsequent laboratory investigations revealed that 

metal oxide coatings on sediments were significantly related 

to the degree of microsphere and oocyst recovery. By contrast, 

grain size was an inadequate predictive tool for microsphere 

or oocyst recovery. This result suggests that the primary mode 

of microsphere and oocyst removal was likely sorptive rather 

than physical filtration. Pretreatment of sediments with low 

levels of natural organic material or SDBS (sodium dodecyl 

benzene sulfonate) anionic surfactant significantly decreased 

sediment efficiency for removal of oocysts or microspheres. 

Finally, while metal oxides on sediment surfaces may 

currently control or limit the transport of oocysts from river 

water to collector wells, our results suggest that slight changes 

in dissolved organic carbon content may reduce oocyst 

removal rates within this operating bank filtration system 

and make this water system more vulnerable to waterborne 

pathogen contamination.
 

 

 

 

 

 

 

 

 

 

 

24 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Examination of the Watershedwide Distribution 

of Escherichia coli along Southern Lake 

Michigan: An Integrated Approach 

By Richard L. Whitman,1 Meredith B. Nevers,1 and 

Muruleedhara N. Byappanahalli1 

1

U.S. Geological Survey, Great Lakes Science Center, Lake Michigan 

Ecological Research Station, 1100 North Mineral Springs Road, Porter, IN 

46304.

Recent research has highlighted the occurrence of 

Escherichia coli in natural habitats not directly influenced 

by sewage inputs. Most studies on E. coli in recreational 

water typically focus on discernable sources (for example, 

effluent discharge and runoff) and fall short of integrating 

riparian, nearshore, onshore, and outfall sources. An integrated 

beachshed approach that links E. coli inputs and interactions 

would be helpful to understand the difference between 

background loading and sewage pollution; to develop more 

accurate predictive models; and to understand the differences 

among potential, net, and apparent culturable E. coli. The 

objective of this study was to examine the interrelatedness of 

E. coli occurrence from various coastal watershed components 

along southern Lake Michigan. The study shows that once 

established in forest soil, E. coli can persist throughout the 

year, potentially acting as a continuous nonpoint source of 

E. coli to nearby streams; year-round background stream 

loading of E. coli can influence beach water quality. E. coli 

is present in highly variable counts in beach sand to depths 

just below the water table and to distances at least 5 meters 

(m) inland from the shore, providing a large potential area 

of input to beach water. In summary, E. coli in the fluviallacustrine system may be stored in forest soils; sediments 

surrounding springs, bank seeps, stream margins, and pools; 

foreshore sand; surface water; and groundwater. While 

rainfall events may increase E. coli counts in the foreshore 

sand and lake water, concentrations quickly decline to prerain 

concentrations. Onshore winds cause an increase in E. coli in 

shallow nearshore water, likely resulting from resuspension of 

E. coli-laden beach sand. When examining indicator bacteria 

source, flux, and context, the entire beachshed as a dynamic 

interacting system should be considered.

Seasonal Stability of Cladophora-Associated 

Salmonella in Lake Michigan Watersheds 

By Muruleedhara N. Byappanahalli,1 Richard Sawdey,2 

Satoshi Ishii,2 Dawn A. Shively,1 John A. Ferguson,2 

Richard L. Whitman,1 and Michael J. Sadowsky2,3 

1

U.S. Geological Survey, Great Lakes Science Center, Lake Michigan 

Ecological Research Station, 1100 North Mineral Springs Road, Porter, IN 

46304.

2

University of Minnesota, Department of Soil, Water, and Climate, 439 

Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108.

3

University of Minnesota, Biotechnology Institute, 1479 Gortner Avenue, 

Suite 140, St. Paul, MN 55108.

The bacterial pathogens Shigella, Salmonella, 

Campylobacter, and shiga toxin-producing E. coli (STEC) 

were recently found to be associated with Cladophora 

growing in southern Lake Michigan. Preliminary results 

indicated that the Salmonella strains associated with 

Cladophora were genetically identical to each other. However, 

because of the small sample size (n=37 isolates) and a lack 

of information on spatial-temporal relationships, the nature 

of the association between Cladophora and Salmonella 

remained speculative. In the present study, we investigated the 

population structure and genetic relatedness of a large number 

of Cladophora-borne Salmonella isolates (n=133) from Lake 

Michigan, as well as those isolated from stream and lake water 

(n=31), aquatic plants (n=8), and beach sands and sediments 

(n=8) from adjacent watersheds. Salmonella isolates were 

collected during 2005–2007 between May and August from 

Lake Michigan beachsheds in Wisconsin, Illinois, and Indiana. 

The genetic relatedness of Salmonella isolates was examined 

by using the horizontal, fluorophore-enhanced repetitive 

polymerase chain reaction (rep-PCR) DNA fingerprinting 

technique called HRERP. While the Salmonella isolates 

associated with Cladophora exhibited a high degree of genetic 

relatedness (≥92 percent similarity), the isolates were not all 

genetically identical. Spatial and temporal relationships were 

evident in the populations examined, with tight clustering of 

the isolates both by year and location. These findings suggest 

that the relationship between Salmonella and Cladophora 

is likely casual and is related to input sources (for example, 

wastewater, runoff, and birds) and the predominant Salmonella 

genotype surviving in the environment during a given season. 

Our studies indicate that Cladophora is likely an important 

reservoir for Salmonella and other enteric bacterial pathogens 

in Lake Michigan beachsheds, which in turn may influence 

nearshore water quality.
 

 

 

 

 

 

 

 

Water Quality 25 

Real-Time Estimation of Taste-and-Odor 

Occurrences in Cheney Reservoir, Kansas 

By Jennifer L. Graham,1 Andrew C. Ziegler,1 and 

Trudy J. Bennett2 

1

U.S. Geological Survey, 4821 Quail Crest Place, Lawrence, KS 66049–

3839.

2

U.S. Geological Survey, 7920 West Kellogg, Wichita, KS 67209.

Cheney Reservoir, Kansas, is one of the City of Wichita’s 

primary drinking-water supplies. Cyanobacteria-related 

taste-and-odor events in reservoirs are a concern because of 

aesthetics and water-treatment costs. Since 2000, the U.S. 

Geological Survey, in cooperation with the City of Wichita, 

has operated real-time water-quality monitors on the North 

Fork of the Ninnescah River, the main tributary to Cheney 

Reservoir, and in Cheney Reservoir. Real-time water-quality 

variables measured since 2000 include water temperature, 

specific conductance, pH, dissolved oxygen, turbidity, and 

chlorophyll fluorescence (an estimate of algal abundance). 

Data collected during 2001–2003 were used to develop a 

real-time water-quality model to estimate Cheney Reservoir 

geosmin (an earthy odor compound) concentrations in real 

time. Multiple regression analysis was used to develop a 

relation between geosmin concentrations and the real-time 

measured sensor variables turbidity and specific conductance. 

The resulting model is used to provide hourly estimates of 

geosmin concentration on the World Wide Web at http://nrtwq.

usgs.gov/ks/. Evaluation of the model indicates that, within 

existing model limits (turbidity of <36 formazin nephelometric 

units (FNU), specific conductance of 790–915 microsiemens 

per centimeter (μS/cm)), geosmin estimates are conservative 

(overestimates are more likely than underestimates). However, 

model probabilities for exceeding the human detection limit of 

10 nanograms per liter (ng/L) are fairly robust (probabilities 

were accurate for 76 percent of measured geosmin values 

during 2001–2008). Several additional real-time sensors have 

been installed in Cheney Reservoir since the development 

of the initial geosmin model including ones to measure 

the following: wind speed and direction, light, nitrate, and 

phycocyanin fluorescence (an estimate of cyanobacterial 

abundance). These new variables may facilitate additional 

model development and enhance understanding of the factors 

driving cyanobacterial bloom development and taste-andodor occurrence. Ongoing studies at Cheney Reservoir will 

refine the relations between reservoir and inflow conditions 

and taste-and-odor occurrences and develop similar models 

for the cyanobacterial toxin microcystin. The City of Wichita 

currently uses the real-time geosmin estimates, along with 

other variables measured in real time, to make management 

decisions that have helped decrease water-treatment costs.

Cyanotoxins in Midwestern Lakes and 

Reservoirs 

By Jennifer L. Graham,1 John R. Jones,2 Susan B. Jones,3 

Keith A. Loftin,1 Michael T. Meyer,1 and Andrew C. Ziegler1 

1

U.S. Geological Survey, 4821 Quail Crest Place, Lawrence, KS 66049–

3839.

2

University of Missouri, 302 Anheuser-Busch Natural Resources Building, 

Columbia, MO 65211.

3

U.S. Geological Survey, Columbia Environmental Research Center, 4200 

New Haven Road, Columbia, MO 65211.

Cyanobacteria (blue-green algae) produce a diverse group 

of toxins that target fundamental cellular processes and affect a 

wide range of organisms. Cyanobacterial toxins (cyanotoxins) 

have been implicated in human and animal illness and death 

in more than 50 countries worldwide, including at least 33 

U.S. States. Human toxicoses associated with cyanotoxins 

most commonly have occurred after exposure through 

drinking water or from contact through recreational water 

activities. The hepatotoxin microcystin is believed to be one 

of the most common cyanotoxins. Because microcystin is a 

potential human-health risk, several studies were conducted to 

determine the occurrence of microcystin in Midwestern water 

resources. During the summers of 1999–2001 and 2004–2006, 

359 lakes in Missouri, Iowa, southern Minnesota, and eastern 

Kansas were sampled for microcystin. Most lakes were 

sampled two to four times in one year or all years. Microcystin 

commonly was detected in the region, and 78 percent of lakes 

sampled had detectable concentrations (≥0.1 microgram per 

liter (μg/L) as determined by enzyme-linked immunosorbent 

assay (ELISA)) at least once. Total microcystin concentrations 

ranged from 0.1 to 52 μg/L (median=0.2 μg/L), with 21 

percent of lakes having concentrations >1 μg/L and 4 percent 

having concentrations >10 μg/L. Microcystin concentrations 

>20 μg/L are considered to have a high risk for adverse health 

effects during recreational exposure. Seasonal studies were 

conducted on nine lakes during 2001–2004. Peak microcystin 

concentrations occurred in June to December; 66 percent of 

the lakes had peaks in September or October. More recent 

studies have examined the presence of other cyanotoxins 

in Midwestern lakes. Resource managers, drinking-water 

treatment-plant operators, lake associations, and local 

officials increasingly are faced with making decisions about 

cyanobacterial blooms that affect public awareness, exposure, 

and health. Although anecdotal reports are common, few 

studies have documented the occurrence of toxins other than 

microcystin in cyanobacterial blooms throughout the United 

States because few analytical methods are available. In 

addition, although the general factors affecting cyanobacterial 

bloom formation are well known, specific factors driving 

individual toxic occurrences are unclear. Understanding the 
 

 

 

 

 

 

 

 

 

 

26 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

range of cyanotoxins that are present and identifying the 

biological, physicochemical, and hydrological factors affecting 

toxin occurrence are key to effective management of water 

resources and minimization of human-health risks.

The South San Francisco Bay Baylands Mercury 

Project: Mercury Status of Pond A8, Alviso 

Slough, and Alviso Marsh, Based on Sediment 

By Mark Marvin-DiPasquale,1 Evangelos Kakouros,1 

Jennifer L. Agee,1 Marisa H. Cox,1 Lisamarie Windham-Myers,1 

Letitia Grenier,2 and Joshua Collins2 

1

U.S. Geological Survey, 345 Middlefield Road, Mail Stop 480, Menlo 

Park, CA 94025–3561.

2

San Francisco Estuary Institute, 7770 Pardee Lane, Oakland, CA 94621.

As part of the South Bay Salt Pond Restoration Project, 

construction is slated to begin in 2009 on a size-adjustable 

notch in the levee between Pond A8 and Alviso Slough. In 

preparation and to establish preconstruction conditions, an 

assessment of mercury (Hg) concentrations and chemical 

form was conducted for the top 2 centimeters (cm) of surface 

sediment of Alviso Slough (main channel and fringing 

marsh), of Pond A8, and in 17 additional reference marsh 

sites throughout the South San Francisco Bay. Total mercury 

(THg) and methylmercury (MeHg) concentrations were 

highest overall within Pond A8. Vegetated marsh sites along 

Alviso Slough also had almost twofold higher average THg 

and inorganic reactive mercury (Hg(II)R) concentrations 

than the combined group of reference marsh sites, although 

MeHg concentrations were not significantly different between 

Alviso and reference marsh groupings. Across all sites, 

Hg(II)R concentration was related to sediment oxidationreduction conditions, such that the most chemically reducing 

sites (for example, Pond A8) had the lowest percentage of 

Hg(II)R (0.08 ± 0.06 percent of THg) and the most chemically 

oxidized sites (for example, vegetated marshes) had the 

highest percentage of Hg(II)R (2.4 ± 1.4 percent of THg). 

In spite of the lower Hg(II)R concentrations in Pond A8, the 

higher MeHg concentrations in this habitat (compared to both 

vegetated marshes and Alviso Slough main channel) appear to 

be driven by high rates of microbial activity that are stimulated 

by the high loading of readily degraded organic matter, in 

the form of phytoplankton. We predict that by facilitating the 

tidal flushing of Pond A8, and thus decreasing the amount of 

phytoplankton deposition to the benthos, MeHg concentrations 

in surface sediment will eventually decrease within Pond A8.

Microbial Ecology 

Enumeration of Viruses and Prokaryotes in 

Deep-Sea Sediments and Cold Seeps of the Gulf 

of Mexico 

By Christina A. Kellogg1 

1

U.S. Geological Survey, Florida Integrated Science Center-St. Petersburg, 

Coastal and Watershed Studies Team, 600 4th Street, St. Petersburg, FL

33701.

Little is known about the distribution and abundance 

of viruses in deep-sea cold-seep environments. Like 

hydrothermal vents, seeps support communities of macrofauna 

that are sustained by chemosynthetic bacteria. It was 

hypothesized that sediments close to these communities would 

be more microbially active and therefore would host higher 

numbers of viruses than nonseep areas.

Methods.—Push cores were taken at six Gulf of Mexico 

sites at water depths below 1,000 meters. These sites included 

reference sediment near coral gardens, brine seeps, microbial 

mats, an urchin field, and a pogonophoran worm community. 

Once on deck, cores were immediately transferred to a 10°C 

cold room where sediment samples (0–2 centimeters (cm)) 

were collected from the core tops. Replicates were sonicated 

in sterile, 0.02-micrometer (μm)-filtered deionized water 

for 30 seconds on ice to extract the viruses and bacteria, 

followed by a low-speed centrifugation (800 xg) for 1 minute 

to pelletize the larger particles. Immediately after extraction, 

aliquots of the supernatant were filtered onto 0.02-μm filters, 

stained with SYBR Gold, mounted on glass slides, and 

frozen at –20°C. The slides were counted by epifluorescence 

microscopy within 48 hours.

Results.—Bacterial counts were an order of magnitude 

lower in sediments directly in contact with macrofauna 

(urchins, pogonophorans) than counts for all other samples 

(107

 vs. 108 cells/gram dry weight) and were highest in 

areas of elevated salinity (brine seeps). Viral counts were 

lowest in the reference sediments and pogonophoran cores 

(108 virus-like particles/gram dry weight), high in brine 

seeps (109 VLP/g dry wt), and highest in the microbial mats 

(1010 VLP/g dry wt). Virus-bacteria ratios (VBR) ranged from 

<5 in the reference sediment to >30 in the microbial mats and 

>60 in the urchin field.

Summary.—Viral counts and VBR ratios were all 

significantly greater than those reported from sediments in the 

deep Mediterranean Sea and in some cases were higher but 

on par with recent data from cold seeps off Japan. This result 

indicates that greater microbial activity in or near cold-seep 

environments results in greater viral production and higher 

numbers of viruses.
 

 

 

 

 

 

 

 

 

 

27 

2

Microbial Decomposer Communities in Alaskan 

Permafrost Soils and Their Response to Thaw 

By Mark P. Waldrop,1 Kimberly P. Wickland,2,3 

Jennifer W. Harden,1 Robert G. Striegl,2 and George R. Aiken3 

1

U.S. Geological Survey, Geology Discipline, 345 Middlefield Road, Menlo 

Park, CA 94025–3561.

U.S. Geological Survey, Water Resources Discipline, Denver Federal 

Center, Box 25046, Denver, CO 80225–0046.

3

U.S. Geological Survey, Water Resources Discipline, University of 

Colorado-Boulder, 3215 Marine Street, Suite E–127, Boulder, CO 80303.

Permafrost-protected soil carbon in boreal forest 

ecosystems represents a significant portion of the 

approximately 500 gigatons (Gt) of C in the soil organic 

matter of boreal regions. The magnitude of this thermally 

protected carbon pool makes it particularly important to the 

global C cycle within the context of global climatic change. 

Permafrost has acted as a C sink for thousands of years, yet 

it currently has been warming at a rate of 1°C per decade, 

making the C contained within it potentially available for 

decomposition. Thawing permafrost opens a latch into a 

globally important C reservoir that could be released to 

the atmosphere (as CO2

) and rivers (as dissolved organic 

carbon, DOC), affecting greenhouse warming and aquatic 

chemistry. A gap in our current knowledge is the extent to 

which permafrost-protected C is available for microbial 

metabolism once soils thaw. Current indications are that 

organic matter contained within permafrost is relatively labile, 

since it is not protected from decomposition by physical 

protection or humification mechanisms. However, we have 

little understanding of the microbiology of permafrost soils, 

which could significantly affect the rate of decomposition 

of permafrost C after thaw. Our aim was to use quantitative 

molecular techniques to examine the abundance of microbial 

decomposer functional groups in permafrost soils, the 

enzymes they encode, and their rates of respiration under both 

aerobic and anaerobic conditions in a simulated summer thaw 

at 5°C. We compared microbial and chemical characteristics 

of active layer and permafrost soils from black spruce stands 

in three distinct geographic regions: Coldfoot, Hess Creek, 

and Smith Lake, Alaska. We chose these regions because they 

span a range of permafrost conditions from shallow active 

layers and mineral-associated permafrost layers to thick active 

layers and deep organic permafrost soils. Soil carbon and 

nitrogen concentrations did not differ between active layer 

and permafrost soils within sites, and neither did the relative 

abundance of total bacteria and methanogens. In contrast, total 

fungal abundance and basidiomycete abundance were strongly 

reduced in permafrost soils. We tested whether the reduction in 

fungal abundance in permafrost soils could affect the turnover 

of soil carbon in thawed permafrost. We incubated soils under 

aerobic and anaerobic conditions at 5°C for 3 months. We are 

currently examining the changes in microbial respiration and 

Microbial Ecology 

enzyme activities that result from the incubation, as well as 

microbial population shifts. We are testing the hypothesis that 

low fungal biomass in permafrost soils will reduce the rate of 

decomposition of organic matter during summer thaw.

Fungal and Methanogen Functional Groups in 

Boreal Forests and Wetlands in Interior Alaska: 

Abundance, Diversity, and Process in the Face 

of Environmental Change 

By Mark Waldrop,1 Jennifer Harden,1 Lee Pruett,1 

Renata Mendieta,1 David McGuire,1,2 Neville Millar,3 and 

Merrit Turetsky3 

1

U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA

94025–3561.

2

University of Alaska-Fairbanks, Department of Biology and Wildlife, 216 

Irving I Building, Fairbanks, AK 99775.

3

Michigan State University, Department of Plant Biology, Plant Biology 

Building, East Lansing, MI 48824.

Boreal forest ecosystems cover nearly 1.2 billion 

hectares (ha) of the surface of the Earth, equivalent to 17 

percent of the total land surface, and contain approximately 

90 gigatons (Gt) of carbon (C) in vegetation and 470 Gt C in 

soil organic matter and forest floor litter. Such large pools of 

C within the boreal ecosystem, equivalent to half of the total 

carbon within all terrestrial ecosystems, make it particularly 

important to the global carbon cycle and global climatic 

change. If the carbon balance in boreal ecosystems were 

significantly altered, then the rate of accumulation of carbon 

within the atmosphere could accelerate, resulting in a positive 

feedback to climate change. Moisture is a primary control 

over plant community distributions and C cycling processes 

in interior Alaska. Most soil carbon is contained in saturated 

soils having low decomposition rates. Changes in moisture 

and temperature have the potential to release large quantities 

of soil carbon to the atmosphere. Therefore, we have begun 

a comprehensive assessment of pools and fluxes of carbon 

across a moisture gradient, fungal and bacterial communities 

affecting C cycling, and the sensitivities of microorganisms to 

environmental change.
 

 

 

 

 

 

 

 

 

 

28 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Fire and Ice: Examining Fungal Mechanisms of 

Recalcitrant Carbon Decomposition in Response 

to Fire in the Boreal Forest Landscape 

By Mark Waldrop1 and Jennifer Harden1 

1

U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA

94025–3561.

Heterotrophic microbial communities within boreal 

forest ecosystems control the fate of large pools of soil organic 

carbon (C) through decomposition and mineralization, yet 

the factors that control microbial communities are not well 

understood. Boreal forest ecosystems contain approximately 

470 gigatons (Gt) of C in soil organic matter and forest floor 

litter and thus have a significant effect on the global C cycle. 

Here we examine the landscape-level variation in microbial 

community composition in order to understand (1) the primary 

factors that control microbial communities in boreal forest 

ecosystems and (2) the effects of variations in community 

composition on the cycling of C. Soil drainage and fire are 

two of the most important factors affecting boreal forest 

structure and function. We hypothesized that the biomass 

and diversity of soil fungi would increase with successional 

stage (5 and 60–120 years after a fire) and with decreasing 

soil moisture. We further hypothesized that increased fungal 

biomass and diversity would increase the capacity of the 

soil microbial community to decompose recalcitrant carbon. 

Fungal community composition and diversity were analyzed 

by denaturing gradient gel electrophoresis (DGGE) and 

denaturing high performance liquid chromatography (DHPLC) 

of the fungal internal transcribed spacer (ITS) region of 

community DNA. Fungal biomass was determined by 

quantitative polymerase chain reaction (qPCR) analysis of the 

ITS region. Functional analysis of the microbial community 

was performed by using oxidative enzyme activities (required 

to degrade recalcitrant C) and qPCR of phenol oxidase 

functional genes. Fire and higher soil moisture reduced the 

diversity and size of the soil fungal community by 50 to 75 

percent, correlating to reduced (50 to 75 percent) phenol 

oxidase enzyme activities, primarily in the fibric (F) horizon. 

Lower phenol oxidase enzyme activities may, in turn, reduce 

the decomposition of recalcitrant carbon, or the “slow” pool 

of carbon used in modeling studies. We also discovered fungal 

mats appearing in a small number of F horizon samples from 

unburned soils that had tenfold higher phenol oxidase enzyme 

activities than the surrounding soil community. The organism 

composing the fungal mat, when present, dominates the soil 

fungal community. As such, it may be an example of a single 

microbial population that strongly affects the turnover of soil 

C at small scales within boreal ecosystems, yet what controls 

its distribution or activity is unknown.

In situ Measurement of Microbially Catalyzed 

Nitrification and Denitrification Rates in 

Stream Sediments Receiving Coalbed-Methane 

Discharge, Powder River Basin, Wyoming 

By Steve H. Harris, Jr.,1 and Richard L. Smith1 

1

U.S. Geological Survey, Water Resources Discipline, University of 

Colorado-Boulder, 3215 Marine Street, Suite E–127, Boulder, CO 80303.

Dissolved methane collected from deep subsurface coal 

beds is a significant source of domestic energy production. 

Water from coalbed-methane (CBM) wells typically contains 

several reduced chemical species including ammonium (1–8 

milligrams nitrogen per liter (mg N/L)) that can affect the 

quality of surface water and groundwater. The transport and 

fate of ammonium are influenced by microbial activities 

occurring in sediments of streams receiving water discharged 

after CBM recovery. In the presence of oxygen, nitrifying 

bacteria oxidize ammonium, producing nitrite and nitrate, 

both of which can be subsequently reduced to nitrogen gas 

by denitrifying microorganisms. Thus, microbial activity can 

potentially influence the nitrogen status of CBM discharge 

waters and serves as the only mechanism for permanent 

nitrogen removal in situ. We examined microbially catalyzed 

nitrification and denitrification in CBM discharge streams 

using in situ sampling chambers designed to capture a parcel 

of water and sediment and observed short-term temporal 

changes in stream chemistry. Rates of dissolved inorganic 

nitrogen (DIN) removal were highest (3.5 milligrams nitrogen 

per square centimeter per hour (mg N/cm2

*hr)) in light 

incubations when oxygen levels were temporally high at 

locations where ammonium levels were elevated (>4.9 mg 

N/L). This high rate of DIN removal resulted in accumulation 

of nitrite and nitrate. However, these endproducts accounted 

for <15 percent of the ammonium consumed, suggesting 

that an additional fate for ammonium exists at this site. At 

the same location, the rate of DIN removal in the dark (0.3 

mg N/cm2

*hr) was <10 percent of the value observed in the 

light. Although microbial nitrate and nitrite consumption was 

observed under both light and dark incubations, the rate was 

faster under the latter condition when oxygen levels were 

lowest. Nitrogen cycling in CBM discharge water exhibits a 

diel pattern that is likely related to the flux of oxygen in stream 

sediments. In situ sampling chambers can be used to estimate 

microbial activity rates in CBM discharge streams and gage 

the impact of those processes on stream geochemistry.
 

 

 

 

 

 

 

 

 

 

 

29 

Microbial Methanogenesis in Laboratory 

Incubations of Coal: Implications for a 

Sustainable Energy Resource in Subsurface 

Coal Beds 

Microbial Ecology 

supports microbial growth. Furthermore, the observation of 

rapid hydrogen consumption uncoupled from methanogenesis 

suggests that competition exists for this compound. The 

success of efforts to stimulate methanogenesis in subsurface 

coal beds will likely be influenced by the nature of the electron 

By Steve H. Harris, Jr.,1 Charles E. Barker,2 and Richard L. Smith1 

1

U.S. Geological Survey, Water Resources Discipline, University of 

Colorado-Boulder, 3215 Marine Street, Suite E–127, Boulder, CO 80303.

2

U.S. Geological Survey, Geology Discipline, Denver Federal Center, Box 

25046, Mail Stop 977, Denver, CO 80225–0046.

Methane desorbed from subsurface coal seams 

contributes about 8 percent of the total natural gas produced in 

the United States. This value is expected to increase over the 

next several years as a growing proportion of energy demands 

is supplied from unconventional reservoirs. Isotopic analyses 

of gas samples from several geographically separate coal beds 

indicate that a substantial proportion of the sorbed methane is 

biogenic in origin. Furthermore, previous studies have shown 

the ability of microbial consortia to degrade coal in aerobic 

laboratory incubations. These findings suggest that stimulation 

of microbial methane production in subsurface coals may 

provide a sustainable source of domestic energy. To address 

this prospect, we assessed the ability of indigenous microbial 

populations to produce methane in coal maintained under 

anaerobic conditions in the laboratory and investigated factors 

that influenced the rate and extent of the process. Several 

freshly collected coals of different rank were examined for 

their ability to support methanogenesis in mineral medium 

alone or amended with different nutrients such as hydrogen (4 

kilopascals (kPa)), formate (20 millimolar (mM)), or acetate 

(25 mM). Microbial methane production was distinguished 

from abiotic desorption by subtracting methane generated in 

replicate incubations that contained bromoethanesulfonic acid 

(5 mM), an inhibitor of methanogenesis. The extent and rate 

of methane production varied among the different coals. A

relatively shallow (400 meters (m)), immature coal exhibited 

a rate of 700 nanomoles of methane per day per gram of coal 

(nmole CH4

*day–1*g coal–1), a value comparable to previous 

observations of contaminated sediments. Methane production 

was negligible in a deeper (650 m), relatively mature coal 

obtained from the same borehole, although the same material 

exhibited a rate of about 80 nmole CH4*day–1*g coal–1 

after a formate amendment. In contrast, hydrogen proved 

to be ineffective as a methanogenic substrate, although this 

electron donor was rapidly consumed in coal incubations. 

A filter-sterilized warm water extract of spent coal renewed 

methanogenesis in incubations no longer generating methane, 

suggesting the cessation of methane production was not 

due to moribund cells or the accumulation of an inhibitory 

compound, but rather the lack of suitable electron donor. 

Viable methanogenic consortia were present in most of the 

coal samples examined in this study, and their activity could 

be enhanced by electron donor amendment, which presumably 

donor.

Chemical Character and Lability of Carbon 

Across a Chronosequence of Drained Sediments 

of a Drying Arctic Lake, Interior Alaska 

By Kimberly P. Wickland,1 Jonathan A. O’Donnell,2 

Joshua C. Koch,1 M. Torre Jorgenson,3 Jennifer W. Harden,4 

Robert G. Striegl,5 and Lysanna Anderson4 

1

U.S. Geological Survey, Water Resources Discipline, University of 

Colorado-Boulder, 3215 Marine Street, Suite E–127, Boulder, CO 80303.

2

University of Alaska-Fairbanks, Department of Biology and Wildlife, 211 

Irving I Building, Fairbanks, AK 99775.

3

ABR, Inc., P.O. Box 80410, Fairbanks, AK 99708.

4

U.S. Geological Survey, Geology Discipline, 345 Middlefield Road, Menlo 

Park, CA 94025–3561.

5

U.S. Geological Survey, Water Resources Discipline, Denver Federal 

Center, Box 25046, Denver, CO 80225–0046.

Drying of lakes over large regions in the arctic and 

subarctic has been occurring during the past several decades, 

exposing lake sediments to aerobic conditions. This drying 

likely leads to changes in sediment carbon (C) chemistry and 

lability due to microbial degradation and encroachment of 

terrestrial vegetation. Characterization of C chemistry and 

lability in these drained sediments is critical to understanding 

its role as a biotic substrate and as a source of greenhouse 

gases. We collected sediments from a drying lake in 

interior Alaska, including flooded sediments (T0) and areas 

continuously or intermittently drained for approximately 5 

years (T1), 15 yrs (T2), and 30 yrs (T3). We characterized 

sediment C chemistry (elemental and pyrolysis-gas 

chromatography/mass spectrometry analyses) and lability of 

solid and leachable C. Organic C content of surface sediments 

decreased from 16 to 10 grams of carbon per gram of sediment 

(g C/g sediment) from T0 to T3, while dissolved organic 

carbon (DOC) yield and aromaticity were greatest from T3 

sediments. Incubation results (3.5 months, 10°C) indicate 

that C in T3 sediments is least labile. This finding suggests 

that C is quickly oxidized from drained sediments, leaving 

recalcitrant C behind.
 

 

 

 

 

 

 

 

30 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Indicators of Ecosystem Health and the Impact 

of Mineralized Terrane 

By Steve Blecker,1 Lisa Stillings,1 Mike Amacher,2 Jim Ippolito,3 

Larry Gough,4 and Nicole DeCrappeo5 

1

U.S. Geological Survey, Western Mineral Resources Science Center, 

Mackay School of Earth Sciences, Reno, NV 89557–0047.

2

U.S. Department of Agriculture, Forest Service, Rocky Mountain Research 

Station, Logan, UT 84321.

3

U.S. Department of Agriculture, Agricultural Research Service, Northwest 

Irrigation and Soils Research Lab, Kimberly, ID 83341.

4

U.S. Geological Survey, Alaska Mineral Resources Program, 4210 

University Drive, Anchorage, AK 99508.

5

U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, 

3200 S.W. Jefferson Way, Corvallis, OR 97331.

Studies of soil quality and ecosystem health employ a 

wide variety of approaches designed to monitor ecosystem 

functioning within an array of natural and anthropogenic 

disturbances. Definitions of soil health vary, but they typically 

include the soil’s role in mediating nutrient, water, and energy 

cycles in support of associated flora and fauna. The limited 

mobility and inherent sensitivity of soil microbial communities 

to external stressors make them potentially well suited for the 

study of stressors on ecosystem health. Additional measures of 

plant community characteristics can provide a more complete 

picture of the impact of a natural or anthropogenic disturbance 

on an ecosystem due in part to the roles of vegetation in 

phytoremediation, the hydrologic cycle, and nutritional value 

to fauna. This study is focused on metal-microbe-vegetation 

interactions in mineralized terrane of terrestrial ecosystems 

and impacts on ecosystem functioning. Relationships among 

microbial and plant activity and composition and abiotic 

soil parameters will be used to develop ecosystem health 

indices that could be used in support of geoenvironmental 

assessments and reclamation monitoring. An extensive 

reconnaissance study within several Western U.S. mining 

districts of contrasting mineralogy and climate is underway, 

examining the differences in metal-biogeochemical interaction 

between mineralized and adjoining nonmineralized areas in 

various ecosystems. Study areas include a sage-grassland 

site impacted by copper/molybdenum, an oak-pine-grass site 

impacted by nickel/chromium, and two sage-pinyon-juniper 

sites impacted by acid sulfate mineralization. Preliminary data 

will include (1) soil biota: microbial biomass (phospholipid 

fatty acids analysis, PFLA), enzyme activity (fluorescein 

diacetate (FDA) hydrolysis), functional diversity (Biolog 

Ecoplate), and C/N mineralization potential (lab incubation); 

(2) vegetation: density, cover, and biomass; and (3) soil abiotic 

measures: total and bioavailable metals, pH, texture, electrical 

conductivity, and bulk density.

Climate-Induced Changes in Nitrogen Dynamics 

in Loch Vale Watershed, Rocky Mountain 

National Park 

By Jill S. Baron,1 Travis S. Schmidt,2 and Melanie D. Hartman3 

1

U.S. Geological Survey, Fort Collins Science Center and Natural Resource 

Ecology Laboratory, Colorado State University, 1499 Campus Mail, Fort 

Collins, CO 80523–1499.

2

U.S. Geological Survey, Denver Federal Center, Box 25046, Mail Stop 

973, Denver, CO 80225–0046.

3

Colorado State University, Natural Resource Ecology Laboratory, 1499 

Campus Mail, Fort Collins, CO 80523–1499.

Mountain terrestrial and aquatic ecosystems are 

responsive to external drivers of change, especially climate 

change and atmospheric deposition of nitrogen (N). We 

explored the consequences of an overlay of climate change 

on an alpine and subalpine watershed in the Colorado Front 

Range that has long been the recipient of elevated atmospheric 

N deposition. Mean annual nitrate concentrations increased 

by 33 percent, and mean annual nitrogen export has increased 

by 28 percent from the Loch Vale watershed since 2000. 

Measured inorganic nitrogen values since 2000 are the highest 

observed since monitoring began in 1982. The substantial 

increase in nitrogen dynamics comes as a surprise, because 

atmospheric N deposition has not increased during this period. 

Coincident with the increase in watershed nitrogen loss and 

stream nitrogen concentrations, there has been a period of 

below-normal precipitation and an increase in temperatures, 

especially mean annual temperature, which increased from a 

mean of 1.3°C for the years 1985–1999 to a mean of 1.7°C 

for 2000–2006. The temperature increase is driven by a strong 

increase in July mean and minimum temperatures. Nitrate 

concentrations, as well as the weathering products calcium 

and sulfate, were higher for the period 2000–2006 in rock 

glacier meltwater at the top of the watershed, suggesting 

minimal influence of alpine and subalpine vegetation and 

soils. We conclude that the observed N increases in Loch Vale 

are climatically induced, caused by melting ice in glaciers 

and rock glaciers that have exposed microbially active 

sediments. The phenomenon observed in Loch Vale may be 

indicative of nitrogen release from ice features worldwide 

as mountain glaciers retreat. In regions that are chronically 

ultra-oligotrophic, additional nitrate may stimulate algal 

productivity and affect species assemblages, such as we have 

already observed.
 

 

 

 

 

 

 

 

 

 

 

 

Metabolic Processes 31 

Metabolic Processes 

Laboratory Studies of Biogenic Methane 

Production from Coal by Microbial Consortia: 

Identifying Organisms, Reactions, and 

Intermediate Products 

By Elizabeth J.P. Jones,1 Mary A. Voytek,1 William H. Orem,1 

Margo D. Corum,1 Anne L. Bates,1 and Harry E. Lerch1 

1

U.S. Geological Survey, 12201 Sunrise Valley Drive, Reston, VA

20192–0002.

Many isotopic studies have indicated that some coal 

beds produce biogenic methane. Little is known, however, 

about the organisms, reactions, and intermediate products 

involved in the process of biogenic methane formation from 

geopolymers like coal. Laboratory microcosms of coal and 

nutrients, some with an added microbial consortium (WBC–2) 

enriched from a modern wetland, were used to study the 

production of methane from coal. Subbituminous coal samples 

from the Wilcox Group (Zavala County, Tex.) and the Fort 

Union Formation (Campbell County, Wyo.), both known to 

produce biogenic methane in the field, released 56 and 16 

standard cubic feet per ton (scf/ton) of methane, respectively, 

in laboratory experiments with WBC–2 added. Generation of 

methane from coal involves a consortium of microorganisms 

that ferment complex organic compounds to methanogenic 

substrates, which are then converted to methane. Microbial 

biomass in the coals was low and methane generation was 

limited by methanogen growth, which did not always occur. 

When WBC–2 was added, organic compounds released from 

the coal, including aromatics and long-chain hydrocarbons 

(fatty acids and alkanes), were degraded over about 70 days. 

Acetate accumulated initially, then decreased as methane 

was formed. WBC–2 also produced methane in coal-free 

treatments with organic compounds such as octadecanoic, 

hexadecanoic, benzoic, and vanillic acids, confirming that coal 

intermediate products can be fermented to methane precursors. 

There was a shift in the WBC–2 microbial population 

grown in coal microcosms, indicating growth of some new 

dominant members specific to coal fermentation. Phylogenetic 

identification of community members in the coal incubations 

will be useful for understanding and manipulating in situ coalbed populations.

Microbially Induced Temperature Changes in a 

Petroleum Hydrocarbon Plume 

By Ean Warren1 and Barbara Bekins1 

1

U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA

94025–3561.

The degradation reactions of organic contaminants are 

often exothermic. Given this, the degradation of organic 

contaminants in an aquifer should produce measurable 

temperature increases if the heat is generated faster than 

it is dissipated. The groundwater contaminant plume at a 

crude oil spill site near Bemidji, Minn., has been undergoing 

aerobic and anaerobic biodegradation for 28 years. At this 

site, the theoretical degradation of 100 milligrams per liter 

(mg/L) of phenol, a representative compound, under aerobic 

conditions could generate a 2°C increase in groundwater 

temperature with no heat loss and an aquifer heat capacity 

of 2,494 joules per liter per degree Celsius (J/L-°C). The 

temperature in the aquifer was measured with an accurate 

thermistor (≤±0.01°C) that was lowered to multiple depths 

in 13 monitoring wells along a groundwater flowpath. The 

measurements were taken from 0.15 to 12.62 meters (m) 

below the water table. Temperatures ranged from 6.35°C in 

the background aquifer to 9.19°C just under the crude oil 

source. These data revealed a thermal plume co-located with 

a previously observed area of benzene, toluene, ethylbenzene, 

and xylene (BTEX) biodegradation under iron-reducing and 

methanogenic conditions. The results indicate that evidence 

of exothermal microbial reactions within contaminant plumes 

can be detected by using sensitive and detailed temperature 

measurements in wells.

Denitrification-Coupled Iron Oxidation in 

Cultures from Aquifer Sediments from Cape Cod, 

Massachusetts 

By Deborah A. Repert,1 Richard L. Smith,1 

Laura K. Baumgartner,2 and Charles P. Hart1 

1

U.S. Geological Survey, Water Resources Discipline, University of 

Colorado-Boulder, 3215 Marine Street, Suite E–127, Boulder, CO 80303.

2

University of Colorado, Molecular, Cellular and Developmental Biology, 

UCB 347, Boulder, CO 80303.

The ability of microorganisms to use Fe(II) as an electron 

donor for the reduction of nitrate via the denitrification 

pathway was examined within a groundwater contaminant 

plume on Cape Cod, Mass. The plume originated from 

the disposal of treated wastewater and contained high 

concentrations of nitrate. Field studies had previously shown 

nitrate reduction occurring in an anoxic Fe(II) zone along 

with a decrease in the concentration of Fe(II). Core material 
 

 

 

 

 

 

 

 

 

 

32 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

was collected from this reduced-iron zone within the aquifer 

and used to create anaerobic enrichment cultures containing 

reduced iron, organic carbon, and nitrate. The enrichments 

exhibited anoxic iron oxidation in conjunction with nitrate 

reduction to nitrogen over a period of several weeks. Growth 

experiments showed that nitrate (2 millimolar (mM)) and 

acetate (1 mM) concentrations were depleted within 2 weeks 

while Fe(II) decreased at a much slower rate with about half of 

the initial concentration oxidized to Fe(III) after 12 weeks. The 

enrichments were also capable of autotrophic denitrification 

when grown with Fe(II) and hydrogen as electron donors 

but were not capable of autotrophic growth solely on Fe(II). 

Preliminary studies indicate that these enrichments are able 

to reduce perchlorate, a contaminant found in some drinking 

water and groundwater sources, when substituted for nitrate. 

Several bacterial strains were isolated from the enrichments 

and subsequently identified using 16S rRNA gene sequencing. 

Most of the isolates belonged to the phyla Proteobacteria 

(mostly Burkholdera and Xanthomonads) and Actinobacteria 

(Cellulomonads) and were distinct from known strains of ironoxidizing denitrifiers. Growth experiments with the isolates 

indicated differences in their ability to reduce various nitrogen 

oxides in the presence of iron. The results of these studies 

provide details of a potentially important redox reaction 

occurring in nitrate-contaminated aquifers because nitrate 

intrusion into iron-reducing zones may be an increasingly 

common situation in many subsurface environments.

Cycling of Methylmercury in the Sediments of 

the Penobscot River Estuary, Maine 

By Aria Amirbahman,1 Karen A. Merritt,1,2 Mary A. Voytek,3 and 

Celia Y. Chen4 

1

University of Maine, 319A Boardman Hall, Orono, ME 04469.

2

Environ Int’l Corp., 20 West Street #6, Portland, ME 04102.

3

U.S. Geological Survey, 12201 Sunrise Valley Drive, Reston, VA

20192–0002.

4

Dartmouth College, 6044 Gilman, Room 412, Hanover, NH 03755–3576.

Due to the presence of high concentrations of organic 

matter and sulfate, estuarine sediments may produce a great 

deal of methylmercury (MeHg). Using equilibrium dialysis 

samplers and molecular analysis of the resident microbial 

population in contaminated sediments of the Penobscot River 

estuary (Maine), we observed a correspondence between 

the density of the sediment sulfate-reducing bacteria and 

methylation in pore waters. We also observed rapid MeHg 

demethylation close to the sediment-water interface (SWI) 

that may be due to the presence of iron-reducing bacteria 

that are dominant close to the SWI, or to the presence of mer 

genes that may be expressed in contaminated sediments, such 

as the ones studied here. We studied Hg methylation in intact 

sediment cores by manipulating the location of the redoxcline 

in the laboratory. Induced shoaling of the redoxcline was 

correlated with a shoaling of the net MeHg production zone 

and an increase in the net MeHg production rate. This study 

indicates that environments such as saltpans, where the 

shallow redoxcline leads to the shoaling of the MeHg front, 

are likely to be Hg methylation and release hotspots in coastal 

environments.

Role of Microbes in Attenuation and 

Mobilization of Arsenic at the Lava Cap Mine 

Superfund Site, Nevada County, California 

By Andrea L. Foster,1 Georges Ona-Nguema,2 and 

G.E. Brown, Jr.2 

1

U.S. Geological Survey, 345 Middlefield Road, Mail Stop 901, Menlo 

Park, CA 94025–3561.

2

Stanford University, Department of Geological and Environmental 

Sciences, Building 320, Room 118, Stanford, CA 94305.

Iron-oxidizing, iron-reducing, and arsenic-reducing 

microbial communities at the Lava Cap Mine Superfund 

site (Nevada City, Calif.) were investigated using culturing, 

chemical, and spectroscopic techniques to understand the 

interplay between processes that attenuate and mobilize 

arsenic (As) in surface waters. Sheaths formed by bacteria 

of the genus Leptothrix physically support a community 

of ferrous iron-oxidizing bacteria suspended in the water 

column. This community induces the precipitation of ferric 

(hydr)oxide, which has a high sorptive capacity for As (1,000 

to >10,000 milligrams per kilogram (mg/kg) As, dry weight). 

X-ray absorption spectroscopy indicates that arsenic is sorbed 

to iron (hydr)oxide. This process removes arsenic from water, 

which is desirable, but it is also potentially reversible. Since 

iron- and (or) arsenic-reducing bacteria could enhance the 

desorption of arsenic from iron (hydr)oxide, their numbers 

were estimated using the most-probable-number technique. 

The results indicate that iron- and arsenic-reducing bacteria are 

present in the iron-oxidizing microbial community dominated 

by Leptothrix, and their reducing activity may be responsible 

for the high iron and arsenic concentrations observed in 

soil pore waters. Denaturing gradient high-performance 

liquid chromatography indicates changes in the microbial 

community in space and time; identification of community 

members is ongoing. These lines of evidence suggest that a 

cycle of arsenic mobilization and immobilization exists and is 

associated with blooms of iron-oxidizing bacteria. Additional 

studies are needed to determine the factors controlling the flux 

of arsenic within each compartment of this cycle and the ways 

that the microbial community responds to and (or) influences 

this cycling.
 

 

 

 

 

 

 

 

 

 

Metabolic Processes 33 

Cr(III) Oxidation by Soluble Mn(III) Chelates: 

A Potential Biogeochemical Pathway for the 

Enhanced Mobilization of Cr from Spinels 

By Christopher T. Mills,1 Martin B. Goldhaber,1 Andrea L. Foster,2 

and Jean M. Morrison1 

1

U.S. Geological Survey, Denver Federal Center, Box 25046, Mail Stop 

964, Denver, CO 80225–0046.

2

U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA

94025–3561.

Soils derived from ultramafic (UM) rocks are enriched in 

Cr(III), mainly due to the presence of chromite (FeCr2O4) and 

other Cr(III)-bearing spinels. Weathering of UM rocks in the 

Coast Range and Sierra Nevada mountains of California has 

impacted the geochemistry of alluvial soils in the Sacramento 

Valley, which are enriched in Cr (30–1,420 micrograms per 

gram (μg g–1)) relative to the U.S. geometric mean (37 μg g–1). 

Although much of the Cr in these soils appears to be bound 

in refractory spinels, some mobilization of Cr is apparent 

in the coincidence of enriched soils with elevated Cr(VI) 

in groundwater (up to 50 micrograms per liter (μg L–1)). It 

was recently reported that dissolution of chromite can be 

driven by the oxidation of the released aqueous Cr(III) on 

soil Mn oxides(Oze and others, 2007). We are studying the 

oxidative dissolution of chromite by soluble Mn(III) as a an 

additional Cr mobilization pathway. Free aqueous Mn(III) is 

a strong oxidant but rapidly disproportionates to Mn(II) and 

Mn(IV). Various chelates such as oxalate and pyrophosphate 

can stabilize Mn(III) in solution. Mn(III)-oxalate is produced 

by extracellular enzymes of white-rot fungi and acts as a 

diffusible oxidant in lignin degradation. Pyrophosphate (PP) 

is a hydrolysis product of adenosine triphosphate (ATP) and 

is also a component of some fertilizers. Its reaction with soil 

Mn oxides can result in soluble Mn(III)-PP. We measured 

the reduction potential of a 1-millimolar (mM) solution of 

Mn(III)-PP as a function of pH. The reduction potential 

decreased from ~1.1 volts (versus standard H2

 electrode) 

at a pH of 2 to ~0.6 V at a pH of 7. Consistent with these 

measurements, Mn(III)-PP oxidized a greater percentage of 

aqueous CrCl3 at lower pH levels. After 2 weeks reaction time, 

94, 63, 28, 3, and <1 percent of Cr(III) was oxidized to Cr(VI) 

at pH levels of 3, 4, 5, 6, and 7, respectively. Forty-five times 

as much Cr(VI) was produced from chromite grains (63–150 

micrometers (μm) in diameter) incubated for 8 days in a 

Mn(III)-PP solution at a pH of 3 than from grains incubated 

with solid manganese oxides at the same pH. As expected, the 

chromite and Mn(III)-PP incubation produced one tenth as 

much Cr(VI) at pH 5 as at pH 3. Our initial studies of Mn(III)-

oxalate suggest its ability to oxidize aqueous CrCl3

, but only in 

a narrow, circumneutral pH range.

Reference Cited 

Oze, Christopher, Bird, D.K., and Fendorf, Scott, 2007, 

Genesis of hexavalent chromium from natural sources 

in soil and groundwater: Proceedings of the National 

Academy of Sciences, PNAS, v. 104, no. 16, p. 6544–6549, 

doi:10.1073/pnas.0701085104, available at http://www.

pnas.org/content/104/16.toc.

A Proteomic Profile of a Novel ArseniteOxidizing Bacterium Alkalilimnicola ehrlichii 

strain MLHE-1T 

By Christine Richey,1 Peter Chovanec,1 Shelley E. Hoeft,2 

Ronald S. Oremland,2 Partha Basu,3 and John F. Stolz1 

1

Duquesne University, Department of Biological Sciences, 600 Forbes 

Street, Pittsburgh, PA 94025.

2

U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA

94025–3561.

3

Duquesne University, Department of Chemistry, 600 Forbes Street, 

Pittsburgh, PA 94025.

Arsenic speciation, mobility, and toxicity can be 

greatly influenced by microbial activity (for example, 

arsenate reduction, arsenite oxidation, methylation, and 

demethylation). The arsenite oxidizer Alkalilimnicola ehrlichii 

strain MLHE-1T is a haloalkaliphilic gammaproteobacterium 

isolated from Mono Lake, Calif. It has the unique ability to 

grow both aerobically as a heterotroph and anaerobically 

as a chemolithoautotroph by coupling arsenite oxidation 

to nitrate reduction. The latter ability has implications for 

arsenic and nitrogen cycling, as well as for carbon fixation 

in anoxic environments. The genome of MLHE-1T has 

been sequenced, and the operons for carbon fixation, CO 

oxidation, nitrate reduction, and arsenic resistance have been 

identified. Surprisingly, no homologue for arsenite oxidase 

was found, but two arsenate reductases were discovered. In 

addition to the dissimilatory nitrate reductase, homologues 

for nitric oxide reductase and nitrous oxide reductase were 

found. MLHE-1T lacks a homologue for nitrite reductase, and 

nitrite is the end product of nitrate respiration. A proteomic 

approach was employed to understand the complex physiology 

of this novel bacterium. Two-dimensional polyacrylamide 

gel electrophoresis (PAGE) was used to separate proteins 

present in the soluble (for example, cytosolic) and particulate 

(for example, membrane) cell fractions of the bacteria 

grown under both oxic and anoxic conditions. Blue native 

gels were also used to separate individual proteins of 

membrane-bound complexes. Trypsin-digested samples were 

analyzed with matrix-assisted laser desorption/ionization 

time-of flight (MALDI-TOF) mass spectrometry. Proteins 

involved in aerobic respiration were identified in aerobically 

grown cells (for example, superoxide dismutase, catalase/
 

 

 

 

34 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

peroxidase I). Most of the Calvin cycle proteins (including 

RuBisCo) and nitrate reduction (for example, NarH) were 

identified in the anaerobic fraction. Interestingly, nitrousoxide reductase (for example, NosZ) was a prominent protein 

in the anaerobic fractions. In addition, the catalytic subunit, 

ArrA (designated Mlg_0216 in the annotated genome), of 

one of the two putative arsenate reductases (ArrDCBAB) was 

found. Activity assays were subsequently performed to locate 

potential arsenite oxidases. Blue native and sodium dodecyl 

sulfate-PAGE (SDS-PAGE) gels revealed that the same Arr 

homologue exhibited oxidase activity using either oxidized 

DCIP or methyl viologen, as well as arsenate reductase 

activity using reduced methyl viologen. Our results suggest 

that this “respiratory arsenate reductase” functions in reverse 

as the arsenite oxidase.

Tools and Techniques 

Flow Cytometry: An Essential Tool in Biomarker 

Research 

By Jill A. Jenkins,1 Bruce E. Eilts,2 and Rassa O. Draugelis-Dale1 

1

U.S. Geological Survey, National Wetlands Research Center, 700 

Cajundome Boulevard, Lafayette, LA 70506.

2

Department of Veterinary Clinical Sciences, Louisiana State University, 

Baton Rouge, LA 70803.

Gains in microbiological knowledge are led by 

technological advances. Flow cytometry (FCM) technology 

continues to expand through adaptations of new reagents 

and protocols. Multiple parameters are measured on cells 

and nuclei passing singly through a 488-nanometer (nm) 

laser beam. Data on cell size, light scatter, and specific stain 

emissions are collected and digitized for computer analyses. 

Typically, 10,000 to 100,000 cells are analyzed per sample 

(with replication) within 1.5 minutes. At the USGS National 

Wetlands Research Center, FCM is primarily applied to 

environmental studies with aquatic animals and amphibians 

to study sublethal stress manifested first at the suborganismal 

level (nuclei, cytoplasm, membranes, and extracellular 

fluids). Various biomarkers developed to quantify sublethal 

stress at these different levels of biological organization can 

be diagnostic and contribute to assessments of animal and 

ecosystem health.

Specific studies include those described below:

Immune System

• Research on surface glycoconjugates on the parasite 

(Perkinsus marinus) of the eastern oyster (Crassostrea 

virginica) to further understand pathogenic 

mechanisms. Life cycle changes were noted, similar to 

those in the malarial parasite.

• Investigation of hemocyte responses of the crayfish 

(Procambarus clarkii) as a nontarget species 

impacted by fipronil-coated rice. Noted reductions 

in intraneuronal chloride ions (excitability regulator) 

were similar to pathogen- or wound-induced responses.

Reproductive Success

• Assays for sperm quality (viability, mitochondrial 

function, cell counts, spermatogenic stage, DNA

integrity, and acrosome reactivity) from impacted 

watersheds included western mosquitofish (Gambusia 

affinis) from Sonny Bono Salton Sea National 

Wildlife Refuge and the Imperial Valley in southern 

California; smallmouth bass (Micropterus dolomieu) 

and yellow perch (Perca flavescens) from Chesapeake 

Bay; razorback suckers (Xyrauchen texanus) and 

common carp (Cyprinus carpio) from Lake Mead 

National Recreational Area and the lower Colorado 

River; and green swordtails (Xiphophorus helleri) 

from Oahu, Hawaii. Microscopic image analysis and 

computer-assisted sperm motion analysis (CASA) 

are two complementary tools used for sperm quality 

assessment.

Genetic Integrity

• Examination of possible links of DNA impacts with 

frog abnormalities. Cytogenetic traits of wood frogs 

(Lithobates sylvaticus) from Kenai National Wildlife 

Refuge, Alaska, were studied by measuring blood cell 

DNA integrity, caspase 3 enzyme (apoptosis indicator), 

and DNA repair kinase.

• Exploration of heritable genetic changes and 

embryonic abnormalities resulting from DNA

fragmentation in germ cells; these changes have been 

studied in many species.

Assessing change is central to understanding animal and 

aquatic ecosystem health and is germane to the management 

of their associated resources. The FCM technology has 

applications in a number of fields.
 

 

 

 

 

 

 

 

35 

USGS Interdisciplinary Microbiology Web Site: 

Marketing USGS Microbiology Expertise and 

Capabilities 

By Bernadette LeMasters1 

1

U.S. Geological Survey, 12201 Sunrise Valley Drive, Reston, VA

20192–0002.

For anticipating and meeting research needs, a Web 

presence for USGS microbiology can provide microbiologists 

with a globally accessible marketing tool for potential 

collaborators, resource management decisionmakers, and 

the general public. Web presence in a consolidated Web site 

could not only offer a comprehensive, “big picture” view of 

the species and science topics USGS microbiology covers, 

but also supply information distributed across the Web about 

the diversity of USGS scientists, research activities, science 

centers, publications, data, and available tools. This new Web 

presence could facilitate the interconnection of scientists 

with peers, leaders, and the public for greater collaboration 

opportunities and an improved understanding of the role of 

USGS microbiology in supporting the sound management of 

the Nation’s natural resources.

Application of Phospholipid Fatty Acids in the 

Evaluation of Post-Katrina Wetland Soils 

By JoAnn M. Holloway,1 Christopher Swarzenski,2 Ken Krauss,3 

and Thomas Doyle3 

1

U.S. Geological Survey, Crustal Imaging and Characterization Team, 

Denver Federal Center, Box 25046, Mail Stop 964, Denver, CO 80225–0046.

2

U.S. Geological Survey, Louisiana Water Science Center, 3535 South 

Sherwood Forest Boulevard, Baton Rouge, LA 70816.

3

U.S. Geological Survey, National Wetlands Research Center, 700 

Cajundome Boulevard, Lafayette, LA 70506.

The combined effects of Hurricanes Katrina (landfall 

Aug. 29, 2005) and Rita (landfall Sept. 24, 2005) resulted in 

a catastrophic loss of wetlands, with an estimated decrease 

of 562 square kilometers (km2) of land area (Barras, 2006) 

along the Louisiana coast of the Gulf of Mexico. A study was 

initiated following the 2005 hurricane season to characterize 

storm impacts on coastal marsh soils by measuring soil 

organic carbon, biogeochemistry of soil pore waters, and soil 

microbial communities using phospholipid fatty acids (PLFA). 

Areas selected for study include Caernarvon, which had the 

greatest land loss through Katrina, and the Barataria Preserve, 

a unit within the Jean Lafitte National Historical Park. Marshes 

ranged from freshwater to saline. PLFA concentrations were 

generally greater in surface soils (28–144 nanomoles of PLFA

per gram (nmol PLFA/g) dry soil at 0–5 centimeters (cm)) 

than in deeper soil (27–77 nmol/g at 10–15 cm; 18–20 nmol/g 

Tools and Techniques 

at 35–45 cm) for soils collected in March 2006. There was a 

notable exception to this trend. The concentration of PLFAs 

was greater at 15 cm (51 nmol/g) than at 5 cm (28 nmol/g) 

in a remnant salt marsh soil from Caernarvon. The ratio of 

17:0cy/17:0, a stress indicator, was greater at depths of 5 and 

15 cm for this soil (6.4 and 7.3, respectively) than in other 

soils collected in March 2006 (1.9–6.4 at 5 cm; 1.2–5.4 at 15 

cm). The inverted PLFA biomass and elevated 17:0cy/17:0 

ratio at this location may reflect disturbance from Katrina 6 

months after the storm. Differences in microbial community 

structure were noted between freshwater marshes and salt 

marshes, with a general decrease in PLFA concentrations with 

increasing salinity. A resampling of surface soil in September 

2007 showed an increase in PLFA concentrations (64–148 

nmol/g) and a decrease in 17:0cy/17:0 ratios (1.5–3.8). In 

addition, there were shifts in surface microbial communities, 

including an increase in a16:0 in freshwater marsh soils and 

an overall increase in 18:1ω9c, a biomarker for eukaryotic 

microorganisms, including algae and fungi. These shifts may 

reflect recovery in soil microbial communities 2 years after the 

landfall of Hurricane Katrina.

Reference Cited 

Barras, J.A., 2006, Land area changes in coastal Louisiana 

after the 2005 hurricanes—A series of three maps: U.S. 

Geological Survey Open-File Report 2006–1274, 3 oversize 

sheets, available at http://pubs.usgs.gov/of/2006/1274/.
 

 

 

 

 

36 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Breakout Session Outcomes, 

October 16, 2008 

Five working groups met in breakout sessions on October 

16, 2008, with goals as listed below:

• Working Group I: to plan a Fact Sheet on 

interdisciplinary microbiology in the USGS
 

• Working Group II: to plan a USGS interdisciplinary 

microbiology Web site

• Working Group III: to suggest ways to broadcast and 

publicize the types of microbiology conducted at the 

USGS

• Working Group IV: to identify emerging issues in 

USGS interdisciplinary microbiology research

• Working Group V: to identify potential opportunities 

for interdisciplinary microbiology work at the USGS

The highlights for each working group are summarized in 

table 1.

Working Group I: To Plan a Fact Sheet 

on Interdisciplinary Microbiology in 

the USGS 

The seven topical sections in the agenda highlight the 

different types of microbiology conducted within the USGS 

and showcase the multidisciplinary nature of our research. 

The task for Working Group I was to consider the topics 

within each section and develop an outline for a Fact Sheet 

that would showcase each of these sections. The goal was not 

to show each and every person’s research but to show general 

research areas that can be highlighted with a few specific 

USGS examples. A guide would be Fact Sheet 2006–3108, 

“Conservation Genetics in the USGS” (Jacobs and others, 

2006). The purpose of an interdisciplinary microbiology Fact 

Sheet would be to provide an overview of our microbiological 

activities for those groups that would use it (customers, 

collaborators, and the public). It is important to list single 

discipline contacts at the end of the Fact Sheet and their email 

addresses and to note that these are the people who could 

provide more information.

Working Group I members.—Jay Hestbeck, Andrea 

Foster, Ean Warren, Don Stoeckel, Chris Ottinger, Richard 

Smith, Jennifer Underwood, Deborah Repert, JoAnn 

Holloway, David Blehert, Lee De Cola

Microbiology in the USGS, theme of Fact Sheet.—

USGS microbiologists conduct prominent, interdisciplinary 

microbiology research encompassing viruses, bacteria, 

protozoa, and fungi relevant to central issues facing society 

today. Leading scientists conduct research spanning 

disciplines including wildlife health and disease, microbial 

ecology, public health and water quality, geomicrobiology, and 

ecosystem function.

Wildlife and Fish Disease 

(Wording excerpted from the conservation genetics 

Fact Sheet:) Infectious disease is a natural component of all 

ecosystems, affecting the health and abundance of terrestrial, 

aquatic, and marine animals. Understanding the role of 

microbes (pathogens) causing these diseases enables managers 

to adopt strategies to mitigate their influence when necessary. 

Disease control can be particularly urgent in situations where 

pathogens alter wildlife population structures or functions 

within an ecosystem. In general, we strive to understand 

disease processes, develop diagnostic methods, describe 

incidence and distribution of significant pathogens, and 

develop strategies for prevention and control.

Examples.—Bat white-nose syndrome; disease impacts 

on wild marine fish

Other examples.—Epidemiology and evolution of 

rhabdoviruses in fish; North American avian flu surveillance; 

ecology and pathogenicity of Avipoxvirus and malaria in 

Pacific Island birds; mycobacteriosis in Chesapeake Bay; 

studies on monkeypox pathogenesis in rodents using in vivo 

imaging; role of wild rodents in environmental transport of 

prions; microbiology in marine wildlife disease

Wildlife and fish disease contact on Fact Sheet.—David 

Blehert, dblehert@usgs.gov

Microbial Ecology 

Microbial ecology addresses the interaction of 

microorganisms with the environment. Microbes are 

ubiquitous in the environment, thriving in aquatic, 

atmospheric, and terrestrial settings. Microorganisms perform 

essential functions in these ecosystems, including microbes 

nutrient (carbon and nitrogen) cycling, organic matter 

decomposition, and contaminant degradation. Ecosystem 

health depends on symbiosis between microorganisms and the 

plant community.

Examples.—Endosymbiotic fungi in plants and their 

ecology and implications for climate change; soil crusts 

and their importance to prevention of desertification, 

ecosystem services, carbon sequestration, and water-quality 

improvements

Other examples.—Microbiology of deep-sea corals; 

chromatography for microbial analysis; soil community 

dynamics in sagebrush steppe and cheatgrass-invaded areas of 

the northern Great Basin

Microbial ecology contact on Fact Sheet.—Nicole 

DeCrappeo, ndecrappeo@usgs.gov
Table 1. Summary of breakout session outcomes from Working Groups I–V. [Detailed notes for each group are in the text, where acronyms are defined]

Working group number 

and mission Suggested products Topics 

I, To plan a Fact Sheet Fact Sheet Fact Sheet should contain examples of USGS microbiology in the following areas: Implement 

on interdisciplinary • Wildlife and fish diseasemicrobiology in the • Microbial ecologyUSGS • Geographic patterns/visualization

• Public health and water quality• Geomicrobiology• Ecosystem function 

II, To plan a USGS Interdisciplinary Web page A survey taken by workshop participants to determine Web page emphasis Highly suc

interdisciplinary indicated the following four highest ranking areas: Web pagmicrobiology Web site • Educate public about USGS microbiology and how it applies to national See http

priorities such as health and resource management

• Provide information about the diverse expertise of USGS microbiologists 

and include contact information

• Provide links to USGS centers with microbiology expertise and (or) 

laboratories

• Display USGS publications about USGS microbiology

III, To suggest ways List of suggested broadcast • Broadcast: Web site; Fact Sheet; posters • We

to broadcast and avenues • Notify of capabilities: other DOI Bureaus, NOAA, State Department, • Popublicize the types USAID, EPA, USDA, DOD, State and local governments, NGOs meof microbiology • In all media, include appropriate USGS microbiologist’s contact • Weconducted at the information FeUSGS • Consider: development of environmental microbiology course; conducting 

USGS science meeting; accepting graduate students

IV, To identify emerging Identification of emerging Priorities: • Pa

issues in USGS issues in microbiology • Technology and tools ag

interdisciplinary and ways to remain • Wildlife and ecosystem health • Whmicrobiology research relevant and cutting edge • Basic and applied research inc

• Environmental impacts of energy and resource development lev• Environmental impacts on human and ecological health • Co• Skill set needs including new scientists and highly skilled and trained seq

biological technicians

V, To identify potential Identification of challenges, • Identify opportunities for interdisciplinary work • Re

opportunities for opportunities, and • Consider impediments including cost differences between disciplines po

interdisciplinary impediments to (salaries and overhead) opmicrobiology work at interdisciplinary research • Address funding issues and recommend dedicated funding, nontargeted dis

the USGS money for integrated science efforts

• Develop advisory group to address impediments and develop strategy to 

encourage interdisciplinary approach
 

 

38 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Geographic Patterns/Visualization 

Geographic science contributes to microbiology in 

four ways. (1) All scientific data should have a spatial and 

temporal component so that they can be organized and 

integrated. Geography offers key tools for this integration. 

(2) The production of useful visualizations of scientific data 

allows USGS scientists to understand spatial and temporal 

patterns. These visualizations can benefit from well-developed 

cartographic and information architecture. (3) Spatial 

analysis uses fundamental concepts of geographic science 

to test hypotheses about spatial patterns, interactions among 

processes, and forecasts of future states. (4) Finally, through 

the exploration of scale, geography is helping biologists 

develop new ways of understanding regional health not only 

as the states of organisms but as the application of clinical 

principles (homeostasis, resilience, diversity) to the welfare of 

regions such as islands, watersheds, and even ecoregions.

Example.—Public health and geospatial distribution 

(mapping vector-borne human diseases such as Lyme disease, 

plague, West Nile virus, H5N1 avian influenza)

Other examples.—Microbial mapping: stimulating 

hypothesis and informing the public; medical geography: 

multiscale insights on the health of regions; identification 

of human plague risk: the importance of habitat diversity 

measures

Geographic patterns/visualization contact on Fact 

Sheet.—Lee De Cola, ldecola@usgs.gov

Public Health and Water Quality 

Our population relies upon clean water for drinking and 

recreation. Microbiological risks to water quality include 

(un)sanitary waste, fecal contamination from domesticated 

animals and wildlife, and proliferation of pathogens and 

toxin-producing cyanobacteria in the environment. The USGS 

addresses these issues through monitoring fecal-indicator 

bacteria, pathogens, and cyanobacteria. USGS scientists 

also work to improve tools such as real-time modeling of E. 

coli concentrations at beaches, to develop and validate rapid 

methods for beach monitoring, to improve our understanding 

of the fate and transport of pathogens, and to apply new tools 

such as fecal source tracking to management of water quality 

for the protection of human health.

Examples.—Rapid methods for beach health models; 

harmful algal blooms

Other examples.—Pathogens and antibiotic-resistant 

bacteria in the environment; bacterial source tracking; 

transport of microbes in the subsurface/physical interactions of 

microbes and particles; flow cytometry in microbiology

Public health and water-quality contact on Fact Sheet.—

Richard L. Smith, rlsmith@usgs.gov

Geomicrobiology 

Geomicrobiology is the study of interaction of microbes 

with physical processes in soils, surface water and ground 

water, ice, and the deep subsurface (for example, caves and 

underground mines). Microbes are Earth’s earliest living 

organisms. The earliest microbes in all likelihood utilized 

inorganic compounds exclusively for all life functions. 

Microbes have since evolved to fill all ecological niches, but 

these earliest life strategies are still important in the modern 

Earth. USGS scientists are studying the mechanisms by which 

microbes are involved in the cycling and transformation of 

potentially toxic trace elements such as arsenic, chromium, 

mercury, selenium, and tellurium; in the breakdown of 

silicate and sulfide minerals in soils and mining wastes; in the 

utilization of inorganic carbon compounds such as methane; 

and in the stabilization of desert soils. Research sites include 

the deep subsurface, extreme saline lakes, mining-impacted 

sites, wetlands, and arid lands.

Examples.—Geomicrobiology/nanoscience of toxic 

elements As, Se, and Te; microbial methylation of mercury

Other examples.—Geomicrobiology of weathering; using 

natural abundance δ13C and ∆14C values of phospholipid fatty 

acids to characterize bacterial carbon cycling pathways in 

deep aquifers; geochemical controls on microbial methylation 

of mercury in the Florida Everglades; microbial influence on 

sulfide and weathering

Geomicrobiology contact on Fact Sheet.— Mark C. 

Marvin-DiPasquale, mmarvin@usgs.gov

Ecosystem Function 

Microbes and microbially mediated processes impact 

nutrient and material flux and transport, energetics, and 

diversity of ecosystems and ecosystem dynamics. These 

processes include human-derived changes at global and 

local levels, microbial responses to these changes, and 

ecosystem-ecosystem interactions such as transport of 

microbially derived products from terrestrial to oceanic or 

freshwater environments. Ecosystem scale can range from 

soil and subsurface pores to ecotone, oceanic, and continental 

perspectives.

Examples.—Biogeochemistry of mountain watersheds, 

evaluating ecosystem function with integrated approaches in 

environmental microbiology, ecosystem service markets, and 

carbon sequestration

Other examples.—Tale of disappearing toads: The 

amphibian chytrid fungus in the Rocky Mountains; natural 

and enhanced bioremediation of nitrate contamination in 

groundwater; microbial communities and carbon cycling in 

response to global change; microbial genetics in groundwater 

models

Ecosystem function contact on Fact Sheet.—JoAnn 

Holloway, jholloway@usgs.gov
 

 

 

 

 

 

 

Working Group II: To Plan a USGS Interdisciplinary Microbiology Web Site 39 

Reference Cited 

Jacobs, Ruth, Haig, Susan, Talbot, Sandy, Winton, James, 

King, Tim, and Kendall, Kate, 2006, Conservation genetics 

in the USGS: U.S. Geological Survey Fact Sheet 2006–

3108, 4 p., available at http://pubs.usgs.gov/fs/2006/3108/.

Working Group II: To Plan a USGS 

Interdisciplinary Microbiology Web 

Site 

Ms. Bernadette LeMasters, USGS Bioinformatics, 

led the breakout session for Working Group II (fig. 1). The 

purpose of this group was to develop ideas on the creation of 

an interdisciplinary microbiology Web site, if funding were to 

become available. Ms. LeMasters had a prototype available 

as a strawman to give the group a starting point from which 

to work. The group was asked to address the following during 

the discussions:

• Define target audiences

• List known customers

• List potential customers

• Discuss titles of the different general microbiology 

categories and the types of research that might fall 

under each

• Discuss sample projects that could be highlighted

Moderator’s Notes on Focus Group To 

Discover Attitudes, Beliefs, and Desires for an 

Interdisciplinary Microbiology Web Site and 

Reactions to a Prototype 

Introduction 

Six USGS scientists with experience or expertise in 

microbiology were assigned to develop ideas for a potential 

interdisciplinary microbiology Web site. With assistance 

from moderator Bernadette LeMasters, the group members 

discussed their information needs and their reactions to a 

mockup Web site, version 1.

Following is a compilation of the notes the moderator 

took during the focus group discussion. Despite the 

organization of the notes into topics, the discussion itself 

was loosely structured and moved fluidly from topic to 

topic. Without prompts from the moderator to focus on 

particular issues, the loose structure often revealed the 

depth of knowledge that respondents had about Web sites. 

Without prompting, respondents identified their information 

Figure 1. Moderator and members of Working Group II. 

Moderator: Bernadette LeMasters, National Biological 

Information Infrastructure (standing, top right). Group members, 

counterclockwise from top right: Joseph E. Bunnell, Geology 

Discipline, Eastern Energy Resources Team, Reston; 

Margo D. Corum, Geology Discipline, Eastern Energy Resources 

Team; Patricia Dick, Biological Resources Discipline, 

Headquarters; Gael Kurath, Biological Resources Discipline, 

Western Fisheries Research Center; Christina Kellogg, Geology 

Discipline, Florida Integrated Science Center; Sandra S. Embrey, 

Water Resources Discipline, Washington Water Science Center; 

Christopher Mills, Geology Discipline, Denver Federal Center. 

Photograph by Cheryl W. Caldwell, USGS. 

needs, explained keyword search terms that would indicate 

Web site success, identified the costs and benefits of the 

mockup interface for retrieval of information, and referred 

to other USGS Web sites as models. The notes from these 

discussions are compiled for the benefit of future Web site 

developers within categories of relevance to creating a USGS 

interdisciplinary microbiology Web site.

Outline of the Discussion 

1.	 Welcome

2.	 Moderator explained who she is and her purpose as a 

moderator

3.	 Assigned timekeeper

4.	 Asked respondents how they would like to proceed: 

take a survey, view past National Biological Information 

Infrastructure (NBII) projects, view related microbiology 

Web sites, or view the mockup? Participants decided on 

first viewing the mockup (figs. 2, 3, 4).

5.	 Passed out hard copies of the mockup pages

6.	 Took notes as participants give their views
 

 

40 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Figure 2. Mockup (version 1) of USGS interdisciplinary microbiology Web site—Home page. After the workshop, the draft Web site 

was updated and activated at http://microbiology.usgs.gov/. 

7.	 When timer called 30 minutes, passed out the survey 

about the top goals for the site

8.	 Reviewed points on chart paper

9.	 After another 30 minutes, closing questions: Would 

making a mockup site be worthwhile?

10. Statement of thanks for participating

Materials 

• Survey

•	 This survey asked participants to complete the 

statement “A USGS interdisciplinary microbiology 

Web site should do the following:” by checking 

“Strongly Agree,” “Agree,” “Disagree,” “Strongly 

Disagree,” or “No opinion” next to a list of 

predefined goals. Respondents were instructed to 

complete the survey individually and silently and 

were encouraged to add their own comments or 

notes.

• Hard copies of Web site mockup version 1 [After 

the workshop, the draft Web site was updated and 

activated at http://microbiology.usgs.gov/.]

Part I: General Goals for a USGS Microbiology Web Site 

Introduction 

Defining the purpose of a Web site is a critical first 

step to creating a site that is successful and useful. The 
Working Group II: To Plan a USGS Interdisciplinary Microbiology Web Site 41 

Figure 3. Mockup (version 1) of USGS interdisciplinary microbiology Web site—Research activities page. 

following are the ideas, suggestions, and responses of focus 

group participants related to the goals and needs for a USGS 

microbiology Web site. Combined are comments made during 

more loosely structured parts of the discussion, as well as 

responses to a survey each participant was asked to complete 

individually.

Information Needs 

• Knowing what others in USGS are doing in 

microbiology [noted by one respondent as the greatest 

benefit of the workshop itself]

• Knowing who is in my discipline related to 

microbiology—a list of everyone [One respondent 

explained he or she was once asked for this 

information and used Google to search for names.]

• Knowing the capabilities of different USGS 

laboratories. When a certain expertise is needed, say 

for a special technique, it is cost-effective to work 

with a laboratory that already has the expertise and 

equipment. However, there is no easy way to know 

which USGS facilities have a needed expertise. [One 

respondent further explained that he or she used 

journal article searches to find the best person/lab 

available.]

Expectations, Requirements, and Preferences 

• Top search engines find the Web site within the first 

page using the key terms “Federal microbiology 

research.” [One respondent said: “No one will search 

‘USGS microbiology.’”]
42 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Figure 4. Mockup (version 1) of USGS interdisciplinary microbiology Web site—Page of microbiology scientist profiles. 

• Web sites to model: Ohio Water Science Center 

and how it shows the center’s capabilities; Florida 

Integrated Science Center Web site and how it 

organizes each discipline by tabs

Survey Identifying Web Site Goals 

Respondents were asked to finish the statement “A

USGS interdisciplinary microbiology Web site should do the 

following:” and check whether they strongly agreed, agreed, 

disagreed, or strongly disagreed with, or had no opinion 

about, a list of predefined goals (table 2). The following four 

goals received “Strongly agreed” or “Agreed” from every 

participant.

1.	 Educate the public about USGS microbiology and how it 

applies to national priorities such as health and resource 

management

Comments: (1) Make sure Web page is designed with 

USGS science strategy in mind; (2) Yes, but mostly by 

linking to other sites like ASM’s [American Society 

for Microbiology’s] Microbe World; (3) Two most 

important goals [Respondent drew a line between 

“Educate the public” goal and “Provide information 

about the diverse expertise” goal]

.	 Provide information about the diverse expertise of USGS 

microbiologists (e.g., name, title, contact information, and 

links to project pages)

Comments: (1) Two most important goals [Respondent 

drew a line between “Educate the public” goal and 

“Provide information about the diverse expertise” goal]

.	 Provide links to USGS centers with microbiology 

2

3

expertise and (or) laboratories
Working Group II: To Plan a USGS Interdisciplinary Microbiology Web Site 43 

Table 2. Results of a survey about the proposed USGS interdisciplinary microbiology Web site. 

[At the workshop held in October 2008, a survey was conducted of the members of Working Group II; members chose the options below in completing the 

statement: A USGS interdisciplinary microbiology Web site should do the following: ...]

No. Goal Strongly 

agree Agree Disagree Strongly disagree No opinion 

1. Educate the public about USGS microbiology and 

how it applies to national priorities such as health 

and resource management

5/6 1/6 -- -- --

2. Educate the public about basic microbiology 1/6 3/6 1/6 1/6 --

concepts

3. Show potential partnering scientists the relatedness 

of other science topics, such as ecosystem 

function, to USGS microbiology

3/6 2/6 1/6 -- --

4. Provide information about the diverse expertise of 

USGS microbiologists (e.g., name, title, contact 

information, and links to project pages)

5/6 1/6 -- -- --

5. Display USGS news releases and broadcasts about 

USGS microbiology

3/6 2/6 -- -- 1/6

6. Display links to USGS microbiology data sources 

such as the National Water-Quality Assessment 

(NAWQA) Program and Wildlife Disease 

Information Node (WDIN)

2/6 3/6 1/6 -- --

7. Display USGS publications about USGS 

microbiology

5/5 -- -- -- --

8. Display future and past meetings, discussion 

groups, and conferences of interest to USGS 

microbiologists

-- 3/6 1/6 -- 2/6

9. Display for other scientists how-to materials about 

microbiology techniques such as rapid detection 

methods

2/6 1/6 2/6 -- 1/6

10. Provide links to USGS centers with microbiology 

expertise and (or) laboratories

5/6 1/6 -- -- --

11. Provide links to related Web sites about 

microbiology from U.S. agencies

-- 4/6 2/6 -- --

4.	 Display USGS publications about USGS microbiology

Comments: (1) [5/5 Strongly agreed, but one 

participant did not respond: “Not sure what you mean 

by display—links to pdf files? Journal articles”]; (2) 

For the most part provide links to pubs, methods, 

etc. only if published. If the material is not published 

contact info should be provided; (3) Searchable by 

scientist; (4) Don’t duplicate—don’t want to update ten 

pages on the Web about my publications

The following goals also are from the survey but received 

mixed responses. The goals are ordered highest to lowest after 

responses were weighted.

1.	 Display USGS news releases and broadcasts about USGS 

microbiology

2.	 Show potential partnering scientists the relatedness of 

other science topics, such as ecosystem function, to USGS 

microbiology

Comments: (1) Show potential partnering scientists 

(job seekers) what USGS has to offer in microbiology; 

(2) Yes, but indirectly, by showcasing the research 

rather than spelling it out

3.	 Display links to USGS microbiology data sources such 

as the National Water-Quality Assessment (NAWQA) 

Program and Wildlife Disease Information Node (WDIN)

4.	 Display for other scientists how-to materials about 

microbiology techniques such as rapid detection methods

Comment: (1) Yes, methods section and an equipment/

technique list so you know where to go
 

 

 

 

 

44 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

5.	 Educate the public about basic microbiology concepts • 

Display future and past meetings, discussion groups, and 

conferences of interest to USGS microbiologists • Provide 

links to related Web sites about microbiology from U.S. 

agencies [Three goals having similar weights.]

Comments: (1) Ok, but of minor importance [in 

reference to “Display future and past meetings” goal]; 

(2) Yes, but again, minor component [in reference to 

“Provide links to related” goal]

Part II: Responses to the Mockup Version 1 

Offering a prototype is often one of the best ways to 

generate feedback and check whether Web designers are on 

the right track. The following are responses from focus group 

participants to hardcopies of the USGS interdisciplinary 

microbiology Web site mockup version 1. The prototype also 

was made available online; after the workshop, the draft Web 

site was updated and activated at http://microbiology.usgs.

gov/.

Home Page (fig. 2) 

• Keep research activities as the main focus of the home 

page

• Thumbnail image menu should stay; makes scanning 

easy

• Change research topics to:

•	 Climate Change

•	 Ecosystem Function

•	 Geographic Patterns

•	 Geomicrobiology

•	 Human Health (simply “Health” is too general—say 

“Human”)

•	 Microbial Ecology

•	 Water Quality (to include Monitoring Programs, 

Recreational Health, and Drinking Water)

•	 Wildlife Disease (“Wildlife” naturally is understood 

to include foxes, deer, etc. To include fish and coral, 

have the photo thumbnail depict fish over coral. 

After clicking on the thumbnail, have subcategories 

for terrestrial, invertebrates, aquatic)

Navigation 

• “Scientists” in the left-hand navigation: you assume 

that you will reach a list of people from USGS 

microbiology. Would be helpful to someone who 

knows whom they are looking for.

• “Methods and Techniques” may or may not belong 

separate from research

Research Activities (fig. 3) 

• Lists are difficult to navigate; instead, have general 

information about research activities, then underneath 

a thumbnail menu that shows research topics

• Looks like a site map; listings such as this should be in 

a separate “Site map” page

• Be sure to list projects under all possible categories so 

as not to miss a project because of poor sorting

Microbiology Scientist Profiles (fig. 4) 

• List the following for each scientist:

•	 Name

•	 Research

•	 Facility

•	 Discipline. List this last, if at all, for the following 

reasons:

•	 A poor reflection of expertise (a person in 

“Geology” is not necessarily a geologist)

•	 Further divides the scientists when the site should 

be “interdisciplinary”

•	 If included, have this deemphasized, perhaps with 

abbreviations

Working Group III: To Suggest Ways To 

Broadcast and Publicize the Types of 

Microbiology Conducted at the USGS 

Working Group III was charged to consider several 

things, including how to broadcast and publicize more broadly 

the different types of microbiology conducted at the USGS. 

It would be useful to understand and have a good idea of 

how people should be notified and who should be notified of 

USGS work and techniques, methodologies, and products we 

can provide. This group was charged with coming up with the 

names of organizations, Federal and State agencies, and other 

groups that would have needs for USGS skills and services 

and that would be in a position to spread the word about our 

capabilities. It was also recommended that the group provide 

actual contact information of individuals in these suggested 

groups if they had contact information.
Working Group III: To Suggest Ways To Broadcast and Publicize the Types of Microbiology Conducted at the USGS 45 

Microbiology Workshop 

Breakout Session Recommendations 

Group III Chart Notes 

Questions: 

• How should we broadcast/publicize the different types 

of microbiology conducted at the USGS?

• How should people be notified and who should be 

notified of our work/products, etc.?

• What are names of organizations (State, Federal, NGO 

[nongovernmental organization], etc.) that would be in 

a position to spread the word?

• What is the contact information for these 

organizations?
 

How should we broadcast/publicize? 

• Web site

• Fact Sheet/posters/newsletter

• DOI (Department of the Interior) Highlight

• ASM/ASV (American Society for Microbiology, 

American Society for Virology)—become player 

within professional societies

• ISSM (International Society for Subsurface 

Microbiology)
 

Who should be notified of our work/products? 

• NPS (National Park Service)

• FWS (U.S. Fish and Wildlife Service)

• USDA (U.S. Department of Agriculture)

• EPA (U.S. Environmental Protection Agency)

• NAS (National Academy of Science)

• DOI (U.S. Department of the Interior)

• DOD (U.S. Department of Defense)

• BLM (U.S. Bureau of Land Management)

• NOAA (National Oceanic and Atmospheric 

Administration)
 

• CDC (Centers for Disease Control)

• State Department/USAID (U.S. Agency for 

International Development)
 

• USGS (U.S. Geological Survey)

What are names of organizations that would be in a 

position to spread the word? 

• States/environment/health

• Local government

• NGO (nongovernmental organizations)

• TNC (The Nature Conservancy)

• TWS (The Wildlife Society)

• Audubon

• AFWA (Association of Fish and Wildlife Agencies)

• Conservation International

• SI (Smithsonian Institution)

• CGIAR (Consultative Group on International 

Agricultural Research)

• Gates Foundation

• Rockefeller Foundation

• UNESCO (United Nations Educational, Scientific and 

Cultural Organization)

• UNEP (United Nations Environment Programme)

• Environmental journals

• NEON (National Ecological Observatory Network)

How should we acquire contact information? 

• Ask for specific names in email distribution to ensure 

information is received by appropriate contact

• In-person presentations

• Micro-day/conference

• Science tube

• Pod cast

• Educational materials

• National research project

• Environmental journalist

Additional suggestions: 

• Environmental micro course

• Graduate students

• Open access

• DVDs

• Develop identity/logo

• USGS science meeting/Need to know what everyone 

else is doing
 

 

 

46 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Working Group IV: To Identify Emerging 

Issues in USGS Interdisciplinary 

Microbiology Research 

Working Group IV was to consider what emerging 

microbiology issues and technologies will be facing USGS 

microbiologists in the near future. Where should we be 

headed to remain relevant and cutting edge? How can these 

suggestions help define our next steps to take after this 

workshop ends?

Members: Carter Atkinson, Matthew Bachmann, 

Muruleedhara Byappanahalli, Brian Cole, Nicole DeCrappeo, 

Jeffrey Hall, Bane Schill, Mark Stanton, Erin Stelzer, Bruce 

Taggart, Mark Waldrop.

Priority 1 – Technology and Tools 

• Remote sensing

• Geographic information systems

• Spatial-temporal models

• Deployable sampling analysis

• Bio-indicators to identify and analyze environmental 

change

• Microbial biodiversity in soils

• Next generation of microbiology including analytical 

technology

• Early detection of biological agents for homeland 

security

Where should we be heading to remain relevant and cutting 

edge?

• Leverage existing resources and partner up with other 

agencies and private companies to develop and ground 

truth these technologies

Resource needs:

• The introduction of new scientists (engineers, 

biochemists) with appropriate skills and experience on 

a continual basis

• Highly skilled and trained biological technicians

• Commitment to ongoing professional training and 

development

• Up-to-date analytical equipment, supplies, and 

facilities

Priority 2 – Wildlife and Ecosystem Health 

• Emerging zoonotic diseases

• How to manage invasive species and pathogens

Where should we be heading to remain relevant and cutting 

edge?

• Wildlife disease surveillance is a key to early detection 

of problems in ecosystems. This activity needs to be 

supported.

• USGS must partner up with other agencies and 

organizations to exploit its niche and complement 

partner agency missions that will enhance our ability 

to detect and manage disease. This includes, but is not 

limited to, development of new diagnostic technologies 

and assessment of invasive issues in terrestrial and 

aquatic (freshwater and marine) systems.

• We need to not only identify new threats, but also 

determine how they will be addressed. USGS must 

partner with other agencies and NGOs to develop 

creative approaches to managing and controlling 

adverse effects of invasive organisms.

• In order to address invasive issues on a timely basis, 

USGS needs to be more nimble and be able to shift 

priorities and resources as needed.

Resource needs:

• Stable funding for wildlife disease surveillance. While 

not necessarily sexy, this is the best way to enhance 

our ability to detect problems early before they become 

difficult to address or out of control.

• The introduction of new scientists with appropriate 

skills and experience on a continual basis

• Highly skilled and trained biological technicians

• Commitment to ongoing professional training and 

development

• Up-to-date analytical equipment, supplies, and 

facilities

Priority 3 – Basic and Applied Research 

• Functional genomics

• Metagenetics

• Proteomics

• Metabolomics

• Drug discovery

• Extremophiles

Where should we be heading to remain relevant and cutting 

edge?

• Integrate genomics, metabolomics, proteomics, and 

microbiome to understand small- and large-scale 
Working Group IV: To Identify Emerging Issues in USGS Interdisciplinary Microbiology Research 47 

processes in biogeochemistry, disease, and ecosystem 

health on a nano to tera scale

• Apply our capacity for microbiology in novel uses such 

as biochips, drug discovery, or energy generation. This 

application would require USGS partnering with other 

governmental organizations and industry.

Resource needs:

• Commitment to ongoing professional training and 

development

• Biochemists

• Highly skilled and trained biological technicians

• Soil microbiologists

• Computational biologists (with associated computing 

power)

• Distributed computing capability

• Sufficient dedicated laboratory space

Priority 4 – Environmental Impacts of Energy and 

Resource Development 

• Microbiological applications to address energy 

development and mineral extraction impacts

• Carbon capture

• Linked microbiological, geochemical, and hydrologic 

impacts of injecting supercritical CO2

 for geologic 

carbon sequestration

Where should we be heading to remain relevant and cutting 

edge?

• Study the capture or release of CO2 through microbial 

responses to climate change at Arctic latitudes

• Conduct investigations to evaluate effects on microbes 

if CO2

 is injected or ejected

• Determine and evaluate methods to extract carbon out 

of waste streams

• Contribute to other governmental agency efforts

• Study effects of carbon sequestration on 

microbiological communities in subsurface, wetland, 

and forested ecosystems and how those community 

changes may in turn affect sequestration

• Evaluate environmental impact of mineral extraction 

technologies on microbial communities (tar sands, gas 

extraction, metals, etc.)

Resource needs:

• The introduction of new scientists with appropriate 

skills and experience on a continual basis

• Highly skilled and trained biological technicians

• Commitment to ongoing professional training and 

development

• Up-to-date analytical equipment, supplies, and 

facilities

• Improvements to existing USGS software to 

accommodate the unique physical and microbiological 

aspects of CO2 sequestration; for example, linking 

PHREEQC to SEAWAT

Priority 5 – Environmental Impacts on Human and 

Ecological Health 

• Emerging contaminants

• Impacts of nanotechnology on the environment

Where should we be heading to remain relevant and cutting 

edge?

Continuing research on emerging contaminants:

• Pharmaceuticals

• Hormones

• Personal care products

• Antimicrobial agents

• Industrial effluents

• Landfill capacity

• Metals

• Pesticides and fertilizers

Continuing research on impacts of nanotechnology on the 

environment:

• Nanotech impacts on biological systems
 

Continuing research on both:
 

• Biotechnology cooperative research with industry

• Unintended consequences

Resource needs:

• The introduction of new scientists with appropriate 

skills and experience on a continual basis

• Highly skilled and trained biological technicians

• Up-to-date analytical equipment, supplies, and 

facilities
 

 

 

 

48 Proceedings, USGS Interdisciplinary Microbiology Workshop, October 15–17, 2008 

Final Thoughts 

Knowledge information needs to effectively promote 

emerging issues

Recommended scientist actions:

• Educate ourselves about USGS Communications 

Office resources, capabilities, and contacts in order to 

communicate scientific results to our partners and the 

general public

• Work together with managers in presenting USGS 

science to Congressional Members on the Hill in 

order to most effectively increase their awareness and 

appreciation of the relevance of USGS science

• Identify and more effectively leverage USGS 

microbiological scientific capabilities, expertise, and 

resources in collaboration with one another and with 

outside partners

• Increase peer-to-peer communications to reduce 

duplication and cost and maximize research effort. In 

other words, leverage existing USGS microbiological 

resources more effectively.

 Recommended organizational actions:

• Develop one funding business model that benefits 

all scientists and disciplines and facilitates broad 

interdisciplinary collaboration throughout the USGS

• Have managers require less administrative work by 

scientists, thus allowing a greater focus on research by 

scientists

• Find ways to streamline and minimize overhead costs 

at all levels of the organization to maximize available 

science funding in the USGS

• Work with scientists in developing greater highthroughput analytical capacity

• Recognize the need to solve problems/issues of our 

partners to remain relevant

• Managers need to listen to and trust our scientists 

in identifying and developing future microbiology 

science needs and issues. Through peer-to-peer 

interactions, our scientists understand microbiology 

science needs and issues.

• Develop better top down/bottom up communication 

between scientists and managers. For example, 

managers (headquarters, regions, areas, and programs) 

attend many internal and external meetings throughout 

the year; very seldom do they report to scientists on 

the issues and opportunities they hear about, nor do 

scientists see any tangible benefits (such as funding) 

from these efforts.

• Encourage microbiological researchers and managers 

to work together in presenting USGS science to 

Congressional Members on the Hill in order to most 

effectively increase their awareness and appreciation of 

the relevance of USGS science

• Identify and more effectively leverage USGS 

microbiological scientific capabilities, expertise, and 

resources that other governmental agencies don’t 

possess

Working Group V: To Identify Potential 

Opportunities for Interdisciplinary 

Microbiology Work at the USGS 

The task of Working Group V was to identify potential 

opportunities for interdisciplinary work. The ideas could 

include general topics to specifics. The group was to identify 

impediments and enhancements for interdisciplinary 

microbiology to work at the USGS. How can we 

encourage interdisciplinary microbiological research? Are 

interdisciplinary microbiology projects useful?

Questions: 

• What are potential opportunities for interdisciplinary 

work?

• What are the impediments and enhancements?

• How can we encourage interdisciplinary research?

• Are interdisciplinary projects useful? Yes 

Impediments: 

• Funding challenges; for example, the Water Resources 

Discipline (WRD) is difficult to work with because of 

cost (salaries, overhead)

• Leadership is unaware of what is happening in the field

• Want leadership to recognize “good” interdisciplinary 

work

• Need more face time with each other

• Need dedicated funding

• It’s about effective communication, collaboration, and 

funding
Working Group V: To Identify Potential Opportunities for Interdisciplinary Microbiology Work at the USGS 49 

Recommendations:
	

How can we encourage interdisciplinary research?
	

Clarify term “interdisciplinary”:

• Identify what defines interdisciplinary

• Foster awareness of others

Meetings/information sharing/networking:

• Host scientific meetings routinely or biannually 

(include field trips)

• Regional meetings can occur more frequently

• Biannual national meetings

Create a virtual community to link other USGS groups 

together to include:

• Wiki sites

• Web sites

• Chat room

• Sponsor webinars

• Roster/listing of who’s who and what technology is 

available

• Incorporate Face Book and (or) Community of Practice 

technology (from Cheryl)

• Video conferencing: we need an effective way to find 

out what others are doing

• Incorporate technology that will allow folks to have 

access 24 hours

• Ensure leadership/decisionmakers are connected to this 

technology as well

Funding:

• Finance people’s efforts (especially in Water Science 

Centers)

• Need dedicated funding

• Have nontargeted money for integrated science efforts

Highlight:

• Identify what interdisciplinary microbiology projects 

have worked

• Use their success as a model

• Encourage interdisciplinary meetings with other 

disciplines outside of microbiology where this 

information can be shared.

• Challenge: Beware of meeting burnout

Web site:

• Set up Web site

• Survey groups who are working in microbiology and 

build a resource list

• Include who has what technology

• Create a wiki site

Advisory group:

• Recommend creating an advisory group to address 

the impediments and develop strategy to encourage 

interdisciplinary research

• Recognize some impediments need to be addressed 

top-down, collaboration bottom-up

• Establish a email list and have conference calls on 

science-related areas

Leadership awareness/involvement:

• Important for leaders to have access and utilize these 

“virtual networks”

• Need for them to know internal capabilities

• Need leadership to be involved in communication loop

• Need a liaison to find a way to get information to the 

top and make aware of the impediments

• Communication needs to go through center to region to 

headquarters

Internal/external funding and opportunities:

• Remember collaboration not just internal

• Look for internal and external opportunities to help 

microbiology to get funding

• Hire staff whose specific function is to find external 

funding opportunities




     

Briggs, K.M., ed.—Proceedings, USGS Interdisciplinary Microbiology Workshop, Estes Park, Colorado, October 15–17, 2008—SIR 2010–5146 

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