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Geomicrobiology

Researchers investigate how microbes interact with the nonliving parts of Earth such as soils, sediment, and atmosphere.

Microbiology

Mercury

Browse samples of USGS research about geomicrobiology and mercury. For related links, see Related Links and References at the bottom of page.

Collaborators Karen Merrit and Aria Amirbahman setting up experiments at Penobscot Estuary. Photo credit: Celia Chen

Cycling of Mercury in Estuarine Sediments (Voytek)

Dave Krabbenhoft and George Aiken sampling a cypress swamp slough channel near Blind River, Louisiana. Photo Credit: Dennis Demcheck, USGS

Mercury Cycling and Transformations across Louisiana Estuarine and Wetland Gradients (Marvin-DiPasquale, et al.)

Sediment core from the USGS-NAWQA sampling site at St. Mary’s River, FL. Photo Credit: Mark Brigham, USGS

Mercury Cycling in Stream Ecosystems
(Marvin-DiPasquale, et al.)

Wetland on margin of Davis Creek Reservoir, Yolo County, CA. Photo credit: J. Holloway, USGS

Mercury Methylation and Microbial Community Structure
(Holloway, Goldhaber)

Dense root biomass associated with white rice. Photo credit: Mark C. Marvin-DiPasquale, USGS

Plant-Microbe Interactions in Wetland Sediments
(Windham-Myers, Marvin-DiPasquale)

With South San Francisco Bay in the background, the vegetated habitat to the left of the levee represents healthy tidal marsh. To the right is a former salt pond. Photo credit: Mark C. Marvin-DiPasquale, USGS

San Francisco Bay Salt Pond Restoration (Marvin-DiPasquale, Windham-Myers, Ackerman, Eagles-Smith)

At the foot of San Francisco’s historic Presidio, Crissy Marsh consists of a mix of subtidal, intertidal and upland habitats. Photo Credit: Lisamarie Windham-Myers, USGS

Urban Salt Marsh Restoration (Windham-Myers, Marvin-DiPasquale)

 


Cycling of Mercury in Estuarine Sediments – Biogeochemical Controls on Fate, Transport and Bioaccumulation along Physical and Chemical Gradients
Collaborators Karen Merrit and Aria Amirbahman setting up experiments at Penobscot Estuary. Photo credit: Celia Chen
Collaborators Karen Merrit and Aria Amirbahman setting up experiments at Penobscot Estuary. Photo credit: Celia Chen
Penobscot Estuary. Photo credit: Celia Chen
Penobscot Estuary. Photo credit: Celia Chen

Mercury (Hg) in the environment is a global and national problem because its source is largely atmospheric and it is a neurotoxin known to affect humans via consumption of fish and shellfish. Hg and its highly toxic form, methylmercury (MeHg), move up the food chain, such that in higher trophic level animals, MeHg concentration could increase up to a factor of 107. Recent studies have shown the presence of biological Hg “hotspots” where inorganic Hg is transformed to MeHg and bioaccumulated in fish and wildlife at a significant rate. Wetlands have been identified as such hotspots, and numerous studies have documented their role as areas of high Hg methylation and bioaccumulation. However, the role of sediments in estuarine and coastal wetlands in Hg methylation and bioaccumulation is less well documented. We are investigating the role of sediments at two field sites in Maine and two in New Hampshire. We are evaluating several factors: the abundance and activity of the microbial community and benthic infauna, redox conditions close to the sediment-water interface (SWI) and the degree of sediment Hg contamination.

The project is unique in that the combination of geochemical, microbial and ecological approaches  simultaneously addresses issues regarding Hg geochemical dynamics and in situ microbial transformation processes, and links them to Hg bioaccumulation and potential biotransfer via intertidal organisms.

For more information contact Mary Voytek, Voytek Microbiology; Aria Amirbahman, University of Maine; and Celia Chen, Dartmouth College.

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Mercury Cycling and Transformations across Louisiana Estuarine and Wetland Gradients
Dave Krabbenhoft and George Aiken sampling a cypress swamp slough channel near Blind River, Louisiana. Photo Credit: Dennis Demcheck, USGS
Dave Krabbenhoft and George Aiken sampling a cypress swamp slough channel near Blind River, Louisiana. Photo Credit: Dennis Demcheck, USGS
Chris Swarzenski and Britt Hall sampling sediment pore water from a cord grass (Spartina patens) dominated marsh near Lake Felicity, Louisiana.
Chris Swarzenski and Britt Hall sampling sediment pore water from a cord grass (Spartina patens) dominated marsh near Lake Felicity, Louisiana.

The mosaic of land and water that make up southern Louisiana and the Gulf Coast face numerous challenges including wetland habitat loss and mercury contamination of aquatic-based food webs. While all sources of mercury to this region have not been fully identified, it has been shown that the Gulf Coast experiences enhanced total mercury deposition from the atmosphere. Further, human blood mercury levels are elevated in this region, in comparison to most other regions of the United States, and this may be partially due to a comparatively high level of regional fish consumption. Wetlands have been often shown to represent zones of enhanced methylmercury production, and it is this methylated-mercury form that most readily accumulates in aquatic food webs and is most toxic to people and wildlife. Yet wetland types vary greatly as a function of salinity, hydrology and vegetation type. This ongoing research effort is focused on exploring the factors that control methylmercury production by sediment bacteria, as well as the speciation (chemical form), transport and transformations of mercury across a wide variety of wetland habitats in Southeastern Louisiana. These habitat types range from cypress-dominated freshwater swamps to peat marshes to cordgrass (Spartina spp.) - dominated saltmarshes, and include both vegetated (emergent plants) and non-vegetated (slough channels, ponds and river main channels) regions.

Publications:

  • Hall, B.D., Aiken, G.R., Krabbenhoft, D.P., Marvin-DiPasquale, M., and Swarzenski, C.M., 2008, Wetlands as principal zones of methylmercury production in southern Louisiana and the Gulf of Mexico region; Environmental Pollution, v. 154, no. 1, p. 124-134. (online abstract of journal articleExternal link)
  • Engle, M.A., Tate, M.T., Krabbenhoft, D.P., Kolker, A., Olson, M.L., Edgerton, E.S., DeWild, J.F., and McPherson, A.K., 2008, Characterization and cycling of atmospheric mercury along the central U.S. Gulf of Mexico Coast, Applied Geochemistry 23 (2008), pp. 419–437. (online pdf file, 1728 KB Acrobat)
  • Kolker, A., Engle, M.A., Krabbenhoft, D.P., and Olson, M.L., 2007, Investigating Atmospheric Mercury with the U.S. Geological Survey Mobile Mercury Laboratory, U.S. Geological Survey Fact Sheet 2007-3071. (online fact sheet)

For more information contact the following scientists:

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Mercury Cycling in Stream Ecosystems
Wintertime sediment sampling at the USGS-WEBB site at Sleeper’s River, VT. Photo Credit: Paul Schuster, USGS
Wintertime sediment sampling at the USGS-WEBB site at Sleeper’s River, VT. Photo Credit: Paul Schuster, USGS
Sediment core from the USGS-NAWQA sampling site at St. Mary’s River, FL. Photo Credit: Mark Brigham, USGS
Sediment core from the USGS-NAWQA sampling site at St. Mary’s River, FL. Photo Credit: Mark Brigham, USGS

The USGS National Water Quality Assessment (NAWQA) Program, the Water, Energy and Biogeochemical Budgets (WEBB) Program, and the Toxic Substances Hydrology Program all focus on water quality and biogeochemistry research associated with U.S. watersheds. With their extensive geographic scope and long-term databases, these programs have provided unique opportunities for investigations into the biogeochemical cycling of mercury in freshwater stream ecosystems. Recent research has found that toxic methylmercury (MeHg) produced by microbes in the headwater and/or in the terrestrial catchment areas of these watersheds may be the primary source of MeHg to streams. Out-of-channel MeHg production, and regional contrast/comparison studies regarding the environmental controls on microbial MeHg production are active and ongoing areas of research in the context of these USGS programs.

For more information view the publications under Related Links and References.

Also contact the following scientists:

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Spatial and Seasonal Variations in Mercury Methylation and Microbial Community Structure in a Historic Mercury Mining Area, Yolo County, California
Davis Creek Reservoir, December 2004, showing ring of senescent wetland vegetation around shoreline. Photo credit: J. Holloway, USGS
Davis Creek Reservoir, December 2004, showing ring of senescent wetland vegetation around shoreline. Wetland soils are a sink for methyl-Hg and organic carbon. Photo credit: J. Holloway, USGS
Image Gallery
Wetland on margin of Davis Creek Reservoir, Yolo County, CA. Photo credit: J. Holloway, USGS
Wetland on margin of Davis Creek Reservoir, Yolo County, CA. This watershed was historically mined for Hg. Photo credit: J. Holloway, USGS
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The relationships between soil parent lithology, nutrient concentrations, microbial biomass and community structure were evaluated in soils from a small watershed impacted by historic Hg mining. Soils from different parent materials had distinct phospholipid fatty acid (PLFA) biomass and community structures that are related to nutrient concentrations and toxicity effects of trace metals including Hg. The formation of methyl-Hg appears to be most strongly linked to soil moisture, which in turn has a correlative relationship with PLFA biomass in wetland soils. Mercury methylation was associated with sulfate-reducing bacteria, including Desulfobacter sp. and Desulfovibrio sp., although these organisms are not exclusively responsible for Hg methylation.

Publication:

Holloway, J.M., Goldhaber, M.B., Scow, K.M & Drenovsky, R. 2009., Spatial and seasonal variations in mercury methylation and microbial community structure in an historic mercury mining area, Yolo County, California, Chemical Geology (2009), doi:10.1016/j.chemgeo.2009.03.031

For more information contact JoAnn M. Holloway, Crustal Imaging & Characterization Team; Martin B. Goldhaber, Crustal Imaging & Characterization Team; Kate M. Scow, U.C. Davis; and Rebecca E. Drenovsky, John Carroll University.

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Plant-Microbe Interactions in San Francisco Bay Wetland Sediments: Impacts on Mercury Biogeochemistry
Lisamarie Windham-Myers in a pickleweed (Salicornia spp.) dominated marsh. Photo credit: Mark C. Marvin-DiPasquale, USGS
Lisamarie Windham-Myers in a pickleweed (Salicornia spp.) dominated marsh near Petaluma River, California, with one of the ‘devegetation’ plots used to examine plant-microbe interactions. Photo credit: Mark C. Marvin-DiPasquale, USGS
Dense root biomass associated with white rice. Photo credit: Mark C. Marvin-DiPasquale, USGS
Dense root biomass associated with white rice (Oryza sativa) from agricultural fields of the Yolo Bypass in California’s central valley, a study site used to explore the linkage between emergent plants, microbial activity and methylmercury production. Photo credit: Mark C. Marvin-DiPasquale, USGS
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Wetland vegetation density and type can influence key microbial processes both through the resupply of key electron acceptors (e.g. sulfate) and the release of electron donors (e.g. acetate and low molecular weight organics) that fuel microbial processes. Conversely, microorganisms are involved in the generation of compounds that are both stimulatory (e.g. the generation of ammonium) and inhibitory (e.g. the generation of sulfide) to plant growth. Due partially to enhanced microbial activity associated with the root zone (rhizosphere) of emergent wetland plants, wetland environments are generally known to be zones of enhanced methylmercury (MeHg) production. However, the extensive variation in wetland types, as dictated by variations in hydrology, salinity and dominant plant species, leads to a wide range in microbial MeHg production rates. The San Francisco Bay watershed is contaminated with mercury as a result of historic mining practices, making the need to better understand the linkages between wetland plants and the microbial community that produces MeHg from inorganic mercury, particularly relevant. Experimental and comparative studies throughout the SFB region have demonstrated that active photosynthetic organic inputs through live roots and into the rhizosphere promote biogeochemical and microbial processes that in turn lead to enhanced MeHg production. Further, plant root density has been found to be proportional to the activity of the microbes associated with MeHg production, across a range of SFB wetland types. Thus, the structural and physiological characteristics of plants also may be also useful in developing landscape-scale predictions of MeHg production in wetland settings. Ongoing studies in a range of SFB wetland types – from freshwater natural floodplains and flooded agricultural fields to saltmarshes – seek to develop a more quantitative understanding of the these plant-microbe relationships, and their impact on MeHg production and export, in this historically mercury contaminated ecosystem.

Publication:

Windham-Myers, L., M. Marvin-DiPasquale, D.P. Krabbenhoft, J.L. Agee, M.H. Cox, P. Heredia-Middleton, C. Coates, and E. Kakouros. 2009. Experimental removal of wetland emergent vegetation leads to decreased methylmercury production in surface sediments. Journal of Geophysical Research 114, G00C05, doi:10.1029/2008JG000815

For more information contact Lisamarie Windham-Myers and Mark C. Marvin-DiPasquale, Menlo Park Regional Office.

See also Microbial Ecology: Plant-Microbe Interactions >>

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San Francisco Bay Salt Pond Restoration Project: Mercury Biogeochemistry and Bioaccumulation
With South San Francisco Bay in the background, the vegetated habitat to the left of the levee represents healthy tidal marsh. To the right is a former salt pond. Photo credit: Mark C. Marvin-DiPasquale, USGS
With South San Francisco Bay in the background, the vegetated habitat to the left of the levee represents healthy tidal marsh. To the right is a former salt pond. Photo credit: Mark C. Marvin-DiPasquale, USGS
Image Gallery
Historic tidal sloughs in the surface of the former salt ponds. Photo credit: Mark C. Marvin-DiPasquale, USGS
Historic tidal sloughs, such as the one above, are still visible in the surface of the former salt ponds. One management goal is to reinstate tidal flushing to these hydrologically disconnected areas and to restore healthy marsh function, without increasing methylmercury production. Photo credit: Mark C. Marvin-DiPasquale, USGS
Image Gallery

The San Francisco Bay (SFB) in California (USA) is contaminated with mercury as a result of historic mining practices in the region; one of the largest point sources being the New Almaden mercury mining district, which drains into the South SFB through Alviso Slough. The State of California recently purchased over 16,000 acres of former salt production ponds for the purpose of wetland habitat restoration, with a majority of these ponds being in South SFB. Research in this area includes: a) the current status of mercury cycling by microbial processes in former salt ponds, Alviso Slough and South SFB reference sites, b) the interaction of wetland plants and the microbial mercury cycle, c) toxic methylmercury production by bacteria, and its incorporation into the local food web, d) trophic transfer of methylmercury and effects on avian reproduction, and e) proposed wetland restoration scenarios and their impact on mobilizing mercury buried in sediment, as well their affect on the status of mercury cycling and bioaccumulation in this region. 

Related Link:

South Bay Salt Pond Restoration Project External link

Publication:

Marvin-DiPasquale, M., and Cox, M.H., 2007, Legacy Mercury in Alviso Slough, South San Francisco Bay, California: Concentration, Speciation and Mobility U.S. Geological Survey Open-File Report number 2007-1240, p 98. (online open-file report)

For more information contact Mark C. Marvin-DiPasquale, Menlo Park Regional Office; Lisamarie Windham-Myers, Menlo Park Regional Office; Josh T. Ackerman, Western Ecological Research Center; and Collin A. Eagles-Smith, Western Ecological Research Center.

See also Ecosystem Function: Habitat Restoration >>

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Urban Salt Marsh Restoration: Crissy Field, Golden Gate National Recreation Area
At the foot of San Francisco’s historic Presidio, Crissy Marsh consists of a mix of subtidal, intertidal and upland habitats. Photo Credit: Lisamarie Windham-Myers, USGS
At the foot of San Francisco’s historic Presidio, Crissy Marsh consists of a mix of subtidal, intertidal and upland habitats. Photo Credit: Lisamarie Windham-Myers, USGS
Water sampling the Crissy Marsh inlet to the San Francisco Bay, with Alcatraz Island seen in the background. The inlet is subject to periodic closure events, resulting from longshore sand migration and a muted tidal prism. Photo Credit: Hillary Harms, USGS
Water sampling the Crissy Marsh inlet to the San Francisco Bay, with Alcatraz Island seen in the background. The inlet is subject to periodic closure events, resulting from longshore sand migration and a muted tidal prism. Photo Credit: Hillary Harms, USGS

As part of the Golden Gate National Recreation Area, Crissy Field is a popular recreational destination in San Francisco, California, for both residents and tourists. The restoration of 18-acres of historic tidal marsh at this site has had great success in terms of public outreach and visibility, but less success in terms of revegetated marsh sustainability. Native cordgrass (Spartina foliosa) has experienced dieback and has failed to recolonize following extended flooding events resulting from periodic closures of the inlet channel, which inhibits daily tidal flushing. These inlet closure events are attributed to the marsh’s small tidal prism and to sand deposition near the inlet mouth. The National Park Service (NPS) currently manages the marsh by dredging the inlet channel to reinstate tidal flow approximately once per year during the spring (at the beginning of the active growing season). The joint USGS-NPS Water Quality Monitoring Program is sponsoring ecosystem-level research at the Crissy Field marsh to help advise NPS wetland managers as to the impacts of these closure events on marsh sustainability, both in terms of plant stress (e.g. fermentative respiration) and the microbial cycling of sulfur and mercury. Specifically we are investigating to what extent closure events are associated with a) increased reduced sulfur concentrations (generated by microbial sulfate reduction) in sediment and pore water, which might be toxic to juvenile or newly recolonized plants, and b) increased toxic methylmercury production by microbes in the sub-tidal and intertidal zones. This research, and that of collaborators in USGS Coastal and Marine Geology, is providing a scientific basis for determining how rapidly and how often to dredge the tidal channel after a closure event, and to inform habitat enhancement projects including a current design to daylight a perennial creek that drains into the marsh and to expand transitional wetland habitats.

Related Links:

For more information contact Lisamarie Windham-Myers, Menlo Park Regional Office, Mark C. Marvin-DiPasquale, Menlo Park Regional Office, and Kristen Ward, NPS Golden Gate National Recreation Area (NPS-GGNRA).

See also Ecosystem Function: Habitat Restoration >>
See also Microbial Ecology: Plant-Microbe Interactions >>

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Related Links and References

USGS Programs and Topics

USGS Laboratories

Mercury Cycling in Stream Ecosystems

  • Marvin-DiPasquale, M., Lutz, M.A., Brigham, M.E., Krabbenhoft, D.P., Aiken, G.R., Orem, W.H., and Hall, B.D., 2009, Mercury cycling in stream ecosystems: 2. Benthic methylmercury production and bed sediment-pore water partitioning: Environmental Science and Technology, v. 43, p. 2726-2732.
  • Marvin-DiPasquale, M.C., Lutz, M.A., Krabbenhoft, D.P., Aiken, G.R., Orem, W.H., Hall, B.D., DeWild, J.F., and Brigham, M.E., 2008, Total Mercury, Methylmercury, Methylmercury Production Potential, and Ancillary Streambed-Sediment and Pore-Water Data for Selected Streams in Oregon, Wisconsin, and Florida, 2003–04: U.S. Geological Survey Data Series  375,  p. View the Publication
  • Lutz, M.A., Brigham, M.E., and Marvin-DiPasquale, M., 2008, Procedures for collecting and processing streambed sediment and pore water for analysis of mercury as part of the National Water-Quality Assessment Program: U.S. Geological Survey Open-File Report 2008-1279,  p  68. View the Publication
  • Schuster, P.F., Shanley, J.B., Marvin-DiPasquale, M., Reddy, M.M., Aiken, G., Roth, D.A., Taylor, H.E., Krabbenhoft, D.P., and DeWild, J.F., 2008, Mercury and organic carbon dynamics during runoff episodes from a Northeastern USA watershed: Water Air and Soil Pollution, v. 187, p. 89-108.

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