Researchers Investigate Oil-Eating Microbes in Gulf Sands

A new Florida State University study is investigating how quickly the Deepwater Horizon oil carried into Gulf of Mexico beach sands is being degraded by the sands' natural microbial communities, and whether native oil-eating bacteria that wash ashore with the crude are helping or hindering that process.

Sediment cores and water samples collected at St. George Island on June 8. These samples are not affected by oil and provide the reference data to compare with data generated in case oil affects this beach. (Photo courtesy of Markus Huettel)

What oceanography professors Markus Huettel and Joel E. Kostka learn will enable them to predict when most of the oil in the beaches will be gone. Their findings may also reveal ways to accelerate the oil degradation rate — and speed matters, because toxic crude components that remain buried on Gulf Coast beaches may seep into the groundwater below.

Samples provided to professors Kostka and Huettel that consist of heavily oiled sediments from a barrier island off the coast of Louisiana. (Photo courtesy of Joel E. Kostka)

"This enormous oil spill affects hundreds of miles of beaches in the Gulf of Mexico," Huettel said. "We can remove the oil from the beach surface, but oil is also carried deeper into the sand, and we need to understand what happens to that oil. Preventing groundwater contamination is crucial not only to Gulf Coast residents but also to coastal management and local economies like fisheries and tourism that depend on water quality."

"We will also study the effect of the dispersant known as Corexit on oil metabolism by natural microbial communities," Kostka said. "Through contacts in the field, my laboratory has acquired Corexit and source oil from the MC252 (Deepwater Horizon) well head for use in our experiments."

St. George Island, Fla., and Dauphin Island, Ala., have served as the primary research sites since early June, when the one-year study began. In addition, the researchers have obtained heavily oiled sand from Pensacola Beach, Fla., and from a barrier island off the Louisiana coast. If warranted by the oil's movement, they will also collect near-shore water and sediment samples from other Gulf beaches.

Click here to read the whole article

New Report out: Oil Spills and Microbes

A new FAQ report from the American Academy of Microbiology (the honorific leadership group within the American Society for Microbiology) has just come out addressing questions regarding the role of microbes in helping to clean up oil spills.

A variety of questions are addressed, including:

What does it mean to say that microbes can ‘clean up’ an oil spill?

Where do the ‘oil-eating’ microbes come from? Are they everywhere? Does that mean we don’t need to worry about oil spills because microbes will always clean them up? What are they doing when there isn’t any oil?

What do the microbes need in order to biodegrade oil and how long does it take? What are the end-products of microbial degradation? How is biodegradation measured in the environment?

and many more. Click here to download and read a pdf of the report.
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Kostka/Huettel Research Profiled in the Tallahassee Democrat


Click here to read the Front Page, Page 2

Gulf Oil Cleanup Crews Trample Nesting Birds

Joel was interviewed by National Geographic News for this story on the impact of beach clean-up operations on birds and Gulf sand dwellers.

See the whole article here.

New Papers Out on the Role of Marine Sands as the Kidneys of the Earth’s Estuaries.

The Kostka Lab has several new publications that have come out in the first part of 2009:

Identification of phytodetritus-degrading microbial communities in sublittoral Gulf of Mexico sands.

In the first paper, published in Limnology & Oceanography from Dr. Tom Gihring's Ph.D. research, microbial taxa that catalyze phytodetritus degradation and denitrification in permeable coastal sediments were identified in the northeast Gulf of Mexico. In this study, stable isotope probing experiments were used to track the assimilation of isotopically labeled substrate into bacterial deoxyribonucleic acid (DNA) and directly link the taxonomic identification of benthic microorganisms with particulate organic matter degradation and denitrification activity. This study provides the first identification of microorganisms responsible for organic matter degradation in marine sediments by DNA sequence analysis. Microbial assemblages recognized for high-molecular-weight organic matter oxidation in the marine water column were important in catalyzing these processes in permeable sediments.
Photo: Dr. Thomas Gihring in the Apalachicola Salt Marsh.

Denitrification in shallow, sublittoral Gulf of Mexico permeable sediments.

In the second paper, published in Limnology & Oceanography from Dr. Tom Gihring's Ph.D. research, we examined nitrogen cycling over a one-year period in shallow sandy sediments at two contrasting sites near a barrier island in the northeastern Gulf of Mexico and provide the first direct determinations of N2 production at ambient nitrate concentrations in permeable marine sediments. Nitrogen stable isotope tracer techniques were used to quantify N2 production rates and pathways in sediment cores and slurries. To simulate pore-water advection, the dominant transport process in the upper layer of the permeable sand beds, intact sediment cores were perfused with aerated seawater. This perfusion increased denitrification rates up to 2.5-fold in Apalachicola Bay sands and 15-fold in Gulf of Mexico sublittoral sands, respectively, relative to static cores. Seasonal N2 production rates were highest in spring and fall. Denitrified nitrate originated almost entirely from benthic nitrification at the exposed Gulf site, whereas water column nitrate dominated sedimentary denitrification at the sheltered Bay site. Sediment incubations in stirred chambers were used to determine net fluxes of O2, N2, nitrate, and ammonium across the sediment-water interface during varied degrees of continuous pore-water exchange. Rates of N2 efflux correlated with rates of pore-water flow increasing from 0.12 mmol N m-2 d-1 under diffusion-limited transport conditions up to 0.87 mmol N m-2 d-1 with pore water advection. Mineralized nitrogen was completely converted to N2 gas in Gulf of Mexico sediments. Our results demonstrate the role of coastal permeable sediments as important sites for nitrogen removal, and the influence of pore-water flow on denitrification and N2 flux.

Rapid organic matter mineralization coupled to iron cycling in intertidal mud flats of the Han River estuary, Yellow Sea.
This new paper, published in the journal Biogeochemistry, reports on a collaborative study conducted with Jung-Ho Hyun, a professor at Hanyang University in Korea and longtime collaborator with the Kostka lab. The study examines the rates and pathways of anaerobic carbon (C) oxidation in an unvegetated mud flat (UMF) and a vegetated mud flat (VMF) of the Ganghwa intertidal zone of the macro-tidal Han River estuary, South Korea. This study found high rates of C mineralization, suggesting that the primarily open and unvegetated Ganghwa intertidal mud flats are a significant sink against the external loading of organic compounds, and that organic matter mineralization is enhanced by chemical exchange regulated by extreme tidal flushing and macro-microorganisms interactions.
Photo: The Han River Estuary, Yellow Sea. Credit:

Identification of sulfate-reducing bacteria in methylmercury contaminated mine tailings by analysis of SSU ribosomal RNA genes.

This paper, published in the journal FEMS Microbiology Ecology, characterizes the bacterial communities of two geochemically contrasting, high-methylmercury mine tailing environments, with emphasis on sulfate reducing bacteria, by analyzing small subunit (SSU) rRNA genes present in the tailings sediments and in enrichment cultures inoculated with tailings. The results of this study provide new insights into the novelty and diversity of bacteria colonizing mine tailings, and identifies specific organisms that warrant further investigation with regard to their roles in mercury methylation and sulfur cycling in these environments.
Photo: Mine tailings from a gold mine in Nova Scotia. Source:

T.M. Gihring, M. Humphrys, H.J. Mills, M. Huettel, J.E. Kostka. 2009 Identification of phytodetritus-degrading microbial communities in sublittoral Gulf of Mexico sands. Limnol. Oceanogr., 54: 1073–1083.

T. M. Gihring, A. Canion, A. Riggs, M. Huettel, and J. E. Kostka. 2009. Denitrification in shallow, sublittoral Gulf of Mexico permeable sediments. Limnology and Oceanography (in press).

J.-H. Hyun, J. S. Mok, H. Y. Cho, S. H. Kim, J. E. Kostka. 2009 Rapid organic matter mineralization coupled to iron cycling in intertidal mud flats of the Han River estuary, Yellow Sea. Biogeochemistry 92: 231–224.

S. Winch, H. J. Mills, J. E. Kostka, D. Fortin, D. R.S. Lean. 2009 Identification of sulfate-reducing bacteria in methylmercury contaminated mine tailings by analysis of SSU ribosomal RNA genes. FEMS Microbiol. Ecol. FEMS Microbiol Ecol 68: 94–107.

Research in Review Features Kostka Lab Research

Research by Professors Joel Kostka and Marcus Huettel on nutrient cycling by microbes in coastal sands is profiled in this month’s FSU Research in Review. The story by Frank Stevenson emphasizes the shift in thinking by scientists as to the roll of sandy bottoms, long thought to be “biological wastelands” and have little to no ecological value in ocean systems. Permeable sediment research, such as that by professors Kostka and Huettel is painting a much more interesting picture of the role of coastal sands.

“Ask any Floridian about what healthy beaches mean to the state’s economy and get ready for an earful.

If state nicknames made any sense at all, “The Sunshine State” would be called “The Beach State.” Take away half of Florida’s sunny days, and the state’s sandy shoreline would still be a perpetual magnet for people and money year-round—a gritty goldmine that defies every natural force known—from hurricanes to red tide—to keep the state’s tourism-based economy the envy of every landlocked state (and others, too.)

Still, most people don’t have a clue what the real story is behind the value of sandy coastlines—not just in Florida but also around the world. Just in the past 20 years, researchers have begun amassing tantalizing evidence that is revolutionizing scientists’ appreciation of coastal sands and their vital role in the overall health not of seaside economies but of the world’s oceans.

What’s happening is nothing less than a sea change in scientists’ thinking about the vast, sandy bottoms and beaches laid up against the third of the planet that’s dry land. For decades, marine biologists have taught that most of the shallow, near-shore bottoms of the globe’s continental shelf are largely biological wastelands—little more than an immense submarine desert largely devoid of life and of little ecological value. Now, these and a host of other researchers are beginning to realize just how wrong they’ve been all along. . . ” Continue reading here >