New Species Publication

We are proud to announce a new paper coming out in the International Journal of Systematic and Evolutionary Microbiology, “Geobacter daltonii sp. nov., an iron(III)- and uranium(VI)-reducing bacterium isolated from the shallow subsurface exposed to mixed heavy metal and hydrocarbon contamination,” by Om Prakash, Tom Gihring, Dava Dalton, Kuki Chin, Stefan Green, Denise Akob, Greg Wanger, and Joel Kostka. This paper describes a new species of Geobacter isolated from the contaminated subsurface of a nuclear legacy waste site in Oak Ridge, Tennessee, managed by the U.S. Dept. of Energy.


Dr. Om Prakash, the lead author on this paper, cultivated a full 3 grams of G. daltonii to show that the genotype of the new strain is very different from its closest relative, G. uraniireducens (DNA-DNA hybridization value of 21 %). Here is Om with a giant flask of the uranium-breathing bug.

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: http://wliasia2008.org.

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: www.nrcan.gc.ca.

Citations:
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.
Article

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.
Article

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.
Article

Sequencing proposal for JGI funded

We have just received news that our proposal to the Department of Energy's Joint Genome Institute (JGI), "Sequencing the genomes of six novel denitrifying bacterial isolates from the uranium and nitrate contaminated subsurface at the U.S. DOE Oak Ridge Integrated Field Research Center (OR-IFRC)," has been funded and sequencing will begin over the next 6 months.

Above: A picture of the wells at the FRC site where these denitrifying bacteria originated

Kostka named associate director at IESES

The Institute for Energy Systems, Economics and Sustainability, a research and policy group established earlier this year at The Florida State University to address sustainability and alternative power issues, has announced $6.5 million in grant awards for research in the areas of fuel cycles, governance and energy delivery systems.

The 29 grants were selected from research proposals seeking nearly $14 million in funding and covering a variety of sustainable energy topics. Given the excellent quality of the proposals submitted and limited dollars available in this funding cycle, the IESES review and selection process was highly competitive.

"Florida has a critical need for new energy technologies and policies that will reduce our reliance on foreign oil, decrease our production of greenhouse gases and stimulate our economy," said Kirby Kemper, Florida State's Vice President for Research. "The grants awarded today will support important research that will address all three of these pressing issues."

Three major research areas were defined during the review process:

• Sustainable Energy Governance and Decision Making, to be led by Professor Richard Feiock of the Reubin O'D. Askew School of Public Administration and Policy
• Excellence in Fuel Cycles, Including Bio-Fuels and Marine Bio-Energy, to be led by Joel Kostka, a professor in Florida State's Department of Oceanography
• Energy Delivery, to be led by Steinar Dale, director of the Center for Advanced Power Systems

In addition to the major awards, planning grants also were announced to provide resources to assist researchers in writing proposals for funding from outside agencies.

"The fundamental problem with sustainable energy technologies is that they rarely achieve market penetration and become successful ventures," said David Cartes, an associate professor of mechanical engineering in the Florida A&M University-Florida State University College of Engineering and director of IESES.

"This is true because we have a very expensive 'technology push' mindset in today's local and federal energy policies — investing in economically non-competitive alternatives. There is a serious need for progressive governance and economic practices that provide pragmatic and affordable technologies, for which a public education plan can lead to 'market pull' — making investments and policy changes that overcome the primary risk factor, competition. Market pull will provide the right choices of sustainable energy investment in the future.

"IESES is all about governance and planning for a sustainable energy future, driven by market pull — one in which my grandchildren won't have to compromise the quality of life I enjoy today," Cartes said.

IESES was formed in summer 2008 by The Florida State University to meet the challenges of Florida's rapidly evolving sustainable energy economy. The institute is staffed by a new generation of engineers, scientists, policymakers and planners — those with a comprehensive understanding of complex sustainable energy systems who stand ready to tackle the challenges and opportunities related to an energy-based future.

Denise's Trip to Germany

As a graduate student in the Kostka Lab, Denise Akob had the opportunity to spend the summer of 2007 as a guest scientist in the lab of Dr. Kirsten Küsel at the Friedrich-Schiller University Jena, Germany. The visit was supported by the Microbe-Mineral Interactions Graduate Research School which promotes international exchange of graduate students and scholars. During her time in Kirsten’s lab she worked in conjunction with Janna Sitte and Eva-Maria Burkhardt and focused on the biogeochemistry of microbial communities in surficial soils contaminated with radionuclides and heavy metals.



The Ronneburg Mining District during active uranium mining and before physical remediation efforts. Photo: http://www.centennialpark.de/page/en/geschichte/geschichte
The site was within the former Ronneburg Mining District, which was an area that was heavily mined for uranium from 1946-1990. Much of the Ronneburg Mining District has now been physically remediated but groundwater runoff from a former leaching heap has contaminated the water and soils of the aquifer with acid mine drainage (AMD). The Gessen Creek, downstream from the former leaching site, is heavily impacted by AMD and processes in the creek soils are affecting transport of heavy metal contaminants. The research performed during Denise’s trip was focused on identifying the active microorganisms in Gessen Creek soils and relating microbial activity to mobilization/immoblization of heavy metals. The work started in the summer of 2007 is still in progress and will be a part of both Jana and Eva's PhD dissertations. In addition to this work, research has continued on microbial communities in Gessen Creek soils through the work of 1 bachelor’s student, 2 diploma students and a new PhD student. Stay tuned for more updates!

Photo of a drainage pond at a former leaching heap in the former Ronneburg Mining District. Photo: D. M. Akob, May 2007
Sampling of porewater profiles in Gessen Creek soils. Photo: D. M. Akob, May 2007

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 >