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Chuanlun Zhang
Savannah River Ecology Laboratory
Since I arrived at the University of Georgia in August 2002, the overarching goal of our
research has been to integrate genomics, lipid biomarkers, and stable isotopes to study microbial
functions in geochemical processes in both natural and contaminated environments. This line of research is currently focused on carbon cycle and energy metabolism by microorganisms from terrestrial hot springs, the Gulf of Mexico deep-sea gas hydrates, the Mississippi River-Gulf of Mexico continental margins, and the saline lakes on the Tibetan Plateau. Another line of research focuses on biomineralization, particularly the role of microorganisms in the formation and destruction of iron minerals that are important in near-surface processes. Currently, this research is being conducted to examine microbe-mineral interactions in heavy metal- and organic solvent-contaminated soil and sediments at the Department of Energy Savannah River Site. Below is a brief description of each research topic.
For research in terrestrial hot springs, our long-term goal is to characterize the archaeal
communities that use different or novel mechanisms for carbon and energy metabolism in the
geothermal system. Our approach is to integrate lipid biomarkers, stable carbon isotopes, and
functional-genes to understand the community structure and to quantify different populations
fixing CO2 in the natural environments. This research was funded by the National Science
Foundation’s Microbial Interactions and Processes Program. A Significant outcome includes
the first discovery of the archaeal biomarker crenarchaeol in terrestrial hot springs (Pearson et al.,
2004). This study was expanded by Zhang et al. (2006) and Pearson et al. (2008). In particular,
Zhang et al. (2006) hypothesized that the evolutionary history of crenarchaeol is longer and more
complex than its distribution in the modern ocean. Our findings also suggest that the crenarchaeol
may have facilitated colonization of the ocean by (hyper)thermophilic archaea and the major
marine radiation of Crenarchaeota. This research was featured on the UGA homepage (2006)
and in the UGA Research Magazine (Fall 2006). Most recently, we demonstrated the global
occurrence of archaeal amoA genes and their endemism in terrestrial hot springs, which indicate
that thermophilic ammonia-oxidizing archaea, previously unrecognized,may play important roles
in nitrogen metabolism in these extreme environments (Zhang et al., ASM meeting abstract 2007;
Zhang et al., 2008). This new finding was featured by Astrobiology Magazine (May 2007) and Science Daily (May 2007). We are seeking funding from the NSF Microbial Systems in the
Biosphere initiative to continue this research.
For research in the Gulf of Mexico, our goal is to delineate the community structure and
ecological functions of microorganisms for carbon and energy metabolism in both sediments and
water column near gas hydrates or cold seeps. We are using the same integrative approach as
mentioned above; however, the focus here is on lipid biomarkers, isotope signatures, and
functional genes related to sulfate reduction, methanogenesis, aerobic/anaerobic oxidation of
methane, and aerobic ammonia oxidation. The Gulf of Mexico project was originally funded by
the NSF Biocomplexity program and is currently funded by the National Institute for Undersea
Science and Technology, sponsored by a consortium of agencies including National Oceanic and
Atmospheric Administration, Mineral Management Services, and the Department of Energy. A
Significant outcome includes the first report of bacterial and archaeal biomarkers associated
with gas hydrates in the Gulf of Mexico (Zhang et al., 2002, 2003) and the presence of diverse and
distinct methanotrophic bacteria in marine sediments associated with gas hydrates (Yan et al.,
2006). We also demonstrated that sulfur-oxidizing bacteria (i.e., Beggiatoa) in surface mats near
gas hydrates use non-methane organic carbon for chemoorganotrophic growth (Zhang et al.,
2005). Another finding was that bacterial lipid biomarkers can effectively distinguish
sulfur-oxidizing and sulfate-reducing bacteria from different environments in the Gulf of Mexico (Li
et al., 2007). Recently, we have been focusing on delineating the dynamics of archaeal
community structures affected by gas hydrates in both the sediments (Pi et al., 2008, in revision)
and in the water column above the cold seeps (Liu et al., manuscript in preparation). Also, major
research opportunities are emerging in the South China Sea as enormous gas hydrate potential
has been identified there. We are collaborating with Tongji University in Shanghai to study
microbial carbon and energy metabolisms in deep water and marine sediments in the SCS.
For research on the Mississippi River (MS) and the Gulf of Mexico (GOM) continental margin,
our goal is to understand the roles that microorganisms play in the overall ecosystem functions in
the land-ocean margins. In the Gulf of Mexico, our objectives are twofold: 1) to quantify the fluxes
of microorganisms from the lower MR into the GOM and to examine changes in the community
structure and functions of microorganisms along the MR to GOM transition zone, and 2) to link
microbial structure and functions to the overall cycling of organic matter (rates of primary
production and respiration of organic matter) in this river-coastal transition system. We
hypothesize that: 1) the lower MR contributes significant biomass of freshwater prokaryotes (both
autotrophs and heterotrophs) into the GOM and rates of primary production and respiration vary
in the MR as a function of physical, hydrological, and geochemical conditions. 2) The river plume
transition to the GOM is a dynamic system with biogeochemical cycles of carbon and nitrogen
mediated by both freshwater and marine microorganisms. Community structure, diversity, and
functional activities (primary production and respiration) are influenced or controlled by the
frequency and magnitude of freshwater input (high discharge vs. low discharge) and associated
constituents. These hypotheses will be tested by: 1) determination of microbial abundance,
community structure and functions using advanced molecular DNA/RNA techniques (e.g.,
FISH/CARD-FISH, RT-qPCR), 2) comprehensive measurements of nutrients and
organic/inorganic species in the river and river plumes, 3) modeling of carbon flux and oxygen
demand in the lower MR, and 4) characterization of particle dynamics in the lower MR and plume
to the GOM. Preliminary results show that the MR has considerably high diversity of archaea and
photoheterotrophic bacteria, which may play important roles in organic matter degradation in the
riverine system (Liu et al., manuscript in preparation). In collaboration with Tongji University, we
are linking the MS-GOM continental margin project to the East China Sea Coastal Seafloor
Observatory to better understand the roles of nonthermophilic archaea in organic carbon
degradation, CO2 fixation, and nitrification because these organisms have been demonstrated to
play an important role in carbon cycle and nitrogen metabolism in the coastal and open ocean environments. One important question we are addressing is how the Three Gorges Dam may
impact the sedimentary, nutrient, and microbial processes in the Yangtze River that flows into the
East China Sea.
For research in saline lakes on the Tibetan Plateau, we have been collaborating with Dr.
Hailiang Dong at Miami University to study microbial responses to changes in environmental
variables in high-elevation lakes on the Tibetan Plateau. Our efforts are focusing on the archaeal
communities and their function in carbon and nitrogen cycles affected by changing salinity. A
Significant outcome includes the observation that increase in salinity in Chaka Lake over the
geological history selected halophilic euryarchaeota over crenarchaeota (Jiang et al., 2007). In
Qinghai Lake (the largest saline lake in China) we observed that the euryarchaeotal populations
in lake sediments are strikingly similar to those present in the methane rich marine environment
(e.g., gas hydrates or cold seeps) (Ye et al., 2006, meeting abstract, American Geophysical
Union, San Francisco), suggesting certain populations of the archaea may be involved in
methane cycling the same way as the marine archaea. Archaeal lipids including the crenarchaeol
biomarker (specific to the crenarchaeota) were observed to be abundant in selected layers of
shallow sediments (less than 50 cm deep), suggesting that the growth and biomass of archaea
may be affected by changing conditions in the lake. While ammonia-oxidizing archaea are being
increasingly reported for marine and soil environments, their role in lake environments is less
studied.
For research on biomineralization at the Savannah River Site, our goal has been to provide
independent environmental assessment of metal and/or organic contamination from the
operation of DOE’s Savannah River Site (SRS). This project has been funded through the U.S.
Department of Energy Financial Assistance to the University of Georgia Research Foundation. A
significant outcome includes the observation of enhanced dissolution of iron and clay minerals
by sulfate-reducing bacteria (Li et al., 2004, 2006), which may have implications for
transformation and mobility of radionuclides or heavy metals associated with iron minerals. Our
genomic studies at the SRS have indicated that a variety of microbial populations have known
capacities to degrade organic contaminants or to transform heavy metals or radionuclides (Ye,
Ph.D.; thesis in preparation). This work also provided physical biosignatures that may be used for
detection of microbial life in extra-terrestrial planets (Vali et al., 2004). I have worked on
mesophilic and thermophilic iron-reducing bacteria for my postdoctoral research at the Oak Ridge
National Laboratory (1994-1998; Zhang et al., 1997, 1998; Liu et al., 1997) and during my
tenure-track teaching at the University of Missouri (1998-2002; Zhang et al., 2001). Research
opportunities along this line are being pursued in collaboration with the Third Institute of
Oceanography, Xiamen, China to explore the microbial role in mineral weathering at
hydrothermal vents and along the flanks of mid-ocean ridges.
I am also developing a new research line on petroleum microbiology to take advantage of my background in petroleum geology (BS, East China Petroleum Institute). The goal here is to understand microbial community structure and function for biodegradation of residual oil and subsequent production of methane in oil reservoirs. Collaborations are being developed with colleagues from several institutions in China.
SELECTED PUBLICATIONS 2008 Jiang, H., Dong, H., Yu, B., Ye, Q., Ji, S., Liu, Y., Shen, J., and Zhang C.L. 2008. Dominance of putative marine benthic archaea in sediments from an inland lake: Qinghai Lake, northwestern China. Environ. Microbiol.doi:10.1111/j.1462-2920.2008.01661.x. Pearson A., Pi Y., Zhao W., Li W., Li Y., Inskeep W., Bonch-Osmolavskaya L., Romanek C., Li S., and Zhang C.L. 2008. Factors controlling the distribution of archaeal tetraethers in terrestrial hot springs. Appl. Environ. Microbiol. 74: 3523–3532. Smith J. L., Campbell B. J., Hanson T. E., Zhang C. L., and Cary S. C. 2008. Nautilia profundicola sp. nov., a thermophilic, sulfur-reducing epsilonproteobacterium from deep-sea hydrothermal vents. Intl’ J. Syst. Evol. Microbiol. 58, 1598–1602. Zhang C.L., Ye Q., Huang Z., Li W., Chen J., Song Z., Hedlund B. P., Zhao W., Gao L., Bagwell C., Inskeep B., Wiegel J., Romanek C.S. 2008 Global occurrence and biogeographic patterning of putative archaeal amoA genes from terrestrial hot springs. Appl. Environ. Microbiol. 74: 6417–6426. Zhao W., Zhang C.L., Romanek C., Wiegel J. 2008. Description of Caldalkalibacillus uzonensis sp. nov. and emended description of the genus Caldalkalibacillus. Int’l. J. System. Evol. Microbiol. 58: 1106–1108. 2007 Boyd E. S., Jackson R. A., Encarnacion G., Zahn J. A., Beard T., Leavitt W.D., Pi Y., Zhang C. L., Pearson A., D’Imperio S., McDermott T. R., and Geesey G. G. 2007. Isolation, characterization, and ecology of sulfur-respiring Crenarchaea inhabiting acid-sulfate-chloride geothermal springs in Yellowstone National Park. Appl. Environ. Microbiol.73: 6669-6677. Huang Z., Wiegel J., Zhou J., Hedlund B., Zhang C.L. 2007. Molecular phylogeny of uncultivated Crenarchaeota in hot springs of moderately elevated temperatures. Geomicrobiol. J. 24: 535-542. Jiang H., Dong H., Yu B., Li Y., Ji S., Liu X., and Zhang C.L. 2007. Microbial response to salinity change in Lake Chaka, a hypersaline lake on the Tibetan Plateau. Environ. Microbiol. 9: 2603-2621. Li Y.-L., Peacock A., White D.C., Geyer R., Zhang C.L. 2007. Spatial patterns of bacterial signature lipid biomarkers in marine sediments of the Gulf of Mexico. Chem. Geol. 238: 168-179. Zhang C.L., Huang Z., Li Y.-L., Romanek C. S., Mills G., Wiegel J., Culp R., Noakes J., and White D. C. 2007. Lipid biomarkers and carbon-isotope signatures of bacteria in Nevada hot springs. Geomicrobiol. J. 24: 519-534. 2006 Li Y.-L., Vali H., Yang J., Phelps T. J., and Zhang C. L. 2006. Reduction of iron oxides enhanced by a sulfate-reducing bacterium and biogenic H2S. Geomicrobiol. J. 23: 103-117. Williams T.J., Zhang C.L., Scott J.H., and Bazylinski D.A. 2006. Evidence for autotrophy via the reverse tricarboxylic acid cycle in the marine magnetotactic coccus strain MC-1. Appl. Environ. Microbiol. 72: 1322-1329. Yan T., Ye Q., Zhou J., and Zhang C.L. 2006. New functional genes for methanotrophs in gas-hydrate and hydrocarbon-seep environments in the Gulf of Mexico. FEMS Microbiol. Ecol. 57: 251-259. Zhang C.L., Pearson A., Li Y.-L., Mills G., Wiegel J. 2006. A thermophilic temperature optimum for crenarchaeol and its implication for archaeal evolution. Appl. Environ. Microbiol. 72: 4419-4422. Zhao W., Wiegel J., Zhang C.L., Romanek C.S., Mills G., King G. 2006. Thermalkaliphus uzonensis gen. nov. sp. nov, a new aerobic thermophilic carbon-monoxide-tolerant bacterium isolated from a hot spring in Uzon Caldera, Kamchatka. Extremophiles. 10: 337-345. 2005 Pancost R.D., Zhang C.L., Tavacoli J., Talbot H.M., Farrimond P., Schouten S., Damste J.S.S., Sassen R. 2005. Lipid biomarkers preserved in hydrate-associated authigenic carbonate rocks of the Gulf of Mexico. Palaeogeography, Palaeoclimatology, Palaeoecology 227: 48-66. Tuo J., Chen J., Yao S., Li Y.-L., Ji J., and Zhang C.L. 2005. Qinghai Lake: A natural laboratory for geomicrobiological research. Geosci. J. China Univ. 2: 187-193. Wang Y., Huang Z., and Zhang C.L. 2005. Knowing the unknown: Statistical approaches towards understanding microbial diversity. Geosci. J. China Univ. 2: 224-233. Zhang C.L., Huang Z., Cantu J., Pancost R. D, Brigmon, R. L., Lyons T. W., and Sassen R. 2005. Lipid Biomarkers and Carbon-Isotope Signatures of a Microbial (Beggiatoa) Mat Associated with Gas Hydrates in the Gulf of Mexico. Appl. Environ. Microbiol. 71: 2106-2112. |
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