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Microbial Ecology

 Microbial diversity and mechanisms shaping microbial diversity patterns

Microorganisms inhabit almost every imaginable environment on earth.  In contrast to plant and animal diversity, however, the extent of microbial diversity is largely unknown. Another key research direction in my laboratory is to use genomic technology to understand microbial diversity and the mechanisms controlling microbial community diversity.  My laboratory was the first to discover unusual microbial community diversity patterns in surface soils that had never been observed in plant or animal communities before.  In cooperation with other scientists, we also demonstrated that spatial isolation is the key mechanism that shapes microbial community structure.  We also discovered several novel divisions of bacteria in soil environments.  We recovered many novel functional gene sequences (e.g. nirS, nirK, amoA, nifH, dsrA/B) from a variety of environmental samples. Unlike previous studies that focused on simply characterizing microbial diversity, our research focused on the mechanisms that control microbial diversity. Our studies have shifted the research direction of microbial ecology toward understanding the mechanisms that shape diversity and hence, the means of manipulating a community.

Dynamics of microbial communities associated with bioremediation

My laboratory is actively involved in several large-scale integrated projects related to bioremediation of mixed wastes. Our focus is to use genomic technology to understand microbial diversity, and the factors and mechanisms shaping microbial community structure in contaminated sites. Understanding the mechanisms controlling the microbial community is extremely important because the knowledge gained may provide novel approaches to the manipulation of microbial communities for desired functions, and will be critical for successful bioaugmentation and biostimulation.

We have used functional gene arrays to investigate microbial communities in six groundwater samples heavily contaminated with uranium and other metals. Our results indicated that microbial populations containing important genes involved in contaminant degradation and immobilization exist but their distribution is heterogeneous. This implies that it is feasible to biostimulate the indigenous microbial populations for contaminant remediation but the process could be very complicated due to highly heterogeneous microbial distributions. By collaborating with environmental engineers, we are also using functional gene arrays to monitor the community dynamics in denitrifying bioreactors and groundwaters for bioremediating uranium and nitrates at the ERSP Field Research Center. In addition, we are collaborating with several other scientists to characterize microbial communities with different contaminant samples.  

Dynamics of microbial communities associated with global changes

As a part of the DOE Center for Carbon Sequestration, we are using microarray technology to understand how different management practices affect microbial community structure and activities, and consequently on carbon sequestration. The results on microbial community structure and activities will provide insightful information about the strategies for carbon sequestration.

Continental margin sediments are the dominant sites of carbon sequestration (via permanent burial) and nitrogen cycling.  Despite their importance, the potential factors and mechanisms controlling carbon sequestration through permanent burial and denitrification in margin sediments are controversial.  Thus, we are using microarrays and other molecular techniques to study microbial diversity and dynamics of marine sediment samples from Washington, Mexico and Arctic, and the mechanisms and organisms that control carbon burial and denitrification.  Hopefully, these studies will provide the basis for better predictions of C and N dynamics in marine sediment.   

Thermophilic iron-reducing bacteria

Ancient thermophilic iron-reducing bacteria from the deep subsurface (2000m below surface) were enriched and characterized.  A part of this work, together with physiological studies, was highlighted by CNN News in April 1997, and published in Science in 1997. A research accomplishment award for this work was received from Oak Ridge National Laboratory in 1998. We also isolated and characterized five pure bacterial strains capable of reducing iron as well as degrading xylan and cellulose. These strains are very close to Thermoanaerobacter ethanolicus. Geological evidence indicates that these bacteria are about 200 million years old and they appear to be the oldest viable cultured bacteria available now from the deepest subsurface. These ancient bacteria could be potentially valuable in studying life evolutionary processes, stress responses and astrobiology.

To date evolutionary events using molecular data, the molecular chronometers must be calibrated with known divergence times for particular lineages (i.e. reference times). However, calibration of molecular clocks in prokaryotes is extremely difficult because of the lack of reliable fossil records for microorganisms.  This represents a grand challenge for studying prokaryote evolution.  Since these ancient isolates were obtained from geologically separated subsurface and their separation times (~200M years) from modern organisms covered up to 5% of the life history on Earth, they are extremely valuable for calibrating molecular chronometers. Therefore, the genome sequences from these isolates will be also very useful in studying microbial evolution in general. 

Psychrophilic and alkaliphilic metal-reducing bacteria

We have obtained about 30 psychrophilic/psychrotolerant iron-reducing bacteria from Siberia and Alaska permafrost soils, Pacific marine sediments and sea water around Naha hydrothermal vents near Hawaii. The closest relatives to these psychrophilic/psychrotolerant iron-reducing bacteria are members of the genus Shewanella. Some of which are able to produce magnetite at 0¡ãC and to reduce iron and cobalt at ¨C4¡ãC.   In addition, alkaliphilic iron-reducing bacterium (i.e., isolate QYMF) was isolated from leachate ponds at the U.S. Borax Mines in Boron, CA. Phylogenetic and physiological analysis indicates that this isolate represents a novel metal-reducing, alkaliphilic species, named as Alkaliphilus metalliredigens.  These iron-reducing bacteria also formed diverse minerals including green rust, rhodochrosite, siderite, vivianite, and uraninite.

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