Tiedje Lab - Projects


The Rhizosphere: An important habitat for microorganisms (Stephan Gantner)

Bacteria can be found nearly everywhere in nature in many unique habitats, including in association with plants. Plants provide an important ecological niche for many different organisms, not only above ground but also below ground. In comparison to bare soil, the soil associated with plant roots contains significantly higher densities of microorganisms. Many of these microbes live there as a part of a distinct community surrounding plant roots. Heterotrophic bacteria are able to use organic compounds excreted in root exudates (Sorensen, 1997), whereas their metabolites can be used by other microbes, which in the end creates a network of closely connected microorganisms (Goddard et al., 2001). This phenomenon of highly active microorganisms in root-associated soil is known as the "rhizosphere effect" (Whipps, 1990). The expression "Rhizosphere" was first used in 1904 by Prof. Lorenz Hiltner (1862-1923) from the Technical University of Munich, Germany (Curl & Truelove, 1986). It described the zone in which plant roots (Greek: Rhizos) interact with the surrounding soil (Sphere). The rhizosphere was originally defined as the important portion of soil near roots responsible for plant growth (by providing nutrients) or as source for plant diseases. Today its definition is much narrower, referring to the root with closely associated soil where microorganisms are influenced by the root. The rhizosphere is commonly subdivided spatially into the endo-rhizosphere (including root cortex, epiderma and root hairs) and the ecto-rhizosphere with root associated soil compartments up to a distance of 5 mm (Belandreau & Knowles, 1978).

The rhizosphere is an interesting area in which to study the interactions between plants and microbes. Plants alter the rhizobacterial community by releasing different substrates, which can vary from single sugar components to complex aromatic structures, and therefore selecting for increased numbers of certain taxa and/or functional groups of bacteria (Kravchenko et al, 2003). Microorganisms can also influence the plant by promoting or inhibiting growth (Glick et al, 1998).

Many of the interactions between microbes and plants are still unknown. In following projects of the Tiedje group the relationship between plants and rhizosphere bacteria are being investigated in the context of global climate change, bioremediation and the ecology of the genus Burkholderia.


Influence of global climate changes on microbial rhizosphere populations of grass land plants (Stephan Gantner)

The rhizosphere of plants harbors a microbial community potentially more responsive to ecosystem changes such as those induced by global climate change. Environmental changes affect the growth and metabolism of plants, and potentially root exudation of polyaromatic compounds which may influence the microbial population of polyaromatic degraders in the rhizosphere.

In this project we are investigating the influence of simulated global climate change effects on microbial diversity in the rhizosphere of grassland plants. We are using the 6-year old FACE (Free Air CO2 Enrichment) grass land field area at Jasper Ridge ( near Stanford, California. This work is part of the Jasper Ridge Global Change Experiment (JRGCE) coordinated by Prof C Field ( at the Carnegie Institute of Washington at Stanford University in California.

The grassland plants were exposed to treatments simulating effects of climate changes including higher levels of carbon dioxide, nitrate or/and higher temperatures. Avena and Geranium were selected as representative grassland plants and dynamic changes of the rhizobacterial community of were determined by t-RFLP-analysis. Results indicated that Geranium plants subjected to the climate change treatments influenced the microbial community. Community studies based on t-RFLP analysis and sequencing studies revealed differences between the rhizosphere population of non-treated grassland plants compared to those treated with elevated CO2 and higher NO3 concentrations. Bacteria that degrade different aromatic compounds were also analyzed using stable isotope probing (SIP) techniques [more about SIP - insert link to previous SIP section in bioremediation]. SIP experiments using 13C-labelled benzoate and biphenyl as substrates to detect aromatic compound degraders in the rhizosphere are currently underway.

Universal primers for aromatic oxygenase degrading genes were designed to identify aromatic compound degrading bacteria in environmental samples including the rhizosphere of plants. The functional genes of interest were biphenyl-2,3-dioxygenases (bphA) and benzoate-1,2-dioxygenase (benA), both involved in the first step of oxidizing the aromatic ring structure of the target molecules biphenyl and benzoate. In a cooperation with Prof. J Cole of the RDPII group ( in the Center for Microbial Ecology at Michigan State University we applied the biostatistical tool, HMMER, to implement a Hidden Markov Model (HMM) for biological sequence analysis. It allowed the collection of all protein structures similar to the targeted functional gene sequence from all online available databases, and compared those sequences to known sequences of biphenyl and benzoate degraders. Alignments of conserved gene regions performed with ARB yielded suitable primers to detect functional genes of aromatic compound degrading bacteria in the rhizosphere. Functional gene microarrays are being used to characterize the functional gene diversity of the rhizobacterial population of those grassland plants that have responded simulated global climate change conditions.

Contact: Stephan Gantner can be reached by e-mail at


Burkholderia (Alban Ramette)

(See summary under Organisms)


Rhizosphere bioremediation of PCBs (Mary Beth Leigh)

(See summary in Bioremediation)