Burkholderia species have tremendous versatility: they can efficiently degrade pollutants in water and soil, fix atmospheric nitrogen, or help plants fight against their pathogens; hence they contribute to a healthy, CO₂-fixing ecosystem. Burkholderia also occupy diverse habitats from soil to rhizosphere (root zone) to water to intimate associations with plants and animals, even living intracellularly in amoebas, for example. They have among the largest prokaryote genomes (7 to 9.7 Mb), consisting of three replicons, the smaller two exhibiting a faster evolutionary rate and considerable plasticity. This rather unique genome structure is thought to contribute to Burkholderia’s characterization as a “versaphile”.

Thus far , the members of the Burkholderia cepacia complex (Bcc) and the narrow group of Burkholderia pathogens outside the Bcc have been sequenced. This selection gives a very narrow insight into the genomics of the genus. Most of the Burkholderia in nature are non-pathogenic, probably are not members of the Bcc, and probably live in the rhizosphere of plants. This project logically extends Burkholderia genomics in two significant ways: by gaining genomic insight into environmentally important members outside the Bcc and pathogen groups, and by helping elucidate what traits are important to rhizosphere competence and plant benefit. Burkholderia are major nitrogen fixing associates of plants in the two largest CO₂-sequestering ecosystems in the western hemisphere, the Amazon rainforest and the Cerrado (Brazilian savannah). These soil-microbe-plant communities are the functional unit of an ecosystem, not the plant in isolation. Of the three species to be sequenced for this project, one was isolated from the Amazon rain forest, one comes from the Cerrado, and one is the type strain of grass root colonizers.

Principal Investigators: James M. Tiedje, Jorge M. Rodrigues, and Terence L. Marsh (Michigan State Univ.); Mariangela Hungria (EMBRAPA, Londrina, Brazil); Fatima S. Moreira (Univ. Fed. de Lavras, Brazil); Ana Tereza R Vasconcelos (Lab. Nac. de Computacao Cientifica, Brazil); and Patrick G. Chain (Lawrence Livermore Natl. Lab.)

Burkholderia strains are involved in carbon cycling and contribute to a healthy, carbon dioxide-fixing environment by fixing atmospheric nitrogen and helping to counter plant pathogens. The bacteria are also known for their ability to break down pollutants in soil and water such as the organic chemical trichloroethene. The abundance of these bacteria in nature suggests they have a larger role in maintaining the biogeochemistry of the planet than is currently known.

Isolated from an onion field, the B. cenocepacia strain isolated from an onion field was previously sequenced by the DOE JGI. Researchers have tracked this strain over several hundred generations and found that the bacteria favor forming biofilms, microbial communities that adhere to a solid substrate. Bacterial communities in the form of biofilms are found throughout the environment but the cause of their diversity remains unclear. In studying the biofilms formed by B. cenocepacia, researchers have found that the bacteria have developed into three distinct morphological genotypes: Studded (S), Ruffled (R) and Wrinkly (W). Researchers now intend to resequence Burkholderia, specifically, these S, W and R mutants, to identify the molecular bases of the mutations that led to these adaptations and to learn more about whether or not biofilm adaptation and diversification is predictable.

Principal Investigators: Vaughn Cooper, University of New Hampshire

Program: CSP 2010