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Genome Studies Reveal Insight into Unique Soil Bacterial PhylumMembers of the bacterial phylum, Acidobacteria, were found to be dominant members of the soil microbial community, when LANL scientists [Cheryl Kuske (B-6) and colleagues] and others discovered them in environmental surveys using molecular techniques over a decade ago. Although Acidobacteria have been detected by DNA-based techniques in all soils and sediments worldwide and in a wide variety of marine and freshwater environments, they have been extremely difficult to culture using standard microbiology techniques. Several thousand sequence types exist in nature, yet less than six isolated species have been cultured and characterized. Because of the difficulty culturing this group of microbes, little is known about their biology, physiology or roles in the environment. However, the abundance of acidobacteria in soils and their ability to withstand polluted and extreme environments suggest that they play important roles in cycling carbon and other processes affecting plant growth and terrestrial ecosystems. The Kuske lab used flow cytometry cell sorting to isolate cells of Acidobacteria from environmental samples. In collaboration with Peter Janssen (University of Melbourne, Australia), who had successfully cultured two Acidobacteria isolates from soil, and the DOE Joint Genome Institute, the Kuske lab used the genome sequences from the two cultured isolates to identify potential physiological traits in these bacteria that would provide insight into their lifestyles in soil. In parallel, the Institute for Genomic Research (TIGR) sequenced the genome of a third Acidobacteria species from an acid mine drainage. The LANL, Joint Genome Institute, and TIGR researchers published a paper on the three Acidobacteria genomes and traits suggested by their genome sequence. The researchers’ goal was to identify potential acidobacterial traits that indicate ecological roles for members of this phylum in soil so that these might be tested more directly in soil environments. They scientists focused on acidobacterial traits that may contribute to survival and growth in soil, including their transporters and their abilities to use carbon, cycle nitrogen, scavenge iron, and produce antimicrobial compounds. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. The bacteria share metabolic traits with other bacteria, and, surprisingly, with fungi. The scientists conclude that individual bacterial cells are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration. These culture and genomic traits are consistent with a broad metabolic capability and a lifestyle suited to slow growth in nutrient-limited environments. Reference: “Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils”, Applied and Environmental Microbiology 75, 2046 (2009). LANL researchers include Jean F. Challacombe, Ravi D. Barabote, Thomas S. Brettin, David Bruce, J. Chris Detter, Cliff S. Han, Hajnalka Kiss, Roxanne Tapia, L. Sue Thompson, and Cheryl R. Kuske. The DOE Microbial Genome Program and the DOE Joint Genome Institute supported the LANL work. |
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