Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils

Naomi L. Ward, Jean F. Challacombe, Peter H. Janssen, Bernard Henrissat, Pedro M. Coutinho, Martin Wu, Gary Xie, Daniel H. Haft, Michelle Sait, Jonathan Badger, Ravi D. Barabote, Brent Bradley, Thomas S. Brettin, Lauren M. Brinkac, David Bruce, Todd Creasy, Sean C. Daugherty, Tanja M. Davidsen, Robert T. DeBoy, J. Chris Detter & 26 others Robert J. Dodson, A. Scott Durkin, Anuradha Ganapathy, Michelle Gwinn-Giglio, Cliff S. Han, Hoda Khouri, Hajnalka Kiss, Sagar P. Kothari, Ramana Madupu, Karen E. Nelson, William C. Nelson, Ian Paulsen, Kevin Penn, Qinghu Ren, M. J. Rosovitz, Jeremy D. Selengut, Susmita Shrivastava, Steven A. Sullivan, Roxanne Tapia, Sue Thompson, Kisha L. Watkins, Qi Yang, Chunhui Yu, Nikhat Zafar, Liwei Zhou, Cheryl R. Kuske

Research output: Contribution to journalArticle

473 Citations (Scopus)

Abstract

The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenese analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobac-teria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N 2 fixation or denitriflcation. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. 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. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.

Original languageEnglish
Pages (from-to)2046-2056
Number of pages11
JournalApplied and Environmental Microbiology
Volume75
Issue number7
DOIs
Publication statusPublished - Apr 2009
Externally publishedYes

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