title: Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.
abstract: The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, 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 denitrification. 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.
authors.affiliation: The Institute for Genomic Research, Rockville, Maryland 20850, USA.
authors.forename: Naomi L
authors.initials: NL
authors.lastname: Ward
authors.forename: Jean F
authors.initials: JF
authors.lastname: Challacombe
authors.forename: Peter H
authors.initials: PH
authors.lastname: Janssen
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Coutinho
authors.forename: Martin
authors.initials: M
authors.lastname: Wu
authors.forename: Gary
authors.initials: G
authors.lastname: Xie
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Haft
authors.forename: Michelle
authors.initials: M
authors.lastname: Sait
authors.forename: Jonathan
authors.initials: J
authors.lastname: Badger
authors.forename: Ravi D
authors.initials: RD
authors.lastname: Barabote
authors.forename: Brent
authors.initials: B
authors.lastname: Bradley
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Brettin
authors.forename: Lauren M
authors.initials: LM
authors.lastname: Brinkac
authors.forename: David
authors.initials: D
authors.lastname: Bruce
authors.forename: Todd
authors.initials: T
authors.lastname: Creasy
authors.forename: Sean C
authors.initials: SC
authors.lastname: Daugherty
authors.forename: Tanja M
authors.initials: TM
authors.lastname: Davidsen
authors.forename: Robert T
authors.initials: RT
authors.lastname: DeBoy
authors.forename: J Chris
authors.initials: JC
authors.lastname: Detter
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Dodson
authors.forename: A Scott
authors.initials: AS
authors.lastname: Durkin
authors.forename: Anuradha
authors.initials: A
authors.lastname: Ganapathy
authors.forename: Michelle
authors.initials: M
authors.lastname: Gwinn-Giglio
authors.forename: Cliff S
authors.initials: CS
authors.lastname: Han
authors.forename: Hoda
authors.initials: H
authors.lastname: Khouri
authors.forename: Hajnalka
authors.initials: H
authors.lastname: Kiss
authors.forename: Sagar P
authors.initials: SP
authors.lastname: Kothari
authors.forename: Ramana
authors.initials: R
authors.lastname: Madupu
authors.forename: Karen E
authors.initials: KE
authors.lastname: Nelson
authors.forename: William C
authors.initials: WC
authors.lastname: Nelson
authors.forename: Ian
authors.initials: I
authors.lastname: Paulsen
authors.forename: Kevin
authors.initials: K
authors.lastname: Penn
authors.forename: Qinghu
authors.initials: Q
authors.lastname: Ren
authors.forename: M J
authors.initials: MJ
authors.lastname: Rosovitz
authors.forename: Jeremy D
authors.initials: JD
authors.lastname: Selengut
authors.forename: Susmita
authors.initials: S
authors.lastname: Shrivastava
authors.forename: Steven A
authors.initials: SA
authors.lastname: Sullivan
authors.forename: Roxanne
authors.initials: R
authors.lastname: Tapia
authors.forename: L Sue
authors.initials: LS
authors.lastname: Thompson
authors.forename: Kisha L
authors.initials: KL
authors.lastname: Watkins
authors.forename: Qi
authors.initials: Q
authors.lastname: Yang
authors.forename: Chunhui
authors.initials: C
authors.lastname: Yu
authors.forename: Nikhat
authors.initials: N
authors.lastname: Zafar
authors.forename: Liwei
authors.initials: L
authors.lastname: Zhou
authors.forename: Cheryl R
authors.initials: CR
authors.lastname: Kuske
mesh_terms: D000900:Anti-Bacterial Agents / Q000096:biosynthesis; D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification*; D001692:Biological Transport; D050260:Carbohydrate Metabolism; D000458:Cyanobacteria / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D005658:Fungi / Q000235:genetics; D016680:Genome, Bacterial; D018942:Macrolides / Q000378:metabolism; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000378:metabolism; D010802:Phylogeny; D020560:Proteobacteria / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D012988:Soil Microbiology
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D018942:Macrolides; D009584:Nitrogen