Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.
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.
Ward
Naomi L
NL
The Institute for Genomic Research, Rockville, Maryland 20850, USA.
Challacombe
Jean F
JF
Janssen
Peter H
PH
Henrissat
Bernard
B
Coutinho
Pedro M
PM
Wu
Martin
M
Xie
Gary
G
Haft
Daniel H
DH
Sait
Michelle
M
Badger
Jonathan
J
Barabote
Ravi D
RD
Bradley
Brent
B
Brettin
Thomas S
TS
Brinkac
Lauren M
LM
Bruce
David
D
Creasy
Todd
T
Daugherty
Sean C
SC
Davidsen
Tanja M
TM
DeBoy
Robert T
RT
Detter
J Chris
JC
Dodson
Robert J
RJ
Durkin
A Scott
AS
Ganapathy
Anuradha
A
Gwinn-Giglio
Michelle
M
Han
Cliff S
CS
Khouri
Hoda
H
Kiss
Hajnalka
H
Kothari
Sagar P
SP
Madupu
Ramana
R
Nelson
Karen E
KE
Nelson
William C
WC
Paulsen
Ian
I
Penn
Kevin
K
Ren
Qinghu
Q
Rosovitz
M J
MJ
Selengut
Jeremy D
JD
Shrivastava
Susmita
S
Sullivan
Steven A
SA
Tapia
Roxanne
R
Thompson
L Sue
LS
Watkins
Kisha L
KL
Yang
Qi
Q
Yu
Chunhui
C
Zafar
Nikhat
N
Zhou
Liwei
L
Kuske
Cheryl R
CR
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
D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D018942:Macrolides; D009584:Nitrogen