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PMID: 19088312 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Linking sequence to function in soil bacteria: sequence-directed isolation of novel bacteria contributing to soilborne plant disease suppression.

Applied and environmental microbiology ·Vol. 75 ·No. 4 ·2009-02-00 ·Pages 915-24

Benítez MS, Gardener BB

Abstract

Microbial community profiling of samples differing in a specific ecological function, i.e., soilborne plant disease suppression, can be used to mark, recover, and ultimately identify the bacteria responsible for that specific function. Previously, several terminal restriction fragments (TRF) of 16S rRNA genes were statistically associated with damping-off disease suppression. This work presents the development of sequence-based TRF length polymorphism (T-RFLP)-derived molecular markers to direct the identification and isolation of novel bacteria involved in damping-off pathogen suppression. Multiple sequences matching TRF M139 and M141 were cloned and displayed identity to multiple database entries in the genera incertae sedis of the Burkholderiales. Sequences matching TRF M148, in contrast, displayed greater sequence diversity. A sequence-directed culturing strategy was developed using M139- and M141-derived markers and media reported to be selective for the genera identified within this group. Using this approach, we isolated and identified novel Mitsuaria and Burkholderia species with high levels of sequence similarity to the targeted M139 and M141 TRF, respectively. As predicted, these Mitsuaria and Burkholderia isolates displayed the targeted function by reducing fungal and oomycete plant pathogen growth in vitro and reducing disease severity in infected tomato and soybean seedlings. This work represents the first successful example of the use of T-RFLP-derived markers to direct the isolation of microbes with pathogen-suppressing activities, and it establishes the power of low-cost molecular screening to identify and direct the recovery of functionally important microbes, such as these novel biocontrol strains.

MeSH Terms
Betaproteobacteria/classification,genetics,isolation & purification DNA Fingerprinting DNA, Bacterial/chemistry,genetics DNA, Ribosomal/chemistry,genetics Genes, rRNA Lycopersicon esculentum/microbiology,physiology Molecular Sequence Data Phylogeny Plant Diseases/microbiology Polymorphism, Restriction Fragment Length RNA, Bacterial/genetics RNA, Ribosomal, 16S/genetics Sequence Analysis, DNA Sequence Homology, Nucleic Acid Soil Microbiology Soybeans/microbiology,physiology
Chemicals
DNA, Bacterial DNA, Ribosomal RNA, Bacterial RNA, Ribosomal, 16S
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Benítez María-Soledad
Department of Plant Pathology, The Ohio State University, OARDC, 1680 Madison Avenue, Wooster, OH 44691, USA.
Gardener Brian B McSpadden
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Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
1098-5336
DOI
10.1128/AEM.01296-08
Published
2009-02-00
Epub
2008-00-16
Pages
915-24
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC2643568
Subset
IM
Databases
GENBANK
EU714905, EU714906, EU714907, EU714908, EU714909, EU714910, EU714911, EU714912, EU714913, EU714914, EU714915, EU714916, EU714917, EU714918, EU714919, EU714920, EU714921, EU714922, EU714923, EU714924, EU714925, EU714926, EU714927, EU714928, EU714929, EU714930, EU714931, EU714932, EU714933, EU714934, EU714935, EU714936, EU714937, EU714938, EU714939, EU714940, EU714941, EU714942, EU714943, EU714944, EU714945, EU714946, EU714947, EU714948, EU714949, EU714950, EU714951, EU714952, EU714953, EU714954, EU714955, EU714956
External Links
PubMed source DOI: 10.1128/AEM.01296-08 PMC Full Text View journal details
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