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Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray
Patrick K H Lee1, Dan Cheng, Ping Hu
1Department of Civil and Environmental Engineering, University of California, Berkeley, USA.
The ISME Journal
|January 14, 2011
Summary
Comparative genomics revealed that closely related Dehalococcoides strains can have different dechlorination functions due to varied reductive dehalogenase genes, highlighting the need for detailed genomic analysis.
Area of Science:
- Environmental microbiology
- Genomics
- Bioremediation
Background:
- Dehalococcoides are key microorganisms for reductive dechlorination of chlorinated ethenes.
- Understanding genome-physiology relationships is crucial for optimizing bioremediation strategies.
- Existing genomic data for Dehalococcoides is limited, hindering comprehensive comparative studies.
Purpose of the Study:
- To investigate genome-physiology relationships in newly isolated Dehalococcoides strains using a custom microarray.
- To compare the genomic content and dechlorination capabilities of Dehalococcoides strains ANAS1, ANAS2, and their enrichment source (ANAS).
- To assess the utility of microarrays for high-throughput comparative genomics of Dehalococcoides.
Main Methods:
- Design and validation of a microarray targeting 98.6% of open-reading frames from sequenced Dehalococcoides strains.
- Application of the microarray to query the genomes of Dehalococcoides strains ANAS1, ANAS2, and the ANAS enrichment.
- Physiological characterization of chlorinated ethene reduction by the strains.
- Comparative genomic analysis to identify similarities and differences in gene content.
Main Results:
- Strains ANAS1 and ANAS2 can reduce trichloroethene, cis-dichloroethene, and 1,1-DCE, but not tetrachloroethene or trans-DCE.
- Only strain ANAS2 couples vinyl chloride reduction to growth.
- Genomes of ANAS1 and ANAS2 are similar to each other and strain 195, with variations in high-plasticity regions.
- Physiological differences correlate with the presence of distinct reductive dehalogenase genes (pceA, tceA, vcrA).
Conclusions:
- Closely related Dehalococcoides strains can exhibit distinct physiological capabilities in chlorinated ethene degradation.
- The incongruence between phylogeny and physiology is linked to variations in reductive dehalogenase genes.
- Microarrays serve as effective tools for high-throughput comparative genomics of unsequenced Dehalococcoides, providing insights into dechlorination functions.
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