Abstract
We developed a broad-ranging method for identifying key hydrogen-producing and consuming microorganisms through analysis of hydrogenase gene content and expression in complex anaerobic microbial communities. The method is based on a tiling hydrogenase gene oligonucleotide DNA microarray (Hydrogenase Chip), which implements a high number of probes per gene by tiling probe sequences across genes of interest at 1.67 × –2 × coverage. This design favors the avoidance of false positive gene identification in samples of DNA or RNA extracted from complex microbial communities. We applied this technique to interrogate interspecies hydrogen transfer in complex communities in (i) lab-scale reductive dehalogenating microcosms enabling us to delineate key H2-consuming microorganisms, and (ii) hydrogen-generating microbial mats where we found evidence for significant H2 production by cyanobacteria. Independent quantitative PCR analysis on selected hydrogenase genes showed that this Hydrogenase Chip technique is semiquantitative. We also determined that as microbial community complexity increases, specificity must be traded for sensitivity in analyzing data from tiling DNA microarrays.
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Acknowledgements
This work was supported by the Strategic Environmental Research Defense Project (SERDP) to AMS by Grant ER-1588. IPGM was supported by a Bio-X Graduate Research Fellowship through the Stanford University. We gratefully acknowledge useful comments by the editor and anonymous reviewers, useful discussions with Dagmar Woebken and a useful discussion of statistics with Gerald Teng and Jim Mussared. We also thank Shirley Galbiati for assistance in performing the sensitivity analysis hybridization.
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Marshall, I., Berggren, D., Azizian, M. et al. The Hydrogenase Chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities. ISME J 6, 814–826 (2012). https://doi.org/10.1038/ismej.2011.136
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DOI: https://doi.org/10.1038/ismej.2011.136
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