S126: Comparison of metagenomics technologies to differentiate the effects of elevated CO2 on soil microbial communities

Recent development and application of high throughput metagenomic technologies have revolutionarized the analysis of microbial community structure. Various high throughput metagenomics technologies have been extensively used for characterizing microbial community diversity and structure, including shotgun sequencing, PCR-based amplicon sequencing, GeoChip, PhyloChip, phenotypic arrays, and fatty acid analysis. In this study, the performances of various types of high throughput metageniomic technologies were compared using 24 samples (12 under elevated CO₂, 12 under ambient CO₂). Our results indicated that GeoChip provided the best resolution in separating the effects of elevated CO₂ from ambient CO₂ on microbial community structure compared to 16S rRNA gene-based amplicon pyrosequencing, which has higher resolution than PhyloChip.  While the effects on community structure can be clearly separated based on fatty acid analysis, no differences can be discerned based on phenotypic arrays. Surprisingly, no significant difference can be observed by shotgun sequencing of all 24 soil samples with 454 and Illumina platforms although more than 150Gb sequences were generated, which is mostly due to the effects of random sampling processes. Mathematical simulation indicated that the artifacts associated with random sampling processes are problematic with high throughput sequencing-based detection approaches. However, the array-based approaches could not provide discovery of new genes overall although it has a great advantage in sample comparison by minimizing the effects of random sampling process. Our studies indicated that different high throughput technologies have different advantages and disadvantages and they should be used in a complementary fashion based on biological questions.