In this study, we utilized a shotgun metagenomic approach to examine the multiple effects of NO3- addition on vernal pool microbial communities in a microcosm experiment [17]. Two metagenomes were created, one for replicate microcosms that

received NO3- (labeled +NO3-) and one for replicate microcosms where NO3- was not added (labeled –N). Our previous study using these microcosms found that the addition of NO3- increased denitrification, while denitrification MRT67307 molecular weight was not detected in the absence of NO3- [17]. This functional change was not accompanied by any change in the denitrifier community structure, which was profiled with the nosZ gene using terminal restriction fragment length polymorphism (TRFLP) [17]. It is unclear, however, if this lack of response by the denitrifying community was physiological in nature or related to our functional gene choice. For the

shotgun metagenomic method utilized here, the microbial genomes were randomly amplified, thus allowing for the potential inclusion of multiple N cycling genes, as well as genes involved in other microbial processes. In addition to denitrifier community structure, our previous analyses used TRFLP to profile the structure of general bacteria and fungi, which also did not respond to NO3- addition [17]. Because shotgun metagenomes also provide taxonomic Selleckchem SB-715992 information for microbial selleckchem communities, we hypothesized that inclusion of more than one functional gene and obtaining taxonomic composition using a shotgun metagenomic approach would reveal community structural responses to NO3- pulses not observed with the profiling technique, TRFLP. Results For the +NO3- metagenome, there were 28,688 DNA fragments for a total of 9,085,193 bp and an average sequence length of 316 bp. The PAK5 –N metagenome contained

a larger number of DNA fragments with 81,300 and a total sequence length of 30,630,623 bp with an average fragment size of 376 bp. The metagenomes were uploaded to the Meta Genome Rapid Annotation of Sequence Technology (MG-RAST) server [18] and were analyzed unassembled with a BLASTX comparison to the SEED subsystems [19], which provided both taxonomic composition and metabolic functions. After applying our filters of 10-5 or lower e-value and 50 bp or greater sequence similarity, 7,406 sequences (+NO3-) and 14,063 sequences (−N) from the metagenomes matched with subsystems following the BLASTX analysis. The number of sequence matches to taxa with the BLASTX comparison were 6,342 (+NO3-) and 12,241 (−N). Each of these characterized DNA fragments represented an environmental gene tag (EGT), or a short segment of a gene found in the microcosm samples. The MG-RAST output included metabolic functions at four different levels, with subsystem category as the highest level and a specific gene as the lowest (see Table 1 for an example).