Ecological Archives C006-041-A1
J. S. Norman, L. Lin, and J. E. Barrett. 2015. Paired carbon and nitrogen metabolism by ammonia-oxidizing bacteria and archaea in temperate forest soils. Ecosphere 6:176. http://dx.doi.org/10.1890/es14-00299.1
Appendix A. AOA and AOB community analysis methods.
AOA and AOB community structure was not of primary concern in this study; we only used these data to find the dominant community members of each group. What follows is a brief description of our community analysis methods, which are outlined in more detail elsewhere (Norman 2013). Briefly, replicate DNA extractions were pooled from each site and then shipped to Molecular Research LP (Shallowater, TX, USA) for amlpicon-based pyrosequencing of AOA and AOB functional genes using group-specific primers: amoA-1F* (Stephen et al. 1998) and amoA-2R (Rotthauwe et al. 1997) were used for AOB, while Arch-amoA-1F* and Arch-amoA-2R were used for AOA (Francis et al.2005) (*Indicates sequencing primer). Sequence analysis was performed using MOTHUR (Schloss et al. 2009), following the Schloss lab 454 SOP (Schloss et al. 2011). Sequences were clustered into operational taxonomic units (OTU) at 94% sequence similarity as recommended for functional genes (Konstantinidis and Tiedje 2005) and representative sequences from each OTU were classified using the non-redundant protein database using blast (NCBI).
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