Properties of universal primers and their coverage for phylogenetic and environmental groupings in the nifH database; continued in Table 2.

aData indicate primer binding to all nifH sequences in the database with 0, 1, and 2 mismatches allowed. In some cases highly degenerate primers bind to multiple positions in the sequence generating coverage values that exceed 100%.bData indicate primer binding to specific groupings in the nifH phylogeny. Abbreviations are as follows: Alpha, Beta, and Gamma Proteobacteria (Pr); Cyanobacteria (Cy); Cluster III (III); Cluster IA (IA); Paenibacillus (Pb); Frankia (Fr); Epsilon Proteobacteria Containing Cluster (Ep); paralogous sequences in Cluster IV (IV).cPrimer coverage queried against sequences recovered from specific environments (Environ.) as described in methods. Environments include: soils (Soil), microbial mats (Mat), and pelagic marine samples (Sea).dSequences are given in the 5′ to 3′ direction, IUPAC characters are used, and I = Inosine.ePosition is relative to A. vinelandii nifH (Genbank ACCN# M20568).fDegeneracy is given as the number of oligonucleotides that comprise the primer.gReferences in which the primers are described.hWe altered these primer names in order to distinguish them from primers with similar name and sequence composition that originate from other sources.iThe 5′ linker sequence ATA GGA TCC was removed from this primer.NA: Data not available as described in Methods.