Properties of group-specific primer pairs and their coverage for phylogenetic and environmental groups.

a

Data 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). In some cases highly degenerate primers bind to multiple positions in the sequence generating coverage values that exceed 100%.

b

Primer 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).

c

Position of amplicon in nifH is relative to A. vinelandii nifH (Genbank ACCN# M20568).

d

Length expected for PCR amplicon.

e

Data indicate primer binding with 0 mismatches to all nifH sequences in the database.

f

This binding position for the reverse primer sequence lies beyond the stop codon of Frankia sp. (Genbank ACCN# M21132) and cannot be represented using the A. vinelandii numbering system.

NA Data not available as nucleotide information is not available for the target group in the region of primer binding.