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. 2012 Jul 25;7(7):e42149. doi: 10.1371/journal.pone.0042149

Table 5. Properties of group-specific primer pairs and their coverage for phylogenetic and environmental groups.

Specific groupingsa (%) Environ.b (%)
Primer set Pos.c Len.d nifH e Pr Cy III IA Fr Pb Ep IV Soil Mat Sea
ChenBR1/ChenBR2 18–698 681 19 35 0 0 7 75 0 0 0 NA 0 0
nifH-a1-forA/nifH-a1-rev 19–482 464 5 12 0 0 0 0 0 0 0 NA 0 0
nifH-f1-forA/nifH-f1-rev 19–482 464 3 0 0 0 0 92 0 0 0 NA 0 0
nifHF/nifHI 25–806 782 15 33 0 0 0 0 0 0 0 100 0 0
primer-3/primer-4 = AQE 37–453 417 0 0 0 0 0 0 0 0 0 0 0 0
nifHf1/nifH-269 43–341 299 1 0 0 0 0 19 0 0 0 0 0 0
nifHf1/nifHr 43–690 648 0 0 0 0 0 0 0 0 0 0 0 0
Olsen1/Olsen2 106–494 389 0 0 0 0 0 0 0 0 0 0 0 0
cyanoF/cyanoR 108–482 375 0 0 0 0 0 0 0 0 0 0 0 0
nifH-a1-forB/nifH-a1-rev 112–482 371 5 11 0 0 0 0 0 0 0 2 0 0
nifH-a2-forB/nifH-a2-rev 112–482 371 0 0 0 0 0 0 0 0 0 0 0 0
nifH-b1-forB/nifH-b1-rev 112–482 371 1 2 0 0 6 0 0 0 0 5 0 0
nifH-c1-forB/nifH-c1-rev 112–482 371 1 1 0 3 1 0 0 4 0 4 0 0
nifH-f1-forB/nifH-f1-rev 112–482 371 20 4 0 2 7 87 0 0 0 6 0 0
nifH-g1-forB/nifH-g1-rev 112–482 371 1 1 0 0 0 0 0 1 0 2 0 0
nifHFor/NifHRev 136–452 317 5 9 0 0 1 0 0 0 0 3 0 0
cylnif-F/cylnif-R 156–375 220 0 0 0 0 0 0 0 0 0 0 0 0
NIFH2F/NIFH5R 231–326 96 0 1 0 0 0 0 0 0 0 1 0 0
FGPH750/FGPD913′ 759−f 116 0 0 0 NA NA 0 NA NA 0 NA NA NA
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.