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

Table 1. Properties of universal primers and their coverage for phylogenetic and environmental groupings in the nifH database; continued in Table 2.

nifH a (%) Specific groupingsb (%) Environ.c (%)
Primerd Name Pos.e Deg.f Tm (°C) 0 1 2 Pr Cy III IA Fr Pb Ep IV Soil Mat Sea Ref.g
GCIWTYTAYGGNAARGG Nh21F 19–35 64 51.8–61.9 93 96 103 89 100 100 100 100 91 83 76 78 100 100 [42]
GCIWTITAYGGNAARGGNGG nifH19F 19–38 128 59.5–69.5 94 96 96 89 100 100 100 100 91 100 79 78 100 100 [43]
GCIWTYTAYGGIAARGGIGG Ueda19F 19–38 16 62.4–67.9 93 96 96 89 100 100 100 100 91 83 76 78 100 100 [44]
GCIWTHTAYGGIAARGGIGGIATHGGIAA IGK3 19–47 72 69.4–75.3 92 95 95 87 100 98 96 100 91 100 78 72 100 100 [45]
GCGTTCTACGGTAAGGGCGGTATCGGNAAR K07-F 19–48 8 71.0–72.8 1 3 10 2 0 0 0 0 0 0 0 0 0 0 [27]
TTYTAYGGNAARGGNGG nifH4 22–38 128 49.8–63.5 52 91 94 71 100 4 43 93 91 13 23 43 100 78 [46]
TCTACGGAAAGGGCGGTATCGG primer-f 23–44 1 66.5 10 14 31 13 0 13 0 0 0 23 0 0 0 0 [47]
TACGGCAARGGTGGNATHG FGPH19 25–43 24 58.2–66.2 7 24 63 9 0 4 1 71 0 2 4 3 0 0 [48]
TACGGYAARGGBGGYATCGG IGK-Polyh 25–44 24 60.3–70.6 18 50 72 22 45 6 16 29 17 0 9 6 100 33 [20]
TACGG(P/K)AAKGG(P/G)GG(P/K)ATPGG PicenoF44 25–44 8 NA 50 85 96 59 96 35 25 79 33 59 31 34 100 89 [49]
TAYGGIAARGGIGGIATYGGIAARTC F1 25–50 4096 60.4–74.5 79 95 96 84 100 69 65 93 83 87 80 83 100 100 [18]
GGHAARGGHGGHATHGGNAARTC MehtaF 28–50 1296 57.4–72.9 59 78 87 46 96 77 44 94 44 51 69 67 100 100 [5]
AARGGNGGNATHGGNAAi IGK 31–47 384 62.1–72.5 90 98 104 91 100 93 70 95 89 94 95 95 100 100 [26]
AAAGGYGGWATCGGYAARTCCACCAC nifHF-Röschh 31–56 16 66.0–71.6 14 25 44 11 34 5 9 70 22 14 0 34 100 5 [24]
AAAGGYGGWATCCGYAARTCCACCAC rösch F-1bh 31–56 16 66.0–71.6 0 14 25 0 0 0 0 0 0 0 0 0 0 0 [25]
GGTATYGGYAARTCSACSAC RL28 37–56 32 57.7–64.1 41 70 84 43 21 41 62 57 6 12 3 24 100 5 [50]
ATHGTIGGITGYGAYCCIAARGCIGA KAD3 106–131 16 70.1–76.8 70 84 94 89 90 15 80 97 80 82 1 70 100 24 [45]
GGNTGYGAYCCNAARGC 469 112–128 128 53.4–67.4 88 92 98 82 94 92 95 98 79 96 35 77 100 73 [20]
GGITGTGAYCCNAAVGCNGA nif112 112–131 96 60.9–70.4 29 90 92 21 37 30 34 36 28 69 11 30 60 22 [43]
GGITGYGAYCCNAAVGCNGA nifH-univ-f112 112–131 192 60.9–72.7 88 91 98 82 91 92 96 98 79 97 35 77 100 73 [21]
TGYGAYCCNAARGCNGA nifH2 115–131 128 54.0–68.1 95 98 98 93 98 96 98 98 98 96 37 93 99 89 [16]
TGYGAYCCIAARGCIGA Kadino 115–131 8 60.2–67.9 95 98 98 93 98 96 98 98 98 96 37 93 99 89 [20]
TGYGAYCCIAAIGCIGA F2 115–131 4 62.3–67.9 96 98 98 94 98 98 99 99 98 98 37 94 99 93 [18]
TGCGAYCCSAARGCBGACTC polF 115–134 24 63.8–70.1 39 70 88 51 12 26 41 61 34 6 3 54 15 8 [20]
GAYCCNAARGCNGACTC nifH11 118–134 64 52.7–63.4 72 96 98 79 67 50 82 97 78 48 17 78 66 55 [51]
CTCCGGGCCRCCNGAYTC FGPH273′ 262–279 16 63.7–70.7 11 44 79 11 0 3 6 93 0 3 1 14 2 5 [48]
GMRCCIGGIGTIGGYTGYGC nifH-2f 277–296 16 69.2–78.3 87 99 99 92 80 74 94 98 95 72 20 85 85 79 [19]
CCRCCRCANACMACGTC Cy55Nh428R 388–404 32 56.6–67.5 66 94 99 68 76 49 63 76 55 49 23 56 65 80 [42]
AAICCRCCRCAIACIACRTC Ueda407R 388–407 8 63.9–70.6 91 99 99 92 95 85 90 99 64 79 71 87 95 93 [44]
ATIGCRAAICCICCRCAIACIACRTC DVV 388–413 8 71.7–75.8 94 98 99 93 94 94 96 98 90 95 52 91 96 93 [45]
GGCATNGCRAANCCVCCRCANAC MehtaR 394–416 768 63.2–75.1 92 98 99 92 94 89 95 98 89 89 49 89 97 92 [5]
a

Data 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%.

b

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).

c

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).

d

Sequences are given in the 5′ to 3′ direction, IUPAC characters are used, and I = Inosine.

e

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

f

Degeneracy is given as the number of oligonucleotides that comprise the primer.

g

References in which the primers are described.

h

We altered these primer names in order to distinguish them from primers with similar name and sequence composition that originate from other sources.

i

The 5′ linker sequence ATA GGA TCC was removed from this primer.

NA: Data not available as described in Methods.