1
2 (3)
Methanobacterium thermoautotrophicum Delta H
Methanococcus vannielii SB
Methanococcus maripaludis S2
Azotobacter vinelandii AvOP
Rhodopseudomonas palustris BisA53
Rhodospirillum rubrum TCC 11170
Chloroherpeon thalassium ATCC 35110
Methanosarcina acetivorans C2A
Methanosarcina acetivorans C2A
Clostridium kluyveri NBRC 12016
Azotobacter vinelandii AvOP
Anabaena variabilis ATCC 29413
Anabaena variabilis ATCC 29413
Methanocaldococcus infernus ME
Methanocaldococcus vulcanius M7
Methanocaldococcus sp. FS406 22
Methanothermococcus okinawensis IH1
Methanococcus aeolicus Nankai 3
Syntrophothermus lipocalidus DSM 12680
Candidatus Desulfordis audaxviator MP104C
Caldicellulosiruptor saccharolytics DSM 8903
Rosiflexus castenholzii DSM 13941
Rosiflexus sp. RS 1
Oscillochloris trichoides
Opitutaceae bacterium TAV2
Syntrophobacter fumaroxidans MPOB
Cand. A. pseudotrichonymphae CFP2
Chlorobium tepidum TLS
Chloroherpeton thalassium ATCC 35110
Dehalococcoides ethenogenes 195
Desulfovibrio vulgaris Dp4
Cand. Methanosphaerula palustris E1-9c
Desulftomaculum reducens MI-1
Alkaliphilus metalliredigens QYMF
Clostridium acetobutylicum ATCC 824
Clostridium beijerinckii NCIMB 8052
Methanosarcina mazei Goe1
Methanosarcina acetivorans C2A
Desulfitobacterium hafniense Y51
Heliobacterium modesticaldum Ice1
Pelobacter carbinolicus DSM 2380
Geobacter lovleyi SZ
Geobacter sp. M21
Thermodesulfovibrio yellowstonii DSM 11347
Azotobacter vinelandii AvOP
Klebsiella pneumoniae 342
Nostoc sp. PCC 7120
Synechococcus sp. JA-2-3Ba
Lyngbya sp. PCC 8106
Methylacidiphilum infernorum V4
Rhodobacter sphaeroides ATCC 17025
Magnetospirillum magnetotacticum MS-1
Rhodospirillum centenum SW
Sinorhizobium medicae WSM419
Zymomonas mobilus ZM4
Rhodopsuedomonas palustris HaA2
Acidithiobacillus ferrooxidans ATCC 23270
Methylocella silvestris BL2
Beijerinckia indica ATCC 9039
Anabaena variabilis ATCC 29413 Chl
Chlorobium limicola DSM 245 Bch
Uncharacterized
Uncharacterized nitrogenase
Mo-nitrogenase
V-nitrogenase
Fe-nitrogenase
0.35
4
3 (2)
M.
lot
i
S.
me
lilo
ti
R. rubrum
R. caps ulatu s NifHD
R. sp ah ero ide s
B.
fu ng
or um
R . p a lu
st
ri s
N o ct o c P C C 7 1 2 0
N . pu nc tif or m e
A. vin ela nd ii
K. pneu moni ae NifHD
Frankia NifHD
D. hafni ense
C. acetobutylicum
C. tepid um
M. maze i
M . ac et ivo ra ns
M
.
b
a
rk
e
ri
N
if
H
D
M . th er m oa ut ot ro ph ic um
M
.
ba
rk
er
i
Vn
fH
D
R. capsulatus
R.
palus
tris A.
vin
ela
nd
ii
A . vi ne
la nd ii
R . p a lu st ri s
M
.
a
ce
tiv
o
ra
n
s
R
.
ru
br
um
M.
ac
eti
vo
ran
s
M.
bark
eri
AnfH
D
M. therm oauto troph icum
M. janna schii
M. barke ri NflH2
M
. a ce
tiv
o ra
n s
M . m a ze i
M
. a c e ti v o ra
n s
R
. c a p s u la
tu
s
R . pa lu st ris
D. ha fn ien se
R. pa lus
tri s
R. pal ust ris
D. hafniense
R. rubrum
F. nucleatum
M. ka nd ler i
M. ba rke ri Nif H
R. capsulatus XY
R. sph aer oid es XY
R. ru br um XY
R . pa lu st ris X Y
C
.
a
u
ra
n
ti
a
c
u
s
X
Y
C
.
te
p
id
u
m
X
Y
R . ca ps ul at us LN
R
.
s
p
h
a
e
ro
id
e
s
L
N
R
.
pa
lu
st
ris
LN R.
ru
br
um
LN
C.
au
ran
tia
cu
s
LN
C.
tepid
um
LN
T.
elong
atus
LN
Syne
choc
ystis
LN
No
sto
c
LN
N
.
pu
nc
tif
or
m
e
LN
0.2 subst/site
Mo-dependent
nitrogenase
cluster 1
cluster 3 (2)
cluster 2 (3)
Mo-independent
nitrogenase
uncharacterized
nitrogenase
Pigment
biosynthesis
a
b
Fig.2.2 (a). Concatenated nitrogenase gene phylogeny. Modified from Boyd et al. (2011).
Reprinted with permission. (b). nifH phylogeny (Raymond et al. 2004). Reprinted with permission. Clusters 2 and 3 annotated as in Zehr et al. (2003), with Raymond et al. (2004) annotation in
parentheses. Note that as more sequences and genomes are added, the nomenclature for major
groups may change
2 (3)
Methanobacterium thermoautotrophicum Delta H
Methanococcus vannielii SB
Methanococcus maripaludis S2
Azotobacter vinelandii AvOP
Rhodopseudomonas palustris BisA53
Rhodospirillum rubrum TCC 11170
Chloroherpeon thalassium ATCC 35110
Methanosarcina acetivorans C2A
Methanosarcina acetivorans C2A
Clostridium kluyveri NBRC 12016
Azotobacter vinelandii AvOP
Anabaena variabilis ATCC 29413
Anabaena variabilis ATCC 29413
Methanocaldococcus infernus ME
Methanocaldococcus vulcanius M7
Methanocaldococcus sp. FS406 22
Methanothermococcus okinawensis IH1
Methanococcus aeolicus Nankai 3
Syntrophothermus lipocalidus DSM 12680
Candidatus Desulfordis audaxviator MP104C
Caldicellulosiruptor saccharolytics DSM 8903
Rosiflexus castenholzii DSM 13941
Rosiflexus sp. RS 1
Oscillochloris trichoides
Opitutaceae bacterium TAV2
Syntrophobacter fumaroxidans MPOB
Cand. A. pseudotrichonymphae CFP2
Chlorobium tepidum TLS
Chloroherpeton thalassium ATCC 35110
Dehalococcoides ethenogenes 195
Desulfovibrio vulgaris Dp4
Cand. Methanosphaerula palustris E1-9c
Desulftomaculum reducens MI-1
Alkaliphilus metalliredigens QYMF
Clostridium acetobutylicum ATCC 824
Clostridium beijerinckii NCIMB 8052
Methanosarcina mazei Goe1
Methanosarcina acetivorans C2A
Desulfitobacterium hafniense Y51
Heliobacterium modesticaldum Ice1
Pelobacter carbinolicus DSM 2380
Geobacter lovleyi SZ
Geobacter sp. M21
Thermodesulfovibrio yellowstonii DSM 11347
Azotobacter vinelandii AvOP
Klebsiella pneumoniae 342
Nostoc sp. PCC 7120
Synechococcus sp. JA-2-3Ba
Lyngbya sp. PCC 8106
Methylacidiphilum infernorum V4
Rhodobacter sphaeroides ATCC 17025
Magnetospirillum magnetotacticum MS-1
Rhodospirillum centenum SW
Sinorhizobium medicae WSM419
Zymomonas mobilus ZM4
Rhodopsuedomonas palustris HaA2
Acidithiobacillus ferrooxidans ATCC 23270
Methylocella silvestris BL2
Beijerinckia indica ATCC 9039
Anabaena variabilis ATCC 29413 Chl
Chlorobium limicola DSM 245 Bch
Uncharacterized
Uncharacterized nitrogenase
Mo-nitrogenase
V-nitrogenase
Fe-nitrogenase
0.35
4
3 (2)
M.
lot
i
S.
me
lilo
ti
R. rubrum
R. caps ulatu s NifHD
R. sp ah ero ide s
B.
fu ng
or um
R . p a lu
st
ri s
N o ct o c P C C 7 1 2 0
N . pu nc tif or m e
A. vin ela nd ii
K. pneu moni ae NifHD
Frankia NifHD
D. hafni ense
C. acetobutylicum
C. tepid um
M. maze i
M . ac et ivo ra ns
M
.
b
a
rk
e
ri
N
if
H
D
M . th er m oa ut ot ro ph ic um
M
.
ba
rk
er
i
Vn
fH
D
R. capsulatus
R.
palus
tris A.
vin
ela
nd
ii
A . vi ne
la nd ii
R . p a lu st ri s
M
.
a
ce
tiv
o
ra
n
s
R
.
ru
br
um
M.
ac
eti
vo
ran
s
M.
bark
eri
AnfH
D
M. therm oauto troph icum
M. janna schii
M. barke ri NflH2
M
. a ce
tiv
o ra
n s
M . m a ze i
M
. a c e ti v o ra
n s
R
. c a p s u la
tu
s
R . pa lu st ris
D. ha fn ien se
R. pa lus
tri s
R. pal ust ris
D. hafniense
R. rubrum
F. nucleatum
M. ka nd ler i
M. ba rke ri Nif H
R. capsulatus XY
R. sph aer oid es XY
R. ru br um XY
R . pa lu st ris X Y
C
.
a
u
ra
n
ti
a
c
u
s
X
Y
C
.
te
p
id
u
m
X
Y
R . ca ps ul at us LN
R
.
s
p
h
a
e
ro
id
e
s
L
N
R
.
pa
lu
st
ris
LN R.
ru
br
um
LN
C.
au
ran
tia
cu
s
LN
C.
tepid
um
LN
T.
elong
atus
LN
Syne
choc
ystis
LN
No
sto
c
LN
N
.
pu
nc
tif
or
m
e
LN
0.2 subst/site
Mo-dependent
nitrogenase
cluster 1
cluster 3 (2)
cluster 2 (3)
Mo-independent
nitrogenase
uncharacterized
nitrogenase
Pigment
biosynthesis
a
b
Fig.2.2 (a). Concatenated nitrogenase gene phylogeny. Modified from Boyd et al. (2011).
Reprinted with permission. (b). nifH phylogeny (Raymond et al. 2004). Reprinted with permission. Clusters 2 and 3 annotated as in Zehr et al. (2003), with Raymond et al. (2004) annotation in
parentheses. Note that as more sequences and genomes are added, the nomenclature for major
groups may change