Supplemental Materials:
In situ phylogenetic structure and diversity of wild Bradyrhizobium communities
J. L. Sachs, S.W. Kembel, A. H. Lau, & E. L. Simms
Protocol for MAG media
-
MAG Media Reagents (per liter)
1.1g MES
1.3g HEPES
1.0g Arabinose (DL)
1.0g Gluconic Acid~Sodium Salt)
1.0g Yeast extract
2ml KH2PO4 Solution (110g/L)
4ml Na2SO4 Solution (62.5 g/L)
1ml MgSO4 • 7H2O Solution (180g/L)
2ml NH4Cl Solution (160g/L)
1ml CaCl2 Solution (13g/L)
1ml FeCl3 • 6H2O Solution (6.7g/L)
Adjust pH to 6.6 with KOH
Autoclave for 40 minutes
Supplemental Tables
Supplemental Table 1. Plant numbers and species collected at each unique GPS site
Site GPS Coordinates Plants Collected
1 38o19'070 N, 123o03'560 W L. heermannii 15 and 17, L. strigosus 14 and 16
2 38o19'100 N, 123o03'440 W L. strigosus 20-25
3 38o19'158 N, 123o03'820 W L. strigosus 7, 8 and 11
4 38o19'158 N, 123o03'824 W L. strigosus 1-4
5 38o20'560 N, 123o03'566 W L. heermannii 33
6 38o20'570 N, 123o03'459 W L. heermannii 34
7 38o20'571 N, 123o03'460 W L. micranthus 28
8 38o20'602 N, 123o03'458 W L. micranthus 30
9 38o20'623 N, 123o03'495 W L. micranthus 27
10 38o20'642 N, 123o03'504 W L. micranthus 26
11 38o20'649 N, 123o03'514 W L. micranthus 29
Supplemental Table 2. Number of isolates and sequenced genotypes from different microenvironments and hosts.
A. Samples among all host species
|
All
|
Nodule
|
Root surface
|
Root tips
|
Old Roots
|
Isolates
|
280
|
172
|
108
|
76
|
32
|
Genotypes
|
69
|
25
|
51
|
40
|
23
|
B. Samples within each host species
| L. Angustissimus |
L. Heermannii
|
L. Micranthus
|
L. strigosus
|
Isolates
|
19
|
61
|
42
|
158
|
Genotypes
|
19
|
22
|
25
|
28
|
Supplemental Table 3.
Sampling type and spatial location of all sequenced isolates
Table 3. Sampling type and spatial location of all sequenced isolates. Isolate source = year (05=2005), plant species (LoA = Lotus angustissimus, LoM = L. micranthus, LoH = L. heermannii, LoS = L. strigosus), and nodule or root surface numbers. Genotype ID = isolate name or GenBank accession when unique, multiply recovered genotypes are named with the host species (A, M, H, S), isolate type(s) (N = nodule, R = root surface) and the total number of isolates that share the genotype. Type = isolation type (nod = nodule, old = mature portion of the root surface, tip = root surface tip. Lat = latitude and Long = longitude. Nod =Nodulation status (Y = positive nodulation in all five test plants, N = lack of nodulation in all five test plants, ‘-‘ = untested). Genbank = GenBank Accession number.
Isolate Source
|
Genotype ID
|
Type
|
Lat
|
Long
|
Nod
|
GenBank
|
05LoA29.1
|
LoA29.1
|
Nod
|
38o20'649
|
123o03'514
|
_
|
FJ766042
|
05LoA29.10
|
LoA29.10
|
Nod
|
38o20'649
|
123o03'514
|
_
|
FJ766040
|
05LoA29.12
|
AHMN14
|
Nod
|
38o20'649
|
123o03'514
|
_
|
FJ766047
|
05LoA29.3
|
AHMN14
|
Nod
|
38o20'649
|
123o03'514
|
_
|
FJ766047
|
05LoA29.4
|
AHMN14
|
Nod
|
38o20'649
|
123o03'514
|
_
|
FJ766047
|
05LoA29.5
|
AHMN14
|
Nod
|
38o20'649
|
123o03'514
|
_
|
FJ766047
|
05LoA29R4.2
|
LoA29R4.2
|
Old
|
38o20'649
|
123o03'514
|
_
|
FJ766077
|
05LoA30.1
|
AHMN14
|
Nod
|
38o20'602
|
123o03'458
|
_
|
FJ766047
|
05LoA30.10
|
AHMN14
|
Nod
|
38o20'602
|
123o03'458
|
_
|
FJ766047
|
05LoA30.11
|
AHMN14
|
Nod
|
38o20'602
|
123o03'458
|
_
|
FJ766047
|
05LoA30.3
|
AHMN14
|
Nod
|
38o20'602
|
123o03'458
|
_
|
FJ766047
|
05LoA30.4
|
AHMN14
|
Nod
|
38o20'602
|
123o03'458
|
_
|
FJ766047
|
05LoA30.5
|
AHMN14
|
Nod
|
38o20'602
|
123o03'458
|
_
|
FJ766047
|
05LoA30.6
|
AHMN14
|
Nod
|
38o20'602
|
123o03'458
|
_
|
FJ766047
|
05LoA30.9
|
LoA30.9
|
Nod
|
38o20'602
|
123o03'458
|
_
|
FJ766044
|
05LoA30R6.7
|
AR_HMN3
|
Tip
|
38o20'602
|
123o03'458
|
_
|
FJ766041
|
05LoA30R7.16
|
LoA30R7.16
|
Old
|
38o20'602
|
123o03'458
|
_
|
FJ766091
|
05LoA30R8.17
|
AHR2
|
Old
|
38o20'602
|
123o03'458
|
_
|
FJ766025
|
05LoA30R8.19
|
LoA30R8.19
|
Old
|
38o20'602
|
123o03'458
|
_
|
FJ766082
|
05LoH15.1
|
HSNR34
|
Nod
|
38o19'070
|
123o03'560
|
Y
|
FJ766029
|
05LoH15.10
|
HMSNR94
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766051
|
05LoH15.11
|
HSNR34
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766029
|
05LoH15.12
|
HSNR34
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766029
|
05LoH15.2
|
HSNR34
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766029
|
05LoH15.3
|
HMSNR94
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766051
|
05LoH15.4
|
HMSNR94
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766051
|
05LoH15.5
|
HMSNR94
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766051
|
05LoH15.6
|
HMSNR94
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766051
|
05LoH15.7
|
HSNR34
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766029
|
05LoH15.8
|
HMSNR94
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766051
|
05LoH15.9
|
HSNR34
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766029
|
05LoH15R2.45
|
HMR2
|
Old
|
38o19'070
|
123o03'560
|
N
|
FJ766030
|
05LoH15R2.47
|
LoH15R2.47
|
Old
|
38o19'070
|
123o03'560
|
_
|
FJ766069
|
05LoH15R2.48
|
LoH15R2.48
|
Old
|
38o19'070
|
123o03'560
|
N
|
FJ766031
|
05LoH15R5.50
|
HSNR34
|
Old
|
38o19'070
|
123o03'560
|
Y
|
FJ766029
|
05LoH15R5.51
|
HSR2
|
Old
|
38o19'070
|
123o03'560
|
_
|
FJ766068
|
05LoH15R8.7
|
LoH15R8.7
|
Old
|
38o19'070
|
123o03'560
|
N
|
FJ766055
|
05LoH15R8.9
|
HMSNR94
|
Old
|
38o19'070
|
123o03'560
|
_
|
FJ766051
|
05LoH17.10
|
HSNR34
|
Nod
|
38o19'070
|
123o03'560
|
Y
|
FJ766029
|
05LoH17.11
|
HSNR34
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766029
|
05LoH17.12
|
HMSNR94
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766051
|
05LoH17.13
|
HMSNR94
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766051
|
05LoH17.14
|
HMSNR94
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766051
|
05LoH17.3
|
HMSNR94
|
Nod
|
38o19'070
|
123o03'560
|
_
|
FJ766051
|
05LoH17.4
|
HSNR34
|
Nod
|
38o19'070
|
| |