LEGENDS TO THE SUPPLEMENTARY FIGURES
Supplementary Figure S1: Principal Coordinates Analysis (PCoA) of weighted
UniFrac distances between soil samples. Samples are color-coded to indicate the
different managements: Green corresponds to natural environments (NE), blue to
Good no-till agricultural practices (GAP); red are Poor no-till Agricultural Practices
(PAP). Localities are indicated by symbols: squares (Bengolea), circles (Monte Buey),
diamonds (Pergamino) and triangles (Viale). A) Ellipses are 99% confidence
intervals of group centroids for each geographical location (ordiellipses function in R
vegan package (Oksanen et al. 2012); B) Ellipses are 99% confidence intervals of
group centroids for each management type (Oksanen et al. 2012)
Supplementary Figure S2: Rarefaction curves indicating the observed number of
OTUs within the 16S rRNA gene sequences in each of the twelve sites, considering
the three pseudo-replicates per sampling and the three sampling dates. OTUs are
shown at the 3% genetic distance level. Samples are color-coded to indicate the
different managements: Green corresponds to natural environments (NE), blue to
Good no-till agricultural practices (GAP); red are Poor no-till Agricultural Practices
(PAP). Localities are indicated by symbols: squares (Bengolea), circles (Monte Buey),
diamonds (Pergamino) and triangles (Viale).
Supplementary Figure S3: Species (OTUs) rarefaction curves of 16S sequences
classified at the phylum level for all the soil samples. Purple: Planctomycetes; green:
Proteobacteria; black: Actinobacteria; blue: Acidobacteria; gray: Gemmatimonadetes;
light blue: Verrucomicrobia; yellow: WS3; Red: SPAM.
Supplementary Figure S4: Histograms of pairwise phylogenetic distances for
major phyla, between soils samples from within each soil management type.
Distributions are color-coded to indicate the different managements: Green
corresponds to natural environments (NE), blue to Good no-till agricultural
practices (GAP); red are Poor no-till Agricultural Practices (PAP).
A
0
.
0
0
VIA
MB
PE
−0
.
0
5
B
−0
.
1
0
PCoA 2
0
.
0
5
0
.
1
0
Supplementary Figure S1
−0
.
2
−0
.
1
0
.
0
PCoA 1
0
.
1
0
.
1
0
0
.
0
0
PAP
NE GAP
−0
.
1
0
−0
.
0
5
PCoA 2
0
.
0
5
B
−0
.
2
−0
.
1
0
.
0
PCoA 1
Supplementary Figure S2
0
.
1
Supplementary Figure S3
Number of OTUs
3,000
2,000
1,000
0
0
10,000
20,000
30,000
Number of sequences
40,000
Supplementary Figure S4
Supplementary Figure S4 (cont)
Supplementary Table S1: Measures of α-diversity and pairwise statistics between different soil
managements
Good no-till
Agricultural
Practices
Poor no-till
Agricultural
Practices
Richness (R)1
580 ± 13
563 ± 13
Shannon (H)1
5.69 ± 0.03
5.60 ± 0.04
Diversity Index
1
2
NE vs GAP
PAP vs GAP
NE vs PAP
p value2
p value2
p value2
568 ± 13
0.4
0.3
0.7
5.64 ± 0.04
0.4
0.2
0.6
Natural
Environments
Indices and standard errors are least square estimates from LMM
P values were obtained from F statistics (Satterthwaite approximation to denominator DOF) with difflsmeans in lmer
test, which tested the null hypothesis that means were not significantly different between soil mangements
Supplementary Table S2: Sequence of crops practiced from 2000 to 2011 in the eight agricultural sites examined in this study. PAP
refers to the operational definition of Poor no-till Agricultural Practices; GAP refers to Good no-till Agricultural Practices
Location/Year
2000/2001
2001/2002
2002/2003
2003/2004
PAP Bengolea
N/A
N/A
N/A
N/A
PAP Monte
Buey
Soybean *
PAP
Pergamino
N/A
N/A
PAP Viale
N/A
N/A
GAP Bengolea
Corn
Soybean
Wheat/Soybean
Corn
Corn
Wheat/Soybean
GAP Monte
Buey
Wheat/Soybean
GAP
Pergamino
N/A
GAP Viale
Corn
Wheat/soybean
N/A
Wheat/Soybean
2004/2005
2005/2006
2006/2007
Wheat *
Soybean *
Soybean
Corn
Soybean
Soybean
Wheat/soybean
Corn
N/A
N/A
Soybean
Soybean
Soybean
Corn
Soybean
Wheat/Soybean
Wheat/Soybean
Corn
Wheat/Soybean
Corn
Wheat/Sorghum
Corn
Wheat/Soybean
N/A
Soybean
Wheat/Soybean
Corn
Wheat/Soybean
Ryegrass/Corn
Soybean
Soybean
N/A
Corn
Wheat/Soybean
Soybean
Supplementary Table S2 (cont)
Location/Year
2007/2008
PAP Bengolea
2008/2009
2009/2010
2010/2011
Wheat/Soybean Soybean
Corn
Soybean
PAP Monte
Buey
Soybean
Soybean
Soybean
Wheat/soybean
PAP
Pergamino
Soybean
Soybean
Soybean
Soybean
PAP Viale
Corn
Soybean
Soybean
Wheat/Soybean
GAP Bengolea
Vicia/Corn
Wheat/Soybean Soybean
GAP Monte
Buey
Vicia/Corn
Corn
GAP
Pergamino
Soybean
Wheat/Soybean Corn
GAP Viale
Wheat/Soybean Corn
N/A: Data not available
* Managed under conventional tilling
Corn
Wheat/Soybean Vicia/Corn
Soybean
Soybean
Corn
Suppl. Appendix S1: Mixed effect linear models. Proposed full models containing
agricultural practice as fixed factor and site, sampling, sample and all possible
interactions as random effects. Reduced models derived from automatic backward
elimination of non-significant effects.
1. MEAN NEAREST TAXON DISTANCE
Full model:
fm1= lmer(mntd.obs ~ Land Use +(1|Land Use:Site)+(1|Sampling:Site)+(1|Land
Use:Sampling)+(1|Sample:Sampling)+(1|Sample:Site)+(1|Land
Use:Sample)+(1|Site)+(1|Sample)+(1|Sampling),data=tabla)
Reduced model:
rm1=lmer(mntd.obs ~ Land Use + (1 | Land Use:Sample) + (1 | Site)
2. WIDELY DISTRIBUTED AND ENDEMIC Taxa
a. Endemic Taxa
Full model:
fm2= lmer(Endemic ~ Land Use +(1|Land Use:Site)+(1|Sampling:Site)+(1|Land
Use:Sampling)+(1|Sample:Sampling)+(1|Sample:Site)+(1|Land
Use:Sample)+(1|Site)+(1|Sample)+(1|Sampling),data=tabla)
Reduced model:
rm2=lmer( Endemic ~ Land Use + (1 | Land Use:Sample) + (1 | Site) + (1 | Sampling),
data = tabla)
b. Widely distributed Taxa
Full model:
fm3=lmer(Widely ~ Land Use +(1|Land Use:Site)+(1|Sampling:Site)+(1|Land
Use:Sampling)+(1|Sample:Sampling)+(1|Sample:Site)+(1|Land
Use:Sample)+(1|Site)+(1|Sample)+(1|Sampling),data=tabla)
Reduced model:
rm3=lmer(Widely ~ Land Use + (1 | Sample:Sampling) +
(1 | Site), data = tabla)
(1 | Land Use:Sample) +
3. α diversity
a. Richness
Full model:
fm4= lmer(Taxa ~ Land Use +(1|Land Use:Site)+(1|Sampling:Site)+(1|Land
Use:Sampling)+(1|Sample:Sampling)+(1|Sample:Site)+(1|Land
Use:Sample)+(1|Site)+(1|Sample)+(1|Sampling),data=tabla)
Reduced model:
rm4= lmer(Taxa ~ Land Use + (1 | Land Use:Site) + (1 | Sampling), data = tabla)
b. Shannon Index
Full model:
fm5= lmer(Shannon_H~ Land Use +(1|Land Use:Site)+(1|Sampling:Site)+(1|Land
Use:Sampling)+(1|Sample:Sampling)+(1|Sample:Site)+(1|Land
Use:Sample)+(1|Site)+(1|Sample)+(1|Sampling),data=tabla)
Reduced model:
rm5=lmer(Shannon_H ~ Land Use + (1 | Land Use:Site), data = tabla)
Reference
Oksanen, J., Blanchet, F.G., Kindt, R., Legendre, P., Minchin, R.B., O’Hara, R.B. et al.
(2012). vegan: Community Ecology Package. R Package version 2.0-5. Available at:
http://CRAN.R-project.org/package=vegan