Rangeland plant community and species composition are known to be related to specific soil properties. The current study investigated the ecological influence (soil characteristics) on the selection and distribution of ecological-related genotypes of dominant xerophyte species in WadiSudr of Egypt. AFLP analysis reflected the genetic profile of the samples species from two altitudinal ranges (up and midstream) and was compared statistically with the differences of their inhabiting soil characteristics on two depth levels (20 and 40 cm) using Mantel test. Correlation values (r) ranged from 0.585 - 0.778 when treating the physical and chemical properties of soil samples regardless its altitudinal area. The correlation confirms that the soil chemical and physical properties influence the selection of a certain genotypes of the dominant xerophytes plants collected from Wadi Sudr of Egypt to certain altitude, while depths at 20 and 40 cm play a key role in the early growth and then the colonization of the selected genotypes, respectively. More studies are needed to exactly test the role and the importance of each of the correlated property to the plant growth and colonization.
In arid environments, soils are formed over time as climate and vegetation act on parent rock material. Relatively large rock fragments form due to physical disintegration; while only chemical weathering which can break up these fragments [
Wadi Sudr is one of the largest and most developed valleys of the southern section of the western coast of Sinai. The vegetation of W. Sudr is relatively rich in the variety of communities and species and also in having wide tracts covered by well-developed plant communities [
The most critical gradients in abiotic factors may be related to water presence, including annual precipitation and soil properties [
The objective of the current work was to study the physical and chemical properties of W. Sudr’s soil at two different altitudinal ranges (upstream and midstream), and to test the soil characteristics influence on the distribution of the xerophytic plant species dominate each range.
Wadi Sudr is located in the southern section of the western coast of Sinai, and lies between latitudes 29˚36'32''N - 29˚57'43''N, and longitudes 32˚41'28"E - 32˚17'27"E. It is bounded by Gebel El-Raha (c. 600 m) in the north and Sinn Bishr (c. 618 m) in the south (
Soil samples were collected at the surface (0 - 20 cm) and subsurface (20 - 40 cm) depths from sites were plant materials were collected in W. Sudr. Physical and chemical parameters of soil samples were analyzed. Soil particle size (%) was determined by the dry sieving to separate soil fractions according to Wentworth scale (American System) [
analyzed using principle component analysis (PCA). Groups & clusters defined for each layer based on PCA were used to construct Euclidean matrices for each group using PCO3 [
Three selected common xerophytic plant species were collected from both upstream and midstream ranges of W. Sudr, where they represent the dominant or the co-dominant species in both ranges. Those species are Reaumuria hirtella Jaub. & Spach(family Tamaricaceae), Retam araetam (Forssk.) Webb & Berthel (family Leguminosae) and Zygophyllum dumosum Boiss. (family Zygophyllaceae). Species names were abbreviated in the following text as Reau maria: Reaumuria hirtella, Retama: Retamaraetam, Zygo: Zygophyllum dumosum.
The DNA extractions were carried out from plant leaves of 3 species (2 samples each) using Wizard® Genomic DNA Purification Kit (PROMEGA, USA) by following the manufacturer’s manual. DNA quality was then tested using agrose gel electrophoresis (1%) contain 1 µl of EthBr (100 mg/ml), and electrophoresed for 1 h (4 V/cm).
The original protocol was followed [
Automated AFLP scoring was performed using both programs Peakscanner™ (Applied Biosystems, USA) and Rawgeno V2 for peak calling and automated scoring, according to the software’s manuals. The analysis of the AFLP data was based on the band-binary criterion (i.e. codifying the detected bands to, 1 when presence and 0 when absent) and processed according to [
The effect of the altitude and soil layer on the distribution of the studied plant species was tested using Mantel test (to measure the association between two matrices) implemented in GenAlEx V6 [
Most of the soil surrounding the studied plants in W. Sudr was mainly formed of fine sand and ranged from 10.92% to 55.82% (
Species | Reaumuria | Retama | Zygo | Reaumuria | Retama | Zygo | Reaumuria | Retama | Zygo | Reaumuria | Retama | Zygo |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Depth | 20 cm | 40 cm | ||||||||||
Site | Upstream | Midstream | Upstream | Midstream | ||||||||
V. fine gravel % | 27.28 | 8.28 | 0.08 | 27.57 | 0.00 | 2.86 | 1.70 | 27.75 | 20.38 | 15.59 | 16.65 | 23.21 |
V. coarse sand % | 19.96 | 9.05 | 0.18 | 14.05 | 0.03 | 9.56 | 2.98 | 21.38 | 24.71 | 8.81 | 13.05 | 11.86 |
Coarse sand % | 17.10 | 9.31 | 0.31 | 7.14 | 0.18 | 8.72 | 4.19 | 20.37 | 15.88 | 8.85 | 10.65 | 9.70 |
Medium sand % | 12.05 | 13.64 | 2.89 | 7.45 | 29.44 | 6.75 | 5.82 | 18.58 | 14.88 | 13.33 | 26.18 | 11.32 |
Fine sand % | 13.32 | 35.54 | 51.56 | 20.84 | 55.82 | 24.70 | 14.74 | 10.92 | 16.61 | 31.29 | 30.54 | 15.17 |
V. fine sand % | 8.04 | 19.39 | 37.19 | 15.33 | 12.23 | 28.66 | 40.59 | 0.85 | 5.52 | 17.99 | 2.21 | 18.67 |
Silt & Clay % | 2.25 | 4.79 | 7.79 | 7.62 | 2.30 | 18.75 | 29.98 | 0.15 | 2.02 | 4.14 | 0.72 | 10.07 |
pH | 7.63 | 7.76 | 7.34 | 6.63 | 8.03 | 7.80 | 8.26 | 8.14 | 8.11 | 7.35 | 8.66 | 7.70 |
EC dS∙m−1 | 13.00 | 2.28 | 3.53 | 22.33 | 1.15 | 0.72 | 3.83 | 1.08 | 2.43 | 1.52 | 0.37 | 2.19 |
Na+ meq/L | 114.0 | 10.18 | 25.41 | 178.2 | 3.22 | 2.62 | 26.22 | 4.49 | 12.19 | 3.12 | 2.24 | 3.04 |
K+ meq/L | 2.12 | 0.36 | 0.49 | 1.93 | 0.39 | 0.29 | 0.68 | 0.23 | 0.58 | 0.29 | 0.02 | 0.22 |
Ca2+ meq/L | 41.00 | 8.18 | 4.87 | 68.04 | 5.13 | 2.16 | 8.74 | 4.49 | 5.18 | 7.98 | 0.67 | 8.64 |
Mg2+ meq/L | 19.50 | 4.09 | 4.53 | 41.58 | 2.80 | 2.16 | 2.66 | 1.63 | 6.33 | 3.80 | 0.67 | 9.92 |
Cl− meq/L | 113.6 | 15.59 | 25.59 | 264.6 | 3.65 | 2.46 | 22.72 | 5.19 | 13.52 | 2.98 | 1.49 | 2.20 |
61.19 | 6.54 | 6.93 | 20.83 | 6.94 | 2.96 | 14.44 | 5.02 | 9.59 | 10.69 | 1.96 | 18.82 | |
1.0 | 0.0 | 0.7 | 0.7 | 0.0 | 1.1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.38 | |
1.14 | 0.61 | 1.15 | 0.80 | 0.14 | 1.14 | 0.8 | 0.7 | 2.1 | 1.1 | 0.9 | 3.2 |
12.50 and 76.19. Data indicated that CaCO3% of soil surrounding Retama raetam in the upstream attained the highest values among the soil surrounding the studied species (76.19 at the depth between 20 - 40 cm) and the lowest value in the midstream (12.50 at the depth between 20 - 40 cm).
Xero-halophyte plants are naturally able to inhabit alkaline soils with high EC profile. The current analysis showed that the soil reaction pH was mostly alkaline (pH 6.63 to 8.66). Electrical conductivity (EC) of the soil profiles in midstream-20 cm recorded the highest value (22.33 dS∙m−1) around Reaumuria hirtella that scored the lowest pH value (6.63) (
In the present investigation, the soil chemical properties and very fine soil texture are the most important factors affecting in distribution and vegetation cover of halophytes in the midstream, while the larger soil particles and CaCO3 were the most effective factors on the distribution of xerophytes in the up and midstream of W. Sudr.
By applying t-test between layers for each of the estimated parameter in each altitudinal area (upstream & midstream), no significant differences between the 20 cm and 40 cm depth were found (values are not shown). Four clusters (sets) and two singletons were successfully defined based on the PCA results for upland & midland (20 cm) and upland & midland (40 cm). Set-1 included “Very fine gravel percentage, very coarse sand percentage, and coarse sand percentage”, that all were soil physical properties. Set-2 included “Medium sand percentage and pH”. While Set-3 included “Fine sand percentage, very fine sand percentage and silt & clay percentage”. The largest set, number 4 included the chemical properties of the soil samples (EC, Na+, K+, Ca2+, M2+, Cl− and
The physical and chemical properties of the sampled soil were statistically deviated and grouped in 4 sets and 2 singletons, in which data treatment should address each set and/or singleton separately to avoid any misleading correlation values. While no significant differences between both depths were proved by t-test, the four grouped sets and the two singletons consistently appeared the same between both depths. Based on that fact, the Euclidean matrices based on physical and chemical properties of soil samples were estimated for each set separately considering the altitudinal area (upstream & midstream).
Three selective fluorescently labeled primers (Mse CTC-Eco AGG, Mse CTC-Eco ACA and Mse CTC-Eco ATA) successfully amplified 367 bands (112, 148 and 107, respectively; binary data not shown). Band scoring was successful at fluorescence rate unit of 100 rfu with an average bin size 0.33. Technical homoplasy confirmed the presence of one peak per bin. Average peak rate ranged from 106 - 148 peak/sample, while its molecular size ranged from 50 - 424 bp. After refining only six loci out of the 367 were retained (
Primer Pairs | Mw (bp) | Reaumuria sp. | Retama sp. | Zygo sp. | |||
---|---|---|---|---|---|---|---|
Upstream | Midstream | Upstream | Midstream | Upstream | Midstream | ||
CTC-AGG | 169 | 1 | 0 | 1 | 0 | 1 | 0 |
146 | 1 | 0 | 1 | 0 | 1 | 0 | |
91 | 1 | 0 | 1 | 0 | 1 | 0 | |
CTC-ACA | 237 | 0 | 1 | 0 | 1 | 1 | 0 |
95 | 1 | 0 | 1 | 0 | 1 | 0 | |
CTC-ATA | 191 | 1 | 0 | 0 | 1 | 1 | 0 |
fied due to the natural genetic relatedness of the genomes within the same species and the genetic differentiation of the genomes among the three studied species. The 6 loci should reflect the variation continuum among the species and within each species. In Funaria hygrometrica 13 out of 1864 AFLP loci were detected to be under selection using computer software among samples from Sierra Nevada Mountains of Spain, the 13 loci proved to be correlated to the maximum temperatures of each sampled location [
Refined data is expected to be the candidate loci in which the environmental selection force is applied. To test such hypothesis, correlation tests showed different significant and insignificant correlations between the altitudinal group, physical & chemical properties and the genetic distance based on unrefined and refined data. Euclidean matrices based on the physical and chemical soil properties were estimated for both layers (
Set1 | Reaumuria-U | Retama-U | Zygo-U | Reaumuria-M | Retama-M | Zygo-M |
---|---|---|---|---|---|---|
Reaumuria-U | 0.000 | 35.762 | 30.948 | 15.768 | 19.148 | 23.914 |
Retama-U | 23.253 | 0.000 | 9.250 | 20.942 | 16.943 | 15.003 |
Zygo-U | 37.590 | 15.064 | 0.000 | 18.033 | 13.312 | 14.537 |
Reaumuria-M | 11.585 | 20.045 | 31.539 | 0.000 | 4.727 | 8.252 |
Retama-M | 37.785 | 15.273 | 0.214 | 31.703 | 0.000 | 6.734 |
Zygo-M | 27.834 | 5.476 | 12.901 | 25.164 | 13.112 | 0.000 |
Set2 | Reaumuria-U | Retama-U | Zygo-U | Reaumuria-M | Retama-M | Zygo-M |
Reaumuria-U | 0.000 | 12.761 | 9.061 | 7.565 | 20.364 | 5.528 |
Retama-U | 1.595 | 0.000 | 3.700 | 5.309 | 7.618 | 7.273 |
Zygo-U | 9.165 | 10.758 | 0.000 | 1.726 | 11.313 | 3.584 |
Reaumuria-M | 4.707 | 6.292 | 4.615 | 0.000 | 12.917 | 2.040 |
Retama-M | 17.395 | 15.802 | 26.559 | 22.035 | 0.000 | 14.891 |
Zygo-M | 5.303 | 6.890 | 3.887 | 1.363 | 22.691 | 0.000 |
Set3 | Reaumuria-U | Retama-U | Zygo-U | Reaumuria-M | Retama-M | Zygo-M |
Reaumuria-U | 0.000 | 49.837 | 44.891 | 38.110 | 50.782 | 29.616 |
Retama-U | 25.080 | 0.000 | 7.595 | 26.919 | 19.675 | 20.833 |
Zygo-U | 48.402 | 24.135 | 0.000 | 19.378 | 14.377 | 15.485 |
Reaumuria-M | 11.770 | 15.511 | 37.704 | 0.000 | 16.164 | 17.190 |
Retama-M | 42.706 | 21.650 | 25.909 | 35.518 | 0.000 | 24.384 |
Zygo-M | 28.757 | 19.958 | 30.238 | 17.789 | 38.846 | 0.000 |
Set4 | Reaumuria-U | Retama-U | Zygo-U | Reaumuria-M | Retama-M | Zygo-M |
Reaumuria-U | 0.000 | 29.916 | 18.247 | 30.738 | 35.536 | 32.144 |
Retama-U | 157.545 | 0.000 | 13.192 | 7.480 | 6.649 | 16.991 |
Zygo-U | 142.035 | 18.574 | 0.000 | 14.487 | 18.945 | 17.955 |
Reaumuria-M | 172.722 | 309.576 | 293.909 | 0.000 | 11.992 | 10.256 |
Retama-M | 170.384 | 14.257 | 31.345 | 323.757 | 0.000 | 20.929 |
Zygo-M | 173.576 | 16.869 | 33.027 | 325.925 | 5.204 | 0.000 |
Jaccard’s | Reaumuria-U | Retama-U | Zygo-U | Reaumuria-M | Retama-M | Zygo-M |
---|---|---|---|---|---|---|
Reaumuria-U | 0 | 5 | 1 | 6 | 1 | 5 |
Retama-U | 190 | 0 | 4 | 1 | 6 | 2 |
Zygo-U | 192 | 98 | 0 | 5 | 2 | 6 |
Reaumuria-M | 180 | 120 | 146 | 0 | 5 | 1 |
Retama-M | 185 | 105 | 97 | 157 | 0 | 4 |
Zygo-M | 206 | 104 | 96 | 142 | 111 | 0 |
In
Without refining (regardless the species type effect), the correlation values were insignificant to all uplands sets, while only negatively correlated to Set3 at 40 cm depth with high significance (p-value < 0.0001). However, correlation values ranged from 0.585 - 0.778 when treating the physical and chemical properties of soil samples regardless its altitudinal area with Set1-20 and 40, Set3-40 and Set4-40. The correlation observed between the genetic variation among the sampled species with the physical properties of the soil Set1 (the percentage of, very fine gravel, very coarse sand, and coarse sand) at both depths (20 and 40 cm), reflects the importance of such soil properties to the inhabiting of the collected species germination, early growth and rooting in both depths.
While the correlation to the physical properties of the soil Set3 (the percentage of, fine sand, very fine sand and silt & clay) and to the chemical properties Set4 (EC, Na me/l, K me/l, Ca me/l, Mg me/l, Cl me/l and SO4) at only 40 cm depth. That would draw our attention to importance of such soil properties to later stages of the plant later growth and colonization in these lands. More studies are needed to exactly test the role and the importance of each of the correlated property to the plant growth and colonization.
The correlation signs (negative or positive) are of no biological relevance, as the genetic variation is not directional and it was generated due to the statistical nature of Mantel test [
Other observation worth mentioning that, after refining the correlation was statistically higher (r-value < 0.80) and stronger (p-value < 0.0001) and the genetic variation is only related to uplands or midlands, but not to both (regardless of the altitudinal area) due to the selection of loci, which subsequently proves the quality of the manual refining.
In arid regions, many taxa occurring exhibit a historically fragmented distribution. Soil type contributes in this fragmentation as proven by the current results, in accordance with previous studies [
The AFLP technique treat a certain mutational action (e.g. single nucleotide polymorphism) that impact the absence of a certain band (score 0 in the binary table) vs the presence of the same band (score 1 in the binary table) in the same species but at a different altitudinal area. Thus, the strong statistical correlations between the genetic variation among genotypes and the soil properties reflect the ability of a certain genotype to exist and germinate in a certain soil. In such case, the species is known to have an adaptive genetic variation, and that the environmental factors play an important role in the selection mechanism of such species. The detection of adaptive loci represents only a first step in a comprehensive understanding of how selection shapes genomic divergence between locations. The further step is to identify exactly the genomic regions or genes and ultimately, the
Clusters | Set1-20 | Set1-40 | Set2-20 | Set2-40 | Set3-20 | Set3-40 | Set4-20 | Set4-40 | |
---|---|---|---|---|---|---|---|---|---|
Unrefined AFLP loci | |||||||||
Up | r-value | 0.789 | 0.982 | −0.620 | 0.906 | 0.545 | 0.992 | 0.993 | 0.720 |
p-value | 0.167 | 0.500 | 0.500 | 0.500 | 0.167 | 0.500 | 0.500 | 0.500 | |
Mid | r-value | 1.000 | −0.395 | −0.223 | −0.335 | −0.339 | −0.978 | 0.946 | −0.888 |
p-value | 0.167 | 0.833 | 0.833 | 0.833 | 0.833 | <0.0001 | 0.500 | 0.500 | |
Both | r-value | 0.714 | 0.585 | −0.296 | 0.277 | 0.291 | 0.778 | 0.490 | 0.656 |
p-value | 0.003 | 0.028 | 0.300 | 0.327 | 0.283 | 0.003 | 0.066 | 0.011 | |
Refined AFLP loci | |||||||||
Up | r-value | −0.820 | −0.110 | −0.567 | 0.137 | −0.962 | −0.173 | −0.178 | 0.450 |
p-value | <0.0001 | 0.833 | 0.500 | 0.833 | <0.0001 | 0.833 | 0.833 | 0.833 | |
Mid | r-value | 0.073 | −0.935 | 0.964 | 0.927 | 0.925 | 0.166 | −0.283 | 0.420 |
p-value | 0.833 | <0.0001 | 0.167 | 0.167 | 0.167 | 0.833 | 0.833 | 0.833 | |
Both | r-value | −0.173 | −0.067 | −0.101 | −0.180 | −0.137 | −0.182 | −0.194 | 0.104 |
p-value | 0.545 | 0.802 | 0.712 | 0.526 | 0.631 | 0.495 | 0.473 | 0.706 |
mutations involved in the adaptation. But the lack of sequence information given by anonymous AFLP loci remains a major limitation to undertake this second step. As a solution, recently developed techniques based on Next Generation Sequencing (NGS) like Restriction-Site Associated DNA (RAD) [
As a conclusion, the current results confirm statistically that the soil chemical and physical properties influence the selection of a certain genotypes of the dominant xerophytes plants collected from W. Sudr of Egypt to certain altitude, while depths at 20 and 40 cm play a key role in the early growth and then colonization of selected genotypes, respectively. However, more studies are still needed to complete the background knowledge in order to design an efficient conservation program of such species.
Esraa Attia El Sherbeny,Amal Ahmed Morsy,Mahmoud Magdy, (2016) Soil Characteristics Influence the Selection of Dominant Plant Genotypes Inhabiting Wadi Sudr, Egypt. American Journal of Plant Sciences,07,1304-1315. doi: 10.4236/ajps.2016.78125