plant patchiness effect on microbial community
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Title: Effect of plant patchiness on soil microbial community structure
Authors: A. Nejidat, E. Ben-David, Y. Sher, R. Golden, E. Zaady and Z. Ronen
Department of Environmental Hydrology and Microbiology, Zukerberg Institute for Water Research, Blaunstein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer
Drylands, Deserts and Desertification-14.12.2008, Sede Boqer
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Aim: to examine the effect of plant and plant type on bulk soil microbial community structure and activity in patchy desert
landscape
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Research locationsLong Term Ecological Research SitesSayeret Shaked• Northern Negev• Semiarid grassland• Long term average rainfall - 200 mm
Avdat• Central Negev• Arid land• Long term average rainfall - 90 mm
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Thymelaea hirsute (Th)
Dominant shrubs – Sayeret Shaked
Noaea mucronata (Nm)
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Dominant shrubs - Avdat
Hammada scoparia (Hs)Zygophyllum dumosum (Zd)
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Methods
- Phospholipids fatty acid (PLFA) analysis (major
microbial groups)
- Denaturing gradient gel electrophoresis (DGGE)
of phylogenetic DNA markers (species diversity)
and Real Time PCR for gene copy quantification
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Sampling: Winter 2007
• Soil samples under plant canopy (SUC) samples
• Soil samples from intershrub spaces (ISP):• ISPA- Avdat• ISPS- Shaked
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ResultsSelected soil chemical parameters in Avdat and Shaked sampling sites.
NO3--N
mg/kg
NO2--N
mg/kg
TAN mg/kg
OM (%)
RWC (%)
EC μScm-1
pH Samples
46.17
0.97
9.67
2.38
7.05
2130
8.03
Zd 51.04
0.19
7.47
2.60
4.98
1958
8.40
Hs
25.68
0.01
6.50
1.68
5.28
748
8.41
ISPA 21.31
0.05
6.14
2..28
4.33
287
8.27
Nm
22.04
0.24
6.97
2.30
5.23
232
8.11
Th 18.60
0.01
4.79
1.07
4.35
174
8.39
ISPS
ANOVA Statistics
<0.01 ns <0.05 ns ns <0.001 ns Avdat vs. Shaked <0.01 ns <0.1 ns ns <0.001 ns SUCA vs. SUCB <0.05 ns ns <0.1 ns <0.1 ns SUCA vs. BSCA
Ns ns <0.05 <0.01 ns <0.005 <0.05 SUCS vs. BSCS <0.01 ns <0.05 <0.1 ns <0.1 ns BSCA vs. BSCS
- - - - - - <0.05 Zd vs. Hs, BSCA
Average values and standard deviation are indicated (n=3). Significant difference between groups of
replicates/samples was tested using one-way ANOVA followed by Tukey’s multiple comparison test; p value is
indicated; ns, not significant. SUCA, soil under canopy from Avdat; SUCB, soil under canopy from Shaked; BSCA,
biological soil crust from Avdat; BSCB, biological soil crust from Shaked.
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(a) PCA ordination of the PLFA relative abundance data (mol %) for all of Avdat sampling sites
(b) PCA ordination of the PLFA relative abundance data (mol %) for all of Shaked sampling sites
(a) (b)
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(a) Redundancy ordination (RDA) triplot of sites, PLFA relative abundance (mol %) and soil quality variables for all of Avdat sampling sites (based on first two axes).
(b) RDA triplot of sites, PLFA relative abundance (mol %) and soil quality variables for all of Shaked sampling sites (based on first two axes)
a b
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RDA triplot of sites, PLFA relative abundance (mol %) and soil quality variables for all of Shaked and Avdat ISP replicates.
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Summary: Part IBased on the PCA of the PLFA profile and PLFA biomarkers with structural
group interpretation the results suggest:
• A shift in soil microbial community structure from underneath plants compared with soils between plants.
• Plant primarily influences the character of surrounding microbial community and plant type may produce a secondary influence.
• Location (Avdat vs Shaked) have significant effect on the microbial community in the intershrub spaces; possibly through climatic differences or indirect effect of plant types
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• Dominance of Gram-negative populations
• Higher proportions of Gram-positive populations in SUC samples compared with ISP samples
• Higher proportions of fungi, cyanobacteria and anaerobes in ISP samples compared with SUC samples
• RDAs suggest that nitrate was a major determinant segregating the PLFA profiles of the intershrub spaces from the SUC.
• Nitrate is also a major factor together with organic matter in segregating the intershrub spaces of Avdat and Shaked
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Nitrification• Ammonia oxidation:
• NH3 + 2H+ + 2e- NH2OH +H2O
• NH2OH + H2O HNO2 + 4H+ + 4e-
• Involves Genera belonging to the Bacteria and Archaea(mesophilic crenarchaea) domains
• Nitrite oxidizing bacteria:HNO2 + H2O HNO3 + 2H+ + 2e-
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Diversity of ammonia oxidizing bacteria
Based on 16SrRNA gene fragment sequences extracted from DGGE runs.
Nitrosospira sp. Nsp2 AJ298745
2.4 7.4 3.4
Nitrosospira sp. Nsp2 3.2
Nitrosospira sp. BF16c46 AF386 3.3
3.1 1.3
9.3 Nitrosospira sp. PM2 AY856376
Nitrosospira sp. Nsp17 AY12380 Nitrosospira sp. En284 AY72703 1.2
7.37.1
1.11.4
Nitrosospira sp. Nl20 AJ298729 Nitrosospira sp. PJA1 AF353163
Nitrosospira sp. Is176 AJ62103 Nitrosospira sp.AJ005543 Nitrosospira sp.AJ298724
Nitrosospira sp. L115 AY123796 Nitrosospira sp .X84658
Nitrosospira tenuis Nv1 Nitrosospira tenuis M96404
Nitrosovibrio sp. FJI82 AY6312 Nitrosovibrio sp. FJI423 AY631
Escherichia coli
74
38
96
89
70
66
45
33
46
74
37
36
69
65
16
15
5
14
22 40
1430
23
26
0.02
Zd
16
amoA
copi
esLo
g10(
copi
es/g
soil)
Archaea
Bacteria
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6.5
7
7.5
8
8.5
Zd Avdat ISP Hs Nm ShakedISP
Th
4.5
4.8
5.1
5.4
5.7
6
Zd Avdat ISP Hs Nm ShakedISP
Th
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y = -0.1569x + 8.3925R2 = 0.5086
6.4
6.8
7.2
7.6
8
y = 0.1161x + 4.622R2 = 0.6561
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5.2
5.4
5.6
5.8
4 5 6 7 8 9 10
amoA
copi
esLo
g10(
copi
es/g
soil)
Archaea
Bacteria
NH4mg-N/Kg soil
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Ammonia Oxidation Potential (AOP)
0
50
100
150
200
250
300
350
400
450
500
μgN
/Kg/
h
Zd ISP Hs Nm ISP Th
ShakedAvdat
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y = 86.028x + 250.71R2 = 0.5302
170
280
390
500
0 0.5 1 1.5 2 2.5
Am
mon
i a O
x ida
ti on
Pot e
ntia
lμg
- N/K
g/h
% Bacterial amoA copies of total amoA copies
Numbers vs Activity
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Conclusions
• Plant presence and plant type affect soil microbial community structure and activity.
• The impact on nutrients transformations may affect soil fertility.
• It is suggested to consider these aspects when introducing plants for combating desertification
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Thank you
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