Effect of plant patchiness on soil microbial community structure

1. 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
1

2. Aim: to examine the effect of plant and plant type on bulk soil
microbial community structure and activity in patchy desert
landscape
2

3. Research locations
Long Term Ecological Research Sites
Sayeret Shaked
• Northern Negev
• Semiarid grassland
• Long term average rainfall - 200 mm
Avdat
• Central Negev
• Arid land
• Long term average rainfall - 90 mm
3

4. Dominant shrubs – Sayeret Shaked
Noaea mucronata (Nm) Thymelaea hirsute (Th)
4

5. Dominant shrubs - Avdat
Zygophyllum dumosum (Zd) Hammada scoparia (Hs)
5

6. 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
6

7. Sampling: Winter 2007
• Soil samples under plant canopy (SUC)
samples
• Soil samples from intershrub spaces (ISP):
• ISPA- Avdat
• ISPS- Shaked
7

8. Results
Selected soil chemical parameters in Avdat and Shaked sampling sites.
Samples pH EC RWC OM TAN NO2--N NO3--N
μScm-1 (%) (%) mg/kg
mg/kg mg/kg
Zd 8.03 2130 7.05 2.38 9.67 0.97 46.17
Hs 8.40 1958 4.98 2.60 7.47 0.19 51.04
ISPA 8.41 748 5.28 1.68 6.50 0.01 25.68
Nm 8.27 287 4.33 2..28 6.14 0.05 21.31
Th 8.11 232 5.23 2.30 6.97 0.24 22.04
ISPS 8.39 174 4.35 1.07 4.79 0.01 18.60
ANOVA Statistics
Avdat vs. Shaked ns <0.001 ns ns <0.05 ns <0.01
SUCA vs. SUCB ns <0.001 ns ns <0.1 ns <0.01
SUCA vs. BSCA ns <0.1 ns <0.1 ns ns <0.05
SUCS vs. BSCS <0.05 <0.005 ns <0.01 <0.05 ns Ns
BSCA vs. BSCS ns <0.1 ns <0.1 <0.05 ns <0.01
Zd vs. Hs, BSCA <0.05 - - - - - -
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.
8

9. (a) (b)
(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
9

10. a b
(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
for10 of Shaked sampling sites (based on first two axes)
all

11. RDA triplot of sites, PLFA relative abundance (mol %) and soil quality variables for
all of Shaked and Avdat ISP replicates.
11

12. Summary: Part I
Based 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
12

13. • 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
13

14. 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-
14

15. Nitrosospira sp. Nsp2 AJ298745
Diversity of ammonia oxidizing bacteria 2.4
7.4
26
3.4
Based on 16SrRNA gene fragment Nitrosospira sp. Nsp2
23
sequences extracted from DGGE runs. 3.2
30 Nitrosospira sp. BF16c46 AF386
14
3.3
40 3.1
22
1.3
14
9.3
Nitrosospira sp. PM2 AY856376
5 65 Nitrosos pira sp. Nsp17 AY12380
74 Nitrosos pira sp. En284 AY72703
1.2
66
7.3
15
96 7.1 Zd
38 1.1
74 1.4
36
Nitrosospira sp. Nl20 AJ 298729
16 Nitrosospira sp. PJA1 AF353163
69 Nitrosospira sp. Is176 AJ62103
Nitrosospira sp.AJ005543
33 Nitrosospira sp.AJ298724
37
Nitrosos pira sp. L115 AY123796
46 Nitrosospira sp.X 84658
45 Nitrosospira tenuis N v1
89
Nitrosospira tenuis M96404
Nitr osovibrio sp. FJI82 AY6312
70 Nitrosovibrio s p. FJI423 AY631
Escherichia coli
0.02
15

16. 8.5
8 Archaea
7.5
7
6.5
Log10(copies/gsoil)
amoA copies
6
Zd Avdat ISP Hs Nm Shaked Th
ISP
6
Bacteria
5.7
5.4
5.1
4.8
4.5
16 Zd Avdat ISP Hs Nm Shaked Th
ISP

17. 8
y = -0.1569x + 8.3925
R2 = 0.5086 Archaea
7.6
7.2
Log10(copies/gsoil)
6.8
amoA copies
6.4
5.8
y = 0.1161x + 4.622
R2 = 0.6561
5.6 Bacteria
5.4
5.2
5
4 5 6 7 8 9 10
17 NH4
mg-N/Kg soil

18. Ammonia Oxidation Potential (AOP)
Avdat Shaked
500
450
400
350
μgN/Kg/h
300
250
200
150
100
50
0
Zd ISP Hs Nm ISP Th
18

19. Numbers vs Activity
500
Ammonia Oxidation Potential
y = 86.028x + 250.71
R2 = 0.5302
390
μg-N/Kg/h
280
170
0 0.5 1 1.5 2 2.5
% Bacterial amoA copies
of total amoA copies
19

20. 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
20

21. Thank you
21