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

2

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

landscape

3

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

4

Thymelaea hirsute (Th)

Dominant shrubs – Sayeret Shaked

Noaea mucronata (Nm)

5

Dominant shrubs - Avdat

Hammada scoparia (Hs)Zygophyllum dumosum (Zd)

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

7

Sampling: Winter 2007

• Soil samples under plant canopy (SUC) samples

• Soil samples from intershrub spaces (ISP):• ISPA- Avdat• ISPS- Shaked

8

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.

9

(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)

10

(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

11

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

12

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

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

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-

15

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

6

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

17

y = -0.1569x + 8.3925R2 = 0.5086

6.4

6.8

7.2

7.6

8

y = 0.1161x + 4.622R2 = 0.6561

5

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

18

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

19

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

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

21

Thank you