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Plant patchiness effect on microbial community

Eric Ariel Ben-David
Eric Ariel Ben-David

1) The study examined the effect of plant patches and plant type on soil microbial communities in desert landscapes. 2) Results showed shifts in microbial community structure between soils under plant canopies and intershrub spaces, with plant canopies primarily influencing surrounding microbes. 3) Location and plant type had secondary effects, with different microbial communities found between the two research sites likely due to climatic differences.

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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 1
Aim: to examine the effect of plant and plant type on bulk soil microbial community structure and activity in patchy desert landscape 2
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
Dominant shrubs Sayeret Shaked Noaea mucronata (Nm) Thymelaea hirsute (Th) 4
Dominant shrubs - Avdat Zygophyllum dumosum (Zd) Hammada scoparia (Hs) 5
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
Sampling: Winter 2007 Soil samples under plant canopy (SUC) samples Soil samples from intershrub spaces (ISP): ISPA- Avdat ISPS- Shaked 7
Results Selected soil chemical parameters in Avdat and Shaked sampling sites. Samples pH EC RWC OM TAN NO2--N NO3--N 亮Scm-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 Tukeys 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
(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
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
RDA triplot of sites, PLFA relative abundance (mol %) and soil quality variables for all of Shaked and Avdat ISP replicates. 11
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
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
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
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
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
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
Ammonia Oxidation Potential (AOP) Avdat Shaked 500 450 400 350 亮gN/Kg/h 300 250 200 150 100 50 0 Zd ISP Hs Nm ISP Th 18
Numbers vs Activity 500 Ammonia Oxidation Potential y = 86.028x + 250.71 R2 = 0.5302 390 亮g-N/Kg/h 280 170 0 0.5 1 1.5 2 2.5 % Bacterial amoA copies of total amoA copies 19
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
Thank you 21

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Plant patchiness effect on microbial community

  • 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 亮Scm-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 Tukeys 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 亮gN/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 亮g-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