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Mark A. Williams
I. Study sites
http://map.vbgood.com/world_relief_map.htm
1. Soil development‐pedogenesis (4 locations)
2. Disturbance/til...
II. Study site
Increasing year of soil development
105y
210y
450y
845y
1400y
2400y 4000y
Lake
1Km
Distance from Lakeshore
...
2
Pg
3
Pg
9
Pg
U.S. DOE. 2009
Net increase of annual atm C = 4 Pg
(1Pg = 1 X 1015 g)
Global Carbon Cycle Imbalance
II. Objective/Hypothesis
 Describing, fundamental
mechanisms of soil organic matter
formation (residence time)
 Proteoge...
Carbon K-Edge NEXAFS Spectroscopy
of Soil Organic Matter during soil
ecosystem development (0 to 10 cm)
Amide
Aromatic/Nit...
Amide-C and N
20 -60%
References
Abe and Watanabe, 2004; Leinweber et al., 2007;
Soil Organic C-Nitrogen
Compositions
Ques...
40y 155y 450y
Early successional plant species
Late successional species
pH
Willi t l 2013
Hypothesis
• There may be a pattern of hydrolysable amino acids
during soil development, which indicates the change of
typ...
Theoretical framework
Biologically formed proteins consist of
mostly 20 standard amino acids
Biologically formed proteins ...
Principal component analysis (PCA)
on variation of relative composition of 17
amino acids
Hydrolysable amino acid composit...
Patterns of Hydrolysable
17 Proteinogenic Amino Acids
Years of development
0 1000 2000 3000 4000 5000
NMSAxis1(64.4%)
-0.8...
Hydrolysable amino acid composition changed
between two seasons.
Patterns of change in mineral-
associated pedogenesis
Acidobacteria are rich in 
Ala‐ and Gly‐ peptides 
Phe
His
Arg
Lys
Ala
Gly
Asp+Asn
Years of development
decline
Actinobact...
Summary
• Clear pattern of proteogenic amino acid 
change associated with active soil pools 
associated with pedogenesis
•...
Acknowledgements
Graduate Students
Jude Moon
Li Ma
Rosana Pineda
Collaborators
Dr. Kang Xia
Li Ma
Undergrad students
Haley...
Amide‐C and N
20 ‐60%
References
Abe and Watanabe, 2004; Leinweber et al., 2007; 
Soil Organic C-Nitrogen
Compositions
Que...
Sub-Hypothesis
• Sub-hypothesis
The change of hydrolysable amino acids may
be influenced by the shift of their source and
...
Acidobacteria are rich in 
Ala‐ and Gly‐ peptides 
Phe His
Arg
Lys
Ala
Gly
Asp+Asn
Years of development
decline
Actinobact...
Sub-hypothesis
The change of hydrolysable amino acids
may be influenced by the shift of their
source and sink.
Plants
SOM
...
Source Hypothesis
Actinobacteria
(high GC content)
Marker Amino Acids Dominant Bacterial Phylum
Phe
Lys
Gly
Ala
Year of de...
Sink Hypothesis
pH
Na *kg/ha
K
Ca
Mg
Acidic AA
(organic anions)
Basic AA
(organic cations)
Summary
• Clear pattern of proteogenic amino acid 
change associated with active soil pools 
associated with pedogenesis
•...
Acknowledgements
Graduate Students
Jude Moon
Li Ma
Rosana Pineda
Collaborators
Dr. Kang Xia
Li Ma
Undergrad students
Haley...
Years of development
0 1000 2000 3000 4000 5000
NMSAxis1(64.4%)
-0.8
-0.6
-0.4
-0.2
0.0
0.2
0.4
0.6
0.8
Plant Community Ba...
Theoretical framework
Biologically formed proteins consist of
mostly 20 standard amino acids
Biologically formed proteins ...
Hydrolysable amino acids
Waters AccQ Fluor Derivatization Kit 
(6‐aminoquinolyl‐N‐hydroxysccinimidyl carbamate, AQC)
HPLC
...
http://www.picstopin.com/
Limitations of the method
Question
Does the types of protein change
during soil development?
Unpublished, Williams and Xia
Age of soilAge of soil
% ...
Principal component analysis (PCA)
on variation of relative composition of 17 amino acids
Hydrolysable amino acid composit...
Principal component analysis (PCA)
on variation of relative composition of 17 amino acids
Hydrolysable amino acid composit...
Older
Winter
Summer
Younger
Carbon K‐Edge NEXAFS Spectroscopy of Soil 
Organic Matter during soil ecosystem 
development (0 to 10 cm)
Relativecontentt...
Year of development
Changeofrelativeabundanceofaminoacids
Phe
His
Arg
Lys
Ala
Gly
Asp+Asn
Actinobacteria, a dominant phylu...
Plants
SOM
Microbes Source
Sink
Physical and Chemical Protection → Accumulation
Year of development
Changeofrelativeabunda...
Peptide/Protein Stabilization and C and N Sequestration in Soils: Contributions of Mineralogy in  Native and Agro-managed ...
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Peptide/Protein Stabilization and C and N Sequestration in Soils: Contributions of Mineralogy in Native and Agro-managed Soils

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Mark Williams

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Peptide/Protein Stabilization and C and N Sequestration in Soils: Contributions of Mineralogy in Native and Agro-managed Soils

  1. 1. Mark A. Williams
  2. 2. I. Study sites http://map.vbgood.com/world_relief_map.htm 1. Soil development‐pedogenesis (4 locations) 2. Disturbance/tillage, resoration (6 locations)
  3. 3. II. Study site Increasing year of soil development 105y 210y 450y 845y 1400y 2400y 4000y Lake 1Km Distance from Lakeshore Elevation above Lakeshore 105y 210y155y70y 260y 450y
  4. 4. 2 Pg 3 Pg 9 Pg U.S. DOE. 2009 Net increase of annual atm C = 4 Pg (1Pg = 1 X 1015 g) Global Carbon Cycle Imbalance
  5. 5. II. Objective/Hypothesis  Describing, fundamental mechanisms of soil organic matter formation (residence time)  Proteogenic amino acid species will show patterns of change related to:  Pedogenesis • Aluminum silicates • Organic matter  Vegetation  Microbial communities .
  6. 6. Carbon K-Edge NEXAFS Spectroscopy of Soil Organic Matter during soil ecosystem development (0 to 10 cm) Amide Aromatic/Nitro- aromatic
  7. 7. Amide-C and N 20 -60% References Abe and Watanabe, 2004; Leinweber et al., 2007; Soil Organic C-Nitrogen Compositions Question: Do the types of amide-N change during soil development? Mikutta et al., 2011 Question: Do the changes in amide-N support theory about mechanisms of SOM formation?
  8. 8. 40y 155y 450y Early successional plant species Late successional species pH Willi t l 2013
  9. 9. Hypothesis • There may be a pattern of hydrolysable amino acids during soil development, which indicates the change of types of protein in soil. • Sub-hypothesis The change of hydrolysable amino acids will be influenced by the shift of their source and sink. • Conceptual Model of Soil Organic Matter Formation Plants SOM Microbes Source Sink Physical and Chemical Protection → Accumulation
  10. 10. Theoretical framework Biologically formed proteins consist of mostly 20 standard amino acids Biologically formed proteins consist of mostly 20 standard amino acids The standard amino acids can be released by thermo-chemical hydrolysis procedure The standard amino acids can be released by thermo-chemical hydrolysis procedure Therefore, we can quantify and determine distribution of the “hydrolysable” amino acids (whole-Soil, mineral-associated) Therefore, we can quantify and determine distribution of the “hydrolysable” amino acids (whole-Soil, mineral-associated) This will help understand the changes in patterns of peptides/proteins in soil This will help understand the changes in patterns of peptides/proteins in soil
  11. 11. Principal component analysis (PCA) on variation of relative composition of 17 amino acids Hydrolysable amino acid composition changed during soil development. Age MRPP: P value<0.001 Changes are consistent with general hypotheses of soil organic matter formation and accrual
  12. 12. Patterns of Hydrolysable 17 Proteinogenic Amino Acids Years of development 0 1000 2000 3000 4000 5000 NMSAxis1(64.4%) -0.8 -0.6 -0.4 -0.2 0.0 0.2 0.4 0.6 0.8
  13. 13. Hydrolysable amino acid composition changed between two seasons.
  14. 14. Patterns of change in mineral- associated pedogenesis
  15. 15. Acidobacteria are rich in  Ala‐ and Gly‐ peptides  Phe His Arg Lys Ala Gly Asp+Asn Years of development decline Actinobacteria are rich in  Phe and His‐ peptides  Microbial markers Increase % Abundance Years of development His+His+‐
  16. 16. Summary • Clear pattern of proteogenic amino acid  change associated with active soil pools  associated with pedogenesis • Working hypotheises: The pattern of  pedogenic organic change derived from plants  and microbes (source) combined with mineral  associations (sink)
  17. 17. Acknowledgements Graduate Students Jude Moon Li Ma Rosana Pineda Collaborators Dr. Kang Xia Li Ma Undergrad students Haley Randolph Yoonji Ha Kelsey Weber
  18. 18. Amide‐C and N 20 ‐60% References Abe and Watanabe, 2004; Leinweber et al., 2007;  Soil Organic C-Nitrogen Compositions Question: Do the types of amide-N change during soil development? Mikutta et al., 2011 Question: Do the changes in amide- N support theory about mechanisms of SOM formation?
  19. 19. Sub-Hypothesis • Sub-hypothesis The change of hydrolysable amino acids may be influenced by the shift of their source and sink. • Conceptual Model of Soil Organic Matter Formation Plants SOM Microbes Source Sink Physical and Chemical Protection → Accumulation
  20. 20. Acidobacteria are rich in  Ala‐ and Gly‐ peptides  Phe His Arg Lys Ala Gly Asp+Asn Years of development decline Actinobacteria are rich in  Phe and His‐ peptides  Microbial markers Increase % Abundance Years of development
  21. 21. Sub-hypothesis The change of hydrolysable amino acids may be influenced by the shift of their source and sink. Plants SOM Microbes Source Sink Physical and Chemical Protection → Accumulation
  22. 22. Source Hypothesis Actinobacteria (high GC content) Marker Amino Acids Dominant Bacterial Phylum Phe Lys Gly Ala Year of development Changeofrelativeabundanceofaminoacids Williams et al., 2013 R2 P value Ala (positive) 0.82 0.0019 Gly (positive) 0.41 0.1670 Lys (negative) 0.22 0.0190 Phe (negative) 0.01 0.4040
  23. 23. Sink Hypothesis pH Na *kg/ha K Ca Mg Acidic AA (organic anions) Basic AA (organic cations)
  24. 24. Summary • Clear pattern of proteogenic amino acid  change associated with active soil pools  associated with pedogenesis • Working hypotheises: The pattern of  pedogenic organic change derived from plants  and microbes (source) combined with mineral  associations (sink)
  25. 25. Acknowledgements Graduate Students Jude Moon Li Ma Rosana Pineda Collaborators Dr. Kang Xia Li Ma Undergrad students Haley Randolph Yoonji Ha
  26. 26. Years of development 0 1000 2000 3000 4000 5000 NMSAxis1(64.4%) -0.8 -0.6 -0.4 -0.2 0.0 0.2 0.4 0.6 0.8 Plant Community Bacterial Community Early successional species Late successional species Williams et al., 2013 Hydrolysable Amino Acids
  27. 27. Theoretical framework Biologically formed proteins consist of mostly 20 standard amino acids Biologically formed proteins consist of mostly 20 standard amino acids The standard amino acids can be released by thermo-chemical hydrolysis procedure The standard amino acids can be released by thermo-chemical hydrolysis procedure Therefore, we can quantify and determine distribution of the “hydrolysable” amino acids Therefore, we can quantify and determine distribution of the “hydrolysable” amino acids This will help understand the changes in patterns of peptides/proteins in soil This will help understand the changes in patterns of peptides/proteins in soil
  28. 28. Hydrolysable amino acids Waters AccQ Fluor Derivatization Kit  (6‐aminoquinolyl‐N‐hydroxysccinimidyl carbamate, AQC) HPLC 110oC, 24h, 1g soil R‐SO3Na →  R‐SO3AA (acidic) →  R‐SO3NH4 NH4+(Orange) in NH4OH  (basic) eluent will be  replaced in the exchange  site of the resin and amino  acids (Green) will be  released. http://wiki.biomine.skelleftea.se/ Hellinger et al., 2013
  29. 29. http://www.picstopin.com/ Limitations of the method
  30. 30. Question Does the types of protein change during soil development? Unpublished, Williams and Xia Age of soilAge of soil % % Relative to total organic N (%) Relative to total organic C (%) Amide-N Calculated Amide-C
  31. 31. Principal component analysis (PCA) on variation of relative composition of 17 amino acids Hydrolysable amino acid composition changed during soil development. Age MRPP: P value<0.001
  32. 32. Principal component analysis (PCA) on variation of relative composition of 17 amino acids Hydrolysable amino acid composition changed between two seasons.
  33. 33. Older Winter Summer Younger
  34. 34. Carbon K‐Edge NEXAFS Spectroscopy of Soil  Organic Matter during soil ecosystem  development (0 to 10 cm) RelativecontenttototalC(%) 0 10 20 30 40 50 0 5 10 15 20 25 Aromatic-C Carboxylic-C 5 130 500 2K-y 60K 120K 0 10 20 30 40 50 0 10 20 30 40 50 Aliphatic-C O/N-alkyl-C 60 250 1K 14K 5 130 500 2K-y 60K 60 250 1K 14K 120K -Consistent patterns of change across ecosystem soil types Franz Josef, NZ Wilderness Park, MI
  35. 35. Year of development Changeofrelativeabundanceofaminoacids Phe His Arg Lys Ala Gly Asp+Asn Actinobacteria, a dominant phylum, the relative abundance decreased dramatically at the early  stage of development. Actinobacteria contains high GC on their genome, which drives  positively selection on Ala and Gly (Chen et al., 2012). And the hydrolysis pools of Ala and Gly decreased rapidly at the early stage as Actinobacteria decreased (Ala: R2=0.82, p=0.0019; Gly:R2 = 0.41, p=0.1670). High GC content drives adverse selection on Lys and Phe, (Chen et al., 2012)  and so as hydrolysable pools of Phe and Lys increased. Acidobacteria are the second largest  dominant bacterial phylum and contain relatively high in His composition based on their  genome database.  Acidobacteria are rich in  Ala‐ and Gly‐ peptides  decline in soil
  36. 36. Plants SOM Microbes Source Sink Physical and Chemical Protection → Accumulation Year of development Changeofrelativeabundance ofaminoacids Phe His Arg Lys Ala Gly Asp+Asn

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