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M Stone- Dissertation Defense
1. The microbial contribution to carbon
and nutrient cycling across a variable
tropical landscape
Madeleine M. Stone
Dissertation Defense
November 21, 2014
3. Soils are largest terrestrial carbon pool
(1500 — 2000 Pg C)
Tropical forests contribute disproportionately to
subsoil C stocks, which have high potential for
long-term C stabilization
4. Most carbon in soils exists as soil organic matter
Schmidt et al. 2011, Nature
Dissertation Proposal | October 19, 2012
5. Soil is the most biologically diverse habitat on Earth
(thousands — millions species per gram)
Soil microbial communities produce, maintain and
decompose soil organic matter
6. Exo-enzymes link microbial ecology and soil biogeochemistry
Substrate
signaling
Catabolic repression
Product formation
Enzyme
production
7. Microbial stoichiometry links carbon, nitrogen and phosphorus cycling
Substrate
signaling
Catabolic repression
P
P
N
N
C
C
C
C
C
C
C
C
C
Product formation
60 : 7 : 1
“Redfield ratio” for soil
microbes?
Enzyme
production
8. In their search for energy and nutrients,
microbes drive biogeochemical cycles of
carbon, nitrogen and phosphorus.
But what controls the microbes?
14. What controls the
biogeochemical capacity of soil
microbes throughout the Luquillo
Critical Zone?
15. 1. Patterns in soil resources
Stone, M.M., DeForest, J.L., Plante, A.F. (2014), Soil Biology &
Biochemistry (Dissertation Chapter 3)
Stone, M.M., Hockaday, W.C., Plante, A.F. In Preparation.
(Dissertation Chapter 6)
2. Patterns in soil microbes
Stone, M.M., DeForest, J.L., Plante, A.F. (2014), Soil Biology &
Biochemistry (Dissertation Chapter 3)
Stone M. M., Plante, A.F. (2014) Soil Biology and Biochemistry
(Dissertation Chapter 5)
Stone, M.M., Plante, A.F. In preparation.
16. Sample Set
Variable Forest Types Soil Types Landscape
Positions
Depths
Basic soil
characterization
Colorado,
Tabonuco
Oxisol (VC),
Inceptisol (QD)
Ridge,
(Slope x3),
Valley
0-140 cm
(300 samples)
Carbon
Chemistry
Colorado,
Tabonuco
Oxisol (VC),
Inceptisol (QD)
Ridge, Slope,
Valley
Various [C] >
1%
(34 samples)
Microbial
Biomass,
Activity &
Community
Structure
Colorado,
Tabonuco
Oxisol (VC),
Inceptisol (QD)
Ridge, Slope,
Valley
0, 20, 50, 80,
110 & 140 cm
(72 samples)
17. 1. Patterns in soil resources
Stone, M.M., DeForest, J.L., Plante, A.F. (2014), Soil Biology &
Biochemistry (Dissertation Chapter 3)
Stone, M.M., Hockaday, W.C., Plante, A.F. In Preparation.
(Dissertation Chapter 6)
2. Patterns in soil microbes
Stone, M.M., DeForest, J.L., Plante, A.F. (2014), Soil Biology &
Biochemistry (Dissertation Chapter 3)
Stone M. M., Plante, A.F. (2014) Soil Biology and Biochemistry
(Dissertation Chapter 5)
Stone, M.M., Plante, A.F. In preparation.
18. 1. Carbon and nutrient concentrations will decline rapidly from
Plant inputs
High resource
surface soils
Increased decomposition,
Low resource subsoils
Mineral association
the surface
2. Shifts in SOM chemistry from plant — microbial
19. 1. Leaf litter chemistry (forest) will be important in determining
surface soil organic matter composition
2. Mineral associations (soil type) will be important in
determining subsoil organic matter composition
Plant inputs
Increased decomposition,
Mineral association
20. Basic soil characterization
• Total C and N measured by combustion
analysis
• “Labile” P quantified using partial
sequential Hedley fractionation (NaHCO3
& NaOH-extractable)
• Soil pH measured in DI water
26. Depth trends in
carbon chemistry
observed at the
individual soil profile
level
But different
patterns were
observed in each
pit.
Oxisol Valley Depth Profile
Amide Aromatic O-Alkyl Alkyl
27. Greater amounts of poorer quality C in Colorado forest
No differences across soil types!
Changes in SOM chemistry with depth are observable at the level
of individual profiles
Alkyl C (lipids) may be particularly important for long-term tropical
C storage
28. 1. Patterns in soil resources
Stone, M.M., DeForest, J.L., Plante, A.F. (2014), Soil Biology &
Biochemistry (Dissertation Chapter 3)
Stone, M.M., Hockaday, W.C., Plante, A.F. In Preparation.
(Dissertation Chapter 6)
2. Patterns in soil microbes
Stone, M.M., DeForest, J.L., Plante, A.F. (2014), Soil Biology &
Biochemistry (Dissertation Chapter 3)
Stone M. M., Plante, A.F. (2014) Soil Biology and Biochemistry
(Dissertation Chapter 5)
Stone, M.M., Plante, A.F. In preparation.
29. 1. Soil microbial biomass and activity will decline with
depth, tracking declines in C and nutrients
2. Specific metabolic activities will shift with depth,
reflecting shifts in resource allocation
3. Microbial community structure will shift with depth,
tracking changing environment
High resource
surface soils
Low resource subsoils
30. In subsoils, microbial
In abundance, surface soils, activity microbial
and
structure abundance, will activity relate to and
the
physiochemical environment
structure will relate to vegetation
(soil type)
32. Extract and quantify
phospholipids for :
1. Viable biomass
2. Broad microbial
community structure
Fungi
Actinobacteria
33. Soil Respiration
CO2 evolution
measured during
90-day respiration
experiment
Respiration rate
normalized to soil
C and microbial C
concentrations to
determine specific
metabolic activity
34. Fluorimetric Enzyme Assays
α – glucosidase (starch)
β-glucosidase (cellulose dimers)
Natural process
β-xylosidase (hemicellulose)
cellobiohydrolase (cellulose oligomers)
Fluorimetric assay
N-acetyl glucosaminidase (chitin)
acid phosphatase (organic phosphate)
Total Potential Activity
Specific Activity
(Per carbon or biomass)
35. No substantial differences among landscape
units (3-way ANOVA):
Microbial
biomass
Cumulative
respiration
Total Enzyme
Activity
P value
Soil parent material
(VC vs. QD)
0.85 0.39 0.27
Forest type (Col vs.
Tab)
0.65 0.16 0.13*
*2/4 carbon cycle enzymes significantly higher in Colorado forest
47. 1.7
60.0
What’s up with phosphatase?
40%
P = 0.01
80%
P = 0.01
Increased phosphatase activity relative to C and N cycle enzymes suggests
microbes at depth invest more in P acquisition
Why?
49. Energy availability drives microbial activity—much more than
landscape differences
Microbial biogeochemical capacity remains similar or increases
with depth, per unit biomass
High specific metabolic activity could be a stress response,
decreased enzyme turnover, or community shifts
Prevalence of phosphatase suggests a special role for this
enzyme
50. Implications
Microbes retain metabolic capacity for biogeochemical
processes in low—energy subsoils
“Stability” of deep soil carbon—microbial starvation?
Starving – survival lifestyle?
Tropical forests make major contributions to the global carbon cycle. They harbor roughly 25 % of world’s biomass and account for roughly 1/3 of global annual NPP.
Tropical forest soils store nearly 700 Petagrams of carbon, compared with 400 Petagrams of carbon in temperate and boreal forest soils combined
Subsoils contain ~50% of soil C stocks
10 000 000 000 (10 biliion) individual cells per gram!
And after soil and forest type, we have have DEPTH
Is it the environment (Depth)
Is it the environment (State factors)
Is it the soil resources? (C and nutrient availability, C chemistry?)
Is it community structure?
Other factors
So this was quite an interesting finding for us and we wanted to know why
Remember, based on resource allocation theory microbes have little reason to produce enzymes that target substrates present in abundance. On the other hand…
Stress due to decreased substrate availabiliy…. Then I could follow this slide with one showing the strong correlation between microbial activity and energy
Would be nice to include “free” enzyme activity on these graphs, as well : Does it decline
First point– that we do not see differences across soil types or forest types in microbial activity suggests microbes can obtain energy where it exists
Second point– while everything declines with depth, subsoil microbial communities still have the CAPACITY to participate in cycles of carbon and nutrients. Thus, active carbon exists in deeper parts of these tropical soil profiles than is typically measured / modeled
Third point— we don’t yet know WHY carbon starved microbes are not totally dormant. Are they producing additional enzymes and respiring at higher rates due to stress? Are those enzymes just kicking around for longer? Are community shifts responsible?
Fourth point— microbes need to make ecological tradeoffs between energy and nutrient acquisition and energy investment to acquire those nutrients. Ultimately, the biogeochemical cycles these microbes drive may be the result of cost-benefit analyses on the part of the microbes.