The microbial contribution to carbon
and nutrient cycling across a variable
tropical landscape
Madeleine M. Stone
Dissertation Defense
November 21, 2014
Tropical forests dominate carbon fluxes in the
terrestrial biosphere
Amazon Basin
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
Dissertation Proposal | October 19, 2012
Most carbon in soils exists as soil organic matter
Schmidt et al. 2011, Nature
Soil is the most biologically diverse habitat on Earth (thousands — millions species per gram)
Soil microbial communities produce, maintain and
decompose soil organic matter
Substrate
signaling
Catabolic repression
Product formation
Enzyme
production
Exo-enzymes link microbial ecology and soil biogeochemistry
Substrate
signaling
Catabolic repression
P
P
N
N
C
C
C
C
C
C
C
C
C
Product formation
Microbial stoichiometry links carbon, nitrogen and phosphorus cycling
60 : 7 : 1
“Redfield ratio” for soil
microbes?
Enzyme
production
In their search for energy and nutrients,
microbes drive biogeochemical cycles of
carbon, nitrogen and phosphorus.
But what controls the microbes?
Luquillo Mountains, Puerto Rico
Oxisol Inceptisol
Gradients in climate, vegetation
Pre-montane forest
(Colorado)
Lowland forest
(Tabonuco) ridge
slope
valley
ridge
slope
valley
Environmental gradients with depth
High resource
surface soils
Low resource subsoils
Δ C, Nutrients,
pH, moisture,
oxygen
110 cm
20 cm
50 cm
80 cm
What controls the
biogeochemical capacity of soil
microbes throughout the Luquillo
Critical Zone?
1. Patterns in soil resourcesStone, 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 microbesStone, 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.
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)
1. Patterns in soil resourcesStone, 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 microbesStone, 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.
High resource
surface soils
Low resource subsoils
Plant inputs
Increased decomposition,
Mineral association
1. Carbon and nutrient concentrations will decline rapidly from
the surface
2. Shifts in SOM chemistry from plant — microbial
1. Leaf litter chemistry (forest) will be important in determining
surface soil organic matter composition
Plant inputs
Increased decomposition,
Mineral association
2. Mineral associations (soil type) will be important in
determining subsoil organic matter composition
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
Exponential declines in carbon and nutrients…
mg g-1 soil mg g-1 soil mg kg-1 soil
More carbon in higher elevation
forest
Carbon and nitrogen along the upper 80 cm of soil profiles
13C Nuclear magnetic resonance spectroscopy (NMR)
• High O-alkyl C in soils, plant and microbial tissues
• Enrichment in N-alkyl and amide C in fungal biomass
• Enrichment in Alkyl C in SOM
Carbon Chemistry Distinct Across Forests
−0.2 −0.1 0.0 0.1 0.2
−0.2
−0
.10.0
0.1
0.2
PC1 42 %
PC
2 3
2 %
−4 −2 0 2 4
−4
−2
02
4
Alkyl
Nalkyl
Oalkyl
DiOAlkyl
Amide
ColDys5
Fungi
Root
Litter
Phenolic Aromatic
Alkyl
DiOAlkyl
Oalkyl
RootLitterFungiColorado Forest SoilTabonuco Forest Soil
Distinct Alkyl: O-alkyl ratios
Root: 0.3 ± 0.0
Fungi: 0.4 ± 0.2
Litter: 0.6 ± 0.0
Tabonuco: 0.7 ± 0.1
Colorado: 2.1 ± 0.3
Depth trends in
carbon chemistry
observed at the
individual soil profile
level
But different
patterns were
observed in each
pit.
AlkylO-AlkylAromaticAmide
Oxisol Valley Depth Profile
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
1. Patterns in soil resourcesStone, 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 microbesStone, 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.
High resource
surface soils
Low resource subsoils
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
In surface soils, microbial
abundance, activity and
structure will relate to vegetation
In subsoils, microbial
abundance, activity and
structure will relate to the
physiochemical environment
(soil type)
Phospholipid Fatty Acid Analysis
Wikimedia
Commons
Extract and quantify
phospholipids for :
1. Viable biomass
2. Broad microbial
community structure
Fungi
Actinobacteria
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
Natural process
Fluorimetric assay
Fluorimetric Enzyme Assaysα – glucosidase (starch)
β-glucosidase (cellulose dimers)
β-xylosidase (hemicellulose)
cellobiohydrolase (cellulose oligomers)
N-acetyl glucosaminidase (chitin)
acid phosphatase (organic phosphate)
Total Potential Activity
Specific Activity
(Per carbon or biomass)
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
20 %
P < 0.01
Dep
th (
cm
)
140
110
80
50
20
0
0 2 4 6
Resp rate per unit soil
µg CO2g-1
day-1
−1 0 1
Resp rate per unit soil C
µg CO2mg C-1
day-1
0.2 0.4 0.6
Resp rate per unit microbial C
µg CO2mg Cmic-1
day-1
Dep
th (
cm
)
140
110
80
50
20
0
0 2 4 6
Resp rate per unit soil
µg CO2g-1
day-1
−1 0 1
Resp rate per unit soil C
µg CO2mg C-1
day-1
0.2 0.4 0.6
Resp rate per unit microbial C
µg CO2mg Cmic-1
day-1
7.8 x
P = 0.07
Dep
th (
cm
)
140
110
80
50
20
0
0 2 4 6
Resp rate per unit soil
µg CO2g-1
day-1
−1 0 1
Resp rate per unit soil C
µg CO2mg C-1
day-1
0.2 0.4 0.6
Resp rate per unit microbial C
µg CO2mg Cmic-1
day-1
19 x
P < 0.01
20 x
P < 0.01NSD(Mostly)
NSD
High variability in deep soil enzyme activity
Increased specific activity with depth driven largely by phosphatase
Substrate
signaling
Catabolic repression
Product formation
Enzyme
production
Why high specific metabolic activity in resource
limited subsoils?
Substrate
signaling
Catabolic repression
Product formation
Enzyme
production
Stress due to resource scarcity?
Microbes strongly driven by energy availability
Substrate
signaling
Catabolic repression
Product formation
Enzyme
production
Decreased enzyme turnover rates?
High enzyme activity following sorption
Substrate
signaling
Catabolic repression
Product formation
Enzyme
production
Community shift?
Evidence for this!
Depth P < 0.001
66 %
P = 0.01
1.7
60.0
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?
What’s up with phosphatase?
Phosphatase activity driven by microbial carbon demand?
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
Starving – survival lifestyle?
Microbes retain metabolic capacity for biogeochemical
processes in low—energy subsoils
“Stability” of deep soil carbon—microbial starvation?
Implications
Future Directions
IPCC October, 2014
Thank you!
Artwork: