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: