Evans Slides SoilsDroughtMicrobes

How do soil microbes respond to drought and rainfall?

Sarah Evans Assistant Professor

Kellogg Biological Sta>on

Major ques>ons addressed in this lecture

•  How does rainfall/drought alter the soil environment?

•  What kind of stress does this impose for a microbe?

•  What traits do microbes use to tolerate these stresses?

But first: why should we care?

•  Rainfall drives biology – Biology drives process

• Rainfall changing in future – Process changing in future?

Soil carbon

Climate change

Background: Climate -‐ carbon -‐ microbe interac5ons

CO2

Climate: predicted shiLs in rainfall •  “More intense rainfall regimes” •  = Higher propor>on of rain from large events •  = Fluctua>on in soil moisture (dry then rewet)

More intense rainfall

IPCC 2007

•  Microbes decompose soil C and produce CO2

•  Sudden changes in moisture are stressful to microbes

CO2

Ques5ons: 1.   How do changes in rainfall affect microbes? 2.   How do these changes affect carbon flux?

CO2

How do changes in rainfall affect plants? How does this affect carbon flux? •  Rain affects plant physiology and species composi>on

•  Different plants will have different effects on carbon flux…

Mean annual precipita>on

Mean annu

al te

mpe

rature

How soil water affects microbes

Various ways that soil water affects microbial activity:

•  rate of solute diffusion through soil •  nutrient availability / uptake into cells •  solute concentration; hyperosmotic stress in saline soils •  microbial movement in soil (cells swim in the fluid phase).

Bacterial movement ceases when soil dries sufficiently to produce discontinuous water-filled pores, or when the water film is smaller than what’s needed for the microbe to swim. For microbial motility, water films must be > 0.5 µm for bacteria; ≥ 4 µm for protozoa and flagellated fungal zoospores.

•  Impacts directly on status of soil aeration [especially O2 diffusion] within pore spaces, hence regulates aerobic vs. anaerobic metabolism

•  drying imposes desiccation stress, common in surface soils

•  Physical (solute movement •  Chemical (nutrient limited) •  Biological (osmotic stress) •  Physical (microbe

movement)

•  Chemical (O2 limitation)

•  Biological (desiccation stress)

The soil environment

•  Flight through soil Physical (solute movement Physical (microbe movement) Chemical (nutrient limited) Chemical (O2 limitation) Biological (osmotic stress) Biological (desiccation stress)

1. 2. 3.

Physical constraints •  Physical (solute movement •  Physical (microbe movement)

Chemical •  Chemical (nutrient limited) •  Chemical (O2 limitation)

Drought Large rainfall event

Microbial cell

•  Biological (osmotic stress) •  Biological (desiccation stress)

Biological

I.  Do micro-‐scale mechanisms help explain soil CO2 flux aLer a large rain event?

II.  Can we use life history strategies to understand microbial responses to moisture stress?

Rest of lecture: Two studies

-‐-‐Fill in traits table-‐-‐

Observed Predicted

Li et al. 2005

Moisture pulse

Difficult to predict

I. Do micro-‐scale mechanisms help explain soil CO2 flux aIer a large rain event?

Are there other mechanisms we haven’t accounted for that could be causing this large pulse of CO2?

First, how is CO2 produced in soil?

Enzymes

Organic maPer

Dissolved substrate

1.  Need microbes 2.  Need movement

•  Individual-‐based, theore>cal model •  Micro-‐scale •  3 func>onal groups •  Quan>fies output

Microbial func5onal groups

DOC:DON Enzyme ac5vity Respira5on

1 cm

Biogeochemical -‐ microbial model

Implemented water dynamics

0 20 40 60 80

100 120 140 160 180

Water level (mm

3 )

Time (days)

Evapora>on

Rainfall

Water level linked to: •  Diffusion •  Leaching •  Microbial growth

Mechanisms: processes responding to water

1.  Water-‐dependent growth 2.  Microbial diversity 3.  Substrate diffusion

Patches Diffusion of substrates Growth of different microbial groups

Cheaters (red) respond

Rainfall pahern:

Cheaters Producers

Simula>ons

1.  Water-‐dependent growth 2.  Microbial diversity 3.  Substrate diffusion

Reproducing CO2 pulse with model

One water pulse With mechanisms, simulated pulse

CO2

What is the rela>ve influence of different mechanisms on CO2 pulse?

Time

CO2

Mechanisms, in different combina>ons: 1.  Water-‐dependent growth 2.  Microbial diversity 3.  Substrate diffusion

Rela>ve influence of different mechanisms Produced highest: Diffusion + Water-‐dependent growth

Exclud

e Diffu

sion

Exclud

e Grow

th

Add microbial diversity

CO

2 res

pire

d (fm

ol C

/hou

r)

Proportion of m

aximum

pulse (%)

100 %

Diffusion contributed more Effect of diversity depends on: •  Compe>>ve

interac>ons •  Specific func>onal

groups present

86 % ± 22%

Conclusions: study 1 •  Reproduced biogeochemical pulse with a model •  Once separated, physical factors (diffusion) might influence CO2 flux more than biological stress

•  CO2 flux did depend on microbial func>onal groups that were present, but needs more work

I.  Do micro-‐scale mechanisms help explain soil CO2 flux aLer a large rain event?

II.  Can we use life history strategies to understand microbial responses to moisture stress?

Outline of talk: Two studies

Exercise

•  What traits would be useful to survive under drought?

Trait Does it contribute to drought tolerance? How?

What are the disadvantages and costs?

Can move (mo5lity)

Cheat off of others’ enzyme produc5on

Ability to store resources

Synthesizes intra-‐cellular solutes

Can change metabolism (plas5c)

Large cell size

Responds quickly to environment

Can form spores

Other?

How can we understand microbial diversity in an ecologically meaningful way? Ambient rainfall

•  Want to categorize microbes based on their ecology

•  Can’t measure all species traits directly

•  Way of organizing organisms based on growth or stress response

•  e.g. r-‐ and k-‐ strategists (MacArthur and Wilson 1967)

•  “life history strategy” in plants (Grime 1979)

– opportunist, ruderal, tolerant

•  Do we see ecological strategies in microbes?

Ecological strategies

Strategy based on historical condi>ons

•  Certain disturbance regime results in certain life strategy

•  Evidence accumula>ng, history mahers for microbes too

Disturbance regime (history)

Specific ques>ons: study 2 1.  Do microbial species express certain

“strategies” when responding to a stress? Are these strategies related to phylogeny?

2.  Does the distribu>on of these strategies change with disturbance history? Is this due to shi4s in species or in strategy?

Disturbance regime: fluctua>on in moisture condi>ons

Methods: describing life strategies •  Used 454 pyrosequencing

to describe rela>ve abundance of each species

•  Visualize on heatmap •  Hierarchical clustering

N=5

MODERATE HIGH LOW

Results: Q1: Do species cluster into strategies?

Tolerant Opportunis>c Sensi>ve

Strategy


Related to phylogeny? à Plot strategy on phylogene>c tree


Does strategy relate to phylogeny?

Sensi>ve clustered, tolerant overdispersed

Ques>ons

1. Do microbial species express certain “strategies” when responding to a stress?

•  Are these strategies related to phylogeny?

2. Does the distribu@on of these strategies change with disturbance history?

•  Is this due to shiLs in species or shiLs in organism strategy?

Yes

Varies

KONZA Biological Research Sta>on

Rainfall Manipula>on Plot Study (RaMPS)

•  Manipulated plot: altered rainfall >ming – more >me between rainfall events, larger events

More drying rewesng

Ambient rainfall Lab drying-‐rewesng

Evans and Wallenstein 2012 Biogeochemistry

Konza biological sta@on

Results: Q2: Does history affect distribu>on of strategies?

Exposed to moisture fluctua>on Ambient rainfall in the field Tolerant Opportunis>c Sensi>ve

Specula>on: related to carbon flux? •  “Tolerance” to drying-‐rewesng could mean more

carbon for growth, less carbon respired. •  Communi>es from Intense Rainfall plots did respire less

when exposed to moisture pulse1

1Evans and Wallenstein 2012 Biogeochemistry

Lower soil respira@on because more tolerant species?

Exposed to moisture fluctua>on Ambient rainfall in the field

Tolerant strategy

Change species or change strategy?

Opportunis>c Sensi>ve Tolerant

Change species or change strategy?

•  75% were different spp

•  Do the species that responded from both historical treatments respond in the same way? Is life strategy conserved?

Opportunis>c Sensi>ve Tolerant

Previously exposed to moisture pulses 25%

overlap

Control

Inside: drying-‐reweMng disturbance history

82% of species changed strategy


Change strategy?

Outside: Control field treatment

Colors of tree = Phyla

Results summary

1. Do microbial species express certain “strategies” when responding to a stress?

•  Are these strategies related to phylogeny?

2. Does the distribu@on of these strategies change with disturbance history?

•  Is this due to shiLs in species or shiLs in organism strategy?

Yes

Varies

Yes

Both occur

Review: What makes a Tolerant, Opportunis>c, or Sensi>ve taxa?


Strategy


Review: Drought in soils imposes physical, chemical, and biological stress on microbes

Physical (solute movement Physical (microbe movement) Chemical (nutrient limited) Chemical (O2 limitation) Biological (osmotic stress) Biological (desiccation stress)

1. 2. 3.

Like any disturbance, need specific traits to survive. Traits come at a cost Impacts carbon cycling

Trait

Can move (mo5lity)

Cheat off of others’ enzyme produc5on

Ability to store resources

Synthesizes intra-‐cellular solutes

Can change metabolism (plas5c)

Large cell size

Responds quickly to environment

Can form spores

Other?

Soil carbon

Climate change

Climate -‐ carbon -‐ microbe interac5ons

CO2

Evans Slides SoilsDroughtMicrobes

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