George Kowalchuk: Combining Large- and Small-Scale Studies to Uncover Soil-Borne Microbial Diversity

George A. Kowalchuk

Nederlands Institute of Ecology (NIOO-KNAW)Dept. Microbial Ecology

Wageningen

Combining large- and small-scale studies to uncover soil-borne

microbial diversity

Royal Academy of Arts and Sciences (KNAW)

Institute for Ecological Sciences (IEW)

George A. Kowalchuk

Nederlands Institute of Ecology (NIOO-KNAW)Dept. Microbial Ecology

Wageningen

What microbial ecology has to gain from the EMP?

Royal Academy of Arts and Sciences (KNAW)

Institute for Ecological Sciences (IEW)

hybrid title

“Why the EMP is important, and what

we need to keep in mind as we

attempt this grand challenge”

• Brief introduction to microbial diversity

• Why the EMP?

• Microbial diversity: the need to think big and small

Stuff I plan to discuss

Soil-borne microbial diversity

• Central to the functioning of terrestrial ecosystems e.g. nutrient cycling, plant growth, biodegradation

• Huge numbers: >109 cells per gram soil; > 1032 cells on the planet

Soil-borne microbial diversity is by far the

greatest source of biodiversity on the planet!

Estimates = 107 – 1012 species

“it’s basically like, wow, there are way more species than you can imagine…”

Accelerating rate of discovery

100 + years

< 30 years

Ernst Haeckel’s tree of life The Evolution of Man (1879)

Major fields to be governed by microbial (meta)-

genomics• Climate change (understanding the problems and the solutions)

• Energy

• Human Health and nutrition (personal genomics)

• Industry and agriculture • Ecological and evolutionary understanding

Climate change

The Netherlands 50 years from

now??

Genomics past: history of our planet

Let’s go back in time – way back

Climate change

The Earth does not support life because it is a nice place to live.

It is a nice place to live principally because living organisms, in particular microorganisms, have shaped it to be that way.

Microbes are Earth’s principle

climate engineers, and the fate of our

planet relies on understanding how

this works

Energy

• Production of H2

• Biological light harvesting machines (coupled to harvesting H2)

• Biofuel cells

• Artificial cell factories

Human Health and Nutrition

Personalized medicine: personalized to you and

your sickness

Medicine based upon you, your symbionts and

your pathogens (or gene expression)

Industry and agriculture

• Over half of all natural products and enzymes come from soil-borne microbes

• Given that only a small fraction of soil microbes are known, it follows that a wealth of biology is waiting to be utilized

• Need to look are microbes in their natural habitat (importance of interactions)

• Increasing need for sustainable agriculture, relying on microbial partnerships

• How many species are there on Earth?

Ecological and evolutionary understanding(basic global questions to be addressed by EMP)

• How many species are there on Earth?

• What is the global gene pool?

Ecological and evolutionary understanding(basic global questions to be addressed by EMP)

• How many species are there on Earth?

• What is the global gene pool?

• How do ecosystems function?

Ecological and evolutionary understanding(basic global questions to be addressed by EMP)

Ecological and evolutionary understanding(basic global questions to be addressed by EMP)

• How many species are there on Earth?

• What is the global gene pool?

• How do ecosystems function?

• What are the patterns of microbial diversity and function?

Microbial diversity:

the need to think big and small

Microbial diversity:

the need to think big and small

To date, we have mostly concentrated on scales of convenience as opposed to

those of greatest relevance

Microbial diversity:

the need to think big and small

To date, we have mostly concentrated on scales of convenience as opposed to

those of greatest relevance

•Drivers of microbial community organization and activity (perspective of the microbes and their local environment)

•Global patterns of microbial diversity and impact (ecosystem and planetary perspective)

Spacelog

Timelog

Coverage of traditional

approaches in microbial ecology

Greatest relevance to microbial organization & activity

Greatest relevance to global environ-

mental impact

The need to think big and smallStepping outside the typical boundaries of microbial

ecology

On the big side

• How are microbial properties linked to large-scale climatic and biogeochemical properties of the planet?

• Global patterns of microbial diversity and biogeography

(and have humans disrupted these)

• Effects of unlimited dispersal and huge total population sizes

On the big side

• How are microbial properties linked to large-scale climatic and biogeochemical properties of the planet?

• Global patterns of microbial diversity and biogeography

(and have humans disrupted these)

• Effects of unlimited dispersal and huge total population sizes

Is everything everywhere?

Does microbial diversity fluctuate in time?

Has microbial diversity been accumulating over time and/or is it being lost?

HTP sequencing methods and ancient DNA approaches hold the potential to answer some of

these very basic questions of diversity on Earth

Tracking microbial diversity across past climate change events

0 10000 20000 30000 40000 50000 60000

Baskura Upper Taymyr River Main River 1

Main River 2 Main River 3 Christie Mine

Goldbottom Quartz Creek Purgatory

Duvanny Yar

Years

root

Thinking really small…

A Sledge-o-matic approach to microbial ecology

Soil sample

Sledge-o-matic: It slices , it dices, it even … circumcises

But it doesn’t describe in situ

microbial communities

well

environmental genome sequencing

(inter)activities of players may

be deduced from all of their individual genome

sequences

Are soil-borne microbes living on islands?

Charles Darwin

Soil Microbial Ecology at the Micro-Scale

• Detailed environmental analysis• Meta-transcriptomic analysis of soil

aggregate classes • Meta-genomic & community analysis

of individual soil aggregates• 3-D mapping of microbial populations

Physical Structure - Tomography - ESEM

- Activity

Micro-habitats - Micro-electrodes - EDX (ESEM)

-Metagenomics

Microbial Community- Spatial distribution- Phylogeny-

Aggregate

Micro-colony

Soil Fractions

Use of protein-encoding gene (rpoB) to help examine selection versus neutral patterns of community assembly

Micro-scale patterns of microbial distribution

12 3

11

5

176

16

12

1015

13

147

4

8

9

18 1920

+1.0-1.0 CCA Prin. Comp. #1 = 37.2%

CC

A P

rin.

Com

p. #

2 =

24.

1%

Soil Microbial Ecology at the Micro-Scale

• Detailed environmental analysis• Meta-transcriptomic analysis of soil

aggregate classes • Meta-genomic & community analysis

of individual soil aggregates• 3-D mapping of microbial populations

Physical Structure - Tomography - ESEM

- Activity

Micro-habitats - Micro-electrodes - EDX (ESEM)

-Metagenomics

Microbial Community- Spatial distribution- Phylogeny-

Aggregate

Micro-colony

Soil Fractions

Some thoughts as the EMP moves forward

• Take scale into account – also consider samples with reduced diversity to allow more complete assembly

Some thoughts as the EMP moves forward

• Take scale into account – also consider samples with reduced diversity to allow more complete assembly

• Special focus to well established experimental sites: i.e. with enhanced meta-data

Some thoughts as the EMP moves forward

• Take scale into account – also consider samples with reduced diversity to allow more complete assembly

• Special focus to well established experimental sites: i.e. with enhanced meta-data

• Examine samples in time (long-term and short-term)

Some thoughts as the EMP moves forward

• Take scale into account – also consider samples with reduced diversity to allow more complete assembly

• Special focus to well established experimental sites: i.e. with enhanced meta-data

• Examine samples in time (long-term and short-term)

• Consider the meta-transcriptome

Some thoughts as the EMP moves forward

• Take scale into account – also consider samples with reduced diversity to allow more complete assembly

• Special focus to well established experimental sites: i.e. with enhanced meta-data

• Examine samples in time (long-term and short-term)

• Consider the meta-transcriptome

• Continue to engage the broad scientific community

Some thoughts as the EMP moves forward

• Take scale into account – also consider samples with reduced diversity to allow more complete assembly

• Special focus to well established experimental sites: i.e. with enhanced meta-data

• Examine samples in time (long-term and short-term)

• Consider the meta-transcriptome

• Continue to engage the broad scientific community

• Don’t be afraid to hype it up…

Thanks…

(destructive) sampling after 0, 2, 4, 7, 10, and 14 days

Inoculation of microcosms

Cell enumeration & in situ visualization

• same matrix potential (-20kPa)

• different vol. water content: 4,99%, 10,91%, and 37,49%

• all pores up to 7.5 um filled with water

pore size distributions of the three artificial soils

0%

5%

10%

15%

20%

25%

0-0.2

0.2-

11-

55-

10

10-2

0

20-4

0

40-6

0

60-8

0

80-1

00

100-

200

>200

pore size classes [mm]

% p

ore

siz

e c

lass

/ to

tal s

oil

volu

me

coarse

medium

fine

Artificial communities in artificial soils

(VU-Amsterdam) Erik Verbruggen, Marcel van Heijden, James Weedon, Rien Aerts, Toby Kiers

(University of Vienna) Tim Urich, Christa Schleper

(O.U. Environ. Genomics) Sanghoon Kang, Zhiang He, Jizhong (Joe) Zhou

(BAS) Kevin Newsham, David Pearce, Pete Convey

(LBNL-Berkeley) Yvette Piceno, Eoine Brodie, Todd De Santis, Gary Andersen

(U of Copenhagen) Eske Willerslev

(U. Glasgow) Chris Quince, Bill Sloan

(RUG) Rampal Etienne

Acknowledgements

(NIOO) Barbara Drigo (U. New South Wales; Sydney, Australia), Etienne Yergeau (Biotechnology Research Institute; Montréal), Eiko Kuramae, Remy Hillikens, Anna Kielak (RU Groningen), Matthias de Hollander, Agata Pijl, Hans van Veen, Wietse de Boer, Michiel Vos, Sarah Jennings, Alexandra Wolf, Juliet Huet

Latest Impact Factor = 6.397

Covering the breadth of microbial ecology