george kowalchuk: combining large- and small-scale studies to uncover soil-borne microbial diversity
DESCRIPTION
George Kowalchuk's talk at the 1st Earth Microbial Project Meeting in ShenzhenTRANSCRIPT
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 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
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
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
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…
(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