2015 soil science of america meeting
TRANSCRIPT
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THE DIRT ON METAGENOMIC APPROACHES FOR TACKLING
OUR SOILSAdina Howe
Iowa State UniversityAgricultural and Biosystems Engineering
Genomics and Environmental Research in Microbial Systems (GERMS) Lab
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SOIL AS THE MOST COMPLEX ECOSYSTEM.
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UBER-DIVERSE!
Biodiversity in the dark, Wall et al., Nature Geoscience, 2010 Jeremy Burgress
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HETEROGENEOUS
http://www.fao.org/ www.cnr.uidaho.edu
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DYNAMIC
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wikipedia: DNA sequencing
Enrichment Mixed Cultures
Natural systems
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wikipedia: DNA sequencing
Enrichment Mixed Cultures
Natural systems
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QUESTIONS TO EXPLORE SOIL AND NUTRIENT DYNAMICS
• What are the most important gene signals and interactions related to nutrient dynamics?
• What does that sequence encode for and what do we know about it?
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SIGNAL FROM NOISE
• Experimental Design
• Choosing the right model
• Statistical Power (repeated observations / data types)
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A TYPICAL WORKFLOW
Sequences, Genes, Enzymes, Abundances
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EXAMPLES OF CO-OCCURENCE ANALYSIS
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AN EXAMPLE OF CO-OCCURENCE ANALYSIS OVER TIME
Decay of wood rotting community
What is the shape and connectivity of relationships in this system?
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Decay of wood rotting community
https://github.com/ryanjw/co-occurrence
Ryan Williams / Petr Baldrian
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CARBON DEGRADATION ACROSS SPACE: SOIL AGGREGATES
Kirsten Hofmockel, PNNL
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SOIL FUNGI AND ENZYME POTENTIAL: STRONG CO-OCCURENCE SIGNALS
https://www.nics.tennessee.edu/biofuel-surprising-discovery
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-1
0
1
2
-1 0 1 2Slope Between GH5 and CB
Slo
pe B
etw
een
GH
5 an
d A
crem
oniu
m
Soil Fraction
Large Macro
Micro
Whole Soil
unclassified Orbilliaceae
unclassified Phaeosphaeriaceae
Cellulose Decomp.
Ryan Williams
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unclassified Orbilliaceae
unclassified Phaeosphaeriaceae
Phomatospora
Cyberlindnera
Cellulose Decomp.
Ryan Williams
-1
0
1
2
-1 0 1 2Slope Between GH5 and CB
Slo
pe B
etw
een
GH
5 an
d A
crem
oniu
m
Soil Fraction
Large Macro
Micro
Whole Soil
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unclassified Ascomycota
unclassified Orbilliaceae
unclassified Phaeosphaeriaceae
Cladosporium
Acremonium
Phomatospora
Cyberlindnera
Cellulose Decomp.
Ryan Williams
-1
0
1
2
-1 0 1 2Slope Between GH5 and CB
Slo
pe B
etw
een
GH
5 an
d A
crem
oniu
m
Soil Fraction
Large Macro
Micro
Whole Soil
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IMPLICATIONS
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FROM DATA TO INFORMATION:
ANNOTATE A GENE LATELY?
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How many legs does a dog have if you call the tail a leg? Four. Calling a tail a leg doesn't make it a leg.
Abraham Lincoln
90%+ of soil microbes have yet to be cultivated or characterized.
My rescue dog Bentley
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FROM SEQUENCE TO GENE
Jin Choi
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THE HMP: A GREAT COMMUNITY EFFORT MODEL
Jin Choi
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THE HMP: A GREAT COMMUNITY EFFORT MODEL
https://github.com/germs-lab/RefSoil
RHIZOSPHERE SOIL
Jin ChoiErick Cardenas, Aaron Garoutte, Jim Tiedje,
NSF Terragenome (ANL Workshop)
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Jin Choi
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Jin Choi
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REFSOIL
Jin Choi
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ACCESS TO THE INVISIBLE
Kim Lewis, ASM
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HOW REPRESENTATIVE ARE OUR REFERENCES?
16s rRNA amplicon project 14 k samples 3 k samples in soil Jin Choi
www.earthmicrobiome.org
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PHYLOGENETIC DISTRIBUTION OF GLOBAL SOIL COMMUNITIES
Jin Choi
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PRESENCE OF REFSOIL ISOLATES / REFERENCES IN GLOBAL SOIL
COMMUNITIES
Jin Choi
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OTU$ID$ Counts$ Taxonomy$assignment$
4457032$ 8007453$ Verrucomicrobia.Spartobacteria.Chthoniobacterales$
4471583$ 2937242$ Verrucomicrobia.Spartobacteria.Chthoniobacterales$
Novel.OTU.5$$ 2025859$ Proteobacteria.Gammaproteobacteria.Xanthomonadales$
101868$ 1828706$ Verrucomicrobia.Spartobacteria.Chthoniobacterales$
Novel.OTU.22$ 1214770$ Cyanobacteria.Chloroplast.Streptophyta$
204154$ 994864$ Acidobacteria.Chloracidobacteria.RB41$
284946$ 903641$ Bacteroidetes.Bacteroidia.Bacteroidales$
807954$ 875988$ Bacteroidetes.Saprospirae.Saprospirales$
86097$ 868055$ Acidobacteria.Chloracidobacteria.RB41$
4423681$ 689209$ GemmaPmonadetes.GemmaPmonadetes$ Jin Choi
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SINGLE CELL SORTING AND GENOMICS
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GREAT COLLABORATORS
Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences 315 Cells
116 16S rRNA
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HOT OFF THE PRESS
Jin Choi
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HOT OFF THE PRESS
Jin Choi
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HOT OFF THE PRESS
Jin Choi
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TAKE HOMES• Understanding complex systems (such as soil) through
omics-based data / new tools is the opportunity of our generation of research
• The tools (microbiology, statistics, modeling, bioinformatics) and datasets (!) are increasingly entangled
• The questions we need to answer need more training and collaboration than ever but have large impacts
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THANKS FOR YOUR ATTENTION! QUESTIONS?
The GERMSJin Choi Phil ColganJared FlaterRyan Williams Fan Yang
James Tiedje (MSU)C. Titus Brown (UC Davis)