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

adina@iastate.edu

SOIL AS THE MOST COMPLEX ECOSYSTEM.

UBER-DIVERSE!

Biodiversity in the dark, Wall et al., Nature Geoscience, 2010 Jeremy Burgress

HETEROGENEOUS

http://www.fao.org/ www.cnr.uidaho.edu

DYNAMIC

wikipedia: DNA sequencing

Enrichment Mixed Cultures

Natural systems

wikipedia: DNA sequencing

Enrichment Mixed Cultures

Natural systems

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?

SIGNAL FROM NOISE

• Experimental Design

• Choosing the right model

• Statistical Power (repeated observations / data types)

A TYPICAL WORKFLOW

Sequences, Genes, Enzymes, Abundances

EXAMPLES OF CO-OCCURENCE ANALYSIS

AN EXAMPLE OF CO-OCCURENCE ANALYSIS OVER TIME

Decay of wood rotting community

What is the shape and connectivity of relationships in this system?

Decay of wood rotting community

https://github.com/ryanjw/co-occurrence

Ryan Williams / Petr Baldrian

CARBON DEGRADATION ACROSS SPACE: SOIL AGGREGATES

Kirsten Hofmockel, PNNL

SOIL FUNGI AND ENZYME POTENTIAL: STRONG CO-OCCURENCE SIGNALS

https://www.nics.tennessee.edu/biofuel-surprising-discovery

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Soil Fraction

Large Macro

Micro

Whole Soil

unclassified Orbilliaceae

unclassified Phaeosphaeriaceae

Cellulose Decomp.

Ryan Williams

unclassified Orbilliaceae

unclassified Phaeosphaeriaceae

Phomatospora

Cyberlindnera

Cellulose Decomp.

Ryan Williams

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Soil Fraction

Large Macro

Micro

Whole Soil

unclassified Ascomycota

unclassified Orbilliaceae

unclassified Phaeosphaeriaceae

Cladosporium

Acremonium

Phomatospora

Cyberlindnera

Cellulose Decomp.

Ryan Williams

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pe B

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Soil Fraction

Large Macro

Micro

Whole Soil

IMPLICATIONS

FROM DATA TO INFORMATION:

ANNOTATE A GENE LATELY?

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

FROM SEQUENCE TO GENE

Jin Choi

THE HMP: A GREAT COMMUNITY EFFORT MODEL

Jin Choi

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)

Jin Choi

Jin Choi

REFSOIL

Jin Choi

ACCESS TO THE INVISIBLE

Kim Lewis, ASM

HOW REPRESENTATIVE ARE OUR REFERENCES?

16s rRNA amplicon project 14 k samples 3 k samples in soil Jin Choi

www.earthmicrobiome.org

PHYLOGENETIC DISTRIBUTION OF GLOBAL SOIL COMMUNITIES

Jin Choi

PRESENCE OF REFSOIL ISOLATES / REFERENCES IN GLOBAL SOIL

COMMUNITIES

Jin Choi

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

SINGLE CELL SORTING AND GENOMICS

GREAT COLLABORATORS

Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences 315 Cells

116 16S rRNA

HOT OFF THE PRESS

Jin Choi

HOT OFF THE PRESS

Jin Choi

HOT OFF THE PRESS

Jin Choi

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

THANKS FOR YOUR ATTENTION! QUESTIONS?

The GERMSJin Choi Phil ColganJared FlaterRyan Williams Fan Yang

James Tiedje (MSU)C. Titus Brown (UC Davis)

germslab.orgadina@iastate.du