This document discusses the need for a soil-specific reference database to connect soil metagenomic sequencing data at different levels and enable broader understanding of soil health and productivity. It outlines challenges in soil metagenomics like incredible microbial diversity and lack of reference genomes. Lessons are drawn from the Human Microbiome Project reference genome effort. A targeted sequencing approach could benefit soil studies by providing frameworks for sequencing and identification. Challenges include defining soil organisms and important metadata. Initial efforts like RefSoil and NCBI Reference Genomes from soil are noted but require further curation. Contributions to developing such a database are welcomed.

2. Is it time for a (community) effort
towards a soil reference
database?
Erick Cardenas, James Cole, Maude David, Aaron
Garoutte, Adina Howe, Janet Jansson, Dave
Myrold, James Tiedje, and you?
Modified version of slides will be available after presentation:
http://www.slideshare.net/adinachuanghowe

3. The most important hands in soil
microbiology

4. Significance of a soil-specific reference
• Need standardized resource to
connect sequencing data at
different levels
• Integrate sequencing data
towards soil health and
productivity
• Broadly enable “connecting the
dots”
Genes
Organisms
Communities
Ecosystems

5. Soil metagenomic challenges
• The amount we know…
• Incredible microbial diversity
• Spatial heterogeneity
• Complex dynamics
• Lack of reference genomes (bacteria,
archaea, fungal)

6. HUMAN MICROBIOME PROJECT

7. Lessons from HMP
• 2009 Goals:
– Take advantage of high throughput technologies
to characterize human microbiome of large
number of samples
– Determine whether associations between changes
in the microbiome and health disease
– Provide a standardized data resource and new
technological approaches to enable such studies
to be undertaken broadly in scientific community

8. HMP metagenomic challenges
Soil
• Incredible microbial
diversity
• Spatial heterogeneity
• Complex dynamics
• Lack of reference
genomes (bacteria,
archaea, fungal)
HMP
• Microbial diversity
• Individual variation
• Complex host-associated
dynamics
• Lack of reference
genomes?

9. The HMP reference genome effort
• Add at least 900-3000 additional reference
bacterial genome sequences to public
database
• Thorough representation of domains and
major body sites

10. Not only sequencing….but access to
data
Currently, over 1000 bacterial genomes at various stages of
sequencing

11. Tools: Opening doors broadly
Metaphlan, Nature Methods 9, 811-814 (2012)
Nature Reviews Genetics, 15,
577-584 (2014)
Vital et al., mBio, Vol 5., 2014

12. Another example: GEBA
Comparison of
• rRNA tree of life
• genome
sequence in the
DSMZ culture
collection
Are there any general benefits that come from this
"phylogeny driven" approach?

13. Simpact of “targeted” sequencing of
improved references
Higher rate of discovery
and characterization of
new gene families
New ways to link distantly
related homologs that
would otherwise go
undetected
Significant phylogenetic
expansions of known
protein families
Enrichment of genetic
diversity

14. Can a similar strategy benefit soil
studies?

15. What could we use it for?
• Target isolation and sequencing efforts; creation of a “most
wanted” list
• Soil specific framework for larger scale sequencing and
proteomic efforts to identify taxonomic and functional
information
• Genome-centric investigation of soil genomes (e.g., distribution
of shared genes among soil phyla); development of improved
biomarkers for high throughput assays
• Providing data to tool developers to make
bioinformatics/visualization easier for soil-specific studies

16. What are the challenges?
• How do we defined a soil organism?
– Origin form soil?
– 16S rRNA gene sequence matched one from soil?
– What level of finishing is adecuate?

17. What are the challenges?
• What is the most critical/practical metadata?
– Soil location
– Soil taxonomy
– Links to RefSeq IDs
– Is the strain available and where?

18. What are the challenges?
• Who to include?
– Fungi! Archaea!

19. What are the challenges?
• Expert curators?
– You?
– Tiered hierarchy of curation level

20. Some initial efforts
RefSoil (2011)
Erick Cardenas, Aaron Garoutte, Adina Howe, Jim Tiedje
Bacterial genomes retrieved from Gold
database , and , and selected those
associated with soil habitats
Manually curated to exclude obligated
human pathogens and extremophiles
Databases can be biased and redundant
Proteobacteri
a, 267
Firmicutes, 92
Tenericutes, 5
Cyanobacteria
, 7
Bacteroidetes,
12
Actinobacteri
a, 75
Acidobacteria,
5
Other, 29
492 organisms
19 phyla

21. NCBI Reference Genomes described as
originating from soil
Proteobacteria
Actinobacteria
Firmicutes
Bacteroidetes
Cyanobacteria
Acidobacteria

22. Protein Models for Functions:
FOAM Database
Nucl. Acids Res. (2014)
doi: 10.1093/nar/gku702

23. Some Motivation
60 terrestrial NEON sites distributed across 20 ecoclimatic domains
Terrestrial scale streaming of lots of data including sequencing data for each site

24. If you’d like to contribute
• Join the breakout session Thursday evening
(6-7 pm)
• Know someone with genomes / database, let
us know? Want to contribute? Have an
opinion? Have funding?
Adina Howe, adina.howe@gmail.com