RefSoil ANL talk

Agricultural and Biosystems Engineering

RefSoil – Continuous Progress

in Soil Reference DatabaseJinlyung Choi, Erick Cardenas,

Ryan Williams, Adina Howe

October 21, 2015 11:40 am

7th Annual Argonne Soil Metagenomics

Meeting


Soil metagenomic challenges

• The amount we know…

• Incredible microbial diversity

• Spatial heterogeneity

• Complex dynamics

• Lack of reference genomes (bacteria,

archaea, fungal)


Do we have a useful dictionary for soil?


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


HMP: A good example of curated DB


HMP: A good example of curated DB

Rhizosphere

/ Bulk Soil


Lessons from HMP• 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

• Identify elusive organisms and identify a most

wanted list


Proteobacteria, 267

Firmicutes, 92

Actinobacteria, 75

Bacteroidetes, 12

Cyanobacteria, 7

Tenericutes, 5

Acidobacteria, 5 Other, 29

Some initial efforts• Bacterial genomes

retrieved from Gold

database, JGI-IMG,

and selected those

associated with soil

habitats

• Manually curated to

exclude obligated

human pathogens and

extremophiles

• Databases are biased

and redundant

RefSoil (2011)Erick Cardenas, Aaron Garoutte,

Adina Howe, Jim Tiedje

492 organisms

19 phyla


What is included and not included

Included

• Have Full genome

sequence available

• Listed in RefSeq

• Associated with soil

habitats

Not included

• Human pathogens

• Extremophile


Here are Updates

• Increase DB size

: • Organisms:

• 492 1043

• Phyla:

• 19 21

• evaluate the

breadth and

diversity of this

database and its

ability to inform

soil microbiology Proteobacteria, 428

Firmicutes, 177

Actinobacteria, 103

Cyanobacteria, 25

Bacteroidetes, 19

Euryarchaeota, 18

Spirochaetes, 8

Other, 25


What could we use it for?• Soil specific database to identify “who” and “what” -

linked to organisms where strains are available for

future efforts

• Making data analysis easier for soil scientists

• Identify targets for culturing efforts




future efforts




RefSoil can be used to Identify functional

information

Antibiotic Resistant Genes and

integrases found in RefSoilWilliams, Choi et al.

In preparation


RefSoil can be used to Identify functional

information

KEGG Metabolic pathway mapping

Glycan Biosynthesis

Metabolism of

Terpenoid and Polyketides


RefSoil can be used to identify

differences in soil

-3

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PC1: 40% variance

PC

2: 1

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varia

nce

group

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CC P PF

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Sulfurihydrogenibium azorense Zymomonas mobilis subsp.

Acidovorax sp.Candidatus Chloracidobacterium

thermophilum B

Corn PrairieFertilized

PrairieCorn Prairie

Fertilized

Prairie

Corn PrairieFertilized

PrairieCorn Prairie

Fertilized

Prairie

Corn

Prairie

Fertilized

Prairie

Corn

Prairie

Fertilized

Prairie




future efforts




Defined Soil-specified resources

makes your analysis easier




future efforts




Earth Microbiome Project (EMP)

16s rRNA amplicon project

14 k samples

3 k samples in soil


Tree of Soil specific in EMP

Soil specific EMP

1.8 million nodes


What are we missing?

– 1) by placement in tree

Some genus missing

Phylum missing

Most genera

missing




Some genus missing

Phylum missing

Most genera

missing




Some genus missing

Phylum missing

Most genera

missing




Some genus missing

Phylum missing

Most genera

missing

Parvarchaeota, AC1, AD3, AncK6, BHI80-139, BRC1,

Caldiserica, Caldithrix, CD12, Chlamydiae,Deferribacteres,

Elusimicrobia, FBP, FCPU426, Fibrobacteres, Fusobacteria,

GAL15, GN01, GN02, GN04, GOUTA4, H-178, Hyd24-12,

Kazan-3B-28, KSB3, LCP-89, LD1, Lentisphaerae, MVP-21, ,

MVS-104, NC10, NKB19, OC31, , OD1, OP11, OP1, OP3,

OP8, OP9, , PAUC34f, Poribacteria, SAR406, SBR1093, SC4,

SR1, TA06, TM6, TM7, TPD-58, VHS-B3-43, WPS-2, WS1,

WS2, WS3, WS4, WS5, WS6, WWE1, ZB3


What are we missing? – 2) by abundance

Highly presence in the soil but not listed in the Reference

OTU ID Counts Taxonomy assignment

4457032 8007453 Verrucomicrobia.Spartobacteria.Chthoniobacterales


Novel.OTU.5 2025859 Proteobacteria.Gammaproteobacteria.Xanthomonadales


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 Gemmatimonadetes.Gemmatimonadetes


Summary


Summary


acknowledgement

Science

RefSoil ANL talk