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Study

Study Name: Avena fatua rhizosphere microbial communities from Hopland, California, USA

Projects

Biosamples

Organisms

Biosamples: 23 Seq. Projects: 63
STUDY INFORMATION
GOLD Study ID Gs0110148
Study Name Avena fatua rhizosphere microbial communities from Hopland, California, USA
Other Names Unraveling the rhizosphere carbon cycle: Using comparative metatranscriptomics to identify key processes involved in root-enhanced decomposition of organic matter
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
SRA Studies
SRA Study Id SRP099800
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H4_Bulk_46 metatranscriptome
Study Abstract
  
SRA Study Id SRP107666
Study Title Acidimicrobiales bacterium JGI 006 Genome sequencing
Study Abstract
  
SRA Study Id SRP099801
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H4_Rhizo_45 metatranscriptome
Study Abstract
  
SRA Study Id SRP107664
Study Title bacterium Ellin6075 strain:JGI 003 Genome sequencing
Study Abstract
  
SRA Study Id SRP099682
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H1_Bulk_28 metatranscriptome
Study Abstract
  
SRA Study Id SRP099684
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H1_Bulk_29 metatranscriptome
Study Abstract
  
SRA Study Id SRP099683
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H1_Rhizo_26 metatranscriptome
Study Abstract
  
SRA Study Id SRP099685
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H1_Rhizo_27 metatranscriptome
Study Abstract
  
SRA Study Id SRP107678
Study Title Sphingobacteriaceae bacterium JGI 017 Genome sequencing
Study Abstract
  
SRA Study Id SRP107679
Study Title Gemmatimonadetes bacterium JGI 022 Genome sequencing
Study Abstract
  
SRA Study Id SRP107676
Study Title Solirubrobacterales bacterium strain:JGI 014 Genome sequencing
Study Abstract
  
SRA Study Id SRP093054
Study Title Arenimonas sp. JGI 044 Genome sequencing
Study Abstract
  
SRA Study Id SRP107677
Study Title Solirubrobacterales bacterium strain:JGI 015 Genome sequencing
Study Abstract
  
SRA Study Id SRP099678
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H1_Bulk_30 metatranscriptome
Study Abstract
  
SRA Study Id SRP099799
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H3_Bulk_42 metatranscriptome
Study Abstract
  
SRA Study Id SRP107674
Study Title Sporichthyaceae bacterium JGI 012 Genome sequencing
Study Abstract
  
SRA Study Id SRP107675
Study Title Sphingobacteriaceae bacterium JGI 016 Genome sequencing
Study Abstract
  
SRA Study Id SRP093050
Study Title Agrobacterium sp. JGI 035 Genome sequencing
Study Abstract
  
SRA Study Id SRP107672
Study Title Actinomycetales bacterium strain:JGI 008 Genome sequencing
Study Abstract
  
SRA Study Id SRP107673
Study Title Nocardioidaceae bacterium strain:JGI 011 Genome sequencing
Study Abstract
  
SRA Study Id SRP107670
Study Title Acidimicrobiales bacterium JGI 007 Genome sequencing
Study Abstract
  
SRA Study Id SRP107671
Study Title Frankiaceae bacterium JGI 009 Genome sequencing
Study Abstract
  
SRA Study Id SRP099792
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H3_Rhizo_37 metatranscriptome
Study Abstract
  
SRA Study Id SRP099791
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H3_Rhizo_39 metatranscriptome
Study Abstract
  
SRA Study Id SRP099670
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H1_Rhizo_25 metatranscriptome
Study Abstract
  
SRA Study Id SRP099796
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H4_Rhizo_43 metatranscriptome
Study Abstract
  
SRA Study Id SRP099798
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H4_Rhizo_44 metatranscriptome
Study Abstract
  
SRA Study Id SRP099797
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H3_Bulk_41 metatranscriptome
Study Abstract
  
SRA Study Id SRP093057
Study Title Flavobacterium sp. JGI 052 Genome sequencing
Study Abstract
  
SRA Study Id SRP099789
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H2_Bulk_36 metatranscriptome
Study Abstract
  
SRA Study Id SRP107687
Study Title Sphingomonadaceae bacterium strain:JGI 037 Genome sequencing
Study Abstract
  
SRA Study Id SRP093044
Study Title Rhodoplanes sp. JGI 031 Genome sequencing
Study Abstract
  
SRA Study Id SRP099788
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H2_Rhizo_32 metatranscriptome
Study Abstract
  
SRA Study Id SRP107688
Study Title Sphingomonadaceae bacterium strain:JGI 036 Genome sequencing
Study Abstract
  
SRA Study Id SRP107685
Study Title Rhizobiales bacterium strain:JGI 029 Genome sequencing
Study Abstract
  
SRA Study Id SRP093041
Study Title Edaphobacter sp. JGI 001 Genome sequencing
Study Abstract
  
SRA Study Id SRP093042
Study Title Mesorhizobium sp. JGI 033 Genome sequencing
Study Abstract
  
SRA Study Id SRP107686
Study Title Xanthomonadaceae bacterium strain:JGI 043 Genome sequencing
Study Abstract
  
SRA Study Id SRP107683
Study Title Caulobacteraceae bacterium JGI 027 Genome sequencing
Study Abstract
  
SRA Study Id SRP107681
Study Title bacterium Ellin329 strain:JGI 028 Genome sequencing
Study Abstract
  
SRA Study Id SRP107682
Study Title Alphaproteobacteria bacterium strain:JGI 026 Genome sequencing
Study Abstract
  
SRA Study Id SRP107680
Study Title bacterium Ellin5290 strain:JGI 023 Genome sequencing
Study Abstract
  
SRA Study Id SRP093049
Study Title Devosia sp. JGI 030 Genome sequencing
Study Abstract
  
SRA Study Id SRP099783
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H2_Bulk_35 metatranscriptome
Study Abstract
  
SRA Study Id SRP099785
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H2_Rhizo_33 metatranscriptome
Study Abstract
  
SRA Study Id SRP093047
Study Title Methylibium sp. JGI 040 Genome sequencing
Study Abstract
  
SRA Study Id SRP099784
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H2_Rhizo_31 metatranscriptome
Study Abstract
  
SRA Study Id SRP093048
Study Title Sphingomonas sp. JGI 038 Genome sequencing
Study Abstract
  
SRA Study Id SRP093045
Study Title Agrobacterium sp. JGI 034 Genome sequencing
Study Abstract
  
SRA Study Id SRP093046
Study Title Sphingomonas bacterium strain:JGI 039 Genome sequencing
Study Abstract
  
SRA Study Id SRP099786
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H2_Bulk_34 metatranscriptome
Study Abstract
  
SRA Study Id SRP087328
Study Title Cellulomonas sp. JGI 051 Genome sequencing
Study Abstract
  
SRA Study Id SRP087684
Study Title bacterium JGI 053 Genome sequencing
Study Abstract
  
SRA Study Id SRP099891
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H3_Bulk_40 metatranscriptome
Study Abstract
  
SRA Study Id SRP099893
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H4_Bulk_47 metatranscriptome
Study Abstract
  
SRA Study Id SRP099892
Study Title Grassland soil microbial communities from Hopland, California, USA - Sample H4_Bulk_48 metatranscriptome
Study Abstract
  
Legacy ER Study ID 63481
Legacy GOLD ID Gm0063481
Added By Michelle Isbandi on 2013-12-30
Last Modified By Michelle Isbandi on 2014-02-07
PI Jennifer Pett-Ridge
Description The soil surrounding plant roots, known as the rhizosphere, is a nexus for the transformation of soil carbon. Rhizosphere microorganisms provide precursors to stabilized soil organic matter by transforming plant root exudates into microbial biomass and by mediating the breakdown of complex plant tissues and cell-derived macromolecules. However, the soil microbial communities and carbohydrate/lignolytic gene transcripts mediating root-accelerated decomposition are largely unidentified. Our goal is to determine how root exudates alter the decomposition of both simple and complex C substrates in the rhizosphere. We hypothesize that the root-exudate stimulation of soil microbial populations results in elevated expression of transcripts for the decomposition of macromolecular C compounds. To address this hypothesis, we propose to use JGI CSP sequencing to: 1. tSequence metatranscriptomes from experimentally manipulated soil, analyzing specifically for transcripts related to carbohydrate decomposition. Treatments include: a)    Rhizosphere soil b)    Rhizosphere soil in direct contact with decaying root litter c)    Decaying root litter in soil d)    Soil that does not contact roots or decaying litter. 2.    Use stable isotope probing (SIP)-assisted metatranscriptomics to analyze the functional subset of the total soil transcriptome that is directly involved in the decomposition of root C. SIP-assisted transcriptomics uses density gradient fractionation to isolate only the 13C-enriched mRNA transcribed by organisms who have consumed a 13C labeled substrate. We will isolate 13C mRNA from soil using the following 13C labeled substrates: a)    13C root exudates b)    13C root exudates + 12C root litter c)    13C root litter d)    13C root litter + 12C root exudates. 3.    SIP-targeted single cell sorting and genome sequencing of taxa involved in the decomposition of 13C-labeled root litter. We hope to target up to 10 phylotypes from each of three root zones (root tip, root hair, mature root) in the following treatments: a)    13C root exudates b)    13C root litter For whole and SIP-assisted metatranscriptome sequencing, we request mRNA HiSeq analysis via paired-end Illumina sequencing of 24 HiSeq lanes (1 lane per treatment, 3 replicates each). This translates to approximately 216 Gb (at ~ 9 Gb per lane). For the single cell sorted genome sequences, cells recovered would be prioritized for paired end-Illumina sequencing (~three preps per lane), yielding up to 20 lanes of Illumina sequencing. Our total project request = ~ 44 lanes Illumina (~400 Gb, assuming 9Gb per lane). This work would significantly augment a project currently funded by the DOE Genomic Science program (FOA DE-PS02-09ER09-25), and would leverage a metagenomic sequencing project of the same Hopland CA soil, currently part of an existing JGI CSP (#653). The isotope labeling experiments described above have already been conducted and high quality RNA extracted. To achieve the high replication and sequence resolution required to address our proposed hypotheses, the sequencing capabilities of JGI will be critical.
Relevance
Study Information Link
Study Information Visibility Public
Metagenomic Study Yes
Publication
Is GEBA No
Is HMP No
ECOSYSTEM CLASSIFICATION
Ecosystem Host-associated
Ecosystem Category Plants
Ecosystem Type Rhizoplane
Ecosystem Subtype
Specific Ecosystem
STUDY COMPOSITION
Number of Biosamples 23
Number of Organisms 40
Number of Seq Projects 63
Number of Analysis Projects 971
Number of Related Studies 0

 

 

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