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Study

Study Name: Bacterial and archaeal communities from various locations to study Microbial Dark Matter (Phase II)

Projects

Biosamples

Organisms

Biosamples: 1824 Seq. Projects: 2067
STUDY INFORMATION
GOLD Study ID Gs0111485
Study Name Bacterial and archaeal communities from various locations to study Microbial Dark Matter (Phase II)
Other Names Microbial Dark Matter project phase II - stepping deeper into unknown territory
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
SRA Studies
SRA Study Id SRP112182
Study Title Glacier valley bacterial and archeal communities from Borup Fiord, Nunavut, Canada, to study Microbial Dark Matter (Phase II) - frozenSSSS metaG metagenome
Study Abstract
  
SRA Study Id SRP112183
Study Title Glacier valley bacterial and archeal communities from Borup Fiord, Nunavut, Canada, to study Microbial Dark Matter (Phase II) - lysozymeSSSS metaG metagenome
Study Abstract
  
SRA Study Id SRP112184
Study Title Glacier valley bacterial and archeal communities from Borup Fiord, Nunavut, Canada, to study Microbial Dark Matter (Phase II) - groundupSSSS metaG metagenome
Study Abstract
  
SRA Study Id SRP106219
Study Title candidate division GAL15 bacterium JGI MDM2-000218CP-D13 Genome sequencing
Study Abstract
  
SRA Study Id SRP106215
Study Title Candidatus Omnitrophica bacterium JGI MDM2 000217CP-K11 Genome sequencing
Study Abstract
  
SRA Study Id SRP106213
Study Title Candidatus Omnitrophica bacterium JGI MDM2 000217CP-N5 Genome sequencing
Study Abstract
  
SRA Study Id SRP107665
Study Title Freshwater lake bacterial and archeal communities from Alinen Mustajarvi, Finland, to study Microbial Dark Matter (Phase II) - Alinen Mustajärvi 5m metaG metagenome
Study Abstract
  
SRA Study Id SRP106214
Study Title Candidatus Omnitrophica bacterium JGI MDM2 000217CP-F19 Genome sequencing
Study Abstract
  
SRA Study Id SRP110205
Study Title Groundwater microbial communities from Cold Creek, Nevada to study Microbial Dark Matter (Phase II) - Lower Cold Creek metagenome
Study Abstract
  
SRA Study Id SRP107663
Study Title Hot spring sediment bacterial and archeal communities from British Columbia, Canada, to study Microbial Dark Matter (Phase II) - Larsen N4 metaG metagenome
Study Abstract
  
SRA Study Id SRP106212
Study Title Candidatus Omnitrophica bacterium JGI MDM2 000217CP-I15 Genome sequencing
Study Abstract
  
SRA Study Id SRP107661
Study Title Hot spring sediment bacterial and archeal communities from British Columbia, Canada, to study Microbial Dark Matter (Phase II) - Dewar Creek DC16 2012 metaG metagenome
Study Abstract
  
SRA Study Id SRP107662
Study Title Freshwater lake bacterial and archeal communities from Alinen Mustajarvi, Finland, to study Microbial Dark Matter (Phase II) - Alinen Mustajärvi 4m metaG metagenome
Study Abstract
  
SRA Study Id SRP107660
Study Title Hot spring sediment bacterial and archeal communities from British Columbia, Canada, to study Microbial Dark Matter (Phase II) - Dewar Creek DC9 2012 metaG metagenome
Study Abstract
  
SRA Study Id SRP098352
Study Title Anoxic lake water microbial communities from Lake Kivu, Rwanda to study Microbial Dark Matter (Phase II) - Lake Kivu water 52m metaG metagenome
Study Abstract
  
SRA Study Id SRP112348
Study Title Freshwater bacterial and archeal communities from Indian Creek, Illinois, USA - 4C3 metaG metagenome
Study Abstract
  
SRA Study Id SRP098354
Study Title Glacier valley bacterial and archeal communities from Borup Fiord, Nunavut, Canada, to study Microbial Dark Matter (Phase II) - ?SSSS metaG metagenome
Study Abstract
  
SRA Study Id SRP112349
Study Title Freshwater bacterial and archeal communities from Indian Creek, Illinois, USA - JTO22cm metaG metagenome
Study Abstract
  
SRA Study Id SRP112347
Study Title Freshwater bacterial and archeal communities from Indian Creek, Illinois, USA - 3C3 metaG metagenome
Study Abstract
  
SRA Study Id SRP104969
Study Title Hot spring microbial communities from Sandy''s Spring West, USA to study Microbial Dark Matter (Phase II) - SSWsed_130316 metagenome
Study Abstract
  
SRA Study Id SRP104966
Study Title Lake sediment microbial communities from Lake Baikal, Russia to study Microbial Dark Matter (Phase II) - Lake Baikal sediment 0-5 cm metagenome
Study Abstract
  
SRA Study Id SRP104967
Study Title Hot spring microbial communities from Sandy''s Spring West, USA to study Microbial Dark Matter (Phase II) - SSWsed_matched metagenome
Study Abstract
  
SRA Study Id SRP098347
Study Title Anoxic lake water microbial communities from Lake Kivu, Rwanda to study Microbial Dark Matter (Phase II) - Lake Kivu water 325m metaG metagenome
Study Abstract
  
SRA Study Id SRP106224
Study Title candidate division GAL15 bacterium JGI MDM2-000218CP-L22 Genome sequencing
Study Abstract
  
SRA Study Id SRP098348
Study Title Hot spring microbial communities from South Africa to study Microbial Dark Matter (Phase II) - Sagole hot spring metaG metagenome
Study Abstract
  
SRA Study Id SRP098469
Study Title Lake sediment bacterial and archeal communities from Gulf of Boni, Indonesia to study Microbial Dark Matter (Phase II) - ?I19B2 metaG metagenome
Study Abstract
  
SRA Study Id SRP098349
Study Title Hot spring microbial communities from South Africa to study Microbial Dark Matter (Phase II) - Tshipise hot spring metaG metagenome
Study Abstract
  
SRA Study Id SRP106222
Study Title candidate division WPS-2 bacterium JGI MDM2-000215CP-D13 Genome sequencing
Study Abstract
  
SRA Study Id SRP106221
Study Title candidate division Gal15 bacterium JGI MDM2-000215CP-H10 Genome sequencing
Study Abstract
  
SRA Study Id SRP098341
Study Title Hot spring sediment microbial communities from Zodletone spring, Oklahoma to study Microbial Dark Matter (Phase II) - Zodletone Spring source 0.5m metaG metagenome
Study Abstract
  
SRA Study Id SRP098342
Study Title Hot spring sediment microbial communities from Zodletone spring, Oklahoma to study Microbial Dark Matter (Phase II) - Zodletone Spring source 2m metaG metagenome
Study Abstract
  
SRA Study Id SRP098344
Study Title Marine hydrothermal vent microbial communities from Guaymas Basin, Gulf of California to study Microbial Dark Matter (Phase II) - Marker 14 Mat core 4571-4 33-36 cm metaG metagenome
Study Abstract
  
SRA Study Id SRP098345
Study Title Marine hydrothermal vent microbial communities from Guaymas Basin, Gulf of California to study Microbial Dark Matter (Phase II) - Marker 14 Mat core 4571-4 3-6 cm metaG metagenome
Study Abstract
  
SRA Study Id SRP098346
Study Title Anoxic lake water microbial communities from Lake Kivu, Rwanda to study Microbial Dark Matter (Phase II) - Lake Kivu water 275m metaG metagenome
Study Abstract
  
SRA Study Id SRP098467
Study Title Lake sediment bacterial and archeal communities from Gulf of Boni, Indonesia to study Microbial Dark Matter (Phase II) - ?I18A1 metaG metagenome
Study Abstract
  
SRA Study Id SRP143862
Study Title Freshwater microbial communities from subterranean cave lake in Wind Cave National Park, South Dakota, United States - WICALVC2017 metagenome
Study Abstract
  
SRA Study Id SRP104977
Study Title Hot spring microbial communities from Jinze hot spring, China to study Microbial Dark Matter (Phase II) - JNZ 20120812A metagenome
Study Abstract
  
SRA Study Id SRP104976
Study Title Hot spring microbial communities from Jinze hot spring, China to study Microbial Dark Matter (Phase II) - JNZ 110809A metagenome
Study Abstract
  
SRA Study Id SRP104978
Study Title Wastewater microbial communities from Netherlands to study Microbial Dark Matter (Phase II) - VDW unchlorinated drinking water metagenome
Study Abstract
  
SRA Study Id SRP104973
Study Title Hot spring microbial communities from Little Hot Creek, USA to study Microbial Dark Matter (Phase II) - LHC4sed_replicate metagenome
Study Abstract
  
SRA Study Id SRP104972
Study Title Hot spring microbial communities from Sandy''s Spring West, USA to study Microbial Dark Matter (Phase II) - SSWTFFsm_matched metagenome
Study Abstract
  
SRA Study Id SRP104975
Study Title Hot spring microbial communities from Gongxiaoshe hot spring, China to study Microbial Dark Matter (Phase II) - GXS 110809B metagenome
Study Abstract
  
SRA Study Id SRP104974
Study Title Hot spring microbial communities from Gongxiaoshe hot spring, China to study Microbial Dark Matter (Phase II) - GXS 20120812B metagenome
Study Abstract
  
SRA Study Id SRP109228
Study Title Calescamantes bacterium JGI MDM2 SSWTFF-3-M14 Genome sequencing
Study Abstract
  
SRA Study Id SRP130156
Study Title Freshwater microbial communities from Lake Kivu, Western Province, Rwanda to study Microbial Dark Matter (Phase II) - Kivu_160m metagenome
Study Abstract
  
SRA Study Id SRP130155
Study Title Freshwater microbial communities from Lake Malawi, Central Region, Malawi to study Microbial Dark Matter (Phase II) - Malawi_45m_30L metagenome
Study Abstract
  
SRA Study Id SRP098338
Study Title Marine hydrothermal vent microbial communities from Guaymas Basin, Gulf of California to study Microbial Dark Matter (Phase II) - Marker 14 Mat core 4569-2 3-6 cm metaG metagenome
Study Abstract
  
SRA Study Id SRP104971
Study Title Hot spring microbial communities from Little Hot Creek, USA to study Microbial Dark Matter (Phase II) - LHC4sed_matched metagenome
Study Abstract
  
SRA Study Id SRP109226
Study Title Calescamantes bacterium JGI MDM2 SSWTFF-3-I7 Genome sequencing
Study Abstract
  
SRA Study Id SRP130157
Study Title Freshwater microbial communities from Lake Kivu, Western Province, Rwanda to study Microbial Dark Matter (Phase II) - Kivu_220m metagenome
Study Abstract
  
SRA Study Id SRP130152
Study Title Freshwater microbial communities from Powell Lake, British Columbia, Canada to study Microbial Dark Matter (Phase II) - PL_2010_330m metagenome
Study Abstract
  
SRA Study Id SRP109224
Study Title Calescamantes bacterium JGI MDM2 SSWTFF-2-E14 Genome sequencing
Study Abstract
  
SRA Study Id SRP130151
Study Title Freshwater microbial communities from Powell Lake, British Columbia, Canada to study Microbial Dark Matter (Phase II) - PL_2010_200m metagenome
Study Abstract
  
SRA Study Id SRP130153
Study Title Freshwater microbial communities from Powell Lake, British Columbia, Canada to study Microbial Dark Matter (Phase II) - PL_2010_300m metagenome
Study Abstract
  
SRA Study Id SRP130161
Study Title Freshwater microbial communities from Lake Kivu, Western Province, Rwanda to study Microbial Dark Matter (Phase II) - Kivu_15m_20L metagenome
Study Abstract
  
SRA Study Id SRP104224
Study Title Iron sulfur acid spring bacterial and archeal communities from Banff, Canada, to study Microbial Dark Matter (Phase II) - Paint Pots PPM 11 metaG metagenome
Study Abstract
  
SRA Study Id SRP109234
Study Title Candidatus Fervidibacteria bacterium JGI MDM2 SSWTFF-3-K9 Genome sequencing
Study Abstract
  
SRA Study Id SRP109233
Study Title Calescamantes bacterium JGI MDM2 SSWTFF-3-M19 Genome sequencing
Study Abstract
  
SRA Study Id SRP110210
Study Title Hot spring microbial communities from Beatty, Nevada to study Microbial Dark Matter (Phase II) - OV2 TP2 metagenome
Study Abstract
  
SRA Study Id SRP110213
Study Title Hot spring microbial communities from Beatty, Nevada to study Microbial Dark Matter (Phase II) - OV2 TP3 metagenome
Study Abstract
  
SRA Study Id SRP110212
Study Title Hot spring microbial communities from Beatty, Nevada to study Microbial Dark Matter (Phase II) - OV2 TP1 metagenome
Study Abstract
  
SRA Study Id SRP110214
Study Title Lake sediment microbial communities from Walker lake, Nevada to study Microbial Dark Matter (Phase II) - Walker Lake 11/02/13 Deep Sediment metagenome
Study Abstract
  
SRA Study Id SRP120288
Study Title Freshwater bacterial and archeal communities from Indian Creek, Illinois, USA to study Microbial Dark Matter (Phase II) - 3A3 metaG metagenome
Study Abstract
  
SRA Study Id SRP088629
Study Title Rhodoplanes sp. JGI PP 4-K5 Genome sequencing
Study Abstract
  
SRA Study Id SRP106417
Study Title Thaumarchaeota archaeon JGI MDM2 GXS-3-L12 Genome sequencing
Study Abstract
  
SRA Study Id SRP109248
Study Title Calescamantes bacterium JGI MDM2 SSWsed-3-M6 Genome sequencing
Study Abstract
  
SRA Study Id SRP109244
Study Title Calescamantes bacterium JGI MDM2 SSWsed-3-L9 Genome sequencing
Study Abstract
  
SRA Study Id SRP109243
Study Title Calescamantes bacterium JGI MDM2 SSWsed-3-M4 Genome sequencing
Study Abstract
  
SRA Study Id SRP109242
Study Title Euryarchaeota archaeon JGI MDM2 SSWsed-3-L11 Genome sequencing
Study Abstract
  
SRA Study Id SRP109241
Study Title Calescamantes bacterium JGI MDM2 SSWsed-3-D14 Genome sequencing
Study Abstract
  
SRA Study Id SRP110366
Study Title Freshwater microbial communities from Finland to study Microbial Dark Matter (Phase II) - AM7a DNA metaG metagenome
Study Abstract
  
SRA Study Id SRP110196
Study Title Groundwater microbial communities from Big Spring, Nevada to study Microbial Dark Matter (Phase II) - Ash Meadows Crystal Spring metagenome
Study Abstract
  
SRA Study Id SRP110195
Study Title Groundwater microbial communities from Big Spring, Nevada to study Microbial Dark Matter (Phase II) - Ash Meadows Big Spring metagenome
Study Abstract
  
SRA Study Id SRP088632
Study Title Rhodoplanes sp. JGI PP 4-B12 Genome sequencing
Study Abstract
  
SRA Study Id SRP088631
Study Title Rhodoplanes sp. JGI PP 4-N16 Genome sequencing
Study Abstract
  
SRA Study Id SRP109258
Study Title Candidatus Hydrothermae bacterium JGI MDM2 LHC4sed-1-H6 Genome sequencing
Study Abstract
  
SRA Study Id SRP109257
Study Title Candidatus Fervidibacteria bacterium JGI MDM2 LHC4sed-1-G17 Genome sequencing
Study Abstract
  
SRA Study Id SRP134980
Study Title Candidatus Microgenomates bacterium strain:JGI MDM2 000217CP-F20 Genome sequencing
Study Abstract
  
SRA Study Id SRP110198
Study Title Groundwater microbial communities from Cold Creek, Nevada to study Microbial Dark Matter (Phase II) - Cold Creek Source metagenome
Study Abstract
  
SRA Study Id SRP110197
Study Title Groundwater microbial communities from Devils Hole, Nevada to study Microbial Dark Matter (Phase II) - Devils Hole metagenome
Study Abstract
  
SRA Study Id SRP109251
Study Title Crenarchaeota archaeon JGI MDM2 LHC4sed-1-G16 Genome sequencing
Study Abstract
  
SRA Study Id SRP109250
Study Title Candidatus Hydrothermae bacterium JGI MDM2 LHC4sed-1-C16 Genome sequencing
Study Abstract
  
SRA Study Id SRP130148
Study Title Freshwater microbial communities from Powell Lake, British Columbia, Canada to study Microbial Dark Matter (Phase II) - PL_2010_150m metagenome
Study Abstract
  
SRA Study Id SRP112285
Study Title Lake sediment bacterial and archeal communities from Gulf of Boni, Indonesia to study Microbial Dark Matter (Phase II) - ?I17A3 metaG metagenome
Study Abstract
  
SRA Study Id SRP098490
Study Title Hot spring sediment bacterial and archeal communities from California, USA to study Microbial Dark Matter (Phase II) - Elbow Spring sediment metaG metagenome
Study Abstract
  
SRA Study Id SRP142737
Study Title Sediment microbial communities from Great Boiling Springs, Gerlach, Nevada, United States - GBS 70_MetaG metagenome
Study Abstract
  
SRA Study Id SRP120296
Study Title Freshwater sediment bacterial and archeal communities from Indian Creek, Illinois, USA to study Microbial Dark Matter (Phase II) - Sed-PBS metaG metagenome
Study Abstract
  
SRA Study Id SRP106208
Study Title candidate division GAL15 bacterium JGI MDM2 000223CP-C16 Genome sequencing
Study Abstract
  
SRA Study Id SRP106209
Study Title Candidatus Gracilibacteria bacterium JGI MDM2 000217CP-N10 Genome sequencing
Study Abstract
  
SRA Study Id SRP107658
Study Title Hot spring sediment bacterial and archeal communities from British Columbia, Canada, to study Microbial Dark Matter (Phase II) - Dewar Creek DC2 2012 metaG metagenome
Study Abstract
  
SRA Study Id SRP107659
Study Title Hot spring sediment bacterial and archeal communities from British Columbia, Canada, to study Microbial Dark Matter (Phase II) - Dewar Creek DC8 2012 metaG metagenome
Study Abstract
  
SRA Study Id SRP142744
Study Title Sediment microbial communities from Great Boiling Springs, Gerlach, Nevada, United States - GBS 60_MetaG metagenome
Study Abstract
  
SRA Study Id SRP142746
Study Title Sediment microbial communities from Great Boiling Springs, Gerlach, Nevada, United States - GBS 85_MetaG metagenome
Study Abstract
  
SRA Study Id SRP107657
Study Title Hot spring sediment bacterial and archeal communities from British Columbia, Canada, to study Microbial Dark Matter (Phase II) - Dewar Creek DC4 2012 metaG metagenome
Study Abstract
  
SRA Study Id SRP107655
Study Title Iron sulfur acid spring bacterial and archeal communities from Banff, Canada, to study Microbial Dark Matter (Phase II) - Paint Pots PPA 5.5 metaG metagenome
Study Abstract
  
SRA Study Id SRP109275
Study Title Candidatus Hydrothermae bacterium JGI MDM2 LHC4sed-1-H12 Genome sequencing
Study Abstract
  
SRA Study Id SRP109274
Study Title Candidatus Acetothermia bacterium JGI MDM2 LHC4sed-1-H19 Genome sequencing
Study Abstract
  
SRA Study Id SRP120292
Study Title Freshwater bacterial and archeal communities from Indian Creek, Illinois, USA to study Microbial Dark Matter (Phase II) - 3B3 metaG metagenome
Study Abstract
  
SRA Study Id SRP120290
Study Title Freshwater bacterial and archeal communities from Indian Creek, Illinois, USA to study Microbial Dark Matter (Phase II) - JTO19cm metaG metagenome
Study Abstract
  
SRA Study Id SRP098487
Study Title Hot spring microbial mat communities from California, USA to study Microbial Dark Matter (Phase II) - Cone Pool mat layer C metaG metagenome
Study Abstract
  
SRA Study Id SRP098521
Study Title Freshwater bacterial and archeal communities from Indian Creek, Illinois, USA - JTO16cm metaG metagenome
Study Abstract
  
SRA Study Id SRP098488
Study Title Hot spring sediment bacterial and archeal communities from California, USA to study Microbial Dark Matter (Phase II) - Blank Spring sediment metaG metagenome
Study Abstract
  
SRA Study Id SRP098522
Study Title Freshwater bacterial and archeal communities from Indian Creek, Illinois, USA - Floc-Cal metaG metagenome
Study Abstract
  
SRA Study Id SRP098489
Study Title Hot spring microbial mat communities from California, USA to study Microbial Dark Matter (Phase II) - Cone Pool mat layer H metaG metagenome
Study Abstract
  
Legacy ER Study ID 75008
Legacy GOLD ID Gm0075008
Added By Jyothi Mallajosyula on 2014-07-03
Last Modified By JGI automated process on 2019-06-17
PI Ramunas Stepanauskas
Description Reconstructing bacterial and archaeal genomes has revolutionized our understanding of microbial metabolism as well as evolutionary processes, and significantly sped up discoveries made in bioprospecting. The vast majority of bacterial and archaeal genomes sequenced to date are of rather limited phylogenetic diversity as they were largely chosen as based on their physiology and/ or medical importance. These findings gave rise to the initiation of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) Project (Wu et al 2009), which populated the tree of life with phylogenetically diverse reference genomes.Following into the footsteps of the GEBA project, we initiated the Microbial Dark Matter (MDM) Project in 2011 to massively expand genomic representation further by targeting 200 representatives of candidate phyla (phyla proposed on the basis of environmental sequences that have no, or very few cultivated representatives) via high throughout single-cell sequencing. The insight derived from the ~200 MDM genomes belonging to 28 major uncharted branches of the tree were invaluable (Rinke at al 2013), providing a first glimpse into the coding potential and the phylogeny of candidate phyla. The single-cell data enabled us to resolve numerous intra- and inter-phylum level relationships and propose new superphyla. In addition we proposed names for 18 candidate phyla for which we greatly expanded sequence space. Here we propose phase II of the MDM project to further deepen our understanding of dark matter by targeting 1000 genomes from candidate phyla. Habitats of highest phylogenetic diversity (PD) value, as based on SSU rRNA surveys, are selected for single-cell sorting and shotgun metagenomics. Thousands to tens of thousands of single cells will be anonymously sorted, whole genomes will be amplified and screened by SSU rRNA PCR and sequencing to allow their taxonomic placement and selection for the draft genome sequencing. We propose to only target taxonomic groups within candidate phyla with no or few sequenced representatives to maximize phylogenetic coverage, the selection of which will in part be driven by the outcome of the single-cell sorts.We moreover propose to generate metagenome shotgun data for each sampling site undergoing single-cell sorting. Single cell genomes will be assembled and QC?d by single-cell specific pipelines previously developed at the JGI. Genomes will be assembled from metagenomes by algorithms developed in the Hugenholtz laboratory. The resulting genome sequences of candidate phyla representatives generated in this project will then be used for metabolic reconstruction to assess functional diversity and link these to the habitat metadata. Genomes will be mined for unique and unexpected functions. Population genomes will be used for pangenome analysis of natural populations to assess heterogeneity and deepen our insights into population structure. Lastly, including our genomes as part of the reference database, we aim to carry out large-scale phylogenetic anchoring analysis of all public metagenomes to study co-occurrence patterns in shotgun sequenced habitats worldwide. Based on phylogenetic diversity analysis of existing SSU rRNA data, ecosystem DOE-relevance and sample access and availability, we selected a target list of 12 environments. All samples harbour a high percentage of candidate phyla. Two of these environments (Sakinaw Lake and Etoliko lagoon) were part of our previous work and SAGs for sequencing as well as metagenomic sequence data are already in hand. For the additional target environments, various Co-PIs will be responsible for providing sample for both, single-cell sequencing (cryo-preserved frozen stocks) and metgenome sequencing (extracted DNA) according to Bigelow and JGI instructions. Samples will be processed at the DOE JGI and with the assistance of the Woyke lab.
Relevance
Study Information Link
Study Information Visibility Public
Metagenomic Study Yes
Publication
Is GEBA No
Is HMP No
ECOSYSTEM CLASSIFICATION
Ecosystem Environmental
Ecosystem Category Aquatic
Ecosystem Type
Ecosystem Subtype
Specific Ecosystem
STUDY COMPOSITION
Number of Biosamples 1824
Number of Organisms 467
Number of Seq Projects 2067
Number of Analysis Projects 2006
Number of Related Studies 0

 

 

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