Dataset: Single amplified genomes
Deployment: Bigelow_Stepanauskas_2012

Single amplified genomes (SAGs)

Principal Investigator:

Dr Ramunas Stepanauskas (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Ocean's dark energy: Global inventory of chemoautotrophs in the aphotic realm (Dark ocean chemoautotrophs)

Version:

Version Date:

2016-11-29

Data URL:

https://www.bco-dmo.org/dataset-deployment/666294/data

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Description

Some of the accessions are not yet available [2017-10-27]. A free login account is required to access some of the pages at IMG, in particular, those located at img.jgi.doe.gov/cgi-bin/mer/.

Publications using this dataset:
Pachiadaki MG, Sintes E, Bergauer K, Brown JM, Record NR, Swan BK, Mathyer ME, Hallam SJ, Lopez-Garcia P, Takaki Y, Nunoura T, Woyke T, Herndl GJ, Stepanauskas R (2017). Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science 358 (6366): 1046-1051.

Bergauer K, Fernandez-Guerra A, Garcia JA, Sprenger RR, Stepanauskas R, Pachiadaki MG, Jensen ON, Herndl GJ (2017). Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics. PNAS doi: 10.1073/pnas.1708779115.

Methods & Sampling

Dataset acquisition description

Samples were collected by collaborators, cryopreserved and shipped frozen to Bigelow Laboratory Single Cell Genomics Facility Center (SCGC). Cells were sorted, identified and sequenced by the SCGC, following SCGC’s standard practices: https://scgc.bigelow.org/PDFs/SCGC_Services_Description.pdf

On average, at least 5 million 2x150 bp or longer paired-end reads were generated per SAG using in-house MiSeq and with a NextSeq (Illumina) instruments. The obtained reads are were pre-processed and, de novo assembled, and quality-controlled using algorithms SCGC's standard protocols that are optimized for single cell MDA products . A combination of tetramer homogeneity tests and blast searches against reference databases is were used to detect potential DNA contaminants among the assembled contigs. Benchmark data demonstrating SCGC SAG WGS whole genome sequencing pipeline performance are available here: from the SCGC website: http://data.bigelow.org/~scgc/WGS_benchmark_data/.

Genome annotation was performed through IMG (http://img-stage.jgi-psf.org/cgi-bin/submit/main.cgi).

Further information on Bigelow Laboratory Single Cell Genomics Center (SCGC) Facilities (pdf)

Relevant References:

In preparation:

Pachiadaki M, Record N, Bergauer K, Nunoura T, Lopez-Garcia P, Herndl G, Stepanauskas R (2017) Global biogeography of bacterioplankton in the aphotic realm. Status = in preparation; Acknowledgment of Federal Support = Yes; Peer Reviewed = NA
Stepanauskas R, Brown J, Fergusson E. (2017) Improved genomic sequencing and de novo assembly of microbial single cells. Status = in preparation; Acknowledgment of Federal Support = Yes; Peer Reviewed = NA
Landry Z, Swan BK, Herndl JG, Vergin K, Stepanauskas R, Giovannoni S (2017) SAR202 genomes from the dark ocean predict pathways for the oxidation of recalcitrant dissolved organic matter. Status = in preparation; Acknowledgment of Federal Support = Yes; Peer Reviewed = NA
Nunoura T, Takaki Y, Minegishi H, Hirai M, Shuto A, Yoshida Y, Nishizawa M, Makabe A, Yanagawa K, Kuroiwa M, Makita T, Kodama T, Yoshida M, Koba K, Kondo R, Yokokawa T, Sunamura M, Stepanauskas R, Takai K (2017) Niche separation of MGI thaumarchaeotes along the water column on the three Northwest Pacific trenches. Status = in preparation; Acknowledgment of Federal Support = Yes; Peer Reviewed = NA
Labonté JM, Tupper B, Brown J, Harris C, Record NR, Stepanauskas R (2017) ViruSCope: A bioinformatics pipeline for viral sequence detection in microbial single cell genomes. Status = in preparation; Acknowledgment of Federal Support = Yes; Peer Reviewed = NA

In review:

Stepanauskas R, Fergusson EA, Brown J, Poulton NJ, Tupper B, Labonté JM, Becraft ED, Brown JM, Pachiadaki MG, Povilaitis T, Jeremian R, Alzbutas G, Thompson BP, Mascena CJ, Bellows WK, Petronis A, Lubys A. Genomics of individual cells and viruses revamped: enhanced gDNA amplification and direct, high throughput matching of cell's genomic and physical properties (2017) Status = in review; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Schulz F, Doud D, Reddy TBK, Jarett J, Rivers A, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Schriml L, Podar M, Bork P, Weinstock GM, Banfield JF, Garrity GM, Hugenholtz P, Parks DH, Tyson GW, Rinke C, Dodsworth JA, Yooseph S, Sutton GG, Yilmaz P, Glöckner FO, Meyer F, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema T, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen J, Hedlund BP, McMahon KD, Fierer N, Knight R, Finn RD, Mizrachi I, Eren AM, Woyke T (2017) Genome Standards for Single Amplified Genomes and Genomes From Metagenomes of Bacteria and Archaea. Status = in review; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Kashtan N, Roggensack SE, Thompson SE, Stepanauskas R, Chisholm SW (2017) Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus. Status = in review; Acknowledgment of Federal Support = Yes; Peer Reviewed = NA
Hawley AK, Nobu MK, Wright JJ, Durno WE, Morgan-Lang C, Sage B, Schwientek P, Swan B, Rinke C, Liu WT, Stepanauskas R, Woyke T, Hallam SJ (2017) Co-metabolic innovation along eco-thermodynamic gradients. Status = in review; Acknowledgment of Federal Support = Yes; Peer Reviewed = NA
Collingro A, Köstlbacher S, Mussmann M, Stepanauskas R, Hallam SJ, Horn M (2017) Marine Chlamydiae encode flagella. Status = in review; Acknowledgment of Federal Support = Yes; Peer Reviewed = NA
Jungbluth SP , del Rio TG, Tringe SG, Stepanauskas R, Rappé MS (2017) Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems. Status = in review; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Luo H, Huang Y, Stepanauskas R, Tang J (2017) Excess of Non-Conservative Amino Acid Changes in Marine Bacterioplankton Lineages with Reduced Genomes. Status = in review; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes

Published:

Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker BJ, Petersen DJ, Jørgensen BB, Stepanauskas R, Reinhardt R, Schramm A, Loy A and Adrian L (2016). Single cell genome and group-specific dsrAB sequencing implicate marine members of the class Dehalococcoidia (phylum Chloroflexi) in sulfur cycling. Mbio 7:e00266-16. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Dyksma S, Bischof K, Fuchs BM, Hoffmann K, Meier D, Meyerdierks A, Pjevac P, Probandt D, Richter M, Stepanauskas R, Mußmann M. (2016). Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. The ISME Journal, 10: 1939-1953. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Ngugi DK, Blom J, Stepanauskas R, Stingl U. (2016). Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines. The ISME Journal, 10: 1383-1399. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Zhang Y, Sun Y, Jiao N, Stepanauskas R, Luo H. (2016). Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5. Applied and Environmental Microbiology, 82(7): 2100-11
Labonte JM, Field EK, Lau M, Chivian D, van Heerden E, Wommack KE, Kieft TL, Onstott TC, Stepanauskas R. (2015). Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Frontiers in Microbiology, 6: 349. Status = PUBLISHED; Acknowledgment of Federal Support= Yes; Peer Reviewed = Yes
Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, Sullivan MB, Woyke T, Wommack KE, Stepanauskas R. (2015). Single cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. The ISME Journal, 9: 2386-2399. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
. Martijn J, Schullz F, Zaremba-Niedzwiedzka K, Viklund J, Stepanauskas R, Andersson SGE, Horn M, Guy L, Ettema TJG. (2015). Single cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution. The ISME Journal, 9: 2373-2385. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Stepanauskas R (2015). Wiretapping into microbial interactions by single cell genomics. Frontiers in Microbiology, 6: 258. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Stepanauskas R. (2015). Crystal Ball: Re-defining microbial diversity from its single-celled building blocks. Environmental Microbiology Reports , 7: 36-37. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Eiler A, Zaremba-Niedzwiedzka K, Martinez-Garcia M, McMahon KD, Stepanauskas R, Andersson SGE, Bertilsson S. (2014). Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics. Environmental Microbiology, 16: 2682-2698. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Ghylin TW, Garcia SL, Moya F, Oyserman BO, Schwientek P, Forest KT, Mutschler J, Dwulit-Smith J, Chan LK, Martinez-Garcia M, Sczyrba A, Stepanauskas R, Grossart HP, Woyke T, Warnecke F, Malmstrom R, Bertilsson S, McMahon KD. (2014). Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The ISME Journal, 8: 2503-2516. Status = PUBLISHED; Acknowledgment of Federal Support =Yes; Peer Reviewed = Yes
Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom R, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW (2014). Single cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science, 344: 416-420. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Kminek G, Conley C, Allen CC, Bartlett DH, Beaty DW, Benning LG, Bhartia R, Boston PJ, Duchaine C, Farmer JD,Flynn GJ, Glavin DP, Gorby Y, Hallsworth JE, Mogul R, Moser D, Buford Price P, Pukall R, Fernandez-Remolar D, Smith CL, Stedman K, Steele A, Stepanauskas R, Sun H, Vago JL, Voytek MA, Weiss PS, Westall F (2014). Report of the workshop for life detection in samples from Mars. Life Sciences in Space Research, 2: 1. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Luo H, Tolar B, Swan B, Zhang C, Stepanauskas R, Moran MA, Hollibaugh JT (2014). Single-cell genomics shedding light on marine Thaumarchaeota diversification. The ISME Journal, 8: 732-736. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Luo H, Swan BK, Stepanauskas R, Hughes AL, Moran MA (2014). Comparing Effective Population Sizes of Dominant Marine Alphaproteobacteria Lineages. Environmental Microbiology Reports, 6: 167-172. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Luo H, Swan BK, Stepanauskas R, Hughes AL, Moran MA (2014). Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters. The ISME Journal, 8: 1428-1439. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Rinke C, Lee J, Nath N, Goudeau D, Thompson B, Poulton N, Ferguson E, Malmstrom R, Stepanauskas R, Woyke T. (2014). Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics. Nature Protocols, 9: 1038-1048. Status= PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Roux S, Hawley AK, Beltran MT, Scofield M, Schwientek P, Stepanauskas R, Woyke T, Hallam SJ, Sullivan MB. (2014). Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell and metagenomics. eLife, 3: e03125. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Swan BK, Chaffin M, Martinez-Garcia M, Morrison HG, Field E, Poulton N, Masland EDP, Harris CC, Sczyrba A, Chain PSG, Koren S, Woyke T, StepanauskasR (2014). Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. PLoS ONE, 9: e95380. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Thrash JC, Temperton B, Swan BK, Landry Z, Woyke T, DeLong EF, Stepanauskas R, Giovannoni SJ (2014). Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. The ISME Journal, 8: 1440-1451. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Wasmund K, Schreiber L, Lloyd KG, Petersen DG, Schramm A, Stepanauskas R, Jørgensen BB, Adrian L. (2014). Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi. The ISME Journal, 8: 383-397. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam S, Kyrpides N, Stepanauskas R, Rubin E, Hugenholtz P, Woyke T (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499: 431-437. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes;
Swan ΒK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, González JM, Luo H, Wright JJ, Landry ZC, Hanson NW, Thompson BP, Poulton NJ, Schwientek P, Acinas SG, Giovannoni SJ, Moran MA, Hallam SJ, Cavicchioli R, Woyke T, Stepanauskas R (2013). Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proceedings of the National Academy of Sciences, 110: 11463-11468. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes
Lloyd KG, Schreiber L, Petersen DG, Kjeldsen K, Lever MA, Stepanauskas R, Richter M, Kleindienst S, Lenk S, Schramm A, Jorgensen BB. 2013. Predominant archaea in marine sediments degrade detrital proteins. Nature 496:215-218. Status = PUBLISHED; Acknowledgment of Federal Support = Yes; Peer Reviewed = Yes

Data Processing Description

Dataset Processing Description

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- replaced spaces with underscores

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1232982	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: MiSeq and NextSeq 500 (Illumina)

Supplied Description:

Used to read base pairs

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

plate reader

Supplied Name: high-throughput plate reader (BMG)

Supplied Description:

Instrument Type

Generic Name: plate reader

Generic Description:

Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.

Thermal Cycler

Supplied Name: Roche LC480

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

ultrasonic cell disrupter (sonicator)

Supplied Name: Covaris focused ultrasonicator

Supplied Description:

Instrument Type

Generic Name: ultrasonic cell disrupter (sonicator)

Generic Description:

Instrument that applies sound energy to agitate particles in a sample.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
SAG	Single amplified genome identifier	unitless	sample
IMG_Genome_ID	Accession number from IMG/M (Integrated Microbial Genomes and Microbiome Samples)	unitless	accession_number
date_collection	sample collection date; formatted as yyyy-mm-dd	unitless	date
site_collection_growth_cond	Collection or isolation site; or growth conditions	unitless	site
depth	Collection depth	meters	depth
lat	Latitude; north is positive	decimal degrees	lat
lon	Longitude; east is positive	decimal degrees	lon
Assembled_Genome_Size	Assembled genome size	base pairs	no_bcodmo_term
Gene_Count	Gene count	genes	no_bcodmo_term
Scaffold_Count	Scaffold count	scaffolds	no_bcodmo_term
Availability	Availability: whether the accession is public or date when release is expected	unitless	no_bcodmo_term
IMG_accession_link	Link to IMG accession page	unitless	external_link

Database

Contribute Data

Dataset: Single amplified genomes
Deployment: Bigelow_Stepanauskas_2012

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Single amplified genomesDeployment: Bigelow_Stepanauskas_2012

Dataset acquisition description

Dataset Processing Description

Dataset: Single amplified genomes
Deployment: Bigelow_Stepanauskas_2012