http://lod.bco-dmo.org/id/dataset/771936 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2019-06-26 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Whole-genome sequence accessions for the Alcanivorax sp. strain 97CO-6 isolated from a crude oil-consuming bacterial consortium, enriched from Yellow Sea sediments from China in April of 2007. 2019-06-26 publication 2019-06-26 revision BCO-DMO Linked Data URI 2019-06-26 creation http://lod.bco-dmo.org/id/dataset/771936 David L. Valentine University of California-Santa Barbara principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Valentine, D. L. (2019) Whole-genome sequence accessions for the Alcanivorax sp. strain 97CO-6 isolated from a crude oil-consuming bacterial consortium, enriched from Yellow Sea sediments from China in April of 2007. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-06-26 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/771936 [access date] Dataset Description: Whole-genome sequence accessions for the Alcanivorax sp. strain 97CO-6 isolated from a crude oil-consuming bacterial consortium, enriched from Yellow Sea sediments from China in April of 2007. The genetic accessions can be found at The National Center for Biotechnology Information (NCBI) under master accession number PIXQ01000000 (https://www.ncbi.nlm.nih.gov/nuccore/PIXQ01000000). These results were published in Yin et al. (2018). Methods and Sampling: Project accession number PIXQ01000000 Species name Alicanivorax sp. 97CO-6 Description of types of sequences: The draft genome of strain 97CO-6, which contains 3,253,423 bp, with a G+C content of 54.53%, as well as 2,931 protein-coding genes and 42 tRNAs. Locations where species were collected Alcanivorax sp. Strain 97CO-6 was isolated from a crude oil-consuming bacterial consortium, enriched from Yellow Sea sediments from China Sequencing and analysis methods Whole-genome shotgun sequencing of the Alcanivorax sp. 97CO-6 genome was done using Solexa paired-end sequencing technology by Shanghai Majorbio Bio-Pharm Technology Co., Ltd (Shanghai, China). A total of 13,445,638 paired-end reads (180-bp and 800-bp libraries) were generated to reach a 398-fold depth of coverage using the Illumina HiSeq 2000 platform (Illumina, Inc., San Diego, CA, USA). The reads were assembled using SOAPdenovo version 1.05. The resulting genome sequence of Alcanivorax sp. 97CO-6 comprises  43 contigs (N90 = 78,739), with 3,253,423 bp and an average G+C content of 54.53%. Gene annotation was carried out using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (https://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html), which was followed by manual editing. The annotation of the genome includes 2,931 candidate protein-encoding genes (with an average size of 960 bp), yielding a coding intensity of 86.50%. A total of 2,118 proteins could be assigned to clusters of orthologous (COG) groups; 42 tRNAs for all 20 amino acids and one 16S-23S-5S rRNA operon were identified using tRNAscan version 1.23 (8) and rRNAmmer version 1.2 (9), respectively. All of the above information is from the published article “Genome Sequence of a Marine Alkane Degrader, Alcanivorax sp. Strain 97CO-6.” Xiafei Yin, Xiao Luan, Angela Xu, Qian Li, Zhisong Cui, and David L. Valentine, Genome Announcements 2018 6 (8): e00087-18 doi: 10.1128/genomeA.00087-18 Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1333162 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1333162 completed David L. Valentine University of California-Santa Barbara 805-893-2973 Department of Earth Science 1006 Webb Hall Santa Barbara CA 93106 USA valentine@ucsb.edu pointOfContact asNeeded Dataset Version: 1 Unknown otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. Collaborative Research: Oxygenation of Hydrocarbons in the Ocean https://osprey.bco-dmo.org/project/748112 Collaborative Research: Oxygenation of Hydrocarbons in the Ocean <p>NSF abstract:<br /> More than 400,000 tons of petroleum hydrocarbons are released annually into the ocean, where they are subject to physical, chemical and biological processes, known as weathering, that are known to remove select hydrocarbons from the ocean. However, little attention has been given to the residues left by the weathering of oil, and studies indicate that oxygenation of these hydrocarbons can play a part in the formation of recalcitrant tar and toxic compounds. To address this gap, researchers from Woods Hole Oceanographic Institution, University of Mary Washington, and University of California Santa Barbara will conduct research to lay a scientific foundation for understanding 1) which processes control the formation of oxygenated hydrocarbons, 2) the rates of these processes, 3) the identity of the major products, 4) the rates at which they are formed and destroyed, and 5) for distinguishing photochemical oxygenation from biological oxygenation. The results from these experiments will contribute to a better understanding of the petroleum oxygenation processes and the environmental fate of understudied oxygenation products.</p> <p>Broader Impacts: This study will provide for several undergraduates and two postdoctoral scholars to be trained in innovative analytical and experimental techniques. The results of this effort will help regulatory agencies to define new analytical methods and target compounds for oil spill research, and will add to our understanding regarding the fate and impacts of hydrocarbons released into the ocean.</p> Oxygenation of Hydrocarbons largerWorkCitation project eng; USA oceans 121.99 121.99 36.67 36.67 2017-04-19 2017-04-19 Gulf of Mexico between Mississippi Slope, Gould Basin, and Castillo Basin (27 N 91 W) 0 BCO-DMO catalogue of parameters from Whole-genome sequence accessions for the Alcanivorax sp. strain 97CO-6 isolated from a crude oil-consuming bacterial consortium, enriched from Yellow Sea sediments from China in April of 2007. Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact https://osprey.bco-dmo.org/dataset/771936/data/download download onLine dataset Project accession number PIXQ01000000 Species name Alicanivorax sp. 97CO-6 Description of types of sequences: The draft genome of strain 97CO-6, which contains 3,253,423 bp, with a G+C content of 54.53%, as well as 2,931 protein-coding genes and 42 tRNAs. Locations where species were collected Alcanivorax sp. Strain 97CO-6 was isolated from a crude oil-consuming bacterial consortium, enriched from Yellow Sea sediments from China Sequencing and analysis methods Whole-genome shotgun sequencing of the Alcanivorax sp. 97CO-6 genome was done using Solexa paired-end sequencing technology by Shanghai Majorbio Bio-Pharm Technology Co., Ltd (Shanghai, China). A total of 13,445,638 paired-end reads (180-bp and 800-bp libraries) were generated to reach a 398-fold depth of coverage using the Illumina HiSeq 2000 platform (Illumina, Inc., San Diego, CA, USA). The reads were assembled using SOAPdenovo version 1.05. The resulting genome sequence of Alcanivorax sp. 97CO-6 comprises  43 contigs (N90 = 78,739), with 3,253,423 bp and an average G+C content of 54.53%. Gene annotation was carried out using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (https://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html), which was followed by manual editing. The annotation of the genome includes 2,931 candidate protein-encoding genes (with an average size of 960 bp), yielding a coding intensity of 86.50%. A total of 2,118 proteins could be assigned to clusters of orthologous (COG) groups; 42 tRNAs for all 20 amino acids and one 16S-23S-5S rRNA operon were identified using tRNAscan version 1.23 (8) and rRNAmmer version 1.2 (9), respectively. All of the above information is from the published article “Genome Sequence of a Marine Alkane Degrader, Alcanivorax sp. Strain 97CO-6.” Xiafei Yin, Xiao Luan, Angela Xu, Qian Li, Zhisong Cui, and David L. Valentine, Genome Announcements 2018 6 (8): e00087-18 doi: 10.1128/genomeA.00087-18 Specified by the Principal Investigator(s) asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact