19:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1a:T50f,The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL. https://ndsf.whoi.edu/jason/1b:T1798,Description from NSF award abstract: A grand challenge in microbial ecology is to understand what drives the structure of microbial communities. A recently discovered novel class of Proteobacteria, the Zetaproteobacteria, are associated with microbial mats at iron rich hydrothermal vents at submarine volcanoes deep in the ocean. These bacteria only grow using iron as an energy source and fix carbon dioxide. Within iron rich microbial mats, Zetaproteobacteria are the dominant bacterial population; however they are rare in most other deep-sea or marine habitats, suggesting they may be restricted to specific niches characterized by gradients of oxygen and iron. Recent discoveries have expanded their range to fluids collected from deep ocean crust boreholes, iron deposits in coastal saltmarshes, and with steel associated bio-corrosion, demonstrating that marine Zetaproteobacteria are cosmopolitan. A unique property of these marine iron oxidizing bacteria is that they produce morphologically distinct iron oxide structures in the form of filamentous sheaths or stalk-like structures. These structures are easily recognized by light microscopy, and electron microscopy is beginning to reveal subtle differences among them that may be diagnostic of different populations of iron oxidizing bacteria. Another unusual aspect of iron oxidizing bacteria is that they produce large quantities of oxides with relatively little bacterial biomass. As a result, the oxides form a matrix that influences water and nutrient flow in the microbial mats where they grow, and in turn, may influence the growth of other groups of bacteria and archaea that live in the mats. In an ecological context, the PIs believe this makes them a keystone species that form the predominant structural matrix of the mat, and engineer an environment conducive for growth of specific bacterial populations within the mat ecosystem. The PIs propose to use high resolution mat sampling techniques to investigate the architecture of mat ecosystems and couple these with modern molecular methods (i.e., single-cell metagenomics) and geochemical measurements of the vent fluid to couple morphological and functional diversity to phylogenetic and physiological diversity. Because the Zetaproteobacteria are ancient, have unique metabolic and morphological attributes, and appear to be restricted to a well-defined habitat, they offer an interesting model for understanding fundamental ecological concepts that drive microbial diversity and evolution. A better understanding of iron oxidizing bacteria that include Zetaproteobacteria is of fundamental interest to scientists interested in areas of earth science and oceanography because they illustrate how microbes can fundamentally influence geochemical cycling and mineral deposition. Furthermore, morphological structures similar to those produced by Zetaproteobacteria can still be identified hundreds of millions (and possibly billions) of years back in the geological record, making them of paleontological, and potentially of exobiological, interest. As knowledge of extant populations grow, it is possible they will also help to inform us of environmental change in past Earth history. A wealth of educational and outreach opportunities will be made possible by this work, including graduate and postdoctoral education, research experiences for undergraduates, and teacher training. In addition the participating scientists are involved in a number of programs to make the general public aware of the process of how scientific research is conducted, and how discoveries of a fundamental nature can ultimately benefit humankind. Additional information/resources: TN293 (Loihi 2013) Loihi Summit Map (PDF) Cruise blog: https://zetahunters.wordpress.com/ Jason Virtual Control Van: http://4dgeo.whoi.edu/webdata/virtualvan/html/VV-tn293/index.html Related Publications: Fullerton, H., K. W. Hager, S. M. McAllister, and C. L. Moyer. 2017. Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō’ihi Seamount, Hawai’i. ISMEJ 11:1900–1914. doi:10.1038/ismej.2017.40 Emerson, D., J. J. Scott, A. Leavitt, E. Fleming, and C. L. Moyer. 2016. In situ estimates of iron-oxidation and accretion rates for iron-oxidizing bacterial mats at Loihi Seamount. bioRxiv 095414. doi:10.1101/095414 Scott, J. J., B. T. Glazer, and D. Emerson. 2017. Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lō’ihi Seamount. Environmental Microbiology 19:301–316. doi:10.1111/1462-2920.13607 Chan, C.S., S.M. McAllister, A.H. Leavitt, B.T. Glazer, S.T. Krepski, and D. Emerson. 2016. The architecture of iron microbial mats reflects the adaptation of chemolithotrophic iron oxidation in freshwater and marine environments. Frontiers in Microbiology 7:796. doi:10.3389/fmicb.2016.00796 Fullerton, H., K. W. Hager, and C. L. Moyer. 2015. Draft genome sequence of Mariprofundus ferrooxydans strain JV-1, isolated from Loihi Seamount, Hawaii. Genome announcements 3:e01118-15. doi:10.1128/genomeA.01118-15 Field, E.K., A. Sczyrba, A.E. Lyman, C.C. Harris, T. Woyke, R. Stepanauskas, and D. Emerson. 2015. Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount. ISMEJ 9:857–870. doi:10.1038/ismej.2014.183 Jesser, KJ, Fullerton H, Hager KW, Moyer CL. 2015. Quantitative PCR analysis of functional genes in iron-rich microbial mats at an active hydrothermal vent system (Lō'ihi Seamount, Hawai'i). Appl Environ Microbiol 81:2976–2984. doi:10.1128/AEM.03608-14. (PDF) RR1413 (Mariana 2014) RR1413 Cruise Report (5.2 MB PDF) Urushima to Rota Map (PDF) Jason Virtual Control Van website: http://4dgeo.whoi.edu/webdata/virtualvan/html/VV-rr1413/index.html Related Publications: Hager, K. W., H. Fullerton, D. A. Butterfield, and C. L. Moyer. 2017. Community structure of lithotrophically-driven hydrothermal microbial mats from the Mariana Arc and Back-Arc. Frontiers in Microbiology 8:1578. doi:10.3389/fmicb.2017.015786:["$","$L19",null,{"dataset":{"_id":"719770","description":"

This dataset includes accession numbers and links to NCBI SRA for metagenomic and metatranscriptomic reads from BioProject PRJNA412510. Samples were collected during the R/V Thomas G. Thompson cruise TN293 at Loihi Seamount. A single Fe mat was sampled (J2-674-BM1-C123456) at Pohaku (Mkr #57), with syringe J2-674-BM1-C3 used for metagenomic sequencing and syringe J2-674-BM1-C6 used for metatranscriptomic sequencing. Latitude: 18.901418 N; Longitude: 155.258191 W; Depth: 1179.43 meters below sea level.

Further details on sequencing are available on the NCBI BioProject page.

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Microbial mat samples were acquired with sub-centimeter sampling resolution from the seafloor using a novel microbial mat sampling device (see Breier, et al. 2012 for details) operated by the ROV Jason 2. Microbial mat samples were collected at the seafloor with RNALater within each collection syringe, fixing RNA activity on collection (in situ RNA expression profiles). On return to the ship, samples were allowed to settle, and the settled floc was stored at -80 degrees C until extraction and analysis.

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DNA and RNA were extracted as described in Chan et al. (2018). Raw metagenomic sequences were quality controlled, assembled, and binned (metagenome-assembled genomes [MAGs]), after which quality controlled RNA sequences were recruited to MAGs to estimate gene expression.

\n","bcodmoProcessing":"","title":"Sample accession numbers for raw metagenome and metatranscriptome Illumina HiSeq 2500 sequencing from an Fe mat sampled during cruise TN293 to Loihi Seamount, Hawaii on 03/25/2013","nickname":"Raw metagenome and metatranscriptome from an Fe mat at Loihi Seamount","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"20 November 2017","version_date":"2017-11-20T05:00:00.000Z","abstract":"","citation":"Chan, C. (2017) Sample accession numbers for raw metagenome and metatranscriptome Illumina HiSeq 2500 sequencing from an Fe mat sampled during cruise TN293 to Loihi Seamount, Hawaii on 03/25/2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 20 November 2017) Version Date 2017-11-20 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/719770 [access date]","citationParts":{"identifier":"http://lod.bco-dmo.org/id/dataset/719770","versionDate":"2017-11-20","versionId":"20 November 2017","year":"2017","title":"Sample accession numbers for raw metagenome and metatranscriptome Illumina HiSeq 2500 sequencing from an Fe mat sampled during cruise TN293 to Loihi Seamount, Hawaii on 03/25/2013","authors":"Chan, C.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"","release_date":null,"field_dataset_location":"","temporal_extent":{"start":"2013-03-25T04:00:00.000Z","end":"2013-03-25T04:00:00.000Z"},"temporal":{"resolution":"time:unitDay","type":"time:Instant","start":{"value":"","label":""},"end":{"value":"","label":""}},"spatial_extent":{"shape":"point","center":{"latitude":18.901418,"longitude":-155.258191},"wkt":" POINT (-155.258191 18.901418)","north":0,"east":0,"south":0,"west":0},"dataset_type":["Other Field Results"],"keywords":["biota","oceans"],"data_files":[{"id":"901865","title":"Fe_mat_accessions_Chan.csv","url":"https://datadocs.bco-dmo.org/dataset/719770/file/ZZZgxYjTo5nJ7J/Fe_mat_accessions_Chan.csv","showTableUrl":"https://www.bco-dmo.org/dataset/719770/data/view/901865","description":"Primary data file for dataset ID 719770","filename":"Fe_mat_accessions_Chan.csv","bytesize":308,"checksum":{"value":"4b81965ae165b96ee8e06fffa641d5b9","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"text/csv","fileType":{"_id":"192","name":"Comma Separated Values (.csv)"},"isErddap":"","date":"","isPublicDuringEmbargo":false,"primaryDataFile":true,"showTable":true,"restricted":false}],"supplemental_files":[],"roles":[{"role":{"_id":"138","name":"Principal Investigator"},"performedBy":{"_id":"557468","name":"Clara Chan"},"performedAtOrganization":{"_id":"70","name":"University of Delaware"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"51498","name":"Shannon Rauch"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[{"_id":"659705","name":"TN293","synonyms":["Loihi 2013"],"dates":{"start":"2013-03-16T00:00:00.000Z","end":"2013-04-01T00:00:00.000Z"},"platform":{"_id":"54017","name":"R/V Thomas G. Thompson"},"chiefScientists":[{"id":"557455","name":"Craig L. Moyer","role":"Chief Scientist"}]}],"funding":[{"_id":"557466","name":"OCE-1155290","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=1155290"}],"instruments":[{"_id":"719849","name":"ROV Jason 2","description":"","type_id":"638","type_name":"ROV Jason","type_desc":"$1a","type_acronym":"ROV Jason"}],"parameters":[{"_id":"719845","name":"accession_id","format":"","frictionlessType":"","description":"

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Database identifier assigned by repository and linked to GenBank or other repository.

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Link to accession at NCBI

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Latitude where sample was collected; N = positive.

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latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

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Longitude where samples were collected. E = positive.

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longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

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