FISH_ROCK : a tool for identifying and counting benthic organisms in bottom photographs

Recent advances in underwater robotics and imaging technology now enable the rapid acquisition of large datasets of near-bottom high-resolution digital imagery. These images provide the potential for developing a non-invasive technique for fisheries data acquisition that reveals the organisms in their natural habitat and can be used to identify important habitat characteristics. Using these large datasets effectively, however, requires the development of computer-based techniques that increase the efficiency of data analysis. This document describes one such tool, FISH_ROCK, which was developed for a group of fisheries researchers using the SeaBED AUV during a research cruise in October 2005. FISH_ROCK is a graphical user interface (GUI) that is executed within Matlab, and allows users digitally generate a database that includes organism identification, quantity, size and distribution as well as details about their habitat. Further development of this GUI will enable its use in different oceanographic environments including the deep sea, and will include modules that perform data analysis.Funding was provided by the National Oceanic and Atmospheric Administration under Grant No. AB133F05SE5828

Integrative Acoustic Mapping Reveals Hudson River Sediment Processes and Habitats

Rivers and estuaries around the world are the focus of human settlements and activities. Needs for clean water, ecosystem preservation, commercial navigation, industrial development, and recreational access compete for the use of estuaries, and management of these resources requires a detailed understanding of estuarine morphology and sediment dynamics. This article presents an overview of the first estuary-wide study of a heavily used estuary, the Hudson River, based on high-resolution acoustic mapping of the river bottom. The integration of three high-resolution acoustic methods with extensive sampling reveals an unexpected complexity of bottom features and allows detailed classification of the benthic environment in terms of riverbed morphology, sediment type, and sedimentary processes

Submeter bathymetric mapping of volcanic and hydrothermal features on the East Pacific Rise crest at 9°50′N

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 8 (2007): Q01006, doi:10.1029/2006GC001333.Recent advances in underwater vehicle navigation and sonar technology now permit detailed mapping of complex seafloor bathymetry found at mid-ocean ridge crests. Imagenex 881 (675 kHz) scanning sonar data collected during low-altitude (~5 m) surveys conducted with DSV Alvin were used to produce submeter resolution bathymetric maps of five hydrothermal vent areas at the East Pacific Rise (EPR) Ridge2000 Integrated Study Site (9°50′N, “bull's-eye”). Data were collected during 29 dives in 2004 and 2005 and were merged through a grid rectification technique to create high-resolution (0.5 m grid) composite maps. These are the first submeter bathymetric maps generated with a scanning sonar mounted on Alvin. The composite maps can be used to quantify the dimensions of meter-scale volcanic and hydrothermal features within the EPR axial summit trough (AST) including hydrothermal vent structures, lava pillars, collapse areas, the trough walls, and primary volcanic fissures. Existing Autonomous Benthic Explorer (ABE) bathymetry data (675 kHz scanning sonar) collected at this site provide the broader geologic context necessary to interpret the meter-scale features resolved in the composite maps. The grid rectification technique we employed can be used to optimize vehicle time by permitting the creation of high-resolution bathymetry maps from data collected during multiple, coordinated, short-duration surveys after primary dive objectives are met. This method can also be used to colocate future near-bottom sonar data sets within the high-resolution composite maps, enabling quantification of bathymetric changes associated with active volcanic, hydrothermal and tectonic processes.This work was supported by an NSF Ridge2000 fellowship to V.L.F. and a Woods Hole Oceanographic Institution fellowship supported by the W. Alan Clark Senior Scientist Chair (D.J.F.). Funding was also provided by the Censsis Engineering Research Center of the National Science Foundation under grant EEC-9986821. Support for field and laboratory studies was provided by the National Science Foundation under grants OCE-9819261 (D.J.F. and M.T.), OCE-0096468 (D.J.F. and T.S.), OCE-0328117 (SMC), OCE-0525863 (D.J.F. and S.A.S.), OCE-0112737 ATM-0427220 (L.L.W.), and OCE- 0327261 and OCE-0328117 (T.S.). Additional support was provided by The Edwin Link Foundation (J.C.K.)

Rolling Deck to Repository: Supporting the marine science community with data management services from academic research expeditions

Direct observations of the oceans acquired on oceanographic research ships operated across the international community support fundamental research into the many disciplines of ocean science and provide essential information for monitoring the health of the oceans. A comprehensive knowledge base is needed to support the responsible stewardship of the oceans with easy access to all data acquired globally. In the United States, the multidisciplinary shipboard sensor data routinely acquired each year on the fleet of coastal, regional and global ranging vessels supporting academic marine research are managed by the Rolling Deck to Repository (R2R, rvdata.us) program. With over a decade of operations, the R2R program has developed a robust routinized system to transform diverse data contributions from different marine data providers into a standardized and comprehensive collection of global-ranging observations of marine atmosphere, ocean, seafloor and subseafloor properties that is openly available to the international research community. In this article we describe the elements and framework of the R2R program and the services provided. To manage all expeditions conducted annually, a fleet-wide approach has been developed using data distributions submitted from marine operators with a data management workflow designed to maximize automation of data curation. Other design goals are to improve the completeness and consistency of the data and metadata archived, to support data citability, provenance tracking and interoperable data access aligned with FAIR (findable, accessible, interoperable, reusable) recommendations, and to facilitate delivery of data from the fleet for global data syntheses. Findings from a collection-level review of changes in data acquisition practices and quality over the past decade are presented. Lessons learned from R2R operations are also discussed including the benefits of designing data curation around the routine practices of data providers, approaches for ensuring preservation of a more complete data collection with a high level of FAIRness, and the opportunities for homogenization of datasets from the fleet so that they can support the broadest re-use of data across a diverse user community

The East Pacific Rise Between 9°N and 10°N: Twenty-Five Years of Integrated, Multidisciplinary Oceanic Spreading Center Studies

The East Pacific Rise from ~ 9–10°N is an archetype for a fast-spreading mid-ocean ridge. In particular, the segment near 9°50'N has been the focus of multidisciplinary research for over two decades, making it one of the best-studied areas of the global ridge system. It is also one of only two sites along the global ridge where two historical volcanic eruptions have been observed. This volcanically active segment has thus offered unparalleled opportunities to investigate a range of complex interactions among magmatic, volcanic, hydrothermal, and biological processes associated with crustal accretion over a full magmatic cycle. At this 9°50'N site, comprehensive physical oceanographic measurements and modeling have also shed light on linkages between hydrodynamic transport of larvae and other materials and biological dynamics influenced by magmatic processes. Integrated results of high-resolution mapping, and both in situ and laboratory-based geophysical, oceanographic, geochemical, and biological observations and sampling, reveal how magmatic events perturb the hydrothermal system and the biological communities it hosts

DataSheet_1_Rolling Deck to Repository: Supporting the marine science community with data management services from academic research expeditions.docx

Direct observations of the oceans acquired on oceanographic research ships operated across the international community support fundamental research into the many disciplines of ocean science and provide essential information for monitoring the health of the oceans. A comprehensive knowledge base is needed to support the responsible stewardship of the oceans with easy access to all data acquired globally. In the United States, the multidisciplinary shipboard sensor data routinely acquired each year on the fleet of coastal, regional and global ranging vessels supporting academic marine research are managed by the Rolling Deck to Repository (R2R, rvdata.us) program. With over a decade of operations, the R2R program has developed a robust routinized system to transform diverse data contributions from different marine data providers into a standardized and comprehensive collection of global-ranging observations of marine atmosphere, ocean, seafloor and subseafloor properties that is openly available to the international research community. In this article we describe the elements and framework of the R2R program and the services provided. To manage all expeditions conducted annually, a fleet-wide approach has been developed using data distributions submitted from marine operators with a data management workflow designed to maximize automation of data curation. Other design goals are to improve the completeness and consistency of the data and metadata archived, to support data citability, provenance tracking and interoperable data access aligned with FAIR (findable, accessible, interoperable, reusable) recommendations, and to facilitate delivery of data from the fleet for global data syntheses. Findings from a collection-level review of changes in data acquisition practices and quality over the past decade are presented. Lessons learned from R2R operations are also discussed including the benefits of designing data curation around the routine practices of data providers, approaches for ensuring preservation of a more complete data collection with a high level of FAIRness, and the opportunities for homogenization of datasets from the fleet so that they can support the broadest re-use of data across a diverse user community.</p

The 2005 Chios Ancient Shipwreck Survey: New Methods for Underwater Archaeology

In 2005 a Greek and American interdisciplinary team investigated two shipwrecks off the coast of Chios dating to the 4th-century b.c. and the 2nd/1st century. The project pioneered archaeological methods of precision acoustic, digital image, and chemical survey using an autonomous underwater vehicle (AUV) and in-situ sensors, increasing the speed of data acquisition while decreasing costs. The AUV recorded data revealing the physical dimensions, age, cargo, and preservation of the wrecks. The earlier wreck contained more than 350 amphoras, predominantly of Chian type, while the Hellenistic wreck contained about 40 Dressel 1C amphoras. Molecular biological analysis of two amphoras from the 4th-century wreck revealed ancient DNA of olive, oregano, and possibly mastic, part of a cargo outbound from Chios. Author(s): Brendan P. Foley 1 | Katerina Dellaporta 2 | Dimitris Sakellariou 3 | Brian S. Bingham 4 | Richard Camilli 5 | Ryan M. Eustice 6 | Dionysis Evagelistis 7 | Vicki Lynn Ferrini 8 | Kostas Katsaros 9 | Dimitris Kourkoumelis 10 | Aggelos Mallios 11 | Paraskevi Micha 12 | David A. Mindell 13 | Christopher Roman 14 | Hanumant Singh 15 | David S. Switzer 16 | Theotokis Theodoulou 17Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/86047/1/bfoley-11.pd

Toward a Cenozoic history of atmospheric CO₂

The geological record encodes the relationship between climate and atmospheric carbon dioxide (CO2) over long and short timescales, as well as potential drivers of evolutionary transitions. However, reconstructing CO2 beyond direct measurements requires the use of paleoproxies and herein lies the challenge, as proxies differ in their assumptions, degree of understanding, and even reconstructed values. In this study, we critically evaluated, categorized, and integrated available proxies to create a high-fidelity and transparently constructed atmospheric CO2 record spanning the past 66 million years. This newly constructed record provides clearer evidence for higher Earth system sensitivity in the past and for the role of CO2 thresholds in biological and cryosphere evolution.</p