Deciphering ocean carbon in a changing world

Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 113 (2016): 3143-3151, doi:10.1073/pnas.1514645113.Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. A vast number of compounds are present in DOM and they play important roles in all major element cycles, contribute to the storage of atmospheric CO2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.Support was provided by National Science Foundation grants OCE1356010, OCE1154320, and OCE1356890, and Gordon and Betty Moore Foundation Grant #3304

OOI Biogeochemical Sensor Data: Best Practices and User Guide. Version 1.0.0.

The OOI Biogeochemical Sensor Data Best Practices and User Guide is intended to provide current and prospective users of data generated by biogeochemical sensors deployed on the Ocean Observatories Initiative (OOI) arrays with the information and guidance needed for them to ensure that the data is science-ready. This guide is aimed at researchers with an interest or some experience in ocean biogeochemical processes. We expect that users of this guide will have some background in oceanography, however we do not assume any prior experience working with biogeochemical sensors or their data. While initially envisioned as a “cookbook” for end users seeking to work with OOI biogeochemical (BGC) sensor data, our Working Group and Beta Testers realized that the processing required to meet the specific needs of all end users across a wide range of potential scientific applications and combinations of OOI BGC data from different sensors and platforms couldn’t be synthesized into a single “recipe”. We therefore provide here the background information and principles needed for the end user to successfully identify and understand all the available “ingredients” (data), the types of “cooking” (end user processing) that are recommended to prepare them, and a few sample “recipes” (worked examples) to support end users in developing their own “recipes” consistent with the best practices presented here. This is not intended to be an exhaustive guide to each of these sensors, but rather a synthesis of the key information to support OOI BGC sensor data users in preparing science-ready data products. In instances when more in-depth information might be helpful, references and links have been provided both within each chapter and in the Appendix

Ebb And Flow: What We Learn From Visible Circulation Patterns in the Salish

We present here a set of visualizations of particle motion in the turbulent and complex environment of Puget Sound. We are interested in superposition of flow patterns particularly related to nutrient flux including: Estuarine input, exchange with the continental shelf and deep ocean through the Strait of Juan de Fuca, tidal circulation and other components of ocean dynamics. We begin with a computational fluid dynamics model and choose initial conditions (particle locations) based on motivating questions: Where does the water go that has been measured by instruments emplaced at NANOOS moorings? Where does fresh water from the Skagit River go, in relation to river stage? How does deep ocean water make its way into the Strait of Juan de Fuca? Does the prevalent Puget Sound circulation pattern resemble a conveyor belt? What is the half-life of the water in Hood Canal? The visualization is generated using the Layerscape research toolkit provided by Microsoft Research. Layerscape combines the Worldwide Telescope visualization engine (large data and time capacity) with a supportive \u27learn/collaborate\u27 website (http://layerscape.org) and data manipulation and ingest tools and software

Signal to noise: Key needs and strategies for communicating ecosystem science

The special session Emerging tools for synthesizing and communicating ecosystem information includes a 30-minute panel discussion divided into two 15-minute blocks within the allotted session time. Panelists include Joel Baker, UW Puget Sound Institute; Rob Fatland, Microsoft Research; Amy Merten, NOAA\u27s Office of Response and Restoration; Ian Perry, Fisheries and Oceans Canada; and Charles Simenstad, UW School of Aquatic and Fishery Science. The panel will discuss strategies for improving information flow among scientists, stakeholders and policymakers within the Salish Sea region. Questions will touch on key information needs and gaps, the potential value or hindrance of new technologies in addressing these needs, and how emerging media is changing the way scientists conduct, define and convey ecosystem synthesis

A model for community-driven development of best practices: the Ocean Observatories Initiative Biogeochemical Sensor Data Best Practices and User Guide

The field of oceanography is transitioning from data-poor to data-rich, thanks in part to increased deployment of in-situ platforms and sensors, such as those that instrument the US-funded Ocean Observatories Initiative (OOI). However, generating science-ready data products from these sensors, particularly those making biogeochemical measurements, often requires extensive end-user calibration and validation procedures, which can present a significant barrier. Openly available community-developed and -vetted Best Practices contribute to overcoming such barriers, but collaboratively developing user-friendly Best Practices can be challenging. Here we describe the process undertaken by the NSF-funded OOI Biogeochemical Sensor Data Working Group to develop Best Practices for creating science-ready biogeochemical data products from OOI data, culminating in the publication of the GOOS-endorsed OOI Biogeochemical Sensor Data Best Practices and User Guide. For Best Practices related to ocean observatories, engaging observatory staff is crucial, but having a “user-defined” process ensures the final product addresses user needs. Our process prioritized bringing together a diverse team and creating an inclusive environment where all participants could effectively contribute. Incorporating the perspectives of a wide range of experts and prospective end users through an iterative review process that included “Beta Testers’’ enabled us to produce a final product that combines technical information with a user-friendly structure that illustrates data analysis pipelines via flowcharts and worked examples accompanied by pseudo-code. Our process and its impact on improving the accessibility and utility of the end product provides a roadmap for other groups undertaking similar community-driven activities to develop and disseminate new Ocean Best Practices