Seagrass metabolism across a productivity gradient using the eddy covariance, Eulerian control volume, and biomass addition techniques

Author Posting. © American Geophysical Union, 2015. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 120 (2015): 3624–3639, doi:10.1002/2014JC010352.The net ecosystem metabolism of the seagrass Thalassia testudinum was studied across a nutrient and productivity gradient in Florida Bay, Florida, using the Eulerian control volume, eddy covariance, and biomass addition techniques. In situ oxygen fluxes were determined by a triangular Eulerian control volume with sides 250 m long and by eddy covariance instrumentation at its center. The biomass addition technique evaluated the aboveground seagrass productivity through the net biomass added. The spatial and temporal resolutions, accuracies, and applicability of each method were compared. The eddy covariance technique better resolved the short-term flux rates and the productivity gradient across the bay, which was consistent with the long-term measurements from the biomass addition technique. The net primary production rates from the biomass addition technique, which were expected to show greater autotrophy due to the exclusion of sediment metabolism and belowground production, were 71, 53, and 30 mmol carbon m−2 d−1 at 3 sites across the bay. The net ecosystem metabolism was 35, 25, and 11 mmol oxygen m−2 d−1 from the eddy covariance technique and 10, −103, and 14 mmol oxygen m−2 d−1 from the Eulerian control volume across the same sites, respectively. The low-flow conditions in the shallow bays allowed for periodic stratification and long residence times within the Eulerian control volume that likely reduced its precision. Overall, the eddy covariance technique had the highest temporal resolution while producing accurate long-term flux rates that surpassed the capabilities of the biomass addition and Eulerian control volume techniques in these shallow coastal bays.This research was conducted under Everglades National Park permit # EVER-2011-SCI-0057. This study received financial support from the Jones Environmental and Barley Scholars Program at the University of Virginia and the National Science Foundation (Chemical Oceanography grant OCE-0536431).2015-11-2

The intertidal hydraulics of tide-dominated reef platforms

A 2 week field experiment investigated the hydrodynamics of a strongly tidally forced tropical intertidal reef platform in the Kimberley region of northwestern Australia, where the spring tidal range exceeds 8 m. At this site, the flat and wide (∼1.4 km) reef platform is located slightly above mean sea level, such that during low tide the offshore water level can fall 4 m below the platform. While the reef always remained submerged over each tidal cycle, there were dramatic asymmetries in both the water levels and velocities on the reef, i.e., the flood duration lasted only ∼2 h versus ∼10 h for the ebb. These dynamics were investigated using a one-dimensional numerical model (SWASH) to solve the nonlinear shallow water equations with rapid (sub to supercritical) flow transitions. The numerical model revealed that as water drains off the reef, a critical flow point was established near the reef edge prior to the water discharging down the steep forereef. Despite this hydraulic control, bottom friction on the reef was still found to make a far greater contribution to elevating water levels on the reef platform and keeping it submerged over each tidal cycle. Finally, a simple analytical model more broadly shows how water levels on intertidal reef platforms functionally depend on properties of reef morphology, bottom roughness, and tidal conditions, revealing a set of parameters (a reef draining time-scale and friction parameter) that can be used to quantify how the water depth will fall on a reef during ebb tide.This is the publisher’s final pdf. The article is copyrighted by American Geophysical Union and published by John Wiley & Sons, Inc.. It can be found at: http://agupubs.onlinelibrary.wiley.com/agu/jgr/journal/10.1002/%28ISSN%292169-9291

First ROV exploration of the Perth Canyon: Canyon setting, faunal observations, and anthropogenic impacts.

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Trotter, J. A., Pattiaratchi, C., Montagna, P., Taviani, M., Falter, J., Thresher, R., Hosie, A., Haig, D., Foglini, F., Hua, Q., & McCulloch, M. T. First ROV exploration of the Perth Canyon: Canyon setting, faunal observations, and anthropogenic impacts. Frontiers in Marine Science, 6, (2019):173, doi:10.3389/fmars.2019.00173.This study represents the first ROV-based exploration of the Perth Canyon, a prominent submarine valley system in the southeast Indian Ocean offshore Fremantle (Perth), Western Australia. This multi-disciplinary study characterizes the canyon topography, hydrography, anthropogenic impacts, and provides a general overview of the fauna and habitats encountered during the cruise. ROV surveys and sample collections, with a specific focus on deep-sea corals, were conducted at six sites extending from the head to the mouth of the canyon. Multi-beam maps of the canyon topography show near vertical cliff walls, scarps, and broad terraces. Biostratigraphic analyses of the canyon lithologies indicate Late Paleocene to Late Oligocene depositional ages within upper bathyal depths (200–700 m). The video footage has revealed a quiescent ‘fossil canyon’ system with sporadic, localized concentrations of mega- and macro-benthos (∼680–1,800 m), which include corals, sponges, molluscs, echinoderms, crustaceans, brachiopods, and worms, as well as plankton and nekton (fish species). Solitary (Desmophyllum dianthus, Caryophyllia sp., Vaughanella sp., and Polymyces sp.) and colonial (Solenosmilia variabilis) scleractinians were sporadically distributed along the walls and under overhangs within the canyon valleys and along its rim. Gorgonian, bamboo, and proteinaceous corals were present, with live Corallium often hosting a diverse community of organisms. Extensive coral graveyards, discovered at two disparate sites between ∼690–720 m and 1,560–1,790 m, comprise colonial (S. variabilis) and solitary (D. dianthus) scleractinians that flourished during the last ice age (∼18 ka to 33 ka BP). ROV sampling (674–1,815 m) spanned intermediate (Antarctic Intermediate Water) and deep waters (Upper Circumpolar Deep Water) with temperatures from ∼2.5 to 6°C. Seawater CTD profiles of these waters show consistent physical and chemical conditions at equivalent depths between dive sites. Their carbonate chemistry indicate supersaturation (Ωcalcite ∼ 1.3–2.2) with respect to calcite, but mild saturation to undersaturation (Ωaragonite ∼ 0.8–1.4) of aragonite; notably some scleractinians were found living below the aragonite saturation horizon (∼1,000 m). Seawater δ13C and nuclear bomb produced Δ14C compositions decrease in the upper canyon waters by up to ∼0.8‰ (<800 m) and 95‰ (<500 m), respectively, relative to measurements taken nearby in 1978, reflecting the ingress of anthropogenic carbon into upper intermediate waters.This work was supported by research funding from the Australian Research Council to MM (FL120100049) and JT (FT160100259), the Italian National Programme of Antarctic Research (PNRA16-00069 Graceful Project) to PM and MT, the Australian Institute of Nuclear Science and Engineering to MM, JT, JF, RT, MT, PM (AINSE Award 16/009). Supplementary oceanographic data are funded through Integrated Marine Observing System (IMOS) supported by the Australian Government

Near-zero environmental impact aircraft

The fundamental challenge facing today's aviation industry is to achieve net zero climate impacts while simultaneously sustaining growth and global connectivity. Aviation's impact on surface air quality, which is comparable to aviation's climate impact when monetized, further heightens this challenge. Prior studies have proposed solutions that aim to mitigate either aviation's climate or air quality impacts. No previous work has proposed an aircraft-energy system that simultaneously addresses both aviation's climate and air quality impacts. In this paper we (1) use a multi-disciplinary design approach to optimize aircraft and propulsion systems, (2) estimate lifecycle costs and emissions of producing sustainable fuels including the embodied emissions associated with electricity generation and fuel production, (3) use trajectory optimization to quantify the fuel penalty to avoid persistent contrail formation based on a full year of global flight operations (including, for the first time, contrail avoidance for a hydrogen burning aircraft), and (4) quantify climate and air quality benefits of the proposed solutions using a simplified climate model and sensitivities derived from a global chemistry transport model. We propagate uncertainties in environmental impacts using a Monte-Carlo approach. We use these models to propose and analyze near-zero environmental impact aircraft, which we define as having net zero climate warming and a greater than 95% reduction in air quality impacts relative to present day. We contrast the environmental impacts of today's aircraft-energy system against one built around either "drop-in" fuels or hydrogen. We find that a "zero-impact" aircraft is possible using either hydrogen or power-to-liquid "drop-in" fuels. The proposed aircraft-energy systems reduce combined climate and air quality impacts by 99%, with fuel costs increasing by 40% for hydrogen and 70% for power-to-liquid fueled aircraft relative to today's fleet (i.e., within the range of historical jet fuel price variation). Beyond the specific case presented here, this work presents a framework for holistic analysis of future aviation systems that considers both climate and air quality impacts.The fundamental challenge facing the aviation industry is to achieve near-zero environmental impacts while sustaining growth. We propose a near-zero impact aircraft, taking a lifecycle perspective across fuels, aircraft design, and operation

The next generation of training for arabidopsis researchers: Bioinformatics and Quantitative Biology

It has been more than 50 years since Arabidopsis (Arabidopsis thaliana) was first introduced as a model organism to understand basic processes in plant biology. A well-organized scientific community has used this small reference plant species to make numerous fundamental plant biology discoveries (Provart et al., 2016). Due to an extremely well-annotated genome and advances in high-throughput sequencing, our understanding of this organism and other plant species has become even more intricate and complex. Computational resources, including CyVerse,3 Araport,4 The Arabidopsis Information Resource (TAIR),5 and BAR,6 have further facilitated novel findings with just the click of a mouse. As we move toward understanding biological systems, Arabidopsis researchers will need to use more quantitative and computational approaches to extract novel biological findings from these data. Here, we discuss guidelines, skill sets, and core competencies that should be considered when developing curricula or training undergraduate or graduate students, postdoctoral researchers, and faculty. A selected case study provides more specificity as to the concrete issues plant biologists face and how best to address such challenges

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Mass transfer limits to nutrient uptake by shallow coral reef communities

Thesis (Ph. D.)--University of Hawaii at Manoa, 2002.Mode of access: World Wide Web.Includes bibliographical references (leaves 119-126).Electronic reproduction.Also available by subscription via World Wide Webxiv, 126 leaves, bound ill. (some col.) 29 cmUptake and assimilation of nutrients is essential to the productivity of coral reefs. Nutrient uptake rates by coral reef communities have been hypothesized to be limited by rates of mass transfer across a concentration boundary layer. The mass transfer coefficient S (m day-1) relates the maximum nutrient flux allowed by mass transfer to the nutrient concentration in the ambient water (Jmax =S[N]). The goal of this dissertation is to determine the maximum rate at which a coral reef flat community can take up nutrients according to mass transfer theory. Nutrient mass transfer coefficients for a Kaneohe Bay Barrier Reef flat community were determined two ways. In the first method, S was estimated from in situ measurements of wave-driven flow speeds (Uh = 0.08-0.22 m s-1) and the friction coefficient of the reef flat (Cf = 0.22±0.03) using a mass transfer correlation. S calculated from this method was 5.8±0.8 m day-1 for phosphate and 9.7±1.3 m day-1 for nitrate and ammonium. The second method compared the dissolution of artificial plaster forms (surface area = 0.1-1.0 m2) of varying roughness scale (0.001-0.1 m) under wave-driven and steady flows (Uh = 0.02-0.21 m s -1). Results showed 1) rates of mass transfer were linearly proportional to surface area regardless of roughness scale and flow conditions, and 2) rates of mass transfer were 1.4-2.0 times higher under wave-driven flows (~8-s in period) than under steady flows. Using appropriate surface areas from the plaster dissolution experiments, S for the reef flat community was 7±3 m day -1 for phosphate and 12±5 m day -1 for nitrate and ammonium. Using the wave enhancement obtained from the plaster dissolution experiments, S could be as high as 9.3±1.3 m day -1 and 15.5±2.1 m day -1. The phosphate uptake rate coefficient from flow respirometry for the same reef flat community was 4.5-9 m day -1. Thus, rates of phosphate uptake by the this community are at the limits of mass transfer. Scaling maximum phosphate uptake rates by the average C:P of benthic autotrophic tissue indicates that net primary production within this community is limited by nutrient uptake

Active modulation of the calcifying fluid carbonate chemistry (δ11B, B/Ca) and seasonally invariant coral calcification at sub-tropical limits

Geochemical and coral growth rate dat

Perennial growth of hermatypic corals at Rottnest Island, Western Australia (32°S)

To assess the viability of high latitude environments as coral refugia, we report measurements of seasonal changes in seawater parameters (temperature, light, and carbonate chemistry) together with calcification rates for two coral species, Acropora yongei and Pocillopora damicornis from the southernmost geographical limit of these species at Salmon Bay, Rottnest Island (32°S) in Western Australia. Changes in buoyant weight were normalised to colony surface areas as determined from both X-ray computed tomography and geometric estimation. Extension rates for A. yongei averaged 51 ± 4 mm y−1 and were comparable to rates reported for Acroporid coral at other tropical and high latitude locations. Mean rates of calcification for both A. yongei and P. damicornis in winter were comparable to both the preceding and following summers despite a mean seasonal temperature range of ∼6 °C (18.2°–24.3 °C) and more than two-fold changes in the intensity of downwelling light. Seasonal calcification rates for A. yongei (1.31–2.02 mg CaCO3 cm−2 d−1) and P. damicornis (0.34–0.90 mg CaCO3 cm−2 d−1) at Salmon Bay, Rottnest Island were comparable to rates from similar taxa in more tropical environments; however, they appeared to decline sharply once summer temperatures exceeded 23 °C. A coral bleaching event observed in December 2013 provided further evidence of how coral at Rottnest Island are still vulnerable to the deleterious effects of episodic warming despite its high latitude location. Thus, while corals at Rottnest Island can sustain robust year-round rates of coral growth, even over cool winter temperatures of 18°–19 °C, there may be limits on the extent that such environments can provide refuge against the longer term impacts of anthropogenic climate change