Horizontal refraction of propagating sound due to seafloor scours over a range-dependent layered bottom on the New Jersey shelf

Author Posting. © Acoustical Society of America, 2012. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 131 (2012): 2587-2598, doi:10.1121/1.3687446.Three-dimensional propagation effects of low frequency sound from 100 to 400 Hz caused by seafloor topography and range-dependent bottom structure over a 20 km range along the New Jersey shelf are investigated using a hybrid modeling approach. Normal modes are used in the vertical dimension, and a parabolic-equation approximate model is applied to solve the horizontal refraction equation. Examination of modal amplitudes demonstrates the effect of environmental range dependence on modes trapped in the water column, modes interacting with the bottom, and modes trapped in the bottom. Using normal mode ray tracing, topographic features responsible for three-dimensional effects of horizontal refraction and focusing are identified. These effects are observed in the measurements from the Shallow Water 2006 experiment. Specifically, signals from a pair of fixed sources recorded on a horizontal line array sitting on the seafloor show an intensification caused by horizontal focusing due to the seabed topography of 4 dB along the array.Work sponsored by the Office of Naval Research under Grants No. N00014-04-1-0146, No. N00014-10-1-0040, and No. N00014-10-1-0649

Effects of frequency-dependent spatial variation in soundscape settlement cues for reef fish larvae

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Salas, A. K., Ballard, M. S., Mooney, T. A., & Wilson, P. S. Effects of frequency-dependent spatial variation in soundscape settlement cues for reef fish larvae. Marine Ecology Progress Series, 687, (2022): 1-21, https://doi.org/10.3354/meps14012.The mechanisms that link reef soundscapes to larval fish settlement behaviors are poorly understood, yet the management of threatened reef communities requires we maintain the recruitment processes that recover and sustain populations. Using a field-calibrated sound propagation model, we predicted the transmission loss in the relevant frequency band as a function of range, depth, and azimuth to estimate the spatial heterogeneity in the acoustic cuescape. The model highlighted the frequency- and depth-dependence of the sound fields fishes may encounter, and we predict these complex spatial patterns influence how sounds function as settlement cues. Both modeling and field measurements supported a non-monotonic decline in amplitude with distance from the reef. We modeled acoustic fields created by sounds at frequencies from 2 common soniferous reef-based animals (snapping shrimps and toadfish) and estimated detection spaces of these sounds for larvae of 2 reef fish species. Results demonstrated that larval depth will influence cue availability and amplitude, and these spatial patterns of detection depend on cue frequency and the larval receiver’s auditory sensitivity. Estimated spatial scales of detection coupled with field measurements suggest cue amplitudes might allow some larvae to detect reef-based sounds at a range exposing them to the predicted spatial variation in the acoustic cuescape. In an individual-based model, cues available to even the shortest modeled distances improved settlement success. Our results emphasize the need to consider the frequency- and depth-dependence of the acoustic cues larval fishes encounter to increase understanding of the role of soundscapes in larval settlement.We thank the following funding sources for partial support: The University of Texas at Austin Integrative Biology Department’s Zoology Scholarship Endowment for Excellence award (A.K.S.), Smithsonian Tropical Research Institute (STRI) Short-term Fellowship (A.K.S.), Office of Naval Research (P.S.W. and M.S.B), and National Science Foundation (OCE-15-36782; T.A.M). We thank P. Gondola for support through the STRI Bocas del Toro Research Station and Dr. Andrew Altieri for assistance in site selection and knowledge of local ecosystem

Toward the Ultrasonic Sensing of Organic Carbon in Seagrass-Bearing Sediments

Ten percent of all organic carbon (Corg) absorbed by the ocean each year is stored in seagrass-bearing sediments. The preservation of these carbon stores is considered a vital method to mitigate climate change. Seagrass-bearing sediments have been correlated with sediment geophysical properties yet have not been related to sediment acoustic properties. For this purpose, sediment cores were collected from a Thalassia testudinum seagrass meadow in South Texas, USA, where geophysical, acoustical, and Corg properties were measured. It is hypothesized that when deposits of Corg adsorb onto mineral surfaces and are stored in pore spaces, compliant layers between grain contacts and the formation of an organic-rich suspension reduce sediment stiffness. Results from this seagrass meadow demonstrated a strong correlation between sediment P wave modulus and Corg and show promise toward the development of an in situ ultrasonic sediment probe to more rapidly quantify and monitor seagrass carbon stores

Application of acoustical remote sensing techniques for ecosystem monitoring of a seagrass meadow

Seagrasses provide a multitude of ecosystem services and serve as important organic carbon stores. However, seagrass habitats are declining worldwide, threatened by global climate change and regional shifts in water quality. Acoustical methods have been applied to assess changes in oxygen production of seagrass meadows since sound propagation is sensitive to the presence of bubbles, which exist both within the plant tissue and freely floating the water as byproducts of photosynthesis. This work applies acoustic remote sensing techniques to characterize two different regions of a seagrass meadow: a densely vegetated meadow of Thalassia testudinum and a sandy region sparsely populated by isolated stands of T. testudinum. A Bayesian approach is applied to estimate the posterior probability distributions of the unknown model parameters. The sensitivity of sound to the void fraction of gas present in the seagrass meadow was established by the narrow marginal probability distributions that provided distinct estimates of the void fraction between the two sites. The absolute values of the estimated void fractions are biased by limitations in the forward model, which does not capture the full complexity of the seagrass environment. Nevertheless, the results demonstrate the potential use of acoustical methods to remotely sense seagrass health and density

Inter-seasonal comparison of acoustic propagation in a Thalassia testudinum seagrass meadow in a shallow sub-tropical lagoon

Acoustic propagation measurements were collected in a seagrass meadow in a shallow lagoon for periods of over 65 h in winter and 93 h in summer. A bottom-deployed sound source transmitted chirps (0.1–100 kHz) every 10 min that were received on a four-receiver horizontal hydrophone array. Oceanographic probes measured various environmental parameters. Daytime broadband acoustic attenuation was 2.4 dB greater in summer than winter, and the median received acoustic energy levels were 8.4 dB lower in summer compared to winter. These differences were attributed in part to seasonal changes in photosynthesis bubble production and above-ground seagrass biomass

Inter-seasonal comparison of acoustic propagation in a Thalassia testudinum seagrass meadow in a shallow sub-tropical lagoon

Acoustic propagation measurements were collected in a seagrass meadow in a shallow lagoon for periods of over 65 h in winter and 93 h in summer. A bottom-deployed sound source transmitted chirps (0.1–100 kHz) every 10 min that were received on a four-receiver horizontal hydrophone array. Oceanographic probes measured various environmental parameters. Daytime broadband acoustic attenuation was 2.4 dB greater in summer than winter, and the median received acoustic energy levels were 8.4 dB lower in summer compared to winter. These differences were attributed in part to seasonal changes in photosynthesis bubble production and above-ground seagrass biomass

Broadband sound propagation in a seagrass meadow throughout a diurnal cycle

Acoustic propagation measurements were conducted in a Thalassia testudinum meadow in the Lower Laguna Madre, a shallow bay on the Texas Gulf of Mexico coast. A piezoelectric source transmitted frequency-modulated chirps (0.1 to 100 kHz) over a 24-h period during which oceanographic probes measured environmental parameters including dissolved oxygen and solar irradiance. Compared to a nearby less vegetated area, the received level was lower by as much as 30 dB during the early morning hours. At the peak of photosynthesis-driven bubble production in the late afternoon, an additional decrease in level of 11 dB was observed

Temporal and spatial dependence of a yearlong record of sound propagation from the Canada Basin to the Chukchi Shelf

Author Posting. © Acoustical Society of America, 2020. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 148(3),(2020): 1663, doi:10.1121/10.0001970.The Pacific Arctic Region has experienced decadal changes in atmospheric conditions, seasonal sea-ice coverage, and thermohaline structure that have consequences for underwater sound propagation. To better understand Arctic acoustics, a set of experiments known as the deep-water Canada Basin acoustic propagation experiment and the shallow-water Canada Basin acoustic propagation experiment was conducted in the Canada Basin and on the Chukchi Shelf from summer 2016 to summer 2017. During the experiments, low-frequency signals from five tomographic sources located in the deep basin were recorded by an array of hydrophones located on the shelf. Over the course of the yearlong experiment, the surface conditions transitioned from completely open water to fully ice-covered. The propagation conditions in the deep basin were dominated by a subsurface duct; however, over the slope and shelf, the duct was seen to significantly weaken during the winter and spring. The combination of these surface and subsurface conditions led to changes in the received level of the sources that exceeded 60 dB and showed a distinct spacio-temporal dependence, which was correlated with the locations of the sources in the basin. This paper seeks to quantify the observed variability in the received signals through propagation modeling using spatially sparse environmental measurements.This work was supported by the Office of Naval Research Ocean Acoustics Program (ONR OA322) under Grant Nos. N00014-15-1-2144, N00014-15-1-2119, N00014-15-1-2017, N00014-15-1-2068, N00014-15-1-2110, N00014-19-1-2721, N00014-15-1-2898, N00014-15-1-2806, and N00014-18-1-2140. The basin moored environmental data were supported by the ONR Arctic and Global Prediction Program (ONR AG322) under Grant No. N00014-15-1-2782. Mooring and hydrographic data were collected and made available by the Beaufort Gyre Exploration Program based at the Woods Hole Oceanographic Institution (http://www.whoi.edu/beaufortgyre) in collaboration with researchers from Fisheries and Oceans Canada at the Institute of Ocean Sciences. The ITP data were collected and made available by the ITP Program (Krishfield et al., 2008; Toole et al., 2011) based at the Woods Hole Oceanographic Institution (http://www.whoi.edu/itp). We acknowledge the use of imagery from the Worldview Snapshots application (https://wvs.earthdata.nasa.gov), part of the Earth Observing System Data and Information System (EOSDIS).2021-03-2

Transmission Spectra of Transiting Planet Atmospheres: Model Validation and Simulations of the Hot Neptune GJ 436b for JWST

We explore the transmission spectrum of the Neptune-class exoplanet GJ 436b, including the possibility that its atmospheric opacity is dominated by a variety of non- equilibrium chemical products. We also validate our transmission code by demonstrating close agreement with analytic models that use only Rayleigh scattering or water vapor opacity. We find broad disagreement with radius variations predicted by another published model. For GJ 436b, the relative coolness of the planet's atmosphere, along with its implied high metallicity, may make it dissimilar in character compared to "hot Jupiters." Some recent observational and modeling efforts suggest low relative abundances of H2O and CH4 present in GJ 436b's atmosphere, compared to calculations from equilibrium chemistry. We include these characteristics in our models and examine the effects of absorption from methane-derived higher order hydrocarbons. Significant absorption from HCN and C2H2 are found throughout the infrared, while C2H4 and C2H6 are less easily seen. We perform detailed simulations of JWST observations, including all likely noise sources, and find that we will be able to constrain chemical abundance regimes from this planet's transmission spectrum. For instance, the width of the features at 1.5, 3.3, and 7 microns indicates the amount of HCN versus C2H2 present. The NIRSpec prism mode will be useful due to its large spectral range and the relatively large number of photo-electrons recorded per spectral resolution element. However, extremely bright host stars like GJ 436 may be better observed with a higher spectroscopic resolution mode in order to avoid detector saturation. We find that observations with the MIRI low resolution spectrograph should also have high signal-to-noise in the 5 - 10 micron range due to the brightness of the star and the relatively low spectral resolution (R ~ 100) of this mode.Comment: 33 pages, 12 figures, Accepted to Ap

Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens

Viola is a large genus with worldwide distribution and many traits not currently exemplified in model plants including unique breeding systems and the production of cyclotides. Here we report de novo genome assembly and transcriptomic analyses of the non-model species Viola pubescens using short-read DNA sequencing data and RNA-Seq from eight diverse tissues. First, V. pubescens genome size was estimated through flow cytometry, resulting in an approximate haploid genome of 455 Mbp. Next, the draft V. pubescens genome was sequenced and assembled resulting in 264,035,065 read pairs and 161,038 contigs with an N50 length of 3,455 base pairs (bp). RNA-Seq data were then assembled into tissue-specific transcripts. Together, the DNA and transcript data generated 38,081 ab initio gene models which were functionally annotated based on homology to Arabidopsis thaliana genes and Pfam domains. Gene expression was visualized for each tissue via principal component analysis and hierarchical clustering, and gene co-expression analysis identified 20 modules of tissue-specific transcriptional networks. Some of these modules highlight genetic differences between chasmogamous and cleistogamous flowers and may provide insight into V. pubescens’ mixed breeding system. Orthologous clustering with the proteomes of A. thaliana and Populus trichocarpa revealed 8,531 sequences unique to V. pubescens, including 81 novel cyclotide precursor sequences. Cyclotides are plant peptides characterized by a stable, cyclic cystine knot motif, making them strong candidates for drug scaffolding and protein engineering. Analysis of the RNA-Seq data for these cyclotide transcripts revealed diverse expression patterns both between transcripts and tissues. The diversity of these cyclotides was also highlighted in a maximum likelihood protein cladogram containing V. pubescens cyclotides and published cyclotide sequences from other Violaceae and Rubiaceae species. Collectively, this work provides the most comprehensive sequence resource for Viola, offers valuable transcriptomic insight into V. pubescens, and will facilitate future functional genomics research in Viola and other diverse plant groups