Warm Shallow Waters Research Articles

Dolphin Whistle Signal Enhancement Using Nonconvex Time-Frequency Regularized Overlapping Group Shrinkage in Warm Shallow Water

Dolphin Whistle Signal Enhancement Using Nonconvex Time-Frequency Regularized Overlapping Group Shrinkage in Warm Shallow Water

Living together in dead coral rocks: macrosymbiotic communities associated with Bonellia echiuran worms (Annelida: Thalassematidae: Bonelliinae), involving new commensal bivalve and amphipod species

Abstract Dead coral rocks are prevalent hard substrates in shallow warm waters, providing habitat for various infaunal and boring invertebrates. Despite this, the nature of species interactions, especially symbiotic relationships, among them remains poorly understood. Bonellia (Annelida: Thalassematidae: Bonelliinae) is a group of greenish echiuran worms commonly inhabiting cavities inside dead coral rocks. Although echiuran burrows in marine sediments are known to harbour various host-specific macrosymbionts, it remains unclear whether such associations also occur in hard substrates. To address this, we investigated the diversity of macrosymbionts associated with the burrows of Bonellia sp. aff. minor in the warm-temperate coast of the Kii Peninsula, Japan, and the evolutionary origins of those symbionts. The host’s burrow morphology was also examined using micro-computed tomography (CT) scanning. Our field survey revealed that the burrows of Bo. sp. aff. minor hosted three commensal species including a polychaete, Oxydromus fauveli, and two new species, a bivalve (Basterotia bonelliphila sp. nov.) and an amphipod (Leucothoe bonelliae sp. nov.). Our molecular phylogenetic analyses showed that each symbiont species belongs to a clade comprising commensal species specific to echiurans or annelids. Overall, our findings contribute to a better understanding of symbiotic associations in marine hard substrates.

Stratigraphic Analysis and Depositional Environment of the Newly Recorded Umm Er Rhadhuma Formation (Paleocene) from the Borehole K.H12/7, South Anah City, Western Iraq

The Paleocene benthic foraminiferal zonation of the Umm Er Rhadhuma Formation from the borehole (K.H 12/7), South Anah City (Western Iraq), has been re-studied and re-analyzed precisely based on the large benthic foraminifera (LBF). They are represented by two biozone Rotorbinella hensoni Partial Range Zone, recorded from the Lower and middle parts of the Umm Er Rhadhuma Formation and Lockhartia praehaimei Partial Range Zone determined Uppermost of this unit, and dated to be the Selandian – Thanetian stage. Almost all the biogenic (micro and macro) and non-biogenic constituents, including large benthic foraminifera, Algae, Echinoderm, Bryozoans, Oyster, Gastropod fragments, and peloids, in addition to lithofacies types, indicate that this succession belongs to the Umm Er Rhadhuma Formation. Furthermore, the Paleocene shallowing upwards succession is recognized from seven identified microfacies (MF1 to MF7), which suggests three significant facies associations. A broad inner ramp represents them and is warm shallow open normal marine water (FA1). In contrast, the second facies association represents by the predominated bioclastic sand shoal facies association (FA2) and finally reaches the semi-restricted lagoon facies associations (FA3). The interaction between the local tectonic disturbance along Rutba high and eustatic sea level mainly controls the development of two sequence boundaries of Type-1 (SB1) that occurred respectively at the Cretaceous /Palaeogene K- Pg boundary and Paleocene /Eocene boundary. The Paleocene depositional system starts with major transgression during the Selandian above a sequence boundary of type one (SB.1), that separates the Late Cretaceous (Maastrichtian) successions of the Tayarat Formation from the overlying Paleocene succession with a significant gap, covering the whole Danian age (That is the top of Tectonic Megasequence AP. 9). The predominance of retrogradation staking tract indicated the transgressive system tract during the late Selandian and early Thanetian as a result of an increase in the sea level rise and expanded accommodation space. The highstand system tracts show aggradational and then change to a progradational stacking pattern by the end of the Thanetian and mark significant sea level drawdown with a new sequence boundary of type one between them.

Molecular data, ecological niche, and dispersal models reveal a trans-Atlantic shallow-water octopus species

The tropical Octopus insularis is a shallow-water species widely distributed in the western Atlantic. Recent studies of niche models have identified suitable habitats for its settlement also on the east coast of the Atlantic. Considering the pelagic larval period and the high tolerance of this species to environmental variations, this study aimed to analyze the possibility of O. insularis occurrence in the West Atlantic (São Tomé Island) through molecular analyses, dispersion, and niche models. The molecular analyses were performed using fragments of 481 bp of the mitochondrial gene (cox1) from three muscle samples collected in São Tomé Island. The O. insularis long-range connectivity between South America and Western Africa was analyzed using a Lagrangian particle tracking model. Additionally, O. insularis records across its entire known distribution were applied to run the ecological niche model (ENM) using the Maxent algorithm. The Bayesian phylogenetic reconstruction showed that two of the three octopus sequences from São Tomé island (Central-Western Africa) belong to a monophyletic and well-supported O. insularis clade. The third octopus sample revealed a new species related to the clade with the Octopus vulgaris species complex. The dispersal models pointed out that passive particles could potentially reach the seamounts region at Africa coast via oceanic currents (mainly the North Equatorial Countercurrent) from São Pedro and São Paulo archipelago (Central-Western Region of the Atlantic) in a period of ∼30–60 days. This suggests that São Pedro and São Paulo archipelago could act as a potential source of paralarvae to Western Africa, although we hypothesize that this connection was more common during the Pleistocene, when sea level was around 120 m lower. In addition to the already known areas of O. insularis occurrence, the ENM pointed suitable habitats to the octopus settlement from Guinea-Bissau down to Equatorial Guinea and Gabon, and African Islands, such as São Tomé and Príncipe. The new record of O. insularis in Africa raises important questions regarding regional fisheries management. Considering that O. insularis is highly tolerant to environmental variations and very adapted to warm shallow waters, there is a possibility that octopus fisheries stocks on the African coast have a mixed composition (O. vulgaris, O. insularis, and Octopus sp.) and therefore the fisheries must follow management measures suitable for each species. In addition, further studies should be carried out in order to characterize and describe the potential new octopus species found only in São Tomé Island according to our genetic survey.

Unique thermal sensitivity imposes a cold-water energetic barrier for vertical migrators

Alterations of marine species’ ranges with climate change are often attributed to oxygen limitation in warming oceans. Here we report unique metabolic temperature sensitivities for the myriad of vertically migrating oceanic species that daily cross depth-related gradients in temperature and oxygen. In these taxa, selection favours high metabolic activity for predator–prey interactions in warm shallow water and hypoxia tolerance in the cold at depth. These diverging selective pressures result in thermal insensitivity of oxygen supply capacity and enhanced thermal sensitivity of active metabolic rate. Aerobic scope is diminished in the cold, well beyond thermodynamic influences and regardless of ambient oxygen levels, explaining the native distributions of tropical migrators and their recent range expansions following warming events. Cold waters currently constitute an energetic barrier to latitudinal range expansion in vertical migrators. As warming due to climate change approaches, and eventually surpasses, temperatures seen during past warming events, this energetic barrier will be relieved.

REAL-TIME MARINE ANIMAL DETECTION USING YOLO-BASED DEEP LEARNING NETWORKS IN THE CORAL REEF ECOSYSTEM

Abstract. In recent years, with the advancement of marine resources and environment research, the ecological functions of reef-building coral reef ecosystems distributed in warm shallow waters of the ocean are being continuously discovered and valued by people. It is important for ecosystem protection to monitor the population of marine animals. Besides, many projects of Autonomous Underwater Vehicle (AUV) also need technology to perceive and understand environment information in real-time for better decision-making. Therefore, marine animal detection has become a challenge for researchers to study nowadays. Deep neural network models have been used to solve fish-related tasks and gained encouraging achievements, but there are still many problems in this field. In this paper, several YOLO-based methods are chosen for comparison. Experiment results indicate that these methods can recognize the marine animals in coral reef quickly and accurately. Finally, several recommendations for model improvement according to assessment results are presented.

Sedimentological study of Khalsi Formation of Ladakh "Implications for Paleogeographic reconstruction"

Carbonates of the Tethys Himalaya in the Ladakh region present a complex relation with rocks of the Indus group and subduction-related volcanics. The present study involves field recognition of the limestone units, collection of mega fossils, petrographic analysis, elemental and mineral composition of Khalsi Formation of Indus group. We present the results on depositional environment, field relation, paleogeographic conditions, and regional significance of Khalsi Formation. The field relation of Khalsi Formation suggests a complex interaction with the igneous intrusion, foredeep turbidite association, metamorphism, and tectonic deformation. The structural disturbance is evidenced by the folding in shale, imprints of sinistral movement, and localized compaction of limestone. The fossil assemblage collected during this study includes Auroradiolites biconvexus, rudists, crinoids, forams (Orbitolinid) corals, colonial bryozoans, belemnite, and some unidentified marine organisms. The faunal assemblage reflects a shallow-water depositional environment. The petrographic analysis of the samples of Khalsi Formation suggests bioclasts as a major component mainly enriched with the fragments of forams, micrite as cementing material, and pyrite and zircon crystals as noncarbonate constituents. The SEM-EDX data suggest significant calcite content in the samples. The SEM-EDX data suggest significant calcite content in the samples. We suggest the rudists, corals, forams (Orbitulina), crinoids, and bryozoans colonies were widely distributed as a reefal framework along tropical and subtropical tethyan ocean margin having a close affinity with the south Asian-Pacific faunal province. These fossils represent a shallow warm water environment of deposition for Khalsi Formation due to the uplifting of the ocean floor in this region after completion of subduction of the Indian plate beneath Eurasian.

Behavioural thermoregulation linked to foraging in blue sharks.

Large pelagic fishes often dive and surface repeatedly as if they were airbreathers, raising a question about the functions of these movements. Some species (e.g., bigeye tuna, ocean sunfish) apparently alternate foraging in deep cold waters and rewarming in shallow warm waters. However, it is unclear how prevalent this pattern is among species. Blue sharks are the widest-ranging pelagic shark with expanded vertical niches, providing a model for studying foraging–thermoregulation associations. We used electronic tags, including video cameras, to record the diving behaviour, muscle temperature, and foraging events of two blue sharks. During repeated deep dives (max. 422 m), muscle temperature changed more slowly than ambient water temperature. Sharks shifted between descents and ascents before muscle temperature reached ambient temperature, leading to a narrower range (8 °C) of muscle temperature than ambient temperature (20 °C). 2.5-h video footage showed a shark catching a squid, during which a burst swimming event was recorded. Similar swimming events, detected from the entire tag data (20 − 22 h), occurred over a wide depth range (5 − 293 m). We conclude that, instead of alternating foraging and rewarming, blue sharks at our study site forage and thermoregulate continuously in the water column. Furthermore, our comparative analyses showed that the heat exchange rates of blue sharks during the warming and cooling process were not exceptional among fishes for their body size. Thus, behavioural thermoregulation linked to foraging, rather than enhanced abilities to control heat exchange rates, is likely key to the expanded thermal niches of this ectothermic species.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00227-021-03971-3.

The Role of Clouds in Coral Bleaching Events Over the Great Barrier Reef

AbstractThermal coral bleaching events (CBEs) over the Pacific, including those over the Great Barrier Reef (GBR), have commonly been linked to the El Niño–Southern Oscillation (ENSO), with bleaching reported to be a direct result of sea surface temperature (SST) anomalies driven by El Niño. However, such a relationship cannot explain CBEs that occurred during La Niña or the neutral phase of the ENSO. Here, we show that the GBR is characterized by a significant negative correlation between total cloud cover anomaly (TCCA) and lagged SST anomaly (SSTA) whose magnitude and spatial extent are greater than the SSTA‐ENSO correlation. This significant negative TCCA‐SSTA (lagged) correlation prevails over two‐thirds of the study domain even after the ENSO signal is removed, which suggests that local‐scale reduced cloud cover is a key component of the regional warm shallow water formation over the GBR and the occurrence of thermal CBEs.

Short‐lived fishes: Annual and multivoltine strategies

AbstractThe diversity of life histories across the animal kingdom is enormous, with direct consequences for the evolution of lifespans. Very short lifespans (maximum shorter than 1 year in their natural environment) have evolved in several vertebrate lineages. We review short‐lived fish species which complete either single (annual/univoltine) or multiple (multivoltine) generations within a year. We summarize the commonalities and particulars of their biology. Apart from annual killifishes (with >350 species), we detected 60 species with validated lifespan shorter than 1 year in their natural environment. Considering the low number of reports on fish lifespan (<5% of 30,000+ fish species; 1,543 species), the total number of short‐lived fish species may be relatively high (>1,200 species). Short‐lived fish species are scattered across 12 orders, indicating that short lifespan is not a phylogenetically conserved trait but rather evolves under specific ecological conditions. In general, short‐lived fish species are small (typically 55 ± 35 mm), experience high predation (making them important part of ecosystem trophodynamics) and live in shallow warm waters with high productivity and stable abiotic conditions (e.g. Gobiidae, Clupeidae). Others utilize temporally constrained environments, where they survive unfavourable conditions as dormant stages (annual killifishes). They also utilize less productive environments; in this case, they migrate between productive and un‐productive environments (e.g. Myctophidae, Salangidae). These species include the putatively shortest‐lived (Schindleria pietschmanni: Schindleriidae) and earliest maturing (Nothobranchius furzeri: Nothobranchiidae) vertebrates and represent the lower limit of vertebrate longevity. Their examination may provide important insights into the evolutionary and mechanistic understanding of ageing.

The sedimentology and sequence stratigraphy of contourites and associated rocks at the northeastern passive margin of Gondwana during the Early Triassic (Induan - Mirga Mir Formation), Iraqi Kurdistan

Contourite deposits are recognized for the first time from the Lower Triassic Mirga Mir Formation in the Kurdistan region, Northern Iraq. The formation represents deposition on the southern passive margin of the Neo-Tethys during its early opening stages. The contourites are characterized by lenticular and sorted siltstones to fine-grained sandstones with current ripples, cross beddings and scour surfaces. These current structures are associated with thin-bedded (5–20 cm) limestones and shales. Petrographic investigations of the associated carbonate successions show both skeletal and non-skeletal grains such as peloids, ooids, intraclasts and extraclasts. Deposition occurred in a ramp setting at the southern passive margin of the Neo-Tethys and the skeletal grains reveal deep open marine and shallow warm water. Four different facies associations are recognized: Offshoal/basinal, foreshoal/slope, shoal and back shoal/lagoon. Field observations and thin section analysis revealed four main contourite facies in the studied outcrops, namely muddy contourites, silty contourites, sandy contourites and calcareous sandy contourites. The contourites are integrated with the basinal, offshoal, foreshoal and slope deposits. Stable isotope data from the carbonates of Mirga Mir Formation show that the δ18O (‰) values are negatives but the δ13C data shows negative and positive values. They show that had underwent meteoric diagenesis and that the δ13C values still preserving their primary depositional signal. The carbon isotopes data conforms to available data from the surrounding countries and by comparison with Early Triassic δ13C stratigraphic trends, it had captured at least two of the well-known positive spikes and at least one of the negative dips. Sequence stratigraphic analysis and stacking patterns revealed that the Mirga Mir Formation can be divided into two third-order depositional sequences. Each sequence is characterized by TST deposits followed by HST deposits and without LST.

Free gait in a shallow pool accelerates recovery after exercise in model mice with fibromyalgia.

This study aimed to determine the effect of pool gait exercise using fibromyalgia-induced model mice. The sensory threshold, locomotive behavior, electrocardiogram, and onset time after the gait test in shallow water using male C57BL/6J mice (weight, 30–35 g; n=21) were investigated. To induce fibromyalgia in model mice, reserpine was injected intraperitoneally into wild-type mice once a day for 3 days. Subsequently, the fibromyalgia-induced model mice were randomly classified into two groups as follows: the control group (n=11) and the pool gait group (n=10). The mice in the pool gait group walked in the same cage containing shallow warm water 5 times per week. Both groups underwent sensory thresholds and video recordings to determine locomotive behaviors weekly. Further, both heart rate and video recordings for observation of a recovery after the gait test in shallow water were undertaken (control group; n=5, pool gait group; n=5). The pool gait did not affect sensory thresholds and locomotive behavior; however, in the pool gait group, both the recovery after the test, such as onset time and gait distance, were considerably better than those of the control group. Furthermore, changes in heart rate and heart rate irregularity after the test were more apparent in the control group than in the pool gait group. The free gait in a shallow pool accelerated recovery after exercise, unlike the sensory threshold.

Excessive exercise induces cardiac arrhythmia in a young fibromyalgia mouse model.

Fibromyalgia patients experience cardiovascular complications in addition to musculoskeletal pain. This study aimed to investigate the cardiac effects of a prolonged shallow water gait in a fibromyalgia-induced young mouse model. To produce a fibromyalgia mouse model, wild-type mice were administered an intraperitoneal injection of reserpine once a day for three days, and two primary experiments were performed. First, three types of gait tests were performed before and after the reserpine injections as follows: (i) 5 minutes of free gait outside the water, (ii) 1 minute of free gait in shallow warm water, and (iii) 5 minutes of free gait in shallow warm water. Second, electrocardiogram recordings were taken before and after the three gait tests. The average heart rate and heart rate irregularity scores were analyzed. Exercise-induced cardiac arrhythmia was observed at 1-minute gait in shallow water during the acute stage of induced FM in young mice. Further, both cardiac arrhythmia and a decrease in HR have occurred at 5-minute gait in shallow water at the same mice. However, this phenomenon was not observed in the wild-type mice under any test conditions. Although a short-term free gait in shallow warm water may be advantageous for increasing the motor activity of FM-model mice, we should be aware of the risk of prolonged and excessive exercise-induced cardiac arrhythmia. For gait exercises in shallow water as a treatment in FM patients. We suggest a gradual increase in exercise duration may be warranted.

Lionfish envenomation in Caribbean and Atlantic waters: Climate change and invasive species.

The concept of emerging diseases is well understood; however, the concept of emerging injuries is not. We describe the introduction of two species of lionfish, native to the Indian and Pacific Oceans, into the warm shallow coastal waters of the Western Atlantic Ocean and the Caribbean Sea. Lionfish thrive in the same coastal waters that attract recreational swimmers, snorkelers, and divers. Because lionfish have ornate colors, people often swim close to have a better look. Lionfish have venomous spines and, in a defensive reaction, frequently envenomate curious humans. The fish are voracious predators and disrupt the coral ecosystems of the Atlantic. Furthermore, their range is spreading through a combination of lack of natural predators and the expansion of hospitable warm waters into higher latitudes as part of climate change.

Bulk and Export Production Fluxes in the Gulf of Aqaba, Northern Red Sea

Marine particulate fluxes were studied between 2014 and 2017 in the oligotrophic Gulf of Aqaba (GOA), northern Red Sea. A bottom tethered mooring mounted with 5 sediment trap stations (KC Denmark Inc.) at approximately equal depth intervals between 120 and 570 m (water depth of ∼610 m) was rotated monthly. The bulk particulate fluxes were determined for the entire period, with organic C and N, CaCO3, and lithogenic fluxes determined for the first two and half years of the deployment. The results are evaluated in the context of monthly resolved records of seawater temperature, chlorophyll-a concentrations, and macro-nutrient concentrations, as well as hourly to weekly dust load records and rare fluvial events. The results are further compared to core-tops collected from varying water depths and are combined to produce a basin source-to-sink mass balance of particulate fluxes. The GOA undergoes strong seasonal changes expressed by surface water temperatures and water column stratification and mixing, which control the vertical and temporal distribution of nutrients and primary and export production. Accordingly, the seasonal variability in particulate fluxes varies over a wide range, typically displaying peak bulk fluxes in bottom waters during the winter (∼5–7 g m–2 d–1) and minimum values in shallow waters during summer (<0.5 g m–2 d–1). Organic C and N fluxes are the highest in shallow waters and display strong vertical attenuation that varies seasonally, a-priori reflecting enhanced remineralization in the warm shallow waters during summer. In contrast, particulate organic carbon and nitrogen fluxes are enhanced in bottom waters during winter, due to the combined effect of the increased presence of mineral ballasts and vertical water column mixing. The quantification of particulate fluxes in the GOA suggests that, while most of the bulk particulates are introduced into the basin via episodic fluvial events, with direct dust inputs contributing approximately an order of magnitude less material, the internal cycling of terrigenous material is complex, with a lag between the initial deposition of influxing material along shallow margins and seasonal reworking and transport of sediments to the deep seafloor. Nevertheless, the fluxes of terrigenous and organic particulates are largely independent of each other, with export production fluxes driven by water column mixing and nutrient availability in the photic zone. In addition to being the first quantitative report of bulk and export production fluxes in the region, our results provide an improved understanding of the interplay between export production and terrigenous fluxes as well as an interpretation of the paleo-record in the GOA and in comparable environments. On a wider scale, the findings reported here relate to the role of dust deposition and hemipelagic sedimentation in the oceans and their impact on export production and particle cycling in coastal regions. Combined, these findings illuminate the factors impacting marine habitats and ecosystems, the cycling and sequestration of trace elements and anthropogenic components in the oceans, and facilitate better understanding of the interplay between solid and dissolved phases in the oceans and reconstructing past oceanographic and climatic conditions from marine sediment cores.

Paleobiogeographic distribution of rudist bivalves (Hippuritida) in the Oxfordian–early Aptian (Late Jurassic–Early Cretaceous)

In the Late Jurassic and Cretaceous the warm shallow water seas were characterized, within benthic marine organisms, by rudist bivalves, a peculiar group of mollusks that originated in the Late Jurassic and became extinct at the end of the Cretaceous. In this paper their global distribution in neritic carbonates is considered since their first appearance in the middle Oxfordian up to the first main extinction event at the end of the early Aptian. The information and data regarding global rudist occurrences throughout neo-Tethys and paleo-Pacific oceans are critically reprised from literature and organized in an Oxfordian-early Aptian Rudist database (OXAP_RDB) that encompasses 235 rudist-bearing localities all across the world, with 845 total rudist occurrences, 34 valid genera and 148 species. Actual rudist geographic distribution is investigated in order to contribute to the identification of the paleobiogeographic pattern of these benthic organisms in the paleoclimatic and paleogeographic setting of neo-Tethys and paleo-Pacific oceans, allowing to reconstruct dispersal patterns and to define four broad paleobiogeographic Provinces in the Barremian–early Aptian.

Crucian Carp (Carassius carassius) Strongly Affect C/N/P Stoichiometry of Suspended Particulate Matter in Shallow Warm Water Eutrophic Lakes

Crucian carp (Carassius carassius) is a key fish species in most Chinese subtropical and tropical shallow lakes. Through sediment feeding, crucian carp could greatly change water turbidity and nutrient levels, as well as the abundance of herbivorous consumers, which may have important influences on seston element stoichiometry. However, so far, experimental studies on this topic are lacking. We conducted a 36-day mesocosm experiment to explore the effects of crucian carp on water physicochemical and biological properties, and C/N/P ratios in suspended particulate matter (SPM) under eutrophic conditions. Our results provided three major findings: (1) Crucian carp resuspended sediments and along with them, reduced light penetration and lower light/total phosphorus (TP) ratios. (2) Crucian carp reduced biomasses of both zooplankton and macrozoobenthos, whereas their effect on phytoplankton was weak, potentially because of resuspension-induced light limitation. (3) Both C/P and N/P ratios in SPM were significant lower in mesocosms with crucian carp than in fish-free controls, which may be attributed to the high contribution of P-rich sediments and low light to nutrient supply caused by fish-induced resuspension. Our results suggest that besides planktivorous fish, benthivore (e.g., crucian carp) in warm shallow waters could also affect pelagic C/N/P stoichiometry via sediment feeding, which may further influence energy transfer efficiency in lake food chain.

Localizing Snapping Shrimp Noise Using a Small-Aperture Array

In warm shallow waters, one can consistently hear the crackling sound due to snapping shrimp. An individual sound or “snap” is highly impulsive. Knowing the source locations of these snaps facilitates the development of some unique passive sensing applications. One common approach in localizing these snaps is to calculate the time difference of arrival (TDoA) of snaps across sensors of an array. For a snap originating from a short distance away, in terms of a few multiples of the array aperture size, the signal from the snap forms a curved wavefront, such that both the direction of arrival (DoA) and the range of the snap can be obtained by studying the TDoA of the wavefront. However, this method is infeasible for long-range 3-D localization due to the need for large-aperture 3-D arrays. Smaller aperture arrays allow estimation of DoA for far-field sounds, but not the range. Since the ocean surface acts like an acoustic mirror that reflects the snaps, we can estimate the range of the snaps by measuring the TDoA between the direct arrivals and their surface reflections, even if the snaps occur in the far-field of the array. Given a set of perfectly associated direct and surface-reflected snaps, we derive a range estimator parameterized by nominal receiver depth and receiver orientation. In practice, we know these parameters only approximately. The problem is further complicated by the fact that snaps are acoustically similar to each other, and so associating a snap with its surface reflection can be difficult. We propose an algorithm that solves the problem of estimation of snap locations, snap associations, and receiver parameters, jointly. We verify the method through numerical simulation and through experimental results.

Environmental Controls of Oyster-Pathogenic Vibrio spp. in Oregon Estuaries and a Shellfish Hatchery.

ABSTRACTVibrio spp. have been a persistent concern for coastal bivalve hatcheries, which are vulnerable to environmental pathogens in the seawater used for rearing larvae, yet the biogeochemical drivers of oyster-pathogenic Vibrio spp. in their planktonic state are poorly understood. Here, we present data tracking oyster-pathogenic Vibrio bacteria in Netarts Bay and Yaquina Bay in Oregon, USA, as well as in adjacent coastal waters and a local shellfish hatchery, through the 2015 upwelling season. Vibrio populations were quantified using a culture-independent approach of high-throughput Vibrio-specific 16S rRNA gene sequencing paired with droplet digital PCR, and abundances were analyzed in the context of local biogeochemistry. The most abundant putative pathogen in our samples was Vibrio coralliilyticus. Environmental concentrations of total Vibrio spp. and V. coralliilyticus were highest in Netarts Bay sediment samples and higher in seawater from Netarts Bay than from nearshore coastal waters or Yaquina Bay. In Netarts Bay, the highest V. coralliilyticus concentrations were observed during low tide, and abundances increased throughout the summer. We hypothesize that the warm shallow waters in estuarine mudflats facilitate the local growth of the V. coralliilyticus pathogen. Samples from larval oyster tanks in Whiskey Creek Shellfish Hatchery, which uses seawater pumped directly from Netarts Bay, contained significantly lower total Vibrio species concentrations, but roughly similar V. coralliilyticus concentrations, than did the bay water, resulting in a 30-fold increase in the relative abundance of the V. coralliilyticus pathogen in hatchery tanks. This suggests that the V. coralliilyticus pathogen is able to grow or persist under hatchery conditions.IMPORTANCE It has been argued that oyster-pathogenic Vibrio spp. have contributed to recent mortality events in U.S. shellfish hatcheries (R. A. Elston, H. Hasegawa, K. L. Humphrey, I. K. Polyak, and C. Häse, Dis Aquat Organ 82:119–134, 2008, https://doi.org/10.3354/dao01982); however, these events are often sporadic and unpredictable. The success of hatcheries is critically linked to the chemical and biological composition of inflowing seawater resources; thus, it is pertinent to understand the biogeochemical drivers of oyster-pathogenic Vibrio spp. in their planktonic state. Here, we show that Netarts Bay, the location of a local hatchery, is enriched in oyster-pathogenic V. coralliilyticus compared to coastal seawater, and we hypothesize that conditions in tidal flats promote the local growth of this pathogen. Furthermore, V. coralliilyticus appears to persist in seawater pumped into the local hatchery. These results improve our understanding of the ecology and environmental controls of the V. coralliilyticus pathogen and could be used to improve future aquaculture efforts, as multiple stressors impact hatchery success.

A Giant Underwater, Encrusted Stalactite from the Blue Hole, Lighthouse Reef, Belize, Revisited: a Complex History of Biologically Induced Carbonate Accretion Under Changing Meteoric and Marine Conditions

A late Pleistocene to Holocene submerged and encrusted speleothem exhibits a complex history including a meteoric phase and two marine phases. A combined study using petrography, mineralogy, and inorganic and organic geochemistry, as well as geochronology has shown that phototrophic and heterotrophic biological activity impacted carbonate precipitation during all phases of carbonate accretion. The stalactite formed ca. 30 m below modern sea level at a marginal overhang in the Blue Hole of Lighthouse Reef Atoll. Unlike purely meteoric speleothems, the Belize example consists of a meteoric core, a marine aragonite crust, and a serpulid-micrite-rich outer crust as a result of postglacial flooding of the karst cave. The core of the stalactite has a tufaceous texture, containing algal or microbial remains, and consists entirely of low-magnesium calcite, formed 19.55-10.68 kyr BP. The texture suggests that the stalactite formed at the cave entrance, and, hence, the former cave ceiling had apparently collapsed earlier during the Pleistocene. Oxygen (δ18O) and carbon (δ13C) isotopes across the core suggest a trend towards drier conditions and reduced soil and plant cover after the last glacial maximum. The marine aragonite crust consists of stacked botryoids in which individual crystals up to 700 lm have dark terminations enriched in high-magnesium calcite. This crust accreted from 10.82 to 9.95 kyr BP in warm shallow water during the early Holocene thermal optimum. Carbonate accretion rates were considerable and averaged 125 μm/yr. The crust has a dense, laminated texture on one side and a porous, shrubby texture on the other. The presence of n-C16:1ω5, n-C17:1ω6, and 10Me-C16 fatty acids in the laminated crust suggests that sulfate-reducing bacteria contributed to aragonite formation in an environment that was less open than the formation environment of the porous crust, where these biomarkers are lacking (n-C16:1ω5,n-C17:1ω6) or are less abundant (10Me-C16). Enrichment of 34S and 18O in carbonate-associated sulfate (CAS) relative to seawater sulfate also suggests sulfate reduction during carbonate formation. The greater contribution of heterotrophic processes to aragonite precipitation in the laminated crust is also reflected in δ13C values as low as -1.3%, whereas no such depletion is observed in the aragonite of the porous crust (δ13C values as low as 0.0%). A pronounced isotopic variability and excursions to positive δ13C values as high as +3.5%0 in the inner half of the laminated crust indicate an episodic, local impact of photosynthesis on aragonite precipitation, whereas the lack of such excursions in the porous crust (δ13C values as high as +1.5%0) is again best explained by a more open environment of formation. After a ca. 5 kyr hiatus, from 4.39 kyr BP, a biogenic crust of abundant serpulids and finely crystalline, microbial and detrital carbonate, consisting of high-magnesium calcite and aragonite, accreted on the outer surface of the stalactite. Outermost crust accretion was probably influenced by the inundation of the Lighthouse Reef lagoon that started to shed abundant fine-grained carbonate sediment into the Blue Hole. The stalactite broke off the cave ceiling either before or after the formation of the outermost crust, likely due to seismic movements along the nearby plate boundary. The study demonstrates that like speleothems from the terrestrial realm, submerged stalactites may have had complex histories with great potential as paleoenvironmental archives.