Environmental drivers of the abundance and distribution of forage fishes on the Northeast US shelf, with a particular emphasis on northern sand lance

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.Small pelagic fishes, also termed forage fishes, represent a critical link between secondary production and myriad top predators in marine ecosystems, including the Northeast US shelf. In this dissertation, I analyze the drivers of forage fish distribution throughout the Northeast US shelf and the drivers of the abundance of the ecologically important northern sand lance. Chapter 2 examines the basic ecology of northern sand lance and uses these insights to identify mechanistic drivers of their abundance. I then explore different scenarios of these drivers to project sand lance abundance through the end of the 21st century, which appears precarious for adult sand lance unless current trajectories change. Chapter 3 analyzes the environmental drivers of the distribution of the six dominant, offshore forage fish species (northern sand lance, Atlantic herring, alewife, blueback herring, Atlantic mackerel, and Atlantic butterfish) on the Northeast US shelf to elucidate the role of environmental covariates in shelf occupancy by these taxa. The results of this chapter indicate shelf occupancy of butterfish and Atlantic mackerel are increasing through time while occupancy of sand lance is decreasing with time. The occurrence of most of these species is also moving deeper and northward with time. Chapter 4 assesses the source-sink dynamics of three sand lance hotspots through Lagrangian particle tracking models simulating larval sand lance transport. Connectivity varies among these hotspots with Georges Bank and Stellwagen Bank having notable retention while the Great South Channel relies on larvae from other hotspots. Retention on Stellwagen Bank and Georges Bank are linked to strong wind events during the larval period of sand lance. Collectively, this dissertation improves our understanding of the dynamics driving variability in the Northeast US shelf forage fish complex, particularly for northern sand lance.The research within this dissertation was funded by a National Science Foundation Graduate Research Fellowship (awarded to JJS), Woods Hole Sea Grant (NA18OAR4170104, Project No. R/O-57), the Bureau of Ocean Energy Management (IA agreement M17PG0019), and the National Marine Sanctuary Foundation

Trophic ecology of barrelfish (Hyperoglyphe perciformis) in oceanic waters of southeast Florida

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Bulletin of Marine Science 93 (2017): 987-996, doi:/10.5343/bms.2017.1003.Deep-water demersal fishes represent an understudied but ecologically important group of organisms. Select species of demersal fishes rely on pelagic prey items, representing a direct transport of surface carbon to greater depths. Barrelfish Hyperoglyphe perciformis (Mitchell, 1818), which inhabit deep slope waters, are a species that has been suggested to fill this role, as congeners consume primarily pelagic gelatinous zooplankton; however, there is a dearth of information on the trophic ecology of barrelfish. Stomach content and stable isotope analyses were conducted on barrelfish caught by recreational fishers off Miami, Florida to improve our understanding of the feeding of this species. Pyrosoma atlanticum (Péron, 1804), a pelagic, vertically migrating tunicate, represented 89% of the barrelfish diet by weight. Mesopelagic fish and shrimp contributed much smaller proportions. Standard ellipse areas corrected for sample size (SEAc) showed a substantially smaller isotopic niche width for barrelfish (0.606 ‰2) than dolphinfish (2.16 ‰2), king mackerel (3.04 ‰2), or wahoo (1.97 ‰2). Coupled with dependence on a singular prey item, the low SEAc of barrelfish suggests they occupy a limited trophic niche space. Overlap of barrelfish SEAc with dolphinfish (99.5% overlap) and king mackerel (100% overlap) indicate that the carbon sources as well as the number of trophic steps for barrelfish are similar to king mackerel and dolphinfish and are linked to surface waters. This trophic linkage suggests that barrelfish may play a role in carbon export and further study into their behavior and daily consumption rates is warranted for quantifying this role.Funding was provided to JJS from a Small Undergraduate Research Grant Experience (SURGE). JKL was supported as a Cooperative Institute for the North Atlantic Region fellow with funds from NOAA

Characterizing larval swordfish habitat in the western tropical North Atlantic

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Fisheries Oceanography, 27 (2018): 246-258, doi:10.1111/fog.12249.Swordfish Xiphias gladius (Linnaeus, 1758) are a circumglobal pelagic fish targeted by multiple lucrative fisheries. Determining the distribution of swordfish larvae is important for indicating reproductive activity and understanding the early life history of swordfish. We identify and characterize larval swordfish distributions during peak swordfish spawning throughout the Gulf of Mexico and western Caribbean Sea with generalized additive models (GAMs) using catches of swordfish larvae during ichthyoplankton surveys in April and May of 2010, 2011, and 2012. The best fit GAM, as determined by stepwise, backward Akaike Information Criterion selection, included both physiochemical (temperature at 5 m, sea surface height anomaly (SSHA), eddy kinetic energy (EKE)), temporal (lunar illumination, hour of sampling) and spatial (location) variables, while near-surface chlorophyll a concentration residuals remained as a random effect. The highest probability of larval swordfish catch occurred at sub-surface temperatures, SSHA, and EKE values indicative of boundary currents. Standard lengths of larvae were larger further downstream in the boundary currents, despite high variability in length with location due to multiple spawning locations of swordfish near these currents. Probability of larval swordfish catch also peaked during the crescent and gibbous moons, indicating a lunar periodicity to swordfish spawning. These results suggest that swordfish may spawn during select moon phases near boundary currents that transport their larvae to larval and juvenile habitat including the northern Gulf of Mexico and coastal waters of the southeast United States.NASA Grant Numbers: NNX11AP76G, NNX08AL06

Soundscapes influence the settlement of the common caribbean coral porites astreoides irrespective of light conditions

Author Posting. © Royal Society, 2018. This article is posted here by permission of Royal Society for personal use, not for redistribution. The definitive version was published in Proceedings of the Royal Society Open Science 5(12) (2018): 181358. doi: 10.1098/rsos.181358.The settlement of reef-building corals is critical to the survival and recovery of reefs. Recent evidence indicates that coral larvae orient towards reef sound, yet the components of the acoustic environment that may attract coral larvae and induce settlement are unknown. Here we investigated the effects of ambient soundscapes on settlement of Porites astreoides coral larvae using in situ chambers on reefs differing in habitat quality (coral and fish abundance). Mean larval settlement was twice as high in an acoustic environment with high levels of low-frequency sounds, typical of a high-quality, healthy reef; this result was observed in both natural light and dark treatments. Overall, the enhancement of coral settlement by soundscapes typical of healthy reefs suggests a positive feedback where soundscape properties of reefs with elevated coral and fish abundance may facilitate coral recruitment.This study is funded by NSF Biological Oceanography award 15-36782 which supported all authors

Microbial and nutrient dynamics in mangrove, reef, and seagrass waters over tidal and diurnal time scales

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Becker, C. C., Weber, L., Suca, J. J., Llopiz, J. K., Mooney, T. A., & Apprill, A. Microbial and nutrient dynamics in mangrove, reef, and seagrass waters over tidal and diurnal time scales. Aquatic Microbial Ecology, 85, (2020): 101-119, https://doi.org/10.3354/ame01944.In coral reefs and adjacent seagrass meadow and mangrove environments, short temporal scales (i.e. tidal, diurnal) may have important influences on ecosystem processes and community structure, but these scales are rarely investigated. This study examines how tidal and diurnal forcings influence pelagic microorganisms and nutrient dynamics in 3 important and adjacent coastal biomes: mangroves, coral reefs, and seagrass meadows. We sampled for microbial (Bacteria and Archaea) community composition, cell abundances and environmental parameters at 9 coastal sites on St. John, US Virgin Islands that spanned 4 km in distance (4 coral reefs, 2 seagrass meadows and 3 mangrove locations within 2 larger bays). Eight samplings occurred over a 48 h period, capturing day and night microbial dynamics over 2 tidal cycles. The seagrass and reef biomes exhibited relatively consistent environmental conditions and microbial community structure but were dominated by shifts in picocyanobacterial abundances that were most likely attributed to diel dynamics. In contrast, mangrove ecosystems exhibited substantial daily shifts in environmental parameters, heterotrophic cell abundances and microbial community structure that were consistent with the tidal cycle. Differential abundance analysis of mangrove-associated microorganisms revealed enrichment of pelagic oligotrophic taxa during high tide and enrichment of putative sediment-associated microbes during low tide. Our study underpins the importance of tidal and diurnal time scales in structuring coastal microbial and nutrient dynamics, with diel and tidal cycles contributing to a highly dynamic microbial environment in mangroves, and time of day likely contributing to microbial dynamics in seagrass and reef biomes.This research was supported by NSF awards OCE-1536782 to T.A.M., J.K.L., and A.A. and OCE-1736288 to A.A., NOAA Cooperative Institutes award NA19O AR 4320074 to A.A. and E. Kujawinski and the Andrew W. Mellon Foundation Endowed Fund for Innovative Research to A.A

Feeding dynamics of Northwest Atlantic small pelagic fishes

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Progress in Oceanography 165 (2018): 52-62, doi:10.1016/j.pocean.2018.04.014.Small pelagic fishes represent a critical link between zooplankton and large predators. Yet, the taxonomic resolution of the diets of these important fishes is often limited, especially in the Northwest Atlantic. We examined the diets, along with stable isotope signatures, of five dominant small pelagic species of the Northeast US continental shelf ecosystem (Atlantic mackerel Scomber scombrus, Atlantic herring Clupea harengus, alewife Alosa pseudoharengus, blueback herring Alosa aestivalis, and Atlantic butterfish Peprilus triacanthus). Diet analyses revealed strong seasonal differences in most species. Small pelagic fishes predominantly consumed Calanus copepods, small copepod genera (Pseudocalanus/Paracalanus/Clausocalanus), and Centropages copepods in the spring, with appendicularians also important by number for most species. Krill, primarily Meganyctiphanes norvegica, and hyperiid amphipods of the genera Hyperia and Parathemisto were common in the stomach contents of four of the five species in the fall, with hyperiids common in the stomach contents of butterfish in both seasons and krill common in the stomach contents of alewife in both seasons. Depth and region were also found to be sources of variability in the diets of Atlantic mackerel, Atlantic herring, and alewife (region but not depth) with krill being more often in the diet of alewife in more northerly locations, primarily the Gulf of Maine. Stable isotope data corroborate the seasonal differences in diet but overlap of isotopic niche space contrasts that of dietary overlap, highlighting the differences in the two methods. Overall, the seasonal variability and consumer-specific diets of small pelagic fishes are important for understanding how changes in the zooplankton community could influence higher trophic levels.Funding for this work was primarily through a US National Science Foundation (NSF) OCE-RIG grant (OCE 1325451) to JKL, with additional support from NOAA through the Cooperative Institute for the North Atlantic Region (CINAR) under Cooperative Agreement NA14OAR4320158 in the form a CINAR Fellow Award (JKL), an NSF Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE 1655686; JKL), a Hendrix College summer research award (ZRK), and an NSF REU-supported Woods Hole Oceanographic Institution Summer Student Fellowship (SLH)

High collocation of sand lance and protected top predators: implications for conservation and management

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Silva, T. L., Wiley, D. N., Thompson, M. A., Hong, P., Kaufman, L., Suca, J. A., Llopiz, J. K., Baumann, H., & Fay, G. High collocation of sand lance and protected top predators: implications for conservation and management. Conservation Science and Practice, (2021): 3:e274, doi: 10.1111/csp2.274.Spatial relationships between predators and prey provide critical information for understanding and predicting climate‐induced shifts in ecosystem dynamics and mitigating human impacts. We used Stellwagen Bank National Marine Sanctuary as a case study to investigate spatial overlap among sand lance (Ammodytes dubius), a key forage fish species, and two protected predators: humpback whales (Megaptera novaeangliae) and great shearwaters (Ardenna gravis). We conducted 6 years (2013–2018) of standardized surveys and quantified spatial overlap using the global index of collocation. Results showed strong, consistent collocation among species across seasons and years, suggesting that humpback whales and great shearwater distributions are tightly linked to sand lance. We propose that identifying sand lance habitats may indicate areas where humpbacks and shearwaters aggregate and are particularly vulnerable to human activities. Understanding how sand lance influence predator distributions can inform species protection and sanctuary management under present and future scenarios.This work was supported by the Bureau of Ocean Energy Management [IA agreement M17PG0019], NOAA Stellwagen Bank National Marine Sanctuary, U.S. Geological Survey, the Volgenau Foundation, and the Mudge Foundation

Multiscale spatio-temporal patterns of boat noise on U.S. Virgin Island coral reefs

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Marine Pollution Bulletin 136 (2018): 282-290, doi:10.1016/j.marpolbul.2018.09.009.Sound-sensitive organisms are abundant on coral reefs. Accordingly, experiments suggest that boat noise could elicit adverse effects on coral reef organisms. Yet, there are few data quantifying boat noise prevalence on coral reefs. We use long-term passive acoustic recordings at nine coral reefs and one sandy comparison site in a marine protected area to quantify spatio-temporal variation in boat noise and its effect on the soundscape. Boat noise was most common at reefs with high coral cover and fish density, and temporal patterns reflected patterns of human activity. Boat noise significantly increased low-frequency sound levels at the monitored sites. With boat noise present, the peak frequencies of the natural soundscape shifted from higher frequencies to the lower frequencies frequently used in fish communication. Taken together, the spectral overlap between boat noise and fish communication and the elevated boat detections on reefs with biological densities raises concern for coral reef organisms.This research was funded by the National Science Foundation Biological Oceanography Program (award OCE-1536782) and the WHOI Summer Student Fellowship Program

The role of sand lances (Ammodytes sp.) in the Northwest Atlantic ecosystem: a synthesis of current knowledge with implications for conservation and management

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Staudinger, M. D., Goyert, H., Suca, J. J., Coleman, K., Welch, L., Llopiz, J. K., Wiley, D., Altman, I., Applegate, A., Auster, P., Baumann, H., Beaty, J., Boelke, D., Kaufman, L., Loring, P., Moxley, J., Paton, S., Powers, K., Richardson, D., Robbins, J., Runge, J., Smith, B., Spiegel, C., & Steinmetz, H. The role of sand lances (Ammodytes sp.) in the Northwest Atlantic ecosystem: a synthesis of current knowledge with implications for conservation and management. Fish and Fisheries, 00, (2020): 1-34, doi:10.1111/faf.12445.The American sand lance (Ammodytes americanus, Ammodytidae) and the Northern sand lance (A. dubius, Ammodytidae) are small forage fishes that play an important functional role in the Northwest Atlantic Ocean (NWA). The NWA is a highly dynamic ecosystem currently facing increased risks from climate change, fishing and energy development. We need a better understanding of the biology, population dynamics and ecosystem role of Ammodytes to inform relevant management, climate adaptation and conservation efforts. To meet this need, we synthesized available data on the (a) life history, behaviour and distribution; (b) trophic ecology; (c) threats and vulnerabilities; and (d) ecosystem services role of Ammodytes in the NWA. Overall, 72 regional predators including 45 species of fishes, two squids, 16 seabirds and nine marine mammals were found to consume Ammodytes. Priority research needs identified during this effort include basic information on the patterns and drivers in abundance and distribution of Ammodytes, improved assessments of reproductive biology schedules and investigations of regional sensitivity and resilience to climate change, fishing and habitat disturbance. Food web studies are also needed to evaluate trophic linkages and to assess the consequences of inconsistent zooplankton prey and predator fields on energy flow within the NWA ecosystem. Synthesis results represent the first comprehensive assessment of Ammodytes in the NWA and are intended to inform new research and support regional ecosystem‐based management approaches.This manuscript is the result of follow‐up work stemming from a working group formed at a two‐day multidisciplinary and international workshop held at the Parker River National Wildlife Refuge, Massachusetts in May 2017, which convened 55 experts scientists, natural resource managers and conservation practitioners from 15 state, federal, academic and non‐governmental organizations with interest and expertise in Ammodytes ecology. Support for this effort was provided by USFWS, NOAA Stellwagen Bank National Marine Sanctuary, U.S. Department of the Interior, U.S. Geological Survey, Northeast Climate Adaptation Science Center (Award # G16AC00237), an NSF Graduate Research Fellowship to J.J.S., a CINAR Fellow Award to J.K.L. under Cooperative Agreement NA14OAR4320158, NSF award OCE‐1325451 to J.K.L., NSF award OCE‐1459087 to J.A.R, a Regional Sea Grant award to H.B. (RNE16‐CTHCE‐l), a National Marine Sanctuary Foundation award to P.J.A. (18‐08‐B‐196) and grants from the Mudge Foundation. The contents of this paper are the responsibility of the authors and do not necessarily represent the views of the National Oceanographic and Atmospheric Administration, U.S. Fish and Wildlife Service, New England Fishery Management Council and Mid‐Atlantic Fishery Management Council. This manuscript is submitted for publication with the understanding that the United States Government is authorized to reproduce and distribute reprints for Governmental purposes. Any use of trade, firm or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government

Birds of a feather eat plastic together: high levels of plastic ingestion in Great Shearwater adults and juveniles across their annual migratory cycle

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Robuck, A. R., Hudak, C. A., Agvent, L., Emery, G., Ryan, P. G., Perold, V., Powers, K. D., Pedersen, J., Thompson, M. A., Suca, J. J., Moore, M. J., Harms, C. A., Bugoni, L., Shield, G., Glass, T., Wiley, D. N., & Lohmann, R. Birds of a feather eat plastic together: high levels of plastic ingestion in Great Shearwater adults and juveniles across their annual migratory cycle. Frontiers in Marine Science, 8, (2022): 719721, https://doi.org/10.3389/fmars.2021.719721.Limited work to date has examined plastic ingestion in highly migratory seabirds like Great Shearwaters (Ardenna gravis) across their entire migratory range. We examined 217 Great Shearwaters obtained from 2008–2019 at multiple locations spanning their yearly migration cycle across the Northwest and South Atlantic to assess accumulation of ingested plastic as well as trends over time and between locations. A total of 2328 plastic fragments were documented in the ventriculus portion of the gastrointestinal tract, with an average of 9 plastic fragments per bird. The mass, count, and frequency of plastic occurrence (FO) varied by location, with higher plastic burdens but lower FO in South Atlantic adults and chicks from the breeding colonies. No fragments of the same size or morphology were found in the primary forage fish prey, the Sand Lance (Ammodytes spp., n = 202) that supports Great Shearwaters in Massachusetts Bay, United States, suggesting the birds directly ingest the bulk of their plastic loads rather than accumulating via trophic transfer. Fourier-transform infrared spectroscopy indicated that low- and high-density polyethylene were the most common polymers ingested, within all years and locations. Individuals from the South Atlantic contained a higher proportion of larger plastic items and fragments compared to analogous life stages in the NW Atlantic, possibly due to increased use of remote, pelagic areas subject to reduced inputs of smaller, more diverse, and potentially less buoyant plastics found adjacent to coastal margins. Different signatures of polymer type, size, and category between similar life stages at different locations suggests rapid turnover of ingested plastics commensurate with migratory stage and location, though more empirical evidence is needed to ground-truth this hypothesis. This work is the first to comprehensively measure the accumulation of ingested plastics by Great Shearwaters over the last decade and across multiple locations spanning their yearly trans-equatorial migration cycle and underscores their utility as sentinels of plastic pollution in Atlantic ecosystems.This project was supported by the NOAA Fisheries National Seabird Program and the Volgenau Foundation. AR acknowledges support from the National Oceanic and Atmospheric Administration Dr. Nancy Foster Scholarship Program (NOAA Award Number NA17NOS4290028), the Robert and Patricia Switzer Foundation, the STEEP Superfund Research Program (NIEHS Award Number P42ES027706), and the Oak Ridge Institute for Science and Education (ORISE) program. LB was funded by INCT-Mar COI and PQ Grant No. 311409/2018-0, both by the Brazilian National Research Council (CNPq). JS was funded by the National Science Foundation Graduate Research Fellowship program