A decade of monitoring Atlantic cod Gadus morhua spawning aggregations in Massachusetts Bay using passive acoustics

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Caiger, P. E., Dean, M. J., DeAngelis, A. I., Hatch, L. T., Rice, A. N., Stanley, J. A., Tholke, C., Zemeckis, D. R., & Van Parijs, S. M. A decade of monitoring Atlantic cod Gadus morhua spawning aggregations in Massachusetts Bay using passive acoustics. Marine Ecology Progress Series, 635, (2020): 89-103, doi:10.3354/meps13219.Atlantic cod Gadus morhua populations in the northeast USA have failed to recover since major declines in the 1970s and 1990s. To rebuild these stocks, managers need reliable information on spawning dynamics in order to design and implement control measures; discovering cost-effective and non-invasive monitoring techniques is also favorable. Atlantic cod form dense, site-fidelic spawning aggregations during which they vocalize, permitting acoustic detection of their presence at such times. The objective of this study was to detect spawning activity of Atlantic cod using multiple fixed-station passive acoustic recorders to sample across Massachusetts Bay during the winter spawning period. A generalized linear modeling approach was used to investigate spatio-temporal trends of cod vocalizing over 10 consecutive winter spawning seasons (2007-2016), the longest such timeline of any passive acoustic monitoring of a fish species. The vocal activity of Atlantic cod was associated with diel, lunar, and seasonal cycles, with a higher probability of occurrence at night, during the full moon, and near the end of November. Following 2009 and 2010, there was a general decline in acoustic activity. Furthermore, the northwest corner of Stellwagen Bank was identified as an important spawning location. This project demonstrated the utility of passive acoustic monitoring in determining the presence of an acoustically active fish species, and provides valuable data for informing the management of this commercially, culturally, and ecologically important species.Thanks to Eli Bonnell, Genevieve Davis, Julianne Bonell, Samara Haver, and Eric Matzen for assistance in MARU deployments, Dana Gerlach and Heather Heenehan for help in passive acoustic data analysis, and the NEFSC passive acoustics group for useful discussions. Funding for 2007−2012 passive acoustic surveys was provided by Excelerate Energy and Neptune LNG to Cornell University. Fieldwork for 2013−2015 was funded through the 2013−2014 NOAA Saltonstall-Kennedy grant program (Award No. NA14NMF4270027), and jointly funded by The Nature Conservancy, Massachusetts Division of Marine Fisheries, and the Cabot Family Charitable Foundation. Funding for 2016 SoundTrap data was provided by NOAA’s Ocean Acoustics Program (4 Sanctuaries Project)

Jurisdiction Over Endangered Species' Habitat: the Impacts of People and Property on Recovery Planning

Coordinating management among multiple landowners and jurisdictional agencies is one of the greatest challenges confronting conservation planning. In this study, we assessed the impacts on recovery progress of the people and property involved in recovery plan development and implementation. We compared indices of recovery progress among endangered species whose primary habitat falls into one of four federal jurisdiction categories: nonfederal land only, 50% but not all federal land, and all federal land. Species found exclusively on federal land are more likely to be improving in status. This may result from the fact that overall implementation of recovery tasks is lower among species occurring exclusively on nonfederal lands. Revision status, the existence of a centralized database, the designation of a person or committee to coordinate plan implementation, the parties involved in drafting the plan, and those designated as responsible for implementing recovery tasks are also significant factors in determining recovery plan implementation. Specifically, diversity of recovery team membership and the average number of participants increase with increasing federal jurisdiction, and tasks are more likely to be completed when more parties are involved in developing recovery plans. However, fewer recovery tasks are completed as the number of parties involved in implementation increases, suggesting that species on federal lands may benefit from less division of labor among agencies. Differences in drafting plans and administering their implementation appear to be stronger determinants of the observed variation in recovery success than differences in the kinds of threats facing species and their habitats

Exploring movement patterns and changing distributions of baleen whales in the western North Atlantic using a decade of passive acoustic data

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Davis, G. E., Baumgartner, M. F., Corkeron, P. J., Bell, J., Berchok, C., Bonnell, J. M., Thornton, J. B., Brault, S., Buchanan, G. A., Cholewiak, D. M., Clark, C. W., Delarue, J., Hatch, L. T., Klinck, H., Kraus, S. D., Martin, B., Mellinger, D. K., Moors-Murphy, H., Nieukirk, S., Nowacek, D. P., Parks, S. E., Parry, D., Pegg, N., Read, A. J., Rice, A. N., Risch, D., Scott, A., Soldevilla, M. S., Stafford, K. M., Stanistreet, J. E., Summers, E., Todd, S., & Van Parijs, S. M. Exploring movement patterns and changing distributions of baleen whales in the western North Atlantic using a decade of passive acoustic data. Global Change Biology, (2020): 1-30, doi:10.1111/gcb.15191.Six baleen whale species are found in the temperate western North Atlantic Ocean, with limited information existing on the distribution and movement patterns for most. There is mounting evidence of distributional shifts in many species, including marine mammals, likely because of climate‐driven changes in ocean temperature and circulation. Previous acoustic studies examined the occurrence of minke (Balaenoptera acutorostrata ) and North Atlantic right whales (NARW; Eubalaena glacialis ). This study assesses the acoustic presence of humpback (Megaptera novaeangliae ), sei (B. borealis ), fin (B. physalus ), and blue whales (B. musculus ) over a decade, based on daily detections of their vocalizations. Data collected from 2004 to 2014 on 281 bottom‐mounted recorders, totaling 35,033 days, were processed using automated detection software and screened for each species' presence. A published study on NARW acoustics revealed significant changes in occurrence patterns between the periods of 2004–2010 and 2011–2014; therefore, these same time periods were examined here. All four species were present from the Southeast United States to Greenland; humpback whales were also present in the Caribbean. All species occurred throughout all regions in the winter, suggesting that baleen whales are widely distributed during these months. Each of the species showed significant changes in acoustic occurrence after 2010. Similar to NARWs, sei whales had higher acoustic occurrence in mid‐Atlantic regions after 2010. Fin, blue, and sei whales were more frequently detected in the northern latitudes of the study area after 2010. Despite this general northward shift, all four species were detected less on the Scotian Shelf area after 2010, matching documented shifts in prey availability in this region. A decade of acoustic observations have shown important distributional changes over the range of baleen whales, mirroring known climatic shifts and identifying new habitats that will require further protection from anthropogenic threats like fixed fishing gear, shipping, and noise pollution.We thank Chris Pelkie, David Wiley, Michael Thompson, Chris Tessaglia‐Hymes, Eric Matzen, Chris Tremblay, Lance Garrison, Anurag Kumar, John Hildebrand, Lynne Hodge, Russell Charif, Kathleen Dudzinski, and Ann Warde for help with project planning, field work support, and data management. For all the support and advice, thanks to the NEFSC Protected Species Branch, especially the passive acoustics group, Josh Hatch, and Leah Crowe. We thank the field and crew teams on all the ships that helped in the numerous deployments and recoveries. This research was funded and supported by many organizations, specified by projects as follows: data recordings from region 1 were provided by K. Stafford (funding: National Science Foundation #NSF‐ARC 0532611). Region 2 data: D. K. Mellinger and S. Nieukirk, National Oceanic and Atmospheric Administration (NOAA) PMEL contribution #5055 (funding: NOAA and the Office of Naval Research #N00014–03–1–0099, NOAA #NA06OAR4600100, US Navy #N00244‐08‐1‐0029, N00244‐09‐1‐0079, and N00244‐10‐1‐0047). Region 3A data: D. Risch (funding: NOAA and Navy N45 programs). Region 3 data: H. Moors‐Murphy and Fisheries and Oceans Canada (2005–2014 data), and the Whitehead Lab of Dalhousie University (eastern Scotian Shelf data; logistical support by A. Cogswell, J. Bartholette, A. Hartling, and vessel CCGS Hudson crew). Emerald Basin and Roseway Basin Guardbuoy data, deployment, and funding: Akoostix Inc. Region 3 Emerald Bank and Roseway Basin 2004 data: D. K. Mellinger and S. Nieukirk, NOAA PMEL contribution #5055 (funding: NOAA). Region 4 data: S. Parks (funding: NOAA and Cornell University) and E. Summers, S. Todd, J. Bort Thornton, A. N. Rice, and C. W. Clark (funding: Maine Department of Marine Resources, NOAA #NA09NMF4520418, and #NA10NMF4520291). Region 5 data: S. M. Van Parijs, D. Cholewiak, L. Hatch, C. W. Clark, D. Risch, and D. Wiley (funding: National Oceanic Partnership Program (NOPP), NOAA, and Navy N45). Region 6 data: S. M. Van Parijs and D. Cholewiak (funding: Navy N45 and Bureau of Ocean and Energy Management (BOEM) Atlantic Marine Assessment Program for Protected Species [AMAPPS] program). Region 7 data: A. N. Rice, H. Klinck, A. Warde, B. Martin, J. Delarue, and S. Kraus (funding: New York State Department of Environmental Conservation, Massachusetts Clean Energy Center, and BOEM). Region 8 data: G. Buchanan, and K. Dudzinski (funding: New Jersey Department of Environmental Protection and the New Jersey Clean Energy Fund) and A. N. Rice, C. W. Clark, and H. Klinck (funding: Center for Conservation Bioacoustics at Cornell University and BOEM). Region 9 data: J. E. Stanistreet, J. Bell, D. P. Nowacek, A. J. Read, and S. M. Van Parijs (funding: NOAA and US Fleet Forces Command). Region 10 data: L. Garrison, M. Soldevilla, C. W. Clark, R. A. Chariff, A. N. Rice, H. Klinck, J. Bell, D. P. Nowacek, A. J. Read, J. Hildebrand, A. Kumar, L. Hodge, and J. E. Stanistreet (funding: US Fleet Forces Command, BOEM, NOAA, and NOPP). Region 11 data: C. Berchok as part of a collaborative project led by the Fundacion Dominicana de Estudios Marinos, Inc. (Dr. Idelisa Bonnelly de Calventi; funding: The Nature Conservancy [Elianny Dominguez]) and D. Risch (funding: World Wildlife Fund, NOAA, and Dutch Ministry of Economic Affairs)

Human Induced Pluripotent Stem Cells Differentiation into Oligodendrocyte Progenitors and Transplantation in a Rat Model of Optic Chiasm Demyelination

BACKGROUND: This study aims to differentiate human induced pluripotent stem cells (hiPSCs) into oligodendrocyte precursors and assess their recovery potential in a demyelinated optic chiasm model in rats. METHODOLOGY/PRINCIPAL FINDINGS: We generated a cell population of oligodendrocyte progenitors from hiPSCs by using embryoid body formation in a defined medium supplemented with a combination of factors, positive selection and mechanical enrichment. Real-time polymerase chain reaction and immunofluorescence analyses showed that stage-specific markers, Olig2, Sox10, NG2, PDGFRα, O4, A2B5, GalC, and MBP were expressed following the differentiation procedure, and enrichment of the oligodendrocyte lineage. These results are comparable with the expression of stage-specific markers in human embryonic stem cell-derived oligodendrocyte lineage cells. Transplantation of hiPSC-derived oligodendrocyte progenitors into the lysolecithin-induced demyelinated optic chiasm of the rat model resulted in recovery from symptoms, and integration and differentiation into oligodendrocytes were detected by immunohistofluorescence staining against PLP and MBP, and measurements of the visual evoked potentials. CONCLUSIONS/SIGNIFICANCE: These results showed that oligodendrocyte progenitors generated efficiently from hiPSCs can be used in future biomedical studies once safety issues have been overcome

Characterizing the Relative Contributions of Large Vessels to Total Ocean Noise Fields: A Case Study Using the Gerry E. Studds Stellwagen Bank National Marine Sanctuary

In 2006, we used the U.S. Coast Guard’s Automatic Identification System (AIS) to describe patterns of large commercial ship traffic within a U.S. National Marine Sanctuary located off the coast of Massachusetts. We found that 541 large commercial vessels transited the greater sanctuary 3413 times during the year. Cargo ships, tankers, and tug/tows constituted 78% of the vessels and 82% of the total transits. Cargo ships, tankers, and cruise ships predominantly used the designated Boston Traffic Separation Scheme, while tug/tow traffic was concentrated in the western and northern portions of the sanctuary. We combined AIS data with low-frequency acoustic data from an array of nine autonomous recording units analyzed for 2 months in 2006. Analysis of received sound levels (10–1000 Hz, root-mean-square pressure re 1 μPa ± SE) averaged 119.5 ± 0.3 dB at high-traffic locations. High-traffic locations experienced double the acoustic power of less trafficked locations for the majority of the time period analyzed. Average source level estimates (71–141 Hz, root-mean-square pressure re 1 μPa ± SE) for individual vessels ranged from 158 ± 2 dB (research vessel) to 186 ± 2 dB (oil tanker). Tankers were estimated to contribute 2 times more acoustic power to the region than cargo ships, and more than 100 times more than research vessels. Our results indicate that noise produced by large commercial vessels was at levels and within frequencies that warrant concern among managers regarding the ability of endangered whales to maintain acoustic contact within greater sanctuary waters

Isolation, whole-genome sequencing, and annotation of two antibiotic-producing and antibiotic-resistant bacteria, Pantoea rodasii RIT 836 and Pseudomonas endophytica RIT 838, collected from the environment.

Antimicrobial resistance (AMR) is a global threat to human health since infections caused by antimicrobial-resistant bacteria are life-threatening conditions with minimal treatment options. Bacteria become resistant when they develop the ability to overcome the compounds that are meant to kill them, i.e., antibiotics. The increasing number of resistant pathogens worldwide is contrasted by the slow progress in the discovery and production of new antibiotics. About 700,000 global deaths per year are estimated as a result of drug-resistant infections, which could escalate to nearly 10 million by 2050 if we fail to address the AMR challenge. In this study, we collected and isolated bacteria from the environment to screen for antibiotic resistance. We identified several bacteria that showed resistance to multiple clinically relevant antibiotics when tested in antibiotic susceptibility disk assays. We also found that two strains, identified as Pantoea rodasii RIT 836 and Pseudomonas endophytica RIT 838 via whole genome sequencing and annotation, produce bactericidal compounds against both Gram-positive and Gram-negative bacteria in disc-diffusion inhibitory assays. We mined the two strains' whole-genome sequences to gain more information and insights into the antibiotic resistance and production by these bacteria. Subsequently, we aim to isolate, identify, and further characterize the novel antibiotic compounds detected in our assays and bioinformatics analysis

Table_1_Comparing the underwater soundscape of the Hawaiian Islands Humpback Whale National Marine Sanctuary and potential influences of the COVID-19 pandemic.docx

Passive acoustic monitoring is an effective technique for long-term monitoring of the soundscape in marine protected areas. Ocean noise is a key concern for the U.S. Office of National Marine Sanctuaries and has been identified as a research priority. The Sanctuary Soundscape Monitoring Project (“SanctSound”) was implemented to support efforts to address ocean noise across seven U.S. sanctuaries using a comprehensive and standardized approach. In this study, acoustic recordings were collected in the Hawaiian Islands Humpback Whale National Marine Sanctuary during the humpback whale seasons (November-May) from 2018-2022. Data encompassed 14 deployments across four sites in the main Hawaiian Islands: Hawaiʻi, Maui, O’ahu, and Kauaʻi. The soundscape was dominated by biological sources, most prominently the seasonal detection of humpback whale song. Third octave level monthly medians ranged from 70.4-105 dB re 1 µPa across sites with distinct peaks from January to April particularly at both Hawaiʻi and Maui sites. Overall, we reported relatively low vessel detection rates, with Maui having the highest daily average of vessel detections (x = 19.16). No COVID-19 impact could be observed acoustically using soundscape metrics which was likely due to the dominance of humpback whale chorusing. However, vessel detections and AIS data revealed a reduction in vessel activity after the onset of the pandemic at the Maui and Hawaiʻi sites. This study demonstrates that standardized metrics are a useful tool for obtaining long-term, baseline soundscape levels to understand the various contributions to the underwater soundscape and potential changes within marine protected areas in Hawaiʻi.</p

Table_2_Comparing the underwater soundscape of the Hawaiian Islands Humpback Whale National Marine Sanctuary and potential influences of the COVID-19 pandemic.docx

Passive acoustic monitoring is an effective technique for long-term monitoring of the soundscape in marine protected areas. Ocean noise is a key concern for the U.S. Office of National Marine Sanctuaries and has been identified as a research priority. The Sanctuary Soundscape Monitoring Project (“SanctSound”) was implemented to support efforts to address ocean noise across seven U.S. sanctuaries using a comprehensive and standardized approach. In this study, acoustic recordings were collected in the Hawaiian Islands Humpback Whale National Marine Sanctuary during the humpback whale seasons (November-May) from 2018-2022. Data encompassed 14 deployments across four sites in the main Hawaiian Islands: Hawaiʻi, Maui, O’ahu, and Kauaʻi. The soundscape was dominated by biological sources, most prominently the seasonal detection of humpback whale song. Third octave level monthly medians ranged from 70.4-105 dB re 1 µPa across sites with distinct peaks from January to April particularly at both Hawaiʻi and Maui sites. Overall, we reported relatively low vessel detection rates, with Maui having the highest daily average of vessel detections (x = 19.16). No COVID-19 impact could be observed acoustically using soundscape metrics which was likely due to the dominance of humpback whale chorusing. However, vessel detections and AIS data revealed a reduction in vessel activity after the onset of the pandemic at the Maui and Hawaiʻi sites. This study demonstrates that standardized metrics are a useful tool for obtaining long-term, baseline soundscape levels to understand the various contributions to the underwater soundscape and potential changes within marine protected areas in Hawaiʻi.</p