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Nucleotide sequences of CsRV1 virus amplified from blue crabs (Callinectes sapidus) from coastal waters and estuaries in North and South America, including the Caribbean and Gulf of Mexico from 2006 to 2020
Full text linkDataset: CsRV1 virus genotypes across the Atlantic coast of N and S AmericaThis record contains nucleotide sequences of CsRV1 virus amplified from blue crabs (Callinectes sapidus) across the study region. RNA from crabs identified as infected using a sensitive Rt-qPCR assay was amplified using primers specific to segment and segment 9 of the virus genome.
A subset of CsRV1-positive RNA preparations were amplified using a full-genome amplification set of primers to amplify the entire CsRV1 genome. (http://primal.zibraproject.org; Quick et al. 2017).
The segment-specific data: seg9 (960 nt amplicon) and seg8 (807 nt amplicon) were trimmed and used to create maximum likelihood trees. Similarly, the full genome sequences were used for a maximum likelihood tree.
In total, 22 complete or near-complete genomes, 42 seg8 ORF sequences, and 96 seg9 ORF sequences of CsRV1 were collected from 15 geographic locations along the US Atlantic coast, Gulf of Mexico, Caribbean Sea and S. America between 2006 – 2021.
Sequence generation and tree building was accomplished by Mingli Zhao with input from coauthors Plough and Kough. Pairwise analyses and ML trees can be found in the Supplemental Materials of results publication Zhao et al. (2023). The sequences generated in this study are deposited in NCBI GenBank, with accession numbers OP067244-OP067635 and are accessible under BioProject PRJNA939818.
For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/890835NSF Division of Ocean Sciences (NSF OCE) OCE-1658466, NSF Division of Ocean Sciences (NSF OCE) OCE-1658396, NSF Division of Ocean Sciences (NSF OCE) OCE-165838
North Atlantic Right Whale Consortium 2015 Annual Report Card
Full text linkThe North Atlantic right whale (Eubalaena glacialis) remains one of the most endangered large whales in the world. Over the past two decades, there has been increasing interest in addressing the problems hampering the recovery of North Atlantic right whales by using innovative research techniques, new technologies, analyses of existing databases, and enhanced conservation and education strategies. This increased interest demanded better coordination and collaboration among all stakeholders to ensure that there was improved access to data, research efforts were not duplicative, and that findings were shared with all interested parties. The North Atlantic Right Whale Consortium, initially formed in 1986 by five research institutions to share data among themselves, was expanded in 1997 to address these greater needs. Currently, the Consortium membership is comprised of representatives from more than 100 entities including: research, academic, and conservation organizations; shipping and fishing industries; whale watching companies; technical experts; United States (U.S.) and Canadian Government agencies; and state authorities. North Atlantic Right Whale Consortium members agreed in 2004 that an annual “report card” on the status of right whales would be useful. This report card includes updates on the status of the cataloged population, mortalities and injury events, and a summary of management and research efforts that have occurred over the previous 12 months. The Board’s goal is to make public a summary of current research and management activities, as well as provide detailed recommendations for future activities. The Board views this report as a valuable asset in assessing the effects of research and management over time.Island Foundation; Conference Fee
North Atlantic Right Whale Consortium 2014 Annual Report Card
Full text linkThe North Atlantic right whale (Eubalaena glacialis) remains one of the most endangered large whales in the world. Over the past two decades, there has been increasing interest in addressing the problems hampering the recovery of North Atlantic right whales by using innovative research techniques, new technologies, analyses of existing databases, and enhanced conservation and education strategies. This increased interest demanded better coordination and collaboration among all stakeholders to ensure that there was improved access to data, research efforts were not duplicative, and that findings were shared with all interested parties. The North Atlantic Right Whale Consortium, initially formed in 1986 by five research institutions to share data among themselves, was expanded in 1997 to address these greater needs. Currently, the Consortium membership is comprised of representatives from more than 100 entities including: research, academic, and conservation organizations; shipping and fishing industries; whale watching companies; technical experts; United States (U.S.) and Canadian Government agencies; and state authorities. North Atlantic Right Whale Consortium members agreed in 2004 that an annual “report card” on the status of right whales would be useful. This report card includes updates on the status of the cataloged population, mortalities and injury events, and a summary of management and research efforts that have occurred over the previous 12 months. The Board’s goal is to make public a summary of current research and management activities, as well as provide detailed recommendations for future activities. The Board views this report as a valuable asset in assessing the effects of research and management over time.Island Foundation; Conference Fee
2022 Lidar summary data Nantucket
No full textThis zipped content contains Lidar summary data: Daily 10-minute average files from 53-200m amsl for 2022
Measurements of Kr/Ar and N2/Ar ratios in stored dissolved gas samples collected in 1981 through the Transient Tracers in the Ocean (TTO) program North Atlantic Survey (NAS)
Full text linkDataset: Elemental and isotopic noble gas ratios and N2/Ar from the North Atlantic: TTO dataThis dataset includes measurements of Kr/Ar and N2/Ar ratios in stored dissolved gas samples collected in 1981 through the Transient Tracers in the Ocean (TTO) program.
These data were used, along with new observations of heavy noble gas ratios (elemental and isotopic ratios) from the Bermuda Atlantic Time-series (BATS) on cruise 10391 (30 April 2022 - 05 May 2022), to model simulations of these tracers using the Transport Matrix Method (TMM). Together these new measurements and model simulations provide insight into physical processes governing gas exchange in the high-latitude regions of North Atlantic Deep Water formation, and a comparison of physical simulations of N2/Ar ratios to observations in TTO samples reveals excess N2 that arises from benthic denitrification in the deep North Atlantic.
For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/890427NSF Division of Ocean Sciences (NSF OCE) OCE-2122427, NSF Division of Ocean Sciences (NSF OCE) OCE-192391
Martha's Vineyard Coastal Observatory 2022
No full textMartha's Vineyard Coastal Observatory (MVCO) is a leading research and engineering facility operated by Woods Hole Oceanographic Institution. MVCO has been collecting ocean and atmospheric data at 3 sites on and near Martha's Vineyard since 2001. A meteorological mast (met mast) on South Beach in Edgartown, MA has collected atmospheric data since May 31 2001. An Air Sea Interaction Tower (ASIT) has been collecting atmospheric and subsurface oceanic data since August 5, 2004. A seafloor node (12m node) has been collecting oceanic data from the seafloor since June 14, 2001. This dataset encompasses the core data (wind speed and direction, air pressure, temperature and relative humidity, water temperature and salinity, and wave data) that has been collected during this period. To learn more about the facility and see additional data collected during short term deployments, visit the MVCO Website (https://mvco.whoi.edu/)
Exploring the protist microbiome: the diversity of bacterial communities associated with Arcella spp. (Tubulina: Amoebozoa)
Full text link© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gomaa, F., Utter, D. R., Loo, W., Lahr, D. J. G., & Cavanaugh, C. M. Exploring the protist microbiome: the diversity of bacterial communities associated with Arcella spp. (Tubulina: Amoebozoa). European Journal of Protistology, 82, (2022): 125861, https://doi.org/10.1016/j.ejop.2021.125861.Research on protist-bacteria interactions is increasingly relevant as these associations are now known to play important roles in ecosystem and human health. Free-living amoebae are abundant in all environments and are frequent hosts for bacterial endosymbionts including pathogenic bacteria. However, to date, only a small fraction of these symbionts have been identified, while the structure and composition of the total symbiotic bacterial communities still remains largely unknown. Here, we use the testate amoeba Arcella spp. as model organisms to investigate the specificity and diversity of Arcella-associated microbial communities. High-throughput amplicon sequencing from the V4 region of the 16S rRNA gene revealed high diversity in the bacterial communities associated with the wild Arcella spp. To investigate the specificity of the associated bacterial community with greater precision, we investigated the bacterial communities of two lab-cultured Arcella species, A. hemispherica and A. intermedia, grown in two different media types. Our results suggest that Arcella-bacteria associations are species-specific, and that the associated bacterial community of lab-cultured Arcella spp. remains distinct from that of the surrounding media. Further, each host Arcella species could be distinguished based on its bacterial composition. Our findings provide insight into the understanding of eukaryotic-bacterial symbiosis.This project was funded by National Science Foundation Postdoctoral Research Fellowship in Biology to F. Gomaa, Grant Number: PRFB1611514. Support was provided to D.R.U. from the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE1745303 to D.R.U and by Harvard University’s Department of Organismic and Evolutionary Biology program
Home sweet home: spatiotemporal distribution and site fidelity of the reef manta ray (Mobula alfredi) in Dungonab Bay, Sudan
Full text link© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Knochel, A. M., Hussey, N. E., Kessel, S. T., Braun, C. D., Cochran, J. E. M., Hill, G., Klaus, R., Checkchak, T., Elamin El Hassen, N. M., Younnis, M., & Berumen, M. L. Home sweet home: spatiotemporal distribution and site fidelity of the reef manta ray (Mobula alfredi) in Dungonab Bay, Sudan. Movement Ecology, 10(1), (2022): 22, https://doi.org/10.1186/s40462-022-00314-9.Background
Reef manta ray (Mobula alfredi) populations along the Northeastern African coastline are poorly studied. Identifying critical habitats for this species is essential for future research and conservation efforts. Dungonab Bay and Mukkawar Island National Park (DMNP), a component of a UNESCO World Heritage Site in Sudan, hosts the largest known M. alfredi aggregation in the Red Sea.
Methods
A total of 19 individuals were tagged using surgically implanted acoustic tags and tracked within DMNP on an array of 15 strategically placed acoustic receivers in addition to two offshore receivers. Two of these acoustically monitored M. alfredi were also equipped with satellite linked archival tags and one individual was fitted with a satellite transmitting tag. Together, these data are used to describe approximately two years of residency and seasonal shifts in habitat use.
Results
Tagged individuals were detected within the array on 96% of monitored days and recorded an average residence index of 0.39 across all receivers. Detections were recorded throughout the year, though some individuals were absent from the receiver array for weeks or months at a time, and generalized additive mixed models showed a clear seasonal pattern in presence with the highest probabilities of detection occurring in boreal fall. The models indicated that M. alfredi presence was highly correlated with increasing chlorophyll-a levels and weakly correlated with the full moon. Modeled biological factors, including sex and wingspan, had no influence on animal presence. Despite the high residency suggested by acoustic telemetry, satellite tag data and offshore acoustic detections in Sanganeb Atoll and Suedi Pass recorded individuals moving up to 125 km from the Bay. However, all these individuals were subsequently detected in the Bay, suggesting a strong degree of site fidelity at this location.
Conclusions
The current study adds to growing evidence that M. alfredi are highly resident and site-attached to coastal bays and lagoons but display seasonal shifts in habitat use that are likely driven by resource availability. This information can be used to assist in managing and supporting sustainable ecotourism within the DMNP, part of a recently designated UNESCO World Heritage Site.This research was supported by The Deep Aquarium (Grant # 00176; http://www.thedeep.co.uk) and The Darwin Initiative (Grant # 21–019; http://www.gov.uk/government/groups/the-darwin-initiative) in addition to baseline funding from MLB
Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization
Full text link© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schmidbaur, H., Kawaguchi, A., Clarence, T., Fu, X., Hoang, O. P., Zimmermann, B., Ritschard, E. A., Weissenbacher, A., Foster, J. S., Nyholm, S., Bates, P. A., Albertin, C. B., Tanaka, E., & Simakov, O. Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization. Nature Communications, 13(1), (2022): 2172, https://doi.org/10.1038/s41467-022-29694-7.Coleoid cephalopods (squid, cuttlefish, octopus) have the largest nervous system among invertebrates that together with many lineage-specific morphological traits enables complex behaviors. The genomic basis underlying these innovations remains unknown. Using comparative and functional genomics in the model squid Euprymna scolopes, we reveal the unique genomic, topological, and regulatory organization of cephalopod genomes. We show that coleoid cephalopod genomes have been extensively restructured compared to other animals, leading to the emergence of hundreds of tightly linked and evolutionary unique gene clusters (microsyntenies). Such novel microsyntenies correspond to topological compartments with a distinct regulatory structure and contribute to complex expression patterns. In particular, we identify a set of microsyntenies associated with cephalopod innovations (MACIs) broadly enriched in cephalopod nervous system expression. We posit that the emergence of MACIs was instrumental to cephalopod nervous system evolution and propose that microsyntenic profiling will be central to understanding cephalopod innovations.H.S., O.P.H., E.R., and O.S. were supported by the Austrian Science Fund (FWF) grant P30686-B29. O.S. was supported by Whitman Center Early Career Fellowship (Frank R. Lillie Quasi-Endowment Fund, L. & A. Colwin Summer Research Fellowship, Bell Research Award in Tissue Engineering). H.S. was supported by the short-term grant abroad (KWA) of the University of Vienna. H.S. and O.S. were supported by the University of Chicago/Vienna Strategic Partnership Programme Mobility Grant. A.K. was supported by the JSPS Postdoctoral Fellowship for Overseas Researchers program from Japan. C.B.A. was supported by the Hibbitt Early Career Fellowship. Eggs and paralarvae of E. scolopes were generated in part by support by the NASA Space Biology 80NSSC18K1465 awarded to J.S.F. S.V.N. was supported by the National Science Foundation IOS-1557914. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC0001003), the UK Medical Research Council (FC001003), and the Wellcome Trust (FC001003)
Turbulence-induced bubble nucleation in hydrothermal fluids beneath Yellowstone Lake
Full text link© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Caudron, C., Vandemeulebrouck, J., & Sohn, R. A. Turbulence-induced bubble nucleation in hydrothermal fluids beneath Yellowstone Lake. Communications Earth & Environment, 3(1), (2022): 103, https://doi.org/10.1038/s43247-022-00417-6.Volcanic systems generate large amounts of gas, and understanding gas fluxes is a fundamental aspect of volcanology and hazard mitigation. Volcanic gases can be challenging to measure, but acoustic methods hold promise in underwater environments because gas bubbles are powerful sound sources. We deployed an acoustic system to study the nature of gas discharge at a large (~30 MW) thermal field on the floor of Yellowstone Lake, which has experienced numerous hydrothermal explosions since the last glaciation (~13.4 ka). We find that small (<10 Pa) turbulent flow instabilities trigger the nucleation of CO2 bubbles in the saturated fluids. The observation of CO2 bubbles nucleating in hydrothermal fluids due to small pressure perturbations informs our understanding of hydrothermal explosions in Yellowstone Lake, and demonstrates that acoustic data in underwater environments can provide insight into the stability of gas-rich systems, as well as gas fluxes.This research was supported by the National Science Foundation grant EAR-1516361 to R.A.S. All work in Yellowstone National Park was completed under an authorized research permit (YELL-2018-SCI-7018). We also acknowledge the IRGA 2021 Volquan project (funded by Université Grenoble Alpes) and Thomas Jefferson Fund Face Foundation (project TJF20_009 ‘Quantifying underwater volcano degassing using novel seismo-acoustic approaches’)