ALBERT

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cochran, J. E. M., Braun, C. D., Cagua, E. F., Campbell, M. F., Hardenstine, R. S., Kattan, A., Priest, M. A., Sinclair-Taylor, T. H., Skomal, G. B., Sultan, S., Sun, L., Thorrold, S. R., & Berumen, M. L. Multi-method assessment of whale shark (Rhincodon typus) residency, distribution, and dispersal behavior at an aggregation site in the Red Sea. Plos One, 14(9), (2019): e0222285, doi:10.1371/journal.pone.0222285.

Description: Whale sharks (Rhincodon typus) are typically dispersed throughout their circumtropical range, but the species is also known to aggregate in specific coastal areas. Accurate site descriptions associated with these aggregations are essential for the conservation of R. typus, an Endangered species. Although aggregations have become valuable hubs for research, most site descriptions rely heavily on sightings data. In the present study, visual census, passive acoustic monitoring, and long range satellite telemetry were combined to track the movements of R. typus from Shib Habil, a reef-associated aggregation site in the Red Sea. An array of 63 receiver stations was used to record the presence of 84 acoustically tagged sharks (35 females, 37 males, 12 undetermined) from April 2010 to May 2016. Over the same period, identification photos were taken for 76 of these tagged individuals and 38 were fitted with satellite transmitters. In total of 37,461 acoustic detections, 210 visual encounters, and 33 satellite tracks were analyzed to describe the sharks’ movement ecology. The results demonstrate that the aggregation is seasonal, mostly concentrated on the exposed side of Shib Habil, and seems to attract sharks of both sexes in roughly equal numbers. The combined methodologies also tracked 15 interannual homing-migrations, demonstrating that many sharks leave the area before returning in later years. When compared to acoustic studies from other aggregations, these results demonstrate that R. typus exhibits diverse, site-specific ecologies across its range. Sightings-independent data from acoustic telemetry and other sources are an effective means of validating more common visual surveys.

Description: Financial support was provided in part by KAUST baseline research funds (to MLB), KAUST award nos. USA00002 and KSA 00011 (to SRT), and the U.S. National Science Foundation (OCE 0825148 to SRT and GBS).

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zeigler, S. L., Gutierrez, B. T., Sturdivant, E. J., Catlin, D. H., Fraser, J. D., Hecht, A., Karpanty, S. M., Plant, N. G., & Thieler, E. R. Using a Bayesian network to understand the importance of coastal storms and undeveloped landscapes for the creation and maintenance of early successional habitat. Plos One, 14(7), (2019): e0209986, doi:10.1371/journal.pone.0209986.

Description: Coastal storms have consequences for human lives and infrastructure but also create important early successional habitats for myriad species. For example, storm-induced overwash creates nesting habitat for shorebirds like piping plovers (Charadrius melodus). We examined how piping plover habitat extent and location changed on barrier islands in New York, New Jersey, and Virginia after Hurricane Sandy made landfall following the 2012 breeding season. We modeled nesting habitat using a nest presence/absence dataset that included characterizations of coastal morphology and vegetation. Using a Bayesian network, we predicted nesting habitat for each study site for the years 2010/2011, 2012, and 2014/2015 based on remotely sensed spatial datasets (e.g., lidar, orthophotos). We found that Hurricane Sandy increased piping plover habitat by 9 to 300% at 4 of 5 study sites but that one site saw a decrease in habitat by 27%. The amount, location, and longevity of new habitat appeared to be influenced by the level of human development at each site. At three of the five sites, the amount of habitat created and the time new habitat persisted were inversely related to the amount of development. Furthermore, the proportion of new habitat created in high-quality overwash was inversely related to the level of development on study areas, from 17% of all new habitat in overwash at one of the most densely developed sites to 80% of all new habitat at an undeveloped site. We also show that piping plovers exploited new habitat after the storm, with 14–57% of all nests located in newly created habitat in the 2013 breeding season. Our results quantify the importance of storms in creating and maintaining coastal habitats for beach-nesting species like piping plovers, and these results suggest a negative correlation between human development and beneficial ecological impacts of these natural disturbances.

Description: Funding for this work was provided through a U.S. Geological Survey Mendenhall Post-Doctoral Fellowship awarded to S. Zeigler, with funding for this fellowship made through a grant to E.R. Thieler from the North Atlantic Landscape Conservation Cooperative. Funders did not play a role in study design, data collection or analysis, decision to publish, or preparation of the manuscript.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lemkau, K. L., Reddy, C. M., Carmichael, C. A., Aeppli, C., Swarthout, R. F., & White, H. K. Hurricane Isaac brings more than oil ashore: Characteristics of beach deposits following the Deepwater Horizon spill. Plos One, 14(3), (2019):e0213464, doi:10.1371/journal.pone.0213464.

Description: Prior to Hurricane Isaac making landfall along the Gulf of Mexico coast in August 2012, local and state officials were concerned that the hurricane would mobilize submerged oiled-materials from the Deepwater Horizon (DWH) spill. In this study, we investigated materials washed ashore following the hurricane to determine if it affected the chemical composition or density of oil-containing sand patties regularly found on Gulf Coast beaches. While small changes in sand patty density were observed in samples collected before and after the hurricane, these variations appear to have been driven by differences in sampling location and not linked to the passing of Hurricane Isaac. Visual and chemical analysis of sand patties confirmed that the contents was consistent with oil from the Macondo well. Petroleum hydrocarbon signatures of samples collected before and after the hurricane showed no notable changes. In the days following Hurricane Isaac, dark-colored mats were also found on the beach in Fort Morgan, AL, and community reports speculated that these mats contained oil from the DWH spill. Chemical analysis of these mat samples identified n-alkanes but no other petroleum hydrocarbons. Bulk and δ13C organic carbon analyses indicated mat samples were comprised of marshland peat and not related to the DWH spill. This research indicates that Hurricane Isaac did not result in a notable change the composition of oil delivered to beaches at the investigated field sites. This study underscores the need for improved communications with interested stakeholders regarding how to differentiate oiled from non-oiled materials. This is especially important given the high cost of removing oiled debris and the increasing likelihood of false positives as oiled-materials washing ashore from a spill become less abundant over time.

Description: The authors wish to acknowledge support for this project from the Gulf of Mexico Research Initiative (RFP-V), the Deep-C Consortium (SA 16-30), NSF (OCE-1333148) awarded to CMR, and a Gulf Research Program Early-Career Research Fellowship to HKW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Thomas, F., Morris, J. T., Wigand, C., & Sievert, S. M. Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities. Plos One, 14(4), (2019):e0215767, doi:10.1371/journal.pone.0215767.

Description: Coastal climate adaptation strategies are needed to build salt marsh resiliency and maintain critical ecosystem services in response to impacts caused by climate change. Although resident microbial communities perform crucial biogeochemical cycles for salt marsh functioning, their response to restoration practices is still understudied. One promising restoration strategy is the placement of sand or sediment onto the marsh platform to increase marsh resiliency. A previous study examined the above- and below-ground structure, soil carbon dioxide emissions, and pore water constituents in Spartina alterniflora-vegetated natural marsh sediments and sand-amended sediments at varying inundation regimes. Here, we analyzed samples from the same experiment to test the effect of sand-amendments on the microbial communities after 5 months. Along with the previously observed changes in biogeochemistry, sand amendments drastically modified the bacterial communities, decreasing richness and diversity. The dominant sulfur-cycling bacterial community found in natural sediments was replaced by one dominated by iron oxidizers and aerobic heterotrophs, the abundance of which correlated with higher CO2-flux. In particular, the relative abundance of iron-oxidizing Zetaproteobacteria increased in the sand-amended sediments, possibly contributing to acidification by the formation of iron oxyhydroxides. Our data suggest that the bacterial community structure can equilibrate if the inundation regime is maintained within the optimal range for S. alterniflora. While long-term effects of changes in bacterial community on the growth of S. alterniflora are not clear, our results suggest that analyzing the microbial community composition could be a useful tool to monitor climate adaptation and restoration efforts.

Description: This work was supported by NSF grants DEB-1050557 (SMS) and OCE-1637630 (JM), and WHOI Investment in Science Funds (SMS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Radice, V. Z., Brett, M. T., Fry, B., Fox, M. D., Hoegh-Guldberg, O., & Dove, S. G. Evaluating coral trophic strategies using fatty acid composition and indices. Plos One, 14(9), (2019): e0222327, doi:10.1371/journal.pone.0222327.

Description: The ecological success of shallow water reef-building corals has been linked to the symbiosis between the coral host and its dinoflagellate symbionts (herein ‘symbionts’). As mixotrophs, symbiotic corals depend on nutrients 1) transferred from their photosynthetic symbionts (autotrophy) and 2) acquired by host feeding on particulate organic resources (heterotrophy). However, coral species differ in the extent to which they depend on heterotrophy for nutrition and these differences are typically poorly defined. Here, a multi-tracer fatty acid approach was used to evaluate the trophic strategies of three species of common reef-building coral (Galaxea fascicularis, Pachyseris speciosa, and Pocillopora verrucosa) whose trophic strategies had previously been identified using carbon stable isotopes. The composition and various indices of fatty acids were compared to examine the relative contribution of symbiont autotrophy and host heterotrophy in coral energy acquisition. A linear discriminant analysis (LDA) was used to estimate the contribution of polyunsaturated fatty acids (PUFA) derived from various potential sources to the coral hosts. The total fatty acid composition and fatty acid indices revealed differences between the more heterotrophic (P. verrucosa) and more autotrophic (P. speciosa) coral hosts, with the coral host G. fascicularis showing overlap with the other two species and greater variability overall. For the more heterotrophic P. verrucosa, the fatty acid indices and LDA results both indicated a greater proportion of copepod-derived fatty acids compared to the other coral species. Overall, the LDA estimated that PUFA derived from particulate resources (e.g., copepods and diatoms) comprised a greater proportion of coral host PUFA in contrast to the lower proportion of symbiont-derived PUFA. These estimates provide insight into the importance of heterotrophy in coral nutrition, especially in productive reef systems. The study supports carbon stable isotope results and demonstrates the utility of fatty acid analyses for exploring the trophic strategies of reef-building corals.

Description: This study was made possible by funding from the XL Catlin Seaview Survey (OHG and VZR; http://catlinseaviewsurvey.com/), Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies (CE140100020; SD and OHG; https://www.coralcoe.org.au/), an ARC Laureate Fellowship (FL120100066; OHG; https://www.arc.gov.au), the University of Queensland Research Training Scholarship (VZR; https://www.uq.edu.au/), and the University of Washington Dale A. Carlson Endowed Faculty Support Fund (MTB and VZR; https://www.washington.edu/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Description: © The Authors, 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Rogers, K. L., Bosman, S. H., Lardie-Gaylord, M., McNichol, A., Rosenheim, B. E., Montoya, J. P., & Chanton, J. P. (2019). Petrocarbon evolution: Ramped pyrolysis/oxidation and isotopic studies of contaminated oil sediments from the Deepwater Horizon oil spill in the Gulf of Mexico. PLoS One, 14(2), (2019):e0212433, doi:10.1371/journal.pone.0212433.

Description: Hydrocarbons released during the Deepwater Horizon (DWH) oil spill weathered due to exposure to oxygen, light, and microbes. During weathering, the hydrocarbons’ reactivity and lability was altered, but it remained identifiable as “petrocarbon” due to its retention of the distinctive isotope signatures (14C and 13C) of petroleum. Relative to the initial estimates of the quantity of oil-residue deposited in Gulf sediments based on 2010–2011 data, the overall coverage and quantity of the fossil carbon on the seafloor has been attenuated. To analyze recovery of oil contaminated deep-sea sediments in the northern Gulf of Mexico we tracked the carbon isotopic composition (13C and 14C, radiocarbon) of bulk sedimentary organic carbon through time at 4 sites. Using ramped pyrolysis/oxidation, we determined the thermochemical stability of sediment organic matter at 5 sites, two of these in time series. There were clear differences between crude oil (which decomposed at a lower temperature during ramped oxidation), natural hydrocarbon seep sediment (decomposing at a higher temperature; Δ14C = -912‰) and our control site (decomposing at a moderate temperature; Δ14C = -189‰), in both the stability (ability to withstand ramped temperatures in oxic conditions) and carbon isotope signatures. We observed recovery toward our control site bulk Δ14C composition at sites further from the wellhead in ~4 years, whereas sites in closer proximity had longer recovery times. The thermographs also indicated temporal changes in the composition of contaminated sediment, with shifts towards higher temperature CO2 evolution over time at a site near the wellhead, and loss of higher temperature CO2 peaks at a more distant site.

Description: This research was made possible by grants from The Gulf of Mexico Research Initiative through its consortiums: Ecosystem Impacts of Oil & Gas Inputs to the Gulf (ECOGIG), The Center for the Integrated Modeling and Analysis of the Gulf Ecosystem (C-Image), and Deep Sea to Coast Connectivity in the Eastern Gulf of Mexico (Deep-C) and the Resuspension, Redistribution and Deposition of DWH Recalcitrant Material (Re-Direct) project. This is ECOGIG Contribution # 521. Funding was also provided by the National Ocean Sciences Accelerator Mass Spectrometry Facility (NOSAMS) Graduate Student Internship Program (NSF OCE-1239667). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 14(1), (2019):e0204193, doi: 10.1371/journal.pone.0204193.

Description: The resilience of regeneration in vertebrates is not very well understood. Yet understanding if tissues can regenerate after repeated insults, and identifying limitations, is important for elucidating the underlying mechanisms of tissue plasticity. This is particularly challenging in tissues, such as the nervous system, which possess a large number of terminally differentiated cells and often exhibit limited regeneration in the first place. However, unlike mammals, which exhibit very limited regeneration of spinal cord tissues, many non-mammalian vertebrates, including lampreys, bony fishes, amphibians, and reptiles, regenerate their spinal cords and functionally recover even after a complete spinal cord transection. It is well established that lampreys undergo full functional recovery of swimming behaviors after a single spinal cord transection, which is accompanied by tissue repair at the lesion site, as well as axon and synapse regeneration. Here we begin to explore the resilience of spinal cord regeneration in lampreys after a second spinal transection (re-transection). We report that by all functional and anatomical measures tested, lampreys regenerate after spinal re-transection just as robustly as after single transections. Recovery of swimming, synapse and cytoskeletal distributions, axon regeneration, and neuronal survival were nearly identical after spinal transection or re-transection. Only minor differences in tissue repair at the lesion site were observed in re-transected spinal cords. Thus, regenerative potential in the lamprey spinal cord is largely unaffected by spinal re-transection, indicating a greater persistent regenerative potential than exists in some other highly regenerative models. These findings establish a new path for uncovering pro-regenerative targets that could be deployed in non-regenerative conditions.

Description: The authors would like to thank Dr. Cristina Roman-Vendrell and Louie Kerr, Director of the Central Microscopy Facility at the MBL, for technical support. We also thank Dr. Juan Diaz-Quiroz for helpful comments on the manuscript. EG was supported in part by an NSF REU Award (#1659604: Biological Discovery in Woods Hole at the Marine Biological Laboratory).

Description: Atlantic cod (Gadus morhua) is a species of great ecological and economical importance in the Baltic Sea. Here, two genetically differentiated stocks, the western and the eastern Baltic cod, display substantial mechanical mixing, hampering our understanding of cod ecology and impeding stock assessments and management. Based on whole-genome re-sequencing data from reference samples obtained from the study area, we designed two different panels of Single Nucleotide Polymorphisms markers (SNPs), which take into account the exceptional genome architecture of cod. A minimum panel of 20 diagnostic SNPs and an extended panel (20 diagnostic and 18 biologically informative SNPs, 38 in total) were developed and validated to distinguish unambiguously between the western and the eastern Baltic cod stocks and to enable studies of local adaptation to the specific environment in the Baltic Sea, respectively. We tested both panels on cod sampled from the southern Baltic Sea (n = 603) caught in 2015 and 2016. Genotyping results showed that catches from the mixing zone in the Arkona Sea, were composed of similar proportions of individuals of the western and the eastern stock. Catches from adjacent areas to the east, the Bornholm Basin and Gdańsk Deep, were exclusively composed of eastern Baltic cod, whereas catches from adjacent western areas (Belt Sea and Öresund) were composed of western Baltic cod. Interestingly, the two Baltic cod stocks showed strong genetic differences at loci associated with life-history trait candidate genes, highlighting the species’ potential for ecological adaptation even at small geographical scales. The minimum and the extended panel of SNP markers presented in this study provide powerful tools for future applications in research and fisheries management to further illuminate the mixing dynamics of cod in the Baltic Sea and to better understand Baltic cod ecology.

Description: We present the first study to examine the year-round distribution, activity patterns, and habitat use of one of New Zealand's most common seabirds, the fluttering shearwater (Puffinus gavia). Seven adults from Burgess Island, in the Hauraki Gulf, and one individual from Long Island, in the Marlborough Sounds, were successfully tracked with combined light-saltwater immersion loggers for one to three years. Our tracking data confirms that fluttering shearwaters employ different overwintering dispersal strategies, where three out of eight individuals, for at least one of the three years when they were being tracked, crossed the Tasman Sea to forage over coastal waters along eastern Tasmania and southeastern Australia. Resident birds stayed confined to waters of northern and central New Zealand year-round. Although birds frequently foraged over pelagic shelf waters, the majority of tracking locations were found over shallow waters close to the coast. All birds foraged predominantly in daylight and frequently visited the colony at night throughout the year. We found no significant inter-seasonal differences in the activity patterns, or between migratory and resident individuals. Although further studies of inter-colony variation in different age groups will be necessary, this study presents novel insights into year-round distribution, activity patterns and habitat use of the fluttering shearwater, which provide valuable baseline information for conservation as well as for further ecological studies.

Description: The evaluation of large amounts of digital image data is of growing importance for biology, including for the exploration and monitoring of marine habitats. However, only a tiny percentage of the image data collected is evaluated by marine biologists who manually interpret and annotate the image contents, which can be slow and laborious. In order to overcome the bottleneck in image annotation, two strategies are increasingly proposed: “citizen science” and “machine learning”. In this study, we investigated how the combination of citizen science, to detect objects, and machine learning, to classify megafauna, could be used to automate annotation of underwater images. For this purpose, multiple large data sets of citizen science annotations with different degrees of common errors and inaccuracies observed in citizen science data were simulated by modifying “gold standard” annotations done by an experienced marine biologist. The parameters of the simulation were determined on the basis of two citizen science experiments. It allowed us to analyze the relationship between the outcome of a citizen science study and the quality of the classifications of a deep learning megafauna classifier. The results show great potential for combining citizen science with machine learning, provided that the participants are informed precisely about the annotation protocol. Inaccuracies in the position of the annotation had the most substantial influence on the classification accuracy, whereas the size of the marking and false positive detections had a smaller influence.