An overview of marine biodiversity in United States waters

Significant challenges to the sustainability of the California coast considering climate change

Climate change is an existential threat to the environmental and socioeconomic sustainability of the coastal zone and impacts will be complex and widespread. Evidence from California and across the United States shows that climate change is impacting coastal communities and challenging managers with a plethora of stressors already present. Widespread action could be taken that would sustain California's coastal ecosystems and communities. In this perspective, we highlight the main threat to coastal sustainability: the compound effects of episodic events amplified with ongoing climate change, which will present unprecedented challenges to the state. We present two key challenges for California's sustainability in the coastal zone: 1) accelerating sea-level rise combined with storm impacts, and 2) continued warming of the oceans and marine heatwaves. Cascading effects from these types of compounding events will occur within the context of an already stressed system that has experienced extensive alterations due to intensive development, resource extraction and harvesting, spatial containment, and other human use pressures. There are critical components that could be used to address these immediate concerns, including comanagement strategies that include diverse groups and organizations, strategic planning integrated across large areas, rapid implementation of solutions, and a cohesive and policy relevant research agenda for the California coast. Much of this has been started in the state, but the scale could be increased, and timelines accelerated. The ideas and information presented here are intended to help expand discussions to sharpen the focus on how to encourage sustainability of California's iconic coastal region.

Biotic assemblages of gelatinous zooplankton in the Gulf of Mexico and adjacent waters: An evolutionary biogeographic approach

Gelatinous zooplankton constitutes a polyphyletic group with a convergent evolutionary history and poorly known biogeographical patterns. In the Gulf of Mexico, a region with complex geological, hydrological, and biotic histories, the study of this group has been limited to taxonomical and ecological aspects. In this study, we implemented a track analysis to identify distributional patterns of gelatinous zooplankton in the Gulf of Mexico and adjacent waters based on a dataset of 6067 occurrence records corresponding to Hydrozoa, Scyphozoa, Cubozoa, Ctenophora, Chaetognatha, Thaliacea, and Appendicularia. Information was compiled from the Global Biodiversity Facility Information (GBIF) and Ocean Biodiversity Information System (OBIS) databases and peer-reviewed literature. Individual tracks were constructed by joining the minimum distance between the occurrence localities of each taxon using a minimum spanning tree algorithm. We identified generalized tracks using parsimony analysis of endemicity with progressive character elimination (PAE-PCE). The areas where different generalized tracks overlapped were considered to represent panbiogeographical nodes. Seven generalized tracks (two with nested patterns) and six panbiogeographical nodes were recognized, mainly in neritic zones. The distributional patterns of gelatinous zooplankton allowed us to identify four biogeographic areas, supporting previously proposed biogeographic schemes. Gelatinous zooplankton in the Gulf of Mexico showed a convergent spatial distribution that can be explained by vicariant and dispersal events. The historical biogeography of the gelatinous biotas of the Gulf of Mexico has been little studied compared to ecological approaches, and the lack of integrative studies considering historical patterns is evident. This type of research is fundamental to understanding the evolutionary history of natural resources from a spatial perspective, identifying sites of biodiversity and endemism, and establishing a biogeographic baseline of the region for further studies.

Seasonality and relative abundance within an elasmobranch assemblage near a major biogeographic divide

Nearshore waters are utilized by elasmobranchs in various ways, including foraging, reproduction, and migration. Multiple elasmobranch species have been previously documented in the nearshore waters of North Carolina, USA, which has a biogeographic break at Cape Hatteras on the Atlantic coast. However, comprehensive understanding of the elasmobranch community in this region is still lacking. Monthly year-round trawling conducted along two ocean transects (near Cape Lookout and Masonboro Inlet in 5 to 18 m depth) in Onslow Bay, North Carolina provided the opportunity to examine the dynamics and seasonal patterns of this community using a multivariate approach, including permutational multivariate analysis of variance and nonparametric BIO-ENV analysis. From November 2004 to April 2008, 21,149 elasmobranchs comprised of 20 species were caught, dominated by spiny dogfish (Squalus acanthias) and clearnose skate (Rostroraja eglanteria). All species exhibited seasonal variation in abundance, but several key species contributed the most to seasonal differences in species composition within each transect. Spiny dogfish was most abundant in the winter at both locations, comprised mainly of mature females. Although clearnose skate was caught in all seasons, the species was most abundant during the spring and fall. Atlantic sharpnose (Rhizoprionodon terraenovae) was one of the most abundant species in the summer, and two distinct size cohorts were documented. Temperature appeared to be the main abiotic factor driving the community assemblage. The extensive year-round sampling provided the ability to better understand the dramatic seasonal variation in species composition and provides new information on the relative abundance of several understudied elasmobranch species that may be of significant ecological importance. Our results underscore the importance of inner continental shelf waters as important elasmobranch habitat and provide baseline data to examine for future shifts in timing and community structure at the northern portion of the biogeographic break at Cape Hatteras.

A macroplastic vulnerability index for marine mammals, seabirds, and sea turtles in Hawai'i

Plastic pollution is having devastating consequences for marine organisms across the planet. However, the population level effects of macroplastic pollution remain difficult and costly to quantify. As a result, there is a need for alternative approaches to evaluate species risk to plastic pollution and inform management needs. We apply a trait-based framework for macroplastic pollution to develop a relative vulnerability index-informed by three dimensions: likelihood of exposure, species' sensitivity, and population resilience-for marine mammals, seabirds, and sea turtles found in Hawai'i. This index ranks 63 study species based on their population level vulnerability to macroplastic pollution, with the highest scoring species being the most vulnerable. Our results indicate that ducks, waders, and noddies with large populations were the least vulnerable to macroplastics, while the most vulnerable were the Hawaiian monk seal, sea turtles, baleen whales, and some albatross and petrel species. This index can inform species in need of population monitoring in Hawai'i, and direct other management priorities (e.g., locations for clean-ups or booms). More broadly, this work exemplifies the value of qualitative risk assessment approaches for better understanding the population level effects of macroplastic pollution and showcases how vulnerability indices can be used to inform management priorities.

Discovering marine biodiversity in the 21st century

We review the current knowledge of the biodiversity of the ocean as well as the levels of decline and threat for species and habitats. The lack of understanding of the distribution of life in the ocean is identified as a significant barrier to restoring its biodiversity and health. We explore why the science of taxonomy has failed to deliver knowledge of what species are present in the ocean, how they are distributed and how they are responding to global and regional to local anthropogenic pressures. This failure prevents nations from meeting their international commitments to conserve marine biodiversity with the results that investment in taxonomy has declined in many countries. We explore a range of new technologies and approaches for discovery of marine species and their detection and monitoring. These include: imaging methods, molecular approaches, active and passive acoustics, the use of interconnected databases and citizen science. Whilst no one method is suitable for discovering or detecting all groups of organisms many are complementary and have been combined to give a more complete picture of biodiversity in marine ecosystems. We conclude that integrated approaches represent the best way forwards for accelerating species discovery, description and biodiversity assessment. Examples of integrated taxonomic approaches are identified from terrestrial ecosystems. Such integrated taxonomic approaches require the adoption of cybertaxonomy approaches and will be boosted by new autonomous sampling platforms and development of machine-speed exchange of digital information between databases.

Ecological succession of the sponge cryptofauna in Hawaiian reefs add new insights to detritus production by pioneering species

Successional theory proposes that fast growing and well dispersed opportunistic species are the first to occupy available space. However, these pioneering species have relatively short life cycles and are eventually outcompeted by species that tend to be longer-lived and have lower dispersal capabilities. Using Autonomous Reef Monitoring Structures (ARMS) as standardized habitats, we examine the assembly and stages of ecological succession among sponge species with distinctive life history traits and physiologies found on cryptic coral reef habitats of Kāneʻohe Bay, Hawaiʻi. Sponge recruitment was monitored bimonthly over 2 years on ARMS deployed within a natural coral reef habitat resembling the surrounding climax community and on ARMS placed in unestablished mesocosms receiving unfiltered seawater directly from the natural reef deployment site. Fast growing haplosclerid and calcareous sponges initially recruited to and dominated the mesocosm ARMS. In contrast, only slow growing long-lived species initially recruited to the reef ARMS, suggesting that despite available space, the stage of ecological succession in the surrounding habitat influences sponge community development in uninhabited space. Sponge composition and diversity between early summer and winter months within mesocosm ARMS shifted significantly as the initially recruited short-lived calcareous and haplosclerid species initially recruit and then died off. The particulate organic carbon contribution of dead sponge tissue from this high degree of competition-free community turnover suggests a possible new component to the sponge loop hypothesis which remains to be tested among these pioneering species. This source of detritus could be significant in early community development of young coastal habitats but less so on established coral reefs where the community is dominated by long-lived colonial sponges.

Phenolic fingerprints of the Pacific seagrass Phyllospadixtorreyi - Structural characterization and quantification of undescribed flavonoid sulfates

Four undescribed flavonoid sulfates were isolated from Phyllospadix torreyi S. Watson foliar tissue. In addition, nine known flavonoid sulfates and three phenolic acids were isolated from the same extract, of which seven had never been reported for the genus Phyllospadix. Structural elucidation of individual phenolics was assigned using complementary informations from their spectral evidence (HPLC-DAD, LC-MS, NMR, and UV) and chemical behavior. The inter-annual variation in phenolic concentrations was determined by quantitative HPLC-DAD over a three-year period. The results showed a relative constancy of phenolic content over time and the high prevalence of flavonoid disulfates (70-90% of the total flavonoids detected). All samples were found dominated by the unreported nepetin 7, 3'-disulfate and 5-methoxyluteolin 7, 3'-disulfate, followed by luteolin 7, 3'-disulfate. Considering the economic potential of flavonoid sulfates in the pharmaceutical and nutraceutical segments, a sample of detrital leaves was also analyzed. The same phenolic pattern was found and the concentration of the individuals, although lower than in fresh material, makes this abundant biomass of interest for dietary and pharmaceutical applications.

Atrous Pyramid GAN Segmentation Network for Fish Images with High Performance

With the development of computer science technology, theory and method of image segmentation are widely used in fish discrimination, which plays an important role in improving the efficiency of fisheries sorting and biodiversity studying. However, the existing methods of fish images segmentation are less accurate and inefficient, which is worthy of in-depth exploration. Therefore, this paper proposes an atrous pyramid GAN segmentation network aimed at increasing accuracy and efficiency. This paper introduces an atrous pyramid structure, and the GAN module is added before the CNN backbone in order to augment the dataset. The Atrous pyramid structure first fuses the input and output of the dilated convolutional layer with a small sampling rate and then feeds the fused features into the subsequent dilated convolutional layer with a large sampling rate to obtain dense multiscale contextual information. Thus, by capturing richer contextual information, this structure improves the accuracy of segmentation results. In addition to the aforementioned innovation, various data enhancement methods, such as MixUp, Mosaic, CutMix, and CutOut, are used in this paper to enhance the model’s robustness. This paper also improves the loss function and uses the label smoothing method to prevent model overfitting. The improvement is also tested by extensive ablation experiments. As a result, our model’s F1-score, GA, and MIoU were tested on the validation dataset, reaching 0.961, 0.981, and 0.973, respectively. This experimental result demonstrates that the proposed model outperforms all the other contrast models. Moreover, in order to accelerate the deployment of the encapsulated model on hardware, this paper optimizes the execution time of the matrix multiplication method on Hbird E203 based on Strassen’s algorithm to ensure the efficient operation of the model on this hardware platform.

Characterization of Halogenated Organic Compounds in Pelagic Sharks and Sea Turtles Using a Nontargeted Approach

Halogenated organic compounds (HOCs) in marine species collected from the Atlantic Ocean [3 shortfin mako (Isurus oxyrinchus) and 1 porbeagle (Lamna nasus)], and 12 sea turtles collected from the Pacific Ocean [3 loggerhead (Caretta caretta), 3 green (Chelonia mydas), 3 olive ridley (Lepidochelys olivacea), and 3 hawksbill (Eretmochelys imbricata)] were analyzed with a nontargeted analytical method using two-dimensional gas chromatography coupled to high-resolution time-of-flight mass spectrometry. Sharks and sea turtles had distinct HOC profiles. Halogenated methoxyphenols (halo-MeOPs) were the most abundant compound class identified in sea turtle livers, while polychlorinated biphenyls (PCBs) were the most abundant in shark livers. In addition to legacy contaminants and halo-MeOPs, a total of 110 nontargeted/novel HOCs (NHOCs) were observed in the shark livers. Shortfin mako collected from the northern Gulf of Mexico contained the largest number (89) and most diverse structural classes of NHOCs. Among all NHOCs, a group of compounds with the elemental composition C₁₄H_12-nCl_n (n = 5-8) exhibited the highest concentrations, followed by chlorocarbazoles and tris(chlorophenyl) methanes (TCPMs). Using nontargeted workflows, a variety of known and unknown HOCs were observed, which demonstrate the need to develop more complete chemical profiles in the marine environment.

The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain

Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. We used metagenomic analyses to provide significant insight into the potential metabolic capacity of the microbial community in Southern GoM deep sediments. We identified genes for hydrocarbon, nitrogen and sulfur metabolism mostly affiliated with Alpha and Betaproteobacteria, Acidobacteria, Chloroflexi and Firmicutes, in relation to the use of alternative carbon and energy sources to thrive under limiting growth conditions, and metabolic strategies to cope with environmental stressors. In addition, results show amino acids metabolism could be associated with sulfur metabolism carried out by Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor bacterial growth. We identified the tricarboxylic acid cycle (TCA) and aspartate, glutamate, glyoxylate and leucine degradation pathways, as part of the core carbon metabolism across samples. Further, microbial communities from the continental slope and abyssal plain show differential metabolic capacities to cope with environmental stressors such as oxidative stress and carbon limiting growth conditions, respectively. This research combined taxonomic and functional information of the microbial community from Southern GoM sediments to provide fundamental knowledge that links the prokaryotic structure to its potential function and which can be used as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.

Quantitative PCR assays to detect whales, rockfish, and common murre environmental DNA in marine water samples of the Northeastern Pacific

Monitoring aquatic species by identification of environmental DNA (eDNA) is becoming more common. To obtain quantitative eDNA datasets for individual species, organism-specific quantitative PCR (qPCR) assays are required. Here, we present detailed methodology of qPCR assay design and testing, including in silico, in vitro, and in vivo testing, and comment on the challenges associated with assay design and performance. We use the presented methodology to design assays for three important marine organisms common in the California Current Ecosystem (CCE): humpback whale (Megaptera novaeangliae), shortbelly rockfish (Sebastes jordani), and common murre (Uria aalge). All three assays have excellent sensitivity and high efficiencies ranging from 92% to 99%. However, specificities of the assays varied from species-specific in the case of common murre, genus-specific for the shortbelly rockfish assay, and broadly whale-specific for the humpback whale assay, which cross-amplified with other two other whale species, including one in a different family. All assays detected their associated targets in complex environmental water samples.

Coastal and estuarine blue carbon stocks in the greater Southeast Asia region: Seagrasses and mangroves per nation and sum of total

Climate Change solutions include CO₂ extraction from atmosphere and water with burial by living habitats in sediment/soil. Nowhere on the planet are blue carbon plants which carry out massive carbon extraction and permanent burial more intensely concentrated than in SE Asia. For the first time we make a national and total inventory of data to date for "blue carbon" buried from mangroves and seagrass and delineate the constraints. For an area across Southeast Asia of approximately 12,000,000 km², supporting mangrove forests (5,116,032 ha) and seagrass meadows (6,744,529 ha), we analyzed the region's current blue carbon stocks. This estimate was achieved by integrating the sum of estuarine in situ carbon stock measurements with the extent of mangroves and seagrass across each nation, then summed for the region. We found that mangroves ecosystems regionally supported the greater amount of organic carbon (3095.19Tg C_org in 1st meter) over that of seagrass (1683.97 Tg C_org in 1st meter), with corresponding stock densities ranging from 15 to 2205 Mg ha^-1 and 31.3 to 2450 Mg ha^-1 respectively, a likely underestimate for entire carbon including sediment depths. The largest carbon stocks are found within Indonesia, followed by the Philippines, Papua New Guinea, Myanmar, Malaysia, Thailand, Tropical China, Viet-Nam, and Cambodia. Compared to the blue carbon hotspot of tropical/subtropical Gulf of Mexico's total carbon stock (480.48 Tg Corg), Southeast Asia's greater mangrove-seagrass stock density appears a more intense Blue Carbon hotspot (4778.66 Tg Corg). All regional Southeast Asian nation states should assist in superior preservation and habitat restoration plus similar measures in the USA & Mexico for the Gulf of Mexico, as apparently these form two of the largest tropical carbon sinks within coastal waters. We hypothesize it is SE Asia's regionally unique oceanic-geologic conditions, placed squarely within the tropics, which are largely responsible for this blue carbon hotspot, that is, consistently high ambient light levels and year-long warm temperatures, together with consistently strong inflow of dissolved carbon dioxide and upwelling of nutrients across the shallow geological plates.

Chronic PAH exposures and associated declines in fish health indices observed for ten grouper species in the Gulf of Mexico

Ten grouper species grouper (n = 584) were collected throughout the Gulf of Mexico (GoM) from 2011 through 2017 to provide information on hepatobiliary polycyclic aromatic hydrocarbon (PAH) concentrations in the aftermath of the Deepwater Horizon (DWH) oil spill. Liver and bile samples were analyzed for PAHs and their metabolites using triple quadrupole mass spectrometry (GC/MS/MS) and high-performance liquid chromatography with fluorescence detection (HPLC-F), respectively. Data were compared among species and sub-regions of the GoM to understand spatiotemporal exposure dynamics in these economically and ecologically important species. Significant differences in the composition and concentrations of PAHs were detected spatially, over time and by species. The West Florida Shelf, Cuba coast and the Yucatan Shelf had a greater proportion of the pyrogenic PAHs in their livers than the other regions likely due to non-oil industry related sources (e.g., marine vessel traffic) in the regional composition profiles. Mean liver PAH concentrations were highest in the north central region of the GoM where DWH occurred. Biliary PAH concentrations and health indicator biometrics initially decrease during the first three years following the DWH oil spill but significantly increased thereafter. Increased exposures are likely explained by the resuspension of residual DWH oil as well as continued inputs from natural (e.g., seeps) sources and other anthropogenically derived sources (e.g., riverine runoff, other oil spills, and leaking oil and gas infrastructure). The increasing trend in PAH concentrations in the bile and liver of grouper species in the north central region of the GoM post-DWH suggest continued chronic exposures, however the critical stage at which permanent, irreparable damage may occur is unknown. Long-term monitoring of PAH levels and associated fish health biomarkers is necessary to evaluate impacts of chronic exposures, particularly in regions subject to intensive oil extraction activities.

Thalassic Rotifers from the United States: Descriptions of Two New Species and Notes on the Effect of Salinity and Ecosystem on Biodiversity

This study shows the results of a rotifer faunistic survey in thalassic waters from 26 sites located in northeastern U.S. states and one in California. A total of 44 taxa belonging to 21 genera and 14 families were identified, in addition to a group of unidentifiable bdelloids. Of the fully identified species, 17 are the first thalassic records for the U.S., including Encentrum melonei sp. nov. and Synchaeta grossa sp. nov., which are new to science, and Colurella unicauda Eriksen, 1968, which is new to the Nearctic region. Moreover, a refined description of Encentrum rousseleti (Lie-Pettersen, 1905) is presented. During the survey, we characterized samples by different salinity values and ecosystems and compared species composition across communities to test for possible ecological correlations. Results indicate that both salinities and ecosystems are a significant predictor of rotifer diversity, supporting that biodiversity estimates of small species provide fundamental information for biomonitoring. Finally, we provide a comprehensive review of the diversity and distribution of thalassic rotifers in the United States. The results of the present study increase the thalassic rotifer record for the U.S. from about 105 (87 at species level) to 124 (106 at species level) taxa.

It's about time: A synthesis of changing phenology in the Gulf of Maine ecosystem

The timing of recurring biological and seasonal environmental events is changing on a global scale relative to temperature and other climate drivers. This study considers the Gulf of Maine ecosystem, a region of high social and ecological importance in the Northwest Atlantic Ocean and synthesizes current knowledge of (a) key seasonal processes, patterns, and events; (b) direct evidence for shifts in timing; (c) implications of phenological responses for linked ecological-human systems; and (d) potential phenology-focused adaptation strategies and actions. Twenty studies demonstrated shifts in timing of regional marine organisms and seasonal environmental events. The most common response was earlier timing, observed in spring onset, spring and winter hydrology, zooplankton abundance, occurrence of several larval fishes, and diadromous fish migrations. Later timing was documented for fall onset, reproduction and fledging in Atlantic puffins, spring and fall phytoplankton blooms, and occurrence of additional larval fishes. Changes in event duration generally increased and were detected in zooplankton peak abundance, early life history periods of macro-invertebrates, and lobster fishery landings. Reduced duration was observed in winter-spring ice-affected stream flows. Two studies projected phenological changes, both finding diapause duration would decrease in zooplankton under future climate scenarios. Phenological responses were species-specific and varied depending on the environmental driver, spatial, and temporal scales evaluated. Overall, a wide range of baseline phenology and relevant modeling studies exist, yet surprisingly few document long-term shifts. Results reveal a need for increased emphasis on phenological shifts in the Gulf of Maine and identify opportunities for future research and consideration of phenological changes in adaptation efforts.

Six decades of change in pollution and benthic invertebrate biodiversity in a southern New England estuary

Pollution has led to a decline of benthic invertebrate biodiversity of Narragansett Bay, raising questions about effects on ecosystem functions and services including shellfish production, energy flow to fishes, and biogeochemical cycles. Changes in community composition and taxonomic distinctness (biodiversity) were calculated from the 1950s-when quantitative benthic invertebrate data first became available-to 2015. Change in community composition of the bay was correlated with changes in dissolved inorganic nitrogen, dissolved oxygen, and sediment contaminants. A mid-bay reference site showed moderate changes in community composition but no change in biodiversity. In contrast, a more impacted site in the upper bay showed substantial differences in community composition over time and a decline in taxonomic distinctness. Bay-wide, as inputs of some stressors such as nutrients and sediment contaminants have declined, there are signs of recovery of benthic biodiversity but other stressors such as temperature and watershed development are increasing.

Increased Abundance and Nursery Habitat Use of the Bull Shark (Carcharhinus leucas) in Response to a Changing Environment in a Warm-Temperate Estuary

A general northward shift in marine species distributions has been observed in the western North Atlantic Ocean, which may have significant ecological consequences. Large coastal sharks can have wide migratory distributions but show fidelity to specific nursery habitats. Here we show evidence for nursery range expansion into Pamlico Sound, North Carolina by a marine apex predator, the Bull Shark (Carcharhinus leucas). Previous assessments have shown little to no use of estuarine North Carolina waters as nursery habitat by Bull Sharks from 1965–2011. Juvenile sharks were rarely captured in a fishery-independent gillnet survey conducted by the North Carolina Division of Marine Fisheries (NCDMF) from 2003–2011, but were present every year from 2011–2016. Juvenile Bull Shark presence in the Sound was strongly related to early summer temperatures and late summer salinities, which have increased in the estuary over the 13 survey years, and further evidence for increasing water temperatures in Pamlico Sound was found in a 45-year data set for the NCDMF estuarine trawl survey. These results suggest that increasing water temperature and salinity have allowed Bull Sharks to expand their nursery habitat. This shift will have unknown, but potentially strong, impacts on both the local ecosystem and interactions with humans.

Delineation and mapping of coastal shark habitat within a shallow lagoonal estuary

Estuaries function as important nursery and foraging habitats for many coastal species, including highly migratory sharks. Pamlico Sound, North Carolina, is one of the largest estuaries in the continental United States and provides a variety of potential habitats for sharks. In order to identify and spatially delineate shark habitats within Pamlico Sound, shark catch and environmental data were analyzed from the 2007–2014 North Carolina Division of Marine Fisheries (NCDMF) gillnet and longline surveys conducted within the estuary. Principal species were identified and environmental data recorded at survey sites (depth, temperature, salinity, dissolved oxygen, submerged aquatic vegetation (SAV) distance, and inlet distance) were interpolated across Pamlico Sound to create seasonal environmental grids with a 90-m² cell size. Boosted Regression Tree (BRT) analysis was used to identify the most important environmental factors and ranges associated with presence of each principal species, and the resulting models were used to predict shark capture probability based on the environmental values within the grid cells. The Atlantic Sharpnose Shark (Rhizoprionodon terraenovae), Blacktip Shark (Carcharhinus limbatus), Bull Shark (Carcharhinus leucas), Sandbar Shark (Carcharhinus plumbeus), Smooth Dogfish (Mustelus canis), and Spiny Dogfish (Squalus acanthias) were the principal species in Pamlico Sound. Most species were associated with proximity to the inlet and/or high salinity, and warm temperatures, but the Bull Shark preferred greater inlet distances and the Spiny Dogfish preferred lower temperatures than the other species. Extensive Smooth Dogfish habitat overlap with seagrass beds suggests that seagrass may be a critical part of nursery habitat for this species. Spatial delineation of shark habitat within the estuary will allow for better protection of essential habitat and assessment of potential interactions with other species.

Pelagic marine refugia and climatically sensitive areas in an eastern boundary current upwelling system

Refugia are areas relatively buffered from contemporary climate change that enable the persistence of valued physical, ecological, or sociocultural resources. Spatially identifying refugia is important for conservation and applied management. Yet the concept of refugia has not been broadly extended to marine ecosystems. Here, we analyze data from a unique and long-term (1999-2015) standardized survey of pelagic marine and anadromous species off Oregon and Washington in the northern California Current to identify such refugia. We use quantitative approaches to assess locations with high species richness and community persistence relative to local and basin-scale environmental fluctuations. We have identified a potential climate change refugial zone along the continental shelf of Washington State in the Northeastern Pacific Ocean, characterized by a species-rich community with low interannual temporal community change. This region contrasts with adjacent areas to the south and offshore that have lower species richness, and higher temporal species community change. Also, using spatially variant generalized additive mixed models, we identify areas with species compositions that are more influenced by basin-scale climatic fluctuations than others. We propose that upwelling regions with retentive topographic features, such as wide continental shelves, can function as marine refugia for pelagic fauna, whereas offshore locations are potentially more climatically sensitive and experience high temporal change in species composition. Further identification of these marine refugia using in situ data for pelagic biodiversity and climatically sensitive areas can help guide management in the face of inevitable climatically driven change.

Identifying zooplankton community changes between shallow and upper-mesophotic reefs on the Mesoamerican Barrier Reef, Caribbean

Mesophotic coral ecosystems (MCEs, reefs 30–150 m) are understudied, yet the limited research conducted has been biased towards large sessile taxa, such as scleractinian corals and sponges, or mobile taxa such as fishes. Here we investigate zooplankton communities on shallow reefs and MCEs around Utila on the southern Mesoamerican Barrier Reef using planktonic light traps. Zooplankton samples were sorted into broad taxonomic groups. Our results indicate similar taxonomic zooplankton richness and overall biomass between shallow reefs and MCEs. However, the abundance of larger bodied (>2 mm) zooplanktonic groups, including decapod crab zoea, mysid shrimps and peracarid crustaceans, was higher on MCEs than shallow reefs. Our findings highlight the importance of considering zooplankton when identifying broader reef community shifts across the shallow reef to MCE depth gradient.

Postglacial migration and adaptation for dispersal in pitch pine (Pinaceae)

PREMISE OF THE STUDY

Variation in a species is a blend of adaptive, random, and migratory responses. Pitch pine (Pinus rigida), a highly variable eastern conifer, has occupied multiple glacial refugia, whose harsh conditions favored adaptations enhancing subsequent dispersal and recolonization of newly deglaciated sites. We assessed phenotypic diversity in long-term growth trials to elucidate both the adaptations and likely refugia.

METHODS

Pitch pine progeny from 31 areas were grown in common gardens in six locations, from eastern Massachusetts to Korea.

KEY RESULTS

Survival increased with source latitude, but seedlings from southern latitudes were tallest in the first (postplanting) year, but that advantage dissipated in later years. Progeny from northern latitudes were precocious, highly fecund, had smaller seeds, and more seeds per cone. Seed mass decreased with latitude in both parents and progeny. Serotinous cones were notably common in the New Jersey Pine Plains and Acadia National Park. Various disease agents and frost burn exhibited latitudinal trends that were nonlinear, with a break in the regression slope at about 40°N latitude. Cluster analysis identified both northern and southern groups, largely split between unglaciated and deglaciated terrain, but with Acadia and the Pine Plains as unique outliers. Within the southern group, provenances were organized into contiguous subgroups, but geographic structure was less evident in the northern group.

CONCLUSIONS

The present range of pitch pine was colonized by migrants from at least three different refugia, including at least one on the exposed continental shelf during the Last Glacial Maximum.

Record-breaking Lake Erie hypoxia during 2012 drought

Hypoxia has been observed in the central basin of Lake Erie for decades. To understand the impact of various controlling factors, we analyze a record of hypoxic extents for Lake Erie for 1985–2012 and develop a parsimonious model of their interannual variability. We find that the 2012 North American drought and accompanying low tributary discharge was associated with a record-breaking hypoxic event in Lake Erie, whereas a record-setting harmful algal bloom in 2011 was likely associated with only mild hypoxia. River discharge and the timing of nutrient input therefore impact western basin bloom growth and central basin oxygen demand in distinct ways that merit further investigation. Overall, April to June tributary discharge, May to July soluble reactive phosphorus loading, July wind stress, and June northwesterly wind duration explain 82% of the interannual variability of hypoxia, and discharge alone explains 39%, indicating that meteorological factors need to be considered in the development of nutrient management strategies, especially as both extreme precipitation events and droughts become more frequent under a changing climate.

Occupancy models for monitoring marine fish: a bayesian hierarchical approach to model imperfect detection with a novel gear combination

Occupancy models using incidence data collected repeatedly at sites across the range of a population are increasingly employed to infer patterns and processes influencing population distribution and dynamics. While such work is common in terrestrial systems, fewer examples exist in marine applications. This disparity likely exists because the replicate samples required by these models to account for imperfect detection are often impractical to obtain when surveying aquatic organisms, particularly fishes. We employ simultaneous sampling using fish traps and novel underwater camera observations to generate the requisite replicate samples for occupancy models of red snapper, a reef fish species. Since the replicate samples are collected simultaneously by multiple sampling devices, many typical problems encountered when obtaining replicate observations are avoided. Our results suggest that augmenting traditional fish trap sampling with camera observations not only doubled the probability of detecting red snapper in reef habitats off the Southeast coast of the United States, but supplied the necessary observations to infer factors influencing population distribution and abundance while accounting for imperfect detection. We found that detection probabilities tended to be higher for camera traps than traditional fish traps. Furthermore, camera trap detections were influenced by the current direction and turbidity of the water, indicating that collecting data on these variables is important for future monitoring. These models indicate that the distribution and abundance of this species is more heavily influenced by latitude and depth than by micro-scale reef characteristics lending credence to previous characterizations of red snapper as a reef habitat generalist. This study demonstrates the utility of simultaneous sampling devices, including camera traps, in aquatic environments to inform occupancy models and account for imperfect detection when describing factors influencing fish population distribution and dynamics.

Antiviral activities and putative identification of compounds in microbial extracts from the Hawaiian coastal waters

Marine environments are a rich source of significant bioactive compounds. The Hawaiian archipelago, located in the middle of the Pacific Ocean, hosts diverse microorganisms, including many endemic species. Thirty-eight microbial extracts from Hawaiian coastal waters were evaluated for their antiviral activity against four mammalian viruses including herpes simplex virus type one (HSV-1), vesicular stomatitis virus (VSV), vaccinia virus and poliovirus type one (poliovirus-1) using in vitro cell culture assay. Nine of the 38 microbial crude extracts showed antiviral potencies and three of these nine microbial extracts exhibited significant activity against the enveloped viruses. A secosteroid, 5α(H),17α(H),(20R)-beta-acetoxyergost-8(14)-ene was putatively identified and confirmed to be the active compound in these marine microbial extracts. These results warrant future in-depth tests on the isolation of these active elements in order to explore and validate their antiviral potential as important therapeutic remedies.

A survey of marine natural compounds and their derivatives with anti-cancer activity reported in 2010

Although considerable progress in oncology therapeutics has been achieved in the last century, cancer remains one of major death causes in the World and for this reason, the development of novel cancer drugs remains a pressing need. Natural marine compounds represent an interesting source of novel leads with potent chemotherapeutic or chemo-preventive activities. In the last decades, structure-activity-relationship studies have led to the development of naturally-derived or semi-synthetic analogues with improved bioactivity, a simplified synthetic target or less toxicity. We aim here to review a selection of natural compounds with reported anticancer activity isolated of marine sources and their associated analogues published in 2010.

Planktonic microbes in the Gulf of Maine area

In the Gulf of Maine area (GoMA), as elsewhere in the ocean, the organisms of greatest numerical abundance are microbes. Viruses in GoMA are largely cyanophages and bacteriophages, including podoviruses which lack tails. There is also evidence of Mimivirus and Chlorovirus in the metagenome. Bacteria in GoMA comprise the dominant SAR11 phylotype cluster, and other abundant phylotypes such as SAR86-like cluster, SAR116-like cluster, Roseobacter, Rhodospirillaceae, Acidomicrobidae, Flavobacteriales, Cytophaga, and unclassified Alphaproteobacteria and Gammaproteobacteria clusters. Bacterial epibionts of the dinoflagellate Alexandrium fundyense include Rhodobacteraceae, Flavobacteriaceae, Cytophaga spp., Sulfitobacter spp., Sphingomonas spp., and unclassified Bacteroidetes. Phototrophic prokaryotes in GoMA include cyanobacteria that contain chlorophyll (mainly Synechococcus), aerobic anoxygenic phototrophs that contain bacteriochlorophyll, and bacteria that contain proteorhodopsin. Eukaryotic microalgae in GoMA include Bacillariophyceae, Dinophyceae, Prymnesiophyceae, Prasinophyceae, Trebouxiophyceae, Cryptophyceae, Dictyochophyceae, Chrysophyceae, Eustigmatophyceae, Pelagophyceae, Synurophyceae, and Xanthophyceae. There are no records of Bolidophyceae, Aurearenophyceae, Raphidophyceae, and Synchromophyceae in GoMA. In total, there are records for 665 names and 229 genera of microalgae. Heterotrophic eukaryotic protists in GoMA include Dinophyceae, Alveolata, Apicomplexa, amoeboid organisms, Labrynthulida, and heterotrophic marine stramenopiles (MAST). Ciliates include Strombidium, Lohmaniella, Tontonia, Strobilidium, Strombidinopsis and the mixotrophs Laboea strobila and Myrionecta rubrum (ex Mesodinium rubra). An inventory of selected microbial groups in each of 14 physiographic regions in GoMA is made by combining information on the depth-dependent variation of cell density and the depth-dependent variation of water volume. Across the entire GoMA, an estimate for the minimum abundance of cell-based microbes is 1.7×10²⁵ organisms. By one account, this number of microbes implies a richness of 10⁵ to 10⁶ taxa in the entire water volume of GoMA. Morphological diversity in microplankton is well-described but the true extent of taxonomic diversity, especially in the femtoplankton, picoplankton and nanoplankton – whether autotrophic, heterotrophic, or mixotrophic, is unknown.

Gold from the sea: marine compounds as inhibitors of the hallmarks of cancer

Cancer is one of the most deadly diseases in the world. Although advances in the field of chemo-preventive and therapeutic medicine have been made regularly over the last ten years, the search for novel anticancer treatments continues. In this field, the marine environment, with its rich variety of organisms, is a largely untapped source of novel compounds with potent antitumor activity. Although many reviews of marine anticancer compounds have been published, we focus here on selected marine compounds that act on the six hallmarks of cancer presented namely self-sufficiency in growth signals, insensitivity to anti-growth signals, evasion of apoptosis, limitless replication, sustained angiogenesis and tissue invasion and metastasis.

Defining Boundaries for Ecosystem-Based Management: A Multispecies Case Study of Marine Connectivity across the Hawaiian Archipelago

Determining the geographic scale at which to apply ecosystem-based management (EBM) has proven to be an obstacle for many marine conservation programs. Generalizations based on geographic proximity, taxonomy, or life history characteristics provide little predictive power in determining overall patterns of connectivity, and therefore offer little in terms of delineating boundaries for marine spatial management areas. Here, we provide a case study of 27 taxonomically and ecologically diverse species (including reef fishes, marine mammals, gastropods, echinoderms, cnidarians, crustaceans, and an elasmobranch) that reveal four concordant barriers to dispersal within the Hawaiian Archipelago which are not detected in single-species exemplar studies. We contend that this multispecies approach to determine concordant patterns of connectivity is an objective and logical way in which to define the minimum number of management units and that EBM in the Hawaiian Archipelago requires at least five spatially managed regions.

Marine biodiversity in the Caribbean: regional estimates and distribution patterns

This paper provides an analysis of the distribution patterns of marine biodiversity and summarizes the major activities of the Census of Marine Life program in the Caribbean region. The coastal Caribbean region is a large marine ecosystem (LME) characterized by coral reefs, mangroves, and seagrasses, but including other environments, such as sandy beaches and rocky shores. These tropical ecosystems incorporate a high diversity of associated flora and fauna, and the nations that border the Caribbean collectively encompass a major global marine biodiversity hot spot. We analyze the state of knowledge of marine biodiversity based on the geographic distribution of georeferenced species records and regional taxonomic lists. A total of 12,046 marine species are reported in this paper for the Caribbean region. These include representatives from 31 animal phyla, two plant phyla, one group of Chromista, and three groups of Protoctista. Sampling effort has been greatest in shallow, nearshore waters, where there is relatively good coverage of species records; offshore and deep environments have been less studied. Additionally, we found that the currently accepted classification of marine ecoregions of the Caribbean did not apply for the benthic distributions of five relatively well known taxonomic groups. Coastal species richness tends to concentrate along the Antillean arc (Cuba to the southernmost Antilles) and the northern coast of South America (Venezuela-Colombia), while no pattern can be observed in the deep sea with the available data. Several factors make it impossible to determine the extent to which these distribution patterns accurately reflect the true situation for marine biodiversity in general: (1) highly localized concentrations of collecting effort and a lack of collecting in many areas and ecosystems, (2) high variability among collecting methods, (3) limited taxonomic expertise for many groups, and (4) differing levels of activity in the study of different taxa.