Distributions of microplastics and larger anthropogenic debris in Norfolk Canyon, Baltimore Canyon, and the adjacent continental slope (Western North Atlantic Margin, U.S.A.).

Anthropogenic debris has been reported in all studied marine environments, including the deepest parts of the sea. Finding areas of accumulation and methods of transport for debris are important to determine potential impacts on marine life. This study analyzed both sediment cores and Remotely Operated Vehicle video to determine the density and distribution of debris, including both micro- and macroplastics, in Norfolk and Baltimore canyons. The average microplastic density in Norfolk Canyon sediment was 37.30 plastic particles m-2 within the canyon and 21.03 particles m-2 on the adjacent slope, suggesting that microplastics could accumulate within submarine canyons. In video transects from both Norfolk and Baltimore canyons, the largest amounts of macroplastic were recorded near the canyon heads. Our findings contribute to a growing evidence base that canyons and their associated benthic invertebrate communities are important repositories and conduits for debris to the deep sea.

Climate-induced changes in the suitable habitat of cold-water corals and commercially important deep-sea fishes in the North Atlantic.

The deep sea plays a critical role in global climate regulation through uptake and storage of heat and carbon dioxide. However, this regulating service causes warming, acidification and deoxygenation of deep waters, leading to decreased food availability at the seafloor. These changes and their projections are likely to affect productivity, biodiversity and distributions of deep-sea fauna, thereby compromising key ecosystem services. Understanding how climate change can lead to shifts in deep-sea species distributions is critically important in developing management measures. We used environmental niche modelling along with the best available species occurrence data and environmental parameters to model habitat suitability for key cold-water coral and commercially important deep-sea fish species under present-day (1951-2000) environmental conditions and to project changes under severe, high emissions future (2081-2100) climate projections (RCP8.5 scenario) for the North Atlantic Ocean. Our models projected a decrease of 28%-100% in suitable habitat for cold-water corals and a shift in suitable habitat for deep-sea fishes of 2.0°-9.9° towards higher latitudes. The largest reductions in suitable habitat were projected for the scleractinian coral Lophelia pertusa and the octocoral Paragorgia arborea, with declines of at least 79% and 99% respectively. We projected the expansion of suitable habitat by 2100 only for the fishes Helicolenus dactylopterus and Sebastes mentella (20%-30%), mostly through northern latitudinal range expansion. Our results projected limited climate refugia locations in the North Atlantic by 2100 for scleractinian corals (30%-42% of present-day suitable habitat), even smaller refugia locations for the octocorals Acanella arbuscula and Acanthogorgia armata (6%-14%), and almost no refugia for P. arborea. Our results emphasize the need to understand how anticipated climate change will affect the distribution of deep-sea species including commercially important fishes and foundation species, and highlight the importance of identifying and preserving climate refugia for a range of area-based planning and management tools.

Assemblage structure, vertical distributions and stable-isotope compositions of anguilliform leptocephali in the Gulf of Mexico.

In August 2007, October 2008 and September-October 2010, 241 Tucker trawl and plankton net tows were conducted at the surface to depths of 1377 m at six locations in the northern and eastern Gulf of Mexico (GOM) to document leptocephalus diversity and determine how assemblage structure, larval size, abundance and isotopic signatures differ across the region and with depth. Overall, 2696 leptocephali representing 59 distinct taxa from 10 families were collected. Five families accounted for 96% of the total catch with Congridae and Ophichthidae being the most abundant. The top four most abundant species composed 59% of the total catch and included: Ariosoma balearicum, Paraconger caudilimbatus, Rhynchoconger flavus and Ophichthus gomesii. Four anguilliform species not previously documented in the GOM as adults or leptocephali were collected in this study, including Monopenchelys acuta, Quassiremus ascensionis, Saurenchelys stylura and one leptocephalus only known from its larval stage, Leptocephalus proboscideus. Leptocephalus catches were significantly greater at night than during the day. Catches at night were concentrated in the upper 200 m of the water column and significantly declined with increasing depth. Leptocephali abundances and assemblages were significantly different between sites on the upper continental slope (c. 500 m depth) and sites on the middle to lower continental slope (c. 1500-2300 m). Sites on the lower continental slope had a mixture of deep-sea demersal, bathypelagic and coastal species, whereas upper-slope sites contained several numerically dominant species (e.g., A. balearicum, P. caudilimbatus) that probably spawn over the continental shelf and upper slope of the GOM. Standard lengths of the four dominant species differed between sites and years, indicating heterochronic reproduction and potential larval source pools within and outside of the GOM. Stable-isotope analyses (δ13 C and δ15 N) conducted on 185 specimens from six families revealed that leptocephali had a wide range of isotopic values at the family and size-class levels. Species in the families Muraenidae, Congridae and Ophichthidae had similar δ15 N values compared with the broad range of δ15 N values seen in the deep-sea families Nemichthyidae, Nettastomatidae and Synaphobranchidae. Stable-isotope values were variably related to length, with δ15 N values being positively size correlated in ophichthids and δ13 C values being negatively size correlated in A. balearicum and P. caudilimbatus. Results suggest that leptocephali feed in various water depths and masses, and on different components of POM, which could lead to niche partitioning. Ecological aspects of these important members of the plankton community provide insight into larval connectivity in the GOM as well as the early life history of Anguilliformes.

Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype.

Cold-water corals provide critical habitats for a multitude of marine species, but are understudied relative to tropical corals. Primnoa pacifica is a cold-water coral prevalent throughout Alaskan waters, while another species in the genus, Primnoa resedaeformis, is widely distributed in the Atlantic Ocean. This study examined the V4-V5 region of the 16S rRNA gene after amplifying and pyrosequencing bacterial DNA from samples of these species. Key differences between the two species' microbiomes included a robust presence of bacteria belonging to the Chlamydiales order in most of the P. pacifica samples, whereas no more than 2% of any microbial community from P. resedaeformis comprised these bacteria. Microbiomes of P. resedaeformis exhibited higher diversity than those of P. pacifica, and the two species largely clustered separately in a principal coordinate analysis. Comparison of P. resedaeformis microbiomes from samples collected in two submarine canyons revealed a significant difference between locations. This finding mirrored significant genetic differences among the P. resedaeformis from the two canyons based upon population genetic analysis of microsatellite loci. This study presents the first report of microbiomes associated with these two coral species.

Decadal Assessment of Polycyclic Aromatic Hydrocarbons in Mesopelagic Fishes from the Gulf of Mexico Reveals Exposure to Oil-Derived Sources.

This study characterizes a decadal assessment of polycyclic aromatic hydrocarbons (PAHs) in the muscle tissues of mesopelagic fish species as indicators of the environmental health of the Gulf of Mexico (GoM) deep-pelagic ecosystem. Mesopelagic fishes were collected prior to the Deepwater Horizon (DWH) oil spill (2007), immediately post-spill (2010), 1 year after the spill (2011), and 5-6 years post-spill (2015-2016) to assess if the mesopelagic ecosystem was exposed to, and retained, PAH compounds from the DWH spill. Results indicated that a 7- to 10-fold increase in PAHs in fish muscle tissues occurred in 2010-2011 (4972 ± 1477 ng/g) compared to 2007 (630 ± 236 ng/g). In 2015-2016, PAH concentrations decreased close to the levels measured in 2007 samples (827 ± 138 ng/g); however, the composition of PAHs still resembles a petrogenic source similar to samples collected in 2010-2011. PAH composition in muscle samples indicated that natural sources (e.g., Mississippi River and natural seeps) or spatial variability within the GoM do not explain the temporal variability of PAHs observed from 2007 to 2016. Furthermore, analysis of different fish tissues indicated the dietary intake and maternal transfer of PAHs as the primary mechanisms for bioaccumulation in 2015-2016, explaining the elevated levels and composition of PAHs in ovarian eggs.

Bacterial community diversity of the deep-sea octocoral Paramuricea placomus.

Compared to tropical corals, much less is known about deep-sea coral biology and ecology. Although the microbial communities of some deep-sea corals have been described, this is the first study to characterize the bacterial community associated with the deep-sea octocoral, Paramuricea placomus. Samples from five colonies of P. placomus were collected from Baltimore Canyon (379-382 m depth) in the Atlantic Ocean off the east coast of the United States of America. DNA was extracted from the coral samples and 16S rRNA gene amplicons were pyrosequenced using V4-V5 primers. Three samples sequenced deeply (>4,000 sequences each) and were further analyzed. The dominant microbial phylum was Proteobacteria, but other major phyla included Firmicutes and Planctomycetes. A conserved community of bacterial taxa held in common across the three P. placomus colonies was identified, comprising 68-90% of the total bacterial community depending on the coral individual. The bacterial community of P. placomus does not appear to include the genus Endozoicomonas, which has been found previously to be the dominant bacterial associate in several temperate and tropical gorgonians. Inferred functionality suggests the possibility of nitrogen cycling by the core bacterial community.

Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.

Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

Pushing x-ray photon correlation spectroscopy beyond the continuous frame rate limit.

We demonstrate delayed-frame X-ray Photon Correlation Spectroscopy with 120 microsecond time resolution, limited only by sample scattering rates, with a prototype Pixel-array detector capable of taking two image frames separated by 153 ns or less. Although the overall frame rate is currently limited to about 4 frame pairs per second, we easily measured millisecond correlation functions. This technology, coupled to the use of brighter synchrotrons such as Petra III or the NSLS-II should enable X-ray Photon Correlation Spectroscopy on microsecond time scales on a wider variety of materials.

X-ray characterization of a multichannel smart-pixel array detector.

The Voxtel VX-798 is a prototype X-ray pixel array detector (PAD) featuring a silicon sensor photodiode array of 48 × 48 pixels, each 130 µm × 130 µm × 520 µm thick, coupled to a CMOS readout application specific integrated circuit (ASIC). The first synchrotron X-ray characterization of this detector is presented, and its ability to selectively count individual X-rays within two independent arrival time windows, a programmable energy range, and localized to a single pixel is demonstrated. During our first trial run at Argonne National Laboratory's Advance Photon Source, the detector achieved a 60 ns gating time and 700 eV full width at half-maximum energy resolution in agreement with design parameters. Each pixel of the PAD holds two independent digital counters, and the discriminator for X-ray energy features both an upper and lower threshold to window the energy of interest discarding unwanted background. This smart-pixel technology allows energy and time resolution to be set and optimized in software. It is found that the detector linearity follows an isolated dead-time model, implying that megahertz count rates should be possible in each pixel. Measurement of the line and point spread functions showed negligible spatial blurring. When combined with the timing structure of the synchrotron storage ring, it is demonstrated that the area detector can perform both picosecond time-resolved X-ray diffraction and fluorescence spectroscopy measurements.

δ(13)C and δ(15)N in deep-living fishes and shrimps after the Deepwater Horizon oil spill, Gulf of Mexico.

The blowout of the Deepwater Horizon (DWH) drill-rig produced a surface oil layer, dispersed micro-droplets throughout the water column, and sub-surface plumes. We measured stable carbon and nitrogen isotopes in mesopelagic fishes and shrimps in the vicinity of DWH collected prior to, six weeks after, and one year after the oil spill (2007, 2010 and 2011). In 2010, the year of the oil spill, a small but significant depletion of δ(13)C was found in two mesopelagic fishes (Gonostoma elongatum and Chauliodus sloani) and one shrimp (Systellaspis debilis); a significant δ(15)N enrichment was identified in the same shrimp and in three fish species (G. elongatum, Ceratoscopelus warmingii, and Lepidophanes guentheri). The δ(15)N change did not suggest a change of trophic level, but did indicate a change in diet. The data suggest that carbon from the Deepwater Horizon oil spill was incorporated into the mesopelagic food web of the Gulf of Mexico.

Global trophic position comparison of two dominant mesopelagic fish families (Myctophidae, Stomiidae) using amino acid nitrogen isotopic analyses.

The δ(15)N values of organisms are commonly used across diverse ecosystems to estimate trophic position and infer trophic connectivity. We undertook a novel cross-basin comparison of trophic position in two ecologically well-characterized and different groups of dominant mid-water fish consumers using amino acid nitrogen isotope compositions. We found that trophic positions estimated from the δ(15)N values of individual amino acids are nearly uniform within both families of these fishes across five global regions despite great variability in bulk tissue δ(15)N values. Regional differences in the δ(15)N values of phenylalanine confirmed that bulk tissue δ(15)N values reflect region-specific water mass biogeochemistry controlling δ(15)N values at the base of the food web. Trophic positions calculated from amino acid isotopic analyses (AA-TP) for lanternfishes (family Myctophidae) (AA-TP ∼2.9) largely align with expectations from stomach content studies (TP ∼3.2), while AA-TPs for dragonfishes (family Stomiidae) (AA-TP ∼3.2) were lower than TPs derived from stomach content studies (TP∼4.1). We demonstrate that amino acid nitrogen isotope analysis can overcome shortcomings of bulk tissue isotope analysis across biogeochemically distinct systems to provide globally comparative information regarding marine food web structure.

The ABO blood group is a trans-species polymorphism in primates.

The ABO histo-blood group, the critical determinant of transfusion incompatibility, was the first genetic polymorphism discovered in humans. Remarkably, ABO antigens are also polymorphic in many other primates, with the same two amino acid changes responsible for A and B specificity in all species sequenced to date. Whether this recurrence of A and B antigens is the result of an ancient polymorphism maintained across species or due to numerous, more recent instances of convergent evolution has been debated for decades, with a current consensus in support of convergent evolution. We show instead that genetic variation data in humans and gibbons as well as in Old World monkeys are inconsistent with a model of convergent evolution and support the hypothesis of an ancient, multiallelic polymorphism of which some alleles are shared by descent among species. These results demonstrate that the A and B blood groups result from a trans-species polymorphism among distantly related species and has remained under balancing selection for tens of millions of years-to date, the only such example in hominoids and Old World monkeys outside of the major histocompatibility complex.

Feline immunodeficiency virus (FIV) in wild Pallas' cats.

Feline immunodeficiency virus (FIV), a feline lentivirus related to HIV, causes immune dysfunction in domestic and wild cats. The Pallas' cat is the only species from Asia known to harbor a species-specific strain of FIV designated FIV(Oma) in natural populations. Here, a 25% seroprevalence of FIV is reported from 28 wild Mongolian Pallas' cats sampled from 2000 to 2008. Phylogenetic analysis of proviral RT-Pol from eight FIV(Oma) isolates from Mongolia, Russia, China and Kazakhstan reveals a unique monophyletic lineage of the virus within the Pallas' cat population, most closely related to the African cheetah and leopard FIV strains. Histopathological examination of lymph node and spleen from infected and uninfected Pallas' cats suggests that FIV(Oma) causes immune depletion in its' native host.

Improvements in lipoatrophy, mitochondrial DNA levels and fat apoptosis after replacing stavudine with abacavir or zidovudine.

OBJECTIVE: To determine if stavudine (alpha4T)-associated mitochondrial toxicity could be reversed by substitution with another nucleoside reverse transcriptase inhibitor. As apoptosis and dysfunction of electron transport chain (ETC) activities may underlie mitochondrial toxicity, these parameters were also evaluated. DESIGN: The 16 participants (on d4T for >3 years; with lipoatrophy and/or hyperlactatemia) substituted abacavir or zidovudine for stavudine in their antiretroviral regimen. Key parameters including dual-energy X-ray absorptiometry (DEXA) scans, fat apoptosis, mitochondrial DNA (mtDNA) content in peripheral blood mononuclear cells (PBMC), skeletal muscle and fat, as well as skeletal muscle mitochondrial ETC activities were evaluated at study entry and at 48 weeks after the substitution. METHODS: Quantitative PCR was used to evaluate mtDNA levels and the presence of deletions/rearrangements; CLIA-validated methods for ETC activities; terminal deoxynucleotidyl transferase dUTP-digoxigenin nick-end labeling assays to evaluate adipocyte apoptosis; and DEXA scans to measure changes in body fat. RESULTS: MtDNA was depleted at study entry in muscle, adipose tissue and PBMC but levels rebounded with respective mean increases of 141%, 146%, and 369% at week 48. Corresponding fat improvements were noted with DEXA increases of 21%, 11%, and 16% in arm, leg, and trunk, respectively. Quantitative adipocyte apoptosis were significantly increased at baseline (P < 0.01 versus HIV-negative controls), with a significant reduction at week 48 (P < 0.05 versus baseline). Mean values for seven mitochondrial enzyme activities assays at entry indicated substantial loss of function (48% to 85% of controls) with significant improvement of complex I activity by week 48. CONCLUSIONS: Substitution of stavudine with abacavir or zidovudine improves mitochondrial indices and fat apoptosis in the setting of lipoatrophy.

The Ronald McDonald House as an alternative to antepartum hospitalization.

OBJECTIVE: We sought to evaluate the use of the Ronald McDonald House (RMH) for selected high-risk pregnant women. METHODS: Beginning in November of 1999, women on the Maternal Fetal Medicine service at Albany Medical Center Hospital (AMCH) were candidates for antepartum lodging at the Ronald McDonald House (RMH). Women whose only indication for antepartum hospitalization was to maintain proximity to a tertiary care center were offered stays at the RMH. Antenatal and neonatal outcomes were reviewed. RESULTS: A total of 41 antepartum subjects stayed at the RMH during the study period. No adverse perinatal outcomes were identified due to utilization of the RMH. Patients stayed at the RMH instead of staying at AMCH as inpatients for a total of 586 days during the study period. CONCLUSIONS: Outpatient management at the RMH is a cost-effective alternative for selected high-risk pregnancies. No adverse outcomes in the study population were attributable to the utilization of the RMH.