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  • Articles  (15,457)
  • Public Library of Science  (15,457)
  • 2010-2014  (15,457)
  • 2011  (15,457)
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  • 2010-2014  (15,457)
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  • 1
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    Cold-water coral distributions in the Drake Passage area from towed camera observations – initial interpretations (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This article is distributed under the terms of the Creative Commons Public Domain. The definitive version was published in PLoS One 6 (2011): e16153, doi:10.1371/journal.pone.0016153.
    Description: Seamounts are unique deep-sea features that create habitats thought to have high levels of endemic fauna, productive fisheries and benthic communities vulnerable to anthropogenic impacts. Many seamounts are isolated features, occurring in the high seas, where access is limited and thus biological data scarce. There are numerous seamounts within the Drake Passage (Southern Ocean), yet high winds, frequent storms and strong currents make seafloor sampling particularly difficult. As a result, few attempts to collect biological data have been made, leading to a paucity of information on benthic habitats or fauna in this area, particularly those on primarily hard-bottom seamounts and ridges. During a research cruise in 2008 six locations were examined (two on the Antarctic margin, one on the Shackleton Fracture Zone, and three on seamounts within the Drake Passage), using a towed camera with onboard instruments to measure conductivity, temperature, depth and turbidity. Dominant fauna and bottom type were categorized from 200 randomized photos from each location. Cold-water corals were present in high numbers in habitats both on the Antarctic margin and on the current swept seamounts of the Drake Passage, though the diversity of orders varied. Though the Scleractinia (hard corals) were abundant on the sedimented margin, they were poorly represented in the primarily hard-bottom areas of the central Drake Passage. The two seamount sites and the Shackleton Fracture Zone showed high numbers of stylasterid (lace) and alcyonacean (soft) corals, as well as large numbers of sponges. Though data are preliminary, the geological and environmental variability (particularly in temperature) between sample sites may be influencing cold-water coral biogeography in this region. Each area observed also showed little similarity in faunal diversity with other sites examined for this study within all phyla counted. This manuscript highlights how little is understood of these isolated features, particularly in Polar regions.
    Description: This work was funded by the National Science Foundation’s Antarctic Earth Sciences Program (ANT0636787 awarded to LFR and RGW) and a CenSeam minigrant (awarded to RGW), and RGW is supported by a SOEST Young Investigator Fellowship from the University of Hawaii at Manoa.
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  • 2
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    Beaked whales respond to simulated and actual navy sonar (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This article is distributed under the terms of the Creative Commons Public Domain declaration. The definitive version was published in PLoS One 6 (2011): e17009, doi:10.1371/journal.pone.0017009.
    Description: Beaked whales have mass stranded during some naval sonar exercises, but the cause is unknown. They are difficult to sight but can reliably be detected by listening for echolocation clicks produced during deep foraging dives. Listening for these clicks, we documented Blainville's beaked whales, Mesoplodon densirostris, in a naval underwater range where sonars are in regular use near Andros Island, Bahamas. An array of bottom-mounted hydrophones can detect beaked whales when they click anywhere within the range. We used two complementary methods to investigate behavioral responses of beaked whales to sonar: an opportunistic approach that monitored whale responses to multi-day naval exercises involving tactical mid-frequency sonars, and an experimental approach using playbacks of simulated sonar and control sounds to whales tagged with a device that records sound, movement, and orientation. Here we show that in both exposure conditions beaked whales stopped echolocating during deep foraging dives and moved away. During actual sonar exercises, beaked whales were primarily detected near the periphery of the range, on average 16 km away from the sonar transmissions. Once the exercise stopped, beaked whales gradually filled in the center of the range over 2–3 days. A satellite tagged whale moved outside the range during an exercise, returning over 2–3 days post-exercise. The experimental approach used tags to measure acoustic exposure and behavioral reactions of beaked whales to one controlled exposure each of simulated military sonar, killer whale calls, and band-limited noise. The beaked whales reacted to these three sound playbacks at sound pressure levels below 142 dB re 1 µPa by stopping echolocation followed by unusually long and slow ascents from their foraging dives. The combined results indicate similar disruption of foraging behavior and avoidance by beaked whales in the two different contexts, at exposures well below those used by regulators to define disturbance.
    Description: The research reported here was financially supported by the United States (U.S.) Office of Naval Research (www.onr.navy.mil) Grants N00014-07-10988, N00014-07-11023, N00014-08-10990; the U.S. Strategic Environmental Research and Development Program (www.serdp.org) Grant SI-1539, the Environmental Readiness Division of the U.S. Navy (http://www.navy.mil/local/n45/), the U.S. Chief of Naval Operations Submarine Warfare Division (Undersea Surveillance), the U.S. National Oceanic and Atmospheric Administration (National Marine Fisheries Service, Office of Science and Technology) (http://www.st.nmfs.noaa.gov/), U.S. National Oceanic and Atmospheric Administration Ocean Acoustics Program (http://www.nmfs.noaa.gov/pr/acoustics/), and the Joint Industry Program on Sound and Marine Life of the International Association of Oil and Gas Producers (www.soundandmarinelife.org).
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  • 3
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    Evolution of a major drug metabolizing enzyme defect in the domestic cat and other felidae : phylogenetic timing and the role of hypercarnivory (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This is an open-access article, free of all copyright. The definitive version was published in PLoS One 6(2011): e18046, doi:10.1371/journal.pone.0018046.
    Description: The domestic cat (Felis catus) shows remarkable sensitivity to the adverse effects of phenolic drugs, including acetaminophen and aspirin, as well as structurally-related toxicants found in the diet and environment. This idiosyncrasy results from pseudogenization of the gene encoding UDP-glucuronosyltransferase (UGT) 1A6, the major species-conserved phenol detoxification enzyme. Here, we established the phylogenetic timing of disruptive UGT1A6 mutations and explored the hypothesis that gene inactivation in cats was enabled by minimal exposure to plant-derived toxicants. Fixation of the UGT1A6 pseudogene was estimated to have occurred between 35 and 11 million years ago with all extant Felidae having dysfunctional UGT1A6. Out of 22 additional taxa sampled, representative of most Carnivora families, only brown hyena (Parahyaena brunnea) and northern elephant seal (Mirounga angustirostris) showed inactivating UGT1A6 mutations. A comprehensive literature review of the natural diet of the sampled taxa indicated that all species with defective UGT1A6 were hypercarnivores (〉70% dietary animal matter). Furthermore those species with UGT1A6 defects showed evidence for reduced amino acid constraint (increased dN/dS ratios approaching the neutral selection value of 1.0) as compared with species with intact UGT1A6. In contrast, there was no evidence for reduced amino acid constraint for these same species within UGT1A1, the gene encoding the enzyme responsible for detoxification of endogenously generated bilirubin. Our results provide the first evidence suggesting that diet may have played a permissive role in the devolution of a mammalian drug metabolizing enzyme. Further work is needed to establish whether these preliminary findings can be generalized to all Carnivora.
    Description: Binu Shrestha was supported by a Fulbright scholarship from the United States Department of State. This project was funded by grant R01GM061834 from the National Institute of General Medical Sciences, contract N01-CO-12400 from the National Cancer Institute (NCI), and by the Intramural Research Program, NCI Center for Cancer Research, National Institutes of Health (NIH).
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  • 4
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    Diversity and dynamics of a widespread bloom of the toxic dinoflagellate Alexandrium fundyense (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e22965, doi:10.1371/journal.pone.0022965.
    Description: Historically, cosmopolitan phytoplankton species were presumed to represent largely unstructured populations. However, the recent development of molecular tools to examine genetic diversity have revealed differences in phytoplankton taxa across geographic scales and provided insight into the physiology and ecology of blooms. Here we describe the genetic analysis of an extensive bloom of the toxic dinoflagellate Alexandrium fundyense that occurred in the Gulf of Maine in 2005. This bloom was notable for its intensity and duration, covering hundreds of kilometers and persisting for almost two months. Genotypic analyses based on microsatellite marker data indicate that the open waters of the northeastern U.S. harbor a single regional population of A. fundyense comprising two genetically distinct sub-populations. These subpopulations were characteristic of early- and late-bloom samples and were derived from the northern and southern areas of the bloom, respectively. The temporal changes observed during this study provide clear evidence of succession during a continuous bloom and show that selection can act on the timescale of weeks to significantly alter the representation of genotypes within a population. The effects of selection on population composition and turnover would be magnified if sexual reproduction were likewise influenced by environmental conditions. We hypothesize that the combined effects of differential growth and reproduction rates serves to reduce gene flow between the sub-populations, reinforcing population structure while maintaining the diversity of the overall regional population.
    Description: This work was supported by the National Institute of Environmental Health Sciences (1-P50-ES012742 to DMA and DLE), by the National Science Foundation through the Woods Hole Center for Oceans and Human Health (OCE-0430724), and by the ECOHAB program (NOAA Grant NA06NOS4780245).
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  • 5
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    A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Authors, 2007. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 2 (2007): e667, doi:10.1371/journal.pone.0000667.
    Description: For decades it has been recognized that neutrophilic Fe-oxidizing bacteria (FeOB) are associated with hydrothermal venting of Fe(II)-rich fluids associated with seamounts in the world's oceans. The evidence was based almost entirely on the mineralogical remains of the microbes, which themselves had neither been brought into culture or been assigned to a specific phylogenetic clade. We have used both cultivation and cultivation-independent techniques to study Fe-rich microbial mats associated with hydrothermal venting at Loihi Seamount, a submarine volcano. Using gradient enrichment techniques, two iron-oxidizing bacteria, strains PV-1 and JV-1, were isolated. Chemolithotrophic growth was observed under microaerobic conditions; Fe(II) and Fe0 were the only energy sources that supported growth. Both strains produced filamentous stalk-like structures composed of multiple nanometer sized fibrils of Fe-oxyhydroxide. These were consistent with mineralogical structures found in the iron mats. Phylogenetic analysis of the small subunit (SSU) rRNA gene demonstrated that strains PV-1 and JV-1 were identical and formed a monophyletic group deeply rooted within the Proteobacteria. The most similar sequence (85.3% similarity) from a cultivated isolate came from Methylophaga marina. Phylogenetic analysis of the RecA and GyrB protein sequences confirmed that these strains are distantly related to other members of the Proteobacteria. A cultivation-independent analysis of the SSU rRNA gene by terminal-restriction fragment (T-RF) profiling showed that this phylotype was most common in a variety of microbial mats collected at different times and locations at Loihi. On the basis of phylogenetic and physiological data, it is proposed that isolate PV-1T ( = 1ATCC BAA-1019: JCM 14766) represents the type strain of a novel species in a new genus, Mariprofundus ferrooxydans gen. nov., sp. nov. Furthermore, the strain is the first cultured representative of a new candidatus class of the Proteobacteria that is widely distributed in deep-sea environments, Candidatus ζ (zeta)-Proteobacteria cl. nov.
    Description: Funding was provided to DE and CLM by the National Science Foundation (0348330) and to DE through the NASA Astobiology Institute.
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  • 6
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    Superfast vocal muscles control song production in songbirds (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Authors, 2008. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 3 (2008): e2581, doi:10.1371/journal.pone.0002581.
    Description: Birdsong is a widely used model for vocal learning and human speech, which exhibits high temporal and acoustic diversity. Rapid acoustic modulations are thought to arise from the vocal organ, the syrinx, by passive interactions between the two independent sound generators or intrinsic nonlinear dynamics of sound generating structures. Additionally, direct neuromuscular control could produce such rapid and precisely timed acoustic features if syringeal muscles exhibit rare superfast muscle contractile kinetics. However, no direct evidence exists that avian vocal muscles can produce modulations at such high rates. Here, we show that 1) syringeal muscles are active in phase with sound modulations during song over 200 Hz, 2) direct stimulation of the muscles in situ produces sound modulations at the frequency observed during singing, and that 3) syringeal muscles produce mechanical work at the required frequencies and up to 250 Hz in vitro. The twitch kinematics of these so-called superfast muscles are the fastest measured in any vertebrate muscle. Superfast vocal muscles enable birds to directly control the generation of many observed rapid acoustic changes and to actuate the millisecond precision of neural activity into precise temporal vocal control. Furthermore, birds now join the list of vertebrate classes in which superfast muscle kinetics evolved independently for acoustic communication.
    Description: This study was funded by NIH DC04390 and DC06876 to FG, and NIH AR38404-20 and NIH AR46125 to LCR. The work was also supported by a grant from the Pennsylvania Department of Health to LCR.
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  • 7
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    Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Authors, 2007. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 2 (2007): e671, doi:10.1371/journal.pone.0000671.
    Description: Rotifers are among the most common non-arthropod animals and are the most experimentally tractable members of the basal assemblage of metazoan phyla known as Gnathifera. The monogonont rotifer Brachionus plicatilis is a developing model system for ecotoxicology, aquatic ecology, cryptic speciation, and the evolution of sex, and is an important food source for finfish aquaculture. However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking. We generated and partially sequenced a cDNA library from B. plicatilis and constructed a database of over 2300 expressed sequence tags corresponding to more than 450 transcripts. About 20% of the transcripts had no significant similarity to database sequences by BLAST; most of these contained open reading frames of significant length but few had recognized Pfam motifs. Sixteen transcripts accounted for 25% of the ESTs; four of these had no significant similarity to BLAST or Pfam databases. Putative up- and downstream untranslated regions are relatively short and AT rich. In contrast to bdelloid rotifers, there was no evidence of a conserved trans-spliced leader sequence among the transcripts and most genes were single-copy. Despite the small size of this EST project it revealed several important features of the rotifer transcriptome and of individual monogonont genes. Because there is little genomic data for Gnathifera, the transcripts we found with no known function may represent genes that are species-, class-, phylum- or even superphylum-specific; the fact that some are among the most highly expressed indicates their importance. The absence of trans-spliced leader exons in this monogonont species contrasts with their abundance in bdelloid rotifers and indicates that the presence of this phenomenon can vary at the subphylum level. Our EST database provides a relatively large quantity of transcript-level data for B. plicatilis, and more generally of rotifers and other gnathiferan phyla, and can be browsed and searched at gmod.mbl.edu.
    Description: This research was supported by the Nagasaki Prefecture Collaboration of Regional Entities for the Advancement of Technological Excellence, Japan Science and Technology Agency to KS, YT, YS and AH, and US NSF grants EF-0412674 and MCB-0544199 to DMW.
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  • 8
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    Climate change, precipitation and impacts on an estuarine refuge from disease (2011)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e18849, doi:10.1371/journal.pone.0018849.
    Description: Oysters play important roles in estuarine ecosystems but have suffered recently due to overfishing, pollution, and habitat loss. A tradeoff between growth rate and disease prevalence as a function of salinity makes the estuarine salinity transition of special concern for oyster survival and restoration. Estuarine salinity varies with discharge, so increases or decreases in precipitation with climate change may shift regions of low salinity and disease refuge away from optimal oyster bottom habitat, negatively impacting reproduction and survival. Temperature is an additional factor for oyster survival, and recent temperature increases have increased vulnerability to disease in higher salinity regions. We examined growth, reproduction, and survival of oysters in the New York Harbor-Hudson River region, focusing on a low-salinity refuge in the estuary. Observations were during two years when rainfall was above average and comparable to projected future increases in precipitation in the region and a past period of about 15 years with high precipitation. We found a clear tradeoff between oyster growth and vulnerability to disease. Oysters survived well when exposed to intermediate salinities during two summers (2008, 2010) with moderate discharge conditions. However, increased precipitation and discharge in 2009 reduced salinities in the region with suitable benthic habitat, greatly increasing oyster mortality. To evaluate the estuarine conditions over longer periods, we applied a numerical model of the Hudson to simulate salinities over the past century. Model results suggest that much of the region with suitable benthic habitat that historically had been a low salinity refuge region may be vulnerable to higher mortality under projected increases in precipitation and discharge. Predicted increases in precipitation in the northeastern United States due to climate change may lower salinities past important thresholds for oyster survival in estuarine regions with appropriate substrate, potentially disrupting metapopulation dynamics and impeding oyster restoration efforts, especially in the Hudson estuary where a large basin constitutes an excellent refuge from disease.
    Description: Funding was provided by the Hudson River Foundation, grant number 00607A, and the New York State Department of Environmental Conservation (MOU 2008).
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  • 9
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    The taxonomic and functional diversity of microbes at a temperate coastal site : a ‘multi-omic’ study of seasonal and diel temporal variation (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 5 (2010): e15545, doi:10.1371/journal.pone.0015545.
    Description: How microbial communities change over time in response to the environment is poorly understood. Previously a six-year time series of 16S rRNA V6 data from the Western English Channel demonstrated robust seasonal structure within the bacterial community, with diversity negatively correlated with day-length. Here we determine whether metagenomes and metatranscriptomes follow similar patterns. We generated 16S rRNA datasets, metagenomes (1.2 GB) and metatranscriptomes (157 MB) for eight additional time points sampled in 2008, representing three seasons (Winter, Spring, Summer) and including day and night samples. This is the first microbial ‘multi-omic’ study to combine 16S rRNA amplicon sequencing with metagenomic and metatranscriptomic profiling. Five main conclusions can be drawn from analysis of these data: 1) Archaea follow the same seasonal patterns as Bacteria, but show lower relative diversity; 2) Higher 16S rRNA diversity also reflects a higher diversity of transcripts; 3) Diversity is highest in winter and at night; 4) Community-level changes in 16S-based diversity and metagenomic profiles are better explained by seasonal patterns (with samples closest in time being most similar), while metatranscriptomic profiles are better explained by diel patterns and shifts in particular categories (i.e., functional groups) of genes; 5) Changes in key genes occur among seasons and between day and night (i.e., photosynthesis); but these samples contain large numbers of orphan genes without known homologues and it is these unknown gene sets that appear to contribute most towards defining the differences observed between times. Despite the huge diversity of these microbial communities, there are clear signs of predictable patterns and detectable stability over time. Renewed and intensified efforts are required to reveal fundamental deterministic patterns in the most complex microbial communities. Further, the presence of a substantial proportion of orphan sequences underscores the need to determine the gene products of sequences with currently unknown function.
    Description: Funding for this work was provided by a Natural Environmental Research Council (www.nerc.ac.uk) grant, NE/F00138X/1.
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  • 10
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    The relationship among oceanography, prey fields, and beaked whale foraging habitat in the Tongue of the Ocean (2011)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: This article is distributed under the terms of the Creative Commons CC0 public domain dedication. The definitive version was published in PLoS One 6 (2011): e19269, doi:10.1371/journal.pone.0019269.
    Description: Beaked whales, specifically Blainville's (Mesoplodon densirostris) and Cuvier's (Ziphius cavirostris), are known to feed in the Tongue of the Ocean, Bahamas. These whales can be reliably detected and often localized within the Atlantic Undersea Test and Evaluation Center (AUTEC) acoustic sensor system. The AUTEC range is a regularly spaced bottom mounted hydrophone array covering 〉350 nm2 providing a valuable network to record anthropogenic noise and marine mammal vocalizations. Assessments of the potential risks of noise exposure to beaked whales have historically occurred in the absence of information about the physical and biological environments in which these animals are distributed. In the fall of 2008, we used a downward looking 38 kHz SIMRAD EK60 echosounder to measure prey scattering layers concurrent with fine scale turbulence measurements from an autonomous turbulence profiler. Using an 8 km, 4-leaf clover sampling pattern, we completed a total of 7.5 repeat surveys with concurrently measured physical and biological oceanographic parameters, so as to examine the spatiotemporal scales and relationships among turbulence levels, biological scattering layers, and beaked whale foraging activity. We found a strong correlation among increased prey density and ocean vertical structure relative to increased click densities. Understanding the habitats of these whales and their utilization patterns will improve future models of beaked whale habitat as well as allowing more comprehensive assessments of exposure risk to anthropogenic sound.
    Description: The data collection and analysis was funded by the Office of Naval Research as N00014-08-1-1162.
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