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Item Bioluminescence as an ecological factor during high Arctic polar night(Nature Publishing Group, 11/2/16) Cronin,Heather A.; Cohen,Jonathan H.; Berge,Jorgen; Johnsen,Geir; Moline,Mark A.; Heather A. Cronin, Jonathan H. Cohen, J�rgen Berge, Geir Johnsen, Mark A. Moline; Cohen, Jonathan Hirsch; Moline, Mark AlanBioluminescence commonly influences pelagic trophic interactions at mesopelagic depths. Here we characterize a vertical gradient in structure of a generally low species diversity bioluminescent community at shallower epipelagic depths during the polar night period in a high Arctic fjord with in situ bathyphotometric sampling. Bioluminescence potential of the community increased with depth to a peak at 80 m. Community composition changed over this range, with an ecotone at 20-40 m where a dinoflagellate-dominated community transitioned to dominance by the copepod Metridia longa. Coincident at this depth was bioluminescence exceeding atmospheric light in the ambient pelagic photon budget, which we term the bioluminescence compensation depth. Collectively, we show a winter bioluminescent community in the high Arctic with vertical structure linked to attenuation of atmospheric light, which has the potential to influence pelagic ecology during the light-limited polar night.Item Mitochondrial DNA analysis of population structure in the Atlantic croaker, Micropogonias undulatus (Perciformes: Sciaenidae)(United States. National Marine Fisheries Service., 1999) Lankford, Thomas E. Jr.; Targett, Timothy E.; Gaffney, Patrick M.; Thomas E. Lankford Jr., Timothy E. Targett, Patrick M. Gaffney; Lankford, Thomas E. Jr.; Targett, Timothy E.; Gaffney, Patrick M.Genetic population struc- ture in Atlantic croaker ( Micropogonias undulatus Linnaeus) was examined by using the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis of mi- tochondrial DNA (mtDNA). Juvenile croaker from three U.S. Atlantic locali- ties (Delaware, North Carolina, and Florida) and one Gulf of Mexico local- ity (Louisiana) were screened to docu- ment the magnitude and spatial distri- bution of mtDNA variation in M. undulatus ; to evaluate the integrity of Cape Hatteras, North Carolina, as a genetic stock boundary; and to estimate levels of gene flow among Atlantic lo- calities to provide an improved basis for future decisions regarding coastwide management of this fishery resource. RFLP analysis of the ATPase 6 and D-loop mtDNA regions revealed a total of 15 composite haplotypes in 93 indi- viduals. Monte Carlo simulations re- vealed no geographic heterogeneity in mtDNA haplotype frequencies among Atlantic localities and no evidence that juveniles collected north and south of Cape Hatteras originated from sepa- rate gene pools (net sequence diver- gence=–0.002%). There was significant heterogeneity between Atlantic and Gulf of Mexico samples, suggesting re- stricted gene flow between these two re- gions. Analysis of molecular variance also indicated regional (Atlantic versus Gulf) population structure, but pro- vided no evidence that Cape Hatteras represents a genetic stock boundary. AMOVA indicated relatively high gene flow ( N e m U = 12–23 effective female mi- grants per generation) among Atlantic localities. These findings are consistent with 1) a single genetic stock of M . undulatus on the Atlantic coast and 2) separate, weakly differentiated stocks in the Atlantic and Gulf of Mexico.Item The Guaymas Basin Hiking Guide to Hydrothermal Mounds, Chimneys, and Microbial Mats: Complex Seafloor Expressions of Subsurface Hydrothermal Circulation(Frontiers Media Sa, 2/18/16) Teske,Andreas; de Beer,Dirk; McKay,Luke J.; Tivey,Margaret K.; Biddle,Jennifer F.; Hoer,Daniel; Lloyd,Karen G.; Lever,Mark A.; Roy,Hans; Albert,Daniel B.; Mendlovitz,Howard P.; MacGregor,Barbara J.; Andreas Teske, Dirk de Beer, Luke J. McKay, Margaret K. Tivey, Jennifer F. Biddle, Daniel Hoer, Karen G. Lloyd, Mark A. Lever, Hans Roy, Daniel B. Albert, Howard P. Mendlovitz and Barbara J. MacGregor; Biddle, Jennifer FrancesThe hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region.Item Spectral Reflectance of Palauan Reef-Building Coral with Different Symbionts in Response to Elevated Temperature(MDPI Ag, 2/23/16) Russell,Brandon J.; Dierssen,Heidi M.; LaJeunesse,Todd C.; Hoadley,Kenneth D.; Warner,Mark E.; Kemp,Dustin W.; Bateman,Timothy G.; Brandon J. Russell, Heidi M. Dierssen, Todd C. LaJeunesse, Kenneth D. Hoadley, Mark E. Warner, Dustin W. Kemp and Timothy G. Bateman; Hoadley, Kenneth D;Warner, Mark ESpectral reflectance patterns of corals are driven largely by the pigments of photosynthetic symbionts within the host cnidarian. The warm inshore bays and cooler offshore reefs of Palau share a variety of coral species with differing endosymbiotic dinoflagellates (genus: Symbiodinium), with the thermally tolerant Symbiodinium trenchii (S. trenchii) (= type D1a or D1-4) predominating under the elevated temperature regimes inshore, and primarily Clade C types in the cooler reefs offshore. Spectral reflectance of two species of stony coral, Cyphastrea serailia (C. serailia) and Pachyseris rugosa (P. rugosa), from both inshore and offshore locations shared multiple features both between sites and to similar global data from other studies. No clear reflectance features were evident which might serve as markers of thermally tolerant S. trenchii symbionts compared to the same species of coral with different symbionts. Reflectance from C. serailia colonies from inshore had a fluorescence peak at approximately 500 nm which was absent from offshore animals. Integrated reflectance across visible wavelengths had an inverse correlation to symbiont cell density and could be used as a relative indicator of the symbiont abundance for each type of coral. As hypothesized, coral colonies from offshore with Clade C symbionts showed a greater response to experimental heating, manifested as decreased symbiont density and increased reflectance or "bleaching" than their inshore counterparts with S. trenchii. Although no unique spectral features were found to distinguish species of symbiont, spectral differences related to the abundance of symbionts could prove useful in field and remote sensing studies.Item Ecophysiological responses of juvenile summer and winter flounder to hypoxia: experimental and modeling analyses of effects on estuarine nursery quality(Inter-Research, 2006-11-07) Stierhoff, Kevin L.; Targett, Timothy E.; Miller, KerriLynn; Kevin L. Stierhoff, Timothy E. Targett, KerriLynn Miller; Stierhoff, Kevin L.; Targett, Timothy E.; Miller, KerriLynnGrowth and feeding rates were measured in juvenile summer flounder Paralichthys dentatus and winter flounder Pseudopleuronectes americanus exposed to sub-lethal hypoxia (low dissolved oxygen, DO) over a range of temperatures, to determine its potential effects on nursery habitat quality for these 2 estuary-dependent flatfishes. Growth rates of both species were generally reduced as DO decreased, particularly at DO levels of 50 to 70% air saturation, and as temperature increased. Summer flounder were more tolerant of low DO than were winter flounder at both 20 and 25°C. At these temperatures, summer flounder growth was reduced by ~25% (compared to growth at normoxia [7.0 mg O2 l–1]) at 3.5 mg O2 l–1 and by 50 to 60% at 2.0 mg O2 l–1. In contrast, growth of winter flounder at 20°C was reduced by ~50% at both 3.5 and 5.0 mg O2 l–1, and growth was zero at 2.0 mg O2 l–1. At 25°C, winter flounder grew poorly in all DO treatments and lost weight at 2.0 mg O2 l–1. Summer flounder were also tested at 30°C. Growth was significantly reduced even at 5.0 mg O2 l–1, and was reduced by ~90% at 2.0 mg O2 l–1. A significant relationship between feeding rate and growth suggested reduced consumption to be a major cause of growth limitation under hypoxia. There was no evidence of growth acclimation for either species after 7 to 14 d exposure to hypoxia. The effect of hypoxia on growth of summer flounder was reduced at lower salinity (15 vs. 25‰) and was unaffected by the presence of a sand substrate. Similarity between modeled growth under hypoxic conditions, based on our laboratory results, and observed growth of summer flounder in a hypoxic estuarine tributary suggests growth limitation in the wild. These laboratory and field results demonstrate that even moderate hypoxia can adversely affect growth rates, and thus the quality of estuarine nursery habitats for juvenile flatfishes.Item Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes(PLOS (Public Library of Science), 2015-04-30) Fauteux, Lisa; Cottrell, Matthew T.; Kirchman, David L.; Borrego, Carles M.; Garcia-Chaves, Maria Carolina; del Giorgio, Paul A.; Lisa Fauteux, Matthew T. Cottrell, David L. Kirchman, Carles M. Borrego, Maria Carolina Garcia-Chaves, Paul A. del Giorgio; Cottrell, Matthew T.; Kirchman, David L.There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cellsmL-1, representing <1 to 37%of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6%and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes.Our results suggest that photoheterotrophymight represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.Item And on top of all that…: Coping with ocean acidification in the midst of many stressors(The Oceanography Society., 2015-06-01) Breitburg, Denise L.; Salisbury, Joseph; Bernhard, Joan M.; Cai, Wei-Jun; Dupont, Sam; Doney, Scott C.; Kroeker, Kristy J.; Levin, Lisa A.; Long, Christopher; Milke, Lisa M.; Miller, Seth H.; Phelan, Beth; Passow, Uta; Seibel, Brad A.; Todgham, Anne E.; Tarrant, Ann M.; Denise L. Breitburg, Joseph Salisbury, Joan M. Bernhard, Wei-Jun Cai, Sam Dupont, Scott C. Doney, Kristy J. Kroeker, Lisa A. Levin, W. Christopher Long, Lisa M. Milke, Seth H. Miller, Beth Phelan, Uta Passow, Brad A. Seibel, Anne E. Todgham, and Ann M. Tarrant; Cai, Wei-JunOceanic and coastal waters are acidifying due to processes dominated in the open ocean by increasing atmospheric CO2 and dominated in estuaries and some coastal waters by nutrient-fueled respiration. The patterns and severity of acidification, as well as its effects, are modified by the host of stressors related to human activities that also influence these habitats. Temperature, deoxygenation, and changes in food webs are particularly important co-stressors because they are pervasive, and both their causes and effects are often mechanistically linked to acidification. Development of a theoretical underpinning to multiple stressor research that considers physiological, ecological, and evolutionary perspectives is needed because testing all combinations of stressors and stressor intensities experimentally is impossible. Nevertheless, use of a wide variety of research approaches is a logical and promising strategy for improving understanding of acidification and its effects. Future research that focuses on spatial and temporal patterns of stressor interactions and on identifying mechanisms by which multiple stressors affect individuals, populations, and ecosystems is critical. It is also necessary to incorporate consideration of multiple stressors into management, mitigation, and adaptation to acidification and to increase public and policy recognition of the importance of addressing acidification in the context of the suite of other stressors with which it potentially interacts.Item Is Ambient Light during the High Arctic Polar Night Sufficient to Act as a Visual Cue for Zooplankton?(PLOS (Public Library of Science), 2015-06-03) Cohen, Jonathan H.; Berge, Jørgen; Moline, Mark A.; Sørensen, Asgeir J.; Last, Kim; Falk-Petersen, Stig; Renaud, Paul E.; Leu, Eva S.; Grenvald, Julie; Cottier, Finlo; Cronin, Heather; Menze, Sebastian; Norgren, Petter; Varpe, Øystein; Daase, Malin; Darnis, Gerald; Johnsen, Geir; Jonathan H. Cohen, Jørgen Berge, Mark A. Moline, Asgeir J. Sørensen, Kim Last, Stig Falk-Petersen, Paul E. Renaud, Eva S. Leu, Julie Grenvald, Finlo Cottier, Heather Cronin, Sebastian Menze, Petter Norgren, Øystein Varpe, Malin Daase, Gerald Darnis, Geir Johnsen; Cohen, Jonathan H.; Moline, Mark A.; Cronin, HeatherThe light regime is an ecologically important factor in pelagic habitats, influencing a range of biological processes. However, the availability and importance of light to these processes in high Arctic zooplankton communities during periods of 'complete' darkness (polar night) are poorly studied. Here we characterized the ambient light regime throughout the diel cycle during the high Arctic polar night, and ask whether visual systems of Arctic zooplankton can detect the low levels of irradiance available at this time. To this end, light measurements with a purpose-built irradiance sensor and coupled all-sky digital photographs were used to characterize diel skylight irradiance patterns over 24 hours at 79°N in January 2014 and 2015. Subsequent skylight spectral irradiance and in-water optical property measurements were used to model the underwater light field as a function of depth, which was then weighted by the electrophysiologically determined visual spectral sensitivity of a dominant high Arctic zooplankter, Thysanoessa inermis. Irradiance in air ranged between 1–1.5 x 10-5 μmol photons m-2 s-1 (400–700 nm) in clear weather conditions at noon and with the moon below the horizon, hence values reflect only solar illumination. Radiative transfer modelling generated underwater light fields with peak transmission at blue-green wavelengths, with a 465 nm transmission maximum in shallow water shifting to 485 nm with depth. To the eye of a zooplankter, light from the surface to 75 m exhibits a maximum at 485 nm, with longer wavelengths (>600 nm) being of little visual significance. Our data are the first quantitative characterisation, including absolute intensities, spectral composition and photoperiod of biologically relevant solar ambient light in the high Arctic during the polar night, and indicate that some species of Arctic zooplankton are able to detect and utilize ambient light down to 20–30m depth during the Arctic polar night.Item How Spatial Relationships Influence Economic Preferences for Wind Power—A Review(MDPI AG, 2015-06-23) Knapp, Lauren; Ladenburg, Jacob; Lauren Knapp and Jacob Ladenburg; Knapp, LaurenAn increasing number of studies in the environmental and resource economic literature suggest that preferences for changes or improvements in environmental amenities, from water quality to recreation, are spatially heterogeneous. One of these effects in particular, distance decay, suggests that respondents exhibit a higher willingness to pay (WTP) the closer they live to a proposed environmental improvement and vice versa. The importance of spatial effects cannot be underestimated. Several of these studies find significant biases in aggregate WTP values, and therefore social welfare, from models that disregard spatial factors. This relationship between spatial aspects and preferences, however, remains largely ignored in the non-market valuation literature applied to valuing preferences for renewable energy, generally, and wind power, specifically. To our knowledge, fourteen peer-reviewed studies have been conducted to estimate stated preferences (SP) for onshore and/or offshore wind development, yet less than half of those utilize any measure to account for the relationship between spatial effects and preferences. Fewer still undertake more robust measures that account for these spatially dependent relationships, such as via GIS, outside incorporating a single ‘distance’ attribute within the choice experiment (CE) referenda. This paper first reviews the methodologies of the SP wind valuation studies that have integrated measure(s) to account for spatial effects. We then categorize these effects into three dimensions—distance to a proposed wind project, distance to existing wind project(s), and cumulative effects—supporting each with a discussion of significant findings, including those found in the wind hedonic and acceptance literature. Policy implications that can be leveraged to maximize social welfare when siting future wind projects as well as recommendations for additional research to control for preference spatial heterogeneity in wind CEs are also posited.Item Temporal and Spatial Comparisons of Underwater Sound Signatures of Different Reef Habitats in Moorea Island, French Polynesia(PLOS (Public Library of Science), 2015-09-09) Bertucci, Frédéric; Parmentier, Eric; Berten, Laëtitia; Brooker, Rohan M.; Lecchini, David; Frédéric Bertucci, Eric Parmentier, Laëtitia Berten, Rohan M. Brooker, David Lecchini; Brooker, Rohan M.As environmental sounds are used by larval fish and crustaceans to locate and orientate towards habitat during settlement, variations in the acoustic signature produced by habitats could provide valuable information about habitat quality, helping larvae to differentiate between potential settlement sites. However, very little is known about how acoustic signatures differ between proximate habitats. This study described within- and between-site differences in the sound spectra of five contiguous habitats at Moorea Island, French Polynesia: the inner reef crest, the barrier reef, the fringing reef, a pass and a coastal mangrove forest. Habitats with coral (inner, barrier and fringing reefs) were characterized by a similar sound spectrum with average intensities ranging from 70 to 78 dB re 1μPa.Hz-1. The mangrove forest had a lower sound intensity of 70 dB re 1μPa.Hz-1 while the pass was characterized by a higher sound level with an average intensity of 91 dB re 1μPa.Hz-1. Habitats showed significantly different intensities for most frequencies, and a decreasing intensity gradient was observed from the reef to the shore. While habitats close to the shore showed no significant diel variation in sound intensities, sound levels increased at the pass during the night and barrier reef during the day. These two habitats also appeared to be louder in the North than in the West. These findings suggest that daily variations in sound intensity and across-reef sound gradients could be a valuable source of information for settling larvae. They also provide further evidence that closely related habitats, separated by less than 1 km, can differ significantly in their spectral composition and that these signatures might be typical and conserved along the coast of Moorea.Item Mechanisms of extracellular S0 globule production and degradation in Chlorobaculum tepidum via dynamic cell–globule interactions(Microbiology Society, 2016-01-07) Marnocha, C. L.; Levy, A. T.; Powell, D. H.; Hanson, T. E.; Chan, C. S.; ; Marnocha, C. L.; Levy, A. T.; Powell, D. H.; Hanson, T. E.; Chan, C. S.The Chlorobiales are anoxygenic phototrophs that produce solid, extracellular elemental sulfur globules as an intermediate step in the oxidation of sulfide to sulfate. These organisms must export sulfur while preventing cell encrustation during S0 globule formation; during globule degradation they must find and mobilize the sulfur for intracellular oxidation to sulfate. To understand how the Chlorobiales address these challenges, we characterized the spatial relationships and physical dynamics of Chlorobaculum tepidum cells and S0 globules by light and electron microscopy. Cba. tepidum commonly formed globules at a distance from cells. Soluble polysulfides detected during globule production may allow for remote nucleation of globules. Polysulfides were also detected during globule degradation, probably produced as an intermediate of sulfur oxidation by attached cells. Polysulfides could feed unattached cells, which made up over 80% of the population and had comparable growth rates to attached cells. Given that S0 is formed remotely from cells, there is a question as to how cells are able to move toward S0 in order to attach. Time-lapse microscopy shows that Cba. tepidum is in fact capable of twitching motility, a finding supported by the presence of genes encoding type IV pili. Our results show how Cba. tepidum is able to avoid mineral encrustation and benefit from globule degradation even when not attached. In the environment, Cba. tepidum may also benefit from soluble sulfur species produced by other sulfur-oxidizing or sulfur-reducing bacteria as these organisms interact with its biogenic S0 globules.Item Mechanisms of extracellular S0 globule production and degradation in Chlorobaculum tepidum via dynamic cell–globule interactions(Microbiology Society, 2016-01-07) Marnocha, C. L.; Levy, A. T.; Powell, D. H.; Hanson, T. E.; Chan, C. S.; C. L. Marnocha, A. T. Levy, D. H. Powell, T. E. Hanson and C. S. Chan; Marnocha, C. L.; Levy, A. T.; Powell, D. H.; Hanson, T. E.; Chan, C. S.The Chlorobiales are anoxygenic phototrophs that produce solid, extracellular elemental sulfur globules as an intermediate step in the oxidation of sulfide to sulfate. These organisms must export sulfur while preventing cell encrustation during S0 globule formation; during globule degradation they must find and mobilize the sulfur for intracellular oxidation to sulfate. To understand how the Chlorobiales address these challenges, we characterized the spatial relationships and physical dynamics of Chlorobaculum tepidum cells and S0 globules by light and electron microscopy. Cba. tepidum commonly formed globules at a distance from cells. Soluble polysulfides detected during globule production may allow for remote nucleation of globules. Polysulfides were also detected during globule degradation, probably produced as an intermediate of sulfur oxidation by attached cells. Polysulfides could feed unattached cells, which made up over 80% of the population and had comparable growth rates to attached cells. Given that S0 is formed remotely from cells, there is a question as to how cells are able to move toward S0 in order to attach. Time-lapse microscopy shows that Cba. tepidum is in fact capable of twitching motility, a finding supported by the presence of genes encoding type IV pili. Our results show how Cba. tepidum is able to avoid mineral encrustation and benefit from globule degradation even when not attached. In the environment, Cba. tepidum may also benefit from soluble sulfur species produced by other sulfur-oxidizing or sulfur-reducing bacteria as these organisms interact with its biogenic S0 globules.Item Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin(Frontiers Media SA, 2016-01-29) Dowell, Frederick; Cardman, Zena; Dasarathy, Srishti; Kellermann, MatthiasY.; Lipp, Julius S.; Ruff, S. Emil; Biddle, Jennifer F.; McKay, Luke J.; MacGregor, Barbara J.; Lloyd, Karen G.; Albert, Daniel B.; Mendlovitz, Howard; Hinrichs, Kai-Uwe; Teske, Andreas; Frederick Dowell, Zena Cardman, Srishti Dasarathy, Matthias Y. Kellermann, Julius S. Lipp, S. Emil Ruff, Jennifer F. Biddle, Luke J. McKay, Barbara J. MacGregor, Karen G. Lloyd, Daniel B. Albert, Howard Mendlovitz, Kai-Uwe Hinrichs and Andreas Teske; Biddle, Jennifer F.The hydrothermal sediments of Guaymas Basin, an active spreading center in the Gulf of California (Mexico), are rich in porewater methane, short-chain alkanes, sulfate and sulfide, and provide a model system to explore habitat preferences of microorganisms, including sulfate-dependent, methane- and short chain alkane-oxidizing microbial communities. In this study, hot sediments (above 60°C) covered with sulfur-oxidizing microbial mats surrounding a hydrothermal mound (termed “Mat Mound”) were characterized by porewater geochemistry of methane, C2–C6 short-chain alkanes, sulfate, sulfide, sulfate reduction rate measurements, in situ temperature gradients, bacterial and archaeal 16S rRNA gene clone libraries and V6 tag pyrosequencing. The most abundantly detected groups in the Mat mound sediments include anaerobic methane-oxidizing archaea of the ANME-1 lineage and its sister clade ANME-1Guaymas, the uncultured bacterial groups SEEP-SRB2 within the Deltaproteobacteria and the separately branching HotSeep-1 Group; these uncultured bacteria are candidates for sulfate-reducing alkane oxidation and for sulfate-reducing syntrophy with ANME archaea. The archaeal dataset indicates distinct habitat preferences for ANME-1, ANME-1-Guaymas, and ANME-2 archaea in Guaymas Basin hydrothermal sediments. The bacterial groups SEEP-SRB2 and HotSeep-1 co-occur with ANME-1 and ANME-1Guaymas in hydrothermally active sediments underneath microbial mats in Guaymas Basin. We propose the working hypothesis that this mixed bacterial and archaeal community catalyzes the oxidation of both methane and short-chain alkanes, and constitutes a microbial community signature that is characteristic for hydrothermal and/or cold seep sediments containing both substrates.Item Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians(Public Library of Science (PLOS), 2016-03-07) Marsh, Adam G.; Hoadley, Kenneth D.; Warner, Mark E.; Adam G. Marsh, Kenneth D. Hoadley, Mark E. Warner; Marsh, Adam G.; Hoadley, Kenneth D.; Warner, Mark E.Coral reefs are under assault from stressors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stress responses across ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular processes with ecological fitness and have identified putative suites of temperature acclimation genes in a Scleractinian coral Acropora hyacinthus.We wondered what unique characteristics of these genes determined their coordinate expression in response to temperature acclimation, and whether or not other corals and cnidarians would likewise possess these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental stressors. We identify common conserved patterns of cytosine-guanosine dinucleotide (CpG) motif frequencies in upstream promoter domains of different functional gene groups in two cnidarian genomes: a coral (Acropora digitifera) and an anemone (Nematostella vectensis). Our analyses show that CpG motif frequencies are prominent in the promoter domains of functional genes associated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (TSS) are 1.38x higher than genomic background levels upstream of -2000 bp from the TSS. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the TSS. In addition, observed shifts in CpG densities among functional groups of genes suggests a potential role for epigenetic DNA methylation within promoter domains to impact functional gene expression responses in A. digitifera and N. vectensis. Identifying promoter epigenetic sequence motifs among genes within specific functional groups establishes an approach to describe integrated cellular responses to environmental stress in reef corals and potential roles of epigenetics on survival and fitness in the face of global climate change.Item Partitioning of Respiration in an Animal-Algal Symbiosis: Implications for Different Aerobic Capacity between Symbiodinium spp.(Frontiers Media S.A., 2016-04-18) Hawkins, Thomas D.; Hagemeyer, Julia C. G.; Hoadley, Kenneth D.; Marsh, Adam G.; Warner, Mark E.; Thomas D. Hawkins, Julia C. G. Hagemeyer, Kenneth D. Hoadley, Adam G. Marsh and Mark E. Warner; Hawkins, Thomas D.; Hagemeyer, Julia C. G.; Hoadley, Kenneth D.; Marsh, Adam G.; Warner, Mark ECnidarian-dinoflagellate symbioses are ecologically important and the subject of much investigation. However, our understanding of critical aspects of symbiosis physiology, such as the partitioning of total respiration between the host and symbiont, remains incomplete. Specifically, we know little about how the relationship between host and symbiont respiration varies between different holobionts (host-symbiont combinations). We applied molecular and biochemical techniques to investigate aerobic respiratory capacity in naturally symbiotic Exaiptasia pallida sea anemones, alongside animals infected with either homologous ITS2-type A4 Symbiodinium or a heterologous isolate of Symbiodinium minutum (ITS2-type B1). In naturally symbiotic anemones, host, symbiont, and total holobiont mitochondrial citrate synthase (CS) enzyme activity, but not host mitochondrial copy number, were reliable predictors of holobiont respiration. There was a positive association between symbiont density and host CS specific activity (mg protein−1), and a negative correlation between host- and symbiont CS specific activities. Notably, partitioning of total CS activity between host and symbiont in this natural E. pallida population was significantly different to the host/symbiont biomass ratio. In re-infected anemones, we found significant between-holobiont differences in the CS specific activity of the algal symbionts. Furthermore, the relationship between the partitioning of total CS activity and the host/symbiont biomass ratio differed between holobionts. These data have broad implications for our understanding of cnidarian-algal symbiosis. Specifically, the long-held assumption of equivalency between symbiont/host biomass and respiration ratios can result in significant overestimation of symbiont respiration and potentially erroneous conclusions regarding the percentage of carbon translocated to the host. The interspecific variability in symbiont aerobic capacity provides further evidence for distinct physiological differences that should be accounted for when studying diverse host-symbiont combinations.Item Assessing the use of a camera system within an autonomous underwater vehicle for monitoring the distribution and density of sea scallops (Placopecten magellanicus) in the Mid-Atlantic Bight(National Marine Fisheries Service., 2016-04-26) Walker, Justin H.; Trembanis, Arthur C.; Miller, Douglas C.; Justin H. Walker, Arthur C. Trembanis and Douglas C. Miller; Walker, Justin H.; Trembanis, Arthur C.; Miller, Douglas C.The sea scallop (Placopecten magellanicus) fishery in the Atlantic is assessed during annual surveys by using both dredging and surface-deployed imaging techniques. In this pilot study in the Mid-Atlantic Bight, we used an autonomous underwater vehicle (AUV) to photograph the seafloor and to evaluate its use for determining scallop density and size. During 22 surveys in 2011, 257 km of seafloor were photographed, resulting in over 203,000 color images. Using trained annotators and photogrammetric software, we determined scallop density and shell heights for 15,252 scallops. The inshore scallop grounds near Long Island (at depths <40 m) had a density of 0.077 scallops per m2, whereas the inshore grounds of the New York Bight had a density of 0.012 scallops per m2. Shell heights derived from images were found to agree well with measurements from scallops collected with a commercial dredge. We show that images obtained with an AUV can be used to reliably estimate both density and shell height consistent with direct sampling from the same area. Moreover, side-scan sonar images obtained with an AUV can be used to detect dredge scars and, therefore, can provide a simultaneous, relative estimate of fishing effort in that area. AUVs provide a highly accurate suite of data for each survey site and therefore allow the design of experimental studies of fishing practices.Item Agents of change and temporal nutrient dynamics in the Altamaha River Watershed(Ecological Society of America, 2017-01-23) Takagi, Kimberly K.; Hunter, Kimberley S.; Cai, Wei-Jun; Joye, Samantha B.; Kimberly K. Takagi, Kimberley S. Hunter, Wei-Jun Cai, and Samantha B. Joye; Cai, Wei-JunNutrient and carbon dynamics in river ecosystems are shifting, and climate change is likely a driving factor; however, some previous studies indicate anthropogenic modification of natural resources may supersede the effects of climate. To understand temporal changes in river ecosystems, consideration of how these agents act independently and collectively to affect watershed biogeochemistry is necessary. Through the Georgia Coastal Ecosystems Long-Term Ecological Research Project, we assessed nutrient (phosphorus, nitrogen, silicate) and carbon dynamics, with specific regard to import and export, in the Altamaha River Basin from 2000 to 2012. This is the first study in the region to document the biogeochemical patterns in the Altamaha’s four main tributaries, the Little Ocmulgee, Ocmulgee, Oconee, and Ohoopee rivers, and the relationships between biogeochemistry and historical precipitation and discharge patterns as well as agricultural and population census data. As discharge patterns are a primary driver of nutrient loads, we determined that water use was a dominant factor in the shifting ecosystem dynamics. Dissolved inorganic nitrogen loads were primarily driven by population density and dissolved inorganic phosphorus loads were strongly influenced by livestock biomass. Taken together, we conclude that both the transportation and biogeochemical cycling of nutrients within the Altamaha River Watershed were highly impacted by anthropogenic influences, which were then further exacerbated by continued climate change. Furthermore, the N-and P-loads in the Altamaha River and tributaries were dominated by dissolved organic nitrogen and dissolved organic phosphorus, emphasizing a need to further study the bioavailability of these species and the mechanisms driving their potential ecological impacts.Item “Sifarchaeota,” a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy(Applied and Environmental Microbiology, 2021-02-19) Farag, Ibrahim F.; Zhao, Rui; Biddle, Jennifer F.The Asgard superphylum is a deeply branching monophyletic group of Archaea, recently described as some of the closest relatives of the eukaryotic ancestor. The wide application of genomic analyses from metagenome sequencing has established six distinct phyla, whose genomes encode diverse metabolic capacities and which play important biogeochemical and ecological roles in marine sediments. Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off the Costa Rica margin, defining a novel lineage phylogenetically married to “Candidatus Thorarchaeota”; as such, we propose the name “Sifarchaeota” for this phylum. The two Sifarchaeota MAGs encode an anaerobic pathway for methylotrophy enabling the utilization of C1 to C3 compounds (methanol and methylamines) to synthesize acetyl coenzyme A (acetyl-CoA). The MAGs showed a remarkable saccharolytic capabilities compared to other Asgard lineages and encoded diverse classes of carbohydrate active enzymes (CAZymes) targeting different mono-, di-, and oligosaccharides. Comparative genomic analysis based on the full metabolic profiles of different Asgard lineages revealed the close relation between Sifarchaeota and “Candidatus Odinarchaeota” MAGs, which suggested similar metabolic potentials and ecological roles. Furthermore, we identified multiple HGT events from different bacterial donors within Sifarchaeota MAGs, which hypothetically expanded Sifarchaeota capacities for substrate utilization, energy production, and niche adaptation.Item Correcting a major error in assessing organic carbon pollution in natural waters(Science Advances, 2021-04-14) Jiao, Nianzhi; Liu, Jihua; Edwards, Bethanie; Lv, Zongqing; Cai, Ruanhong; Liu,Yongqin; Xiao, Xilin; Wang, Jianning; Jiao, Fanglue; Wang, Rui; Huang, Xingyu; Guo, Bixi; Sun, Jia; Zhang, Rui; Zhang, Yao; Tang, Kai; Zheng, Qiang; Azam, Farooq; Batt, John; Cai, Wei-Jun; He, Chen; Herndl, Gerhard J.; Hill, Paul; Hutchins, David; LaRoche, Julie; Lewis, Marlon; MacIntyre, Hugh; Polimene, Luca; Robinson, Carol; Shi, Quan; Suttle, Curtis A.; Thomas, Helmuth; Wallace, Douglas; Legendre, LouisMicrobial degradation of dissolved organic carbon (DOC) in aquatic environments can cause oxygen depletion, water acidification, and CO2 emissions. These problems are caused by labile DOC (LDOC) and not refractory DOC (RDOC) that resists degradation and is thus a carbon sink. For nearly a century, chemical oxygen demand (COD) has been widely used for assessment of organic pollution in aquatic systems. Here, we show through a multicountry survey and experimental studies that COD is not an appropriate proxy of microbial degradability of organic matter because it oxidizes both LDOC and RDOC, and the latter contributes up to 90% of DOC in high-latitude forested areas. Hence, COD measurements do not provide appropriate scientific information on organic pollution in natural waters and can mislead environmental policies. We propose the replacement of the COD method with an optode-based biological oxygen demand method to accurately and efficiently assess organic pollution in natural aquatic environments.Item A satellite-based mobile warning system to reduce interactions with an endangered species(Ecological Applications, 2021-05-30) Breece, Matthew W.; Oliver, Matthew J.; Fox, Dewayne A.; Hale, Edward A.; Haulsee, Danielle E.; Shatley, Matthew; Bograd, Steven J.; Hazen, Elliott L.; Welch, HeatherEarth-observing satellites are a major research tool for spatially explicit ecosystem nowcasting and forecasting. However, there are practical challenges when integrating satellite data into usable real-time products for stakeholders. The need of forecast immediacy and accuracy means that forecast systems must account for missing data and data latency while delivering a timely, accurate, and actionable product to stakeholders. This is especially true for species that have legal protection. Acipenser oxyrinchus oxyrinchus (Atlantic sturgeon) were listed under the United States Endangered Species Act in 2012, which triggered immediate management action to foster population recovery and increase conservation measures. Building upon an existing research occurrence model, we developed an Atlantic sturgeon forecast system in the Delaware Bay, USA. To overcome missing satellite data due to clouds and produce a 3-d forecast of ocean conditions, we implemented data interpolating empirical orthogonal functions (DINEOF) on daily observed satellite data. We applied the Atlantic sturgeon research model to the DINEOF output and found that it correctly predicted Atlantic sturgeon telemetry occurrences over 90% of the time within a 3-d forecast. A similar framework has been utilized to forecast harmful algal blooms, but to our knowledge, this is the first time a species distribution model has been applied to DINEOF gap-filled data to produce a forecast product for fishes. To implement this product into an applied management setting, we worked with state and federal organizations to develop real-time and forecasted risk maps in the Delaware River Estuary for both state-level managers and commercial fishers. An automated system creates and distributes these risk maps to subscribers’ mobile devices, highlighting areas that should be avoided to reduce interactions. Additionally, an interactive web interface allows users to plot historic, current, future, and climatological risk maps as well as the underlying model output of Atlantic sturgeon occurrence. The mobile system and web tool provide both stakeholders and managers real-time access to estimated occurrences of Atlantic sturgeon, enabling conservation planning and informing fisher behavior to reduce interactions with this endangered species while minimizing impacts to fisheries and other projects.