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The e-newsletter Marine Science Review compiles citations and abstracts of significant marine-related research, selected from more than 710 science journals. Each of its 12 subject areas, which include the range of important issues involving the intersection of human activity with coastal and marine environments, is distributed monthly. You can subscribe to each subject area individually or to all.

Special Edition: 10 Years of Ocean Exploration at NOAA

• Highly Cited Research Articles
• Significant Research: 2009 and 2010

In 2001, the National Oceanic and Atmospheric Administration (NOAA) created a program to explore Earth’s largely unknown ocean for the purpose of discovery and the advancement of knowledge. This program, now part of NOAA’s Office of Ocean Exploration and Research (OER), continues to advance NOAA and national goals to better understand the ocean through discovery, research, technology development, outreach, and education. OER responds to emerging scientific issues leading to discoveries and new technologies that benefit society. The "Highly Cited" and "Significant Research: 2009 and 2010" listed here flowed from ocean expeditions and projects sponsored by OER across 10 years, and are selected from a total of 685 science publications (26 audiovisual publications, including photo galleries and television specials; 34 scientific books and/or book chapters; 118 conference papers; 402 journal articles; 72 magazine articles and 33 technical reports including NOAA technical memoranda) that have been published thus far. A complete list of the journal articles currently known to have been produced with OER support is available online at:

http://www.lib.noaa.gov/researchtools/subjectguides/oceanexplorebib_exped.html

The high number of citations to articles listed in Part I, and the rapid accumulation of citations to articles listed in Part II, indicate that these articles are representative of the most significant research to have been produced as a result of OER support.

Highly Cited Research Articles

• Baums, I.B., Miller, M.W., and Hellberg, M.E.  Regionally isolated populations of an imperiled Caribbean coral, Acropora palmata.  Molecular Ecology 14(5): 1377-1390, 2005.
  Read Abstract >>

  The movements of larvae between marine populations are difficult to follow directly and have been the subject of much controversy, especially in the Caribbean. The debate centres on the degree to which populations are demographically open, such that depleted populations can be replenished by recruitment from distant healthy populations, or demographically closed and thus in need of local management. Given the depressed state of many tropical reef populations, the understanding of these movements now bears critically on the number, placement, and size of marine reserves. Most genetic analyses assume that dispersal patterns have been stable for thousands of generations, thus they commonly reflect past colonization histories more than ongoing dispersal. Recently developed multilocus genotyping approaches, however, have the demonstrated ability to detect both migration and population isolation over far shorter timescales. Previously, we developed five microsatellite markers and demonstrated them to be both Mendelian and coral-specific. Using these markers and Bayesian analyses, we show here that populations of the imperiled reef-building coral, Acropora palmata, have experienced little or no recent genetic exchange between the western and the eastern Caribbean. Puerto Rico is identified as an area of mixing between the two subregions. As a consequence of this regional isolation, populations in the western and eastern Caribbean should have the potential to adapt to local conditions and will require population-specific management strategies.

• Boschi, C., Dini, A., Früh-Green, G.L., and Kelley, D.S.  Isotopic and element exchange during serpentinization and metasomatism at the Atlantis Massif (MAR 30ºN): Insights from B and Sr isotope data.  Geochimica et Cosmochimica Acta 72(7): 1801-1823, 2008.
  Read Abstract >>

  The Lost City hydrothermal system at the southern Atlantis Massif (Mid-Atlantic Ridge, 30ºN) provides a natural laboratory for studying serpentinization processes, the temporal evolution of ultramafic-hosted hydrothermal systems, and alteration conditions during formation and emplacement of an oceanic core complex. Here we present B, 0, and Sr isotope data to investigate fluid/rock interaction and mass transfer during detachment faulting and exhumation of lithospheric sequences within the Atlantis Massif. Our data indicate that extensive serpentinization was a seawater-dominated process that occurred predominately at temperatures of 150-250 ºC and at high integrated W/R ratios that led to a marked boron enrichment (3491 ppm). Boron removal from seawater during serpentinization is positively correlated with changes in δ¹¹B (11-16‰) but shows no correlation with O-isotope composition. Modeling indicates that B concentrations and isotope values of the serpentinites are controlled by transient temperature-pH conditions. In contrast to prior studies, we conclude that low-temperature marine weathering processes are insignificant for boron geochemistry of the Atlantis Massif serpentinites. Talc- and amphibole-rich fault rocks formed within a zone of detachment faulting at temperatures of approximately 270-350 ºC and at low W/R ratios. Talc formation in ultramafic domains in the massif was subsequent to an early stage of serpentinization and was controlled by the access of Si-rich fluids derived through seawater-gabbro interactions. Replacement of serpentine by talc resulted in boron loss and significant lowering of δ¹¹B values (9-10‰), which we model as the product of progressive extraction of boron. Our study provides new constraints on the boron geochemical cycle at oceanic spreading ridges and suggests that serpentinization associated with ultramafic-hosted hydrothermal systems may have important implications for the behavior of boron in subduction zone settings.

• Bosley, K.L., Lavelle, J.W., Brodeur, R.D., Wakefield, W.W., Emmett, R.L., Baker, E.T., and Rehmke, K.M.  Biological and physical processes in and around Astoria submarine Canyon, Oregon, USA.  Journal of Marine Systems 50(1-2): 21-37, 2004.
  Read Abstract >>

  Astoria Canyon represents the westernmost portion of the Columbia River drainage system, with the head of the canyon beginning just 16 km west of the mouth of the Columbia River along the northern Oregon and southern Washington coasts. During the summer of 2001, physical, chemical, and biological measurements in the canyon were taken to better understand the hydrodynamic setting of and the feeding relationships among, the pelagic and benthic communities. Results show that currents were strongly tidal, and transport, where measured, was primarily up and into the canyon below shelf depth as previous studies in the canyon have shown. Temperature time series suggests that the largest diurnal oscillations occurred at, or were trapped near, the bottom of the canyon. Within the upper canyon, subtidal temperature was correlated with upper-level shelf-edge currents, linking subtidal upwelling events in the canyon with near-surface subtidal along-shore flow. Invertebrates, such as shrimp. euphausiids, and squid, as well as mesopelagic fishes, dominated the Isaacs-Kidd midwater trawl catches along the canyon walls. Large trawl catches were comprised mainly of lake and rockfishes (shallow trawls) and macrourids, scorpaenids, stomiids. and zoarcids (bottom trawls). Gut-content analysis of rockfishes and lanternfishes revealed substantial use of midwater prey such as euphausiids and mesopelagic fishes. The δ¹³C values of fishes and invertebrates reflected local primary production, as indicated by particulate organic matter (POM) δ¹³C values from samples collected at various depths along the axis of the canyon, as well as across the canyon at several sites. The δ¹⁵N values of fishes and invertebrates indicated lanternfishes, along with euphausiids, amphipods, shrimp and squid, may be important dietary components of higher-tropic-level fishes in both the benthic and benthopelagic food webs. The δ¹³C and δ¹⁵N values of Sebastes species showed significant enrichment in the adults of species that are largely piscivorous relative to the values of adults of more omnivorous species.

• Cordes, E.E., Carney, S.L., Hourdez, S., Carney, R.S., Brooks, J.M., and Fisher, C.R.  Cold seeps of the deep Gulf of Mexico: Community structure and biogeographic comparisons to Atlantic equatorial belt seep communities.  Deep-Sea Research Part I—Oceanographic Research Papers 54(4): 637-653, 2007.
  Read Abstract >>

  Quantitative collections of tubeworm- and mussel-associated communities were obtained from 3 cold seep sites in the deep Gulf of Mexico: in Atwater Valley at 1890 m depth, in Alaminos Canyon at 2200 in depth, and from the Florida Escarpment at 3300 in depth. A total of 50 taxa of macro- and megafauna were collected including 2 species of siboglinid tubeworms and 3 species of bathymodiolin mussels. In general, the highest degree of similarity was between communities collected from the same site. Most of the dominant families at the well-characterized upper Louisiana slope seep sites of the Gulf of Mexico were present at the deep sites as well; however, there was little overlap at the species level between the upper and lower slope communities. One major difference in community structure between the upper and lower slope seeps was the dominance of the ophiuroid Ophioctenella acies in the deeper communities. The transition between upper and lower slope communities appears to occur between 1300 and 1700m based on the number of shared species with the Barbados seeps at either end of this depth range. Seep communities of the deep Gulf of Mexico were more similar to the Barbados Accretionary Prism seep communities than they were to either the upper slope Gulf of Mexico or Blake Ridge communities based on numbers of shared species and Bray-Curtis similarity values among sites. The presence of shared species among these sites suggests that there is ongoing or recent exchange among these areas. An analysis of bathymodioline mussel phylogeography that includes new collections from the west coast of Africa is presented. This analysis also suggests recent exchange across the Atlantic equatorial belt from the Gulf of Mexico to the seeps of the West Nigerian margin.

• Cordes, E.E., Hourdez, S., Predmore, B.L., Redding, M.L., and Fisher, C.R.  Succession of hydrocarbon seep communities associated with the long-lived foundation species Lamellibrachia luymesi.  Marine Ecology Progress Series 305: 17-29, 2005.
  Open Access >>
  Read Abstract >>

  The vestimentiferan tubeworm Lamellibrachia luymesi lives for over 250 yr and forms aggregations of hundreds to thousands of individuals at hydrocarbon seep sites in the Gulf of Mexico. A succession model has been proposed where changes in the abiotic environment within tubeworm aggregations lead to shifts in the associated community structure. Here, we test this model using new data from communities associated with 13 tubeworm aggregations. We quantify the temporal scale of succession by using a population-growth model to estimate aggregation age. In older tubeworm aggregations, biomass, density, and number of species m^-2 tube surface area decline. In addition, primary producer, primary consumer, and endemic species comprise a smaller proportion of the tubeworm-associated community in old aggregations. These changes in the associated community are attributed to lower epibenthic sulfide concentrations in older aggregations. A number of species' densities show strong correlations to sulfide concentration, and similarity between communities is best explained by a combination of aggregation age and sulfide concentration. Together, these data demonstrate the role of hydrogen sulfide in this seep habitat and the effect that the hypothesized reduction of epibenthic sulfide concentration by L. luymesi would have on the associated community.

• Davis, A.S., Clague, D.A., Bohrson, W.A., Dalrymple, G.B., and Greene, H.G.  Seamounts at the continental margin of California: A different kind of oceanic intraplate volcanism. Geological Society of America Bulletin 114(3): 316-333, 2002.
  Read Abstract >>

  Davidson, Guide, Pioneer, Gumdrop, and Rodriguez Seamounts, located at the continental margin offshore California between latitudes 37.5ºN and 34.0ºN, may represent a previously unrecognized type of intraplate oceanic volcanism. Morphologically unlike typical oceanic-island volcanoes or near-ridge seamounts, they are complex, northeast-trending ridges that reflect the ridge-parallel structure of the underlying oceanic crust. ⁴⁰Ar/³⁹Ar laser fusion ages of mineral separates indicate at least two episodes of volcanism at ca. 16 and ca. 12 Ma, younger by 7-11 m.y. than the underlying ocean crust. Volcanic rocks are predominantly differentiated alkalic basalt, hawaiite, and mugearite. The lack of coherent liquid-lines-of-descent is consistent with small batches of magma forming, fractionally crystallizing, and erupting in isolation from the previous and subsequent batches. The presence of mantle xenoliths suggests that magmas originated in the upper mantle. Xenoliths of alkalic cumulates and xenocrysts of feldspar, amphibole, and titanomagnetite are consistent with fractionation in the upper mantle as well. Sr, Nd, and Pb isotope ratios of some samples are from depleted-mantle sources like those of MORB (mid-oceanic-ridge basalt); others indicate more variably enriched mantle sources. Magmas formed by small-percentage partial melting of variably enriched MORB-source-type mantle, according to the samples' high abundances of incompatible elements such as Nb, Ta, and Th. Coeval middle Miocene basalts in onshore coastal California have a similar isotopic range, but their trace elements show a subduction-related signature. If the coeval volcanic rocks offshore originated in a slab window, as proposed for those onshore, they were not influenced by a slab component. Although a slab-window origin is plausible for the middle Miocene volcanism, later episodes of small, sporadic eruptions on- and offshore probably resulted from decompression melting of mantle rising along existing zones of weakness undergoing extension related to continued movement along transform-fault systems.

• Duperron, S., Sibuet, M., MacGregor, B.J., Kuypers, M.M.M., Fisher, C.R., and Dubilier, N. Diversity, relative abundance and metabolic potential of bacterial endosymbionts in three Bathymodiolus mussel species from cold seeps in the Gulf of Mexico.Environmental Microbiology 9(6): 1423-1438, 2007.
  Read Abstract >>

  Cold seeps in the Gulf of Mexico are often dominated by mussels of the genus Bathymodiolus that harbour symbiotic bacteria in their gills. In this study, we analysed symbiont diversity, abundance and metabolic potential in three mussel species from the northern Gulf of Mexico: Bathymodiolus heckerae from the West Florida Escarpment, Bathymodiolus brooksi from Atwater Valley and Alaminos Canyon, and 'Bathymodiolus' childressi, which co-occurs with B. brooksi in Alaminos Canyon. Comparative 16S rRNA sequence analysis confirmed a single methanotroph-related symbiont in 'B.' childressi and a dual symbiosis with a methanotroph- and thiotroph-related symbiont in B. brooksi. A previously unknown diversity of four co-occurring symbionts was discovered in B. heckerae: a methanotroph, two phylogenetically distinct thiotrophs and a methylotroph-related phylotype not previously described from any marine invertebrate symbiosis. A gene characteristic of methane-oxidzing bacteria, pmoA, was identified in all three mussel species confirming the methanotrophic potential of their symbionts. Stable isotope analyses of lipids and whole tissue also confirmed the importance of methanotrophy in the carbon nutrition of all of the mussels. Analyses of absolute and relative symbiont abundance in B. heckerae and B. brooksi using fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization indicated a clear dominance of methanotrophic over thiotrophic symbionts in their gill tissues. A site-dependent variability in total symbiont abundance was observed in B. brooksi, with specimens from Alaminos Canyon harbouring much lower densities than those from Atwater Valley. This shows that symbiont abundance is not species-specific but can vary considerably between populations.

• Embley, R.W. et al.  Long-term eruptive activity at a submarine arc volcano.  Nature 441(7092): 494-497, 2006.
  Read Abstract >>

  Three-quarters of the Earth's volcanic activity is submarine, located mostly along the mid-ocean ridges, with the remainder along intraoceanic arcs and hotspots at depths varying from greater than 4,000 m to near the sea surface. Most observations and sampling of submarine eruptions have been indirect, made from surface vessels or made after the fact. We describe here direct observations and sampling of an eruption at a submarine arc volcano named NW Rota-1, located 60 km northwest of the island of Rota (Commonwealth of the Northern Mariana Islands). We observed a pulsating plume permeated with droplets of molten sulphur disgorging volcanic ash and lapilli from a 15-m diameter pit in March 2004 and again in October 2005 near the summit of the volcano at a water depth of 555 m (depth in 2004). A turbid layer found on the flanks of the volcano (in 2004) at depths from 700 m to more than 1,400 m was probably formed by mass-wasting events related to the eruption. Long-term eruptive activity has produced an unusual chemical environment and a very unstable benthic habitat exploited by only a few mobile decapod species. Such conditions are perhaps distinctive of active arc and hotspot volcanoes.

• Hopcroft, R.R., Clarke, C., Nelson, R.J., and Raskoff, K.A.  Zooplankton communities of the Arctic's Canada Basin: the contribution by smaller taxa.  Polar Biology 28(3): 2005.
  Read Abstract >>

  Zooplankton was sampled at ten stations in the Canada Basin during August 2002 using both 53- and 236-µm mesh nets to examine the contribution by smaller and less studied species. Copepod nauplii, the copepods Oithona similis, Oncaea borealis and Microcalanus pygmaeus, and the larvacean Fritillaria borealis typica dominated the upper 100 m of the water column numerically, while biomass was dominated by the copepods Calanus hyperboreus, Calanus glacialis and Paraeuchaeta glacialis, and the chaetognath Eukrohnia hamata. Zooplankton biomass ranged from 3.7 to 14.5 mg AFDW m³, with a mean of 9.6 mg AFDW m³. While the three microcopepods contributed less than 5% of the biomass, estimates of their potential growth rates suggest they might contribute upwards of 25% of the metazoan zooplankton production. The true rates of growth and development of these microcopepods in the Arctic need to be determined to conclusively ascertain their importance.

• Iken, K., Bluhm, B.A., and Gradinger, R.R.  Food web structure in the high Arctic Canada Basin: evidence from δ¹³C and δ¹⁵N analysis.  Polar Biology 28(3): 2005.
  Read Abstract >>

  The food-web structure of the Arctic deep Canada Basin was investigated in summer 2002 using carbon and nitrogen stable isotope tracers. Overall food-web length of the range of organisms sampled occupied four trophic levels, based on 3.8‰ trophic level enrichment (δ¹⁵N range: 5.3-17.7‰). It was, thus, 0.5-1 trophic levels longer than food webs in both Arctic shelf and temperate deep-sea systems. The food sources, pelagic particulate organic matter (POM) (δ¹³C = -25.8‰, δ¹⁵N = 5.3‰) and ice POM (δ¹³C = -26.9‰, δ¹⁵N = 4.1‰), were not significantly different. Organisms of all habitats, ice-associated, pelagic and benthic, covered a large range of δ¹⁵N values. In general, ice-associated crustaceans (δ¹⁵N range 4.6 - 12.4‰, mean 6.9‰) and pelagic species (δ¹⁵N range 5.9 - 16.5, mean 11.5‰) were depleted relative to benthic invertebrates (δ¹⁵N range 4.6 - 17.7‰, mean 13.2‰). The predominantly herbivorous and predatory sympagic and pelagic species constitute a shorter food chain that is based on fresh material produced in the water column. Many benthic invertebrates were deposit feeders, relying on largely refractory material. However, sufficient fresh phytodetritus appeared to arrive at the seafloor to support some benthic suspension and surface deposit feeders on a low trophic level (e.g., crinoids, cumaceans). The enriched signatures of benthic deposit feeders and predators may be a consequence of low primary production in the high Arctic and the subsequent high degree of reworking of organic material.

• Joye, S.B., Boetius, A., Orcutt, B.N., Montoya, J.P., Schulz, H.N., Erickson, M.J., and Lugo, S.K. The anaerobic oxidation of methane and sulfate reduction in sediments from Gulf of Mexico cold seeps.  Chemical Geology 205(3-4): 219-238, 2004.
  Read Abstract >>

  We determined the geochemical characteristics of sediments and measured rates of the anaerobic oxidation of methane (AOM) and sulfate reduction (SR) in samples collected near thermogenic (structure II) gas hydrate mounds and in areas lacking hydrates along the continental slope in the Gulf of Mexico. We used radiotracer (¹⁴C and ³⁵S) techniques to determine rates of AOM and SR over depth in sediment cores. Abundant mats of white and orange Beggiatoa spp. were common in areas of active seepage and these sediments were enriched in hydrogen sulfide and methane. In cores collected from areas without Beggiatoa or hydrate, concentrations of redox metabolites showed little variation over depth and these sites were inferred to be areas of low seepage. Integrated AOM rates were low in Beggiatoa-free cores (<0.05 mmol m^-2 day^-1) and averaged 2.8 ± 4.6 mmol m^-2 day^-1 in seep cores that contained Beggiatoa or gas hydrate. Integrated SR rates were also low in Beggiatoa-free cores (<1 mmol m^-2 day^-1) and averaged 54 ± 94 mmol m^-2 day^-1 in cores with Beggiatoa or hydrate. Rates of SR generally exceeded rates of AOM and the two processes were loosely coupled, suggesting that the majority of SR at Gulf of Mexico hydrocarbon seep sites is likely fueled by the oxidation of other organic matter, possibly other hydrocarbons and oil, rather than by AOM.

• Kniemeyer, O. et al.  Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria.  Nature 449(7164): 898-U10, 2007.
  Read Abstract >>

  The short-chain hydrocarbons ethane, propane and butane are constituents of natural gas. They are usually assumed to be of thermochemical origin, but biological formation of ethane and propane has been also observed. Microbial utilization of short-chain hydrocarbons has been shown in some aerobic species but not in anaerobic species of bacteria. On the other hand, anaerobic utilization of short-chain hydrocarbons would in principle be expected because various anaerobic bacteria grow with higher homologues (≥C₆. Indeed, chemical analyses of hydrocarbon-rich habitats with limited or no access of oxygen indicated in situ biodegradation of short-chain hydrocarbons. Here we report the enrichment of sulphate-reducing bacteria (SRB) with such capacity from marine hydrocarbon seep areas. Propane or n-butane as the sole growth substrate led to sediment-free sulphate-reducing enrichment cultures growing at 12, 28 or 60 ºC. With ethane, a slower enrichment with residual sediment was obtained at 12 ºC. Isolation experiments resulted in a mesophilic pure culture (strain BuS5) that used only propane and n-butane (methane, isobutane, alcohols or carboxylic acids did not support growth). Complete hydrocarbon oxidation to CO₂ and the preferential oxidation of ¹²C-enriched alkanes were observed with strain BuS5 and other cultures. Metabolites of propane included iso- and n-propylsuccinate, indicating a subterminal as well as an unprecedented terminal alkane activation with involvement of fumarate. According to 16S ribosomal RNA analyses, strain BuS5 affiliates with Desulfosarcina/Desulfococcus, a cluster of widespread marine SRB. An enrichment culture with propane growing at 60 ºC was dominated by Desulfotomaculum-like SRB. Our results suggest that diverse SRB are able to thrive in seep areas and gas reservoirs on propane and butane, thus altering the gas composition and contributing to sulphide production.

• Lesser, M.P.  Experimental biology of coral reef ecosystems.  Journal of Experimental Marine Biology and Ecology 300(1-2): 217-252, 2004.
  Read Abstract >>

  Coral reef ecosystems are at the crossroads. While significant gaps still exist in our understanding of how "normal" reefs work, unprecedented changes in coral reef systems have forced the research community to change its focus from basic research to understand how one of the most diverse ecosystems in the world works to basic research with strong applied implications to alleviate damage, save, or restore coral reef ecosystems. A wide range of stressors on local, regional, and global spatial scales including over fishing, diseases, large-scale disturbance events, global climate change (e.g., ozone depletion, global warming), and over population have all contributed to declines in coral cover or phase shifts in community structure on time scales never observed before. Many of these changes are directly or indirectly related to anthropogenically induced changes in the global support network that affects all ecosystems. This review focuses on some recent advances in the experimental biology of coral reef ecosystems, and in particular scleractinian corals, at all levels of biological organization. Many of the areas of interest and techniques discussed reflect a progression of technological advances in biology and ecology but have found unique and timely application in the field of experimental coral reef biology. The review, by nature, will not be exhaustive and reflects the authors interests to a large degree. Because of the voluminous literature available, an attempt has been made to capture the essential elements and references for each topic discussed.

• Lupton, J. et al.  Submarine venting of liquid carbon dioxide on a Mariana Arc volcano.Geochemistry Geophysics Geosystems 7(Q08007): 2006.
  Read Abstract >>

  Although CO₂ is generally the most abundant dissolved gas found in submarine hydrothermal fluids, it is rarely found in the form of CO₂ liquid. Here we report the discovery of an unusual CO₂-rich hydrothermal system at 1600-m depth near the summit of NW Eifuku, a small submarine volcano in the northern Mariana Arc. The site, named Champagne, was found to be discharging two distinct fluids from the same vent field: a 103 ºC gas-rich hydrothermal fluid and cold (<4 ºC) droplets composed mainly of liquid CO₂. The hot vent fluid contained up to 2.7 moles/kg CO₂, the highest ever reported for submarine hydrothermal fluids. The liquid droplets were composed of ~98% CO₂, ~1% H₂S, with only trace amounts of CH₄ and H₂. Surveys of the overlying water column plumes indicated that the vent fluid and buoyant CO₂ droplets ascended < 200 m before dispersing into the ocean. Submarine venting of liquid CO₂ has been previously observed at only one other locality, in the Okinawa Trough back-arc basin (Sakai et al., 1990a), a geologic setting much different from NW Eifuku, which is a young arc volcano. The discovery of such a high CO₂ flux at the Champagne site, estimated to be about 0.1% of the global MOR carbon flux, suggests that submarine arc volcanoes may play a larger role in oceanic carbon cycling than previously realized. The Champagne field may also prove to be a valuable natural laboratory for studying the effects of high CO₂ concentrations on marine ecosystems.

• MacDonald, I.R. et al.  Asphalt volcanism and chemosynthetic life in the Campeche Knolls, Gulf of Mexico.  Science 304(5673): 999-1002, 2004.
  Read Abstract >>

  In the Campeche Knolls, in the southern Gulf of Mexico, lava-like flows of solidified asphalt cover more than 1 square kilometer of the rim of a dissected salt dome at a depth of 3000 meters below sea level. Chemosynthetic tubeworms and bivalves colonize the sea floor near the asphalt, which chilled and contracted after discharge. The site also includes oil seeps, gas hydrate deposits, locally anoxic sediments, and slabs of authigenic carbonate. Asphalt volcanism creates a habitat for chemosynthetic life that may be widespread at great depth in the Gulf of Mexico.

• McFadden, C.S., France, S.C., Sánchez, J.A., and Alderslade, P.  A molecular phylogenetic analysis of the Octocorallia (Cnidaria : Anthozoa) based on mitochondrial protein-coding sequences.  Molecular Phylogenetics and Evolution 41(3): 513-527, 2006.
  Read Abstract >>

  Despite their abundance and ecological importance in a wide variety of shallow and deep water marine communities, octocorals (soft corals, sea fans, and sea pens) are a group whose taxonomy and phylogenetic relationships remain poorly known and little studied. The group is currently divided into three orders (0: Alcyonacea, Pennatulacea, and Helioporacea); the large O. Alcyonacea (soft corals and sea fans) is further subdivided into six sub-ordinal groups on the basis of skeletal composition and colony growth form. We used 1429 bp of two mitochondrial protein-coding genes, ND2 and mshl, to construct a phylogeny for 103 octocoral genera representing 28 families. In agreement with a previous 18S rDNA phylogeny, our results support a division of Octocorallia into two major clades plus a third, minor clade. We found one large clade (Holaxonia-Alcyoniina) comprising the sea fan sub-order Holaxonia and the majority of soft corals, and a second clade (Calcaxonia-Pennatulacea) comprising sea pens (O. Pennatulacea) and the sea fan sub-order Calcaxonia. Taxa belonging to the sea fan group Scleraxonia and the soft coral family Alcyoniidae were divided among the Holaxonia-Alcyoniina clade and a third, small clade (Anthomatus-Corallium) whose relationship to the two major clades was unresolved. In contrast to the previous studies, we found sea pens to be monophyletic but nested within Calcaxonia; Our analyses support the sea fan family Ellisellidae as the sister taxon to the sea pens. We are unable to reject the hypothesis that the calcaxonian and holaxonian skeletal axes each arose once and suggest that the skeletal axis of sea pens is derived from that of Calcaxonia. Topology tests rejected the monophyly of sub-ordinal groups Alcyoniina, Scleraxonia, and Stolonifera, as well as 9 of 14 families for which we sampled multiple genera. The much broader taxon sampling and better phylogenetic resolution afforded by our study relative to the previous efforts greatly clarify the relationships among families and subordinal groups within each of the major clades. The failure of these mitochondrial genes as well as previous 18S rDNA studies to resolve many of the deeper nodes within the tree (including its root) suggest that octocorals underwent a rapid radiation and that large amounts of sequence data will be required in order to resolve the basal relationships within the clade.

• Mellinger, D.K., Stafford, K.M., Moore, S.E., Dziak, R.P., and Matsumoto, H.  An overview of fixed passive acoustic observation methods for cetaceans. Oceanography 20(4): 36-45, 2007.
  Open Access >>
  
• Meyer, E. et al.  Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx.  BMC Genomics 10, 2009.
  Open Access >>
  Read Abstract >>

  Background: New methods are needed for genomic-scale analysis of emerging model organisms that exemplify important biological questions but lack fully sequenced genomes. For example, there is an urgent need to understand the potential for corals to adapt to climate change, but few molecular resources are available for studying these processes in reef-building corals. To facilitate genomics studies in corals and other non-model systems, we describe methods for transcriptome sequencing using 454, as well as strategies for assembling a useful catalog of genes from the output. We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora. Results: More than 600,000 reads produced in a single 454 sequencing run were assembled into ~40,000 contigs with five-fold average sequencing coverage. Based on sequence similarity with known proteins, these analyses identified ~11,000 different genes expressed in a range of conditions including thermal stress and settlement induction. Assembled sequences were annotated with gene names, conserved domains, and Gene Ontology terms. Targeted searches using these annotations identified the majority of genes associated with essential metabolic pathways and conserved signaling pathways, as well as novel candidate genes for stress-related processes. Comparisons with the genome of the anemone Nematostella vectensis revealed ~8,500 pairs of orthologs and ~100 candidate coral-specific genes. More than 30,000 SNPs were detected in the coral sequences, and a subset of these validated by re-sequencing. Conclusion: The methods described here for deep sequencing of the transcriptome should be widely applicable to generate catalogs of genes and genetic markers in emerging model organisms. Our data provide the most comprehensive sequence resource currently available for reef-building corals, and include an extensive collection of potential genetic markers for association and population connectivity studies. The characterization of the larval transcriptome for this widely-studied coral will enable research into the biological processes underlying stress responses in corals and evolutionary adaptation to global climate change.

• Mills, H.J., Hodges, C., Wilson, K., MacDonald, I.R., and Sobecky, P.A.  Microbial diversity in sediments associated with surface-breaching gas hydrate mounds in the Gulf of Mexico.  FEMS Microbiology Ecology 46(1): 39-52, 2003.
  Open Access >>
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  A molecular phylogenetic approach was used to characterize the composition of microbial communities from two gas hydrate sedimentary systems in the Gulf of Mexico. Nucleic acids, extracted from sediments directly overlying surface-breaching gas hydrate mounds collected from a research submersible (water depth 550-575 in), were amplified with nine different 16S rDNA gene primer sets. The polymerase chain reaction primers targeted microorganisms at the domain-specific (Bacteria and Archaea) and group-specific (sulfate-reducing bacteria (SRB) and putative anaerobic methane-oxidizing (ANME) archaea) level. Amplicons were obtained with five of the nine primer sets including two of the six SRB Groups (SRB Group 5 and Group 6) and used to generate five different clone libraries. Analysis of 126 clones from the Archaea library revealed that the sediments associated with naturally occurring gas hydrate harbored a low diversity. Sequence analysis indicated the majority of archaeal clones were most closely related to Methanosarcinales, Methanomicrobiales and distinct phylogenetic lineages within the ANME groups. The most frequently recovered phylotypes in the ANME library were related to either ANME-2 or Methanomicrobiales. In contrast to the two archaeal libraries, bacterial diversity was higher with the majority of the 126 bacterial clones most closely related to uncultured clones dominated by the δ- and ε-Proteobacteria. Interestingly, while 82% of the clones in the SRB Group 5 library were affiliated with δ-Proteobacteria, the vast majority (83%) of clones in the SRB Group 6 library was affiliated with the Firmicates. This is the first phylogenetic-based description of microbial communities extant in methane-rich hydrate-associated sediments from a hydrocarbon seep region in the Gulf of Mexico.

• Mills, H.J., Martinez, R.J., Story, S., and Sobecky, P.A.  Identification of members of the metabolically active microbial populations associated with Beggiatoa species mat communities form Gulf of Mexico cold-seep sediments.  Applied and Environmental Microbiology 70(9): 5447-5458, 2004.
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  In this study, the composition of the metabolically active fraction of the microbial community occurring in Gulf of Mexico marine sediments (water depth, 550 to 575 m) with overlying filamentous bacterial mats was determined. The mats were mainly composed of either orange- or white-pigmented Beggiatoa spp. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from three different sediment depths (0 to 2, 6 to 8, and 10 to 12 cm) that had been subjected to reverse transcription-PCR amplification. Domain-specific 16S PCR primers were used to construct 12 different 16S crDNA libraries containing 333 Archaea and 329 Bacteria clones. Analysis of the Archaea clones indicated that all sediment depths associated with overlying orange- and white-pigmented microbial mats were almost exclusively dominated by ANME-2 (95% of total Archaea clones), a lineage related to the methanogenic order Methanosarcinales. In contrast, bacterial diversity was considerably higher, with the dominant phylotype varying by sediment depth. An equivalent number of clones detected at 0 to 2 cm, representing a total of 93%, were related to the γ and δ classes of Proteobacteria, whereas clones related to δ-Proteobacteria dominated the metabolically active fraction of the bacterial community occurring at 6 to 8 cm (79%) and 10 to 12 cm (85%). This is the first phylogenetics-based evaluation of the presumptive metabolically active fraction of the Bacteria and Archaea community structure investigated along a sediment depth profile in the northern Gulf of Mexico, a hydrocarbon-rich cold-seep region.

• Mills, H.J., Martinez, R.J., Story, S., and Sobecky, P.A.  Characterization of microbial community structure in Gulf of Mexico gas hydrates: Comparative analysis of DNA- and RNA-derived clone libraries. Applied and Environmental Microbiology 71(6): 3235-3247, 2005.
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  The characterization of microbial assemblages within solid gas hydrate, especially those that may be physiologically active under in situ hydrate conditions, is essential to gain a better understanding of the effects and contributions of microbial activities in Gulf of Mexico (GoM) hydrate ecosystems. In this study, the composition of the Bacteria and Archaea communities was determined by 16S rRNA phylogenetic analyses of clone libraries derived from RNA and DNA extracted from sediment-entrained hydrate (SEH) and interior hydrate (111). The hydrate was recovered from an exposed mound located in the northern GoM continental slope with a hydrate chipper designed for use on the manned-submersible Johnson Sea Link (water depth, 550 m). Previous geochemical analyses indicated that there was increased metabolic activity in the SEH compared to the III layer (B.N. Orcutt, A. Boetius, S.K. Lugo, I.R. Macdonald, V.A. Samarkin, and S. Joye, Chem. Geol. 205:239-251). Phylogenetic analysis of RNA- and DNA-derived clones indicated that there was greater diversity in the SEH libraries than in the III libraries. A majority of the clones obtained from the metabolically active fraction of the microbial community were most closely related to putative sulfate-reducing bacteria and anaerobic methane-oxidizing archaea. Several novel bacterial and archaeal phylotypes for which there were no previously identified closely related cultured isolates were detected in the RNA- and DNA-derived clone libraries. This study was the first phylogenetic analysis of the metabolically active fraction of the microbial community extant in the distinct SEH and III layers of GoM gas hydrate.

• Orcutt, B., Boetius, A., Elvert, M., Samarkin, V., and Joye, S.B.  Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico cold seeps. Geochimica et Cosmochimica Acta 69(17): 4267-4281, 2005.
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  The anaerobic oxidation of methane in aquatic environments is a globally significant sink for a potent greenhouse gas. Significant gaps remain in our understanding of the anaerobic oxidation of methane because data describing the distribution and abundance of putative anaerobic methanotrophs in relation to rates and patterns of anaerobic oxidation of methane activity are rare. An integrated biogeochemical, molecular ecological and organic geochemical approach was used to elucidate interactions between the anaerobic oxidation of methane, methanogenesis, and sulfate reduction in sediments from two cold seep habitats (one brine site, the other a gas hydrate site) along the continental slope in the Northern Gulf of Mexico. The results indicate decoupling of sulfate reduction from anaerobic oxidation of methane and the contemporaneous occurrence of methane production and consumption at both sites. Phylogenetic and organic geochemical evidence indicate that microbial groups previously suggested to be involved in anaerobic oxidation of methane coupled to sulfate reduction were present and active. The distribution and isotopic composition of lipid biomarkers correlated with microbial distributions, although concrete assignment of microbial function based on biomarker profiles was complicated given the observed overlap of competing microbial processes. Contemporaneous activity of anaerobic oxidation of methane and bicarbonate-based methanogenesis, the distribution of methane-oxidizing microorganisms, and lipid biomarker data suggest that the same microorganisms may be involved in both processes.

• Orcutt, B.N., Boetius, A., Lugo, S.K., MacDonald, I.R., Samarkin, V.A., and Joye, S.B.  Life at the edge of methane ice: microbial cycling of carbon and sulfur in Gulf of Mexico gas hydrates.  Chemical Geology 205(3-4): 239-251, 2004.
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  The processes of methane oxidation and sulfate reduction were examined in subsamples of gas hydrate associated materials collected along the Gulf of Mexico continental slope. Standard radiotracer techniques were used to determine rates of microbial activity in different layers of the hydrate environment, including outer sediment (OS), interface sediment (IS), worm burrow sediment (WB), interior hydrate (IN) and a mixture of hydrate and sediment (MIX). The anaerobic oxidation of methane (AOM) and sulfate reduction (SR) were observed in all hydrate samples examined and the rates of these processes showed similar spatial trends between different hydrate layers. Highest rates of both AOM and SR were observed at interface between the sediment and hydrate. AOM rates were about 3-11 nmol cm^-3 day^-1 in worm burrow and interface sediments as compared to <1 nmol cm^-3 day^-1 in other hydrate material types. Rates of SR ranged from 59 to 490 nmol cm^-3 day^-1 in worm burrow and interface sediments while rates in interior hydrate samples were an order of magnitude lower. These rates observed in hydrate materials are lower than rates from nearby methane-rich sediments at ambient temperatures. Nevertheless, our data show that active microbial populations inhabit all layers of the hydrate environment and suggest their activity may impact biogeochemical methane and sulfur cycling in this unique niche.

• Penn, K., Wu, D.Y., Eisen, J.A., and Ward, N.  Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Applied and Environmental Microbiology 72(2): 1680-1683, 2006.
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  Although microbes associated with shallow-water corals have been reported, deepwater coral microbes are poorly characterized. A cultivation-independent analysis of Alaskan seamount octocoral microflora showed that Proteobacteria (classes Alphaproteobacteria and Gammaproteobacteria), Firmicutes, Bacteroidetes, and Acidobacteria dominate and vary in abundance. More sampling is needed to understand the basis and significance of this variation.

• Proskurowski, G. et al.  Abiogenic hydrocarbon production at Lost City hydrothermal field.  Science 319(5863): 604-607, 2008.
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  Low-molecular-weight hydrocarbons in natural hydrothermal fluids have been attributed to abiogenic production by Fischer-Tropsch type (FTT) reactions, although clear evidence for such a process has been elusive. Here, we present concentration, and stable and radiocarbon isotope, data from hydrocarbons dissolved in hydrogen-rich fluids venting at the ultramafic-hosted Lost City Hydrothermal Field. A distinct "inverse" trend in the stable carbon and hydrogen isotopic composition of C₁ to C₄ hydrocarbons is compatible with FTT genesis. Radiocarbon evidence rules out seawater bicarbonate as the carbon source for FTT reactions, suggesting that a mantle- derived inorganic carbon source is leached from the host rocks. Our findings illustrate that the abiotic synthesis of hydrocarbons in nature may occur in the presence of ultramafic rocks, water, and moderate amounts of heat.

• Reed, J.K., Weaver, D.C., and Pomponi, S.A.  Habitat and fauna of deep-water Lophelia pertusa coral reefs off the southeastern US: Blake Plateau, Straits of Florida, and Gulf of Mexico.  Bulletin of Marine Science 78(2): 343-375, 2006.
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  Expeditions from 1999 to 2004 for biomedical research explored various deep-sea coral ecosystems (DSCE) off the southeastern U.S. (Blake Plateau, Straits of Florida, and eastern Gulf of Mexico). Habitat and benthos were documented from 57 dives with human occupied submersibles and three with a remotely operated vehicle (ROV), and resulted in ~100 hrs of videotapes, 259 in situ digital images, 621 museum specimens, and >400 microbial isolates. These were the first dives to document the habitat, benthic fauna, and fish diversity of some of these poorly known deep-water reefs. Fifty-eight fish species and 142 benthic invertebrate taxa were identified. High-definition topographic SEABEAM maps and echosounder profiles were also produced. Sites included in this report range from South Carolina on the Blake Plateau to the southwestern Florida slope: 1) Stetson Lophelia reefs along the eastern Blake Plateau off South Carolina; 2) Savannah Lophelia lithoherms along the western Blake Plateau off Georgia; 3) east Florida Lophelia reefs, 4) Miami Terrace escarpment in the Straits of Florida; 5) Pourtales Terrace off the Florida Keys; and 6) west Florida Lophelia lithoherms off the southwestern Florida shelf in the Gulf of Mexico. These are contrasted with the azooxanthellate deep-water Oculina reefs at the shelf-edge off central eastern Florida. The fisheries and biopharmaceutical resource potential of these deep-water habitats remain relatively unknown. Although these habitats are not currently designated as marine protected areas (MPAs) or coral habitat areas of particular concern (HAPCs), they are ecologically diverse, vulnerable to physical destruction, and irreplaceable resources. Activities involving bottom trawling, pipelines, or oil/gas production could negatively impact these reefs. National Oceanic and Atmospheric Administration (NOAA) Fisheries and the South Atlantic Fishery Management Council are currently developing priority mapping sites of the DSCEs within this region, and these data may provide potential targets for new MPAs and HAPCs.

• Robinson, C.A., Bernhard, J.M., Levin, L.A., Mendoza, G.F., and Blanks, J.K.  Surficial hydrocarbon seep infauna from the Blake Ridge (Atlantic Ocean, 2150 m) and the Gulf of Mexico (690-2240 m).  Marine Ecology – An Evolutionary Perspective 25(4): 313-336, 2004.
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  Infauna, including foraminifera and metazoans, were enumerated and identified from five types of seep habitats and two adjacent non-seep habitats. Collections were made with the deep submergence research vessel 'Alvin' from three areas of active seepage in the Gulf of Mexico (Alaminos Canyon [2220 m], Atwater Canyon [1930 m], and Green Canyon lease block 272 [700 m]) and on the Blake Ridge Diapir [2250 m], which is located off the southeastern coast of the United States. The seep habitats sampled included four types of microbial mats (Beggiatoa, Thioploca, thin and thick Arcobacter) and the periphery of a large mussel bed. Sediments under large rhizopod protists, xenophyophores, were sampled adjacent to the mussel bed periphery. A non-seep site, which was >1 km away from active seeps, was also sampled for comparison. Densities of most taxa were higher in the Gulf of Mexico seeps than in Blake Ridge samples, largely because densities in the thick microbial mats of Blake Ridge were significantly lower. Diversity was higher in the Thioploca mats compared to other microbial-mat types. Within an ocean basin (i.e., Atlantic, Gulf of Mexico) we did not observe significant differences in meiofaunal or macrofaunal composition in Beggiatoa versus Thioploca mats or thin versus thick Arcobacter mats. Foraminifera represented up to 16% of the seep community, a proportion that is comparable to their contribution at adjacent non-seep communities. In general, the observed densities and taxonomic composition of seep sites at the genus level was consistent with previous observations from seeps (e.g., the foraminifers Bolivina and Fursenkoina, the dorvilleid polychaete Ophryotrocha).

• Ross, S.W., and Quattrini, A.M.  The fish fauna associated with deep coral banks off the southeastern United States.  Deep-Sea Research Part I–Oceanographic Research Papers, 54(6): 975-1007, 2007.
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  Deep-sea or cold-water corals form substantial habitat along many continental slopes, including the southeastern United States (SEUS). Despite increasing research on deep coral systems and growing appreciation of their importance to fishes, quantitative data on fish communities occupying these ecosystems are relatively lacking. Our overall goals were to document the fish species and their relative abundances and to describe the degree of general habitat specificity of the fishes on and around deep coral habitats on the SEUS slope. From 2000 to 2006, we used the Johnson-Sea-Link (JSL) submersible (65 dives, 366–783m), supplemented with otter trawls (33 tows, 365–910m) to document fishes and habitats from off North Carolina to east-central Florida. Eight areas with high concentrations of deep-sea corals were surveyed repeatedly. Three general habitat types (prime reef, transition reef, and off reef) were defined to determine large-scale habitat use patterns. Throughout the area, at least 99 fish species were identified, many (19%) of which yielded new distributional data. Most species observed with the JSL were on prime reef (n=50) and transition reef (n=42) habitats, but the off reef habitat supported a well developed, but different fauna (n=25 species). Prime reef was characterized by Laemonema melanurum (21% of total), Nezumia sclerorhynchus (17% of total), Beryx decadactylus (14% of total), and Helicolenus dactylopterus (10% of total). The off reef areas were dominated by Fenestraja plutonia (19% of total), Laemonema barbatulum (18% of total), Myxine glutinosa (8% of total), and Chlorophthalmus agassizi (7% of total). Transition habitat exhibited a mixture of species that were also found on either prime reef or off reef habitats. Nezumia sclerorhynchus was the most abundant (25% of total) transition habitat species, followed by L. barbatulum (16% of total) and L. melanurum (14% of total). Several species (e.g., Anthias woodsi, B. decadactylus, Conger oceanicus, and Dysommina rugosa) demonstrated specificity to deep-reef habitats, while others (e.g., C. agassizi, Benthobatis marcida, F. plutonia, and Phycis chesteri) were always more common away from reefs. In addition to new distributional data, we provide behavioral and biological observations for dominant species.

• Wells, L.E., Cordray, M., Bowerman, S., Miller, L.A., Vincent, W.F., and Deming, J.W.  Archaea in particle-rich waters of the Beaufort Shelf and Franklin Bay, Canadian Arctic: Clues to an allochthonous origin? Limnology and Oceanography 51(1): 47-59, 2006.
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  We used 4',6-diamidino-2-phenylindole (DAPI) staining and fluorescent in situ hybridization to examine total bacterioplankton and archaeal distributions in surface waters and in deeper nepheloid layers and particle-poor waters across the Beaufort Shelf of the Canadian Arctic, including the Mackenzie River and Kugmallit Bay, as well as more distant Franklin Bay. Although the regional distribution of bacterioplankton was best explained by salinity (r_s = -0.89, n = 28, p < 0.001) and indicators of primary production (chlorophyll a [Chl a], total organic carbon, and the ratio of Chl a to particulate organic carbon [Chl a: POC]), that of Archaea instead reflected measures of particulate matter, specifically microscopically determined particle concentration (r_s = 0.85, n = 30, p < 0.001), suspended particulate matter, POC, particulate organic nitrogen (PON), and the beam attenuation coefficient. Moreover, when compared with similarly deep particle-poor waters, nepheloid layers were significantly enriched in Archaea (median concentration of 6.00 x 10⁴ mL^-1 [15.5% of bacterioplankton] vs. 1.79 x 10⁴ mL^-1 [3.6%]; p < 0.05), but not total bacterioplankton. The relationship between Archaea and particles, the dominance of the Mackenzie River as the regional particle source, the detection of highest archaeal concentrations (11.5–14.4 x 10⁴ mL^-1) in the river, and the highly significant correlation (r_s = 0.97, n = 12, p < 0.001) between Archaea in particle-rich waters and PON (the river providing the upper end member) suggest that many of these Archaea derive from the river.

• Widder, E.A., Robison, B.H., Reisenbichler, K.R., and Haddock, S.H.D. Using red light for in situ observations of deep-sea fishes.  Deep-Sea Research Part I–Oceanographic Research Papers 52(11): 2077-2085, 2005.
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  Observations of animals in the deep ocean typically require the use of bright lights that can damage eyes and disrupt normal behaviors. Although the use of infrared light is an effective means of unobtrusive observation on land, it is far less effective in the ocean where long wavelength light is rapidly attenuated by seawater. Here we describe in situ observations of the behavior of the sablefish, Anoplopoma fimbria, around a baited site under different lighting conditions. Fish were observed with low-light-level imaging that had adequate sensitivity to compensate for the attenuation losses associated with the use of long wavelength light in water. ROV-based experiments compared the number of sablefish seen around bait, illuminated alternately with red vs. white light. Significantly more fish were seen under red light than white light with the average number of sablefish observed per 10min viewing interval under red light being 38.9 ( ± 18.5 SD) compared to 7.5 (± 7.1 SD) under white light. Under both red and white light sablefish spent only brief periods in the illumination field (10.5 s [± 8.7 SD] under red light and 6.6 s [± 8.7 SD] under white light). It appeared that sablefish were responding to competing drives of attraction to the bait and avoidance of the lights and that the avoidance was greater for white light than for red light. Observations were also made with the newly developed deep-sea observatory, Eye-in-the-Sea, using long wavelength LED illumination. The onset of LED illumination did not generally produce a startle response from fish around the bait, and in some cases invoked no response at all. However, in the majority of cases the fish moved out of the circle of red-light illumination during the 7.5 s recording period, indicating that the light was detectable and aversive to these fish. This was true with both 660 and 680 nm LED illuminators. We conclude that while a sharper short-wavelength cutoff of the illumination source is required to achieve truly unobtrusive observation, red light is nonetheless significantly less disruptive than white light for observing deep-sea fish behavior, and can provide adequate illumination when used in combination with image-intensified cameras.

• Wilson, S.G., Polovina, J.J., Stewart, B.S., and Meekan, M.G.  Movements of whale sharks (Rhincodon typus) tagged at Ningaloo Reef, Western Australia.  Marine Biology 148(5): 1157-1166, 2006.
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  Whale sharks (Rhincodon typus Smith) aggregate seasonally (March-June) to feed in coastal waters off Ningaloo Reef, Western Australia. Pop-up archival tags were attached to 19 individuals (total lengths 4.5-11.0 m) at this location in early May of 2003 and 2004 to examine their horizontal and vertical movements. The long-term movement patterns of six whale sharks were documented, all of which travelled northeast into the Indian Ocean after departing Ningaloo Reef. They used both inshore and offshore habitats and made extensive vertical movements, occasionally to a depth of at least 980 m. Frequent up-and-down movements, diel vertical migration, and crepuscular descents were evident in the depth records. The sharks experienced ambient temperatures ranging between 4.2 and 28.7 ºC and encountered gradients of up to 20.8 ºC on dives.

Significant Research: 2009 and 2010

• Andrews, A.H., Stone, R.P., Lundstrom, C.C., and DeVogelaere, A.P.  Growth rate and age determination of bamboo corals from the northeastern Pacific Ocean using refined ²¹⁰Pb dating. Marine Ecology Progress Series 397: 173-185, 2009.
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  Bamboo corals from Davidson Seamount and from the Gulf of Alaska were aged using a refined ²¹⁰Pb dating technique. The goal was to determine growth rates and age for several bamboo corals with higher precision. Radiometric results for 2 Davidson Seamount corals (Keratoisis sp.) converged on a radial growth rate of ~0.055 mm yr^–1. One colony was aged at 98 ± 9 yr, with an average axial growth rate of ~0.7 cm yr^–1. The age of a large colony was >145 yr with an estimated axial growth rate of 0.14 to 0.28 cm yr^–1. Inconsistent rates may indicate nonlinear axial growth. A Keratoisis sp. specimen from the Gulf of Alaska was aged at 116 ± 29 yr from a radial growth rate of ~0.056 mm yr^–1, which led to an average axial growth rate of ~1.0 cm yr^–1. An Isidella tentaculum colony was aged at 53 ± 10 yr and grew most rapidly with a radial growth rate of ~0.10 mm yr^–1 and an average axial growth rate of ~1.4 cm yr^–1; however, the ²¹⁰Pb decay pattern may have provided evidence for either a hiatus in radial growth or environmental changes in ²¹⁰Pb. Our findings of slow growth and long life compared favorably with other bamboo coral studies and provided age estimates with greater precision. The high longevity of bamboo coral is an indication that recovery from disturbance or removal may take decades to a century. These age data provide a basis for a defensible position on the protection of bamboo coral and essential information for describing other life history characteristics.

• Baco, A.R., Rowden, A.A., Levin, L.A., Smith, C.R., and Bowden, D.A.  Initial characterization of cold seep faunal communities on the New Zealand Hikurangi margin.  Marine Geology 272(1-4): 251-259, 2010.
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  Cold-seep communities have been known from the North Atlantic and North Pacific for more than 20 years, but are only now being explored in the Southern Hemisphere. While fisheries bycatch had suggested the presence of cold seeps on the New Zealand margin, the biodiversity and distribution of these communities remained unknown. Explorations using towed cameras and direct sampling gear revealed that cold seep sites are abundant along the New Zealand Hikurangi margin. Initial characterization of the faunal communities at 8 of these sites indicates a fauna that is associated with particular sub-habitats but which varies in abundance between sites. Community composition is typical, at higher taxonomic levels, of cold seep communities in other regions. The dominant symbiont-bearing taxa include siboglinid (tube) worms, vesicomyid clams and bathymodiolin mussels. At the species level, much of the seep-associated fauna identified so far appears either to be new to science, or endemic to New Zealand seeps, suggesting the region may represent a new biogeographic province for cold-seep fauna. Some overlap at the species and genus level is also indicated between the sampled seep communities and the fauna of hydrothermal vents on the Kermadec Arc in the region. Further taxonomic and genetic identifications of fauna from this study will allow us to fully test the levels of species overlap with other New Zealand chemosynthetic ecosystems as well as with other cold seep sites worldwide. These apparently novel communities exhibit evidence of disturbance from a deep bottom-trawl fishery and appear to be threatened along the entire New Zealand margin. As bottom fisheries, mining, and fossil-fuel exploitation move into deeper waters, seep communities may be endangered worldwide, necessitating the initiation of conservation efforts even as new seep ecosystems are discovered and explored. Our findings highlight the unique nature of anthropogenic impacts in the deep-sea, in which reservoirs of biodiversity can be impacted long before they are even known.

• Becker, E.L., Cordes, E.E., Macko, S.A., and Fisher, C.R.  Importance of seep primary production to Lophelia pertusa and associated fauna in the Gulf of Mexico.  Deep-Sea Research Part I–Oceanographic Research Papers 56(5): 786-800, 2009.
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  To investigate the importance of seep primary production to the nutrition of Lophelia pertusa and associated communities and examine local trophic interactions, we analyzed stable carbon, nitrogen, and sulfur compositions in seven quantitative L. pertusa community collections. A significant seep signature was only detected in one of the 35 species tested (Provanna sculpta, a common seep gastropod) despite the presence of seep fauna at the three sample sites. A potential predator of L. pertusa was identified (Coralliophila sp.), and a variety of other trophic interactions among the fauna occupying the coral framework were suggested by the data, including the galatheid crab Munidopsis sp. 2 feeding upon hydroids and the polychaete Eunice sp. feeding upon the sabellid polychaete Euratella sp. Stable carbon abundances were also determined for different sections of L. pertusa skeleton representing different stages in the growth and life of the aggregation. There was no temporal trend detected in the skeleton isotope values, suggesting that L. pertusa settles in these areas only after seepage has largely subsided. Isotope values of individual taxa. that were collected from both L. pertusa and vestimentiferan habitats showed decreasing reliance upon seep primary production with average age of the vestimentiferan aggregation, and finally, no seep signature was detected in the coral collections. Together our data suggest that it is the presence of authigenic carbonate substrata, a product of past seep microbial activity, as well as hydrodynamic processes that drive L. pertusa occurrence at seep sites in the Gulf of Mexico, not nutritional dependence upon primary production by seep microbes.

• Brazelton, W.J., and Baross, J.A.  Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm.  ISME Journal 3(12): 1420-1424, 2009.
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  The carbonate chimneys of the Lost City Hydrothermal Field on the Mid-Atlantic Ridge are coated in thick microbial biofilms consisting of just a few dominant species. We report a preliminary analysis of a biofilm metagenome that revealed a remarkable abundance and diversity of genes potentially involved in lateral gene transfer (LGT). More than 8% of all metagenomic reads showed significant sequence similarity to transposases; all available metagenomic data sets from other environments contained at least an order of magnitude fewer transposases. Furthermore, the sequence diversity of transposase genes in the biofilm was much greater than that of 16S rRNA genes. The small size and high sequencing coverage of contigs containing transposases indicate that they are located on small but abundant extragenomic molecules. These results suggest that rampant LGT among members of the Lost City biofilm may serve as a generator of phenotypic diversity in a community with very low organismal diversity.

• Brazelton, W.J. et al.  Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys.  Proceedings of the National Academy of Sciences of the United States of America 107(4): 1612-1617, 2010.
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  The Lost City Hydrothermal Field, an ultramafic-hosted system located 15 km west of the Mid-Atlantic Ridge, has experienced at least 30,000 years of hydrothermal activity. Previous studies have shown that its carbonate chimneys form by mixing of ~90 ºC, pH 9-11 hydrothermal fluids and cold seawater. Flow of methane and hydrogen-rich hydrothermal fluids in the porous interior chimney walls supports archaeal biofilm communities dominated by a single phylotype of Methanosarcinales. In this study, we have extensively sampled the carbonate-hosted archaeal and bacterial communities by obtaining sequences of >200,000 amplicons of the 16S rRNA V6 region and correlated the results with isotopic (²³⁰Th) ages of the chimneys over a 1,200-year period. Rare sequences in young chimneys were commonly more abundant in older chimneys, indicating that members of the rare biosphere can become dominant members of the ecosystem when environmental conditions change. These results suggest that a long history of selection over many cycles of chimney growth has resulted in numerous closely related species at Lost City, each of which is preadapted to a particular set of reoccurring environmental conditions. Because of the unique characteristics of the Lost City Hydrothermal Field, these data offer an unprecedented opportunity to study the dynamics of a microbial ecosystem's rare biosphere over a thousand-year time scale.

• Bucklin, A., Hopcroft, R.R., Kosobokova, K.N., Nigro, L.M., Ortman, B.D., Jennings, R.M., and Sweetman, C.J.  DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition.  Deep-Sea Research Part II–Topical Studies in Oceanography 57(1-2): 40-48, 2010.
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  Zooplankton species diversity and distribution are important measures of environmental change in the Arctic Ocean, and may serve as 'rapid-responders' of climate-induced changes in this fragile ecosystem. The scarcity of taxonomists hampers detailed and up-to-date monitoring of these patterns for the rarer and more problematic species. DNA barcodes (short DNA sequences for species recognition and discovery) provide an alternative approach to accurate identification of known species, and can speed routine analysis of zooplankton samples. During 2004-2008, zooplankton samples were collected during cruises to the central Arctic Ocean and Chukchi Sea. A ~700 base-pair region of the mitochondrial cytochrome oxiclase I (mtCOI) gene was amplified and sequenced for 82 identified specimens of 41 species, including cnidarians (six hydrozoans, one scyphozoan), arthropod crustaceans (five amphipods, 24 copepods, one decapod, and one euphausiid); two chaetognaths; and one nemertean. Phylogenetic analysis used the Neighbor-joining algorithm with Kimura-2-Parameter (K-2-P) distances, with 1000-fold bootstrapping. K-2-P genetic distances between individuals of the same species ranged from 0.0 to 0.2; genetic distances between species ranged widely from 0.1 to 0.7. The mtCOI gene tree showed monophyly (at 100% bootstrap value) for each of the 26 species for which more than one individual was analyzed. Of seven genera for which more than one species was analyzed, four were shown to be monophyletic: three genera were not resolved. At higher taxonomic levels, only the crustacean order Copepoda was resolved, with bootstrap value of 83%. The mtCOI barcodes accurately discriminated and identified known species of 10 taxonomic groups of Arctic Ocean holozooplankton. A comprehensive DNA barcode database for the estimated 300 described species of Arctic holozooplankton will allow rapid assessment of species diversity and distribution in this climate-vulnerable ocean ecosystem.

• Bucklin, A. et al.  A "Rosetta Stone" for metazoan zooplankton: DNA barcode analysis of species diversity of the Sargasso Sea (Northwest Atlantic Ocean). Deep-Sea Research Part II–Topical Studies in Oceanography 57(24-26): 2234-2247, 2010.
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  Species diversity of the metazoan holozooplankton assemblage of the Sargasso Sea, Northwest Atlantic Ocean, was examined through coordinated morphological taxonomic identification of species and DNA sequencing of a similar to 650 base-pair region of mitochondrial cytochrome oxidase I (mtCOI) as a DNA barcode (i.e., short sequence for species recognition and discrimination). Zooplankton collections were made from the surface to 5,000 meters during April, 2006 on the R/V R.H. Brown. Samples were examined by a ship-board team of morphological taxonomists; DNA barcoding was carried out in both ship-board and land-based DNA sequencing laboratories. DNA barcodes were determined for a total of 297 individuals of 175 holozooplankton species in four phyla, including: Cnidaria (Hydromedusae, 4 species; Siphonophora, 47); Arthropoda (Amphipoda, 10; Copepoda, 34; Decapoda, 9; Euphausiacea, 10; Mysidacea, 1; Ostracoda, 27); and Mollusca (Cephalopoda, 8; Heteropoda, 6; Pteropoda, 15); and Chaetognatha (4). Thirty species of fish (Teleostei) were also barcoded. For all seven zooplankton groups for which sufficient data were available, Kimura-2-Parameter genetic distances were significantly lower between individuals of the same species (mean=0.0114; S.D. 0.0117) than between individuals of different species within the same group (mean=0.3166; S.D. 0.0378). This difference, known as the barcode gap, ensures that mtCOI sequences are reliable characters for species identification for the oceanic holozooplankton assemblage. In addition, DNA barcodes allow recognition of new or undescribed species, reveal cryptic species within known taxa, and inform phylogeographic and population genetic studies of geographic variation. The growing database of "gold standard" DNA barcodes serves as a Rosetta Stone for marine zooplankton, providing the key for decoding species diversity by linking species names, morphology, and DNA sequence variation. In light of the pivotal position of zooplankton in ocean food webs, their usefulness as rapid responders to environmental change, and the increasing scarcity of taxonomists, the use of DNA barcodes is an important and useful approach for rapid analysis of species diversity and distribution in the pelagic community.

• Cordes, E.E., Becker, E.L., Hourdez, S., and Fisher, C.R.  Influence of foundation species, depth, and location on diversity and community composition at Gulf of Mexico lower-slope cold seeps.  Deep-Sea Research Part II–Topical Studies in Oceanography 57(21-23): 1870-1881, 2010.
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  Efforts to understand and preserve the seep communities of the deep Gulf of Mexico (GOM) begin with a comprehensive survey of the biodiversity of these communities. Previous studies have provided a conceptual model of the physiology, population, and community ecology of upper continental slope seeps. However, seeps at water depths below 1000 m in the Gulf of Mexico remain relatively unknown. In this study, data from 47 samples of tubeworm- and mussel-associated communities at depths of 1005-2750 m are examined. Other than tubeworms and mussels, 66 taxa of macro- and megafauna were collected, 43 of which appear to be restricted to water depths of over 1000 m, and 39 that have not been reported previously from the Gulf of Mexico. Diversity in mussel beds was highest at mid-slope depths, but tubeworm-associated communities did not show clear bathymetric trends in diversity. Diversity was higher in tubeworm aggregations at the alpha level (per sample), but higher in mussel beds at the beta level (species turnover among collections). Although both community types were often numerically dominated by the endemic shrimp Alvinocaris muricola, broad differences in the communities hosted by tubeworm aggregations and mussel beds were apparent. The most important factors explaining community similarity within community type were the depth, relative abundance of different mussel species in a bed, and the average size of tubeworms in an aggregation. The high proportion of deep-seep species that were found for the first time in the Gulf of Mexico emphasizes the importance of conservation efforts for these patchy communities.

• Cordes, E.E., Bergquist, D.C., and Fisher, C.R.  Macro-ecology of Gulf of Mexico cold seeps.  Annual Review of Marine Science, 1: 143-168, 2009.
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  Shortly after the discovery of chemosynthetic ecosystems at deep-sea hydrothermal vents, similar ecosystems were found at cold seeps in the Gulf of Mexico. Over the past two decades, these sites have become model systems for understanding the physiology of the symbiont-containing megafauna and the ecology of seep communities worldwide. Symbiont-containing bivalves and siboglinid polychaetes dominate the communities, including five bathymodiolin mussel species and six vestimentiferan (siboglinid polychaete) species in the Gulf of Mexico. The mussels include the first described examples of methanotrophic symbiosis and dual methanotrophic/thiotrophic symbiosis. Studies with the vestimentiferans have demonstrated their potential for extreme longevity and their ability to use posterior structures for subsurface exchange of dissolved metabolites. Ecological investigations have demonstrated that the vestimentiferans function as ecosystem engineers and identified a community Succession Sequence from a specialized high-biomass endemic community to a low-biomass community of background fauna over the life of a hydrocarbon seep site.

• Cordes, E.E. et al.  The influence of geological, geochemical, and biogenic habitat heterogeneity on seep biodiversity.  Marine Ecology–An Evolutionary Perspective 31(1): 51-65, 2010.
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  Cold seeps are among the most heterogeneous of all continental margin habitats. Abiotic sources of heterogeneity in these systems include local variability in fluid flow, geochemistry, and substrate type, which give rise to different sets of microbial communities, microbial symbiont-bearing foundation species, and associated heterotrophic species. Biogenic habitats created by microbial mats and the symbiotic species including vesicomyid clams, bathymodiolin mussels, and siboglinid tubeworms add an additional layer of complexity to seep habitats. These forms of habitat heterogeneity result in a variety of macrofaunal and meiofaunal communities that respond to changes in structural complexity, habitat geochemistry, nutrient sources, and interspecific interactions in different ways and at different scales. These responses are predicted by a set of theoretical metacommunity models, the most appropriate of which for seep systems appears to be the 'species sorting' concept, an extension of niche theory. This concept is demonstrated through predictable patterns of community assembly, succession, and beta-level diversity. These processes are described using a newly developed analytical technique examining the change in the slope of the species accumulation curve with the number of habitats examined. The diversity response to heterogeneity has a consistent form, but quantitatively changes at different seep sites around the world as the types of habitats present and the size-classes of fauna analyzed change. The increase in beta diversity across seep habitat types demonstrates that cold seeps and associated biogenic habitats are significant sources of heterogeneity on continental margins globally.

• Eytan, R.I., Hayes, M., Arbour-Reily, P., Miller, M., and Hellberg, M.E.  Nuclear sequences reveal mid-range isolation of an imperilled deep-water coral population.  Molecular Ecology 18(11): 2375-2389, 2009.
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  The mitochondrial DNA of corals and their anthozoan kin evolves slowly, with substitution rates about two orders of magnitude lower than in typical bilateral animals. This has impeded the delineation of closely related species and isolated populations in corals, compounding problems caused by high morphological plasticity. Here we characterize rates of divergence and levels of variation for three nuclear gene regions, then use these nuclear sequences as markers to test for population structure in Oculina, a taxonomically confused genus of corals. Rates of sequence divergence (obtained by comparison to Solenastrea hyades) were at least five (and sometimes over 10) times faster for the three nuclear markers than for a mitochondrial reference sequence. Nuclear sequence variation was also high within populations, although it tended to decline north of Cape Canaveral. Significant subdivision was evident among samples from 10 locations from between North Carolina and the Florida Panhandle, but neither nominal species designation nor population depth explained much of this variation. Instead, a single population from the unique deep (>70 m) water reefs at the Oculina Banks off central Florida was a strong genetic outlier: all pairwise measures of subdivision involving this population were greater than those involving all other populations, and multilocus clustering recognized the Oculina Banks as distinct from other populations, despite its close proximity (≤36 km) to populations from shallower waters nearby and its location at the centre of the sampled range. Genetic isolation of the Oculina Banks population suggests that focused efforts will be needed to conserve the foundation species of these monotypic reefs and that depth may play a role in isolating marine populations and perhaps facilitating initial steps towards speciation.

• Hopcroft, R.R., Kosobokova, K.N., and Pinchuk, A.I.  Zooplankton community patterns in the Chukchi Sea during summer 2004.  Deep-Sea Research Part II–Topical Studies in Oceanography 57(1-2): 27-39, 2010.
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  Zooplankton were sampled in the Chukchi Sea along three transects between Alaska and Russia, plus four high-speed transects across the axis of Herald Valley in August of 2004. A total of 50 holoplanktonic species, along with a prominent assemblage of meroplankton were encountered; most were of Pacific Ocean origin. Copepods represented the most diverse group with 23 species, and contributed the bulk (3100ind.m⁻³, 30mg dry weightm⁻³) of the total holozooplankton community abundance (3500ind.m⁻³) and biomass (42mg DWm⁻³) at most stations. Meroplanktonic larvae were, on average, almost as abundant (2260ind.m⁻³) as the holozooplankton. Copepods were dominated numerically by four species of Pseudocalanus, Oithona similis, and the neritic copepods Acartia longiremis and Centropages abdominalis. The larger-bodied copepods, Calanus glacialis/marshallae and three Neocalanus species, equalled or exceeded the biomass of Pseudocalanus, followed by contributions from Metridia pacifica and Eucalanus bungii. Considerable abundance (256ind.m⁻³) and biomass (42mg DWm⁻³) of the larvacean Oikopleura vanhoeffeni was observed throughout the sampling area. The chaetognath Parasagitta elegans (4.8mg DWm⁻³) and a diverse assemblage of cnidarians (~1.2mg DWm⁻³) comprised the dominant predators. Six major assemblages of zooplankton were identified, and each was closely tied to physical properties of water masses: Euryhaline species in the warm fresh Alaska Coastal Current, a Bering Sea assemblage of both shelf and oceanic species in cool salty Bering Sea Water, a transitional group between these two, a neritic Bering Sea assemblage in cold salty Bering Winter Water, and a small cluster of Arctic Shelf species in cold, fresh Resident Chukchi Water. Ongoing climate change may alter the boundaries, extent of penetration, size spectra, and productivities of these communities, thus warranting regular monitoring of the zooplankton communities of this gateway into the Arctic.

• Iken, K., Bluhm, B., and Dunton, K.  Benthic food-web structure under differing water mass properties in the southern Chukchi Sea.  Deep-Sea Research Part II–Topical Studies in Oceanography 57(1-2): 71-85, 2010.
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  We used carbon and nitrogen stable isotope ratios as markers of food source connections and trophic position to evaluate whether benthic food-web structure varied among water masses with different productivity regimes in the southern Chukchi Sea. Benthic communities and suspended particulate organic matter (POM) were sampled at nine stations located in four water masses during the 2004 Russian-American Long-term Census of the Arctic (RUSALCA) cruise. POM δ¹³C values were depleted in the relatively unproductive Alaska Coastal Water (ACW, −24.2‰) and at the Russian Coast (RC, −24.5) compared to the enriched signatures of highly productive Anadyr Water (AW, −21.1‰) and the intermediate value (−23.6‰) of Bering Shelf Water (BSW). Corresponding differences in POM C/N reflected higher nutritive content of AW (6.19) compared to ACW (8.45). Carbon isotopic values of sediments were also most depleted in the nearshore waters of the ACW (−24.8‰) and RC (−23.4‰), versus BSW (−22.8‰) and AW (−22.1‰). In addition, the low δ¹⁵N values and high C/N ratios associated with sediments under the ACW (2.9‰ and 10.0, respectively) compared to the other three water masses (range 4.5–4.9‰ and 6.8–7.5, respectively) are likely explained by a terrestrial signal associated with the higher freshwater input into the ACW. Consequently, the δ¹³C value of POM in the ACW is likely driven by a large fraction of refractory material of terrestrial origin, and POM may not always be a reliable baseline for trophic level calculations in the ACW. Excluding POM, δ¹⁵N isotope spread among the same 42 taxa of invertebrates and fishes was 8.5‰ in ACW and 7.5‰ in AW, compared to 12.0‰ and 9.6‰ with the inclusion of δ¹⁵N POM values. Almost without exception, consumers in the ACW had higher δ¹⁵N values than their AW counterparts (average difference 2.5‰). However, food webs in ACW and AW (as well as in the BSW and RC) did not differ substantially in length (four trophic levels) when based on primary consumers as the baseline. The relatively high proportion of consumers within the first trophic level in AW suggests that there is a more direct coupling of benthic consumers to the very high pelagic primary production in these waters, which is also reflected in the high benthic infaunal biomass at low trophic levels (TL2) reported in the literature for this area. We conclude that differences in regional water column productivity in the southern Chukchi Sea may be manifested primarily in the quantitative representation of various trophic levels and less in qualitative characteristics such as food-web length or relative distribution of trophic levels.

• Jones, A.T., Greinert, J., Bowden, D.A., Klaucke, I., Petersen, C.J., Netzeband, G.L., and Weinrebe, W. Acoustic and visual characterisation of methane-rich seabed seeps at Omakere Ridge on the Hikurangi Margin, New Zealand.  Marine Geology 272(1-4): 154-169, 2010.
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  Six active methane seeps and one cold-water reef that may represent a relict seep were mapped at Omakere Ridge on New Zealand's Hikurangi Margin during cruises SO191 and TAN0616. Hydroacoustic flares interpreted to be bubbles of methane rising through the water column were identified in the area. The seep sites and the cold-water reef were characterised by regions of high backscatter intensity on sidescan sonar records, or moderate backscatter intensity where the seep was located directly below the path of the sidescan towfish. The majority of sites appear as elevated features (2-4 m) in multibeam swath data. Gas blanking and acoustic turbidity were observed in sub-bottom profiles through the sites. A seismic section across two of the sites (Bear's Paw and LM-9) shows a BSR suggesting the presence of gas hydrate as well as spots of high amplitudes underneath and above the BSR indicating free gas. All sites were ground truthed with underwater video observations, which showed the acoustic features to represent authigenic carbonate rock structures. Live chemosynthetic biotic assemblages, including siboglinid tube worms, vesicomyid clams, bathymodiolin mussels, and bacterial mats, were observed at the seeps. Cold-water corals were the most conspicuous biota of the cold-water reef but widespread vesicomyid clam shells indicated past seep activity at all sites. The correlation between strong backscatter features in sidescan sonar images and seep-related seabed features is a powerful tool for seep exploration, but differentiating the acoustic features as either modern or relict seeps requires judicial analysis and is most effective when supported by visual observations.

• Joye, S.B., Bowles, M.W., Samarkin, V.A., Hunter, K.S., and Niemann, H.  Biogeochemical signatures and microbial activity of different cold-seep habitats along the Gulf of Mexico deep slope.  Deep-Sea Research Part II–Topical Studies in Oceanography 57(21-23): 1990-2001, 2010.
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  Microorganisms and the processes they mediate serve as the metabolic foundation of cold seeps. We characterized a suite of biogeochemical constituents and quantified rates of two key microbial processes, Sulfate Reduction (SR) and Anaerobic Oxidation of Methane (AOM), to assess variability between habitats at water depths exceeding 1000 m in the northern Gulf of Mexico. Rates of SR were highest in sediments beneath microbial mats, lower in brine-influenced and oil-influenced sediments, and lowest in animal habitats. Sediments collected near tubeworms had the highest SR rates for animal habitats. Rates of AOM generally were low, but higher rates were associated with brine-influenced, oil-influenced, tubeworm- and urchin-inhabited sediments. Rates of both SR and AOM were orders of magnitude lower at deep-slope sites compared to upper-slope sites examined previously. As observed at upper-slope sites. SR and AOM rates were often loosely coupled. At one site, AOM rates exceeded SR rates, suggesting that an alternate electron acceptor for AOM is possible. Extremely depleted δ¹³C values in methane illustrated the broad significance of biogenic methane production at deep-slope sites. Brine-influenced habitats were characterized by extremely high concentrations of ammonium and dissolved organic carbon, serving as important focused sources of these chemicals to adjacent environments.

• Klaucke, I., Weinrebe, W., Petersen, C.J., and Bowden, D.  Temporal variability of gas seeps offshore New Zealand: Multi-frequency geoacoustic imaging of the Wairarapa area, Hikurangi margin.  Marine Geology 272(1-4): 49-58, 2010.
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  Cold seeps on Opouawe Bank, situated in around 1000 m water depth on the Hikurangi Margin offshore North Island New Zealand, were investigated using multibeam bathymetry, 75 and 410 kHz sidescan sonar imagery, and 2-8 kHz Chirp sediment echosounder data. Towed video camera observations allowed ground-truthing the various geoacoustic data. At least eleven different seep locations displaying a range of seep activity were identified in the study area. The study area consists of an elongated, northward-widening ridge that is part of the accretionary Hikurangi Margin and is well separated from direct terrigenous input by margin channels surrounding the ridge. The geoacoustic signature of individual cold-seep sites ranged from smooth areas with slightly elevated backscatter intensity resulting from high gas content or the presence of near-surface gas hydrates, to rough areas with widespread patches of carbonates at the seafloor. Five cold seeps also show indications for active gas emissions in the form of acoustic plumes in the water column Repeated sidescan sonar imagery of the plumes indicates they are highly variable in intensity and direction in the water column, probably reflecting the control of gas emission by tides and currents Although gas emission appears strongly focused in the Wairarapa area, the actual extents of the cold seep structures are much wider in the subsurface as is shown by sediment echosounder profiles, where large gas fronts were observed.

• Kosobokova, K.N., and Hopcroft, R.R.  Diversity and vertical distribution of mesozooplankton in the Arctic's Canada Basin.  Deep-Sea Research Part II–Topical Studies in Oceanography 57(1-2): 96-110, 2010..
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  The composition and biomass of the zooplankton community within the Canada Basin down to 3000 m was studied during July 2005 at 12 stations. A total of 111 species including 74 species of crustaceans (55 species of copepods, 2 euphausiids, 11 amphipods, 1 decapod, 5 ostracods), 17 cnidarians (12 hydromedusae, 1 scyphomedusae, 4 siphonophora), 1 foraminifera, 4 ctenophores, 2 pteropods, 4 larvaceans, 4 chaetognaths, and 5 polychaetes were identified. Most of the species observed are typical of the Arctic waters, with the notable exception of several Pacific expatriate copepod species, suggesting no zoogeographical barrier between the Canadian and Eurasian basins. Overall species inventories appear unchanged over the past 50 years, and were similar to the Eurasian Basins. Zooplankton biomass averaged 3.6 ± 0.23 g DW m^-2, with ~50% of the biomass concentrated within the upper 100 m; nonetheless significant biomass and the majority of species diversity occurred below 100 m. Copepods represented 91% of the community numerically, followed by pteropods (2.6%), larvacean (1.8%) and shelled protists (1.5%), with other groups each contributing 1% or less. While copepods represented 85% of the total biomass, chaetognaths represented 13% on average (ca. 50% of non-copepod biomass), followed by cnidarians plus ctenophores (4.6%), ostracods (3.6%), and other groups (~2% or less). Species-specific depth preferences and ranges resulted in statistically distinct communities in different depth strata and showed an orderly departure in similarity with increasing distance between strata. In Arctic waters, because temperature varied relatively little over the water column, so should respiratory rates; hence deep-water species are likely to play a greater role in the transfer or recycling of surface production than is typical of other deep ocean communities.

• Lesser, M.P., Slattery, M., and Leichter, J.J.  Ecology of mesophotic coral reefs.  Journal of Experimental Marine Biology and Ecology 375(1-2): 1-8, 2009.
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  Mesophotic coral reefs, reefs at depths of 30 m to 150 m, are receiving renewed interest from coral reef scientists and managers because they are linked physically and biologically to their shallow water counterparts, have the potential to be refugia for shallow coral reef taxa such as coral and sponges, and can be a source of larvae that could contribute to the resiliency of shallow water reefs. Here we review what is currently known about how mesophotic reef communities are structured and identify critical areas where new information is needed. The review covers two primary taxa, coral and sponges, where a majority of the ecological work on mesophotic coral reefs has been done, and physical processes (e.g., the attenuation of visible irradiance and internal waves) that exert significant abiotic control on the structure of these deep fore reef communities. Understanding the ecology of mesophotic coral reefs, and the connectivity between them and their shallow water counterparts, should be a primary focus of future reef studies as the worldwide degradation of shallow coral reefs, and the ecosystem services they provide, continues.

• Levin, L.A., and Dayton, P.K.  Ecological theory and continental margins: where shallow meets deep.   Trends in Ecology and Evolution 24(11): 606-617, 2009.
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  Continental margins, where land becomes ocean and plunges to the deep sea, provide valuable food and energy resources, and perform essential functions such as carbon burial and nutrient cycling. They exhibit remarkably high species and habitat diversity, but this is threatened by our increasing reliance on the resources that margins provide, and by warming, expanding hypoxia and acidification associated with climate change. Continental margin ecosystems, with environments, constituents and processes that differ from those in shallow water, demand a new focus, in which ecological theory and experimental methods are brought to bear on management and conservation practices. Concepts of disturbance, diversity-function relationships, top-down versus bottom-up control, facilitation and meta-dynamics offer a framework for studying fundamental processes and understanding future change.

• Levin, L.A., Mendoza, G.F., Gonzalez, J.P., Thurber, A.R., and Cordes, E.E.  Diversity of bathyal macrofauna on the northeastern Pacific margin: the influence of methane seeps and oxygen minimum zones. Marine Ecology–An Evolutionary Perspective 31(1): 94-110, 2010.
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  The upper continental slope in the northeastern Pacific Ocean is intercepted by a deep oxygen minimum zone (OMZ; 650-1100 m) and punctuated by conduits of methane seepage. We examined the effects of these two dominant sources of heterogeneity on the density, composition and diversity of heterotrophic macrofauna off Hydrate Ridge, Oregon (OR; 800 m water depth), where the seeps co-occur within an OMZ, and off the Eel River, Northern California (CA; 500 m), where seeps are overlain by better oxygenated waters. We hypothesized that seeps (containing clam beds and microbial mats) should contribute a suite of distinct species to the regional margin species pool but that OMZ-associated hypoxia would dampen seep-related heterogeneity. Macrofaunal densities were highest (23,000-33,510 ind.m^-2) in the CA seep sediments and in the OR near-seep samples, intermediate in the OR seep, CA near seep and CA and OR 500-m margin sediments (10,05419,777 ind.m^-2), and lowest in the CA and OR OMZ habitats at 800 m (42697847 ind.m^-2). Annelids constituted over 50% of the taxa in all but the CA clam bed and OR microbial mat sediments, where mollusks were abundant. Approximately 50% of seep species appeared to be habitat endemic; species present in microbial mats largely formed a subset of those present in the clam beds. Dorvilleid and ampharetid polychaetes were dominant in the seep sediments; non-seep margin sediments at 500 and 800 m were populated heavily by branckiate polychaetes including cossurids and paraonids. Alpha diversity (Es[20] calculated per core) was lowest and rank 1 dominance was highest in the CA and OR microbial mat habitats. Pooled analyses of Es[100] revealed highest species richness in the CA clam bed and near-seep habitats (30.3 and 29.6, respectively), and lowest species richness in the OR microbial mat and near-seep habitats (16.5 and 17.9, respectively). Non-seep sediments (500 and 800 m) off both CA and OR were more homogeneous (55-57% within-habitat similarity) than clam bed and microbial mat sediments (only 32-37% within-habitat similarity). CA sediment macrofauna generally exhibit higher alpha diversity, and as habitats are combined, a higher rate of increase in the slope of the species accumulation curves than do OR margin macrofauna. Methane seeps in the NE Pacific introduce significant heterogeneity that increases margin biodiversity at multiple spatial scales. However, our hypothesis that the OMZ would lessen the seep contributions to diversity was not supported. The better oxygenated CA seeps at 500 in shared more of the background margin fauna (at 500 m) than did the OR seeps at 800 m (with OMZ fauna at 800 in). Geographical differences in the fluxes of methane-rich fluids and the increased reliance on chemosynthetic food sources with increased depth could explain these results.

• Lundsten, L., Barry, J.P., Cailliet, G.M., Clague, D.A., DeVogelaere, A.P., and Geller, J.B. Benthic invertebrate communities on three seamounts off southern and central California, USA.  Marine Ecology Progress Series 374: 23-32, 2009.
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  Seamounts are unique and biologically productive deep-sea habitats that have often been described as having high levels of endemism, highly productive fisheries, and benthic communities vulnerable to trawl fishing. We describe the abundance and distribution of benthic megafaunal invertebrates found on 3 seamounts off central and southern California. Video observations were taken during 27 dives of a remotely operated vehicle (ROV) and were annotated in detail using the Monterey Bay Aquarium Research Institute's (MBARI) video annotation reference system (VARS, http://vars.sourceforge.net/). Video analysis yielded 134 477 observations of 202 identified invertebrate taxa. Video transects were analyzed to quantify organism density. Thirteen new species were observed and collected. Invertebrate communities at Davidson and Pioneer Seamounts were dominated by passive suspension-feeding cnidarians (mostly corals), but at Rodriguez Seamount, a guyot, the invertebrate community was dominated by holothurian echinoderms. We found no evidence of endemism among the megafauna a: these 3 seamounts, which are all in close proximity to each other and the continental margin.

• McClain, C.R., Lundsten, L., Ream, M., Barry, J., and DeVogelaere, A.  Endemicity, biogeography, composition, and community structure on a northeast Pacific seamount. PLOS One 4(1): e4141, 2009.
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  The deep ocean greater than 1 km covers the majority of the earth's surface. Interspersed on the abyssal plains and continental slope are an estimated 14000 seamounts, topographic features extending 1000 m off the seafloor. A variety of hypotheses are posited that suggest the ecological, evolutionary, and oceanographic processes on seamounts differ from those governing the surrounding deep sea. The most prominent and oldest of these hypotheses, the seamount endemicity hypothesis (SMEH), states that seamounts possess a set of isolating mechanisms that produce highly endemic faunas. Here, we constructed a faunal inventory for Davidson Seamount, the first bathymetric feature to be characterized as a 'seamount', residing 120 km off the central California coast in approximately 3600 m of water. We find little support for the SMEH among megafauna of a Northeast Pacific seamount; instead, finding an assemblage of species that also occurs on adjacent continental margins. A large percentage of these species are also cosmopolitan with ranges extending over much of the Pacific Ocean Basin. Despite the similarity in composition between the seamount and non-seamount communities, we provide preliminary evidence that seamount communities may be structured differently and potentially serve as source of larvae for suboptimal, non-seamount habitats.

• Meyer, E. et al.  Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx.  BMC Genomics 10, 2009.
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  Background: New methods are needed for genomic-scale analysis of emerging model organisms that exemplify important biological questions but lack fully sequenced genomes. For example, there is an urgent need to understand the potential for corals to adapt to climate change, but few molecular resources are available for studying these processes in reef-building corals. To facilitate genomics studies in corals and other non-model systems, we describe methods for transcriptome sequencing using 454, as well as strategies for assembling a useful catalog of genes from the output. We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora. Results: More than 600,000 reads produced in a single 454 sequencing run were assembled into similar to 40,000 contigs with five-fold average sequencing coverage. Based on sequence similarity with known proteins, these analyses identified ~11,000 different genes expressed in a range of conditions including thermal stress and settlement induction. Assembled sequences were annotated with gene names, conserved domains, and Gene Ontology terms. Targeted searches using these annotations identified the majority of genes associated with essential metabolic pathways and conserved signaling pathways, as well as novel candidate genes for stress-related processes. Comparisons with the genome of the anemone Nematostella vectensis revealed ~8,500 pairs of orthologs and ~100 candidate coral-specific genes. More than 30,000 SNPs were detected in the coral sequences, and a subset of these validated by re-sequencing. Conclusion: The methods described here for deep sequencing of the transcriptome should be widely applicable to generate catalogs of genes and genetic markers in emerging model organisms. Our data provide the most comprehensive sequence resource currently available for reef-building corals, and include an extensive collection of potential genetic markers for association and population connectivity studies. The characterization of the larval transcriptome for this widely-studied coral will enable research into the biological processes underlying stress responses in corals and evolutionary adaptation to global climate change.

• Mosher, C.V., and Watling, L.  Partners for life: a brittle star and its octocoral host. Marine Ecology Progress Series 397: 81-88, 2009.
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  Throughout the New England and Corner Rise seamounts of the western North Atlantic Ocean, several ophiuroid species are conspicuously epizoic on octocorals. One species, Ophiocreas oedipus, was found only on the chrysogorgiid octocoral Metallogorgia melanotrichos. Colonies of M. melanotrichos were collected from 11 seamounts during expeditions in 2003, 2004, and 2005 at depths between 1300 and 2200 m. O. oedipus is obligately associated with M. melanotrichos, leading a solitary existence on all octocorals observed. Evidence suggests that a young brittle star settles directly on a young octocoral and the 2 species then grow, mature, and senesce together. The brittle star benefits directly by being above the bottom for suspension feeding and is passively protected by the octocoral, but the latter, as far as we have been able to determine, seems neither to benefit nor be disadvantaged by the relationship.

• Naehr, T.H., Birgel, D., Bohrmann, G., MacDonald, I.R., and Kasten, S.  Biogeochemical controls on authigenic carbonate formation at the Chapopote "asphalt volcano", Bay of Campeche.  Chemical Geology 266(3-4): 399-411, 2009.
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  The Campeche Knolls in the Bay of Campeche, southern Gulf of Mexico, were investigated through detailed seafloor mapping, ROV surveys, and sediment and pore water sampling. The knolls are elongated submarine, hills created by salt tectonics with a positive relief of up to 800 m above the surrounding seafloor. Several of the knolls are associated with sea-surface oil slicks identified from satellite data, indicating the presence of hydrocarbon seeps on the seafloor. One of the knolls, named "Chapopote", was studied in detail during two international research expeditions (SO174/2 and M67/2) and is characterized by extensive hydrocarbon seepage including large asphalt flows, oil and gas seeps, and seafloor gas hydrate deposits. Chemosymbiotic biological communities and authigenic carbonate deposits are associated with the seeps and are the result of both biogeochemical turnover and the interaction between downward-diffusing seawater and hydrocarbon-rich pore fluids at shallow sediment depth. Authigenic carbonates are characterized by aragonite exhibit a, porous texture, and are cemented by a matrix of microsparitic to sparitic aragonite. Macropores of the carbonates were completely filled with liquid oil. Carbonate microfabrics include peloidal or clotted fabrics that may indicate the existence of microenvironments resulting from microbial metabolism. Banded/botryoidal aragonite cements line the intra- and bioclasts and incompletely fill the pore spaces. The stable carbon isotopic composition ofauthigenic aragonite varies between -28.6‰ and -17.9‰ (PDB), identifying oil oxidation as the primary source of carbon to the DIC pool, while lipid biomarker data demonstrate the concurrent existence of microbial communities responsible for anaerobic oxidation of methane (AOM). These observations indicate the presence of additional, AOM-independent reactions responsible for carbon sequestration at hydrocarbon seeps and demonstrate the complexity of biogeochemical processes at seep sites in the Gulf of Mexico basin. Oxygen isotope data of authigenic aragonite vary from +2.5‰ to +3.8‰ (PDB), indicating carbonate precipitation in slight disequilibrium with the surrounding pore fluids.

• Palumbi, S.R. et al.  Managing for ocean biodiversity to sustain marine ecosystem services.  Frontiers in Ecology and the Environment 7(4): 204-211, 2009.
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  Managing a complex ecosystem to balance delivery of all of its services is at the heart of ecosystem-based management. But how can this balance be accomplished amidst the conflicting demands of stakeholders, managers, and policy makers? In marine ecosystems, several common ecological mechanisms link biodiversity to ecosystem functioning and to a complex of essential services. As a result, the effects of preserving diversity can be broadly beneficial to a wide spectrum of important ecosystem processes and services, including fisheries, water quality, recreation, and shoreline protection. A management system that conserves diversity will help to accrue more "ecoservice capital" for human use and will maintain a hedge against unanticipated ecosystem changes from natural or anthropogenic causes. Although maintenance of biodiversity cannot be the only goal for ecosystem-based management, it could provide a common currency for evaluating the impacts of different human activities on ecosystem functioning and can act as a critical indicator of ecosystem status.

• Shank, T.M.  Seamounts: Deep-ocean laboratories of faunal connectivity, evolution, and endemism.   Oceanography 23(1): 108-122, 2010.
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  Seamount systems that are geographically, hydrographically, topographically, and/or genetically "isolated" are likely to have developed highly endemic taxa and ecosystems. Although current estimates of endemism are challenged by inconsistencies in sampling approaches, the physical, biological, and geological processes intrinsic to seamount systems can undeniably serve to connect or isolate populations, stimulate genetic divergence, drive the formation of new species, and structure diversity and endemism. In fact, the large variety of interconnected mechanisms that promote or impede the genetic connectivity of seamount communities via dispersal (and the long-term maintenance of species or the subsequent divergence of populations leading to speciation) are key unknowns to understanding the fundamental evolutionary processes that structure both the diversity and biogeography of deep-sea fauna. Fortunately, the net results of these ecological interactions at seamounts are represented in the patterns of genetic connectivity of the constituent species. The conclusions of the relatively few genetic connectivity studies across seamount fish, coral, and invertebrates are largely inconsistent, reflecting the ecological and evolutionary complexities of seamount systems. Yet, identifying the "connectivity" of seamount populations and their diverse ecosystems, which are increasingly vulnerable to threats from destructive fisheries and mining practices, is vital for developing and evaluating conservation and management strategies for seamount resources. Integrated, multidisciplinary studies of the physical, chemical, geological, an ecological dynamics of seamounts will continue to reveal the value of seamounts as natural laboratories in which to gain insights into the factors that elucidate the role these systems play in the dispersal, evolution, and biodiversity of deep-sea fauna. These studies will also direct the management of seamount biological diversity, which is increasingly susceptible to anthropogenic disturbance.

• Thoma, J.N., Pante, E., Brugler, M.R., and France, S.C.  Deep-sea octocorals and antipatharians show no evidence of seamount-scale endemism in the NW Atlantic.  Marine Ecology Progress Series 397: 25-35, 2009.
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  Seamounts are undersea mountains commonly characterized by accelerated currents, exposed hard-substrates, and relatively high biomass and biodiversity. Hydrographic features associated with seamounts have led authors to hypothesize that benthic invertebrate populations from geographically separated searnounts (and the continental slope) may experience varying degrees of genetic isolation, resulting in high levels of endemism. While this hypothesis has been tested for multiple taxonomic groups in the Pacific, it has rarely been addressed in the Atlantic. We tested the null hypothesis that the geographic ranges of corals from NW Atlantic seamounts are restricted to individual seamounts. We examined 188 octocoral and 50 antipatharian colonies (representing 6 and 2 genera, respectively) from 14 seamounts, spanning 1700 km, and the adjacent continental margin and estimated their genetic variation using mitochondrial loci (msh1 for all octocorals, as well as an intergenic region for isidids, and 3 multi-gene spanning segments for antipatharians). Well-sampled haplotypes were not geographically isolated on individual seamounts, thus refuting the hypothesis of local endemism of coral fauna on the New England and Corner Seamounts. The narrow geographic distribution of rare haplotypes is most likely due to undersampling rather than endemism. Our results do not preclude that cryptic variation and endemism not revealed by mitochondrial DNA may become evident should more variable markers be developed.

• Thurber, A.R., Kroger, K., Neira, C., Wiklund, H., and Levin, L.A.  Stable isotope signatures and methane use by New Zealand cold seep benthos. Marine Geology 272(1-4): 260-269, 2010..
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  The carbon isotopic composition of seep faunal tissue represents a time-integrated view of the interaction between biology and the biogeochemical gradients within the environment. Here we provide an initial description of carbon and nitrogen stable isotope signatures of dominant symbiont-bearing megafauna and heterotrophic mega- and macrofauna from 10 methane-seep sites on the continental margin of the North Island of New Zealand (662-1201 m water depth). Isotopic signatures suggest that sulfide oxidation supports symbiont-bearing taxa including solemyid and vesicomyid bivalves, and methanotrophic symbionts are present in the seep mussel Bathymodiolus sp. Multiple species of Frenulata (Siboglinidae) are present and have a range of isotopic values that are indicative of both thiotroph- and methanotroph-based nutrition. Isotopic composition of the tubeworm Lamellibrachia sp. varied by 23.3‰ among individuals although there was no consistent difference among sites Variation in methane use by heterotrophic fauna appears to reflect the availability of hard vs. soft substrate, macrofauna on hard substrates had high δ¹³C signatures, reflecting consumption of photosynthetic-derived organic matter. Two unique, biotic assemblages were discovered to be fueled largely by methane: a hard-substrate, multi-phyla sponge-associated community (inhabiting the sponge Pseudosuberites sp.) and a soft-sediment assemblage dominated by ampharetid polychaetes Isotope signatures yield estimates of 38-100% and 6-100% methane-derived carbon in sponge associates and ampharetid-bed macrofauna. respectively. These estimates are comparable to those made for deeper methane seeps at the Florida Escarpment (3290 m) and Kodiak. Alaska seeps (4445 m) The overall high use of methane as a carbon source by both symbiont-bearing and heterotrophic fauna suggests that New Zealand methane seeps are an ideal model system to study the interaction among metazoans, bacteria, archaea, and their resulting effect on methane cycles.

• Tunnicliffe, V., Davies, K.T.A., Butterfield, D.A., Embley, R.W., Rose, J.M., and Chadwick, W.W. Survival of mussels in extremely acidic waters on a submarine volcano.  Nature Geoscience, 2(5): 344-348, 2009.
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  Increasing atmospheric carbon dioxide levels are causing ocean acidification, compromising the ability of some marine organisms to build and maintain support structures as the equilibrium state of inorganic carbon moves away from calcium carbonate. Few marine organisms tolerate conditions where ocean pH falls significantly below today's value of about 8.1 and aragonite and calcite saturation values below 1. Here we report dense clusters of the vent mussel Bathymodiolus brevior in natural conditions of pH values between 5.36 and 7.29 on northwest Eifuku volcano, Mariana arc, where liquid carbon dioxide and hydrogen sulphide emerge in a hydrothermal setting. We find that both shell thickness and daily growth increments in shells from northwest Eifuku are only about half those recorded from mussels living in water with pH >7.8. Low pH may therefore also be implicated in metabolic impairment. We identify four-decade-old mussels, but suggest that the mussels can survive for so long only if their protective shell covering remains intact: crabs that could expose the underlying calcium carbonate to dissolution are absent from this setting. The mussels' ability to precipitate shells in such low-pH conditions is remarkable. Nevertheless, the vulnerability of molluscs to predators is likely to increase in a future ocean with low pH.

• Vetter, E.W., Smith, C.R., and De Leo, F.C.  Hawaiian hotspots: enhanced megafaunal abundance and diversity in submarine canyons on the oceanic islands of Hawaii. Marine Ecology–An Evolutionary Perspective 31(1): 183-199, 2010.
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  Submarine canyons are important sources of habitat heterogeneity on the slopes of continents and islands, but the study of canyon ecology has been largely restricted to continental margins. Here we use visual and video surveys from 36 submersible dives to evaluate the role of canyons as abundance and diversity hotspots for megafauna in the Hawaiian Archipelago, an island chain embedded in an oligotrophic ocean. We surveyed megafauna in canyon and slope settings at depths of 350-1500 m along the margins of four islands: the low 'islands' of Nihoa and Maro Reef, and the high islands of Oahu and Moloka'i. Megafaunal communities in canyons differed significantly from those in nearby slope habitats at all depths. Highly mobile fishes and invertebrates were consistently more abundant in canyons than on nearby slopes at the same depth off all islands, suggesting that canyons may be important sources of larvae for surrounding habitats. In the few cases where megafaunal abundances were similar or higher on the slope, the differences were typically driven by higher slope abundance of sessile suspension feeders or animals with limited mobility, i.e. by organisms which are likely to have difficulty with high currents and sediment transport in canyons. Megafaunal species richness and diversity generally trended higher within canyons, especially for the highly mobile taxa. Canyons contained 41 megafaunal species never observed on the slope, and increased estimated regional species richness by 25-30 species, indicating that canyons enhanced beta and gamma (regional) biodiversity. An expected trend of greater enhancement of diversity and abundance in canyons on the margins of high versus low oceanic islands was not observed, although megafauna were generally more abundant in both canyon and slope habitats on the high islands (Oahu and Moloka'i). We conclude that submarine canyons on both low and high islands in the Hawaiian Archipelago may provide keystone structures, enhancing megafaunal abundance, providing source populations for the open slope, and enhancing local and regional species diversity.

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