Showing papers in "Deep-sea Research Part Ii-topical Studies in Oceanography in 2010"

Mesopelagic zone ecology and biogeochemistry - a synthesis

Abstract: The mesopelagic zone is the oceanic region through which carbon and other elements must pass in order to reach deeper waters or the sea floor. However, the food web interactions that occur in the mesopelagic zone are difficult to measure and so, despite their crucial importance to global elemental cycles, are not very well known. Recent developments in technology and new approaches have advanced the study of the variability in and controls upon the distribution and diversity of organisms in the mesopelagic zone, including the roles of respiration, recycling, and repackaging of particulate and dissolved organic material. However, there are remarkably few syntheses of the ecology and biogeochemistry of the microbes and metazoa that permanently reside or habitually visit this ‘twilight zone’. Without this synthesis, it is difficult to assess the impact of ongoing changes in ocean hydrography and chemistry, due to increasing atmospheric carbon dioxide levels, on the biological carbon pump. This paper reviews what is known about the distribution of microbes and metazoa in the mesopelagic zone in relation to their activity and impact on global biogeochemical cycles. Thus, gaps in our knowledge are identified and suggestions made for priority research programmes that will improve our ability to predict the effects of climate change on carbon sequestration.

Assessing the apparent imbalance between geochemical and biochemical indicators of meso- and bathypelagic biological activity: What the @#! is wrong with present calculations of carbon budgets?

Abstract: Metabolic activity in the water column below the euphotic zone is ultimately fuelled by the vertical flux of organic material from the surface. Over time, the deep ocean is presumably at steady state, with sources and sinks balanced. But recently compiled global budgets and intensive local field studies suggest that estimates of metabolic activity in the dark ocean exceed the influx of organic substrates. This imbalance indicates either the existence of unaccounted sources of organic carbon or that metabolic activity in the dark ocean is being over-estimated. Budgets of organic carbon flux and metabolic activity in the dark ocean have uncertainties associated with environmental variability, measurement capabilities, conversion parameters, and processes that are not well sampled. We present these issues and quantify associated uncertainties where possible, using a Monte Carlo analysis of a published data set to determine the probability that the imbalance can be explained purely by uncertainties in measurements and conversion factors. A sensitivity analysis demonstrates that the bacterial growth efficiencies and assumed cell carbon contents have the greatest effects on the magnitude of the carbon imbalance. Two poorly quantified sources, lateral advection of particles and a population of slowly settling particles, are discussed as providing a means of closing regional carbon budgets. Finally, we make recommendations concerning future research directions to reduce important uncertainties and allow a better determination of the magnitude and causes of the unbalanced carbon budgets.

Eddy-mean flow interaction in the decadally modulating Kuroshio Extension system

Abstract: Satellite altimeter sea-surface height (SSH) data of the past 16 years are used to investigate the decadal changes of the Kuroshio Extension (KE) system that oscillated between a stable and an unstable dynamic state. During the stable state of 10/1992–06/1995 and 01/2002–12/2004, the KE jet was intense and had a northerly zonal mean path and a well-defined southern recirculation gyre. During the unstable state of 07/1995–12/2001 and 01/2005–present, the KE jet had a reduced eastward transport and a more southerly flow path. Transitions between the two dynamic states are caused by the basin-scale wind-stress curl forcing in the eastern North Pacific related to the Pacific decadal oscillations (PDOs) or the North Pacific Gyre Oscillations (NPGOs). During the positive PDO (or negative NPGO) phase, the intensified Aleutian Low generates negative SSH anomalies in the eastern North Pacific through Ekman divergence. As these wind-induced negative SSH anomalies propagate to the west as baroclinic Rossby waves, they weaken the zonal KE jet and shift its path southward. As its path is pushed southward ( ∼ 32 ∘ N ) , the deep-reaching KE jet has to ride over the shallow Shatsky Rise, generating localized disturbances that lead to their subsequent development along the KE jet west of the Shatsky Rise. The sequence opposite to that listed above occurs when the PDO (NPGO) changes to its negative (positive) phase. After the KE system transitions from a stable to unstable state, the enhanced eddy interaction is found to strengthen both the southern recirculation gyre and quasi-stationary meanders along the KE's upstream path. This nonlinear eddy interaction is important in determining the amplitude of the observed decadal KE variability.

Dissolved organic carbon export and subsequent remineralization in the mesopelagic and bathypelagic realms of the North Atlantic basin

Abstract: Dissolved organic carbon (DOC) data are presented from three meridional transects conducted in the North Atlantic as part of the US Climate Variability (CLIVAR) Repeat Hydrography program in 2003. The hydrographic sections covered a latitudinal range of 61 St o 631N along longitudes 201W (CLIVAR line A16), 521W (A20) and 661W (A22). Over 3700 individual measurements reveal unprecedented detail in the DOC distribution and systematic variations in the mesopelagic and bathypelagic zones of the North Atlantic basin. Latitudinal gradients in DOC concentrations combined with published estimates of ventilation rates for the main thermocline and North Atlantic Deep Water (NADW) indicate a net DOC export rate of 0.081 Pg C yr � 1 from the epipelagic zone into the mesopelagic and bathypelagic zones.

Phytoplankton community structure and stocks in the Southern Ocean (30–80°E) determined by CHEMTAX analysis of HPLC pigment signatures

Abstract: The geographic distribution, stocks and vertical profiles of phytoplankton of the seasonal ice zone off east Antarctica were determined during the 2005–2006 austral summer during the Baseline Research on Oceanography, Krill and the Environment-West (BROKE-West) survey. CHEMTAX analysis of HPLC pigment samples, coupled with microscopy, permitted a detailed survey along seven transects covering an extensive area between 30°E and 80°E, from 62°S to the coast. Significant differences were found in the composition and stocks of populations separated by the Southern Boundary of the Antarctic Circumpolar Current (SB), as well as a small influence of the Weddell Gyre in the western sector of the ‘zone south of the Antarctic Circumpolar Current’ (SACCZ). Within the SACCZ, we identified a primary bloom under the ice, a secondary bloom near the ice edge, and an open-ocean deep population. The similarity of distribution patterns across all transects allowed us to generalise a hypothesized sequence for the season. The primary phytoplankton bloom, with stocks of Chl a up to 239 mg m−2, occurred about 35 days before complete disappearance of the sea ice, and contained both cells from the water column and those released from melting ice. These blooms were composed of haptophytes (in particular, colonies and gametes of Phaeocystis antarctica), diatoms and cryptophytes (or the cryptophyte symbiont-containing ciliate Myrionecta rubrum). Aggregates released by melting ice quickly sank from the upper water column and Chl a stocks declined to 56–92 mg m−2, but the bloom of diatoms and, to a lesser extent, cryptophytes continued until about 20 days after ice melt. The disappearance of sea ice coincided with a sharp increase in P. antarctica and grazing, as indicated by increasing phaeophytin a and phaeophorbide a. Chlorophyllide content suggests that the diatom bloom then senesced, probably due to iron exhaustion. Stocks rapidly declined, apparently due to grazing krill that moved southward following the retreating sea ice. We suggest that grazing of the bloom and export of faecal pellets stripped the upper water column of iron (as suggested by low Fv/Fm ratios and CHEMTAX pigment ratios in Haptophytes – iron was not measured). Thus, export of iron by grazing, and possibly sedimentation, created a southward migrating iron gradient, limiting growth in the upper water column. North of the postulated iron gradient, a nanoflagellate community developed at depth, with Chl a stocks from 36–49 mg m−2. This community was probably based on regenerated production, sustained by residual and/or upwelling iron, as indicated by a close correspondence between distributions of Chl a and profiles of Fv/Fm. The community consisted of haptophytes (chiefly Phaeocystis gametes), dinoflagellates, prasinophytes, cryptophytes, and some small diatoms. Selective grazing by krill may have fashioned and maintained the community. North of the SB, Chl a ranged from 40–67 mg m−2 and was found predominantly in the mixed layer, but Fv/Fm ratios remained low, suggesting the community of P. antarctica and diatoms was iron-limited. These interpretations provide a cogent explanation for the composition and structure of late summer microbial populations in the marginal ice zone.

Biodiversity of the white coral bank off Cape Santa Maria di Leuca (Mediterranean Sea): An update

Abstract: The biodiversity of the Santa Maria di Leuca (SML) coral bank is summarized and its description is updated using data collected by means of underwater video systems, benthic samplers and fishing gears. A total of 222 living species have been recorded within the coral bank area in the depth range 280–1121 m. The most abundant benthic taxa recorded are Porifera (36 species) followed by Mollusca (35) and Cnidaria (31). The scleractinian corals Madrepora oculata and Lophelia pertusa are the main colonial species in the structure of the SML bank. Annelida, Crustacea and Bryozoa have been found with 24, 23 and 19 species, respectively. A total of 40 species of demersal fish have been recorded. Other faunal taxa were found with small numbers of species. One hundred and thirty-five species are new for the SML bank, 31 of which represent new records for the north-western Ionian Sea (2 Porifera, 17 Cnidaria, 1 Mollusca, 3 Annelida, 2 Crustacea, 4 Bryozoa and 4 Echinodermata). The finding of the annelid Harmothoe vesiculosa represents the first record for the Mediterranean Sea. The SML coral bank represents a biodiversity “hot-spot” on the bathyal bottoms of the Mediterranean Sea.

Fluorescence characteristics of dissolved organic matter in the deep waters of the Okhotsk Sea and the northwestern North Pacific Ocean

Abstract: Fluorescent dissolved organic matter (DOM), a fraction of chromophoric DOM, is known to be produced in the deep ocean and is considered to be bio-refractory. However, the factors controlling fluorescence properties of DOM in the deep ocean are still not well understood. In this study, we determined the fluorescence properties of DOM in the deep waters of the Okhotsk Sea and the northwestern North Pacific Ocean using excitation-emission matrix (EEM) fluorescence and parallel factor analysis (PARAFAC). One protein-like, two humic-like components, and one uncertain component, which might be derived from a fluorometer artifact, were identified by EEM-PARAFAC. Fluorescence intensity levels of the protein-like component were highest in the surface waters, decreased with depth, but did not change systematically in the bathypelagic layer (1000 m - bottom). Fluorescence characteristics of the two humic-like components were similar to those traditionally defined as marine and terrestrial humic-like fluorophores. The fluorescence intensity levels of the two humic-like components were lowest in the surface waters, increased with depth in the mesopelagic layer (200 - 1000 m), and then slightly decreased with depth in the bathypelagic layer. The ratio of the two humic-like components remained in a relatively narrow range in the bathypelagic layer compared to that in the surface layer, suggesting a similar composition of humic-like fluorophores in the bathypelagic layer. In addition, the fluorescence intensities of the two humic-like components were linearly correlated to apparent oxygen utilization (AOU) in the bathypelagic layer, suggesting that both humic-like components are produced in situ as organic matter is oxidized biologically. These findings imply that optical characteristics of humic-like fluorophores once formed might not be altered further biologically or geochemically in the deep ocean. On the other hand, relationships of fluorescence intensities with AOU and Fe(III) solubility were different between the two humic-like components in the mesopelagic layer, suggesting different environmental dynamics and biogeochemical roles for the two humic-like components.

Impact of natural oil and higher hydrocarbons on microbial diversity, distribution, and activity in Gulf of Mexico cold-seep sediments

Abstract: Gulf of Mexico cold seeps characterized by variable compositions and magnitudes of hydrocarbon seepage were sampled in order to investigate the effects of natural oils, methane, and non-methane hydrocarbons on microbial activity, diversity, and distribution in seafloor sediments. Though some sediments were characterized by relatively high quantities of oil, which may be toxic to some microorganisms, high rates of sulfate reduction (SR, 27.9714.7 mmol m

Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic’s interior

Abstract: Current estimates point to a mismatch of particulate organic carbon supply derived from the surface ocean and the microbial organic carbon demand in the meso- and bathypelagic realm. Based on recent findings that chemoautotrophic Crenarchaeota are abundant in the mesopelagic zone, we quantified dissolved inorganic carbon (DIC) fixation in the meso- and bathypelagic North Atlantic and compared it with heterotrophic microbial activity. Measuring 14C-bicarbonate fixation and 3H-leucine incorporation revealed that microbial DIC fixation is substantial in the mesopelagic water masses, ranging from 0.1 to 56.7 μmol C m−3 d−1, and is within the same order of magnitude as heterotrophic microbial activity. Integrated over the dark ocean’s water column, DIC fixation ranged from 1–2.5 mmol C m−2 d−1, indicating that chemoautotrophy in the dark ocean represents a significant source of autochthonously produced ‘new organic carbon’ in the ocean’s interior amounting to about 15–53% of the phytoplankton export production. Hence, chemoautotrophic DIC fixation in the oxygenated meso- and bathypelagic water column of the North Atlantic might substantially contribute to the organic carbon demand of the deep-water microbial food web.

Benthic food-web structure under differing water mass properties in the southern Chukchi Sea

Abstract: 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.

Long-term change in the abyssal NE Atlantic: The ‘Amperima Event’ revisited

Abstract: The results from a time series study (1989 to 2005) at a depth of 4850m on the Porcupine Abyssal Plain, NE Atlantic, are presented showing radical changes in the density of large invertebrates (megafauna) over time. Major changes occurred in a number of different taxa between 1996 and 1999 and then again in 2002. One species of holothurian, Amperima rosea, was particularly important, increasing in density by over three orders of magnitude. There were no significant changes in total megafaunal biomass during the same period. Peaks in density were correlated to reductions in mean body size indicating that the increases were related to large-scale recruitment events. The changes occurred over a wide area of the Porcupine Abyssal Plain. Comparisons made with changes in the density of protozoan and metazoan meiofauna, and with macrofauna, showed that major changes in community structure occurred in all size fractions of the benthic community at the same time. This suggests that the faunal changes were driven by environmental factors rather than being stochastic population imbalances of one or two species. Large-scale changes in the flux of organic matter to the abyssal seafloor have been noted in the time series, particularly in 2001 and may be related to the sudden mass occurrence of A. rosea the following year. Time-varying environmental factors are important in influencing the occurrence of megafauna on the abyssal seafloor.

Emerging concepts on microbial processes in the bathypelagic ocean-ecology, biogeochemistry, and genomics

Abstract: This paper synthesizes recent findings regarding microbial distributions and processes in the bathypelagic ocean (depth >1000 m). Abundance, production and respiration of prokaryotes reflect supplies of particulate and dissolved organic matter to the bathypelagic zone. Better resolution of carbon fluxes mediated by deep microbes requires further testing on the validity of conversion factors. Archaea, especially marine Crenarchaeota Group I, are abundant in deep waters where they can fix dissolved inorganic carbon. Viruses appear to be important in the microbial loop in deep waters, displaying remarkably high virus to prokaryote abundance ratios in some oceanic regions. Sequencing of 18S rRNA genes revealed a tremendous diversity of small-sized protists in bathypelagic waters. Abundances of heterotrophic nanoflagellates (HNF) and ciliates decrease with depth more steeply than prokaryotes; nonetheless, data indicated that HNF consumed half of prokaryote production in the bathypelagic zone. Aggregates are important habitats for deep-water microbes, which produce more extracellular enzymes (on a per-cell basis) than surface communities. The theory of marine gel formation provides a framework to unravel complex interactions between microbes and organic polymers. Recent data on the effects of hydrostatic pressure on microbial activities indicate that bathypelagic microbial activity is generally higher under in situ pressure conditions than at atmospheric pressures. High-throughput sequencing of 16S rRNA genes revealed a remarkable diversity of Bacteria in the bathypelagic ocean. Metagenomics and comparative genomics of piezophiles reveal not only the high diversity of deep sea microbes but also specific functional attributes of these piezophilic microbes, interpreted as an adaptation to the deep water environment. Taken together, the data compiled on bathypelagic microbes indicate that, despite high-pressure and low-temperature conditions, microbes in the bathypelagic ocean dynamically interact with complex mixtures of organic matter, responding to changes in the ocean’s biogeochemical state.

Benthic habitat characterization and distribution from two representative sites of the deep-water SML Coral Province (Mediterranean)

Abstract: Two sites (MS04 and MS06) from the Santa Maria di Leuca (SML) Coral Province were analyzed by a video and acoustic survey during the National Italian Project Apulian Plateau Bank Ecosystem Study (APLABES). Site MS04 (Atlantis Mound) is characterized by a sub-conical mound, 500 m wide and 25 m high, located at a water depth of about 650 m. Site MS06 (Yellow Chain) comprises several elongated reliefs (NNW–SSE-oriented), up to 25 m high and 500 m in maximum lateral extent, located at a depth of between 490 and 540 m. At both sites, two main mesohabitats (mound and intermound) containing several coral-bearing and -barren macrohabitats were observed in recorded videos and detected in side-scan sonographs. The coral-rich macrohabitats, characterized by densely packed colonies of the scleractinians Madrepora oculata and, secondarily, Lophelia pertusa ( M / L ), are typically restricted to the mound areas. The mud-dominated ones, almost devoid of M/L colonies, are more common within the intermound mesohabitat. However, on the most extensive mounds, both macrohabitat typologies exist. They are heterogeneously distributed on the mound surface, often showing a clear differentiation along two opposite flanks of the same topographic feature. M / L -rich macrohabitats are preferentially located on top and along the mound northeastern flank, showing a typical step-like distribution, probably reflecting the arrangement of hard substrate outcrops. Along this flank, fan-shaped Madrepora colonies and sponges are often oriented NNW–SSE, implying, together with other evidence, a primary southwestern current flow. The hard-bottom macrohabitats of the southwestern mound flank are generally restricted to sparse exposed, subvertical to overhanging scarps as well as to heterometric boulders located at the scarp base. Their fauna is mainly characterized by small-sized organisms (such as sponges and solitary scleractinians) although m-sized boulders may locally host very large antipatharian colonies ( Leiopathes glaberrima ). The heterogeneous distribution of the observed benthic macrohabitats seems to be strictly related to the local topography, the main current flow (and consequently larvae/food supply per unit of time), and the substrate typology (hard- vs. soft-bottom).

Zooplankton community patterns in the Chukchi Sea during summer 2004

Abstract: 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 (3100 ind. m−3, 30 mg dry weight m−3) of the total holozooplankton community abundance (3500 ind. m−3) and biomass (42 mg DW m−3) at most stations. Meroplanktonic larvae were, on average, almost as abundant (2260 ind. 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 (256 ind. m−3) and biomass (42 mg DW m−3) of the larvacean Oikopleura vanhoeffeni was observed throughout the sampling area. The chaetognath Parasagitta elegans (4.8 mg DW m−3) and a diverse assemblage of cnidarians (∼1.2 mg DW m−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.

Dynamics of the cross-shelf circulation in the Yellow and East China Seas in winter

Abstract: A general ocean circulation model is used to study the dynamics of the cross-shelf circulation in the Yellow and East China Seas in winter. The model results show that the shelf circulation in winter is induced primarily by the northerly monsoonal winds. Compared with the wind-driven circulation, the Kuroshio-forced circulation over the shelf is very weak. The westward shift of the Yellow Sea Warm Current is produced by the northerly winds through the generation of a sea-level trough off the Subei coasts and a sea-level ridge along the center of the Yellow Sea topographic trough. The sea-level trough off the Subei coasts is produced because the sea level at the coast is tied to the depression in the northern Yellow Sea and is moderated by the surface Ekman transport of the northerly monsoon. The sea-level ridge along the center of the Yellow Sea topographic trough is produced because the sea level along both the east China and the west Korea coasts decreases. The structure of the sea level gives rise to a geostrophic intrusion against the wind along the western side of the Yellow Sea trough and southward movement of the Korean coastal currents along the eastern side of the trough.

Effects of deep-water coral banks on the abundance and size structure of the megafauna in the Mediterranean Sea

Abstract: The Santa Maria di Leuca (SML) coral banks represent a rare example of living Lophelia-Madrepora -bearing coral mounds in the Mediterranean Sea. They are located between 350 and 1100 m in depth, in the northern Ionian Sea (eastern-central Mediterranean). Using a multi-beam echo sounder, side-scan sonar, high-resolution seismics and underwater video, the zones were identified for the sampling demersal fauna without damaging the coral colonies. During September–October 2005 experimental samplings were carried out with longlines and trawl nets inside the coral habitat and outside, where fishery exploitation occurs. No significant differences were shown between the abundance of fish recorded using longlines in the coral and non-coral habitat even though some selachians and teleosts were more abundant in the former than in the latter. Large specimens of rockfish ( Helicolenus dactylopterus ) and blackspot seabream ( Pagellus bogaraveo ) were commonly caught using longlines in the coral habitat. Data from trawling revealed refuge effects in the coral habitat and fishing effects outside. Significant differences were detected between the recorded abundances in the two study areas. Greater densities and biomasses were obtained inside the coral area, and fish size spectra and size distributions indicate a greater abundance of large fish inside the coral habitat. The SML coral habitat is a spawning area for H. dactylopterus . The remarkable density of the young-of-the-year of the deep-water shark Etmopterus spinax as well as of Merluccius merluccius , Micromesistius poutassou , Phycis blennoides and H. dactylopterus , indicates that the coral habitat also acts as nursery area for these demersal species, which are exploited outside. Considering the evidence of the negative impact of bottom trawling and, to a lesser extent, of longlining, the coral banks can provide a refuge for the conservation of unique species and habitats as well as in providing benefit to adjacent fisheries through the spill-over effect both of eggs, larvae, juveniles and adults.

A “Rosetta Stone” for metazoan zooplankton: DNA barcode analysis of species diversity of the Sargasso Sea (Northwest Atlantic Ocean)

Abstract: 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 ∼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.

DOC dynamics in the meso and bathypelagic layers of the Mediterranean Sea

Abstract: Seven years (2001–2008) of dissolved organic carbon (DOC) vertical profiles were examined in order to assess the main processes determining DOC concentration and distribution in the meso- and bathypelagic layers of the Mediterranean Sea. As expected, DOC showed high and highly variable concentrations in the surface layer of 57–68 μM (average values between 0 and 100 m), with a decrease to 44–53 μM between 200 and 500 m. Deep DOC distribution was strongly affected by deep-water formation, with a significant increase to values of 76 μM in recently ventilated deep waters, and low concentrations, comparable to those observed in the open oceanic waters (34–45 μM), where the oldest, deep waters occurred. In winter 2004/2005 a deep-water formation event was observed and the consequent DOC export at depth was estimated to range between 0.76–3.02 Tg C month–1. In the intermediate layer, the main path of the Levantine Intermediate Water (LIW) was followed in order to estimate the DOC consumption rate in its core. Multiple regression between DOC, apparent oxygen utilization (AOU), and salinity indicated that 38% of the oxygen consumption was related to DOC mineralization when the effect of mixing was removed. In deep waters of the southern Adriatic Sea a DOC decrease of 6 μM, together with an AOU increase of 9 μM, was observed between the end of January 2008 and the end of June 2008 (5 months). These data indicate a rate of microbial utilization of DOC of about 1.2 μM C month−1, with 92% of the oxygen consumption due to DOC mineralization. These values are surprisingly high for the deep sea and represent a peculiarity of the Mediterranean Sea.

Evolution and dynamics of the flow through Herald Canyon in the western Chukchi Sea

Abstract: The flow of summer and winter Pacific water masses through Herald Canyon is investigated using data from a high-resolution hydrographic/velocity survey conducted in summer 2004. The survey was part of the Russian-American Long Term Census of the Arctic (RUSALCA) program, and consisted of four cross-canyon transects occupied over a 2-day period. At the time of the survey dense winter water was entering the western side of the canyon from the Chukchi Sea, flowing alongside a poleward jet of summer water on the canyon’s eastern flank. As the dense water progressed northward it switched sides of the canyon and underwent a sudden increase in layer thickness. This coincided with vertical mixing near the interface of the winter and summer water, producing a new water mass mode exiting the canyon. All of these features are consistent with the notion of hydraulic activity occurring in the canyon. A three-layer hydraulic theory is applied to the flow, which suggests that it is supercritical and that hydraulic control is likely. A lock-exchange formulation accurately predicts the northward transport of the winter water. The origin of the winter water and the manner in which it drains into the canyon is investigated using satellite ice-concentration data, atmospheric re-analysis fields, historical in-situ data, and a simple circulation model. Finally, the fate of the Pacific water exiting the canyon, and its connection to the Chukchi shelfbreak current, is discussed.

Polymer dynamics of DOC networks and gel formation in seawater

Abstract: The ocean plays a major role in global biogeochemical carbon cycling; it holds an important reservoir of reduced organic carbon, mostly in the form of dissolved organic carbon (DOC), and processes about one-half of the total primary production of the planet. Dissolved molecules present between living and assimilable size extremes (∼1000 nm -1 nm), constitute the most abundant form of remnant biochemicals in the ocean, outweighing the total living biomass by a factor of roughly 200. Because DOC is the fundamental substrate for marine microorganisms, and is primarily composed by small refractory biopolymers, this prompted the idea that the ocean might function as a huge repository of recalcitrant carbon. The missing link that elucidates this paradox and explains how the rich and vast stock of DOC becomes available to bacteria was the discovery that DOC throughout the water column remains in reversible assembly/dispersion equilibrium forming porous microscopic gels (Chin et al., Nature 391, 568-572, 1998). This abiotic DOC-POM shunt yields a microgel pool containing ∼70 gigatons of carbon forming discrete patches of high nutrient concentration that can be readily colonized by microorganisms. The presence of this huge gel mass in seawater extending far into the dark ocean has ramifications that might well scale nonlinearly through the microbial loop to the World Ocean and global climate system and it is fundamentally changing how oceanographers think about processes linking the microbial loop and biological pump to the rest of the biosphere and the geosphere. Even if a small fraction of DOC remains self-assembled, marine scientists will have to revise the rationale of established aquatic paradigms ranging from trace metal chelation, size–reactivity relationships, the microbial loop, the biological pump, colloid pumping, and humification. A ubiquitous, reversible DOC assembly/dispersion process implies a dynamic “patchiness” spanning from the molecular to the micron scale, where the assignment of static bulk features including dimension, concentration, functionalities and vertical fluxes can be open to question. This brief revision illustrates two case studies that show how simple methods and principles of polymer networks theory can be used to advance the understanding of one of the most intriguing and significant processes taking place in the ocean. Namely, the kinetics and thermodynamics of: (a) Ca-driven DOC self-assembly, and (b) hydrophobic bond-driven self assembly of DOC by amphiphilic exopolymers released by marine bacteria.

Cold-seep carbonates of the middle and lower continental slope, northern Gulf of Mexico

Abstract: Authigenic carbonates from cold seeps on the middle and lower continental slope of the northern Gulf of Mexico (GOM) exhibit a wide range of mineralogical and stable isotopic compositions. These carbonates consist of concretions and nodules in surface sediments, hardgrounds of crusts and isolated slabs, and mounded buildups of blocks and slabs of up to over 10 meters in relief above the surrounding seafloor. Mineralogically, the carbonates are dominated by high-Mg calcite (HMC) and aragonite. However, low levels (<5 wt%) of dolomite are present in most samples. Petrographically, Mg-calcite peloidal matrix and acicular to botryoidal aragonitic void-filling cements are the most frequent associations. The carbon isotopic compositions of the carbonates range from −60.8 to 14.0‰ PDB, indicating complex carbon sources that include 13C-depleted biogenic and thermogenic methane, biodegraded crude oil, seawater CO2, and 13C-enriched residual CO2 from methanogenesis. A similarly large variability in δ18O values (2.5 to 6.7‰ PDB) demonstrates the geochemical complexity of the slope, with some samples pointing toward an 18O-enriched oxygen source that is possibly related to advection of 18O-enriched formation water and/or to the decomposition of gas hydrate. A considerable range of mineralogical and isotopic variations in cold-seep carbonate composition was noted even within individual study sites. However, common trends occur across multiple geographic areas. This situation suggests that local controls on fluid and gas flux, types of seep hydrocarbons, the presence or absence of gas hydrate in the near-surface sediment, and chemosynthetic communities, as well as the temporal evolution of the local hydrocarbon reservoir, all may play a part in determining carbonate mineralogy and isotope geochemistry. The carbon isotope data clearly indicate that between-site variation is greater than within-site variation. Seep carbonates formed on the middle and lower continental slope of the GOM do not appear to be substantially different from those found on the upper slope (<1000-m water depth). The highly variable fluids and gases that leave their geochemical imprints on seep carbonate of the middle and lower continental slope are similar to their outer shelf and upper slope counterparts.

DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition

Abstract: 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 oxidase 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.

Diversity and vertical distribution of mesozooplankton in the Arctic's Canada Basin

Abstract: 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 varies 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.

Phytoplankton community at warm eddies in the northern South China Sea in winter 2003/2004

Abstract: Two anti-cyclonic (warm) eddies were located in the northern South China Sea (SCS) during winter 2003/2004. They were monitored using sea-level anomaly data provided by satellite altimetry, surface drifters and in situ hydrographic data. Phytoplankton Chl a biomass as well as community structure were determined using high-performance liquid chromatography. Both warm eddies displayed positive sea-level anomaly, high sea-surface temperature and similar phytoplankton Chl a biomass compared with the reference area. However, phytoplankton communities we observed in these two eddies were significantly different. In one warm eddy which was formed by the Kuroshio intrusion, the phytoplankton community was dominated by prochlorophyceae within the euphotic zone. In the other warm eddy, which might be formed in coastal waters of northern SCS, haptophyceae dominated in the euphotic zone. This difference in the phytoplankton community was due to the different origins and ages of the two warm eddies. (C) 2010 Elsevier Ltd. All rights reserved.

Long-term variability of downward particle flux in the deep northeast Atlantic: Causes and trends

Abstract: At 3000 m depth the downward flux of particulate matter shows substantial seasonal and interannual variation. Complete annual records for eight of the past 14 years have been examined in the light of mixing depths derived from the OCCAM general circulation model and euphotic zone chlorophyll concentration and productivity, which were derived from the SeaWiFS satellite colour sensor. The annual flux was particularly high in 2001 due to a late summer deposition exceeding previous records several fold and this year was also characterised by very early shoaling of the mixing depth in spring and a very high surface spring chlorophyll concentration. Other years that were somewhat unusual in having either high or low flux at depth were not in general associated with unusual patterns of mixing or productivity. The percentage of the annual organic carbon primary production which reaches 3000 m varies from 0.6 to 1.2% except in 2001 when it reached 3.4%. A mechanistic relationship between upper-ocean processes and deep-ocean particle flux remains elusive and various explanations are suggested for this which need now to be addressed. In the spring, the timing of first shoaling of mixing, enhancement of productivity and increased particle flux at depth have all advanced during the 14 years of study by about 2 days per year, suggesting a similar trend as has been observed for surface phytoplankton, mesozooplankton, fish and seabirds probably caused by wide-scale environmental changes.

The circulation and water masses of the Antarctic shelf and continental slope between 30 and 80∘E

Abstract: The circulation and water masses from the Antarctic continental shelf to 62 ∘ S between 30 and 80 ∘ E are described using hydrographic data collected on seven hydrographic sections during the Baseline Research on Oceanography, Krill and the Environment-West (BROKE-West) experiment. The eastern limb of the Weddell Gyre dominates circulation between 30 and 40 ∘ E , and is significantly cooler and fresher than the region to the east. The Antarctic Circumpolar Current (ACC) extends from the north into the survey region east of 40 ∘ E , reaching as far south as 65 . 5 ∘ S at 60 ∘ E . This results in increasing observed maximum temperature and salinities progressively towards the east, peaking at 80 ∘ E due to the intrusion of the southern ACC Front (sACCF) to 63 ∘ S . This southward extension is steered by the southern end of Kerguelen Plateau, causing a horizontal shear of over 0.15 m s - 1 between the eastward ACC and westward-flowing Antarctic Slope Current (ASC). The ASC is observed at all six meridional sections immediately north of the shelf break. It is strongly barotropic and transports a total of 15.8 ± 7.4 Sv westwards, while the bottom referenced baroclinic component only contributes 1.3 ± 0.3 Sv . At each section this current intensifies to a narrow westward ‘jet’ with absolute velocities up to 0.3 m s - 1 over the steepest shelf slope gradients. At 70 ∘ E a ‘V’ shape is observed in the ASF. This, and the nearby presence of denser shelf water and ice-shelf water, is characteristic of Antarctic Bottom Water (AABW) formation, but no new AABW is found on this section. Instead, significantly warmer, saltier and less oxygenated AABW to the east and newly formed AABW high on the continental slope immediately to the west suggest a formation region just west of 70 ∘ E . This newly formed AABW progressively becomes warmer and saltier west of 60 ∘ E and is observed extending offshore and moving westward below eastward flowing water masses. ACC frontal positions are found to be 1–2° farther north in the survey region than suggested by historical climatology.

Blocking and Westward Passage of Eddies in the Luzon Strait

Abstract: Satellite observations have shown the abundance of generally westward-propagating eddies in the subtropical regions in the North Pacific Ocean, especially north of 10°N. Eddies transport mass, and can significantly impact the circulation as well as the heat, salt and nutrient balances of the western Pacific marginal seas. This paper uses a numerical model to examine the conditions when eddies can or cannot freely propagate westward through the Luzon Strait into the South China Sea (SCS). Composite analyses on the 10-year model data show that the fates of eddies depend on the strength and path of the Kuroshio. In one path that exists mostly during fall and winter, the Kuroshio loops westward into the SCS, the potential vorticity (PV) across the current is weak, and eddies are likely to propagate freely through the Luzon Strait. In another path, which exists mostly during spring and summer, the Kuroshio tends to leap directly northward bypassing the SCS, the PV across it strengthens, and eddies are then blocked and are constrained to also follow the northward path. Nonlinear eddy-current interaction and the existence of a cyclone north of the Luzon Island during the looping phase explain why eddies of both signs can pass through the strait. It is shown also that the upstream state of the Kuroshio in the western tropical Pacific plays an important role in dictating the different paths of the Kuroshio. The looping (leaping) path is caused by a weakened (stronger) Kuroshio transport related to the northward (southward) shift of the North Equatorial Current in wintertime (summertime).

Biogeochemical signatures and microbial activity of different cold-seep habitats along the Gulf of Mexico deep slope

Abstract: 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.

DNA Barcoding the Medusozoa using mtCOI

Abstract: The Medusozoa are a clade within the Cnidaria comprising the classes Hydrozoa, Scyphozoa, and Cubozoa. Identification of medusozoan species is challenging, even for taxonomic experts, due to their fragile forms and complex, morphologically-distinct life history stages. In this study 231 sequences for a portion of the mitochondrial Cytochrome Oxidase I (mtCOI) gene were obtained from 95 species of Medusozoans including; 84 hydrozoans (61 siphonophores, eight anthomedusae, four leptomedusae, seven trachymedusae, and four narcomedusae), 10 scyphozoans (three coronatae, four semaeostomae, two rhizostomae, and one stauromedusae), and one cubozoan. This region of mtCOI has been used as a DNA barcode (i.e., a molecular character for species recognition and discrimination) for a diverse array of taxa, including some Cnidaria. Kimura 2-parameter (K2P) genetic distances between sequence variants within species ranged from 0 to 0.057 (mean 0.013). Within the 13 genera for which multiple species were available, K2P distance between congeneric species ranged from 0.056 to 0.381. A cluster diagram generated by Neighbor Joining (NJ) using K2P distances reliably clustered all barcodes of the same species with ≥99% bootstrap support, ensuring accurate identification of species. Intra- and inter-specific variation of the mtCOI gene for the Medusozoa are appropriate for this gene to be used as a DNA barcode for species-level identification, but not for phylogenetic analysis or taxonomic classification of unknown sequences at higher taxonomic levels. This study provides a set of molecular tools that can be used to address questions of speciation, biodiversity, life-history, and population boundaries in the Medusozoa.

The intricacies of dinoflagellate pellicle cysts: The example of Alexandrium minutum cysts from a bloom-recurrent area (Bay of Baiona, NW Spain)

Abstract: The terms “temporary”, “pellicle”, and “ecdysal” cyst have been employed arbitrarily in the literature of the dinoflagellate life cycle to describe a non-motile and single-layered-wall stage with no mandatory dormancy period, of asexual or sexual origin. These three terms have been used more or less synonymously, but more specific definitions, taking into account morphological and physiological aspects and their roles in dinoflagellate population dynamics, are still needed. To clarify the current terminology, we examine and discuss the usages and foundations of those terms. The background for this discussion is provided by a comparison of the morphology and germination times of three different types of Alexandrium minutum cysts collected during a seasonal bloom in the Bay of Baiona (NW Spain). The double-walled cysts were similar to the resting cysts reported for this species, but other, thin-walled and thecate cysts were also observed. These latter cyst types needed between 1 and 17 days to germinate and were therefore considered as short-term cysts, in contrast to the 1.5-month dormancy period of resting (hypnozygotic) cysts. Our results showed that the temporal distribution of these short-term cysts during the bloom period followed a pattern very similar to that of vegetative cells. However, resting cysts were only detected at the end of the bloom. In the context of our present knowledge regarding the dormancy and quiescence of dinoflagellate cysts, “temporary” is a very misleading and uncertain term and must be rejected. The term “ecdysal” has been used in reference to thin-walled cysts when ecdysis has been proven; however, ecdysis is not unique to this type of cysts as thick-walled zygotic cysts can be formed thorough ecdysis of a thecate planozygote. In conclusion, based on our current understanding of cysts, the term “pellicle” more appropriately describes single-layered-wall stages.