Sea-ice derived meltwater stratification slows the biological carbon pump: results from continuous observations

The ocean moderates the world's climate through absorption of heat and carbon, but how much carbon the ocean will continue to absorb remains unknown. The North Atlantic Ocean west (Baffin Bay/Labrador Sea) and east (Fram Strait/Greenland Sea) of Greenland features the most intense absorption of anthropogenic carbon globally; the biological carbon pump (BCP) contributes substantially. As Arctic sea-ice melts, the BCP changes, impacting global climate and other critical ocean attributes (e.g. biodiversity). Full understanding requires year-round observations across a range of ice conditions. Here we present such observations: autonomously collected Eulerian continuous 24-month time-series in Fram Strait. We show that, compared to ice-unaffected conditions, sea-ice derived meltwater stratification slows the BCP by 4 months, a shift from an export to a retention system, with measurable impacts on benthic communities. This has implications for ecosystem dynamics in the future warmer Arctic where the seasonal ice zone is expected to expand.

In situ experimental evidences for responses of abyssal benthic biota to shifts in phytodetritus compositions linked to global climate change

Abyssal plains cover more than half of Earth's surface, and the main food source in these ecosystems is phytodetritus, mainly originating from primary producers in the euphotic zone of the ocean. Global climate change is influencing phytoplankton abundance, productivity, and distribution. Increasing importance of picoplankton over diatom as primary producers in surface oceans (especially projected for higher latitudes) is projected and hence altering the quantity of organic carbon supplied to the abyssal seafloor as phytodetritus, consequences of which remain largely unknown. Here, we investigated the in situ responses of abyssal biota from viruses to megafauna to different types of phytoplankton input (diatoms or cyanobacteria which were labeled with stable isotopes) at equatorial (oligotrophic) and temperate (eutrophic) benthic sites in the Pacific Ocean (1°N at 4277 m water depth and 39°N at 5260 m water depth, respectively). Our results show that meiofauna and macrofauna generally preferred diatoms as a food source and played a relatively larger role in the consumption of phytodetritus at higher latitudes (39°N). Contrarily, prokaryotes and viruses showed similar or even stronger responses to cyanobacterial than to diatom supply. Moreover, the response of prokaryotes and viruses was very rapid (within 1-2 days) at both 1°N and 39°N, with quickest responses reported in the case of cyanobacterial supply at higher latitudes. Overall, our results suggest that benthic deep-sea eukaryotes will be negatively affected by the predicted decrease in diatoms in surface oceans, especially at higher latitudes, where benthic prokaryotes and viruses will otherwise likely increase their quantitative role and organic carbon cycling rates. In turn, such changes can contribute to decrease carbon transfer from phytodetritus to higher trophic levels, with strong potential to affect oceanic food webs, their biodiversity and consequently carbon sequestration capacity at the global scale.

Sophistication in a seemingly simple creature: a review of wild holothurian nutrition in marine ecosystems

Holothurians are marine invertebrates that are among the most widespread benthic megafauna communities by both biomass and abundance in shallow‐water and deep‐sea ecosystems, their functions supporting important ecological services worldwide. Despite their simple appearance as sea cucumbers, holothurians show a wide range of feeding practices. However, information on what and how these animals eat is scattered and potentially confusing. We provide a comprehensive review of holothurian nutrition in coastal and deep‐sea ecosystems. First, we describe morphological aspects of holothurian feeding and the ultrastructure of tentacles. We discuss the two processes for food capture, concluding that mucus adhesion is likely the main method; two mucous cells, type‐1 and type‐2, possibly allow the adhesion and de‐adhesion, respectively, of food particles. Secondly, this review aims to clarify behavioural aspects of holothurian suspension‐ and deposit‐feeding. We discuss the daily feeding cycle, and selective feeding strategies. We conclude that there is selectivity for fine and organically rich particles, and that feeding through the cloaca is also a route for nutrient absorption. Third, we provide a wide description of the diet of holothurians, which can be split into two categories: living and non‐living material. We suggest that Synallactida, Molpadida, Persiculida, Holothuriida and Elasipodida, ingest the same fractions, and emphasise the importance of bacteria in the diet of holothurians.

Investigating the environmental drivers of deep-seafloor biodiversity: A case study of peracarid crustacean assemblages in the Northwest Atlantic Ocean

The deep-sea benthos covers over 90% of seafloor area and hosts a great diversity of species which contribute toward essential ecosystem services. Evidence suggests that deep-seafloor assemblages are structured predominantly by their physical environment, yet knowledge of assemblage/environment relationships is limited. Here, we utilized a very large dataset of Northwest Atlantic Ocean continental slope peracarid crustacean assemblages as a case study to investigate the environmental drivers of deep-seafloor macrofaunal biodiversity. We investigated biodiversity from a phylogenetic, functional, and taxonomic perspective, and found that a wide variety of environmental drivers, including food availability, physical disturbance (bottom trawling), current speed, sediment characteristics, topographic heterogeneity, and temperature (in order of relative importance), significantly influenced peracarid biodiversity. We also found deep-water peracarid assemblages to vary seasonally and interannually. Contrary to prevailing theory on the drivers of deep-seafloor diversity, we found high topographic heterogeneity (at the hundreds to thousands of meter scale) to negatively influence assemblage diversity, while broadscale sediment characteristics (i.e., percent sand content) were found to influence assemblages more than sediment particle-size diversity. However, our results support other paradigms of deep-seafloor biodiversity, including that assemblages may vary inter- and intra-annually, and how assemblages respond to changes in current speed. We found that bottom trawling negatively affects the evenness and diversity of deep-sea soft-sediment peracarid assemblages, but that predicted changes in ocean temperature as a result of climate change may not strongly influence continental slope biodiversity over human timescales, although it may alter deep-sea community biomass. Finally, we emphasize the value of analyzing multiple metrics of biodiversity and call for researchers to consider an expanded definition of biodiversity in future investigations of deep-ocean life.

Chronic effects of brine discharge form large-scale seawater reverse osmosis desalination facilities on benthic bacteria

Seawater desalination facilities continuously discharge hyper-saline brine into the coastal environment which often flows as a concentrated plume over the seafloor, hence possibly impacting benthic microorganisms. Yet, the effects of brine discharge from desalination plants on benthic bacteria, key players in biodegradation of organic material and nutrient recycling is unknown. In this study, we tested the chronic (years) effects of brine discharge from three large-scale desalination facilities on the abundance, metabolic activity and community composition of benthic bacteria. To this end, four sampling campaigns were carried at the outfall areas of the Ashkelon, Sorek and Hadera desalination facilities. The effects of the brine were compared to corresponding reference stations which were not influenced by the brine (i.e., water temperature and salinity). Our sampling data indicate that bacterial abundance and activity that includes bacterial growth efficiency were 1.3-2.6-fold higher at the outfall area than the reference station. Concomitant analysis pointed out that the bacterial community structure at the brine discharge area was also different than the reference station, yet varied between each desalination facility. Our results demonstrate that the impact of brine effluent from desalination facilities on benthic bacteria are site-specific and localized (<1.4 Km²) around the discharge point. Namely, that the effects on benthic bacteria are prominent at the brine mixing zone and change according to the discharge method used to disperse the brine as well as local stressors (e.g., eutrophication and elevated water temperature). Our results contribute new insights on the effects of desalination-brine to benthic microbes, while providing scientifically-based aspects on the ecological impacts of brine dispersion for decision makers.

Fish mitigate trophic depletion in marine cave ecosystems

Dark marine habitats are often characterized by a food-limited condition. Peculiar dark habitats include marine caves, characterized by the absence of light and limited water flow, which lead to reduced fluxes of organic matter for cave-dwelling organisms. We investigated whether the most abundant and common cave-dwelling fish Apogon imberbis has the potential to play the role of trophic vector in Mediterranean marine caves. We first analysed stomach contents to check whether repletion changes according to a nycthemeral cycle. We then identified the prey items, to see whether they belong to species associated with cave habitats or not. Finally, we assessed whether A. imberbis moves outside marine caves at night to feed, by collecting visual census data on A. imberbis density both inside and outside caves, by day and by night. The stomach repletion of individuals sampled early in the morning was significantly higher than later in the day. Most prey were typical of habitats other than caves. A. imberbis was on average more abundant within caves during the day and outside during the night. Our study supports the hypothesis regarding the crucial trophic role of A. imberbis in connecting Mediterranean marine caves with external habitats.

Food supply and size class depending variations in phytodetritus intake in the benthic foraminifer Ammonia tepida

Ammonia tepida is a common and abundant benthic foraminifer in intertidal mudflats. Benthic foraminifera are primary consumers and detritivores and act as key players in sediment nutrient fluxes. In this study, laboratory feeding experiments using isotope-labeled phytodetritus were carried out with A. tepida collected at the German Wadden Sea, to investigate the response of A. tepida to varying food supply. Feeding mode (single pulse, constant feeding; different incubation temperatures) caused strong variations in cytoplasmic carbon and nitrogen cycling, suggesting generalistic adaptations to variations in food availability. To study the influence of intraspecific size to foraminiferal carbon and nitrogen cycling, three size fractions (125-250 µm, 250-355 µm, >355 µm) of A. tepida specimens were separated. Small individuals showed higher weight specific intake for phytodetritus, especially for phytodetrital nitrogen, highlighting that size distribution within foraminiferal populations is relevant to interpret foraminiferal carbon and nitrogen cycling. These results were used to extrapolate the data to natural populations of living A. tepida in sediment cores, demonstrating the impact of high abundances of small individuals on phytodetritus processing and nutrient cycling. It is estimated that at high abundances of individuals in the 125-250 µm size fraction, Ammonia populations can account for more than 11% of phytodetritus processing in intertidal benthic communities.

Surviving anoxia in marine sediments: The metabolic response of ubiquitous benthic foraminifera (Ammonia tepida)

High input of organic carbon and/or slowly renewing bottom waters frequently create periods with low dissolved oxygen concentrations on continental shelves and in coastal areas; such events can have strong impacts on benthic ecosystems. Among the meiofauna living in these environments, benthic foraminifera are often the most tolerant to low oxygen levels. Indeed, some species are able to survive complete anoxia for weeks to months. One known mechanism for this, observed in several species, is denitrification. For other species, a state of highly reduced metabolism, essentially a state of dormancy, has been proposed but never demonstrated. Here, we combined a 4 weeks feeding experiment, using 13C-enriched diatom biofilm, with correlated TEM and NanoSIMS imaging, plus bulk analysis of concentration and stable carbon isotopic composition of total organic matter and individual fatty acids, to study metabolic differences in the intertidal species Ammonia tepida exposed to oxic and anoxic conditions. Strongly contrasting cellular-level dynamics of ingestion and transfer of the ingested biofilm components were observed between the two conditions. Under oxic conditions, within a few days, intact diatoms were ingested, degraded, and their components assimilated, in part for biosynthesis of different cellular components: 13C-labeled lipid droplets formed after a few days and were subsequently lost (partially) through respiration. In contrast, in anoxia, fewer diatoms were initially ingested and these were not assimilated or metabolized further, but remained visible within the foraminiferal cytoplasm even after 4 weeks. Under oxic conditions, compound specific 13C analyses showed substantial de novo synthesis by the foraminifera of specific polyunsaturated fatty acids (PUFAs), such as 20:4(n-6). Very limited PUFA synthesis was observed under anoxia. Together, our results show that anoxia induced a greatly reduced rate of heterotrophic metabolism in Ammonia tepida on a time scale of less than 24 hours, these observations are consistent with a state of dormancy.

Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters

Estuaries are highly dynamic ecosystems in which freshwater and seawater mix together. Depending on tide and river inflows, particles originating from rivers or from the remobilization of sediments accumulate in the water column. Due to the salinity gradient and the high heterotrophic activity in the estuarine plume, hypoxic and anoxic microniches may form in oxygenated waters, sustaining favorable conditions for resuspended anaerobic microorganisms. In this context, we tested the hypothesis that anaerobic sulfate-reducing prokaryotes may occur in the water column of the Adour River. Using 16S ribosomal RNA (rRNA) and dsrAB-based terminal restriction fragment length polymorphism (T-RFLP) techniques, we characterized total prokaryotic and sulfate-reducing communities along a gradient from estuarine to marine bay waters. Sulfate-reducing prokaryotes were further characterized by the description of dsrB genes and the cultivation of sulfidogenic anaerobic microorganisms. As a result, physical-chemical parameters had a significant effect on water bacterial diversity and community structure along the studied gradient. The concentration of cultured sulfidogenic microorganisms ranged from 1 to 60 × 10³ cells l^-1 in the water column. Sulfate-reducing prokaryotes occurring in estuarine waters were closely related to microorganisms previously detected in freshwater sediments, suggesting an estuarine origin, mainly by the remobilization of the sediments. In the marine bay station, sediment-derived sulfate-reducing prokaryotes were not cultured anymore, probably due to freshwater dilution, increasing salinity and extended oxic stress. Nevertheless, isolates related to the type strain Desulfovibrio oceani were cultured from the diluted plume and deep marine waters, indicating the occurrence of autochthonous sulfate-reducing bacteria offshore.

Exploration of the Canyon-Incised Continental Margin of the Northeastern United States Reveals Dynamic Habitats and Diverse Communities

The continental margin off the northeastern United States (NEUS) contains numerous, topographically complex features that increase habitat heterogeneity across the region. However, the majority of these rugged features have never been surveyed, particularly using direct observations. During summer 2013, 31 Remotely-Operated Vehicle (ROV) dives were conducted from 494 to 3271 m depth across a variety of seafloor features to document communities and to infer geological processes that produced such features. The ROV surveyed six broad-scale habitat features, consisting of shelf-breaching canyons, slope-sourced canyons, inter-canyon areas, open-slope/landslide-scar areas, hydrocarbon seeps, and Mytilus Seamount. Four previously unknown chemosynthetic communities dominated by Bathymodiolus mussels were documented. Seafloor methane hydrate was observed at two seep sites. Multivariate analyses indicated that depth and broad-scale habitat significantly influenced megafaunal coral (58 taxa), demersal fish (69 taxa), and decapod crustacean (34 taxa) assemblages. Species richness of fishes and crustaceans significantly declined with depth, while there was no relationship between coral richness and depth. Turnover in assemblage structure occurred on the middle to lower slope at the approximate boundaries of water masses found previously in the region. Coral species richness was also an important variable explaining variation in fish and crustacean assemblages. Coral diversity may serve as an indicator of habitat suitability and variation in available niche diversity for these taxonomic groups. Our surveys added 24 putative coral species and three fishes to the known regional fauna, including the black coral Telopathes magna, the octocoral Metallogorgia melanotrichos and the fishes Gaidropsarus argentatus, Guttigadus latifrons, and Lepidion guentheri. Marine litter was observed on 81% of the dives, with at least 12 coral colonies entangled in debris. While initial exploration revealed the NEUS region to be both geologically dynamic and biologically diverse, further research into the abiotic conditions and the biotic interactions that influence species abundance and distribution is needed.

Field Documentation of Unusual Post-Mortem Arthropod Activity on Human Remains

During a forensic investigation, the presence of physical marks on human remains can influence the interpretation of events related to the death of an individual. Some tissue injury on human remains can be misinterpreted as ante- or peri-mortem wounds by an investigator when in reality the markings resulted from post-mortem arthropod activity. Unusual entomological data were collected during a study examining the decomposition of a set of human remains in San Marcos, Texas. An adult female Pediodectes haldemani (Girard) (Orthoptera: Tettigoniidae) and an Armadillidium cf. vulgare (Isopoda: Armadilidiidae) were documented feeding on the remains. Both arthropods produced physical marks or artifacts on the remains that could be misinterpreted as attack, abuse, neglect, or torture. Additionally, red imported fire ants, Solenopsis invicta Buren (Hymenoptera: Formicidae), were observed constructing structures in the mark produced by the P. haldemani feeding. These observations provide insight into the potential of post-mortem arthropod damage to human remains, which previously had not been described for these taxa, and therefore, physical artifacts on any remains found in similar circumstances may result from arthropod activity and not ante- or peri-mortem wounds.

Sinking jelly-carbon unveils potential environmental variability along a continental margin

Particulate matter export fuels benthic ecosystems in continental margins and the deep sea, removing carbon from the upper ocean. Gelatinous zooplankton biomass provides a fast carbon vector that has been poorly studied. Observational data of a large-scale benthic trawling survey from 1994 to 2005 provided a unique opportunity to quantify jelly-carbon along an entire continental margin in the Mediterranean Sea and to assess potential links with biological and physical variables. Biomass depositions were sampled in shelves, slopes and canyons with peaks above 1000 carcasses per trawl, translating to standing stock values between 0.3 and 1.4 mg C m² after trawling and integrating between 30,000 and 175,000 m² of seabed. The benthopelagic jelly-carbon spatial distribution from the shelf to the canyons may be explained by atmospheric forcing related with NAO events and dense shelf water cascading, which are both known from the open Mediterranean. Over the decadal scale, we show that the jelly-carbon depositions temporal variability paralleled hydroclimate modifications, and that the enhanced jelly-carbon deposits are connected to a temperature-driven system where chlorophyll plays a minor role. Our results highlight the importance of gelatinous groups as indicators of large-scale ecosystem change, where jelly-carbon depositions play an important role in carbon and energy transport to benthic systems.

Resource quality affects carbon cycling in deep-sea sediments

Deep-sea sediments cover ~70% of Earth's surface and represent the largest interface between the biological and geological cycles of carbon. Diatoms and zooplankton faecal pellets naturally transport organic material from the upper ocean down to the deep seabed, but how these qualitatively different substrates affect the fate of carbon in this permanently cold environment remains unknown. We added equal quantities of (13)C-labelled diatoms and faecal pellets to a cold water (-0.7 °C) sediment community retrieved from 1080 m in the Faroe-Shetland Channel, Northeast Atlantic, and quantified carbon mineralization and uptake by the resident bacteria and macrofauna over a 6-day period. High-quality, diatom-derived carbon was mineralized >300% faster than that from low-quality faecal pellets, demonstrating that qualitative differences in organic matter drive major changes in the residence time of carbon at the deep seabed. Benthic bacteria dominated biological carbon processing in our experiments, yet showed no evidence of resource quality-limited growth; they displayed lower growth efficiencies when respiring diatoms. These effects were consistent in contrasting months. We contend that respiration and growth in the resident sediment microbial communities were substrate and temperature limited, respectively. Our study has important implications for how future changes in the biochemical makeup of exported organic matter will affect the balance between mineralization and sequestration of organic carbon in the largest ecosystem on Earth.

Increase in Alphaproteobacteria in association with a polychaete, Capitella sp. I, in the organically enriched sediment

We conducted bioremediation experiments on the organically enriched sediment on the sea floor just below a fish farm, introducing artificially mass-cultured colonies of deposit-feeding polychaete, Capitella sp. I. To clarify the association between the Capitella and bacteria on the efficient decomposition of the organic matter in the sediment in the experiments, we tried to identify the bacteria that increased in the microbial community in the sediment with dense patches of the Capitella. The relationship between TOC and quinone content of the sediment as an indicator of the bacterial abundance was not clear, while a significant positive correlation was found between Capitella biomass and quinone content of the sediment. In particular, ubiquinone-10, which is present in members of the class Alphaproteobacteria, increased in the sediment with dense patches of the Capitella. We performed denaturing gradient gel electrophoresis (DGGE) analyses to identify the alphaproteobacterial species in the sediment with dense patches of the worm, using two DGGE fragments obtained from the sediment samples and one fragment from the worm body. The sequences of these DGGE fragments were closely related to the specific members of the Roseobacter clade. In the associated system with the Capitella and the bacteria in the organically enriched sediment, the decomposition of the organic matter may proceed rapidly. It is very likely that the Capitella works as a promoter of bacteria in the organically enriched sediment, and feeds the increased bacteria as one of the main foods, while the bacteria decompose the organic matter in the sediment with the assistance of the Capitella.

Habitat heterogeneity, disturbance, and productivity work in concert to regulate biodiversity in deep submarine canyons

Habitat heterogeneity is a major structuring agent of ecological assemblages promoting beta diversity and ultimately contributing to overall higher global diversity. The exact processes by which heterogeneity increases diversity are scale dependent and encompass variation in other well-known processes, e.g., productivity, disturbance, and temperature. Thus, habitat heterogeneity likely triggers multiple and cascading diversity effects through ecological assemblages. Submarine canyons, a pervasive feature of the world's oceans, likely increase habitat heterogeneity at multiple spatial scales similar to their terrestrial analogues. However, our understanding of how processes regulating diversity, and the potential for cascading effects within these important topographic features, remains incomplete. Utilizing remote-operated vehicles (ROVs) for coring and video transects, we quantified faunal turnover in the deep-sea benthos at a rarely examined scale (1 m-1 km). Macrofaunal community structure, megafaunal density, carbon flux, and sediment characteristics were analyzed for the soft-bottom benthos at the base of cliff faces in Monterey Canyon (northeast Pacific Ocean) at three depths. We documented a remarkable degree of faunal turnover and changes in overall community structure at scales < 100 m, and often < 10 m, related to geographic features of a canyon complex. Ultimately, our findings indicated that multiple linked processes related to habitat heterogeneity, ecosystem engineering, and bottom-up dynamics are important to deep-sea biodiversity.

Temporal change in deep-sea benthic ecosystems: a review of the evidence from recent time-series studies

Societal concerns over the potential impacts of recent global change have prompted renewed interest in the long-term ecological monitoring of large ecosystems. The deep sea is the largest ecosystem on the planet, the least accessible, and perhaps the least understood. Nevertheless, deep-sea data collected over the last few decades are now being synthesised with a view to both measuring global change and predicting the future impacts of further rises in atmospheric carbon dioxide concentrations. For many years, it was assumed by many that the deep sea is a stable habitat, buffered from short-term changes in the atmosphere or upper ocean. However, recent studies suggest that deep-seafloor ecosystems may respond relatively quickly to seasonal, inter-annual and decadal-scale shifts in upper-ocean variables. In this review, we assess the evidence for these long-term (i.e. inter-annual to decadal-scale) changes both in biologically driven, sedimented, deep-sea ecosystems (e.g. abyssal plains) and in chemosynthetic ecosystems that are partially geologically driven, such as hydrothermal vents and cold seeps. We have identified 11 deep-sea sedimented ecosystems for which published analyses of long-term biological data exist. At three of these, we have found evidence for a progressive trend that could be potentially linked to recent climate change, although the evidence is not conclusive. At the other sites, we have concluded that the changes were either not significant, or were stochastically variable without being clearly linked to climate change or climate variability indices. For chemosynthetic ecosystems, we have identified 14 sites for which there are some published long-term data. Data for temporal changes at chemosynthetic ecosystems are scarce, with few sites being subjected to repeated visits. However, the limited evidence from hydrothermal vents suggests that at fast-spreading centres such as the East Pacific Rise, vent communities are impacted on decadal scales by stochastic events such as volcanic eruptions, with associated fauna showing complex patterns of community succession. For the slow-spreading centres such as the Mid-Atlantic Ridge, vent sites appear to be stable over the time periods measured, with no discernable long-term trend. At cold seeps, inferences based on spatial studies in the Gulf of Mexico, and data on organism longevity, suggest that these sites are stable over many hundreds of years. However, at the Haakon Mosby mud volcano, a large, well-studied seep in the Barents Sea, periodic mud slides associated with gas and fluid venting may disrupt benthic communities, leading to successional sequences over time. For chemosynthetic ecosystems of biogenic origin (e.g. whale-falls), it is likely that the longevity of the habitat depends mainly on the size of the carcass and the ecological setting, with large remains persisting as a distinct seafloor habitat for up to 100 years. Studies of shallow-water analogs of deep-sea ecosystems such as marine caves may also yield insights into temporal processes. Although it is obvious from the geological record that past climate change has impacted deep-sea faunas, the evidence that recent climate change or climate variability has altered deep-sea benthic communities is extremely limited. This mainly reflects the lack of remote sensing of this vast seafloor habitat. Current and future advances in deep-ocean benthic science involve new remote observing technologies that combine a high temporal resolution (e.g. cabled observatories) with spatial capabilities (e.g. autonomous vehicles undertaking image surveys of the seabed).

Bacterial diversity in surface sediments from the Pacific Arctic Ocean

In order to assess bacterial diversity within four surface sediment samples (0-5 cm) collected from the Pacific Arctic Ocean, 16S ribosomal DNA clone library analysis was performed. Near full length 16S rDNA sequences were obtained for 463 clones from four libraries and 13 distinct major lineages of Bacteria were identified (alpha, beta, gamma, delta and epsilon-Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Firmicutes, Planctomycetes, Spirochetes, and Verrucomicrobia). alpha, gamma, and delta-Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria were common phylogenetic groups from all the sediments. The gamma-Proteobacteria were the dominant bacterial lineage, representing near or over 50% of the clones. Over 35% of gamma-Proteobacteria clones of four clone library were closely related to cultured bacterial isolates with similarity values ranging from 94 to 100%. The community composition was different among sampling sites, which potentially was related to geochemical differences.

On the use of benthic foraminiferal δ13C in palaeoceanography: constraints from primary proxy relationships

Recent findings are reviewed from observations in the field on the generation of the δ13C signal in shells of live (Rose Bengal stained) benthic foraminifera, and end up with implications for the interpretation of fossil signatures. The δ13C values of calcite tests of preferentially epifaunal foraminifera principally reflect the δ13C of dissolved inorganic carbon (DIC) of ambient seawater, whereas infaunal species record a porewater signal, both with an offset from equilibrium calcite. Species occupying the deepest average living depth in the sediment usually exhibit lowest δ13C test values, but δ13C values of conspecific specimens at a single site do not decrease with increasing subbottom depth and decreasing porewater δ13CDIC. Organic carbon fluxes to the sediment surface are generally reflected by infaunal species such that lowered δ13C values coincide with high fluxes, but even strictly epifaunal species may reflect seasonally pulsed phytodetritus supply by depleted test δ13C. In high-productivity environments, however, where dissolved oxygen and sedimentary carbonate contents are low, benthic foraminiferal tests show 13C enrichment probably due to carbonate-ion undersaturation. Ontogenetic increase in δ13C values of certain infaunal species suggests a slow-down of metabolic rates during test growth and decreasing fractionation with age. At sites of active methane discharge δ13C values of infaunal species reflect low pore water δ13CDIC values, documenting active methane release in the sediment, whereas lowered δ13C values of strictly epifaunal species are most probably the result of incorporation of 13C depleted methanotrophic biomass.

Modern deep-sea benthic foraminifera: a brief review of their morphology-based biodiversity and trophic diversity

Most fossil deep-sea foraminifera are multichambered and have relatively robust, calcareous or agglutinated shells. Modern assemblages, on the other hand, include many fragile monothalamous (single-chambered) forms and komokiaceans (a superfamily of protist currently placed within the foraminifera) with soft test walls. These groups are poorly known and most of the hundreds of morphospecies recognized in deep-sea samples are undescribed. The relative abundance of robust and fragile taxa varies with water depth and food supply. Calcareous and other hard-shelled species tend to predominate in relatively eutrophic areas, particularly on continental margins, but decrease as a proportion of the ‘entire’ live fauna (i.e. including soft-shelled species) with increasing water depth, even above the CCD (carbonate compensation depth). Most of the species on which the foraminiferal proxies used in palaeoceanography are based live in these bathyal regions. At abyssal depths, and particularly below the CCD, faunas are largely agglutinated and dominated by monothalamous forms. These assemblages have a much lower fossilization potential than those found on continental margins. In addition to carbonate dissolution, these patterns probably reflect adaptations to increasingly oligotrophic conditions on the ocean floor with increasing depth and distance from land. Bathyal species include herbivores and opportunistic deposit feeders (omnivores) that consume labile organic material, in addition to deep-infaunal deposit feeders, and must contribute significantly to carbon cycling. Many abyssal monothalamous foraminifera, in constrast, accumulate stercomata (waste pellets composed of fine sediment particles) and probably ingest sediment, associated bacteria and more refractory organic matter. Some monothalamous species without stercomata may be bacteriovores. Although they probably process organic carbon at a slower rate than calcareous species, the shear abundance of monothalamous taxa at abyssal depths suggests that they are important in carbon cycling on a global scale. The loss of a substantial proportion of foraminiferal biomass and biodiversity from the fossil record should be considered when using foraminifera to reconstruct palaeoproductivity, for example, by using the Benthic Foraminiferal Accummulation Rate (BFAR). Different dietary preferences among calcareous species have implications for the stable carbon isotope signal preserved in their shells.

Comparison of benthic foraminiferal and macrofaunal responses to organic pollution in the Firth of Clyde (Scotland)

By comparing benthic foraminiferal and macrofaunal responses to sewage sludge disposal in the Firth of Clyde (Scotland), we wanted to investigate the possibility of using foraminifera as bio-indicators of marine environmental degradation. Both groups present a similar distributional pattern, with poor faunas composed of species tolerant to strong oxygen depletion near to the disposal site, surrounded by high density of opportunistic species. Farther away, faunal density decreases and equilibrium taxa gradually replace opportunistic species. No more environmental impact is perceptible beyond 3 km. Nevertheless, some differences exist: foraminifera appear to be more impacted at the disposal site, probably as a consequence of the low pH, a supplementary stress factor for organisms provided with a calcareous test. At 3 km west of the disposal site, macrofauna is comparable to the reference station, whereas foraminifera still indicate environmental degradation, suggesting their higher sensitivity to this type of pollution. It appears that benthic foraminifera may add valuable information to open marine environmental monitoring.

Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediments

The prokaryote community activity and structural characteristics within marine sediment sampled across a continental shelf area located off eastern Antarctica (66 degrees S, 143 degrees E; depth range, 709 to 964 m) were studied. Correlations were found between microbial biomass and aminopeptidase and chitinase rates, which were used as proxies for microbial activity. Biomass and activity were maximal within the 0- to 3-cm depth range and declined rapidly with sediment depths below 5 cm. Most-probable-number counting using a dilute carbohydrate-containing medium recovered 1.7 to 3.8% of the sediment total bacterial count, with mostly facultatively anaerobic psychrophiles cultured. The median optimal growth temperature for the sediment isolates was 15 degrees C. Many of the isolates identified belonged to genera characteristic of deep-sea habitats, although most appear to be novel species. Phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether analyses indicated that the samples contained lipid components typical of marine sediments, with profiles varying little between samples at the same depth; however, significant differences in PLFA profiles were found between depths of 0 to 1 cm and 13 to 15 cm, reflecting the presence of a different microbial community. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified bacterial 16S rRNA genes revealed that between samples and across sediment core depths of 1 to 4 cm, the community structure appeared homogenous; however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. Sequencing of DGGE bands and rRNA probe hybridization analysis revealed that the major community members belonged to delta proteobacteria, putative sulfide oxidizers of the gamma proteobacteria, Flavobacteria, Planctomycetales, and Archaea. rRNA hybridization analyses also indicated that these groups were present at similar levels in the top layer across the shelf region.

Bacteria in the cold deep-sea benthic boundary layer and sediment-water interface of the NE Atlantic

This is a short review of the current understanding of the role of microorganisms in the biogeochemistry in the deep-sea benthic boundary layer (BBL) and sediment-water interface (SWI) of the NE Atlantic, the gaps in our knowledge and some suggestions of future directions. The BBL is the layer of water, often tens of meters thick, adjacent to the sea bed and with homogenous properties of temperature and salinity, which sometimes contains resuspended detrital particles. The SWI is the bioreactive interface between the water column and the upper 1 cm of sediment and can include a large layer of detrital material composed of aggregates that have sedimented from the upper mixed layer of the ocean. This material is biologically transformed, over a wide range of time scales, eventually forming the sedimentary record. To understand the microbial ecology of deep-sea bacteria, we need to appreciate the food supply in the upper ocean, its packaging, passage and transformation during the delivery to the sea bed, the seasonality of variability of the supply and the environmental conditions under which the deep-sea bacteria grow. We also need to put into a microbial context recent geochemical findings of vast reservoirs of intrinsically labile organic material sorped onto sediments. These may well become desorped, and once again available to microorganisms, during resuspension events caused by deep ocean currents. As biotechnologists apply their tools in the deep oceans in search of unique bacteria, an increasing knowledge and understanding of the natural processes undertaken and environmental conditions experienced by deep-sea bacteria will facilitate this exploitation.

Transformations of biogenic particles during sedimentation in the northeastern Atlantic

The vertical flux and transformation of biogenic particles are im portant processes in the oceanic carbon cycle. Changes in the magnitude of the biological pump can occur in the north eastern Atlantic on both a seasonal and interannual basis. For example, seasonal variations in vertical flux at 47° N 20° W are linked to seasonal ocean productivity variations such as the spring bloom. The size and organic and inorganic content of phytoplankton species, their development and succession also play a role in the scale and composition of the biological pump. The majority of flux is in the form of fast sinking aggregates. Bacteria and transparent exopolymer particle production by phytoplankton have been implicated in aggregate production and mass flux events. Zooplankton grazing and faecal pellet production, their size and composition and extent of their vertical migration also influence the magnitude of vertical flux. Aggregates are formed in the upper ocean, often reaching a maximum concentration just below the seasonal thermocline and can be a food resource to mesozooplankton as well as to the high concentrations of attached bacteria and protozoa. Attached bacteria remineralize and solubilize the aggregate particulate organic carbon. The degree of particle solubilization is likely to be affected by factors controlling enzyme activity and production, for example temperature, pressure or concentration of specific organic molecules, all of which may change during sinking. Attached bacterial growth is greatest on particulate organic matter collected at 500 m which is the depth where studies of 210 Po reveal that there is greatest break-up of rapidly sinking particles. Break-up of particles by feeding zooplankton can also occur. The fraction of sinking POC lost between 150-3100 m at one station in the north eastern Atlantic could supply about 90% of the bacterial carbon demand. Some larger, faster sinking aggregates escape solubilization and disaggregation in the upper 1000 m and arrive in the deep ocean and on the deep-sea bed. Seasonally varying rates of sedimentation are reflected at the deep-sea floor by deposition of phytodetrital material in summer. Approximately 2-4% of surface water primary production reaches the sea floor in 4500 m depth at 47° N 20° W after a sedimentation time of about 4-6 weeks. In this region, concentrations of chloroplastic pigments increased in summer by an order of magnitude, whereas seasonal changes in activity or biomass parameters were smaller. Breakdown of the generally strongly degraded organic matter deposited on deep-sea sediments is mainly accomplished by bacteria. Rates of degradation and efficiency of biomass production depend largely on the proportion of biologically labile material which decreases with advancing decay. It is likely that different levels of organic matter deposition influence the bioturbation rates of larger benthos, which has an effect on transport processes within the sediment and presumably also on microbial degradation rates.

Fine-scale vertical profiles of meiofauna in muddy subtidal sediments

The fine-scale vertical profile (2-mm intervals to 2 cm) of meiofauna was surveyed at three water depths (20, 50, and 80 m) on the Louisiana continental shelf and at two depths (25 and 55 m) in a subarctic Alaskan bay. Meiofaunal densities at these sites measured through 4 cm were similar to those of other subtidal muddy-sediment sites, nematodes averaging about 1000 and 1500 and harpacticoid copepods averaging 125 and 30 per 10 cm2 in Louisiana and Alaska, respectively. Overall, harpacticoids were numerous at the sediment–water interface and exceptionally shallow in depth profile; densities decreased with increasing depth, with few individuals below 6 mm. Across all sites and water depths, weighted mean depths of harpacticoids averaged 5.4 mm. Nematodes were distributed to much greater depths, and generally increased in density with depth, with highest densities below 6 mm. In the Gulf of Mexico, nematode density peaked in the second centimetre. Across all sites and depths, nematode weighted mean depth averaged 10.5 mm within the upper 2 cm. Harpacticoids were the most abundant meiofaunal taxon in the upper 4 mm in the Gulf of Mexico at the 50- and 80-m sites. Overall, harpacticoids were disproportionately abundant at the sediment–water interface to a depth of 6 mm, and play a more significant role in events that take place at the surface than their down-core abundance would indicate. For example, harpacticoids are potentially more influenced by bottom-feeding fish and erosional events than are nematodes, and may exert an influence over the initial burial of sedimented phytodetritus.

Controls of the microbial loop: Nutrient limitation and enzyme production, location and control

A major controlling factor for bacterial growth is their ability to hydrolyze high molecular weight molecules too complex to be transported directly across the cell's membrane. The utility of such an extracellular enzyme hydrolysis system, location of the enzymes (free or attached), environmental controls of enzyme production, and implications of multiple hydrolysis-uptake systems are explored in relation to free-living oceanic bacteria and bacteria attached to rapidly sinking aggregates.