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Fjords are semi-enclosed marine systems with unique physical conditions that influence microbial community composition and structure. Pronounced organic matter and physical condition gradients within fjords provide a natural laboratory for the study of changes in microbial community structure and metabolic potential in response to environmental conditions. Photosynthetic production in euphotic zones sustains deeper aphotic microbial activity via organic matter sinking, augmented by large terrestrial inputs. Previous studies do not consider both prokaryotic and eukaryotic communities when linking metabolic potential and activity, community composition, and environmental gradients. To address this gap we profiled microbial functional potential (Biolog Ecoplates), bacterial abundance, heterotrophic production (3H-Leucine incorporation), and prokaryotic/eukaryotic community composition (16S and 18S rRNA amplicon gene sequencing). Similar factors shaped metabolic potential, activity and community (prokaryotic and eukaryotic) composition across surface/near surface sites. However, increased metabolic diversity at near bottom (aphotic) sites reflected an organic matter influence from sediments. Photosynthetically produced particulate organic matter shaped the upper water column community composition and metabolic potential. In contrast, microbial activity at deeper aphotic waters were strongly influenced by other organic matter input than sinking marine snow (e.g. sediment resuspension of benthic organic matter, remineralisation of terrestrially derived organic matter, etc.), severing the link between community structure and metabolic potential. Taken together, different organic matter sources shape microbial activity, but not community composition, in New Zealand fjords.

Breakdown of skeletal and lithic hard substrates by organisms, a process referred to as bioerosion, is part of the global carbon cycle and receives increased attention, but little is known about bioerosion in polar environments. Here, we study bioerosion traces (addressed by their respective ichnotaxa) recorded in the barnacle Bathylasma corolliforme from the Ross Sea, Antarctica. Traces were visualized via scanning electron microscopy of epoxy casts prepared with the vacuum cast-embedding technique. In 50 samples from shallow 37 m to bathyal 1680 m water depths, 16 different bioerosion traces were found, classified into microborings presumably produced by cyanobacteria (1), chlorophytes (1), fungi (9), foraminifera (1), unknown organotrophs (5), and macroborings produced by cirripeds (1). Statistical ichnodiversity analysis resulted in a significant (p = 0.001) ANOSIM with moderate differences (R = 0.5) between microbioerosion trace assemblages at different water depths and revealed two main clusters (NMDS, SIMPROF) corresponding to the photic and aphotic stations. A comparison between this study and a corresponding study from the Svalbard archipelago, Arctic Ocean, shows that the ichnodiversity in calcareous barnacle skeletons is similar in polar waters of both hemispheres. This includes several ichnotaxa that are indicative for cool- to cold-water environments, such as Flagrichnus baiulus and Saccomorpha guttulata. Nine of the investigated ichnotaxa occur in both polar regions and seven ichnotaxa show an extensive bathymetrical range down to the deep sea at bathyal 1680 m water depth.

The infaunal living clypeasteroid echinoid genus Echinocyamus is considered a model organism for various ecological and paleontological studies since its distribution ranges from the polar regions to the tropics, and from shallow-marine settings to the deep-sea. Deep-sea analyses of this genus are rare, but imperative for the understanding and function of these important ecosystems. During the 2012 Southern Surveyor expedition, 35 seamounts off the east coast of Australia were dredged in depths greater than 800 m. Of these, six dredges contained a total of 18 deep-sea Echinocyamus tests. The tests have been analyzed for taphonomic alterations including abrasion patterns, macro-borings, micro-borings, depressions on the test, test staining, test filling, encrustation, and fragmentation. Findings are interpreted in the context of the deep-sea setting and are compared to Echinocyamus samples from shallow-water environments. Results show that abrasion in deep-sea environments is generally high, especially in ambulacral and genital pores indicating that tests can persist for a long time on the seafloor. This contrasts with shallow-water Echinocyamus that show lower abrasion due to early test destruction. Macro-borings are present as single or paired holes with straight vertical profiles resembling Lithophaga borings. Micro-borings are abundant and most likely the result of sponge or fungal activity. Depressions on the tests, such as scars or pits, are likely the result of trauma or malformation during ontogeny. Test staining is common, but variable, and is associated with FE/Mn oxidation and authigenic clays based on elemental analyses. Test filling occurs as loose or lithified sediment. Encrustation is present in the form of rudimentary crusts and biofilms. No macro-organisms were found on the tests. Biofilm composition differs from shallow-water environments in that organisms captured in the biofilm reflect aphotic conditions or sedimentation of particles from higher in the water column (e.g., coccoliths). Fragmentation is restricted to the apical system and pore regions. Results of this first comparative study on deep-sea Echinocyamus from Australian seamounts show that the minute tests can survive for a long time in these settings and undergo environmental specific taphonomic processes reflected in various taphonomic alterations.

The data on chlorophyll content in the water and bottom sediments in freshwater Rybinsk Reservoir (Upper Volga) and Aniva Sea Bay (Sea of Okhotsk) are summarized. The average concentration of chlorophyll a in plankton of the reservoir is 23.0 ± 1.9 μg/L, in the bay 0.77 ± 0.06 μg/L, in the bottom sediments 144.2 ± 14.9, and 8.2 ± 0.7 μg/g in the dry sediment, respectively. Correlations between pigment concentrations in the euphotic zone, in the aphotic bottom layer, the whole column of water, and the upper layer of bottom sediments, as well as the relationship of pigments with depth (within 6–100 m) and transparency (from 1 to 18 m), were revealed. It is shown that the general relations for two waterbodies are approximated by nonlinear equations with determination coefficient values (R2) from 0.37 to 0.93. The patterns of the relationship between pigment indices are similar in both waterbodies.

Este artículo contiene 26 páginas, 2 tablas, 14 figuras., Biogeochemical cycling of silicon (Si), largely affected by biological drivers, is pivotal to the ecological functioning of the ocean. Most knowledge regarding biological utilization of Si derives from research on phototrophic organisms circumscribed to the photic ocean (i.e., diatoms). Utilization of Si in the aphotic ocean, where heterotrophic silicifiers become relevant Si users, remains poorly investigated. Here we quantify the flux rates and stocks characterizing Si cycling across dense aggregations of the hexactinellid sponge Vazella pourtalesii established in the aphotic zone of the central Scotian Shelf, Nova Scotia, Canada. Although individual rates of silicic acid consumption were low compared to other sponge species and diatoms, the large abundance of individuals (6.5 million) over the extension of these sponge grounds (2105 km2 ) leads to massive annual silicic acid consumption, invested in producing their siliceous skeletons of biogenic silica. This sponge activity accumulates large biogenic silica stocks both in the living population and in the sediments. Skeletal pieces in sediment revealed that a good portion of biogenic silica deposited to the bottom after sponge death recycles as silicic acid before being permanently buried. This biogenic silica–silicic acid turnover, facilitated by an unconventional silicification pattern that favors delamination and dissolution of V. pourtalesii spicules, causes silicic acid enrichment at oceanographic dimensions in the bottom water of the central Scotian Shelf. Silicic acid efflux from the bottom sustains a feedback mechanism that fulfills sponge needs for silicic acid and facilitates the persistence of sponge aggregations in the long term., This research was completed by funds from the SponGES H2020 grant (BG-01-2015.2. Agreement Number 679849-2), from Fisheries and Oceans Canada SPERA and IGS projects to EK, and from MINECO PBS project (CTM2015-67221-R) to MM.

The construction of artificial weirs as part of the Four Major Rivers Restoration Project is expected to result in the Nakdong River Basin having the characteristics of closed water bodies and properties of water quality that convert suspended components into soluble ones due to a long retention time, thereby leading to the continuous deterioration of water quality. In this regard, this study investigated the changes of water quality on four weirs in the mid-lower Nakdong River Basin. In addition, it examined the organic matters and nutrient salts affecting the water quality, established mass balance with respect to the nutrient salts, and analyzed the load accumulations of each weir to present the directions for water quality management. With regard to the water quality, the items of BOD and COD, T-N and NH4-N, and T-P and PO4-P showed similar tendencies, and most of the items exhibited high concentrations from July to September. Furthermore, it was confirmed that the concentrations of the water quality items were high in Dalseong Weir and Hapcheon-Changnyeong Weir. In July, most of the weirs showed the greatest difference of DO in the surface layer and deepwater layer, while the DO concentration of the deepwater layer dropped below 4.0 mg/L in all four weirs. The sediment survey showed that the SS, T-N, and T-P have a larger amount of sediment in the aphotic zone than in the photic zone, and the amount of sediment per unit area was greatest in Dalseong Weir. According to the sediment release survey results, the release concentration was high in July, which was due to the effects of high water temperature and low DO concentration. T-N was eluted mostly from Dalseong Weir and Gangjeong-Goryeong Weir, and T-P was eluted mostly from Dalseong Weir and Hapcheon-Changnyeong Weir. Among the mass balance, nitrogen balance showed the highest amount of accumulation in Gangjeong-Goryeong Weir (6109 kg/d), and phosphorus balance showed the highest amount of accumulation in Changnyeong-Haman Weir (447 kg/d). These results are expected to be utilized as important materials for setting the management directions for each weir.

Dimethylsulfoniopropionate (DMSP) is an important marine osmolyte. Aphotic environments are only recently being considered as potential contributors to global DMSP production. Here, our Mariana Trench study reveals a typical seawater DMSP/dimethylsulfide (DMS) profile, with highest concentrations in the euphotic zone and decreased but consistent levels below. The genetic potential for bacterial DMSP synthesis via the dsyB gene and its transcription is greater in the deep ocean, and is highest in the sediment.s DMSP catabolic potential is present throughout the trench waters, but is less prominent below 8000 m, perhaps indicating a preference to store DMSP in the deep for stress protection. Deep ocean bacterial isolates show enhanced DMSP production under increased hydrostatic pressure. Furthermore, bacterial dsyB mutants are less tolerant of deep ocean pressures than wild-type strains. Thus, we propose a physiological function for DMSP in hydrostatic pressure protection, and that bacteria are key DMSP producers in deep seawater and sediment., Dimethylsulfoniopropionate (DMSP) is an osmolyte produced by marine microbes that plays an important role in nutrient cycling and atmospheric chemistry. Here the authors go to the Mariana Trench—the deepest point in the ocean—and find bacteria are key DMSP producers, and that DMSP has a role in protection against high pressure.

For the first time, the composition of micromycetes communities was investigated in both photic and aphotic entrance zones of seven caves in Montenegro: Obodska Pecina, Golubinja Pecina, Velustica Pecina, Vrbacka jama, Jama ER-1, Njegos Pecina, and an unnamed cave. In total, 72 species of micromycetes were identified: 46 species from illuminated photic zones of the caves, including 43 species on phototrophs, 10 species from the air, 15 species on substrates, and 50 species from unlit aphotic zones, including 35 species from the air and 37 species on substrates. The most frequently isolated species were Acrodontium salmoneum, Aureobasidium pullulans, Cladosporium oxysporum, Mucor racemosus f. racemosus, Penicillium chrysogenum, and Rhizopus stolonifer. The similarity between micromycetes composition of different biotopes was evaluated using the Jaccard index and cluster analysis. The greatest similarity was observed in the communities isolated from the air of the photic zones of the caves.

Shifts between the alternative stable states have been a popular topic of ecological studies for over 50 years. However, identifying the mechanisms that drive these regime shifts remains a challenging task in the field of applied ecology and ecosystem management. Herein, we applied a Bayesian latent variable regression (BLR) to the dataset obtained for a shallow lake experiencing a shift from the dominance of submerged plants to the dominance of floating plants to classify the observed lake states, determine total phosphorus (TP) thresholds, and establish a steady-state relationship between the phosphorus content and the size of an aphotic zone. In addition, a structural equation model was utilized to elucidate the mechanisms driving this shift and their effects on the trophic web of the ecosystem. The BLR model exhibited high state classification rates (median/mean accuracy > 97.5%) and accurately determined the steady-state relationships between the TP thresholds and the aphotic zone size. We also found that the top-down control via piscivorous fish was stronger in the state dominated by submerged macrophytes, while the bottom-up control via TP was stronger in the state dominated by floating macrophytes. Additionally, the dominance of floating macrophytes was related to the low degree of biodiversity and simplification of the trophic web. Our results show that top predators can be used to control nutrient levels and ensure the dominance of submerged macrophytes. It also provides a new perspective on the theory of alternative states and potential tools for the management of ecosystems experiencing regime shifts.

We analyzed the depth distributions of benthic diatoms in two adjacent, but hydrologically distinct subalpine lakes (Lakes Soiernseen, S-Germany). Lake Unterer Soiernsee is affected by marked water-level fluctuations and is light-penetrated to the bottom most of the year, while Lake Oberer Soiernsee provides more stable conditions and an extended aphotic zone. Mixed samples of epiphytic, epilithic, epipsammic and epipelic periphyton were taken in one-meter depth steps by scuba divers. Most of the common benthic diatoms occurred in distinct depth-areas. RDA analyses showed that depth was strongly correlated with species distribution in both lakes. Depth-constrained cluster analyses indicated three distinct diatom community zones in each lake. A shallow littoral zone hosting mainly epiphytic and epilithic species and a deeper littoral zone with mainly epipsammic and epipelic taxa existed in both lakes. Additionally, a highly disturbed near-shore littoral zone with diatoms adapted to unstable conditions (aerophilic taxa, pioneer species) was found in Lake Unterer Soiernsee, and a deep-water pelagic zone with mainly planktonic taxa in Lake Oberer Soiernsee. Light availability, substrate, physical stressors and nutrient concentrations were linked closely with water depth. While light availability affected the ratio of benthic and planktonic diatoms, substrate type influenced benthic diatom assemblage structures. Diatoms occurring in surficial sediments of the aphotic zone represent an ideal cross-section of the recent diatom assemblage of the lake, including benthic and planktonic species. However, sediment samples taken in light-flooded depths are inappropriate for studies based on shifts between benthic and planktonic taxa, because in situ benthic species dominate the surface-sediment assemblages, while settled tychoplanktonic and planktonic species occur less frequently. A diatom-inferred depth model was created for each lake to prove the usability for down-core studies using weighted-averaging approaches. For both lakes these models are highly appropriate to reconstruct past fluctuations in water-transparency or lake-level. With regard to the development of diatom-based TP-transfer-functions for Bavarian mountain lakes, we found it is highly important to consider lake depth and transparency. Based on the findings of this study we recommend the creation of two different training-sets, one for deep or low-transparency lakes with an aphotic zone including both benthic and planktonic diatoms, and another one for shallow, clear water lakes solely using benthic diatoms.

Current knowledge on the seasonality of benthic nitrate reduction pathways in the aphotic, density stratified coastal zone of the Baltic Sea is largely based on data from muddy sediments, neglecting the potential contribution of sandy sediments. To gain a more comprehensive understanding of seasonality in this part of the Baltic Sea coast, we measured rates of benthic denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA) monthly in the ice-free period of 2016 in both sandy and muddy aphotic sediments, northwestern Gulf of Finland. No anammox was observed. The seasonal cycle of denitrification in both sediment types was related to the hydrography-driven development of bottom water temperature. The seasonal cycle of DNRA was less clear and likely connected to a combination of bottom water temperature, carbon to nitrogen ratio, and substrate competition with denitrification. Denitrification and DNRA rates were 50-80 and 20% lower in the sandy than in the muddy sediment. The share of DNRA in total nitrate reduction, however, was higher in the sandy than in the muddy sediment, being (by similar to 50%) the highest DNRA share in sandy sediments so far measured. Our data add to the small pool of published studies showing significant DNRA in both cold and/or sandy sediments and suggest that DNRA is currently underestimated in the Baltic coastal nitrogen filter. Our results furthermore emphasize that the various environmental conditions of a coastal habitat (light regime, hydrography, and geomorphology) affect biogeochemical element cycling and thus need to be considered in data interpretation.

The planktonic marine diatom Skeletonema marinoi forms resting stages, which can survive for decades buried in aphotic, anoxic sediments and resume growth when re-exposed to light, oxygen, and nutrients. The mechanisms by which they maintain cell viability during dormancy are poorly known. Here, we investigated cell-specific nitrogen (N) and carbon (C) assimilation and survival rate in resting stages of three S. marinoi strains. Resting stages were incubated with stable isotopes of dissolved inorganic N (DIN), in the form of 15 N-ammonium (NH4+ ) or -nitrate (NO3- ) and dissolved inorganic C (DIC) as 13 C-bicarbonate (HCO3- ) under dark and anoxic conditions for 2 months. Particulate C and N concentration remained close to the Redfield ratio (6.6) during the experiment, indicating viable diatoms. However, survival varied between

Pelagic carbonate deposits formed by the thin-shelled, epifaunal, originally bimineralic bivalve Bositra buchi were geographically widely distributed in the Tethyan basins during the Middle Jurassic. Here, to evaluate conditions that allowed the formation of peculiar, metre-scale, densely-packed shell beds primarily formed by Bositra, we assess size distributions and preservation of this bivalve in thin sections at ten sites in the Pieniny Klippen Belt and Peri-Klippen units (Western Carpathians), representing a bathymetric transect from pelagic-platform tops with shell beds up to slope environments where small filaments occur with spicules and radiolarians. Although Bositra shell beds are modulated by transport and winnowing, three types of evidence indicate that they primarily reflect high bivalve productivity. First, we find that size distributions of this species form a bathymetric gradient, from the dominance of remains smaller than 0.5 mm in low- energy slope environments, to 0.5-2 mm on muddy platform edges, up to lensoid shell beds with large valves (~2-15 mm) occurring on platform tops exposed to bottom currents. Although sediment winnowing from shell beds contributed to the rarity of small-sized specimens in platform-top environments, the bathymetric shift in the shape of size distributions is not purely driven by fragmentation and by size-selective transport of small specimens into slope environments because the average valve thickness declines with depth and thick fragments do not occur in slope environments. High abundances of suspension-feeding Bositra preferentially associated with indicators of bottom currents at oligophotic or aphotic depths indicate that plankton productivity was probably sourced by nutrient-rich internal waves that intersected platform tops, leading to low juvenile mortality in Bositra populations. In contrast, populations in deeper environments with the limited input of particulate organic matter failed to achieve maturity. Second, the inner, originally nacreous shell layer of Bositra is now represented by neomorphic calcite that is luminescent, enriched in Mn and depleted in Mg, indicating that this layer was not dissolved in the taphonomic active zone. Third, fibrous- acicular low-Mg calcite cements that characteristically coat Bositra in shell beds show blotchy luminescence and highly irregular Mg distribution, indicating that they were precipitated as high-Mg calcite cements. Fibrous-acicular cements in shell beds do not coat upward- facing sides of valves covered by a first phase of micrite whereas they fully coat elevated portions of the same valves. Therefore, they were precipitated at very high rates concurrently with micrite deposition in shelters. Nutrient-rich bottom currents thus simultaneously increased (1) Bositra survivorship by enhancing primary productivity and (2) cementation rate by renewal of saturation of pore waters in the taphonomic active zone at platform tops. In spite of the association of Bositra shell beds with major hiatal surfaces, (1) the rapid precipitation of fibrous-acicular cements, (2) the rarity of iron-stained Bositra valves in shell beds, and (3) the significantly smaller concentrations of iron in shell-rich muds than in shell-poor muds indicate that shell beds do not represent long-term hiatal or lag concentrations. They rather represent composite shell beds that record high population densities of these bivalves at ecological time scales. Spatial variation in intensity of bottom currents and in sea- floor topography generated by faulted blocks resulted (1) in hiatal surfaces with mineralized hardgrounds at high-energy current-swept sites and (2) in preservation of up to 1 m-thick lensoid shell beds at sites with less intense but persistent currents. Bositra shell beds thus ultimately have patchy horizontal and stratigraphic distribution.

International audience; Studies on microbial communities, and their associated organic biomarkers, that are found thriving in the aphotic euxinic waters in modern stratified ecosystems are scarce compared to those undertaken in euxinic photic zones. The Dziani Dzaha (Mayotte,Indian Ocean) is a tropical, saline, alkaline crater lake that has recently been presentedas a modern analog of Proterozoic Oceans due to its thalassohaline classification (having water of marine origin) and specific biogeochemical characteristics. Continuous intense photosynthetic production and microbial mineralization keep most of the water column permanently aphotic and anoxic preventing the development of a euxinic (sulfidic and anoxic) photic zone despite a high sulfide/sulfate ratio and the presence of permanent or seasonal haloclines. In this study, the molecular composition of the organic matter in Lake Dziani Dzaha was investigated and compared to the microbial diversity evaluated through 16S rRNA gene amplicon sequencing, over two contrasting seasons (rainy vs. dry) that influence water column stratification. Depth profiles of organic biomarker concentrations (chlorophyll-a and lipid biomarkers) and bacterial and archaeal OTU abundances appeared to be strongly dependent on the presence of aphotic haloclines and euxinia. OTU abundances revealed theimportance of specific haloalkaliphilic bacterial and archaeal assemblages in phytoplanktonic biomass recycling and the biogeochemical functioning of the lake, suggesting new haloalkaline non-phototrophic anaerobic microbial precursors for some of the lipid biomarkers. Uncultured Firmicutes from the family Syntrophomonadaceae (Clostridiales), and Bacteroidetes from the ML635J-40 aquatic group, emerged as abundant chemotrophic bacterial members in the anoxic or euxinic waters and were probably responsible for the production of short-chain n-alkenes, wax esters, diplopterol, and tetrahymanol. Halocline-dependent euxinia also had a strong impact on the archaeal community which was dominated by Woesearchaeota in the sulfide-free waters. In the euxinic waters, methanogenic Euryarchaeota from the Methanomicrobia, Thermoplasmata, and WSA2 classes dominated and were likely at the origin of common hydrocarbon biomarkers of methanogens (phytane, pentamethyl-eicosenes, and partially hydrogenated squalene).

Plastic pollution is abundant in aquatic environments worldwide and many of its detrimental impacts are well documented, but it also represents a novel substrate available to a diversity of organisms. Biofilms – assemblages of bacteria, algae, and fungi – colonise hard surfaces in aquatic environments. They are key agents in biogeochemical cycling and are a food source for grazing organisms, representing a keystone aquatic community, and are known to influence the fate of plastic pollution in aquatic environments. In one of the most temporally thorough assessments of biofilm development on freshwater plastics, here we report on the evolution of algal biofilm assemblages on three plastic polymers (Low Density Polyethylene, Polypropylene, and Polyethylene Terephthalate) over six weeks in the photic and aphotic zones of a freshwater reservoir in Staffordshire, UK. Significant differences were found between diatom assemblages on plastics in the photic and aphotic zones, and between diatom assemblages quantified on weeks 2, 4 and 6 of the study, but total algal photosynthetic pigment concentrations did not vary significantly between polymers in either zone. Scanning Electron Microscopy indicates that degradation of polymer surfaces occurs within six weeks in the aphotic zone, with potential implications for plastic fragmentation and microplastic generation.

Dark ocean microbial dynamics are fundamental to understand ecosystem metabolism and ocean biogeochemical processes. Yet, the ecological response of deep ocean communities to environmental perturbations remains largely unknown. Temporal and spatial dynamics of the meso- and bathypelagic prokaryotic communities were assessed throughout a 2-year seasonal sampling across the western Mediterranean Sea. A common pattern of prokaryotic communities’ depth stratification was observed across the different regions and throughout the seasons. However, sporadic and drastic alterations of the community composition and diversity occurred either at specific water masses or throughout the aphotic zone and at a basin scale. Environmental changes resulted in a major increase in the abundance of rare or low abundant phylotypes and a profound change of the community composition. Our study evidences the temporal dynamism of dark ocean prokaryotic communities, exhibiting long periods of stability but also drastic changes, with implications in community metabolism and carbon fluxes. Taken together, the results highlight the importance of monitoring the temporal patterns of dark ocean prokaryotic communities., SI

Rhodolith beds and bioherms formed by ecosystem engineering crustose coralline algae support the northernmost centres of carbonate production, referred to as polar cold‐water carbonate factories. Yet, little is known about biodiversity and recruitment of these hard‐bottom communities or the bioeroders degrading them, and there is a demand for carbonate budgets to include respective rates of polar carbonate build‐up and bioerosion. To address these issues, a 10‐year settlement and bioerosion experiment was carried out at the Arctic Svalbard archipelago in and downslope of a rhodolith bed. The calcifiers recorded on experimental settlement tiles (56 taxa) were dominated by bryozoans, serpulids and foraminiferans. The majority of the bioerosion traces (30 ichnotaxa) were microborings, followed by attachment etchings and grazing traces. Biodiversity metrics show that calcifier diversity and bioerosion ichnodiversity are both elevated in the rhodolith bed, if compared to adjacent aphotic waters, but these differences are statistically insignificant. Accordingly, there were only low to moderate dissimilarities in the calcifier community structure and bioerosion trace assemblages between the two depth stations (46 and 127 m), substrate orientations (up‐ and down‐facing) and substrate types (PVC and limestone), in that order of relevance. In contrast, surface coverage as well as the carbonate accretion and bioerosion rates were all significantly elevated in the rhodolith bed, reflecting higher abundance or size of calcifiers and bioerosion traces. All three measures were highest for up‐facing substrates at 46 m, with a mean coverage of 78.2% (on PVC substrates), a mean accretion rate of 24.6 g m−2 year−1 (PVC), and a mean bioerosion rate of −35.1 g m−2 year−1 (limestone). Differences in these metrics depend on the same order of factors than the community structure. Considering all limestone substrates of the two platforms, carbonate accretion and bioerosion were nearly in balance at a net rate of −2.5 g m−2 year−1. A latitudinal comparison with previous settlement studies in the North Atlantic suggests that despite the harsh polar environment there is neither a depletion in the diversity of hard‐bottom calcifier communities nor in the ichnodiversity of grazing traces, attachment etchings and microborings formed by organotrophs. In contrast, microborings produced by phototrophs are strongly depleted because of limitations in the availability of light (condensed photic zonation, polar night, shading by sea ice). Also, macroborings were almost absent, surprisingly. With respect to carbonate production, the Svalbard carbonate factory marks the low end of a latitudinal gradient while bioerosion rates are similar or even higher than at comparable depth or photic regime at lower latitudes, although this might not apply to shallow euphotic waters (not covered in our experiment), given the observed depletion in bioeroding microphytes and macroborers. While echinoid grazing is particularly relevant for the bioerosion in the rhodolith bed, respective rates are far lower than those reported from tropical shallow‐water coral reefs. The slow pace of carbonate production but relatively high rates of bioerosion (both promoted by low carbonate supersaturation states in Arctic waters), in concert with high retention of skeletal carbonates on the seafloor and no calcite cements forming in open pore space created by microborers, suggest a low fossilisation potential for polar carbonates, such as those formed in the Mosselbukta rhodolith beds., Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659

The Eastern Tropical North Pacific Ocean hosts one of the world's largest oceanic oxygen deficient zones (ODZs). Hot spots for reactive nitrogen (N-r) removal processes, ODZs generate conditions proposed to promote N-r inputs via dinitrogen (N-2) fixation. In this study, we quantified N-2 fixation rates by N-15 tracer bioassay across oxygen, nutrient, and light gradients within and adjacent to the ODZ. Within subeuphotic oxygen-deplete waters, N-2 fixation was largely undetectable; however, addition of dissolved organic carbon stimulated N-2 fixation in suboxic (9 nmol N center dot L-1 center dot day(-1)) were also observed in suboxic waters near volcanic islands where N-2 fixation was quantifiable to 3,000 m. Within the overlying euphotic waters, N-2 fixation rates were highest near the continent, exceeding 500 mu mol N center dot m(-2)center dot day(-1) at one third of inshore stations. These findings support the expansion of the known range of diazotrophs to deep, cold, and dissolved inorganic nitrogen-replete waters. Additionally, this work bolsters calls for the reconsideration of ocean margins as important sources of N-r. Despite high rates at some inshore stations, regional N-2 fixation appears insufficient to compensate for N-r loss locally as observed previously in the Eastern Tropical South Pacific ODZ.

The oxygen minimum zone (OMZ) of the central Arabian Sea is investigated with a biogeochemical model that couples the marine nitrogen and oxygen cycles and includes euphotic, aphotic, aerobic and anaerobic processes. The model is used to quantify the strength, location and relative timing of governing processes, in particular, nitrite generation, nitrogen losses and oxygen consumption. In an idealized two-dimensional physical environment the model is able to reproduce the observed meridional-vertical structure of oxygen and nitrate, as well as the secondary nitrite maximum layer. Characteristic features of vertical profiles are well represented and the modelled nitrogen transformation rates are in good agreement with observed values. The model results show that (i) the OMZ is neither vertically nor horizontally homogeneous, (ii) minute differences in oxygen concentration determine the thickness of the nitrite layer, (iii) there is hardly any seasonal cycle in the extent of the OMZ but a pronounced seasonal cycle in nitrite, and (iv) the nitrogen loss in the OMZ is accomplished by a succession of denitrification and anammox, based on the seasonal supply of labile detritus. We conclude that the nitrogen loss in the Arabian Sea can only be understood by taking into account the diversity, vertical arrangement and temporal succession of microbial processes.

Rocky benthic communities are common in Antarctic coastal habitats; yet little is known about their carbon turnover rates. Here, we performed a broad survey of shallow ( < 65 m depth) rocky ice-scoured habitats of South Bay (Doumer Island, Western Antarctic Peninsula), combining (i) biodiversity assessments from benthic imaging, and (ii) in situ benthic dissolved oxygen (O2) exchange rates quantified by the aquatic eddy covariance technique. The 18 study sites revealed a gradual transition from macroalgae and coralline-dominated communities at ice-impacted depths (15–25 m; zone I) to large suspension feeders (e.g., sponges, bivalves) at depth zone II (25–40 m) and extensive suspension feeders at the deepest study location (zone III; 40–65 m). Gross primary production (GPP) in zone I was up to 70 mmol O2 m−2 d−1 and dark ecosystem respiration (ER) ranged from 15 to 90 mmol m−2 d−1. Zone II exhibited reduced GPP (average 1.1 mmol m−2 d−1) and ER rates from 6 to 36 mmol m−2 d−1, whereas aphotic zone III exhibited ER between 1 and 6 mmol m−2 d−1. Benthic ER exceeded GPP at all study sites, with daily net ecosystem metabolism (NEM) ranging from − 22 mmol m−2 d−1 at the shallow sites to − 4 mmol m−2 d−1 at 60 m. Similar NEM dynamics have been observed for hard-substrate Arctic habitats at comparable depths. Despite relatively high GPP during summer, coastal rocky habitats appear net heterotrophic. This is likely due to active drawdown of organic material by suspension-feeding communities that are key for biogeochemical and ecological functioning of high-latitude coastal ecosystems.

A new species of Geoplaninae from a limestone cave located in northeastern Brazil is described herein. Paraba pankaru Amaral & Leal-Zanchet, sp. n. differs from its congeners by the color pattern and characteristics of the copulatory apparatus, especially regarding the prostatic vesicle. Unlike other species of Paraba, the species shows long, sensory pits, sometimes opening through wide invaginations, which may constitute a troglomorphism. The flatworm was collected in an aphotic and quite moist area, which was not far from one of the cave entrances, creeping over a clay ground. Therefore, this species may be adapted to the cave environment, constituting at least a troglophile. http://www.zoobank.org/urn:lsid:zoobank.org:pub:A80BA3DA-8463-4D0C-9DBB-B662FDE9E088

Dormancy in the Foraminifera has been observed widely across the phylum in reaction to a variety of triggers including, in the diatom symbiont-bearing foraminifer Amphistegina gibbosa, extended periods of darkness. Resumption of activity in the host-symbiont holobiont was noted, but not fully documented, in specimens reintroduced to light following up to 12 months in darkness. Here, criteria for documenting recovery included resumption of reticulopodial activity in the host and return of pre-treatment golden-brown color characteristic of an active symbiotic diatom population. Reticulopodial activity resumed in nearly all treatment specimens (>95%) following 12 months in darkness, and in >70% of the specimens when reintroduced to light following 20 months in darkness. Image analysis using the percent of the foraminiferal surface area showing golden-brown color as a proxy for recovery of the endosymbionts showed return of such color within days for shorter treatments (7 and 12 months in darkness), but slower and less complete return in longer treatments (15 and 20 months), indicating increased susceptibility to photic damage of symbionts as the length of dormancy increased.

Recent studies demonstrate that marine N2 fixation can be carried out without light by heterotrophic N2 fixers (diazotrophs). However, direct measurements of N2 fixation in aphotic environments are relatively scarce. Heterotrophic as well as unicellular and colonial photoautotrophic diazotrophs are present in the oligotrophic Gulf of Aqaba (northern Red Sea). This study evaluates the relative importance of these different diazotrophs by combining biogeochemical models with time series measurements at a 700 m deep monitoring station in the Gulf of Aqaba. At this location, an excess of nitrate, relative to phosphate, is present throughout most of the water column and especially in deep waters during stratified conditions. A relative excess of phosphate occurs only at the water surface during nutrient-starved conditions in summer. We show that a model without N2 fixation can replicate the observed surface chlorophyll but fails to accurately simulate inorganic nutrient concentrations throughout the water column. Models with N2 fixation improve simulated deep nitrate by enriching sinking organic matter in nitrogen, suggesting that N2 fixation is necessary to explain the observations. The observed vertical structure of nutrient ratios and oxygen is reproduced best with a model that includes heterotrophic as well as colonial and unicellular autotrophic diazotrophs. These results suggest that heterotrophic N2 fixation contributes to the observed excess nitrogen in deep water at this location. If heterotrophic diazotrophs are generally present in oligotrophic ocean regions, their consideration would increase current estimates of global N2 fixation and may require explicit representation in large-scale models.

14 pages, 2 figures, The deep sea (i.e., >200 m depth) is a highly dynamic environment where benthic ecosystems are functionally and ecologically connected with the overlying water column and the surface. In the aphotic deep sea, organisms rely on external signals to synchronize their biological clocks. Apart from responding to cyclic hydrodynamic patterns and periodic fluctuations of variables such as temperature, salinity, phytopigments, and oxygen concentration, the arrival of migrators at depth on a 24-h basis (described as Diel Vertical Migrations; DVMs), and from well-lit surface and shallower waters, could represent a major response to a solar-based synchronization between the photic and aphotic realms. In addition to triggering the rhythmic behavioral responses of benthic species, DVMs supply food to deep seafloor communities through the active downward transport of carbon and nutrients. Bioluminescent species of the migrating deep scattering layers play a not yet quantified (but likely important) role in the benthopelagic coupling, raising the need to integrate the efficient detection and quantification of bioluminescence into large-scale monitoring programs. Here, we provide evidence in support of the benefits for quantifying and continuously monitoring bioluminescence in the deep sea. In particular, we recommend the integration of bioluminescence studies into long-term monitoring programs facilitated by deep-sea neutrino telescopes, which offer photon counting capability. Their Photo-Multiplier Tubes and other advanced optical sensors installed in neutrino telescope infrastructures can boost the study of bioluminescent DVMs in concert with acoustic backscatter and video imagery from ultra-low-light cameras. Such integration will enhance our ability to monitor proxies for the mass and energy transfer from the upper ocean into the deep-sea Benthic Boundary Layer (BBL), a key feature of the ocean biological pump and crucial for monitoring the effects of climate-change. In addition, it will allow for investigating the role of deep scattering DVMs in the behavioral responses, abundance and structure of deep-sea benthic communities. The proposed approach may represent a new frontier for the study and discovery of new, taxon-specific bioluminescence capabilities. It will thus help to expand our knowledge of poorly described deep-sea biodiversity inventories and further elucidate the connectivity between pelagic and benthic compartments in the deep-sea, This work was developed within the framework of the Tecnoterra (ICM-CSIC/UPC) and the following project activities: ARIM (Autonomous Robotic sea-floor Infrastructure for benthopelagic Monitoring; MartTERA ERA-Net Cofound) and RESBIO (TEC2017-87861-R; Ministerio de Ciencia, Innovación y Universidades; PIs: JR and JA) and with funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). Ocean Networks Canada was funded through Canada Foundation for Innovation-Major Science Initiative Fund 30199 to FD and BP. The STRAW and STRAW-b experiments deployed and connected through the NEPTUNE cabled observatory are supported by the German Research Foundation through grant SFB 1258 “Neutrinos and Dark Matter in Astro- and Particle Physics,” the cluster of excellence “Origin and Structure of the Universe,” and the University of Alberta

Much of the surface water of the ocean is supersaturated in elemental mercury (Hg0) with respect to the atmosphere, leading to sea-to-air transfer or evasion. This flux is large, and nearly balances inputs from the atmosphere, rivers and hydrothermal vents. While the photochemical production of Hg0 from ionic and methylated mercury is reasonably well-studied and can produce Hg0 at fairly high rates, there is also abundant Hg0 in aphotic waters, indicating that other important formation pathways exist. Here, we present results of gross reduction rate measurements, depth profiles and diel cycling studies to argue that dark reduction of Hg2+ is also capable of sustaining Hg0 concentrations in the open ocean mixed layer. In locations where vertical mixing is deep enough relative to the vertical penetration of UV-B and photosynthetically active radiation (the principal forms of light involved in abiotic and biotic Hg photoreduction), dark reduction will contribute the majority of Hg0 produced in the surface ocean mixed layer. Our measurements and modeling suggest that these conditions are met nearly everywhere except at high latitudes during local summer. Furthermore, the residence time of Hg0 in the mixed layer with respect to evasion is longer than that of redox, a situation that allows dark reduction-oxidation to effectively set the steady-state ratio of Hg0 to Hg2+ in surface waters. The nature of these dark redox reactions in the ocean was not resolved by this study, but our experiments suggest a likely mechanism or mechanisms involving enzymes and/or important redox agents such as reactive oxygen species and manganese (III).

Nitrogen (N2) fixation, the energetically expensive conversion of N2 to ammonia, plays an important role in balancing the global nitrogen budget. Defying historic paradigms, recent studies have detected non-cyanobacterial N2 fixation in deep, dark oceanic waters. Even low volumetric rates can be significant considering the large volume of these waters. However, measuring aphotic N2 fixation is an analytical challenge due to the low particulate nitrogen (PN) concentrations. Here, we investigated N2 fixation rates in aphotic waters in the South China Sea (SCS). To increase the sensitivity of N2 fixation rate measurements, we applied a novel approach requiring only 0.28 μg N for measuring the isotopic composition of particulate nitrogen. We conducted parallel 15N2-enriched incubations in ambient seawater, seawater amended with amino acids and poisoned (HgCl2) controls, along with incubations that received no tracer additions to distinguish biological N2 fixation. Experimental treatments differed significantly from our two types of controls, those receiving no additions and killed controls. Amino acid additions masked N2 fixation signals due to the uptake of added 14N-amino acid. Results show that the maximum dark N2 fixation rates (1.28 ± 0.85 nmol N L−1 d−1) occurred within upper 200 m, while rates below 200 m were mostly lower than 0.1 nmol N L−1 d−1. Nevertheless, N2 fixation rates between 200 and 1000 m accounted for 39 ± 32 % of depth-integrated dark N2 fixation rates in the upper 1000 m, which is comparable to the areal nitrogen inputs via atmospheric deposition. Globally, we found that aphotic N2 fixation studies conducted in oxygenated environments yielded rates similar to those from the SCS (−1 d−1), regardless of methods, while higher rates were occasionally observed in low-oxygen (2 fixation in the SCS and eastern tropical south Pacific. Our results provide the first insight into aphotic N2 fixation in SCS and support the importance of the aphotic zone as a globally-important source of new nitrogen to the ocean.

The orthoquartzite Imawarì Yeuta cave hosts exceptional silica speleothems and represents a unique model system to study the geomicrobiology associated to silica amorphization processes under aphotic and stable physical–chemical conditions. In this study, three consecutive evolution steps in the formation of a peculiar blackish coralloid silica speleothem were studied using a combination of morphological, mineralogical/elemental and microbiological analyses. Microbial communities were characterized using Illumina sequencing of 16S rRNA gene and clone library analysis of carbon monoxide dehydrogenase (coxL) and hydrogenase (hypD) genes involved in atmospheric trace gases utilization. The first stage of the silica amorphization process was dominated by members of a still undescribed microbial lineage belonging to the Ktedonobacterales order, probably involved in the pioneering colonization of quartzitic environments. Actinobacteria of the Pseudonocardiaceae and Acidothermaceae families dominated the intermediate amorphous silica speleothem and the final coralloid silica speleothem, respectively. The atmospheric trace gases oxidizers mostly corresponded to the main bacterial taxa present in each speleothem stage. These results provide novel understanding of the microbial community structure accompanying amorphization processes and of coxL and hypD gene expression possibly driving atmospheric trace gases metabolism in dark oligotrophic caves.

The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (~52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin’s index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose much below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities by interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.

Contains fulltext : 232043.pdf (Publisher’s version ) (Closed access) The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received less attention than other regions of the global Ocean. This has hampered our understanding of the diversity and metabolic potential of the microorganisms that dwell in this habitat. To fill this knowledge gap, we analyzed a collection of 31 metagenomes from the Atlantic Ocean that spanned the epipelagic, mesopelagic and bathypelagic zones (surface to 4000 m). Read-centric and gene-centric analysis revealed the unique taxonomic and functional composition of metagenomes from each depth zone, which was driven by differences in physical and chemical parameters. In parallel, a total of 40 metagenome-assembled genomes were obtained, which recovered one third of the total community. Phylogenomic reconstruction revealed that many of these genomes are derived from poorly characterized taxa of Bacteria and Archaea. Genomes derived from heterotrophic bacteria of the aphotic zone displayed a large apparatus of genes suited for the utilization of recalcitrant organic compounds such as cellulose, chitin and alkanes. In addition, we found genomic evidence suggesting that mixotrophic bacteria from the bathypelagic zone could perform carbon fixation through the Calvin-Benson-Bassham cycle, fueled by sulfur oxidation. Finally, we found that the viral communities shifted throughout the water column regarding their targeted hosts and virus-to-microbe ratio, in response to shifts in the composition and functioning their microbial counterparts. Our findings shed light on the microbial and viral drivers of important biogeochemical processes that take place in the South Atlantic Ocean.

Fjord systems in higher latitudes are unique coastal water ecosystems that facilitate the study of dissolved organic matter (DOM) dynamics from surface to deeper waters. The current work was undertaken in the Trondheim fjord characterized by North Atlantic waters, and compared DOM fractions from three depths - surface (3 m), intermediate (225 m) and deep (440 m) in four seasons, from late spring to winter in 2017. The high-resolution mass spectrometry data showed that DOM composition varies significantly in different seasons rather than in different depths in the fjord systems. The bacterial community composition was comparable except at spring surface and summer intermediate depths. Bacterial production was minimal below the euphotic layer, even with sufficient availability of inorganic nutrients. The bacterial production rate in the surface waters was about 7 times and over 50 times higher than that of the aphotic zone in the winter and the summer seasons, respectively. The surface heterotrophic microbial communities might have rapidly consumed the available labile DOM, with the production of more refractory DOM limiting bacterial production in aphotic layers. The greater number of CRAM-like formulas determined in the surface waters compared to other depths supports our hypothesis. The refractory DOM sequestered in the water column may either be exported into sediments attached to particulate matter and marine gels, or may escape into the atmosphere as carbon dioxide/monoxide during the photochemical oxidation pathways, suggesting that it is involved in climate change scenarios.

The north-western Mediterranean deep convection plays a crucial role in the general circulation and biogeochemical cycles of the Mediterranean Sea. The DEWEX (DEnse Water EXperiment) project aimed to better understand this role through an intensive observation platform combined with a modelling framework. We developed a 3 dimensional coupled physical and biogeochemical model to estimate the cycling and budget of dissolved oxygen in the entire north-western Mediterranean deep convection area over the period September 2012 to September 2013. After showing that the simulated dissolved oxygen concentrations are in a good agreement with the in situ data collected from research cruises and Argo floats, we analyze the seasonal cycle of the air-sea oxygen exchanges, as well as physical and biological oxygen fluxes, and we estimate an annual oxygen budget. Our study indicates that the annual air-to-sea fluxes in the deep convection area amounted to 20 mol m−2 yr−1. 88 % of the annual uptake of atmospheric oxygen, i.e. 18 mol m−2, occurred during the intense vertical mixing period. The model shows that an amount of 27 mol m−2 of oxygen, injected at the sea surface and produced through photosynthesis, was transferred under the euphotic layer, mainly during deep convection. An amount of 20 mol m−2 of oxygen was then gradually exported in the aphotic layers to the south and west of the western basin, notably, through the spreading of dense waters recently formed. The decline in the deep convection intensity in this region predicted by the end of the century in recent projections, may have important consequences on the overall uptake of atmospheric oxygen in the Mediterranean Sea and on the oxygen exchanges with the Atlantic Ocean, that appear necessary to better quantify in the context of the expansion of low-oxygen zones.

The geothermal system of the Salento peninsula (Italy) is characterized by the presence of many hydrogen sulfide-rich underground waters and thermal springs. We focused our attention on the submerged section of Zinzulusa (Castro, Italy), a cave of both naturalistic and archaeological interest. In pioneer studies, some hypotheses about the origin of the sulfurous waters of this area were proposed. The most accredited one is that sulfate-enriched waters of marine origin infiltrate deep along bands with greater permeability, and warm-up going upwards, due to the geothermal gradient. During their route, marine waters interact with organic deposits and generate hydrogen sulfide as a result of sulfate reduction. To date, no studies have been conducted to elucidate the hydrogen sulfide origin in this site. The nature of reducing power and energy sources supporting microbial life in this submerged habitat is currently unknown. Here we present a multidisciplinary experimental approach aimed at defining geochemical features and microbiological diversity of the submerged habitat of Zinzulusa cave. Our integrated data provide strong evidence that the sulfate content of the marine water and the activity of sulfate-reducing bacteria may account for the hydrogen sulfide content of the thermal springs. Anaerobic, sulfate-reducing, thermophilic Thermodesulfovibrio and hyperthermophilic Fervidobacterium genera show a high percentage contribution in 16S rRNA gene metabarcoding analyses, despite the mesophilic conditions of the sampling site. Besides, supported by PICRUSt functional analysis, we propose a chemotrophic model in which hydrocarbon deposits, entrapped in the stratifications of the seafloor, may be exploited by anaerobic oil-degrading bacteria as carbon and energy sources to sustain efficient hydrogen, sulfur, and nitrogen biogeochemical cycles. The Zinzulusa hydrothermal site represents an ecosystem useful to obtain new insights into prokaryotic mutual interactions in oligotrophic and aphotic conditions, which constitute the largest environment of the biosphere.