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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.

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.

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.

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.

BackgroundMarine Group I (MGI)Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGIThaumarchaeotawere present in the deepest part of oceans—the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water.ResultsIn this study, metagenomic data were obtained from 0–10,500 m deep seawater samples from the Mariana Trench. The distribution patterns ofThaumarchaeotaderived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance ofThaumarchaeotapeaked in bathypelagic zone (depth 1000–4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+and Na+respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea.ConclusionsOur study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-seaThaumarchaeotain carbon and nitrogen cycling.

Reefs formed by scleractinian cold-water corals represent unique biodiversity hot spots in the deep sea, preferring aphotic water depths of 200–1000 m. The distribution of the most prominent reef-building species Lophelia pertusa is controlled by various environmental factors including dissolved oxygen concentrations and temperature. Consequently, the expected ocean deoxygenation and warming triggered by human-induced global change are considered as a serious threat to cold-water coral reefs. Here, we present results on recently discovered reefs in the SE Atlantic, where L. pertusa thrives in hypoxic and rather warm waters. This sheds new light on its capability to adapt to extreme conditions, which is facilitated by high surface ocean productivity, resulting in extensive food supply. Putting our data in an Atlantic-wide perspective clearly demonstrates L. pertusa’s ability to develop population-specific adaptations, which are up to now hardly considered in assessing its present and future distributions.

Marine Euryarchaeota remain among the least understood major components of marine microbial communities. Marine group II Euryarchaeota (MG-II) are more abundant in surface waters (4–20% of the total prokaryotic community), whereas marine group III Euryarchaeota (MG-III) are generally considered low-abundance members of deep mesopelagic and bathypelagic communities. Using genome assembly from direct metagenome reads and metagenomic fosmid clones, we have identified six novel MG-III genome sequence bins from the photic zone (Epi1–6) and two novel bins from deep-sea samples (Bathy1–2). Genome completeness in those genome bins varies from 44% to 85%. Photic-zone MG-III bins corresponded to novel groups with no similarity, and significantly lower GC content, when compared with previously described deep-MG-III genome bins. As found in many other epipelagic microorganisms, photic-zone MG-III bins contained numerous photolyase and rhodopsin genes, as well as genes for peptide and lipid uptake and degradation, suggesting a photoheterotrophic lifestyle. Phylogenetic analysis of these photolyases and rhodopsins as well as their genomic context suggests that these genes are of bacterial origin, supporting the hypothesis of an MG-III ancestor that lived in the dark ocean. Epipelagic MG-III occur sporadically and in relatively small proportions in marine plankton, representing only up to 0.6% of the total microbial community reads in metagenomes. None of the reconstructed epipelagic MG-III genomes were present in metagenomes from aphotic zone depths or from high latitude regions. Most low-GC bins were highly enriched at the deep chlorophyll maximum zones, with the exception of Epi1, which appeared evenly distributed throughout the photic zone worldwide This work was supported by projects MEDIMAX BFPU2013–48007-P from the Spanish Ministerio de Economía y Competitividad MaCuMBA Project 311975 of the European Commission FP7 Project AQUAMET II/2014/012 from the Generalitat Valenciana and by the French Agence Nationale de la Recherche (ANR-08-GENM-024–001,EVOLDEEP). JHM was supported with a PhD fellowship from the Spanish Ministerio de Economía y Competitividad.

Some of the best-known disturbances affecting coral reefs are storms, yet their impacts on light are poorly known. Here, we describe the underwater light on a reef off St. John, US Virgin Islands (18°18′37.04N, 63°43′23.17W), during two hurricanes and multiple tropical waves that occurred between 17 August 2017 and 30 November 2017. Photosynthetically active radiation (PAR) was recorded at 19-m depth and at the surface, and rainfall was measured as a cause of turbidity affecting underwater light. Hurricanes Irma and Maria reduced maximum daily underwater photosynthetic photon flux density (PPFD) to

Mesophotic coral ecosystems, which occur at depths of ~40 to 150 m, have received recent scientific attention as potential refugia for organisms inhabiting deteriorating shallow reefs. These ecosystems merit research in their own right, as they harbor both depth-generalist species and a distinctive reef-fish fauna. Reef ecosystems just below the mesophotic are globally underexplored, and the scant recent literature that mentions them often suggests that mesophotic ecosystems transition directly into those of the deep sea. Through submersible-based surveys in the Caribbean Sea, we amassed the most extensive database to date on reef-fish diversity between ~40 and 309 m at any single tropical location. Our data reveal a unique reef-fish assemblage living between ~130 and 309 m that, while taxonomically distinct from shallower faunas, shares strong evolutionary affinities with them. Lacking an existing name for this reef-faunal zone immediately below the mesophotic but above the deep aphotic, we propose “rariphotic.” Together with the “altiphotic,” proposed here for the shallowest reef-faunal zone, and the mesophotic, the rariphotic is part of a depth continuum of discrete faunal zones of tropical reef fishes, and perhaps of reef ecosystems in general, all of which warrant further study in light of global declines of shallow reefs.

Coastal waters are important in linking zoobenthos and fish, as many coastal fishes feed on benthic prey in these habitats. Major drivers, such as eutrophication and climate change, may alter this link, whereas shifts in the importance of these drivers may induce different responses in zoobenthos and fish, respectively, potentially changing productivity of coastal ecosystems. The aim of this study was to assess in which way abundance and distribution of benthic-feeding fish and biomass of zoobenthos have changed over time in response to eutrophication (Secchi depth) and climate change (temperature and salinity), respectively. This was done by analyzing gross changes in the responses over three decades (1983–2012) and across depth zones. Eutrophication and climate change caused different though specific impacts on fish and zoobenthos, respectively. Throughout the 1980s, increasing benthic-feeding fish abundance in shallow waters (

Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large-scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established ‘core' (180 PCs; one-third new to science) and ‘flexible' (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (

The diversity of calcareous epiliths along a bathymetrical transect spanning the intertidal to bathyal (0–500 m) was investigated during a two-year carbonate cycling experiment deployed in the Faial Channel, Azores. The epilith inventory comprises 47 taxa of bryozoans, 9 serpulids, 3 bivalves, 3 cirripeds, 3 foraminiferans, 2 vermetid gastropods, and 1 scleractinian coral, along with 6 rhodophyte morphotypes. Colonised surface area, carbonate accretion rates, and biodiversity peak in the deeper euphotic zone (15 and 60 m), where mature biocoenoses were established after 2 years exposure, whereas colonisation was retarded at dysphotic and aphotic depths. Particularly in the photic zone, colonised surface area, accretion rates, as well as species richness and abundance were higher on down-facing compared to up-facing surfaces. Analyses of similarity (ANOSIM) and non-metrical multidimensional scaling (NMDS) of species abundance data revealed that water depth and substrate orientation were the dominant factors controlling the community structure as a result of direct (photosynthesis) and indirect (bioerosion pressure; nutrient supply) effects of the light regime, while exposure time and substrate type had little influence. The same hierarchy applies for the ichnodiversity of bioerosion traces, but with an inverse pattern in case of substrate orientation, reflecting the interaction of encrustation and bioerosion. Positive net carbonate production rates support the development of oyster bioherms and heterozoan-dominated carbonate/volcaniclastic sediments accumulating in the Faial Channel and adjacent slope. A comparison with biogenic sediments from other Macaronesian archipelagos and seamounts demonstrates the abundance and diversity of non-tropical heterozoan carbonates in oceanic islands.

Although winter conditions play a major role in determining the productivity of the western Antarctic Peninsula (WAP) waters for the following spring and summer, a few studies have dealt with the seasonal variability of microorganisms in the WAP in winter. Moreover, because of regional warming, sea-ice retreat is happening earlier in spring, at the onset of the production season. In this context, this study describes the dynamics of the marine microbial community in the Melchior Archipelago (WAP) from fall to spring 2006. Samples were collected monthly to biweekly at four depths from the surface to the aphotic layer. The abundance and carbon content of bacteria, phytoplankton and microzooplankton were analyzed using flow cytometry and inverted microscopy, and bacterial richness was examined by PCR–DGGE. As expected, due to the extreme environmental conditions, the microbial community abundance and biomass were low in fall and winter. Bacterial abundance ranged from 1.2 to 2.8 × 105 cells ml−1 showing a slight increase in spring. Phytoplankton biomass was low and dominated by small cells (

This paper aims at a synthesis of our conceptual views on the marine nutrient cycling. Based on selected biological, physical and geochemical aspects of the system, we present a framework for the description of the nitrogen cycling in oligotrophic regions of the ocean. Recent findings about the importance of the mesopelagic for remineralization are combined with ideas on the role of primary production, external input and fixation in nitrogen cycling. Instead of the usual distinction between euphotic and aphotic zones (i.e., with and without net primary production), our concept suggests a three-layer model featuring the subsurface production remineralization layer (SPRL) between the base of the surface mixed layer (SML) and the nutrient maximum at about 1000–1200 m depth, which can be used as a biogeochemical definition for the lower boundary of the mesopelagic. The approach leads to revised definitions of new and regenerated production, as well as export into the deep ocean, which are more adequate to characterize the biological pump, at least in the oligotrophic ocean. One of the main conclusions is that the steady state nitrogen export from the SPRL is fully determined by the sum of atmospheric deposition of nitrogen and N2-fixation and can be best quantified at the depth of the nitrogen maximum. While the magnitude of primary production by non-diazotrophic phytoplankton is irrelevant for export into the deep ocean, biological processes are crucial in determining size, shape and density of sinking particles and the remineralization rate of detritus.

In the cold-temperate setting of the Swedish Kosterfjord area, experimental carbonate and PVC substrates were deployed for a 6, 12 and 24-month duration along a transect from euphotic to aphotic depths in order to study bioerosion and carbonate accretion patterns. Among the organisms that contribute to the latter by secreting calcareous skeletons, epibenthic foraminiferans represent a major component, both in terms of diversity (a dozen species) as well as in the number of individuals (exceeding 50,000 individuals per m2 at certain depths). The by far dominating species were found to be Cibicides lobatulus and the agglutinating Lituotuba lituiformis, along with smaller numbers of Planorbulina mediterranensis, Tholosina vesicularis and Nubecularia lucifuga. The foraminiferal distribution exhibits a pronounced abundance maximum in shallow waters at 7 and especially 15 m and a maximum in diversity at 15-50 m water depth. Some of the foraminiferans encountered, such as Cibicides lobatulus and the rare Gypsina vesicularis, were found to contribute also to the bioerosion of the calcareous substrates by etching shallow attachment scars. These prominent traces witness the former presence of benthic foraminiferans on fossil to Recent hardgrounds, inferring a potential applicability as an in situ proxy where tests are not preserved. Estimated minimum carbonate production rates for the dominant Cibicides lobatulus reach a maximum of 0.326 g/m2/year with the highest rates occurring at 7 to 30 m water depth. Carbonate production rates are up to two magnitudes higher on the PVC (0-0.326 g/m2/year) than on the carbonate substrates (0-0.010 g/m2/year) and are considerably higher than estimates previously reported from the western Baltic.

In the cold-temperate setting of the Swedish Kosterfjord, a 2-year experiment was launched in order to assess bioerosion rates and to investigate the endolithic borer communities in relation to light availability (relative bathymetry), hydrography and exposure time. The inventory of microendolithic traces, studied by SEM analysis of epoxy resin casts of planted bivalve shells, yields diverse ichnocoenoses comprising a total of 21 traces produced by boring cyanobacteria (7), chlorophytes (4), fungi (6) and traces of uncertain affinity (4). The link between the endoliths (biotaxa) and the traces they leave (ichnotaxa) is evaluated by the study of the boring organisms in situ by transmission light microscopy of planted Iceland spar and bivalve shells. Additionally, the activity of various macroborers (foraminiferans, polychaetes, echinoids, gastropods and sponges) is documented, adding to a distinct diversity maximum at 7 m water depth. A highly condensed photic zonation, due to the high latitude (59°) and eutrophic conditions, is recorded by the measurement of the Photosynthetically Active Radiation (PAR) and is confirmed by the bathymetric range of the photic related ichnocoenoses. At 1 m water depth, a mature shallow euphotic ichnocoenosis dominated by cyanobacteria and at 7 m, a deep euphotic ichnocoenosis dominated by chlorophytes, respectively, is developed after as little as 12 months exposure. With the vanishing light availability from 15 m downwards, the ichnocoenoses development is significantly slowed and only immature dysphotic and aphotic borer communities (dominated by fungi) are encountered. Strong fluctuations of salinity (down to 8%) and temperature (0–20°C) in the euphotic zone indicate most phototrophs present to be considerably euryhaline and eurytherm, while most endolithic fungi appear preferentially in the deeper, more stable marine waters.

The sulfate-reducing bacterium strain SRB D2 isolated from the photic zone of a hypersaline microbial mat, from Lake Chiprana, NE Spain, respired pyruvate, alanine, and alpha-ketoglutarate but not formate, lactate, malate, succinate, and serine at significant rates under fully oxic conditions. Dehydrogenase enzymes of only the former substrates are likely oxygen-tolerant as all substrates supported anaerobic sulfate reduction. No indications were found, however, that aerobic respiration supported growth. Although strain SRB D2 appeared phylogenetically closely related to the oxygen-tolerant sulfate-reducing bacterium Desulfovibrio oxyclinae, substrate spectra were markedly different. Most-probable-number (MPN) estimates of sulfate-reducing bacteria and aerobic heterotrophic bacteria indicated that the latter were numerically dominant in both the photic and aphotic zones of the mat. Moreover, substrate spectra of representative isolates showed that the aerobic heterotrophic bacteria are metabolically more diverse. These findings indicate that sulfate-reducing bacteria in the fully oxic photic zone of mats have to compete with aerobic heterotrophic bacteria for organic substrates. Porewater analysis revealed that total carbohydrates and low-molecular-weight carbon compounds (LMWC) made up substantial fractions of the total dissolved organic carbon (DOC) pool and that nighttime degradation of the former was concomitant with increased concentration of the latter. Our findings indicate that aerobic respiration by sulfate-reducing bacteria contributes to organic carbon mineralization in the oxic zone of microbial mats as daytime porewater LMWC concentrations are above typical half-saturation constants.

The fate of pelagic diatoms in marine coastal aphotic sediments was investigated from sediment profiles in western Scandinavian waters. We used three independent methods to estimate pigment pools in the sediment: (1) fluorometry, (2) high-performance liquid chromatography and (3) pigments estimated from germinable diatom cells, using the dilution extinction method. A strong positive relationship with an intercept close to zero was observed between fucoxanthin, a marker of diatoms, and chlorophyll a. The fucoxanthin/chl a ratio was on average 1.05, which was similar to monocultures of dominating diatom taxa, indicating that sedimentary chl a was to a large extent of diatom origin. Chl a and fucoxanthin correlated significantly and positively with, and where within the same order of magnitude as, corresponding substances predicted from live diatom cell numbers obtained with the dilution extinction method. This indicates that a major part of surficial sediment chl a was bound in live cells of pelagic diatoms. There was a consistent change in viable cells with sediment depth and with timing of dominating taxa, with the non-spore-forming Skeletonema costatum dominating in the surface sediment in March and May, while the spore forming Chaetoceros spp. dominated deep in the sediment and during periods outside of the spring bloom (February and August). This indicates that chl a is bound in several different cell pools with different degradation rates, depending on diatom taxonomy. Thus, diatoms originating predominantly from the spring bloom may provide an important direct link in the pelagic–benthic coupling in this area.

Primary production and algal composition were studied in the shallow, highly turbid tropical freshwater Lake Baringo (Kenya). The lake's primary productivity was found to be very low when compared to other neighbouring Rift Valley lakes. The mean value of daily gross primary production was 0.56 g O2 m−2 d−1 with a range of 0.22 – 0.70 g O2 m−2 d−1. The study showed that this lake's primary production is strongly influenced by the inorganic turbidity but not the self-shading of algae as observed in the neighbouring soda and alkaline lakes. The lake has a high aphotic:photic zone ratio of 19, thus leading to a low light adapted phytoplankton community capable of vertical movement. This was shown by a uniform chlorophyll-a concentration at night and a gradient with higher values near the water surface observed during day time, too. Mean chlorophyll-a concentration was 55 μg l−1. Lake Baringo is characterised by only low diversity of algae and cyanobacteria, the latter being the major group of phytoplankton in this lake. Few green algae and diatoms were recorded during this study, growing for the most part in gelatinous sheaths of the blue-greens (strategy to get some light), on the stones near the shores of the lake and attached to the macrophytes.

Phylogenetic information from ribosomal RNA genes directly amplified from the environment changed our view of the biosphere, revealing an extraordinary diversity of previously undetected prokaryotic lineages. Using ribosomal RNA genes from marine picoplankton, several new groups of bacteria and archaea have been identified, some of which are abundant2,3,4. Little is known, however, about the diversity of the smallest planktonic eukaryotes, and available information in general concerns the phytoplankton of the euphotic region. Here we recover eukaryotes in the size fraction 0.2–5 µm from the aphotic zone (250–3,000 m deep) in the Antarctic polar front. The most diverse and relatively abundant were two new groups of alveolate sequences, related to dinoflagellates that are found at all studied depths. These may be important components of the microbial community in the deep ocean. Their phylogenetic position suggests a radiation early in the evolution of alveolates.

Cold-seep communities have relatively low diversity, are dominated by one or two taxa present in high density and high biomass in comparison with the surrounding fauna, and are restricted to aphotic habitats. Their associated heterotrophic fauna are usually distinctive from the fauna of their surroundings. In contrast, a more commonplace chemoautotrophically based community occurs in shallow photic habitats. The associated heterotrophic fauna includes many of the species typical of the surrounding communities and typically dominates abundance, whereas the species with chemoautotrophic symbionts dominate biomass. All modern seep assemblages are deeper than 550 m. Many fossil seep assemblages occurred in water as shallow as the mid-shelf (

Respiratory activity and metabolic CO2production of the microplankton in the Otranto Strait (Mediterranean Sea) were determined by monitoring the Electron Transport System activity. Ten stations were repeatedly investigated during two oceanographic surveys in February–March and August 1994. Respiratory activity and CO2 production, estimated from the surface to the bottom, were higher in the euphotic layers (0-200 m) during summer (mean values: Winter = 0.024 μg C h−1 dm−3; Summer = 0.042 μg C h−1 dm−3); in the aphotic zone (deeper than 200 m), the rates were similar throughout different seasons (0.013 and 0.014 μg C h−1 dm−3, respectively). A comparison with data collected by other authors from the euphotic layers of the Mediterranean Sea was made. Respiratory activities decreased from Western to Eastern Mediterranean Basins. The values of CO2 production, integrated between 200 and 1000 m in the Otranto Strait (mean value 237.7 mg C m−2 d−1), were compared with other data collected from the Mediterranean Sea as well as from the Pacific, Atlantic and Indian Oceans. The comparison showed the Otranto Strait to be a site of organic matter oxidation.

The surficial sediments of the Baie de Morlaix, a large embayment at the rocky coast of northern Brittany (48°N), are predominantly composed of bioclastic carbonates. Several different macrophytic communities are the most prominent systems producing skeletal carbonate deposits within the euphotic zone of this shallow water environment. The distribution of these communities is controlled by the strength of the hydrodynamic energy. In the more exposed outer section of the bay, affected by episodically strong storm-wave impact, the rocky seabottom is densely colonized by extended kelp forests ofLaminaria hyperborea, L. digitata andSaccorhiza polyschides. The flexible thalli of the pseudoperennial phaeophytes contain numerous highly differentiated microhabitats, occupied by several carbonate-secreting organisms. Detachment and fragmentation of the epiphytic community generates coarse biogenic debris, mainly of balanids, bryozoans, serpulids and echinoids. In the sheltered parts of the numerous rocky shoals and small islands, which create a morphologically complex coastal platform, autochthonous coralline algal maerl-banks are developed. The biostromal framework of the maerl-banks is constructed by the small branched thalli of the coralline algaeLithothamnium corallioides andPhymatolithon calcareum. Depending on location and energy regime several characteristic parautochthonous to allochthonous subfacies can be recognized. Generally they are found in the deeper parts of the coastal platform whereas the autochthonous maerl-banks are restricted to the shallow (

In aquatic ecosystems, fluctuations in environmental conditions and prokaryotic host physiological states can strongly affect the dynamics of viral life strategies. The influence of prokaryote physiology and environmental factors on viral replication cycles (lytic and lysogeny) was investigated from April to September 2011 at three different strata (epi, meta, and hypolimnion) in the mixolimnion of deep volcanic temperate freshwater Lake Pavin (France). Overall, the euphotic region (epi and metalimnion) was more dynamic and showed significant variation in microbial standing stocks, prokaryotic physiological state, and viral life strategies compared to the aphotic hypolimnion which was stable within sampled months. The prokaryotic host physiology as inferred from the nucleic acid content of prokaryotic cells (high or low nucleic acid) was strongly regulated by the chlorophyll concentration. The predominance of the high nucleic acid (HNA) prokaryotes (cells) over low nucleic acid (LNA) prokaryotes (cells) in the spring (HNA/LNA = 1.2) and vice versa in the summer period (HNA/LNA = 0.4) suggest that the natural prokaryotic communities underwent major shifts in their physiological states during investigated time period. The increase in the percentage of inducible lysogenic prokaryotes in the summer period was associated with the switch in the dominance of LNA over HNA cells, which coincided with the periods of strong resource (nutrient) limitation. This supports the idea that lysogeny represents a maintenance strategy for viruses in unproductive or harsh nutrient/host conditions. A negative correlation of percentage of lysogenic prokaryotes with HNA cell abundance and chlorophyll suggest that lysogenic cycle is closely related to prokaryotic cells which are stressed or starved due to unavailability of resources for its growth and activity. Our results provide support to previous findings that changes in prokaryote physiology are critical for the promotion and establishment of lysogeny in aquatic ecosystems, which are prone to constant environmental fluctuations.

Tubular microfossils are important sediment producers in the aphotic zone of the Red Sea. They occur on forereef slopes and as incrustations on hardgrounds of basinal carbonates as well as encrusting drowned reefs. The tubular microfossils (mean inner diameter 10 μm, outer diameter 50 μm) are straight to slightly curved and commonly branched. Because of their size and mode of calcification, they may represent remnants of fungi or cyanobacteria. Combined growth of the microfossils on protected upper surfaces of substrates and little sedimentation produce strictly geofugal cryptalgal fabrics. Although this fabric suggests phototactic growth, the tubular microfossils are eurytopic. In the Red Sea they occur between 63 and 765 m below present sea level. Within the basin the cryptalgal fabrics formed during last glacial lowstand of sea level and along the slope during Holocene rise of sea level. Limiting factors recognized so far seem to be space competition with faster growing encrusters, mainly the corallinaceans, and burial by sediments. During glacial lowstand of sea level salinity exceeded the tolerance levels of most planktonic taxa resulting in low rates of sedimentation in the basin. Along the cliffed slope sedimentation remained low during Holocene transgression. Before the mid-Mesozoic calcified cyanophyceans were very common. It is proposed that, as a consequence of the radiation of calcareous plankton during that time, suitable conditions of low sedimentation in deep water became less common.

Despite extensive discussions during the last 20 years stromatolites are still used by many geologists as unequivocal indicators of very shallow-water conditions. We investigated four stratigraphic units from the Lower and Middle Jurassic of southern Germany (Posidonien-Schiefer, Amaltheen-Ton) and of the Northern Calcareous Alps (Adneter Kalk, Klauskalk), which were formerly interpreted as shallow marine sediments by some authors due to the occurrence of stromatolites. Our interpretations of the macro-, micro- and ultrafacies of these sediments are not compatible with shallow-water settings. We therefore propose a deep-marine, aphotic origin of these stromatolites. Former interpretations of the Posidonien-Schiefer as a shallow-water deposit are mainly based on the occurrence of stromatolites. We favour the model of a temporarily stagnant, deep, aphotic basin for these planktonrich sediments. Particles resembling ooids, but lying within mudstones cannot be taken as evidence for shallow agitated water. They either formed within the mud or are allochthonous. The deep-water setting of the red limestone of the Alpine Early and Middle Jurassic is indicated by a lack of platform-typical components like coated grains and phototrophic benthos and by shells of plankton and nekton forming a major part of the sediment. Stromatolites occur on the steep slope of a drowned Rhaetian reef with an estimated relief of 50–100 m and immediately below and within radiolarian limestones, deposited below the aragonite compensation depth (ACD). The aphotic stromatolites show some morphological differences to their shallow water counterparts. In all of our sections they occurred during intervals of reduced sedimentation. They form only thin horizons and probably grew very slowly. Mineralizations by Fe−Mn oxides and phosphate are very common. The presence of a microbial film is evident from binding of sedimentary particles, but the nature of the microbes is not known. Growth habits within the very distinct environments of red limestone and black shales show some common features, but also clear differences. The microproblematicumFrutexites Maslov is a very common component in deep-water stromatolites, but may also itself form small crusts or dendrolites. It occurs in two different forms. Opaque, slender forms with indistinct outlines probably grew within the weakly lithified sediment. Thicker, transparent forms with well defined outlines are found in cavities and probably also grew on the seafloor. Well preserved specimens display an internal fabric of radially arranged fibres of Fe−Mn oxides and calcite. It is suggested that calcite or aragonite were one original mineralogy ofFrutexites, which was later replaced by Fe−Mn oxides or phosphate. It is not certain whetherFrutexites is an organic, biomineralized structure or an inorganic mineralization, but the variable mineralogy and growth forms in different environments point to an organic origin. But even if organic, the occurrence in cryptic habitats and negative phototactic growth-directions make it clear thatFrutexites was not phototrophic.

Mathematical modelling was used to explore the seasonal and annual variability of primary, new and secondary production as well as sedimentation between 72° and 80°N in the central Barents Sea during the years 1981 to 1983. 1981 and 1982 were years with extensive ice coverage while 1983 experienced little sea-ice. The phytoplankton “spring” bloom started usually in April/May at about 75°N and was delayed from May/June in the south to August/September in the north as a function of thermal stratification and sea-ice dynamics. The model indicates that several, simultaneous spring bloom events, separated in space, can be found, especially during years with low ice coverage. The annual estimates of primary production, secondary production and sedimentation decreased on average from 73, 7.3 and 48 to 18, 1.8 and 9 g C m−2 year−1 between the southern and the northern part of the Barents Sea respectively. The annual estimates of particulate carbon flux were much higher in 1983 compared to 1981–1982, especially in the north where up to 6 times higher rates were calculated for 1983. The number of zooplankton species present in spring in the southern Barents Sea is governed by over-wintering success, but probably also influenced by advection of Atlantic water. The model was run for Atlantic water with 10,000, 3,000 or none copepods per m2 present in March, indicating that sedimentation can vary between 38 and 61 g C m−2 year−1 due to zooplankton grazing alone. This suggests that the supply of organic carbon to the aphotic zone of the Barents Sea is only partly determined by the strength and duration of phytoplankton blooms, but strongly influenced by zooplankton dynamics.

The plume of particulate DNA (0.7–1μg/l) was extended from a black smoker vent (c.a. 1340 m depth) to the west-southwest directions in the Izena bottom-water region. High concentrations of particulate materials (70–110 μg C/l; 300–570 μg S/l) were also detected in the bottom-waters. Microscopic observation showed that the bottom-waters were rich in alcian blue-stainable large amorphous particles which contained coccoid and rod-shaped microbial cells mostly smaller than 1μm. These microbial matrix compounds appeared to contribute to low P-DNA/P-C ratio (0.011±0.008;n=27) in the vent environment. Sulfur was detected in various kinds of particles in the waters, while the content varied with calcium. Microbial population in the P-DNA plume water was in the order of 105 cells/ml and the most (>99.9%) were non-culturable. The composition of culturable heterotrophs differed between the bottom-waters and surface sediments surrounding the vent; contributions of low temperature (4°C)-culturable bacteria and manganese-oxidizing bacteria to the total heterotrophs were higher in the sediments than in the waters. In contrast, percentages of orange-pigmented heterotrophs and microorganisms capable of growing in thiosulfate- and ammonia-based media to the total heterotrophs were higher in the waters than in the sediments. These results suggest that the culturable bacterial community in the bottom-waters was nutritionally versatile. Izena hydrothermal activities seemed to have a great influence in concentrations and compositions of particulate mateirals and in biomass and compositions of microbial community in the vicinity of this aphotic deep-sea environment.

Murray-Darling Freshwater Research CentreMDFRC item.Biofilms were allowed to develop on wooden slides of the River Red Gum (Eucalyptus camaldulensis Dehnh., Myrtaceae) submerged in two billabongs of south-eastern Australia. The slides were placed in the photic zone and the aphotic zone, and the biofilms sampled after eight week''s growth over the summer of 1989–1990 and winter of 1990. Bacterial numbers, estimated with epifluorescence microscopy, ranged from 4–78 × 106 cells cm–2. Bacteria were more abundant in the photic zone than the aphotic zone, and more abundant in summer than winter. Fewer than 0.5% of the bacteria could be cultivated on nutrient agar plates. Concentrations of phospholipids ranged from 8–79 ng cm–2, which corresponded to bacterial abundances of 2–17 × 106 cells cm–2. Fifty five phospholipid fatty acids (PLFA) were identified, of which 16:0 (13–29% of total PFLA) was the most common. Other abundant PFLA included 16:17c (6–28%), 18:26 (3–16%), 18:33 (4–12%), 18:19c (3–5%), 18:l7c (5–11%) and 18:0 (2–8%). Minor PLFA included 14:0, i and a 15:0, 15:0, 16:l5c, 16:113c, 18:36, 18:43, 20:46 and 20:53. The PLFA profiles of the biofilms were quite different from those of the sediments and plankton. There was a clear distinction between the PLFA profiles of summer and winter biofilms, but less evidence for unequivocal site or light-regime effects.

In the Helgoland region eight sublittoral hard substrate communities occur. These communities were stationary in time during the years 1987–1989. The major governing parameters are the available amount of daylight and the degree of exposure to water movement. In the photic zone, three communities are met with, one of which is widespread and appears to be independent of the exposure to water movement. Under exposed conditions, at the lower border of the photic zone, a second community is observed. A third community is established on erosive muschelkalk substrates. In the aphotic zone also, three communities are found. The distribution of these communities is related to the rate of water movement. One community is divided into three variants, with different preferences regarding the angle of inclination and nature of the substrates. In the artificially constructed harbours, where sedimentation exceeds erosion, two different communities have settled. In the community under moderately sheltered conditions many species are found which also occur in the natural photic zone. Under extremely sheltered conditions a group of species has become dominant which is very rare in the Helgoland region outside the quay-walls but which has been described as being characteristic for sheltered localities elsewhere.

The Danish-Polish Trough—a northwest to southeast striking basin—is bordered by the Fennoscandian Shield in the north and the Ringkobing-Fyn High in the south. During the Late Cretaceous and Early Tertiary carbonate sedimentation prevailed. Locally small bryozoan mounds were formed during the Upper Maastrichtian. The bulk of bryozoan bioherms originated during the Danian B to C. Coral communities and coral mounds are confined to the Danian C. About five coral limestone localities occur within the Danish-Polish Trough; Fakse is the most important one.

During the course of video/still image analysis, some pictures unfortunately appear to have been mixed up. The coral colonies shown in Fig. 1 have not been sampled, and their identity is not confirmed. However, numerous Corallium sp. colonies were found at the same site in greater depth (602–627 m), as shown in Fig. S1 (attached), and their identity was confirmed by DNA barcoding. We would like to emphasize that the main message of our Reef Site article, the first discovery of precious corals on the aphotic reef slope of Osprey Reef, is still unchanged. We thank Rob Beaman (JCU) for pointing this out to us and Sarah Adolf (LMU) for assistance with DNA barcoding.

Sediment-water exchanges of ammonium (NH4 +), nitrate + nitrite (NOx −), filterable reactive phosphorus (FRP, primarily ortho-phosphate), and oxygen (O2) under aphotic (heterotrophic) conditions were determined at 2–5 stations in the Neuse River Estuary, from 1987 to 1989. Shallow (1 m), sandy stations were sampled along the salinity gradient. Fluxes from deep (>2 m) sites were compared to the shallow sites in two salinity zones. Grain size became finer and organic content increased with depth in the oligohaline zone but not in the mesohaline zone. Net release of NH4 + and FRP occurred at all sites. Fluxes varied from slight uptake to releases of 200–500 μmol m−2 h−1 (NH4 +) and 150–900 μmol m−2 h−1 (FRP). Net NOx − exchange was near zero, but were ±100 μmol m−2 h−1 over the year. Release of NH4 + and FRP from the shallow sandy stations decreased with distance down the estuary, but O2 uptake did not change. The deeper oligohaline site had twofold higher rates of NH4 + and FRP release and O2 uptake than the shallow site, but no differences occurred between depths in the mesohaline zone. Temperature and organic content were important controls for all fluxes, but water column NOx − concentration was also important in regulating NOx − exchanges. Ratios of oxygen consumption to NH4 + release were near the predicted ratio (Redfield model) at oligohaline sites but increased down estuary at mesohaline sites. This may be due to greater nitrification rates promoted by autotrophy in the sediments.

The depth distribution and composition of residual amino acids was determined in December 1980 in the Bransfield Strait. The major components were aspartic and glutamic acids together with alanine, glycine and serine. Non-protein amino acids were not found in significant amounts. On the average, the amino acids accounted for 25% of the total organic carbon and 50% of the organic nitrogen. Amino acid nitrogen/chlorophyll ratios indicated that in most euphotic zone samples phytoplankton in good physiological condition was present whereas heavily degraded material was found in deeper water layers. Statistical treatment and cluster analysis show distinct differences between euphotic and aphotic zone samples which could be used to characterize phytoplankton communities.

By comparing primary production (14C) and biomass variation it is possible to calculate the total losses of phytoplankton. For the mesotrophic drinking water reservoir Saidenbach, average loss rates of -0.31 d-1 for the total phytoplankton and -0.99 d-1 for nanoplankton were determined from September 1980 to May 1981. The greater the share of nanoplankton in the total phytoplankton, the less the real activity as reflected in biomass changes observed. The considerable (mainly nanoplankton) losses, however, cannot be explained by grazing or sedimentation. They are assumed to be caused by high mortality of flagellates due to a relatively high depth of mixing and their retention in the aphotic layer.

The plankton of an acidic, polymictic, brown-water lake was investigated over a one-year period. The phytoplankton community was dominated by Chlamydomonas sp., Melosira varians and Peridinium pusillum during different times of the year. Densities were abnormally low, with a maximum of only 13,781 individuals per liter during the March bloom. The water column was nearly void of phytoplankton during the fall. These low densities were attributed to several of the physical and chemical characteristics of the water, including low pH, low levels of nutrients and light limitation. The latter factor was important because of low light transmission into the highly colored water, shading from macrophytes and the nearly continuous transport of the phytoplankton into the aphotic zone due to mixing of the water column by sea breezes.

Salps (mainly Salpa fusiformis and, to a lesser extent, Pegea socia) and a web-building pteropod (Corolla spectabilis) were studied in epipelagic waters of the central California Current. Although both kinds of gelatinous zooplankton trap phytoplankton in a mucus net, a fecal pellet analysis indicated that their diet differs significantly when they feed together, probably because of differences both in the pore sizes of their nets and in their feeding methods. Salps have a finemesh filter, on which they can retain even the smallest phytoplankton; thus, when small coccolithophores are abundant, as they were in our study, salp feces contain such cells and the coccoliths derived from them. In contrast, pteropods feeding in the same area produce fecal pellets consisting chiefly of larger phytoplankton, especially diatoms. Since fecal pellets transport most biogenic material to the deep sea, changes in herbivore species composition at a given geographic location can change the chemistry of materials entering deep water; at our study site, the more salps, the greater the calcite flux, and, the more pteropods, the greater the silica flux. In addition, fecal pellets of both salps and pteropods include partially digested residues of phytoplankton that appear as olive-green spheres, having an ultrastructure identical with that of the socalled olive-green “cells.” Presumably, fecal pellets, after sinking into deep water, ultimately disintegrate. releasing both the viable phytoplankton and the olive-green spheres into aphotic waters. Thus the feces of epipelagic herbivores are likely sources of much of the flora of the deep ocean.

Seasonal and spatial aspects of the net settling velocities of particles in Lake Constance were investigated by measurements of settling fluxes and estimates of the concentrations of suspended matter. Annual mean sinking velocities ranged from 2.6 m d−1 in the euphotic zone to 7.5 m d−1 in the aphotic zone. Summer maxima of 36.6 m d−1 were caused by settling calcite crystals, while minima of 0.4 m d−1 during the clear water phase resulted from particulate matter consisting mostly of phytoplankton and organic debris. Winter settling velocities averaged 1,2 m d−1. The mean residence time for the bulk of particles calculated on an annual basis was 27.8 days. The net settling velocities in this study were higher than those calculated for phytoplankton in other investigations but agreed with estimates for particles from Lake Zurich obtained by an approach similar to this study.

Chla, protein, RNA and DNA were measured in 400 samples taken from the surface down to 5,000 m at 27 oceanographical stations in the North Pacific Ocean. Two section diagrams of these cellular constituents were given along 155°E and 155°W meridians, and several vertical profiles of the four constituents were also given at some stations near Japan. The average concentration ranges of Chla, protein, RNA and DNA obtained in this study area were 0.025–0.862, 11.4–88.1, 1.36–35.3 and 0.13–5.24μg/l, respectively. Chla was distributed mostly in the photic zone as we would expect. However protein, RNA were in high concentrations within the photic zone and sometimes extremely high concentrations in the deep aphotic zone.

The growth characteristics of small (0.2-1.0μm) and large (1.0-3.0 (μm) free-living and attached bacteria were studied in Lake Constance by comparing the spatial and seasonal dynamics of their biomass turnover time (ratio of biomass/production). The biomass of small free-living bacteria usually turned over significantly faster than that of large free-living bacteria throughout the water column. The turnover of attached bacterial biomass was characterized by large fluctuations. Occasionally, in aphotic water layers, it was as long as that of large free-living bacteria, but when large amounts of decaying organic particles were present, it was shorter than that of small free-living cells. Biomass turnover times of free-living bacteria were in the same range as their generation times, which were estimated from the increase in bacterial abundance in 3μm prefiltered samples. The biomass turnover time of actively metabolizing bacteria was comparable to the generation time of actively metabolizing cells. These results indicate that the biomass turnover time is a useful indicator of the growth of different bacterial fractions, as it reflects their different amounts of participation in microbial processes of aquatic ecosystems.

1. Light penetration in sediments is a function of sediment granulometry; it decreases with the decrease in grain size. 2. Light quantities entering the sediments are a function of substrate depth: At 1 mm depth, light penetration ranges between 80 (at medium quartzy sands from Hel) and 2 (at very fine sands from the Black Sea) percent of the light quantities found at the substrate surface; at 2 mm depth light penetration varies between 52 percent and total darkness (when muds replace sand); at 3 mm depth it varies between 0 and 23 per cent; at 4 mm depth, in most samples the aphotic zone was reached; however, in some sediments (quartzy medium or coarse-medium sands) values up to 9 per cent may occur; at 5 mm depth out of 46 analysed samples only 5 contained up to 5 per cent light; at 6 mm depth the lowest readings of down to 3 per cent were obtained. 3. On the basis of these data, the photic zone in sandy sediments is very thin.

Glucose uptake was measured at three different stations in the northwestern Pacific Ocean. The measurements were made at various temperatures (5° to 35°C) and glucose concentrations (3 to 100 μg glucose/l). The uptake of almost all samples taken from the surface to 1,500 m was affected primarily by temperature. The temperature dependence of samples from near the transition region between the Kuroshio and the Oyashio current waters was twice as large as that of both current samples. Furthermore, the samples from the former, transition, region and the aphotic samples of the latter, current, regions showed an optimal temperature 15° to 30°C higher than the in situ temperature; the optimal temperature was only 5° to 10°C higher in the photic samples of the stable region. The average potential glucose uptake at/near the optimal temperature was 0.026 μg glucose/l/h in the photic zone and 0.015 μg glucose/l/h in the aphotic zone. However, after correction by the in situ temperature, the uptake was 0.024 and 0.003 μg glucose/l/h, respectively.

In the past decade, protozoa have been recognized as ubiquitous residents of the upper waters of the sea, where they have key roles in detrital and producer food webs1–4. In contrast, protozoa are almost unknown from aphotic depths, where food chains presumably are supported by detritus. We show here that ciliate protozoans do accompany sinking detritus to bathypelagic depths. In the productive northeastern Pacific Ocean, the biomass of ciliates on particles settling between the surface and 2,000 m far exceeds the biomass of bacteria, which are the only widely recognized detrital microorganisms in deep pelagic communities. Although absolute numbers of ciliates decline below the euphotic zone, their concentrations (number per g detritus) drop only slightly by 2,000 m. Taxonomic data and patterns of abundance5 indicate that the ciliates are endemics and not remnants of surface colonists, and that the deep sea is a favourable environment for them. Their high concentrations, possibly together with other smaller protozoa, indicate that protists may control bacterial mineralization rates on sinking particles, thereby regulating the vertical distribution of many biologically active elements in the sea.

Particulate organic matter (POM) has a central role in the vertical transport of material in the sea1. In the open ocean, POM is produced in the euphotic layer by phytoplankton and degraded in the aphotic layer during sinking to the sea floor. Isotopic abundance of biophilic elements such as C and N in POM is altered by isotopic fractionations associated with biochemical reactions2. Natural abundances of 13C or 15N thus provide useful information on biochemical behaviour of POM in the sea. We report here the first comprehensive data on the vertical distribution of 15N in suspended POM3 collected at a station in the northeastern Indian Ocean. Also, we discuss how nitrogen isotopic analysis could be used for the identification and quantification of the vertical transport processes.