Living benthic foraminifera of the Okhotsk Sea: Faunal composition, standing stocks and microhabitats

Live (Rose Bengal stained) benthic foraminifera were investigated in surface sediment samples from the Okhotsk Sea to reveal the relationship between faunal characteristics and environmental parameters. Live benthic foraminifera were quantified in the size fraction > 125 µm in the upper 8 cm of replicate sediment cores, recovered with a multicorer at five stations along the Sakhalin margin, and at three stations on the southwestern Kamchatka slope. The stations are from water depths between 625 to 1752 m, located close or within the present Okhotsk Sea oxygen minimum zone, with oxygen levels between 0.3 and 1.5 ml l^- 1. At the high-productivity and ice-free Kamchatka stations, live benthic foraminifera are characterized by maximal standing stocks (about 1700-3700 individuals per 50 cm²), strong dominance of calcareous species (up to 87-91% of total live faunas), and maximal habitat depths (down to 5.2-6.7 cm depth). Vertical distributions of total faunal abundances exhibit a clear subsurface maximum in sediments. At the Sakhalin stations, which are seasonally ice-covered and less productive, live benthic foraminifera show lower standing stocks (about 200-1100 individuals per 50 cm²), lower abundance of calcareous species (10-64% of total live faunas), and shallower habitat depths (down to 2.5-5.4 cm depth). Faunal vertical distributions are characterized by maximum in the uppermost surface sediments. It is suggested that 1) lower and strongly seasonal organic matter flux, caused by the seasonal sea ice cover and seasonal upwelling, 2) lower bottom water oxygenation (0.3-1.1 ml l^- 1), and 3) more pronounced influence of carbonate undersaturated bottom water along the Sakhalin margin are the main factors responsible for the observed faunal differences. According to species downcore distributions and average living depths, common calcareous species were identified as preferentially shallow, intermediate and deep infaunal. Foraminiferal microhabitat occupation correlates with the organic matter flux and the depth of the oxygenated layer in sediments.     

Living benthic foraminifera of the Okhotsk Sea: Faunal composition,standing stocks and microhabitats

Live (Rose Bengal stained) benthic foraminifera were investigated in surface sediment samples from the Okhotsk Sea to reveal the relationship between faunal characteristics and environmental parameters. Live benthic foraminifera were quantified in the size fraction > 125 µm in the upper 8 cm of replicate sediment cores, recovered with a multicorer at five stations along the Sakhalin margin, and at three stations on the southwestern Kamchatka slope. The stations are from water depths between 625 to 1752 m, located close or within the present Okhotsk Sea oxygen minimum zone, with oxygen levels between 0.3 and 1.5 ml l^- 1. At the high-productivity and ice-free Kamchatka stations, live benthic foraminifera are characterized by maximal standing stocks (about 1700-3700 individuals per 50 cm²), strong dominance of calcareous species (up to 87-91% of total live faunas), and maximal habitat depths (down to 5.2-6.7 cm depth). Vertical distributions of total faunal abundances exhibit a clear subsurface maximum in sediments. At the Sakhalin stations, which are seasonally ice-covered and less productive, live benthic foraminifera show lower standing stocks (about 200-1100 individuals per 50 cm²), lower abundance of calcareous species (10-64% of total live faunas), and shallower habitat depths (down to 2.5-5.4 cm depth). Faunal vertical distributions are characterized by maximum in the uppermost surface sediments. It is suggested that 1) lower and strongly seasonal organic matter flux, caused by the seasonal sea ice cover and seasonal upwelling, 2) lower bottom water oxygenation (0.3-1.1 ml l^- 1), and 3) more pronounced influence of carbonate undersaturated bottom water along the Sakhalin margin are the main factors responsible for the observed faunal differences. According to species downcore distributions and average living depths, common calcareous species were identified as preferentially shallow, intermediate and deep infaunal. Foraminiferal microhabitat occupation correlates with the organic matter flux and the depth of the oxygenated layer in sediments.     

Morphology and mode of life of the polychaeteRotularia

The serpulidRotularia built rather regular, planispiral or trochospiral tubes with an uncoiled adult portion. Juveniles ofRotularia were cemented to small substrates, and later in ontogeny grew into secondary, reclining epifaunal soft-bottom dwellers in medium- to high-energy environments. The uncoiled adult portion, together with the coiled portion of the tube, constituted a stabilizing structure increasing the effective area of contact with the substrate, and was only exceptionally bent out of the coiling plane, a situation common in other sessile soft-bottom dwellers among polychaetes and gastropods.     

Benthic foraminiferal morphogroups of mid to outer shelf environments of the Late Jurassic (Prebetic Zone, southern Spain): Characterization of biofacies and environmental significance

Benthic foraminiferal assemblages belonging to a mixed carbonate–siliciclastic shelf succession of the Oxfordian (Upper Jurassic) in the Prebetic, southern Spain, were analyzed. The faunal data, obtained on thin sections of strongly lithified sediments, allowed the detailed differentiation of a foraminiferal morphogroups system to be applied to the interpretation of paleoenvironmental conditions. Eleven morphogroups were differentiated according to shell composition, general morphology, number of chambers and mode of coiling. Paleoenvironmental analysis combines these features with inferred life-style (epifaunal, shallow infaunal and deep infaunal) and feeding strategy (suspension-feeder, deposit-feeder, herbivores, etc.) of the foraminifera. Analogies and differences regarding previously established morphogroup systems could be outlined accordingly.

In the Prebetic Oxfordian, distribution trends of foraminiferal morphogroups allow for a comparison of mid to outer shelf environments occupying the South-Iberian paleomargin, indicating that nutrient supply was the most important factor controlling morphogroup development. The mid shelf settings are dominated by epifaunal active herbivores–phytodetritivores, in shallow to deep substrate position of the redox boundary. The outer shelf is dominated by agglutinated and infaunal detritivore-bacterial scavenger morphogroups revealing a deep substrate position of the redox boundary. Particularly favorable trophic conditions in mid shelf environments are related with higher phytodetritus input from more proximal and shallower shelf areas.     

Accumulation of sediment-associated viruses in shellfish.

The present study focused on the importance of contaminated sediments in shellfish accumulation of human viruses. Epifaunal (Crassostrea virginica) and infaunal (Mercenaria mercenaria) shellfish, placed on or in cores, were exposed to either resuspended or undisturbed sediments containing bound poliovirus type 1 (LSc 2ab). Consistent bioaccumulation by oysters (four of five trials) was only noted when sediment-bound viruses occurred in the water column. Virus accumulation was observed in a single instance where sediments remained in an undisturbed state. While the incidence of bioaccumulation was higher with resuspended rather than undisturbed contaminated sediment, the actual concentration of accumulated viruses was not significantly different. The accumulation of viruses from oysters residing on uninoculated sediments. When clams were exposed to undisturbed, virus-contaminated sediments, two of five shellfish pools yielded viral isolates. Bioaccumulation of undisturbed sediments by these bivalves was considered marginal when related to the concentration of virus in contaminated sediments; they would only represent a significant threat when suspended in the water column. Arguments were advanced for water-column sampling in the region of the water-sediment interface to provide an accurate determination of the virological quality of shellfish harvesting waters.     

Accumulation of sediment-associated viruses in shellfish

The present study focused on the importance of contaminated sediments in shellfish accumulation of human viruses. Epifaunal (Crassostrea virginica) and infaunal (Mercenaria mercenaria) shellfish, placed on or in cores, were exposed to either resuspended or undisturbed sediments containing bound poliovirus type 1 (LSc 2ab). Consistent bioaccumulation by oysters (four of five trials) was only noted when sediment-bound viruses occurred in the water column. Virus accumulation was observed in a single instance where sediments remained in an undisturbed state. While the incidence of bioaccumulation was higher with resuspended rather than undisturbed contaminated sediment, the actual concentration of accumulated viruses was not significantly different. The accumulation of viruses from oysters residing on uninoculated sediments. When clams were exposed to undisturbed, virus-contaminated sediments, two of five shellfish pools yielded viral isolates. Bioaccumulation of undisturbed sediments by these bivalves was considered marginal when related to the concentration of virus in contaminated sediments; they would only represent a significant threat when suspended in the water column. Arguments were advanced for water-column sampling in the region of the water-sediment interface to provide an accurate determination of the virological quality of shellfish harvesting waters.     

Living foraminifera and total populations in salt marsh peat cores: Kelsey Marsh (Clinton, CT) and the Great Marshes (Barnstable, MA)

Common species of intertidal agglutinated benthic foraminifera in salt marshes in Massachusetts and Connecticut live predominantly at the marsh surface and in the topmost sediment (0–2.5 cm), but a considerable part of the fauna lives at depths of 2.5–15 cm. Few specimens are alive at depths of 15–25 cm, with rare individuals alive between 25–50 cm in the sediments. Specimens living between the sediment surface and 25 cm deep occur in all marsh settings, whereas specimens living deeper than 25 cm are restricted to cores from the lower and middle marsh, and have an irregular distribution-with-depth. Lower and middle marsh areas are bioturbated by metazoa, suggesting that living specimens reach these depths at least in part by bioturbation. High-marsh sediments in New England consist of very dense mats of Spartina patents or Distichlis spicata roots and are not bioturbated by metazoa. In this marsh region bioturbation by plant roots and vertical fluid motion may play a role in moving the foraminifera into the sediment. The depth-distribution of living specimens varies with species: living specimens of Trochammina inflata consistently occur at the deepest levels. This suggests that species have differential rates of survival in the sediment, possibly because of differential adaptation to severe dysoxia to anoxia, or because of differing food preferences. There is no simple correlation between depth-in-core and faunal diversity, absolute abundance, and species composition of the assemblages. It is therefore possible to derive a signal of faunal changes and thus the environmental changes that may have caused them from the complex faunal signal of fossil assemblages.     

Effects of biotic factors on depth selection by salt marsh nekton

Biotic factors such as interactions among co-occurring taxa are frequently cited as important in determining how nekton use habitat, yet their effects have rarely been tested experimentally. We investigated the general hypothesis that depth distributions of five taxa common in salt marsh intertidal creeks are affected by the presence of other taxa. Two experiments were conducted in a pair of large (15 m³), multi-level (20, 40, and 60 cm water depth) flow-through tanks under fairly stable environmental conditions. During the first experiment, when grass shrimp (Palaemonetes spp.), mummichog (Fundulus heteroclitus), white mullet (Mugil curema), spot (Leiostomus xanthurus), and pinfish (Lagodon rhomboides) were each tested alone, the highest proportions of individuals occupied the intermediate and deepest depths. When all taxa were tested together, the distributions of resident creek taxa, mummichog and grass shrimp, shifted to shallower depths, but the distributions of the seasonal transient taxa, white mullet, spot, and pinfish, did not change. A second experiment was conducted to test the effect of predator presence on grass shrimp depth selection. Neither predatory pinfish nor non-predatory white mullet had a strong influence on grass shrimp depth distribution when tested separately, but grass shrimp shifted to shallower depths in the combined presence of both fish. This suggests that a multiple-taxa effect such as increased disturbance or higher encounter frequency influenced the depth selection of grass shrimp. Our results demonstrate that biotic factors are important in shaping distributions of grass shrimp and mummichog in shallow water habitat.     

The input of foraminiferal infaunal populations to sub-fossil assemblages along an elevational gradient in a salt marsh: application to sea-level studies in the mid-Atlantic coast of North America

The suitability of marsh sites for sea-level studies was examined based on a field study along a transect from high to low marsh. Living foraminifera at Bombay Hook (Delaware, USA) are considered to be shallow infaunal (i.e., uppermost 10 cm). Peak concentrations were found at 1–10 cm in the high marsh, 1–5 cm in the intermediate marsh, and 3–5 cm in the low marsh. However, sporadic deep infaunal inputs in the low marsh could significantly contribute to the sub-fossil assemblage. In the upper 10 cm buried (death + sub-fossil) and living assemblages showed a strong correlation, and the seasonal pattern of the buried assemblage paralleled the living one, suggesting that the buried assemblage reflected the most recent reproductive inputs. The cumulative standing crop of each dominant species was used to estimate their contribution to the buried assemblage in order to assess if the community is vertically homogeneous and, therefore, if the infaunal production causes differential sub-surface enrichment. The results showed that a “shallow” (0–5 cm) infaunal contribution is able to explain much of the sub-fossil assemblage beneath the surface in the high and intermediate marsh plots. However, in the low marsh plot, the deep infaunal contribution was greatest and significantly affected the sub-fossil assemblage. Therefore, modern analogues for sea-level studies in mid-Atlantic North American marshes should include the uppermost 5 cm. The interval proposed for the high and intermediate marsh is thin enough that epifaunal species are not underrepresented and encompasses only ~8 years (based on burial rates) providing a high temporal resolution. Handling editor: J. Saros     

Live (Rose Bengal stained) and dead benthic foraminifera from the oxygen minimum zone of the Pakistan continental margin (Arabian Sea)

Live (Rose Bengal stained) and dead benthic foraminiferal communities (hard-shelled species only) from the Pakistan continental margin oxygen minimum zone (OMZ) have been studied in order to determine the relation between faunal composition and the oxygenation of bottom waters. Samples were taken from 136 m to 1870 m water depth during the intermonsoon season of 2003 (March–April). Live foraminiferal densities show a clear maximum in the first half centimetre of the sediment only few specimens are found down to 4 cm depth. The faunas exhibit a clear zonation across the Pakistan margin OMZ. Down to 500 m water depth, Uvigerina ex gr. U. semiornata and Bolivina aff. B. dilatata dominate the assemblages. These taxa are largely restricted to the upper cm of the sediment. They are adapted to the very low bottom-water oxygen values (≈ 0.1 ml/l in the OMZ core) and the extremely high input of organic carbon on the upper continental slope. The lower part of the OMZ is characterised by cosmopolitan faunas, containing also some taxa that in other areas have been described in deep infaunal microhabitats. The contrast between faunas typical for the upper part of the OMZ, and cosmopolitan faunas in the lower part of the OMZ, may be explained by a difference in the stability of dysoxic conditions over geological time periods. The core of the OMZ has been characterised by prolonged periods of stable, strongly dysoxic conditions. The lower part of the OMZ, on the contrary, has been much more variable over time-scales of 1000s and 10,000 years because of changes in surface productivity and a fluctuating intensity of NADW circulation. We suggest that, as a consequence, well-adapted, shallow infaunal taxa occupy the upper part of the OMZ, whereas in the lower part of the OMZ, cosmopolitan deep infaunal taxa have repeatedly colonised these more intermittent low oxygen environments.     

Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes

Interactions among microbes and stratification across depths are both believed to be important drivers of microbial communities, though little is known about how microbial associations differ between and across depths. We have monitored the free-living microbial community at the San Pedro Ocean Time-series station, monthly, for a decade, at five different depths: 5 m, the deep chlorophyll maximum layer, 150 m, 500 m and 890 m (just above the sea floor). Here, we introduce microbial association networks that combine data from multiple ocean depths to investigate both within- and between-depth relationships, sometimes time-lagged, among microbes and environmental parameters. The euphotic zone, deep chlorophyll maximum and 890 m depth each contain two negatively correlated ‘modules'' (groups of many inter-correlated bacteria and environmental conditions) suggesting regular transitions between two contrasting environmental states. Two-thirds of pairwise correlations of bacterial taxa between depths lagged such that changes in the abundance of deeper organisms followed changes in shallower organisms. Taken in conjunction with previous observations of seasonality at 890 m, these trends suggest that planktonic microbial communities throughout the water column are linked to environmental conditions and/or microbial communities in overlying waters. Poorly understood groups including Marine Group A, Nitrospina and AEGEAN-169 clades contained taxa that showed diverse association patterns, suggesting these groups contain multiple ecological species, each shaped by different factors, which we have started to delineate. These observations build upon previous work at this location, lending further credence to the hypothesis that sinking particles and vertically migrating animals transport materials that significantly shape the time-varying patterns of microbial community composition.     

Diatom assemblages in sediments of Lake Juusa, Southern Estonia with an assessment of their habitat

Diatom analysis of surface sediments and two sediment cores from different sedimentation areas of a small closed lake was undertaken with the aim of acquiring knowledge on the dependence of the distribution of diatom assemblages on lake bathymetry. Lake Juusa was selected for the study because we have for this lake a large data set about the lithological composition of sediments and macrofossil and cladoceran records for the Holocene. A high carbonate content (20–60%) in the sediment sequence indicates high carbonacity and relatively stable pH values during the Holocene. On the basis of comprehensive analysis, abrupt water-level fluctuations and changes in the trophic status were established. Results of this study showed that the fluctuations of the water-level were the leading factor determining the habitats of diatom assemblages in the lake. In the surface sediment samples planktonic species such as Cyclotella spp., Stephanodiscus spp. and Aulacoseira spp. had a depth optimum at 3–4 m and the most abundant periphytic taxa were distributed mostly at depths shallower than 3.5 m. The same regularity was established in sediment cores where a good correlation between planktonic species and lake water depth was found in sediments accumulated at water depths >4 m. Lake Juusa appears to be a proper site for detailed environmental reconstructions over the Holocene, and the results will give us a good opportunity to analyse the history of water-level fluctuations in other small Estonian lakes. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: K. Martens     

Poliovirus retention in 75-cm soil cores after sewage and rainwater application.

The adsorption rate of a guanidine-resistant strain of poliovirus LSc 2ab was measured in Long Island soils with in situ field cores (10.1 by 75 cm). The test virus was chosen because it exhibited soil adsorption and elution characteristics of a number of non-polioviruses. After the inoculation of cores with seeded sewage effluent at a 1-cm/h infiltration rate, cores were extracted, fractionated, and analyzed for total plaque-forming units per each 5-cm fraction. The results showed that 77% of the viruses were adsorbed in the first 5 cm of soil. An additional 11% were found in the 5- to 10-cm fraction, and a total of 96% of the viruses were adsorbed by 25 cm. The remaining 4% were uniformly distributed over the next 50 cm of soil, with a minimum of 0.23% in each soil section. Few viruses (< 0.22%) were observed in core filtrates. Analysis of the viral distribution pattern in seeded cores, after an application of a single rinse of either sewage effluent or rainwater, indicated that large-scale viral mobilization was absent. However, localized areas of viral movement were noted in both of the rinsed cores, with the rainwater-rinsed cores exhibiting more expensive movement. All mobilized viruses were resorbed at lower core depths.     

Biostratigraphie,paléoécologie et zones d’acmé des foraminifères planctoniques au passage Crétacé-Paléogène dans la Téthys (Tunisie et Espagne) et l’Atlantique (France)

Biostratigraphical high-resolution analyses and quantitative data confirm that deposition is continuous across the K-Pg transition in several sections in Tunisia (El Kef, stratotype section) and Spain (Agost and Caravaca sections) located in the Tethyan realm and the Bidart sections in the Atlantic realm, without any relevant hiatus. The Upper Maastrichtian assemblages of planktic foraminifera from these sections are largely dominated by small biserial heterohelicids. They are associated to common species having planispiral test (i.e. globigerinelloids), trochospiral test (i.e. hedbergellids, rugoglobigerinids globotruncanids), to rare triserial heterohelicids (i.e. guembelitriids) and trochospiral species showing tubulospines (i.e. schackoinids). Stratigraphical ranges of these diverse taxa through the late Maastrichtian in the Tethyan and Atlantic realms show very few changes in the planktonic foraminiferal assemblages and most of the species are present in the Abathomphalus mayaroensis biozone. By our high-resolution sampling and the intensive research for the A. mayaroensis index species in the uppermost Maastrichtian samples, we confirm that this species is omnipresent up to the top of the Maastrichtian. Therefore, A. mayaroensis is present in almost all samples which are late Maastrichtian in age, but this species became very scarce in the uppermost Maastrichtian samples. This scarceness could be due to a climate cooling. A sharp decrease in relative abundance of the deep dwellers species, like as Abathomphalus intermedius and A. mayaroensis as well as in other keeled globotruncanids is observed at the studied sections from the Tethyan realm (indicative of low latitude) across the latest Maastrichtian. At the K/Pg boundary, all the globotruncanids disappeared. They are considered specialists living in tropical-subtropical deep seawater habitat. At this boundary, large and ornate heterohelicids also disappeared. Therefore, all the studied sections show that about 90 % of the Maastrichtian species became extinct according to a catastrophic mass extinction pattern. Only about 10 % crossed the K/Pg boundary and survived during the earliest Danian. The minor difference in the number of disappeared taxa is related to their latitude location or environment paleodepth. The changes in the species relative abundance, observed in the successive planktic foraminiferal assemblages, make it possible to recognize the Acme-stage 0 typical of the upper Maastrichtian interval. It is characterized by the highest species richness of Globotruncanids and heterohelicids specialists of tropical to subtropical marine conditions, the Acme-stage 1 typical of the Guembelitria cretacea Zone, and in particular of the Hedbergella holmdelensis Subzone dominated by “opportunists” species belonging to Guembelitria, the Acme-stage 2 which corresponds to the Pv. eugubina Zone dominated mainly by specimens belonging to Palaeoglobigerina and Parvularugoglobigerina and the Acme-stage 3 which characterizes mainly the Ps. pseudobulloides Zone dominated by biserial species belonging to Chiloguembelina and Woodringina.     

From near extinction to recovery: Late Triassic to Middle Jurassic ammonoid shell geometry

The Triassic–Jurassic extinction resulted in the near demise of the ammonoids. Based on a survey of ammonoid expansion rates, coiling geometry and whorl shape, we use the Raup accretionary growth model to outline a universal morphospace for planispiral shell geometry. We explore the occupation of that planispiral morphospace in terms of both breadth and density of occupation in addition to separately reviewing the occurrence of heteromorphs. Four intervals are recognized: pre‐extinction (Carnian to Rhaetian); aftermath (Hettangian); post‐extinction (Sinemurian to Aalenian) and recovery (Bajocian to Callovian). The pre‐extinction and recovery intervals show maximum disparity. The aftermath is marked by the disappearance of heteromorphs and a dramatic reduction in the range of planispiral morphologies to a core area of the morphospace. It is also characterized by an expansion into an evolute, slowly expanding part of the morphospace that was not occupied prior to the extinction and is soon abandoned during the post‐extinction interval. Aftermath and post‐extinction ammonoid data show a persistent negative correlation whereby rapid expansion rates are associated with narrow umbilical widths and often compressed whorls. The permanently occupied core area of planispiral morphospace represents generalist demersals whose shells were probably optimizing both hydrodynamic efficiency and shell stability. All other parts of the planispiral morphospace, and the pelagic modes of life the shells probably exploited, were gradually reoccupied during the post‐extinction interval. Planispiral adaptation was by diffusion away from the morphospace core rather than by radical jumps. Recovery of disparity was not achieved until some 30 Myr after the extinction event.     

SPI-ing on the seafloor: characterising benthic systems with traditional and in situ observations

This work aimed to show that the sea bed of two environmentally-different regions of the North Sea varies both spatially and temporally with respect to their biological communities and bioturbation characteristics. The two contrasting sites studied were north of the Dogger Bank (ND) (85 m) and the Oyster Grounds (OG) (45 m). The physical environment varied between and within sites, mainly influenced by sediment chlorophyll a content and water temperature. Our data revealed that the depth of the apparent Redox Potential Discontinuity (aRPD) layer at OG varied between 2.2 cm in February and 6.5 cm in October; evidence of bioturbation activity (e.g., feeding voids) was observed within the sediment profile. In contrast, at the ND site the aRPD values ranged from 1.7 cm in February to 2.5 cm in May and feeding voids and infaunal burrows were restricted to sediment depths far shallower than those observed at OG. Communities at ND were dominated by a number of surficial-sediment dwelling polychaete species (e.g., Notomastus latericeus, capitellids) while those of OG were dominated by the brittlestar Amphiura filiformis, together with significant numbers of deeper-dwelling taxa such as the ghost shrimp Callianassa subterranea and the bivalve mollusc Corbula gibba. Our data imply that regions of the North Sea which experience dissimilar environmental conditions not only possess different infaunal communities but also contrasting seasonal fluctuations and bioturbation capacities. The ecological implications of these findings, including inferences for carbon and nutrient cycling, are discussed in relation to the wider North Sea ecosystem.     

The dark side of the hyporheic zone: depth profiles of nitrogen and its processing in stream sediments

1. Although it is well known that sediments can be hot spots for nitrogen transformation in streams, many previous studies have confined measurements of denitrification and nitrate retention to shallow sediments (<5 cm deep). We determined the extent of nitrate processing in deeper sediments of a sand plains stream (Emmons Creek) by measuring denitrification in core sections to a depth of 25 cm and by assessing vertical nitrate profiles, with peepers and piezometers, to a depth of 70 cm. 2. Denitrification rates of sediment slurries based on acetylene block were higher in shallower core sections. However, core sections deeper than 5 cm accounted for 68% of the mean depth‐integrated denitrification rate. 3. Vertical hydraulic gradient and vertical profiles of pore water chloride concentration suggested that deep ground water upwelled through shallow sediments before discharging to the stream channel. The results of a two‐source mixing model based on chloride concentrations suggested that the hyporheic zone was very shallow (<5 cm) in Emmons Creek. 4. Vertical profiles showed that nitrate concentration in shallow ground water was about 10–60% of the nitrate concentration of deep ground water. The mean nitrate concentrations of deep and shallow ground water were 2.17 and 0.73 mg NO₃‐N L^?1, respectively. 5. Deep ground water tended to be oxic (6.9 mg O₂ L^?1) but approached anoxia (0.8 mg O₂ L^?1) after passing through shallow, organic carbon‐rich sediments, which suggests that the decline in the nitrate concentrations of upwelling ground water was because of denitrification. 6. Collectively, our results suggest that there is substantial nitrate removal occurring in deep sediments, below the hyporheic zone, in Emmons Creek. Our findings suggest that not accounting for nitrate removal in deep sediments could lead to underestimates of nitrogen processing in streams and catchments.     

Seasonal and microhabitat influences on diatom assemblages and their representation in sediment traps and surface sediments from adjacent High Arctic lakes: Cape Bounty,Melville Island,Nunavut

The spatial (i.e. microhabitat) and temporal (i.e. seasonal) characteristics of diatom assemblages in adjacent High Arctic lakes were studied intensively June–August 2004. These baseline data are used to improve understanding of modern diatom community dynamics, as well to inform paleoenvironmental reconstructions. Diatoms were collected approximately weekly through the melt season from each principal benthic substrate (moss/macrophyte, rock scrapes, littoral sediment), plankton, and sediment traps, and were compared to the uppermost 0.5 cm of a surface core obtained from the deepest part of the lake where sediment cores are routinely collected. Water samples were collected concurrently with diatom samples to investigate species–environment relationships. The lakes share approximately half of their common taxa, the most abundant overall in both lakes being small Cyclotella species. Results of detrended correspondence analysis (DCA) indicate that the largest gradient in species turnover existed between benthic and planktonic communities in both lakes, and that sediment trap and the surface core top samples most closely resemble the planktonic assemblage, with an additional contribution from the lotic environment. Our results indicate clear micro-spatial controls on species assemblages and a degree of disconnection between the benthos and deep lake sediments that manifests as an under-representation of benthic taxa in deep lake surface sediments. These findings are particularly relevant in the context of interpreting the paleoenvironmental record and assessing ecosystem sensitivity to continued climate change.     

Ammonia-oxidizing archaea have similar power requirements in diverse marine oxic sediments

Energy/power availability is regarded as one of the ultimate controlling factors of microbial abundance in the deep biosphere, where fewer cells are found in habitats of lower energy availability. A critical assumption driving the proportional relationship between total cell abundance and power availability is that the cell-specific power requirement keeps constant or varies over smaller ranges than other variables, which has yet to be validated. Here we present a quantitative framework to determine the cell-specific power requirement of the omnipresent ammonia-oxidizing archaea (AOA) in eight sediment cores with 3–4 orders of magnitude variations of organic matter flux and oxygen penetration depth. Our results show that despite the six orders of magnitude variations in the rates and power supply of nitrification and AOA abundances across these eight cores, the cell-specific power requirement of AOA from different cores and depths overlaps within the narrow range of 10⁻¹⁹–10⁻¹⁷ W cell⁻¹, where the lower end may represent the basal power requirement of microorganisms persisting in subseafloor sediments. In individual cores, AOA also exhibit similar cell-specific power requirements, regardless of the AOA population size or sediment depth/age. Such quantitative insights establish a relationship between the power supply and the total abundance of AOA, and therefore lay a foundation for a first-order estimate of the standing stock of AOA in global marine oxic sediments.Subject terms: Microbial ecology, Biogeochemistry, Water microbiology     

Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico

Marine sediments of coastal margins are important sites of carbon sequestration and nitrogen cycling. To determine the metabolic potential and structure of marine sediment microbial communities, two cores were collected each from the two stations (GMT at a depth of 200 m and GMS at 800 m) in the Gulf of Mexico, and six subsamples representing different depths were analyzed from each of these two cores using functional gene arrays containing approximately 2,000 probes targeting genes involved in carbon fixation; organic carbon degradation; contaminant degradation; metal resistance; and nitrogen, sulfur, and phosphorous cycling. The geochemistry was highly variable for the sediments based on both site and depth. A total of 930 (47.1%) probes belonging to various functional gene categories showed significant hybridization with at least 1 of the 12 samples. The overall functional gene diversity of the samples from shallow depths was in general lower than those from deep depths at both stations. Also high microbial heterogeneity existed in these marine sediments. In general, the microbial community structure was more similar when the samples were spatially closer. The number of unique genes at GMT increased with depth, from 1.7% at 0.75 cm to 18.9% at 25 cm. The same trend occurred at GMS, from 1.2% at 0.25 cm to 15.2% at 16 cm. In addition, a broad diversity of geochemically important metabolic functional genes related to carbon degradation, nitrification, denitrification, nitrogen fixation, sulfur reduction, phosphorus utilization, contaminant degradation, and metal resistance were observed, implying that marine sediments could play important roles in biogeochemical cycling of carbon, nitrogen, phosphorus, sulfate, and various metals. Finally, the Mantel test revealed significant positive correlations between various specific functional genes and functional processes, and canonical correspondence analysis suggested that sediment depth, PO(4)(3-), NH(4)(+), Mn(II), porosity, and Si(OH)(4) might play major roles in shaping the microbial community structure in the marine sediments.