Search

Significance A substantial component of the global nitrogen cycle is the production of biologically inaccessible dinitrogen attributed to anaerobic denitrification by prokaryotes. Recent evidence identified a eukaryote, foraminifera, as new key players in this “loss” of bioavailable nitrogen. The evolution of denitrification in eukaryotes is a rare event, and the genetic mechanisms of the denitrification pathway in foraminifera are just starting to be elucidated. We present large-scale sequencing analyses of 10 denitrifying foraminiferal species, which reveals the high conservation of the foraminiferal denitrification pathway. We further find evidence for a complementation of denitrification by the foraminiferal microbiome. Together, these findings provide insights into the early evolution of a previously overlooked component in the marine nitrogen cycle. Abstract: Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.

Phosphorus is essential for all living organisms, being a component of DNA and RNA and the energy carrier ATP. Phosphogenesis is a main sink of reactive phosphorus in the oceans. The present study reports the presence of intracellular dissolved inorganic phosphate (DIP) in benthic foraminifera from the Peruvian oxygen minimum zone (OMZ). The mean intracellular DIP concentration was 28 ± 3 mM; two to three orders-of-magnitude higher than in the ambient pore waters. The biological implications of the high intracellular phosphate enrichment may be related to the synthesis of polyphosphates or phospholipids for cell-membranes. The comparative genomics analysis of multiple species of foraminifera from different environments reveals that foraminifers encode the genes required for both phospholipid and polyphosphate metabolism. Rapid phosphogenesis and phosphorite formation associated with foraminiferal tests is hypothesized due to the pre-concentration of intracellular phosphate in these organisms. The results indicate that foraminifera may play a key and previously overlooked role in the global phosphorus cycle.

Heavy metal pollution originating from anthropogenic sources, e.g. mining, industry and extensive land use, is increasing in many parts of the world and influences coastal marine environments even after the source has ceased to pollute. The elevated input of heavy metals into the marine system potentially affects the biota because of their toxicity, persistence and bioaccumulation. An emerging tool for environmental applications is the heavy metal incorporation into foraminiferal calcite tests, which facilitates monitoring of anthropogenic footprints on recent and past environmental systems. The aim of this study was to investigate whether the incorporation of heavy metals into foraminifera is a direct function of their concentration in seawater. Culturing experiments with a mixture of dissolved chromium (Cr), manganese (Mn), nickel (Ni), copper (Cu), zinc (Zn), silver (Ag), cadmium (Cd), tin (Sn), mercury (Hg) and lead (Pb) in artificial seawater were carried out over a wide concentration range to assess the uptake of heavy metals by the nearshore foraminiferal species Ammonia aomoriensis, Ammonia batava and Elphidium excavatum. Seawater analyses revealed increasing concentrations for most metals between culturing phases and high metal concentrations in the beginning of the culturing phases due to sudden metal addition. Furthermore, a loss of metals during the culturing process was discovered by an offset between the added and the actual concentrations of the metals in seawater. Laser ablation ICP-MS (inductively coupled plasma mass spectrometry) analysis of the newly formed calcite revealed species-specific differences in the incorporation of heavy metals. The foraminiferal calcite of all three species exhibited Pb and Ag concentrations strongly correlated with concentrations in the seawater culturing medium (partition coefficients and standard deviation for Ag – Ammonia aomoriensis, 0.50 ± 0.02; Ammonia batava, 0.17 ± 0.01; Elphidium excavatum, 0.47 ± 0.04; for Pb – Ammonia aomoriensis, 0.39 ± 0.01; Ammonia batava, 0.52 ± 0.01; Elphidium excavatum, 0.91 ± 0.01). Ammonia aomoriensis further showed a correlation with Mn and Cu, A. batava with Mn and Hg, and E. excavatum with Cr and Ni and partially also with Hg. However, Zn, Sn and Cd showed no clear trend for the species studied, which in the case of Sn was maybe caused by the lack of variation in the seawater Sn concentration. The calibrations and the calculated partition coefficients render A. aomoriensis, A. batava and E. excavatum as natural archives that enable the determination of variations in some heavy metal concentrations in seawater in polluted and pristine environments.

Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown and the missing denitrification pathway components are elusive. Analysing transcriptomes and metagenomes of ten foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer of the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteracea, which harbour genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success within oxygen depleted habitats.Significance StatementA substantial component of the global nitrogen cycle is the production of biologically inaccessible dinitrogen attributed to anaerobic denitrification by prokaryotes. Recent evidence identified a eukaryote – foraminifera – as new key players in this ‘loss’ of bioavailable nitrogen. The evolution of denitrification in eukaryotes constitutes a rare event and the genetic mechanisms of the denitrification pathway in foraminifera are just starting to be elucidated. We present large-scale sequencing analyses of ten denitrifying foraminiferal species, which reveals the high conservation of the foraminiferal denitrification pathway. We further find evidence for a complementation of denitrification by the foraminiferal microbiome. Together, these findings provide novel insights on the early evolution of a previously overlooked component in the marine nitrogen cycle.

Supratidal sands are vitally important for coastal defence in the German Wadden Sea. They are less affected by human activities than other areas as they are located far off the mainland shore, touristical and commercial activities are generally prohibited. Therefore, supratidal sands are of high ecological interest. Nevertheless, the faunal inventory and distribution pattern of microorganisms on these sands were studied very little. The composition of living and dead foraminiferal assemblages was therefore investigated along a transect from the supratidal sand Japsand up to Hallig Hooge. Both assemblages were dominated by calcareous foraminifera of which Ammonia batava was the most abundant species. Elphidium selseyense and Elphidium williamsoni were also common in the living assemblage, but Elphidium williamsoni was comparably rare in the dead assemblage. The high proportions of Ammonia batava and Elphidium selseyense in the living assemblage arose from the reproduction season that differed between species. While Ammonia batava and Elphidium selseyense just finished their reproductive cycles, Elphidium williamsoni was just about to start. This was also confirmed by the size distribution patterns of the different species. The dead assemblage revealed 20 species that were not found in the living assemblage of which some were reworked from older sediments (e.g., Bucella frigida) and some were transported via tidal currents from other areas in the North Sea (e.g., Jadammina macrescens). The living foraminiferal faunas depicted close linkages between the open North Sea and the mainland. Key species revealing exchange between distant populations were Haynesina germanica, Ammonia batava and different Elphidium species. All these species share an opportunistic behaviour and are able to inhabit a variety of different environments; hence, they well may cope with changing environmental conditions. The benthic foraminiferal association from Japsand revealed that transport mechanisms via tides and currents play a major ecological role and strongly influence the faunal composition at this site.

Highlights • Foraminifera responded faster to environmental perturbations than macroorganisms. • Population densities doubled and Asterigerinata mamilla bloomed under stronger flow. • Excess of threshold values and changes to new ecosystems induce acme occurrences. Abstract Benthic foraminifera are deemed sensitive indicators of environmental conditions. Triggers and magnitudes of faunal response to environmental changes are yet poorly constrained. Benthic foraminiferal faunas were monitored annually at Ria Formosa (Algarve, Portugal) coastal lagoon since 2013. Distinct environmental changes were recognised during the monitoring period. The relocation of a tidal inlet in winter 2015 effected faster flushing, higher tidal levels, and stronger currents in the Esteiro do Ancão tidal channel. The epibenthic foraminiferal species Asterigerinata mamilla increased in abundance and the population densities of the whole fauna were double as high as before inlet relocation. Enhanced sediment redeposition was recorded and extensive polychaete colonies successively replaced firmground patches with oysters. The standing stock of the foraminiferal fauna declined in the next year due to food impoverishment, while the high hydraulic energy levels and high percentages of Asterigerinata mamilla maintained. Benthic foraminifera responded much faster to environmental perturbations than macroorganisms identifying them as powerful proxies in environmental studies.

Highlights • Investigations of the benthic foraminiferal distribution in the Elbe Estuary. • Low diverse assemblages are dominated by Ammonia species. • Low salinities and high-frequency dredging confines foraminiferal proliferation. • Over 40 years, changes in hydrodynamic conditions induced assemblage modifications. Abstract For the past 200 years, estuarine environments experienced intense and rapid environmental degradations due to human interventions. In addition, Global Changes are modifying the estuarine physiography, leading to a re-structuration of marginal marine benthic communities. The aim of this study is to document, the modern assemblage composition and the species-environment relations of benthic foraminifera upstream the Elbe Estuary (southern North Sea) and to observe what has changed since the first survey in 1981. For this purpose, a surface sampling was carried out from 22 stations along the transitional area of the Elbe Estuary. Living (rose-Bengal stained) and dead foraminiferal assemblages were analysed as well as hydrological and sedimentological parameters (such as salinity, pH, grain-size, and organic matter). Living faunas are characterized by very low densities and largely dominated by Ammonia species. Dead assemblages are more diverse and dominated by Ammonia aomoriensis, Haynesina germanica, and Cribroelphidium selseyense. Salinity and grain-size seem to be the major factors influencing foraminiferal distributions in the transitional area. Under the ongoing climate changes, future strategies will be taken to foster the application of benthic foraminifera as biomonitoring tool in the Elbe Estuary, via this baseline investigation.

A benthic isotope record has been measured for core SO75-26KL from the upper Portuguese margin (1099 m water depth) to monitor the response of thermohaline overturn in the North Atlantic during Heinrich events. Evaluating benthic δ18O in TS diagrams in conjunction with equilibrium δc fractionation implies that advection of Mediterranean outflow water (MOW) to the upper Portuguese margin was significantly reduced during the last glacial (< 15% compared to 30% today). The benthic isotope record along core SO75-26KL therefore primarily monitors variability of glacial North Atlantic conveyor circulation. The 14C-accelerator mass spectrometry ages of 13.54±.07 and 20.46±.12 ka for two ice-rafted detritus (IRD) layers in the upper core section and an interpolated age of 36.1 ka for a third IRD layer deeper in the core are in the range of published 14C ages for Heinrich events H1, H2, and H4. Marked depletion of benthic δ13C by 0.7–1.1‰ during the Heinrich events suggests reduced thermohaline overturn in the North Atlantic during these events. Close similarity between meltwater patterns (inferred from planktonic δ18O) at Site 609 and ventilation patterns (inferred from benthic δ13C) in core SO75-26KL implies coupling between thermohaline overturn and surface forcing, as is also suggested by ocean circulation models. Benthic δ13C starts to decrease 1.5–2.5 kyr before Heinrich events Hl and H4, fully increased values are reached 1.5–3 kyr after the events, indicating a successive slowdown of thermohaline circulation well before the events and resumption of the conveyor's full strength well after the events. Benthic δ13C changes in the course of the Heinrich events show subtle maxima and minima suggesting oscillatory behavior of thermohaline circulation, a distinct feature of thermohaline instability in numerical models. Inferrred gradual spin-up of thermohaline circulation after Hl and H4 is in contrast to abrupt wanning in the North Atlantic region that is indicated by sudden increases in Greenland ice core δ18O and in marine faunal records from the northern North Atlantic. From this we infer that thermohaline circulation can explain only in part the rapid climatic oscillations seen in glacial sections of the Greenland ice core record.

Heavy metal pollution from anthropogenic sources increasingly influence marine environments and biota because of their toxicity, persistence and bioaccumulation. Especially coastal environments act as natural catchments for anthropogenic pollutants because these areas are highly affected by industry, agriculture and urban sewage runoff. In nearly all natural environments that are harmed by heavy metal pollution, a combination of several pollutants occurs at the same time. In marginal seas and coastal areas, benthic foraminifera are common in meiofaunal associations, and they can be used as biomonitoring tool for changes in environmental parameters like temperature, salinity, or redox conditions. Furthermore, foraminifera take up heavy metals from the seawater and incorporate those into their carbonate shells during calcification. Moreover, foraminifera have a short life cycle and can therefore react immediately to contaminations of the environment. Here, we will present results from culturing studies with Ammonia aomoriensis, Elphidium excavatum and Ammonia batava addressing the relationship of heavy metal concentration in the seawater and in the foraminiferal tests. The partitioning factor between the ambient seawater and the calcium carbonate of the foraminifera is constrained by continuous water monitoring and laser ablation ICP – MS measurements on single chambers grown during the experiment in a manipulated culturing medium. The foraminifera were exposed to a combination of ten different heavy metals over a range of concentrations comparable to current conditions in medium to high pollutedhigh-polluted areas. A correlation between the heavy metal concentration in the culture medium and in the foraminiferal calcite was recognised for several heavy metals (e.g. Cd, Cr, Pb). Once the carbonate/seawater metal partitioning coefficients are constrained with certainty, investigations of the chemistry of benthic foraminiferal shells offer an advanced and reliable method to monitor short-term changes in the concentrations and bioavailability of toxic elements in seawater.

Sedimentological, geochemical and benthic foraminiferal proxies were used to interpret changes of depositional environments in a mud entrapment inside the Guadiana River paleo-valley, northern Gulf of Cadiz, to understand the temporal variability of fluvial flooding events and to detect patterns of latitudinal climatic variability in western Iberia. The period between ca. 5800 and ca. 1250 cal yr BP was characterized by slowly accumulating coarse-grained sediments, high content of biogenic sand components, and high abundances of shallow-water benthic foraminiferal species. After ca. 1250 cal yr BP, the sedimentary environment was dominated by fine-grained sediments, with high abundances of opportunistic benthic foraminiferal species and successful colonizers, and high values of geochemical ratios indicative of enhanced terrigenous supply. Sedimentation rates increased drastically over the last ca. 500 years. The genesis of these environments was mainly driven by the variable frequency of fluvial flooding events driven by the regional climate variability. Low terrigenous sediment input under dry conditions prevailed in the older sedimentary unit. Flood frequency and terrigenous sediment supply increased during the younger unit. The variability of the North Atlantic Oscillation at centennial scales highly influenced the sediment supply during the last ca. 500 years, with high terrigenous supply during negative NAO conditions. Our results corroborate an N-S gradient along the Atlantic Iberia during middle and late Holocene, with more humid conditions in the northwestern and drier conditions towards the southeast. The gradient weakened over the past ca. 500 years, with increased rainfalls and flood events during the Little Ice Age., This study was made possible by the CADISED (Cadiz Shelf Sediment Depocentres) survey (MARUM research cruise POS482, Germany), and was also supported by projects UID/0350/2020 CIMA of the Portuguese Science Foundation (FCT) and CGL2011-30302-C02-02 and CTM2017-88237-P of the Spanish Ministry of Economy and Competitiveness. Isabel Mendes also thanks to FCT for Research Assistant contract DL57/2016/CP1361/CT0009.

Background: Clinical trials of bone marrow cell–based therapies after acute myocardial infarction (MI) have produced mostly neutral results. Treatment with specific bone marrow cell–derived secreted proteins may provide an alternative biological approach to improving tissue repair and heart function after MI. We recently performed a bioinformatic secretome analysis in bone marrow cells from patients with acute MI and discovered a poorly characterized secreted protein, EMC10 (endoplasmic reticulum membrane protein complex subunit 10), showing activity in an angiogenic screen. Methods: We investigated the angiogenic potential of EMC10 and its mouse homolog (Emc10) in cultured endothelial cells and infarcted heart explants. We defined the cellular sources and function of Emc10 after MI using wild-type, Emc10 -deficient, and Emc10 bone marrow–chimeric mice subjected to transient coronary artery ligation. Furthermore, we explored the therapeutic potential of recombinant Emc10 delivered by osmotic minipumps after MI in heart failure–prone FVB/N mice. Results: Emc10 signaled through small GTPases, p21-activated kinase, and the p38 mitogen-activated protein kinase (MAPK)–MAPK-activated protein kinase 2 (MK2) pathway to promote actin polymerization and endothelial cell migration. Confirming the importance of these signaling events in the context of acute MI, Emc10 stimulated endothelial cell outgrowth from infarcted mouse heart explants via p38 MAPK-MK2. Emc10 protein abundance was increased in the infarcted region of the left ventricle and in the circulation of wild-type mice after MI. Emc10 expression was also increased in left ventricular tissue samples from patients with acute MI. Bone marrow–derived monocytes and macrophages were the predominant sources of Emc10 in the infarcted murine heart. Emc10 KO mice showed no cardiovascular phenotype at baseline. After MI, however, capillarization of the infarct border zone was impaired in KO mice, and the animals developed larger infarct scars and more pronounced left ventricular remodeling compared with wild-type mice. Transplanting KO mice with wild-type bone marrow cells rescued the angiogenic defect and ameliorated left ventricular remodeling. Treating FVB/N mice with recombinant Emc10 enhanced infarct border-zone capillarization and exerted a sustained beneficial effect on left ventricular remodeling. Conclusions: We have identified Emc10 as a previously unknown angiogenic growth factor that is produced by bone marrow–derived monocytes and macrophages as part of an endogenous adaptive response that can be enhanced therapeutically to repair the heart after MI.

Rapid changes in ocean circulation and climate have been observed in marine-sediment and ice cores over the last glacial period and deglaciation, highlighting the non-linear character of the climate system and underlining the possibility of rapid climate shifts in response to anthropogenic greenhouse gas forcing. To date, these rapid changes in climate and ocean circulation are still not fully explained. One obstacle hindering progress in our understanding of the interactions between past ocean circulation and climate changes is the difficulty of accurately dating marine cores. Here, we present a set of 92 marine sediment cores from the Atlantic Ocean for which we have established age-depth models that are consistent with the Greenland GICC05 ice core chronology, and computed the associated dating uncertainties, using a new deposition modeling technique. This is the first set of consistently dated marine sediment cores enabling paleoclimate scientists to evaluate leads/lags between circulation and climate changes over vast regions of the Atlantic Ocean. Moreover, this data set is of direct use in paleoclimate modeling studies., Design Type(s)modeling and simulation objective • data collection and processing objective • source-based data analysis objectiveMeasurement Type(s)age-depth modelTechnology Type(s)computational modeling techniqueFactor Type(s)geographic location • depthSample Characteristic(s)Atlantic Ocean • marine sediment Machine-accessible metadata file describing the reported data (ISA-Tab format)

Pleistocene and late Pliocene benthic foraminifera from the Manihiki Plateau (southwestern tropical Pacific) were studied at piston-core 34KL. A new benthic foraminiferal biozonation is proposed. It comprises the Nodogenerina sagriensis Partial Range Zone from core base to 566.5 cm and the Fissurina seminiformis Partial Range Zone from this level to core top. The boundary is defined by the last occurence of Nodogenerina sagriensis which is time equivalent to the ‘Stilostomella extinction’ in the Eastern Atlantic. High abundances of Cibicidoides wuellerstorfi indicate a strong influence of near-bottom currents. The absence of high-productivity sensitive species reveals a low flux of organic matter to the sea floor from which a considerable amount is adduced by lateral advection.

Benthic foraminifera have proven to be suitable for environmental monitoring because of their high levels of adaptation, small size and high abundance in Recent sediments and the fossil record. Foraminifera are scarcely used in monitoring studies because a standardization of methods has not been achieved to date. When particular methods were introduced and why they were applied is often hidden in the literature. This paper reviews the development of field and laboratory methods, their constraints and consequences for faunal and data analyses. Multiple and box corers and some grab samplers retrieve reliable surface sediment samples provided the bow wave is minimized as the sampler approaches the sea floor. Most disturbances are created during handling of the unit on deck and subsampling. Ethanol for preservation, rose Bengal as vital stain and a mesh size of 63 µm to wash foraminiferal samples are used extensively. Faunal analyses of a larger size fraction are occasionally necessary. The fractions >125 µm and >150 µm are often preferentially chosen even though this may artificially reduce specimen numbers and faunal diversity. Generally, a much lower level of common practice prevails in sample preparation and faunal analyses than in sampling or laboratory procedures. Increasing preference has been given to quantitative methods and the acquisition of independently revisable census data during recent decades.

Living benthic foraminiferal assemblages were monitored between January and July 2004 in the Kiel Bight, Baltic Sea. Phytoplankton blooms and the deposition of organic detritus were depicted by fluorometer hydro casts and pigment concentrations in surface sediments. Three depositional pulses of organic matter were identified by high phytoplankton concentrations above the sea floor and elevated pigment concentrations in the surface sediment. The foraminiferal assemblage composition remained rather constant but the population density of Elphidium excavatum clavatum showed a two- to six-fold increase within a few days after organic detritus deposition. The foraminiferal assemblage composition was compared to earlier studies in this area. Elphidium excavatum, Ammotium cassis and E. incertum dominated the living fauna in the 1960s and 1970s. The recent survey revealed a predominance of E. excavatum subspecies (more than 90% of the living assemblage). The average population densities were six times higher than in the 1970s. Data structure and model calculations suggested that E. excavatum clavatum is able to reproduce rapidly, with high offspring numbers at elevated food supply. The diminution of A. cassis has occurred in Kiel Bight during the last ten years and was most likely induced by a period of low deep-water salinities in the early 1990s.

Past ocean temperatures and salinities are successfully approximated from combined stable oxygen isotopes (δ18O) and Mg / Ca measurements in fossil foraminiferal tests. To further refine this approach, we collected living planktic foraminifers by net sampling and pumping of seasurface waters from the Caribbean Sea, the eastern Gulf of Mexico, and Florida Straits. Analyses of δ18O and Mg / Ca in eight living planktic species (Globigerinoides sacculifer, Orbulina universa, Neogloboquadrina dutertrei, Pulleniatina obliquiloculata, Globorotalia menardii, Globorotalia ungulata, Globorotalia truncatulinoides and Globorotalia tumida) were compared to measured in situ properties of the ambient seawater (temperature, salinity and δ18Oseawater) and fossil tests of underlying surface sediments. "Vital effects" such as symbiont activity and test growth cause δ18O disequilibria to the ambient seawater and a large scatter in foraminiferal Mg / Ca. Overall, ocean temperature is the most prominent environmental influence on δ18Ocalcite and Mg / Ca. Enrichment of the heavier δ18 isotope in living specimens below the mixed layer and in fossil tests are clearly related to lowered in situ temperatures and gametogenic calcification. Mg / Ca-based temperature estimates of G. sacculifer indicate seasonal maximum accumulation rates on the seafloor in early spring (March) at Caribbean stations and later in the year (May) in the Florida Straits, related to the respective mixed layer temperatures of ~ 26 °C. Notably, G. sacculifer reveals a positive linear relationship between foraminiferal derived δ18Oseawater estimates and both measured in situ δ18Oseawater and salinity. Our results affirm the applicability of existing δ18O and Mg / Ca calibrations for the reconstruction of past ocean temperatures and δ18Oseawater reflecting salinity due to the convincing accordance of proxy data in both living and fossil foraminifers, and in situ environmental parameters. Large "vital effects" and seasonally varying proxy signals, however, need to be taken into account.

Apolipoprotein A-1 (Apo A-1) plays an important role in lipid transfer and obesity. Chemical unfolding of α-helical Apo A-1 is induced with guanidineHCl and monitored with differential scanning calorimetry (DSC) and CD spectroscopy. The unfolding enthalpy and the midpoint temperature of unfolding decrease linearly with increasing guanidineHCl concentration, caused by the weak binding of denaturant. At room temperature, binding of 50–60 molecules guanidineHCl leads to a complete Apo A-1 unfolding. The entropy of unfolding decreases to a lesser extent than the unfolding enthalpy. Apo A-1 chemical unfolding is a dynamic multi-state equilibrium that is analysed with the Zimm-Bragg theory modified for chemical unfolding. The chemical Zimm-Bragg theory predicts the denaturant binding constant KD and the protein cooperativity σ. Chemical unfolding of Apo A-1 is two orders of magnitude less cooperative than thermal unfolding. The free energy of thermal unfolding is ~0.2 kcal/mol per amino acid residue and ~1.0 kcal/mol for chemical unfolding at room temperature. The Zimm-Bragg theory calculates conformational probabilities and the chemical Zimm-Bragg theory predicts stretches of α-helical segments in dynamic equilibrium, unfolding and refolding independently and fast.

Highlights • High abundance of active anaerobic methanotrophs in sediments of the blowout crater suggests adaptation to methane seepage within at most two decades. • Fast exchange processes in permeable surface sediments prevent sulfate depletion and probably methane-derived carbonate precipitation. • Methane seepage impacts isotopic and assemblage composition of benthic foraminifera. Abstract Methane emissions from marine sediments are partly controlled by microbial anaerobic oxidation of methane (AOM). AOM provides a long-term sink for carbon through precipitation of methane-derived authigenic carbonates (MDAC). Estimates on the adaptation time of this benthic methane filter as well as on the establishment of related processes and communities after an onset of methane seepage are rare. In the North Sea, considerable amounts of methane have been released since 20 years from a man-made gas blowout offering an ideal natural laboratory to study the effects of methane seepage on initially “pristine” sediment. Sediment cores were taken from the blowout crater and a reference site (50 m distance) in 2011 and 2012, respectively, to investigate porewater chemistry, the AOM community and activity, the presence of authigenic carbonates, and benthic foraminiferal assemblages. Potential AOM activity (up to 3060 nmol cm−3 sediment d−1 or 375 mmol m−2 d−1) was detected only in the blowout crater up to the maximum sampling depth of 18 cm. CARD-FISH analyzes suggest that monospecific ANME-2 aggregates were the only type of AOM organisms present, showing densities (up to 2.2*107 aggregates cm−3) similar to established methane seeps. No evidence for recent MDAC formation was found using stable isotope analyzes (δ13C and δ18O). In contrast, the carbon isotopic signature of methane was recorded by the epibenthic foraminifer Cibicides lobatulus (δ13C −0.66‰). Surprisingly, the foraminiferal assemblage in the blowout crater was dominated by Cibicides and other species commonly found in the Norwegian Channel and fjords, indicating that these organisms have responded sensitively to the specific environmental conditions at the blowout. The high activity and abundance of AOM organisms only at the blowout site suggests adaptation to a strong increase in methane flux in the order of at most two decades. High gas discharge dynamics in permeable surface sediments facilitate fast sulfate replenishing and stimulation of AOM. The accompanied prevention of total alkalinity build-up in the porewater thereby appears to inhibit the formation of substantial methane-derived authigenic carbonate at least within the given time window.

Present day oceans are well ventilated, with the exception of mid-depth oxygen minimum zones (OMZs) under high surface water productivity, regions of sluggish circulation, and restricted marginal basins. In the Mesozoic, however, entire oceanic basins transiently became dysoxic or anoxic. The Cretaceous ocean anoxic events (OAEs) were characterised by laminated organic-carbon rich shales and low-oxygen indicating trace fossils preserved in the sedimentary record. Yet assessments of the intensity and extent of Cretaceous near-bottom water oxygenation have been hampered by deep or long-term diagenesis and the evolution of marine biota serving as oxygen indicators in today's ocean. Sedimentary features similar to those found in Cretaceous strata were observed in deposits underlying Recent OMZs, where bottom-water oxygen levels, the flux of organic matter, and benthic life have been studied thoroughly. Their implications for constraining past bottom-water oxygenation are addressed in this review. We compared OMZ sediments from the Peruvian upwelling with deposits of the late Cenomanian OAE 2 from the north-west African shelf. Holocene laminated sediments are encountered at bottom-water oxygen levels of < 7 μmol kg−1 under the Peruvian upwelling and < 5 μmol kg−1 in California Borderland basins and the Pakistan Margin. Seasonal to decadal changes of sediment input are necessary to create laminae of different composition. However, bottom currents may shape similar textures that are difficult to discern from primary seasonal laminae. The millimetre-sized trace fossil Chondrites was commonly found in Cretaceous strata and Recent oxygen-depleted environments where its diameter increased with oxygen levels from 5 to 45 μmol kg−1. Chondrites has not been reported in Peruvian sediments but centimetre-sized crab burrows appeared around 10 μmol kg−1, which may indicate a minimum oxygen value for bioturbated Cretaceous strata. Organic carbon accumulation rates ranged from 0.7 and 2.8 g C cm−2 kyr−1 in laminated OAE 2 sections in Tarfaya Basin, Morocco, matching late Holocene accumulation rates of laminated Peruvian sediments under Recent oxygen levels below 5 μmol kg−1. Sediments deposited at > 10 μmol kg−1 showed an inverse exponential relationship of bottom-water oxygen levels and organic carbon accumulation depicting enhanced bioirrigation and decomposition of organic matter with increased oxygen supply. In the absence of seasonal laminations and under conditions of low burial diagenesis, this relationship may facilitate quantitative estimates of palaeo-oxygenation. Similarities and differences between Cretaceous OAEs and late Quaternary OMZs have to be further explored to improve our understanding of sedimentary systems under hypoxic conditions.

An important tool for deep-sea temperature reconstruction is Mg/Ca paleothermometry applied to benthic foraminifera. Foraminifera of the genus Melonis appear to be promising candidates for temperature reconstructions due to their wide geographical and bathymetric distribution, and their infaunal habitat, which was suggested to reduce secondary effects from carbonate ion saturation (Δ[CO3 2−]). Here, we make substantial advances to previous calibration efforts and present new multi-lab Mg/Ca data for Melonis barleeanum and Melonis pompilioides from more than one hundred core top samples spanning in situ bottom temperatures from −1 to 16 °C, coupled with morphometric analyses of the foraminifer tests. Both species and their morphotypes seem to have a similar response of Mg/Ca to growth temperature. Compilation of new and previously published data reveals a linear dependence of temperature on Mg/Ca, with a best fit of Mg/Ca (mmol/mol) = 0.113 ± 0.005 ∗ BWT (°C) + 0.792 ± 0.036 (r2 = 0.81; n = 120; 1σ SD). Salinity, bottom water Δ[CO3 2−], and varying morphotypes have no apparent effect on the Mg/Ca-temperature relationship, but pore water Δ[CO3 2−] might have had an influence on some of the samples from the tropical Atlantic.

Environmental histories that span the last full glacial cycle and are representative of regional change in Australia are scarce, hampering assessment of environmental change preceding and concurrent with human dispersal on the continent ca. 47,000 years ago. Here we present a continuous 150,000-year record offshore south-western Australia and identify the timing of two critical late Pleistocene events: wide-scale ecosystem change and regional megafaunal population collapse. We establish that substantial changes in vegetation and fire regime occurred ∼70,000 years ago under a climate much drier than today. We record high levels of the dung fungus Sporormiella, a proxy for herbivore biomass, from 150,000 to 45,000 years ago, then a marked decline indicating megafaunal population collapse, from 45,000 to 43,100 years ago, placing the extinctions within 4,000 years of human dispersal across Australia. These findings rule out climate change, and implicate humans, as the primary extinction cause., Megafaunal extinction in Australia has been attributed to both climate change and human causation. Here, van der Kaars et al. present a 150,000 year record offshore southwest Australia in which they refine the timing and nature of regional ecosystem changes and megafaunal population collapse.

The benthic foraminiferal inventory and their assemblage composition was documented along five sediment cores from the Peruvian margin between 3°S and 18°S at water depths of 500 to 1250 m, covering the lower boundary of today’s Oxygen Minimum Zone (OMZ). Emphasis was given to certain time intervals during the last 22 thousand years when different climatic and oceanographic conditions prevailed than today. In total three agglutinated and 186 calcareous species were recognised. Bolivina costata, Bolivinita minuta, Cassidulina delicata and Epistominella exigua were most abundant. The foraminiferal distributions revealed a marked change in assemblage composition particularly at the deeper cores during and after the deglaciation. The diversity declined and Bolivina species became dominant. These changes took place gradually over several millennia, and high-frequency fluctuations were not recorded. This pattern provides evidence for rather stable ecological conditions and sluggish changes in bottom water circulation during the last deglaciation.

The transition from benthos to plankton requires multiple adaptations, yet so far it remains unclear how these are acquired in the course of the transition. To investigate this process, we analyzed the genetic diversity and distribution patterns of a group of foraminifera of the genus Bolivina with a tychopelagic mode of life (same species occurring both in benthos and plankton). We assembled a global sequence data set for this group from single-cell DNA extractions and occurrences in metabarcodes from pelagic environmental samples. The pelagic sequences all cluster within a single monophyletic clade within Bolivina. This clade harbors three distinct genetic lineages, which are associated with incipient morphological differentiation. All lineages occur in the plankton and benthos, but only one lineage exhibits no limit to offshore dispersal and has been shown to grow in the plankton. These observations indicate that the emergence of buoyancy regulation within the clade preceded the evolution of pelagic feeding and that the evolution of both traits was not channeled into a full transition into the plankton. We infer that in foraminifera, colonization of the planktonic niche may occur by sequential cooptation of independently acquired traits, with holoplanktonic species being recruited from tychopelagic ancestors

The faunal composition and diversity pattern of Recent benthic foraminifera from the shelf and slope of the South Western Approaches (Celtic Sea) were assessed. The sampling stations cover a depth range from 100 to 500 m. A total number of 294 species was recorded, of which 89 were found exclusively in the living fauna and 118 only in the dead assemblage, whereas 87 species were found in both assemblages. The faunal composition revealed a distinct bisection of the living fauna on the shelf. While certain distribution patterns of living dominant species were recognized along a NE-SW trending transect towards the shelf edge, the living fauna changed within small depth intervals and geographic position on the slope. Causes for these structured slope assemblages were probably along-slope currents of varying strengths, as well as variations in topography and bottom sediments. Analyses of population densities and diversity patterns determined high densities along the shelf edge and at one slope station, as well as an increasing diversity with water depth. A comparison with literature data from the same area yields distinct differences in faunal composition on the shelf and slope. The diversity was similar on the shelf, but higher at corresponding stations on the slope. We conclude that the faunal composition was highly influenced by the time and methods of sampling. In order to obtain consistent results in regional studies, all samples should be taken in a short time interval and by using the same sampling device. In addition, we depicted the influences of environmental parameters on dead faunal assemblages and their consequences for paleoenvironmental interpretations of fossil foraminiferal assemblages.

Paleoenvironmental studies and climate models demonstrate that fl uvial runoff and moisture availability in the Caribbean hinterland react very sensitively to climatic variations. Late Pleistocene and Holocene climate records document pronounced dry and wet periods over tropical South America mainly caused by shifts of the Intertropical Convergence Zone (ITCZ). However, forcing mechanisms for changes in the ITCZ position remain controversial. Here we present high-resolution foraminiferal Ba/Ca and δ18Oseawater records from a core located within the Orinoco River outfl ow documenting abrupt hydrological changes in the Orinoco catchment area during the deglacial and Holocene. Our data, obtained from the surface-dwelling foraminifera Globigerinoides ruber (pink), show an abrupt increase in Ba/ Ca ratios in the early Holocene, starting ~600 yr after the end of the Younger Dryas (YD) cold interval at ca. 10.8 ka and suggesting a massive reorganization of moisture sources in northern South America. In contrast, the salinity dependent δ18Oseawater from the same samples shows a gradual decrease starting at the end of the YD. The offset of our Ba/Ca peak excludes meltwater release in conjunction with the northern Andean glacier retreat well before the end of the YD as a forcing mechanism. We suggest that the Ba/Ca record documents an abrupt increase in Ba-rich waters of a northern Andean source caused by the insolation-driven shift of the ITCZ and/or enhanced monsoon activity.

The eastern Pacific benthic foraminifer Nonionella stella Cushman & Moyer, 1930 was recorded for the first time in the Skagerrak (North Sea) and its fjords. In this short note we evaluate its migration, considering both dispersal by propagules and ship ballast tanks. We suggest that the predominantly southward surface currents along the western European seaboard and Morocco would impede a wide-range dispersal of N. stella propagules and hypothesize transportation by ship ballast tanks as the possible vector of N. stella immigration into northern European seas.

The aim of the present study was to compare preservation, staining and preparation techniques to assess the influence of different sample treatments and analyses on the accuracy of benthic foraminiferal assemblage data from NE Atlantic shelf seas. Replicate surface samples from the SE North Sea were preserved with ethanol–rose Bengal or formalin, some were stained after processing, or foraminifera were concentrated by flotation. Coloration of living specimens was different between samples treated with an ethanol–rose Bengal solution and those stained after washing. In the latter case, only the last two or three chambers were stained. The aliquot sample preserved with formalin showed dissolution features in agglutinated and porcellaneous species. Population density varied between different preservation, picking modes and investigators. The accuracy of picking was in the range of ±2 % (1σ), while external reproducibility ranged from −34 to +16 %. There was no significant difference between wet and dry picking. Samples that were concentrated by flotation generally yielded a lower number of specimens. Agglutinated species were under-represented in samples that were stained after washing and in the flotation concentrate. Size fractions showed a reduction of population density and Fisher alpha diversity index with increasing mesh size. Only half of the specimens and less than two-thirds of the species are captured if the >125 µm rather than >63 µm fraction is analysed. In oxygen minimum zones, where small-sized species dominate the assemblage, the recovery in larger size fractions could be lower.

Thermally-induced protein unfolding is commonly described with the two-state model. This model assumes only two types of protein molecules in solution, the native (N) and the denatured, unfolded (U) protein. In reality, protein unfolding is a multistep process, even if intermediate states are only sparsely populated. As an alternative approach we explore the Zimm–Bragg theory, originally developed for theα-helix-to-random coil transition of synthetic polypeptides. The theory includes intermediate structures with concentrations determined by the cooperativity of the unfolding reaction. We illustrate the differences between the two-state model and the Zimm–Bragg theory with measurements of apolipoprotein A-1 and lysozyme by differential scanning calorimetry (DSC) and CD spectroscopy. Nine further protein examples are taken from the literature. The Zimm–Bragg theory provides a perfect fit of the calorimetric unfolding transitions for all proteins investigated. In contrast, the transition curves and enthalpies predicted by the two-state model differ considerably from the experimental results. Apolipoprotein A-1 is ~50%α-helical at ambient temperature and its unfolding follows the classicalα-helix-to-random coil equilibrium. The unfolding of proteins with littleα-helix content, such as lysozyme, can also be analyzed with the Zimm–Bragg theory by introducing the concept of ‘folded’ and ‘unfolded’ peptide units assuming an average unfolding enthalpy per peptide unit. DSC is the method of choice to measure the unfolding enthalpy,$\Delta H_{\rm exp} ^0 $, but CD spectroscopy in combination with the two-state model is often used to deduce the unfolding enthalpy. This can lead to erroneous result. Not only are different enthalpies required to describe the CD and DSC transition curves but these values deviate distinctly from the experimental result. In contrast, the Zimm–Bragg theory predicts the DSC and CD unfolding transitions with the same set of parameters.

Nat. Med. 21, 140–149 (2015); published online 12 January 2015; corrected after print 19 November 2015 In the version of this article initially published, the article number in reference 13 is incorrectly stated as '100ra190' and should be '100ra90'. The error has been corrected in the HTML and PDF versions of the article.

Static and dynamic light scattering were employed to determine simultaneously the average relative molecular mass, Mr, and the average hydrodynamic radius, Rh, of protein molecules. The new method was applied to the association-dissociation equilibrium of apolipoprotein A-1 (Apo A-1) and its thermal unfolding. As a control, lysozyme was measured as a nonassociating protein. Apo A-1 forms oligomers as a function of concentration and temperature, and the equilibrium can be described by a cooperative association model, consisting of a nucleation step and a growth step. At concentrations of 1 and 2.7 mg/mL, the Apo A-1 solution contained mainly monomers and octamers, with intermediates occurring at very low concentrations. Oligomer formation was maximal at 22 °C and was characterized by a temperature-dependent association constant. The cooperative association model allows the quantitative analysis of both the average relative molecular mass, Mr, and the average hydrodynamic radius, Rh, with the same set of model parameters which, in turn, are also applicable to analytical ultracentrifugation experiments. The light scattering experiments were reversible as long as the Apo A-1 solution was not heated above 60 °C.

It is expected that the calcification of foraminifera will be negatively affected by the ongoing acidification of the oceans. Compared to the open oceans, these organisms are subjected to much more adverse carbonate system conditions in coastal and estuarine environments such as the southwestern Baltic Sea, where benthic foraminifera are abundant. This study documents the seasonal changes of carbonate chemistry and the ensuing response of the foraminiferal community with bi-monthly resolution in Flensburg Fjord. In comparison to the surface pCO2, which is close to equilibrium with the atmosphere, we observed large seasonal fluctuations of pCO2 in the bottom and sediment pore waters. The sediment pore water pCO2 was constantly high during the entire year ranging from 1244 to 3324 μatm. Nevertheless, in contrast to the bottom water, sediment pore water was slightly supersaturated with respect to calcite as a consequence of higher alkalinity (AT) for most of the year. Foraminiferal assemblages were dominated by two calcareous species, Ammonia aomoriensis and Elphidium incertum, and the agglutinated Ammotium cassis. The one-year cycle was characterised by seasonal community shifts. Our results revealed that there is no dynamic response of foraminiferal population density and diversity to elevated sediment pore water pCO2. Surprisingly, the fluctuations of sediment pore water undersaturation (Ωcalc) co-vary with the population densities of living Ammonia aomoriensis. Further, we observed that most of the tests of living calcifying foraminifera were intact. Only Ammonia aomorienis showed dissolution and recalcification structures on the tests, especially at undersaturated conditions. Therefore, the benthic community is subjected to high pCO2 and tolerates elevated levels as long as sediment pore water remains supersaturated. Model calculations inferred that increasing atmospheric CO2 concentrations will finally lead to a perennial undersaturation in sediment pore waters. Whereas benthic foraminifera indeed may cope with a high sediment pore water pCO2, the steady undersaturation of sediment pore waters would likely cause a significant higher mortality of the dominating Ammonia aomoriensis. This shift may eventually lead to changes in the benthic foraminiferal communities in Flensburg Fjord, as well as in other regions experiencing naturally undersaturated Ωcalc levels.

Benthic foraminifera are unicellular eukaryotes inhabiting sediments of aquatic environments. Several species were shown to store and use nitrate for complete denitrification, a unique energy metabolism among eukaryotes. The population of benthic foraminifera reaches high densities in oxygen-depleted marine habitats, where they play a key role in the marine nitrogen cycle. However, the mechanisms of denitrification in foraminifera are still unknown, and the possibility of a contribution of associated bacteria is debated. Here, we present evidence for a novel eukaryotic denitrification pathway that is encoded in foraminiferal genomes. Large-scale genome and transcriptomes analyses reveal the presence of a denitrification pathway in foraminifera species of the genus Globobulimina. This includes the enzymes nitrite reductase (NirK) and nitric oxide reductase (Nor) as well as a wide range of nitrate transporters (Nrt). A phylogenetic reconstruction of the enzymes' evolutionary history uncovers evidence for an ancient acquisition of the foraminiferal denitrification pathway from prokaryotes. We propose a model for denitrification in foraminifera, where a common electron transport chain is used for anaerobic and aerobic respiration. The evolution of hybrid respiration in foraminifera likely contributed to their ecological success, which is well documented in palaeontological records since the Cambrian period.

Ammonia and Elphidium collected in the Kiel Fjord for the present study were first identified on morphological bases as Ammonia beccarii (Linne´, 1758) and Elphidium excavatum (Terquem, 1876). Phylogenetic analyses based on partial SSU rDNA and LSU rDNA sequences show that Ammonia specimens sampled in the Kiel Fjord belong to the phylotype T6, which has a disjunct distribution (Wadden and Baltic Seas/China and Japan) and has been identified as Ammonia aomoriensis (Asano, 1951). Partial SSU rDNA sequence analyses indicate that Elphidium specimens from the Kiel Fjord belong to the clade E. excavatum, confirming the morphological identification. This clade can be further divided in three subclades. Kiel Fjord Elphidium belong to two of these subclades and were identified morphologically as the subspecies E. excavatum excavatum (Terquem, 1876) and E. e. clavatum Cushman, 1930.

Living benthic foraminifera of Flensburg Fjord were surveyed in June 2006. The muddy and organic-rich sediments of the inner fjord were dominated by Elphidium incertum. E. incertum and E. excavatum were frequent in muds and sandy muds of the fjord loop around Holnis Peninsula and in the outer part. Gelting Bay yielded a different biofacies, indicating a brackish and sandy habitat, poor in food supply and with microfauna dominated by Ammonia beccarii and E. albiumbilicatum. The central fjord and nearshore zones of the loop were characterized by sandy muds, relatively poor in food and occupied by A. beccarii, E. incertum and E. excavatum subspecies. High abundances of E. excavatum were encountered in the innermost fjord, with fine-grained and organic-rich muddy sediments.A comparison with previous studies revealed the profound changes in species composition in the outer Flensburg Fjord since the 1970s. A decline in numbers of Ammotium cassis and flourishing of Ammonia beccarii in Gelting Bay were recognized. These changes are most likely associated with decreased intensity and frequency of salt-water inflows into the Baltic Sea since the 1960s. It is inferred that the decline of A. cassis is similar to that of Eggerelloides scaber, which currently is found only in depressions of Kiel Bight with higher salinity.

The Adra River deltaic system, southeast Iberian Peninsula, shows a steep topography and is subjected to strong climatic seasonality. This system has been affected by alternating wet and dry periods, and it has also undergone numerous anthropogenic activities such as deforestation, mining activities, river channel deviations and dam construction, particularly during the last two centuries. Two sediment cores were retrieved off the Adra River, from the western (MS_V9) and eastern (MS_V4) lobes of the subaqueous deltaic deposit. A multi-proxy study was carried out, including grain size, benthic foraminiferal assemblages, magnetic susceptibility and geochemical element analyses, in order to understand the sedimentary expression of recent climatic cycles and anthropogenic interventions in the river basin. Periods of increased deposition of coarse-grained sediments, low absolute abundance of benthic foraminifera and high elemental ratios indicative of terrigenous contributions, were interpreted as periods of increased sediment supply to the shelf. Four flooding events were recorded in core MS_V9 and three events on core MS_V4, of which two were observed in both cores. They were related to periods with major floods that were documented on the southern Iberian Peninsula around 1770e1810 and 1860 e1870 AD. On the other hand, sediment core intervals exhibiting increasing proportion of fine-grained sediments and higher abundances of foraminiferal species assigned as successful colonizers (Textularia earlandi) and opportunistic species that feed on bacteria or terrestrial organic matter (Bolivina ordinaria, Bulimina elongata, Eggerelloides scaber and Ammonia beccarii or tepida), indicate the establishment of new environments with new ecological constraints. They were related to significant decreases of terrigenous sediment input during low rainfall or dry periods. The increase of opportunistic species feeding on fresh phytodetritus (Nonionella iridea, Nonionella stella, Nonionella sp., Brizalina dilatata, Epistominella vitrea and Bolivinellina pseudopuntata), under more stable environmental conditions, also point to a stronger marine influence on the prodeltaic environments during these periods. The human interventions on the river basin after 1872 AD, with the deviation of the main river channel to the east, led to a drastic reduction of the sediment exported to the western delta lobe. This study showed that the sedimentation on the Adra subaqueous deltaic deposit was mainly controlled by rainfall variability from 1663 to 1872 AD, and afterwards by anthropogenic interventions., SI

Summary The dnaK operon of Streptomyces coelicolor encodes the DnaK chaperone machine and HspR, the transcriptional repressor of the operon; HspR confers repression by binding to several inverted repeat sequences in the promoter region, dnaKp. Here, we demonstrate that HspR specifically requires the presence of DnaK protein to retard a dnaKp fragment in gel-shift assays. This requirement is independent of the co-chaperones, DnaJ and GrpE, and it is ATP independent. Furthermore the retarded protein‐DNA complex can be ‘supershifted’ by antiDnaK monoclonal antibody, demonstrating that DnaK forms an integral component of the complex. It was shown in DNase I footprinting experiments that refolding and specific binding of HspR to its DNA target does not require DnaK. We conclude that the formation of the stable DnaK‐HspR‐DNA ternary complex does not depend on the chaperoning activity of DnaK. In affinity chromatography experiments using whole-cell extracts, DnaK was shown to copurify with HspR, providing additional evidence that the two proteins interact in vivo; it was not possible to purify HspR away from DnaK in any experiments unless a powerful denaturant was used. The level of heat shock induction of chromosomal DnaK could be partially suppressed by expressing dnaK extrachromosomally from a heterologous promoter. In addition, it is shown that DnaK confers enhanced HspRmediated repression of transcription in vitro. Taken together, these results suggest that DnaK functions as a transcriptional co-repressor by binding to HspR at its operator sites. In this model, the DnaK‐HspR system would represent a novel example of feedback regulation of gene expression by a molecular chaperone, in which DnaK directly activates a

Present day oceans are generally well ventilated except mid-depth oxygen minimum zones (OMZs) under high surface water productivity regimes, regions of sluggish circulation, and restricted marginal basins. In the Mesozoic, however, entire oceanic basins transiently became dysoxic or even anoxic. In particular the Cretaceous Ocean Anoxic Events (OAEs) were characterised by laminated organic-carbon rich shales and low-oxygen indicating trace fossil assemblages preserved in the sedimentary record. Yet both, qualitative and quantitative assessments of intensity and extent of Cretaceous near-bottom water oxygenation have been hampered by deep or long-term diagenesis and the evolution of marine biota serving as oxygen indicators in today's ocean. Sedimentary features similar to those found in Cretaceous strata were observed in deposits underlying Recent OMZs, where bottom-water oxygen levels, the flux of organic matter, and benthic life are well known. Their implications for constraining past bottom-water oxygenation are addressed in this review, with emphasis on comparing OMZ sediments from the Peruvian upwelling with deposits of the late Cenomanian OAE 2 from the Atlantic NW African shelf. Holocene laminated sediments were encountered at bottom-water oxygen levels of 10 μmol kg−1 showed an inverse exponential relationship of bottom-water oxygen levels and organic carbon accumulation depicting enhanced bioirrigation and decomposition of organic matter with increased oxygen supply. In absence of seasonal laminations and under conditions of low burial diagenesis, this relationship may facilitate quantitative estimates of paleo-oxygenation under suboxic conditions. Similarities and differences between Cretaceous OAEs and late Quaternary OMZs have to be further explored to improve our understanding of sedimentary systems under hypoxic conditions.

Calcifying foraminifera are expected to be endangered by ocean acidification; however, the response of a complete community kept in natural sediment and over multiple generations under controlled laboratory conditions has not been constrained to date. During 6 months of incubation, foraminiferal assemblages were kept and treated in natural sediment with pCO2-enriched seawater of 430, 907, 1865 and 3247 μatm pCO2. The fauna was dominated by Ammonia aomoriensis and Elphidium species, whereas agglutinated species were rare. After 6 months of incubation, pore water alkalinity was much higher in comparison to the overlying seawater. Consequently, the saturation state of Ωcalc was much higher in the sediment than in the water column in nearly all pCO2 treatments and remained close to saturation. As a result, the life cycle (population density, growth and reproduction) of living assemblages varied markedly during the experimental period, but was largely unaffected by the pCO2 treatments applied. According to the size–frequency distribution, we conclude that foraminifera start reproduction at a diameter of 250 μm. Mortality of living Ammonia aomoriensis was unaffected, whereas size of large and dead tests decreased with elevated pCO2 from 285 μm (pCO2 from 430 to 1865 μatm) to 258 μm (pCO2 3247 μatm). The total organic content of living Ammonia aomoriensis has been determined to be 4.3% of CaCO3 weight. Living individuals had a calcium carbonate production rate of 0.47 g m−2 a−1, whereas dead empty tests accumulated a rate of 0.27 g m−2 a−1. Although Ωcalc was close to 1, approximately 30% of the empty tests of Ammonia aomoriensis showed dissolution features at high pCO2 of 3247 μatm during the last 2 months of incubation. In contrast, tests of the subdominant species, Elphidium incertum, stayed intact. Our results emphasize that the sensitivity to ocean acidification of the endobenthic foraminifera Ammonia aomoriensis in their natural sediment habitat is much lower compared to the experimental response of specimens isolated from the sediment.

The discovery that foraminifera are able to use nitrate instead of oxygen as an electron acceptor for respiration has challenged our understanding of nitrogen cycling in the ocean. It was thought before that only prokaryotes and some fungi are able to denitrify. Rate estimates of foraminiferal denitrification have been very sparse and limited to specific regions in the oceans, not comparing stations along a transect of a certain region. Here, we present estimates of benthic foraminiferal denitrification rates from six stations at intermediate water depths in and below the Peruvian oxygen minimum zone (OMZ). Foraminiferal denitrification rates were calculated from abundance and assemblage composition of the total living fauna in both surface and subsurface sediments, as well as from individual species specific denitrification rates. A comparison with total benthic denitrification rates as inferred by biogeochemical models revealed that benthic foraminifera probably account for the total denitrification in shelf sediments between 80 and 250 m water depth. The estimations also imply that foraminifera are still important denitrifiers in the centre of the OMZ around 320 m (29–50% of the benthic denitrification), but play only a minor role at the lower OMZ boundary and below the OMZ between 465 and 700 m (2–6% of total benthic denitrification). Furthermore, foraminiferal denitrification has been compared to the total benthic nitrate loss measured during benthic chamber experiments. The estimated foraminiferal denitrification rates contribute 2 to 46% to the total nitrate loss across a depth transect from 80 to 700 m, respectively. Flux rate estimates range from 0.01 to 1.3 mmol m−2 d−1. Furthermore we show that the amount of nitrate stored in living benthic foraminifera (3 to 3955 μmol L−1) can be higher by three orders of magnitude as compared to the ambient pore waters in near-surface sediments sustaining an important nitrate reservoir in Peruvian OMZ sediments. The substantial contribution of foraminiferal nitrate respiration to total benthic nitrate loss at the Peruvian margin, which is one of the main nitrate sink regions in the world ocean, underpins the importance of the previously underestimated role of benthic foraminifera in global biogeochemical cycles.

Same-area comparison between patterns of Recent (living) and Holocene benthic foraminiferal assemblage composition is essential to validate their utility as proxies for paleoenvironmental reconstructions. Such reconstructions have scarcely been attempted in shelf environments. In this study, we compared living (stained), dead and Holocene benthic foraminiferal assemblages from the Gulf of Cadiz continental shelf off the Guadiana River. On average, 99% of the living benthic foraminiferal species were preserved in the dead assemblage and 95% in the fossil record. Several common species were assessed as indicators for certain environmental factors, including river discharge, supply of terrestrial organic matter, heavy metal concentrations, oxygen levels, substrate properties, hydrodynamic energy levels, sea-level rise and human impact. The paleoenvironmental reconstruction depicted five stages of Holocene environmental evolution of the Guadiana shelf over the last 11,500 cal yr BP. The characteristics of the stages, and the transitions between them, were in particular driven by changes in sea-level, influx of terrestrial organic matter and limits of productivity.

Potassium ions stabilize the DnaK · ADP complex that forms on incubation of nucleotide-free DnaK with ADP or ATP. Generation of the crystallographically defined Mg2+ cluster [Wilbanks, S. M. & McKay, D. B. (1995) J. Biol. Chem. 270, 2251–2257], in which two K+ and the nucleotide are bound together with Mg2+ in the ATPase site, appears to be essential for the ATP-induced acceleration of binding of peptide ligands, the ATP-induced release of peptide ligands and for the peptide-induced increase in ATPase activity. Thus, K+ is instrumental in signal transmission between the ATPase site and the peptide-binding site.

Three contrasting sedimentary environments on the continental shelf off the Guadiana River (northern Gulf of Cadiz) were integrated in a chronological framework and analysed in terms of sedimentology and benthic foraminiferal assemblages to understand the Holocene paleoenvironmental evolution. The analysed environments differ in terms of their depositional regimes and benthic foraminiferal assemblages. However, a dominant fluvial origin of the sand fraction was observed in all three environments. Holocene sedimentary processes were mainly controlled by natural (sea level changes and climate variations) and human-induced processes (e.g. deforestation, agriculture) along four evolutionary stages. The three older stages were mainly influenced by natural processes, such as sea level variations and fluvial inputs, whereas the most recent stage reflects a combination of climatic- and human-induced processes. A deepening of sedimentary environments related to a period of rapid sea level rise, strongly influenced by river discharges occurred from c. 11,500 to c. 10,000 cal. yr BP. A reduction in sediment export to the shelf, as a result of the continuous and rapid sea level rise and enhanced estuary infilling reflects the second stage, from c. 10,000 to c. 5000 cal. yr BP. The beginning of the third stage, from c. 5000 to c. 1500–1000 cal. yr BP, is marked by a sea-level slowdown and the relatively stable climate and environmental conditions. The fourth stage, from c. 1500–1000 cal. yr BP to Recent times, reflects the intensification of human-induced processes and climatic variability in the Guadiana River basin. This stage also reflects modern depositional conditions, with the formation of a proximal prodeltaic wedge and a distal muddy body. PDCTM/P/MAR/15289/1999 info:eu-repo/semantics/publishedVersion

Living (stained) benthic foraminiferal faunas were analyzed in 51 surficial sediment samples taken from the northern Gulf of Cadiz continental shelf between the mouths of the Guadiana and Guadalquivir rivers. The distribution and abundance of 26 species with relative abundance .5% were related to water depth, sediment type, river discharge, water temperature, salinity, turbidity, and primary productivity. Hierarchical classification using R- and Q-mode cluster analyses, and individual distributions, allowed these taxa to be categorized into four general groups. Group 1 is represented by Bolivina ordinaria and Hopkinsina atlantica. These species are linked to river discharge, and are associated with muddy sediments. They are considered the most opportunistic species in the assemblage, and are associated with the limits of productivity. Group 2, contains Ammonia beccarii, Eggerelloides scaber, Elphidium gerthi, Quinqueloculina laevigata, and Q. stelligera, and is characteristic of shallow water depths. Its species are associated with different sediment types and their distribution is influenced by river discharge. Group 3 is dominated by Bulimina aculeata, B. elongata, Elphidium excavatum, E. cuvillieri, Epistominella vitrea, and Rectuvigerina phlegeri. These species display the highest abundances between 30–100 m water depths. They prevail in muds associated with weak hydrodynamics, low oxygenation, and high organic matter. Group 4 includes species that are more abundant in deep stations and is divided into two subgroups. Subgroup 4A includes Bolivina catanensis, B. italica, B. striatula, Cassidulina laevigata, Stainforthia sp., Nouria polymorphinoides, and Nouria sp., with higher abundances in one or two samples. Subgroup 4B, with Brizalina dilatata, B. spathulata, Bulimina marginata, Nonionella iridea, N. stella, and N. turgida, has patchy distribution. Higher abundances of Nonionella species off the Guadiana River are related to low temperature and salinity. info:eu-repo/semantics/publishedVersion

Modeling and proxy studies indicate that a reduction of Atlantic Meridional Overturning Circulation (AMOC) strength profoundly impacts temperatures and salinities in the (sub)tropical Atlantic, especially on subsurface levels. While previous studies focused on prominent periods of AMOC reduction during the last deglaciation, we aim to test whether similar reconfigurations of the subtropical hydrography occurred during the moderate climatic alterations punctuating the last interglacial Marine Isotope Stage (MIS) 5. Here, we present temperature and salinity records from a Florida Straits core by combining d18O and Mg/Ca analyses on surface (Globigerinoides ruber, white) and deep‐dwelling (Globorotalia crassaformis) foraminifera covering MIS 5 in high resolution. The data reveal increasing salinities at intermediate depths during interglacial cooling episodes, decoupled from relatively stable surface conditions. This probably indicates the spatial expansion of saline subtropical gyre waters due to enhanced Ekman downwelling and might also point to a changed density structure and altered geostrophic balance in Florida Straits. Notably, these oceanographic alterations are not consistently occurring during periods of AMOC reduction. The data suggest that the expansion of gyre waters into Florida Straits was impeded by the increasing influence of Antarctic Intermediate Water (AAIW) from MIS 5.5 to ∼107 kyr BP. Afterward, increasingly positive benthic d13C values imply a recession of AAIW, allowing the temporary expansion of gyre waters into Florida Straits. We argue that the inferred transient subtropical salt accumulation and warm pool expansion might have played a pivotal role in reinvigorating meridional overturning and dampen the severity of interglacial cold phases.