Response to technical comment on `meta-analysis reveals negative yet variable effects of ocean acidification on marine organisms'

It has been proposed that crustaceans should be excluded from a comparison of biological responses to ocean acidification among organisms with different calcium carbonate (CaCO3 ) forms in their calcified structures. We re-analysed our data without crustaceans and found high variation in organismal responses within CaCO3 categories. We conclude that the CaCO3 polymorph alone does not predict sensitivity, and a consideration of functional differences among organisms is necessary for predicting variation in response to acidification.     

Quaternary dune carbonates from the Mediterranean Coast of Egypt: Petrography and diagenesis

Summary The Quaternary carbonates of the Mediterranean coast of Egypt between Alexandria and Salum appear as parallel limestone ridges rising up to 100 m above sea level. These ridges are dominated by dunal carbonates which differ not only in their primary composition but also by distinct grades of meteoric water diagenesis. Oolitic facies dominates the younger aeolianites of the first and second ridges. Bioclastic facies with abundant coralline algae, benthonic foraminifers, molluscs, echinoderms and intraclasts represents the major rock type in the older aeolianites. Features of meteoric water diagenesis include precipitation of increasing amounts of avoid-filling low Mg-calcite spar, dissolution of aragonite and stabilization of aragonite and high Mg-calcite to low Mg-calcite. Aeolianites below paleosol horizons contain abundant calcrete cements, micritized fossils and detrital grains which are commonly corroded and replaced by calcite. Three stages of progressive meteoric diagenesis are recognised in the Egyptian Quaternary aeolianites. In stage 1 minor precipitation of low Mg-calcite occurs at the grain boundaries. Stage 2 is marked by partial dissolution of aragonite, partial loss of high Mg-calcite and precipitation of low Mg-calcite in some pore spaces. In stage 3, most of the remaining pores are occluded by cementation. At the end of stage 3, Mg is removed from high Mg-calcite but some aragonite still persists. The early vadose cements are represented by miniscus, bridge and pendant cements. The phreatic cements were precipitated as bladed spar in the isopachous rims and equant spar in the intergranular and mouldic porosity. The late vadose cements are represented by micritic cements that were related to calcrete formation. Elemental behaviour during meteoric water diagenesis indicates that it leads to a gradual decrease in bulk Sr along with Na in progressively altered aeolianites. Mn distribution is controlled by the carbonate mineralogy (aragonite versus calcite) as well as the proximity of the aeolianites to the overlying paleosol horizons.     

Biomineralization of carbonate and phosphate by moderately halophilic bacteria

We investigated the precipitation of carbonate and phosphate minerals by 19 species of moderately halophilic bacteria using media with variable Mg(2+)/Ca(2+) ratios. The precipitated minerals were calcite, magnesium (Mg) calcite, and struvite (MgNH(4)PO(4) x 6H(2)O) in variable proportions depending on the Mg(2+)/Ca(2+) ratio of the medium. The Mg content of the Mg-calcite decreased with increasing Ca(2+) concentration in the medium. According to the saturation indices, other minerals could also have precipitated. We observed important differences between the morphology of carbonate and phosphate, which may help us to recognize these minerals in natural systems. We studied the growth and pH curves of four bacteria in media specific for carbonate and struvite precipitation. We consider the biomineralization processes that produce carbonate and phosphate minerals, and propose a hypothesis for the lack of struvite in natural environments and ancient rocks.     

Exceptional preservation requires fast biodegradation: thylacocephalan specimens from La Voulte-sur-Rhône (Callovian,Jurassic, France)

Konservat-Lagerstätten are seen as snapshots of past biodiversity for a given location and time. However, processes leading to the exceptional morphological preservation of fossils in these deposits remain incompletely understood. This results in a deficient assessment of taphonomic biases and limits the robustness/relevance of palaeobiological reconstructions. Here, we report the mineralogical characterization of crustacean fossils preserved within carbonate-rich concretions from the Jurassic Konservat-Lagerstätte of La Voulte-sur-Rhône (Ardèche, France). The combination of SEM-EDS, TEM, synchrotron-based XRF, XRD and XANES allows the mineralogical phases composing these fossils (i.e. fluorapatite, Fe-sulfides (pyrite, pyrrhotite) and Mg-calcite) and the surrounding matrix (i.e. Mg-calcite, clays and detrital silicates) to be identified. Fluorapatite and pyrite (and pyrrhotite) precipitated during decay under anoxic conditions, replacing delicate organic structures and preserving anatomical details. These mineral structures were subsequently consolidated by a Mg-calcite cement. Of note, histologically similar tissues were replaced by the same mineral phases, confirming that fossilization (in La Voulte) occurred rapidly enough to be influenced by tissue composition. Altogether, the present study shows that exceptional preservation requires fast biodegradation, thereby confirming recent experimental evidence.     

Non-skeletal carbonate production and stromatolite growth within a pleistocene deep ocean (Last glacial maximum, Red Sea)

Summary Quasi modern non-skeletal carbonates and stromatolites occur from the Red Sea shelf, proximal to the reef systems and continuous into the axial basin (512 to 2704 metres below present sea level). The lithified carbonates are intermixed with carbonate ooze forming a hard layer of 50 to 90 cm thickness. Decimetric platey fragments of lithified carbonate exhibit planar to columnar stromatolitic growth forms, lumpy microbial fabrics and internal brecciation features. The ultrastructures of lithified carbonates are formed by cryptocrystalline carbonate, mainly as aragonite spherulites, Mg-calcite peloids, anhedral mosaics of Mg-calcite and aragonite. Biogenic overgrowth, intercalations of calciturbidites and the type of interlocking relationships in the crystalline fabrics all indicate precipitation at the sea floor or close by. Morphological and mineralogical similarity with previously published microfabrics indicate microbial mediation of carbonate precipitation. The hard layer was formed during the last glacial maximum (LGM, approx. 23ka to 13ka), when pelagic sedimentation rates droped to a minimum due to high surface water salinities. Precipitation of the excess calcium carbonate in the deep ocean was strongly enhanced because the Hanish sill at the southern end of the Red Sea blocked input of cold bottom waters which in turn caused bottom water with high temperatures and salinities (>50 ‰), and low oxygen content. The scenario of a starved greenhouse-type ocean for the Red Sea during the LGM compliments models for the origin of ancient (Mesozoic and Palaeozoic) deepwater stromatolites.     

Biogenic and synthetic high magnesium calcite – A review

Systematic studies on the Mg distributions, the crystal orientations, the formation mechanisms and the mechanical properties of biogenic high-Mg calcites in different marine organisms were summarized in detail in this review. The high-Mg calcites in the hard tissues of marine organisms mentioned generally own a few common features as follows. Firstly, the Mg distribution is not uniform in most of the minerals. Secondly, high-Mg calcite biominerals are usually composed of nanoparticles that own almost the same crystallographic orientations and thus they behave like single crystals or mesocrystals. Thirdly, the formation of thermodynamically unstable high-Mg calcites in marine organisms under mild conditions is affected by three key factors, that is, the formation of amorphous calcium (magnesium) carbonate precursor, the control of polymorph via biomolecules and the high Mg/Ca ratios in modern sea. Lastly, the existence of Mg ions in the Mg-containing calcite may improve the mechanical properties of biogenic minerals. Furthermore, the key progress in the synthesis of high-Mg calcites in the laboratory based on the formation mechanisms of the biogenic high-Mg calcites was reviewed. Many researchers have realized the synthesis of high-Mg calcites in the laboratory under ambient conditions with the help of intermediate amorphous phase, mixed solvents, organic/inorganic surfaces and soluble additives. Studies on the structural analysis and formation mechanisms of thermodynamically unstable biogenic high-Mg calcite minerals may shed light on the preparation of functional materials with enhanced mechanical properties.     

Small pits associated with renilla (Cnidaria: Pennatulacea) on a modern low‐energy sandflat,Kiawah Island,South Carolina,U.S.A.

Small, shallow circular pits containing the Atlantic sea pansy, Renilla reniformis, were fairly common at one locality on the lower foreshore of Kiawah Island in June, 1997. Many of the pits were positioned on the stoss side of sand ripples; the organisms were oriented with their bilateral plane of symmetry essentially parallel to ripple crests. If preserved as concave epireliefs or convex hyporeliefs on bedding surfaces, such pits would be difficult not only to attribute to a trace producer or traditional ethologic category, but to identify as trace fossils in the first place.     

Decline in growth of foraminifer Marginopora rossi under eutrophication and ocean acidification scenarios

The combination of global and local stressors is leading to a decline in coral reef health globally. In the case of eutrophication, increased concentrations of dissolved inorganic nitrogen (DIN) and phosphorus (DIP) are largely attributed to local land use changes. From the global perspective, increased atmospheric CO₂ levels are not only contributing to global warming but also ocean acidification (OA). Both eutrophication and OA have serious implications for calcium carbonate production and dissolution among calcifying organisms. In particular, benthic foraminifera precipitate the most soluble form of mineral calcium carbonate (high‐Mg calcite), potentially making them more sensitive to dissolution. In this study, a manipulative orthogonal two‐factor experiment was conducted to test the effects of dissolved inorganic nutrients and OA on the growth, respiration and photophysiology of the large photosymbiont‐bearing benthic foraminifer, Marginopora rossi. This study found the growth rate of M. rossi was inhibited by the interaction of eutrophication and acidification. The relationship between M. rossi and its photosymbionts became destabilized due to the photosymbiont's release from nutrient limitation in the nitrate‐enriched treatment, as shown by an increase in zooxanthellae cells per host surface area. Foraminifers from the OA treatments had an increased amount of Chl a per cell, suggesting a greater potential to harvest light energy, however, there was no net benefit to the foraminifer growth. Overall, this study demonstrates that the impacts of OA and eutrophication are dose dependent and interactive. This research indicates an OA threshold at pH 7.6, alone or in combination with eutrophication, will lead to a decline in M. rossi calcification. The decline in foraminifera calcification associated with pollution and OA will have broad ecological implications across their ubiquitous range and suggests that without mitigation it could have serious implications for the future of coral reefs.     

Bacterial species dominance within a binary culture biofilm.

Studies with two species of bacteria, Pseudomonas putida and Hyphomicrobium sp. strain ZV620, were carried out to evaluate the overall net rate of accumulation of biofilm, the biofilm species composition, and individual species shear-related removal rates. Bacterial cells of either or both species were deposited onto glass or biofilm surfaces to initiate multispecies biofilms. Subsequent biofilm development was carried out under known conditions of nutrient concentration and laminar flow. Establishment of a depositing organism in a biofilm composed of another species was found to be a function of the relative growth rates of the bacterial species. In the case of simultaneous species deposition and subsequent binary culture development, the faster-growing organisms rapidly became the dominant biofilm species, but the slower-growing organisms remained established within the biofilm and continued to increase in numbers over time. The results also indicated that the rate of cell removal by fluid shear for a species was a function of biofilm cell number only if the species concentration was uniform with depth; in essence, only the upper layers of the biofilm were sheared off.     

High Performance,Flexible, Solid‐State Supercapacitors Based on a Renewable and Biodegradable Mesoporous Cellulose Membrane

A flexible, transparent, and renewable mesoporous cellulose membrane (mCel‐membrane) featuring uniform mesopores of ≈24.7 nm and high porosity of 71.78% is prepared via a facile and scalable solution‐phase inversion process. KOH‐saturated mCel‐membrane as a polymer electrolyte demonstrates a high electrolyte retention of 451.2 wt%, a high ionic conductivity of 0.325 S cm^?1, and excellent mechanical flexibility and robustness. A solid‐state electric double layer capacitor (EDLC) using activated carbon as electrodes, the KOH‐saturated mCel‐membrane as a polymer electrolyte exhibits a high capacitance of 110 F g^?1 at 1.0 A g^?1, and long cycling life of 10 000 cycles with 84.7% capacitance retention. Moreover, a highly integrated planar‐type micro‐supercapacitor (MSC) can be facilely fabricated by directly depositing the electrode materials on the mCel‐membrane‐based polymer electrolyte without using complicated devices. The resulting MSC exhibits a high areal capacitance of 153.34 mF cm^?2 and volumetric capacitance of 191.66 F cm^?3 at 10 mV s^?1, representing one of the highest values among all carbon‐based MSC devices. These findings suggest that the developed renewable, flexible, mesoporous cellulose membrane holds great promise in the practical applications of flexible, solid‐state, portable energy storage devices that are not limited to supercapacitors.     

Coral acid rich protein selects vaterite polymorph in vitro

Corals and other biomineralizing organisms use proteins and other molecules to form different crystalline polymorphs and biomineral structures. In corals, it’s been suggested that proteins such as Coral Acid Rich Proteins (CARPs) play a major role in the polymorph selection of their calcium carbonate (CaCO₃) aragonite exoskeleton. To date, four CARPs (1–4) have been characterized: each with a different amino acid composition and different temporal and spatial expression patterns during coral developmental stages. Interestingly, CARP3 is able to alter crystallization pathways in vitro, yet its function in this process remains enigmatic. To better understand the CARP3 function, we performed two independent in vitro CaCO₃ polymorph selection experiments using purified recombinant CARP3 at different concentrations and at low or zero Mg²⁺ concentration. Our results show that, in the absence of Mg²⁺, CARP3 selects for the vaterite polymorph and inhibits calcite. However, in the presence of a low concentration of Mg²⁺ and CARP3 both Mg-calcite and vaterite are formed, with the relative amount of Mg-calcite increasing with CARP3 concentration. In all conditions, CARP3 did not select for the aragonite polymorph, which is the polymorph associated to CARP3 in vivo, even in the presence of Mg²⁺ (Mg:Ca molar ratio equal to 1). These results further emphasize the importance of Mg:Ca molar ratios similar to that in seawater (Mg:Ca equal to 5) and the activity of the biological system in a aragonite polymorph selection in coral skeleton formation.     

Patterns of distribution of calcite crystals in soft corals sclerites

The gross morphology of soft coral surface sclerites has been studied for taxonomic purposes for over a century. In contrast, sclerites located deep in the core of colonies have not received attention. Some soft coral groups develop massive colonies, in these organisms tissue depth can limit light penetration and circulation of internal fluids affecting the physiology of coral tissues and their symbiotic algae; such conditions have the potential to create contrasting calcifying conditions. To test this idea, we analyzed the crystal structure of sclerites extracted from different colony regions in selected specimens of zooxanthellate and azooxanthellate soft corals with different colony morphologies, these were: Sarcophyton mililatensis, Sinularia capillosa, Sinularia flexibilis, Dendronephthya sp. and Ceeceenus levis. We found that the crystals that constitute polyp sclerites differ from those forming stalk sclerites. We also observed different crystals in sclerites located at various depths in the stalk including signs of sclerite breakdown in the stalk core region. These results indicate different modes of calcification within each colonial organism analyzed and illustrate the complexity of organisms usually regarded as repetitive morphological and functional units. Our study indicates that soft corals are ideal material to study natural gradients of calcification conditions. J. Morphol. 2011. © 2011 Wiley‐Liss, Inc.     

CRYSTALLOGRAPHY AND DIAGENESIS IN FOSSIL CRANIID BRACHIOPODS

Abstract:  One of the fundamental questions in biomineralization is how organisms control crystallographic orientation during biomineral production. The understanding of how diagenetic changes influence the preservation of original crystallographic patterns in fossilized biomineral structures provides a priori fundamental information for such an assessment. Fossil craniid brachiopods Petrocrania scabiosa (Late Ordovician) and Crania craniolaris (Late Cretaceous) are analysed using electron backscattered diffraction (EBSD) to provide crystallographic data at high spatial resolution in the structural context. EBSD analyses show that P. scabiosa maintains most of the original crystallographic signature, including data from individual calcite tablets and laminae, while C. craniolaris only retains fragmentary crystallographic data reflecting the crystallographic continuity of tablets across laminae. Data show that the preservation of the original crystallographic signature is independent of that of shell ultrastructure and geological time. In addition, results allow us to propose a series of steps in the evolution of 'crystallographic loss' due to diagenesis.     

Biomineralization by photosynthetic organisms: Evidence of coevolution of the organisms and their environment?

Biomineralization is widespread among photosynthetic organisms in the ocean, in inland waters and on land. The most quantitatively important biogeochemical role of land plants today in biomineralization is silica deposition in vascular plants, especially grasses. Terrestrial plants also increase the rate of weathering, providing the soluble substrates for biomineralization on land and in water bodies, a role that has had global biogeochemical impacts since the Devonian. The dominant photosynthetic biomineralizers in today's ocean are diatoms and radiolarians depositing silica and coccolithophores and foraminifera depositing calcium carbonate. Abiotic precipitation of silica from supersaturated seawater in the Precambrian preceded intracellular silicification dominated by sponges, then radiolarians and finally diatoms, with successive declines in the silicic acid concentration in the surface ocean, resulting in some decreases in the extent of silicification and, probably, increases in the silicic acid affinity of the active influx mechanisms. Calcium and bicarbonate concentrations in the surface ocean have generally been supersaturating with respect to the three common calcium carbonate biominerals through geological time, allowing external calcification as well as calcification in compartments within cells or organisms. The forms of calcium carbonate in biominerals, and presumably the evolution of the organisms that produce them, have been influenced by abiotic variations in calcium and magnesium concentrations in seawater, and calcium carbonate deposition has probably also been influenced by carbon dioxide concentration whose variations are in part biologically determined. Overall, there has been less biological feedback on the availability of substrates for calcification than is the case for silicification.     

Effect of water velocity on the early development of manganese-depositing biofilm in a drinking-water distribution system

Abstract A study of the development of biofilm colonizing the surfaces of pipes in a drinking-water distribution system has shown that water velocity significantly influenced the nature and physiological activity of the biofilm. Biofilm developed at a velocity of 0.5 m s⁻¹ actively oxidized and deposited manganese, but at 0.01 m s⁻¹ no manganese was deposited. Budding bacteria were the dominant microorganisms depositing manganese but a variety of other organisms were also present in the biofilms. The budding bacteria oxidizing manganese were Pedomicrobium manganicum and Metallogenium .     

Antigenic distinctiveness, heterogeneity, and relationships of Methanothrix spp.

A detailed immunologic analysis of Methanothrix soehngenii Opfikon (the type species of the genus), Methanothrix sp. strain CALS-1, and Methanothrix concilii GP6 was performed. A variety of poly- and monoclonal antibody probes for a comprehensive panel of reference organisms were used to determine immunogenicity, antigenicity, and relationships. The three organisms are antigenically distinct but interrelated, forming an immunologically cohesive group, weakly related to methanosarcinae. A prominent feature of the organisms was heterogeneity characterized by antigenic diversity and compartmentation, the latter particularly evident in M. soehngenii Opfikon, which was examined more thoroughly. The complexity of the antigenic profile of this strain and the heterogeneity of the group suggest a high degree of phenotypic diversification within the genus.     

Reverse gyrase, a hallmark of the hyperthermophilic archaebacteria.

Investigation of the presence of a reverse gyrase-like activity in archaebacteria revealed wide distribution of this activity in hyperthermophilic species, including methanogens and sulfur-dependent organisms. In contrast, no reverse gyrase activity was detected in mesophilic and moderately thermophilic organisms, which exhibited only an ATP-independent activity of DNA relaxation. These results suggest that the presence of reverse gyrase in archaebacteria is tightly linked to the high growth temperatures of these organisms. With respect to antigenic properties, the enzyme appeared similar among members of the genus Sulfolobus. In contrast, no close antigenic relatedness was found between the reverse gyrase of members of the order Sulfolobales and that of the other hyperthermophilic organisms.     

Development of albian microbialites and microbialite reefs at marginal platform areas of the Vasco-Cantabrian Basin (Soba reef area,Cantabria, N. Spain)

The Middle Albian sequence from the western marginal area of the Vasco-Cantabrian Basin contains calcified microbialites in different marine depositional environments, individually well defined by microstructure, lamina characteristics and mode of formation. Microbialites may form the primary framework of reefs, which occur as composite stacks in mid to lower slope environments or as isolated bodies in small intraplatform basins. In most areas microbialite reef growth was initiated below the photic zone. Stratiform intercalations of microbialites and composite microbialite/foraminifer oncoids are restricted to well bedded carbonate platform deposits (Urgonian). Three basis types of microbialites are recognized:

Morphology and sedimentology of Halimeda bioherms from the eastern Java Sea (Indonesia)

Halimeda bioherms, occurring primarily along the western and southern margins of Kalukalukuang Bank in the eastern Java Sea, display a wide variety of thicknesses and shapes. In general, high-frequency forms of the northern bank are replaced by thicker and lower frequency forms along the deeper southern margin. Sidescan sonar data suggest aperiodic reworking of shallow bioherm crests of the northern bank into features suggestive of bedforms. These features are not associated with deeper bioherms of the southern bank. Cores from the bioherms indicate that they consist mostly of disarticulated Halimeda plates set in a lime mud matrix composed largely of Halimeda fragments and foraminifera tests. Carbon-14 dating shows that, with exception of some deep southern bank examples, bioherms are actively accreting. Results of mineralogy and elemental chemistry on piston core PC-12 suggest cyclic variations in Mg-calcite (cement in Halimeda utricles), which may be related to periodic excursions of cold Pacific throughflow water onto the bank. Composition of the Mg-calcite (8.6 mole-%) suggests a temperature of formation of about 22 °C, which is 7 °C below average surface water temperatures. The carbon and oxygen isotope compositions of both aragonite and Mg-calcite phases are remarkably homogeneous, but were inconclusive with regard to the cold-water intrusion hypothesis. However, a lack of reef-building corals below a depth of 15 m, abundance of Halimeda bioherms on the western margin of K-Bank, where upwelling is predicted, extensive boring of sedimentary particles by endolithic boring algae, and high nutrient values of water at the thermocline (50–70 m deep) all support the incursion of cold, nutrient-rich water onto the bank. Upwelling and nutrient overloading are suggested as explanations for remarkable algal growth at the expense of reef-building corals.     

Mating behaviour in the mosquito, Anopheles gambiae s.1.save

ABSTRACT. Mating behaviour in the Anopheles gambiae complex was studied in the laboratory, using an infra-red TV system to make observations in the 'dark'. Maximum fertilization occurred when both sexes were at least 2 days old. In LD 12:12 most mating took place in the first hour of the dark phase. At this time, the males had erect fibrillae on the antennae and showed the maximum response to an artificial female flight tone, approaching, landing-on and attempting to clasp the sound source. The cycle of fibrillar erection and of responsiveness to sound continued in constant dark. Males did not appear to discriminate on contact, between their own and other species. Previously mated females actively resisted copulation, but, when tethered, were unable to prevent the deposition of further internal mating plugs. Free-flying, previously inseminated, females prevented the males from depositing internal plugs, but not from ejaculating and depositing external plugs. The differences between A.gambiae and the better known Stegomyia mosquitoes appear to be related to their different habits, A.gambiae males being less likely to encounter females of other species or inseminated females of their own species at the restricted time and place of mating.