Articles | Volume 10, issue 6
Research article 03 Jun 2013
Research article | 03 Jun 2013
Taking nature into lab: biomineralization by heavy metal-resistant streptomycetes in soil
E. Schütze et al.
No articles found.
Juraj Majzlan, Stefan Kiefer, Kristina Lilova, Tamilarasan Subramani, Alexandra Navrotsky, Edgar Dachs, and Artur Benisek
Eur. J. Mineral., 33, 357–371,Short summary
Chapmanite is a seemingly rare mineral, a silicate of the elements iron and antimony. In this work, we evaluated how stable and how soluble this mineral is. The goal was to determine if this mineral can store the toxic element antimony. Our results show that it is possible, but its formation in nature is hindered and slow. Yet, in some special environments, it could store and keep antimony over longer time.
Alexandra M. Plumhoff, Jakub Plášil, Edgar Dachs, Artur Benisek, Jiří Sejkora, Martin Števko, Mike S. Rumsey, and Juraj Majzlan
Eur. J. Mineral., 32, 285–304,
Aileen Meier, Anne Kastner, Dennis Harries, Maria Wierzbicka-Wieczorek, Juraj Majzlan, Georg Büchel, and Erika Kothe
Biogeosciences, 14, 4867–4878,Short summary
Biomineralization of (magnesium) calcite and vaterite by bacterial isolates was observed using isolates from limestone associated groundwater, rock and soil. More than 92 % of isolates could form carbonates with different crystal macromorphologies. Using different conditions like varying temperature, pH or media components but also cocultivation to test for collaborative effects of sympatric bacteria, mechanisms of calcium carbonate formation were studied.
Related subject area
Biogeochemistry: BiomineralizationDecoupling salinity and carbonate chemistry: low calcium ion concentration rather than salinity limits calcification in Baltic Sea musselsTechnical note: A universal method for measuring the thickness of microscopic calcite crystals, based on bidirectional circular polarizationThe patterns of elemental concentration (Ca, Na, Sr, Mg, Mn, Ba, Cu, Pb, V, Y, U and Cd) in shells of invertebrates representing different CaCO3 polymorphs: a case study from the brackish Gulf of Gdańsk (the Baltic Sea)Carbonic anhydrase is involved in calcification by the benthic foraminifer Amphistegina lessoniiDistribution of chlorine and fluorine in benthic foraminiferaRare earth elements in oyster shells: provenance discrimination and potential vital effectsDetermining how biotic and abiotic variables affect the shell condition and parameters of Heliconoides inflatus pteropods from a sediment trap in the Cariaco BasinIntercomparison of four methods to estimate coral calcification under various environmental conditionsTechnical note: The silicon isotopic composition of choanoflagellates: implications for a mechanistic understanding of isotopic fractionation during biosilicificationInsights into architecture, growth dynamics, and biomineralization from pulsed Sr-labelled Katelysia rhytiphora shells (Mollusca, Bivalvia)Subaqueous speleothems (Hells Bells) formed by the interplay of pelagic redoxcline biogeochemistry and specific hydraulic conditions in the El Zapote sinkhole, Yucatán Peninsula, MexicoKinetics of calcite precipitation by ureolytic bacteria under aerobic and anaerobic conditionsCoupled calcium and inorganic carbon uptake suggested by magnesium and sulfur incorporation in foraminiferal calcitePlanktonic foraminiferal spine versus shell carbonate Na incorporation in relation to salinityPrecipitation of calcium carbonate mineral induced by viral lysis of cyanobacteria: evidence from laboratory experimentsMineral formation induced by cable bacteria performing long-distance electron transport in marine sedimentsVariation in brachiopod microstructure and isotope geochemistry under low-pH–ocean acidification conditionsWeaving of biomineralization framework in rotaliid foraminifera: implications for paleoceanographic proxiesMarine and freshwater micropearls: biomineralization producing strontium-rich amorphous calcium carbonate inclusions is widespread in the genus Tetraselmis (Chlorophyta)Carbon and nitrogen turnover in the Arctic deep sea: in situ benthic community response to diatom and coccolithophorid phytodetritusTechnical note: A refinement of coccolith separation methods: measuring the sinking characteristics of coccolithsImproving the strength of sandy soils via ureolytic CaCO3 solidification by Sporosarcina ureaeImpact of salinity on element incorporation in two benthic foraminiferal species with contrasting magnesium contentsCalcification in a marginal sea – influence of seawater [Ca2+] and carbonate chemistry on bivalve shell formationEffect of temperature rise and ocean acidification on growth of calcifying tubeworm shells (Spirorbis spirorbis): an in situ benthocosm approachPhosphorus limitation and heat stress decrease calcification in Emiliania huxleyiAnatomical structure overrides temperature controls on magnesium uptake – calcification in the Arctic/subarctic coralline algae Leptophytum laeve and Kvaleya epilaeve (Rhodophyta; Corallinales)Coral calcifying fluid aragonite saturation states derived from Raman spectroscopyImpact of trace metal concentrations on coccolithophore growth and morphology: laboratory simulations of Cretaceous stressBa incorporation in benthic foraminiferaSize-dependent response of foraminiferal calcification to seawater carbonate chemistryTechnical note: an economical apparatus for the observation and harvest of mineral precipitation experiments with light microscopyPhysiology regulates the relationship between coccosphere geometry and growth phase in coccolithophoresTrends in element incorporation in hyaline and porcelaneous foraminifera as a function of pCO2Decoupled carbonate chemistry controls on the incorporation of boron into Orbulina universaMineralogical response of the Mediterranean crustose coralline alga Lithophyllum cabiochae to near-future ocean acidification and warmingTemperature affects the morphology and calcification of Emiliania huxleyi strainsSkeletal mineralogy of coral recruits under high temperature and pCO2Direct uptake of organically derived carbon by grass roots and allocation in leaves and phytoliths: 13C labeling evidencepH up-regulation as a potential mechanism for the cold-water coral Lophelia pertusa to sustain growth in aragonite undersaturated conditionsIron encrustations on filamentous algae colonized by Gallionella-related bacteria in a metal-polluted freshwater streamOcean acidification does not affect magnesium composition or dolomite formation in living crustose coralline algae, Porolithon onkodes in an experimental systemReconsidering the role of carbonate ion concentration in calcification by marine organismsImpact of seawater carbonate chemistry on the calcification of marine bivalvesImpact of seawater [Ca2+] on the calcification and calciteMg / Ca of Amphistegina lessoniiEvaluation of coral reef carbonate production models at a global scaleNew highlights of phytolith structure and occluded carbon location: 3-D X-ray microscopy and NanoSIMS resultsLimpets counteract ocean acidification induced shell corrosion by thickening of aragonitic shell layersIdentifying vital effects in Halimeda algae with Ca isotopesExperimental evidence for foraminiferal calcification under anoxia
Trystan Sanders, Jörn Thomsen, Jens Daniel Müller, Gregor Rehder, and Frank Melzner
Biogeosciences, 18, 2573–2590,Short summary
The Baltic Sea is expected to experience a rapid drop in salinity and increases in acidity and warming in the next century. Calcifying mussels dominate Baltic Sea seafloor ecosystems yet are sensitive to changes in seawater chemistry. We combine laboratory experiments and a field study and show that a lack of calcium causes extremely slow growth rates in mussels at low salinities. Subsequently, climate change in the Baltic may have drastic ramifications for Baltic seafloor ecosystems.
Luc Beaufort, Yves Gally, Baptiste Suchéras-Marx, Patrick Ferrand, and Julien Duboisset
Biogeosciences, 18, 775–785,Short summary
The coccoliths are major contributors to the particulate inorganic carbon in the ocean. They are extremely difficult to weigh because they are too small to be manipulated. We propose a universal method to measure thickness and weight of fine calcite using polarizing microscopy that does not require fine-tuning of the light or a calibration process. This method named "bidirectional circular polarization" uses two images taken with two directions of a circular polarizer.
Anna Piwoni-Piórewicz, Stanislav Strekopytov, Emma Humphreys-Williams, and Piotr Kukliński
Biogeosciences, 18, 707–728,Short summary
Calcifying organisms occur globally in almost every environment, and the process of biomineralization is of great importance in the global carbon cycle and use of skeletons as environmental data archives. The composition of skeletons is very complex. It is determined by the mechanisms of biological control on biomineralization and the response of calcifying organisms to varying environmental drivers. Yet for trace elements, such as Cu, Pb and Cd, an impact of environmental factors is pronounced.
Siham de Goeyse, Alice E. Webb, Gert-Jan Reichart, and Lennart J. de Nooijer
Biogeosciences, 18, 393–401,Short summary
Foraminifera are calcifying organisms that play a role in the marine inorganic-carbon cycle and are widely used to reconstruct paleoclimates. However, the fundamental process by which they calcify remains essentially unknown. Here we use inhibitors to show that an enzyme is speeding up the conversion between bicarbonate and CO2. This helps the foraminifera acquire sufficient carbon for calcification and might aid their tolerance to elevated CO2 level.
Anne Roepert, Lubos Polerecky, Esmee Geerken, Gert-Jan Reichart, and Jack J. Middelburg
Biogeosciences, 17, 4727–4743,Short summary
We investigated, for the first time, the spatial distribution of chlorine and fluorine in the shell walls of four benthic foraminifera species: Ammonia tepida, Amphistegina lessonii, Archaias angulatus, and Sorites marginalis. Cross sections of specimens were imaged using nanoSIMS. The distribution of Cl and F was co-located with organics in the rotaliids and rather homogeneously distributed in miliolids. We suggest that the incorporation is governed by the biomineralization pathway.
Vincent Mouchi, Camille Godbillot, Vianney Forest, Alexey Ulianov, Franck Lartaud, Marc de Rafélis, Laurent Emmanuel, and Eric P. Verrecchia
Biogeosciences, 17, 2205–2217,Short summary
Rare earth elements (REEs) in coastal seawater are included in bivalve shells during growth, and a regional fingerprint can be defined for provenance and environmental monitoring studies. We present a large dataset of REE abundances from oysters from six locations in France. The cupped oyster can be discriminated from one locality to another, but this is not the case for the flat oyster. Therefore, provenance studies using bivalve shells based on REEs are not adapted for the flat oyster.
Rosie L. Oakes and Jocelyn A. Sessa
Biogeosciences, 17, 1975–1990,Short summary
Pteropods are a group of tiny swimming snails whose fragile shells put them at risk from ocean acidification. We investigated the factors influencing the thickness of pteropods shells in the Cariaco Basin, off Venezuela, which is unaffected by ocean acidification. We found that pteropods formed thicker shells when nutrient concentrations, an indicator of food availability, were highest, indicating that food may be an important factor in mitigating the effects of ocean acidification on pteropods.
Miguel Gómez Batista, Marc Metian, François Oberhänsli, Simon Pouil, Peter W. Swarzenski, Eric Tambutté, Jean-Pierre Gattuso, Carlos M. Alonso Hernández, and Frédéric Gazeau
Biogeosciences, 17, 887–899,Short summary
In this paper, we assessed four methods (total alkalinity anomaly, calcium anomaly, 45Ca incorporation, and 13C incorporation) to determine coral calcification of a reef-building coral. Under all conditions (light vs. dark incubations and ambient vs. lowered pH levels), calcification rates estimated using the alkalinity and calcium anomaly techniques as well as 45Ca incorporation were highly correlated, while significantly different results were obtained with the 13C incorporation technique.
Alan Marron, Lucie Cassarino, Jade Hatton, Paul Curnow, and Katharine R. Hendry
Biogeosciences, 16, 4805–4813,Short summary
Isotopic signatures of silica fossils can be used as archives of past oceanic silicon cycling, which is linked to marine carbon uptake. However, the biochemistry that lies behind such chemical fingerprints remains poorly understood. We present the first measurements of silicon isotopes in a group of protists closely related to animals, choanoflagellates. Our results highlight a taxonomic basis to silica isotope signatures, possibly via a shared transport pathway in choanoflagellates and animals.
Laura M. Otter, Oluwatoosin B. A. Agbaje, Matt R. Kilburn, Christoph Lenz, Hadrien Henry, Patrick Trimby, Peter Hoppe, and Dorrit E. Jacob
Biogeosciences, 16, 3439–3455,Short summary
This study uses strontium as a trace elemental marker in combination with high-resolution nano-analytical techniques to label the growth fronts of bivalves in controlled aquaculture conditions. The growing shells incorporate the labels and are used as
snapshotsvisualizing the growth processes across different shell architectures. These observations are combined with structural investigations across length scales and altogether allow for a detailed understanding of this shell.
Simon Michael Ritter, Margot Isenbeck-Schröter, Christian Scholz, Frank Keppler, Johannes Gescher, Lukas Klose, Nils Schorndorf, Jerónimo Avilés Olguín, Arturo González-González, and Wolfgang Stinnesbeck
Biogeosciences, 16, 2285–2305,Short summary
Unique and spectacular under water speleothems termed as Hells Bells were recently reported from sinkholes (cenotes) of the Yucatán Peninsula, Mexico. However, the mystery of their formation remained unresolved. Here, we present detailed geochemical analyses and delineate that the growth of Hells Bells results from a combination of biogeochemical processes and variable hydraulic conditions within the cenote.
Andrew C. Mitchell, Erika J. Espinosa-Ortiz, Stacy L. Parks, Adrienne J. Phillips, Alfred B. Cunningham, and Robin Gerlach
Biogeosciences, 16, 2147–2161,Short summary
Microbially induced carbonate mineral precipitation (MICP) is a natural process that is also being investigated for subsurface engineering applications including radionuclide immobilization and microfracture plugging. We demonstrate that rates of MICP from microbial urea hydrolysis (ureolysis) vary with different bacterial strains, but rates are similar in both oxygenated and oxygen-free conditions. Ureolysis MICP is therefore a viable biotechnology in the predominately oxygen-free subsurface.
Inge van Dijk, Christine Barras, Lennart Jan de Nooijer, Aurélia Mouret, Esmee Geerken, Shai Oron, and Gert-Jan Reichart
Biogeosciences, 16, 2115–2130,Short summary
Systematics in the incorporation of different elements in shells of marine organisms can be used to test calcification models and thus processes involved in precipitation of calcium carbonates. On different scales, we observe a covariation of sulfur and magnesium incorporation in shells of foraminifera, which provides insights into the mechanics behind shell formation. The observed patterns imply that all species of foraminifera actively take up calcium and carbon in a coupled process.
Eveline M. Mezger, Lennart J. de Nooijer, Jacqueline Bertlich, Jelle Bijma, Dirk Nürnberg, and Gert-Jan Reichart
Biogeosciences, 16, 1147–1165,Short summary
Seawater salinity is an important factor when trying to reconstruct past ocean conditions. Foraminifera, small organisms living in the sea, produce shells that incorporate more Na at higher salinities. The accuracy of reconstructions depends on the fundamental understanding involved in the incorporation and preservation of the original Na of the shell. In this study, we unravel the Na composition of different components of the shell and describe the relative contribution of these components.
Hengchao Xu, Xiaotong Peng, Shijie Bai, Kaiwen Ta, Shouye Yang, Shuangquan Liu, Ho Bin Jang, and Zixiao Guo
Biogeosciences, 16, 949–960,Short summary
Viruses have been acknowledged as important components of the marine system for the past 2 decades, but understanding of their role in the functioning of the geochemical cycle remains poor. Results show viral lysis of cyanobacteria can influence the carbonate equilibrium system remarkably and promotes the formation and precipitation of carbonate minerals. Amorphous calcium carbonate (ACC) and aragonite are evident in the lysate, implying that different precipitation processes have occurred.
Nicole M. J. Geerlings, Eva-Maria Zetsche, Silvia Hidalgo-Martinez, Jack J. Middelburg, and Filip J. R. Meysman
Biogeosciences, 16, 811–829,Short summary
Multicellular cable bacteria form long filaments that can reach lengths of several centimeters. They affect the chemistry and mineralogy of their surroundings and vice versa. How the surroundings affect the cable bacteria is investigated. They show three different types of biomineral formation: (1) a polymer containing phosphorus in their cells, (2) a sheath of clay surrounding the surface of the filament and (3) the encrustation of a filament via a solid phase containing iron and phosphorus.
Facheng Ye, Hana Jurikova, Lucia Angiolini, Uwe Brand, Gaia Crippa, Daniela Henkel, Jürgen Laudien, Claas Hiebenthal, and Danijela Šmajgl
Biogeosciences, 16, 617–642,
Yukiko Nagai, Katsuyuki Uematsu, Chong Chen, Ryoji Wani, Jarosław Tyszka, and Takashi Toyofuku
Biogeosciences, 15, 6773–6789,Short summary
We interpret detailed SEM and time-lapse observations of the calcification process in living foraminifera, which we reveal to be directly linked to the construction mechanism of organic membranes where the calcium carbonate precipitation takes place. We show that these membranes are a highly perforated outline is first woven by skeletal pseudopodia and then later overlaid by a layer of membranous pseudopodia to close the gaps. The chemical composition is related to these structures.
Agathe Martignier, Montserrat Filella, Kilian Pollok, Michael Melkonian, Michael Bensimon, François Barja, Falko Langenhorst, Jean-Michel Jaquet, and Daniel Ariztegui
Biogeosciences, 15, 6591–6605,Short summary
The unicellular microalga Tetraselmis cordiformis (Chlorophyta) was recently discovered to form intracellular mineral inclusions, called micropearls, which had been previously overlooked. The present study shows that 10 Tetraselmis species out of the 12 tested share this biomineralization capacity, producing amorphous calcium carbonate inclusions often enriched in Sr. This novel biomineralization process can take place in marine, brackish or freshwater and is therefore a widespread phenomenon.
Ulrike Braeckman, Felix Janssen, Gaute Lavik, Marcus Elvert, Hannah Marchant, Caroline Buckner, Christina Bienhold, and Frank Wenzhöfer
Biogeosciences, 15, 6537–6557,Short summary
Global warming has altered Arctic phytoplankton communities, with unknown effects on deep-sea communities that depend strongly on food produced at the surface. We compared the responses of Arctic deep-sea benthos to input of phytodetritus from diatoms and coccolithophorids. Coccolithophorid carbon was 5× less recycled than diatom carbon. The utilization of the coccolithophorid carbon may be less efficient, so a shift from diatom to coccolithophorid blooms could entail a delay in carbon cycling.
Hongrui Zhang, Heather Stoll, Clara Bolton, Xiaobo Jin, and Chuanlian Liu
Biogeosciences, 15, 4759–4775,Short summary
The sinking speeds of coccoliths are relevant for laboratory methods to separate coccoliths for geochemical analysis. However, in the absence of estimates of coccolith settling velocity, previous implementations have depended mainly on time-consuming method development by trial and error. In this study, the sinking velocities of cocooliths were carefully measured for the first time. We also provide an estimation of coccolith sinking velocity by shape, which will make coccolith separation easier.
Justin Michael Whitaker, Sai Vanapalli, and Danielle Fortin
Biogeosciences, 15, 4367–4380,Short summary
Materials, like soils or cements, can require repair. This study used a new bacterium (Sporosarcina ureae) in a repair method called "microbially induced carbonate precipitation" (MICP). In three trials, benefits were shown: S. ureae could make a model sandy soil much stronger by MICP, in fact better than a lot of other bacteria. However, MICP-treated samples got weaker in three trials of acid rain. In conclusion, S. ureae in MICP repair shows promise when used in appropriate climates.
Esmee Geerken, Lennart Jan de Nooijer, Inge van Dijk, and Gert-Jan Reichart
Biogeosciences, 15, 2205–2218,
Jörn Thomsen, Kirti Ramesh, Trystan Sanders, Markus Bleich, and Frank Melzner
Biogeosciences, 15, 1469–1482,Short summary
The distribution of mussel in estuaries is limited but the mechanisms are not well understood. We document for the first time that reduced Ca2+ concentration in the low saline, brackish Baltic Sea affects the ability of mussel larvae to calcify the first larval shell. As complete formation of the shell is a prerequisite for successful development, impaired calcification during this sensitive life stage can have detrimental effects on the species' ability to colonize habitats.
Sha Ni, Isabelle Taubner, Florian Böhm, Vera Winde, and Michael E. Böttcher
Biogeosciences, 15, 1425–1445,Short summary
Spirorbis tube worms are common epibionts on brown algae in the Baltic Sea. We made experiments with Spirorbis in the
Kiel Outdoor Benthocosmsat CO2 and temperature conditions predicted for the year 2100. The worms were able to grow tubes even at CO2 levels favouring shell dissolution but did not survive at mean temperatures over 24° C. This indicates that Spirorbis worms will suffer from future excessive ocean warming and from ocean acidification fostering corrosion of their protective tubes.
Andrea C. Gerecht, Luka Šupraha, Gerald Langer, and Jorijntje Henderiks
Biogeosciences, 15, 833–845,Short summary
Calcifying phytoplankton play an import role in long-term CO2 removal from the atmosphere. We therefore studied the ability of a representative species to continue sequestrating CO2 under future climate conditions. We show that CO2 sequestration is negatively affected by both an increase in temperature and the resulting decrease in nutrient availability. This will impact the biogeochemical cycle of carbon and may have a positive feedback on rising CO2 levels.
Merinda C. Nash and Walter Adey
Biogeosciences, 15, 781–795,Short summary
Past seawater temperatures can be reconstructed using magnesium / calcium ratios of biogenic carbonates. As temperature increases, so does magnesium. Here we show that for these Arctic/subarctic coralline algae, anatomy is the first control on Mg / Ca, not temperature. When using coralline algae for temperature reconstruction, it is first necessary to check for anatomical influences on Mg / Ca.
Thomas M. DeCarlo, Juan P. D'Olivo, Taryn Foster, Michael Holcomb, Thomas Becker, and Malcolm T. McCulloch
Biogeosciences, 14, 5253–5269,Short summary
We present a new technique to quantify the chemical conditions under which corals build their skeletons by analysing them with lasers at a very fine resolution, down to 1/100th the width of a human hair. Our first applications to laboratory-cultured and wild corals demonstrates the complex interplay among seawater conditions (temperature and acidity), calcifying fluid chemistry, and bulk skeleton accretion, which will define the sensitivity of coral calcification to 21st century climate change.
Giulia Faucher, Linn Hoffmann, Lennart T. Bach, Cinzia Bottini, Elisabetta Erba, and Ulf Riebesell
Biogeosciences, 14, 3603–3613,Short summary
The main goal of this study was to understand if, similarly to the fossil record, high quantities of toxic metals induce coccolith dwarfism in coccolithophore species. We investigated, for the first time, the effects of trace metals on coccolithophore species other than E. huxleyi and on coccolith morphology and size. Our data show a species-specific sensitivity to trace metal concentration, allowing the recognition of the most-, intermediate- and least-tolerant taxa to trace metal enrichments.
Lennart J. de Nooijer, Anieke Brombacher, Antje Mewes, Gerald Langer, Gernot Nehrke, Jelle Bijma, and Gert-Jan Reichart
Biogeosciences, 14, 3387–3400,
Michael J. Henehan, David Evans, Madison Shankle, Janet E. Burke, Gavin L. Foster, Eleni Anagnostou, Thomas B. Chalk, Joseph A. Stewart, Claudia H. S. Alt, Joseph Durrant, and Pincelli M. Hull
Biogeosciences, 14, 3287–3308,Short summary
It is still unclear whether foraminifera (calcifying plankton that play an important role in cycling carbon) will have difficulty in making their shells in more acidic oceans, with different studies often reporting apparently conflicting results. We used live lab cultures, mathematical models, and fossil measurements to test this question, and found low pH does reduce calcification. However, we find this response is likely size-dependent, which may have obscured this response in other studies.
Chris H. Crosby and Jake V. Bailey
Biogeosciences, 14, 2151–2154,Short summary
In the course of experiments exploring the formation of calcium phosphate minerals in a polymeric matrix, we developed a small-scale, reusable, and low-cost setup that allows microscopic observation over time for use in mineral precipitation experiments that use organic polymers as a matrix. The setup uniquely accommodates changes in solution chemistry during the course of an experiment and facilitates easy harvesting of the precipitates for subsequent analysis.
Rosie M. Sheward, Alex J. Poulton, Samantha J. Gibbs, Chris J. Daniels, and Paul R. Bown
Biogeosciences, 14, 1493–1509,Short summary
Our culture experiments on modern Coccolithophores find that physiology regulates shifts in the geometry of their carbonate shells (coccospheres) between growth phases. This provides a tool to access growth information in modern and past populations. Directly comparing modern species with fossil coccospheres derives a new proxy for investigating the physiology that underpins phytoplankton responses to environmental change through geological time.
Inge van Dijk, Lennart J. de Nooijer, and Gert-Jan Reichart
Biogeosciences, 14, 497–510,Short summary
Culturing foraminifera under controlled pCO2 conditions shows that incorporation of certain elements (Zn, Ba) into foraminiferal shells is impacted by the inorganic carbonate system. Modeling the chemical speciation of these elements suggests that incorporation is determined by the availability of free ions. Furthermore, analyzing and comparing trends in element incorporation in hyaline and porcelaneous species may provide constrains on the differences between their calcification strategies.
Ella L. Howes, Karina Kaczmarek, Markus Raitzsch, Antje Mewes, Nienke Bijma, Ingo Horn, Sambuddha Misra, Jean-Pierre Gattuso, and Jelle Bijma
Biogeosciences, 14, 415–430,Short summary
To calculate the seawater carbonate system, proxies for 2 out of 7 parameters are required. The boron isotopic composition of foraminifera shells can be used as a proxy for pH and it has been suggested that B / Ca ratios may act as a proxy for carbonate ion concentration. However, differentiating between the effects of pH and [CO32−] is problematic, as they co-vary in natural systems. To deconvolve the effects, we conducted culture experiments with the planktonic foraminifer Orbulina universa.
Merinda C. Nash, Sophie Martin, and Jean-Pierre Gattuso
Biogeosciences, 13, 5937–5945,Short summary
We carried out a 1-year experiment on coralline algae to test how higher CO2 and temperature might change the mineral composition of the algal skeleton. We expected there to be a decline in magnesium with CO2 and an increase with temperature. We found that CO2 did not change the mineral composition, but higher temperature increased the amount of magnesium.
Anaid Rosas-Navarro, Gerald Langer, and Patrizia Ziveri
Biogeosciences, 13, 2913–2926,Short summary
The global warming debate has sparked an unprecedented interest in temperature effects on coccolithophores. We show that sub-optimal growth temperatures lead to an increase in malformed coccoliths in a strain-specific fashion and the inorganic / organic carbon has a minimum at optimum growth temperature. Global warming might cause a decline in coccoliths' inorganic carbon contribution to the "rain ratio", as well as improved fitness in some genotypes by reducing coccolith malformation.
T. Foster and P. L. Clode
Biogeosciences, 13, 1717–1722,Short summary
In recent years much research has focussed on whether corals will be able to build their skeletons under predicted ocean acidification. One strategy corals may employ is changing the mineralogy of their skeletons from aragonite to the less soluble polymorph of calcium carbonate; calcite. Here we show that newly settled coral recruits are unable to produce calcite in their skeletons under near-future elevations in pCO2, which may leave them more vulnerable to ocean acidification.
Anne Alexandre, Jérôme Balesdent, Patrick Cazevieille, Claire Chevassus-Rosset, Patrick Signoret, Jean-Charles Mazur, Araks Harutyunyan, Emmanuel Doelsch, Isabelle Basile-Doelsch, Hélène Miche, and Guaciara M. Santos
Biogeosciences, 13, 1693–1703,Short summary
This 13C labeling experiment demonstrates that carbon can be absorbed by the roots, translocated in the plant, and ultimately fixed in organic compounds subject to occlusion in silica particles that form inside plant cells (phytoliths). Plausible forms of carbon absorbed, translocated, and fixed in phytoliths are assessed. Implications for our understanding of the C cycle at the plant-soil-atmosphere interface are discussed.
M. Wall, F. Ragazzola, L. C. Foster, A. Form, and D. N. Schmidt
Biogeosciences, 12, 6869–6880,Short summary
We investigated the ability of cold-water corals to deal with changes in ocean pH. We uniquely combined morphological assessment with boron isotope analysis to determine if changes in growth are related to changes in control of calcification pH. We found that the cold-water coral Lophelia pertusa can maintain the skeletal morphology, growth patterns as well as internal calcification pH. This has important implications for their future occurrence and explains their cosmopolitan distribution.
J. F. Mori, T. R. Neu, S. Lu, M. Händel, K. U. Totsche, and K. Küsel
Biogeosciences, 12, 5277–5289,Short summary
We studied filamentous macroscopic algae growing in metal-rich stream water that leaked from a former uranium-mining district. These algae were encrusted with Fe-deposits that were associated with microbes, mainly Gallionella-related Fe-oxidizing bacteria, and extracellular polymeric substances. Algae with a lower number of chloroplasts often exhibited discontinuous series of precipitates, likely due to the intercalary growth of algae which allowed them to avoid detrimental encrustation.
M. C. Nash, S. Uthicke, A. P. Negri, and N. E. Cantin
Biogeosciences, 12, 5247–5260,
L. T. Bach
Biogeosciences, 12, 4939–4951,Short summary
Calcification by marine organisms reacts to changing seawater carbonate chemistry, but it is unclear which components of the carbonate system drive the observed response. This study uncovers proportionalities between different carbonate chemistry parameters. These enable us to understand why calcification often correlates well with carbonate ion concentration, and they imply that net CaCO3 formation in high latitudes is not more vulnerable to ocean acidification than formation in low latitudes.
J. Thomsen, K. Haynert, K. M. Wegner, and F. Melzner
Biogeosciences, 12, 4209–4220,
A. Mewes, G. Langer, S. Thoms, G. Nehrke, G.-J. Reichart, L. J. de Nooijer, and J. Bijma
Biogeosciences, 12, 2153–2162,Short summary
A culture study with the benthic foraminifer Amphistegina lessonii was conducted at varying seawater [Ca2+] and constant [Mg2+]. Results showed optimum growth rates and test thickness at ambient seawater Mg/Ca and a calcite Mg/Ca which is controlled by the relative seawater ratio. Results support the conceptual biomineralization model by Nehrke et al. (2013); however, our refined flux-based model suggests transmembrane transport fractionation that is slightly weaker than expected.
N. S. Jones, A. Ridgwell, and E. J. Hendy
Biogeosciences, 12, 1339–1356,Short summary
Production of calcium carbonate by coral reefs is important in the global carbon cycle. Using a global framework we evaluate four models of reef calcification against observed values. The temperature-only model showed significant skill in reproducing coral calcification rates. The absence of any predictive power for whole reef systems highlights the importance of coral cover and the need for an ecosystem modelling approach accounting for population dynamics in terms of mortality and recruitment.
A. Alexandre, I. Basile-Doelsch, T. Delhaye, D. Borshneck, J. C. Mazur, P. Reyerson, and G. M. Santos
Biogeosciences, 12, 863–873,Short summary
Phytoliths contain occluded organic compounds called phytC. The nature and location of phytC in biogenic silica structures is poorly understood. Here, we reconstructed the 3-D structure of phytoliths using 3-D Xray microscopy. We further evidenced a pool of phytC, continuously distributed in the silica structure, using nanoscale secondary ion mass spectrometry (NanoSIMS). Our findings allowed the re-evaluation of previous suggestions regarding phytC quantification and environmental meaning.
G. Langer, G. Nehrke, C. Baggini, R. Rodolfo-Metalpa, J. M. Hall-Spencer, and J. Bijma
Biogeosciences, 11, 7363–7368,Short summary
Specimens of the patellogastropod limpet Patella caerulea were collected within and outside a CO2 vent site at Ischia, Italy. The distribution of different crystal structures across shell sections was analysed. Patella caerulea counteracts shell dissolution in corrosive waters by enhanced production of aragonitic parts of the shell. We conclude that it is not possible to predict the dissolution behaviour of a composite biomineral on the basis of the properties of its constituent mineral.
C. L. Blättler, S. M. Stanley, G. M. Henderson, and H. C. Jenkyns
Biogeosciences, 11, 7207–7217,Short summary
Halimeda algae were used as a test organism to untangle some of the specific factors that influence skeletal composition, in particular Ca-isotope composition. Algae were stimulated to precipitate both calcite and aragonite by growth in artificial Cretaceous seawater. Comparison of the skeletal Ca-isotope ratios with inorganic carbonate forms indicates the effects of mineralogy and Rayleigh distillation of Ca on the geochemistry of their carbonate skeletons.
M. P. Nardelli, C. Barras, E. Metzger, A. Mouret, H. L. Filipsson, F. Jorissen, and E. Geslin
Biogeosciences, 11, 4029–4038,
Adele, L. B.: Biomineralization: Conflicts, challenges, and opportunities, J. Cell. Biochem., 72, 83–91, 1998.
Basnakova, G., Spencer, A. J., Palsgard, E., Grime, G. W., and Macaskie, L. E.: Identification of the Nickel Uranyl Phosphate Deposits on Citrobacter sp. Cells by Electron Microscopy with Electron Probe X-ray Microanalysis and by Proton-Induced X-ray Emission Analysis, Environ. Sci. Technol., 32, 760–765, 1998.
Ben Omar, N., Gonzalez-Munoz, M. T., and Penalver, J. M. A.: Struvite crystallization on Myxococcus cells, Chemosphere, 36, 475–481, 1998.
Bhuiyan, M. I., Mavinic, D. S., and Beckie, R. D.: A solubility and thermodynamic study of struvite, Environ. Technol., 28, 1015–1026, 2007.
Bibb, M. J.: Regulation of secondary metabolism in streptomycetes, Curr. Opin. Microbiol., 8, 208–215, 2005.
Cappellen, P. V.: Biomineralization and Global Biogeochemical Cycles, in: Biomineralization, edited by: Dove, P. M., Yoreo, J. J. D., and Weiner, S., Biogeochemistry of Earth Processes – Reviews in Mineralogy and Geochemistry, 2003.
Chen, L., Shen, Y. H., Xie, A. J., Huang, F. Z., Zhang, W. Q., and Liu, S. X.: Seed-Mediated Synthesis of Unusual Struvite Hierarchical Superstructures Using Bacterium, Crystal Growth Des., 10, 2073–2082, 2010.
Da Silva, S., Bernet, N., Delgenès, J. P., and Moletta, R.: Effect of culture conditions on the formation of struvite by Myxococcus xanthus, Chemosphere, 40, 1289–1296, 2000.
Doyle, J. D., Philp, R., Churchley, J., and Parsons, S. A.: Analysis of Struvite Precipitation in Real and Synthetic Liquors, Process Saf. Environ., 78, 480–488, 2000.
Fanfani, L. and Zanazzi, P. F.: Switzerite - Its Chemical Formula and Crystal-Structure, Miner. Petrol., 26, 255–269, 1979.
Gadd, G. M.: Metals, minerals and microbes: geomicrobiology and bioremediation, J. Med. Microbiol., 156, 609–643, 2010.
Gonzalez, H. and Jensen, T. E.: Nickel sequestering by polyphosphate bodies in Staphylococcus aureus, Microbios, 93, 179–185, 1998.
Haferburg, G., Kloess, G., Schmitz, W., and Kothe, E.: "Ni-struvite" – A new biomineral formed by a nickel resistant Streptomyces acidiscabies, Chemosphere, 72, 517–523, 2008.
Hesse, A., Schreyger, F., Tuschewitzki, G. J., Classen, A., and Bach, D.: Experimental investigations on dissolution of incrustations on the surface of catheters, Urol. Int., 44, 364–369, 1989.
Hutnik, N., Wierzbowska, B., Piotrowski, K., and Matynia, A.: Continuous reaction crystallization of struvite from solution containing phosphate(V) and nitrate(V) ions, The Online J. Sci. Technol., 3, 58–66, 2011.
Kamnev, A. A., Antonyuk, L. P., Colina, M., Cherynshev, A. V., and Ignatov, V. V.: Investigation of a microbially produced structural modification of magnesium-ammonium orthophosphate, Monatsh. Chem., 130, 1431–1442, 1999.
Kieser, T., Bibb, M. J., Buttner, M. J., Chater, K. F., and Hopwood, D. A.: Practical Streptomyces Genetics, The John Innes Foundation Norwich, England, 2000.
Kim, D., Ryu, H. D., Kim, M. S., Kim, J., and Lee, S. I.: Enhancing struvite precipitation potential for ammonia nitrogen removal in municipal landfill leachate, J. Hazard. Mater., 146, 81–85, 2007.
Kofina, A. N. and Koutsoukos, P. G.: Spontaneous Precipitation of Struvite from Synthetic Wastewater Solutions, Crystal Growth Des., 5, 489–496, 2005.
Konhauser, K. and Riding, R.: Bacterial Biomineralization, in: Fundamentals of Geobiology, edited by: Knoll, A. H., Canfield, D. E., and Konhauser, K. O., John Wiley & Sons, Ltd, 105–130, 2012.
Le Corre, K. S., Valsami-Jones, E., Hobbs, P., and Parsons, S. A.: Impact of calcium on struvite crystal size, shape and purity, J. Cryst. Growth, 283, 514–522, 2005.
Le Corre, K. S., Valsami-Jones, E., Hobbs, P., and Parsons, S. A.: Impact of reactor operation on success of struvite precipitation from synthetic liquors., Environ. Technol., 28, 1245–1256, 2007a.
Le Corre, K. S., Valsami-Jones, E., Hobbs, P., and Parsons, S. A.: Kinetics of Struvite Precipitation: Effect of the Magnesium Dose on Induction Times and Precipitation Rates, Environ. Technol., 28, 1317–1324, 2007b.
Lee, S. I., Weon, S. Y., Lee, C. W., and Koopman, B.: Removal of nitrogen and phosphate from wastewater by addition of bittern, Chemosphere, 51, 265–271, 2003.
Lowenstam, H. A.: Minerals formed by organisms, Science, 211, 1126–1131, 1981.
Lowenstam, H. A. and Weiner, S.: On biomineralization, Oxford University Press, Inc., New York, 1989.
Mann, S.: Mineralization in biological systems, Struct. Bonding, 54, 125-174, 1983.
McLean, R. J., Downey, J., Clapham, L., Wilson, J. W., and Nickel, J. C.: Pyrophosphate inhibition of Proteus mirabilis-induced struvite crystallization in vitro, Clin. Chim. Acta, 200, 107–117, 1991.
Ohlinger, K. N., Young, T. M., and Schroeder, E. D.: Predicting struvite formation in digestion, Water Res., 32, 3607–3614, 1998.
Párraga, J., Rivadeneyra, A. M., Martín-García, J. M., Delgado, R., and Delgado, G.: Precipitation of Carbonates by bacteria from a Saline Soil, in Matural and Artificial Soil Extracts, Geomicrobiol. J., 21, 55–66, 2004.
Pérez-García, I., Rivadeneyra, M. A., and Ramos, C.: The influence of pH on struvite formation by bacteria, Chemosphere, 18, 1633–1638, 1989.
Prywer, J. and Torzewska, A.: Bacterially Induced Struvite Growth from Synthetic Urine: Experimental and Theoretical Characterization of Crystal Morphology, Crystal Growth Des., 9, 3538–3543, 2009.
Prywer, J. and Torzewska, A.: Biomineralization of struvite crystals by Proteus mirabilis from artificial urine and their mesoscopic structure, Cryst. Res. Technol., 45, 1283–1289, 2010.
Reardon, C. L., Dohnalkova, A. C., Nachimuthu, P., Kennedy, D. W., Saffarini, D. A., Arey, B. W., Shi, L., Wang, Z., Moore, D., McLean, J. S., Moyles, D., Marshall, M. J., Zachara, J. M., Fredrickson, J. K., and Beliaev, A. S.: Role of outer-membrane cytochromes MtrC and OmcA in the biomineralization of ferrihydrite by Shewanella oneidensis MR-1, Geobiology, 8, 56–68, 2010.
Rivadeneyra, M. A., Calvo, C., González-Torres, M. C., Pérez-García, I., and Ramos-Cormenzana, A.: Precipitation of struvite in urine medium by urease-positive and urease-negative Yersinia strains, Urol. Int., 45, 298–301, 1990.
Rivadeneyra, M. A., Pérez-García, I., and Ramos-Cormenzana, A.: Struvite precipitation by soil and fresh water bacteria, Curr. Microbiol., 24, 343–347, 1992.
Rivadeneyra, M. A., Gutierrez-Calderón, A., Rivadeneyra, A. M., and Ramos-Cormenzana, A.: A study of struvite precipitation and urease activity in bacteria isolated from patients with urinary infections and their possible involvement in the formation of renal calculi, Urol. Int., 63, 188–192, 1999.
Roncal-Herrero, T. and Oelkers, E. H.: Experimental determination of struvite dissolution and precipitation rates as a function of pH, Appl. Geochem., 26, 921–928, 2011.
Ronteltap, M., Maurer, M., and Gujer, W.: The behaviour of pharmaceuticals and heavy metals during struvite precipitation in urine, Water Res., 41, 1859–1868, 2007.
Saidou, H., Korchef, A., Ben Moussa, S., and Ben Amor, M.: Struvite precipitation by the dissolved CO2 degasification technique: Impact of the airflow rate and pH, Chemosphere, 74, 338–343, 2009.
Schmidt, A., Haferburg, G., Sineriz, M., Merten, D., Büchel, G., and Kothe, E.: Heavy metal resistance mechanisms in actinobacteria for survival in AMD contaminated soils, Chemie der Erde-Geochem., 65, 131–144, 2005.
Schmidt, A., Haferburg, G., Schmidt, A., Lischke, U., Merten, D., Ghergel, F., Büchel, G., and Kothe, E.: Heavy metal resistance to the extreme: Streptomyces strains from a former uranium mining area, Chemie der Erde-Geochem., 69, 35–44, 2008.
Schütze, E. and Kothe, E.: Heavy Metal-Resistant Streptomycetes in Soil, in: Soil Biology, Springer-Verlag Berlin Heidelberg, 2012.
Skinner, H. C. W.: Biominerals, Mineral. Mag., 69, 621–641, 2005.
Stefov, V., Soptrajanov, B., Kuzmanovski, I., Lutz, H. D., and Engelen, B.: Infrared and Raman spectra of magnesium ammonium phosphate hexahydrate (struvite) and its isomorphous analogues. III. Spectra of protiated and partially deuterated magnesium ammonium phosphate hexahydrate, J. Mol. Struct., 752, 60–67, 2005.
Veis, A.: Mineralization in an organic matrix framework, in: Biomineralization, edited by: Dove, P. M., Yoreo, J. J. D., and Weiner, S., Biogeochemistry of Earth Processes – Reviews in Mineralogy and Geochemistry, 2003.
Wang, X.-W., WangII, P., and Zheng, Y.-Q.: Crystal structure of hexaaquanickel(II) hydrogenphosphate monohydrate, [Ni(H2O)6][HPO4] × H2O, Z. Kristallogr.-New Cryst. St., 220, 321–322, 2005.
Weiner, S. and Dove, P.: An overview of biomineralization and the problem of the vital effect, in: Biomineralization, edited by: Dove, P. M., Yoreo, J. J. D., and Weiner, S., Biogeochemistry of Earth Processes – Reviews in Mineralogy and Geochemistry, 2003.
Yakubovich, O. V., Massa, W., Soboleva, A. A., Dimitrova, O. V., and Urusov, V. S.: Crystal structure of a new synthetic homologue of the switzerite series, Dokl. Chem., 393, 262–269, 2003.
Zantua, M. I., Dumenil, L. C., and Bremner, J. M.: Relationships Between Soil Urease Activity and Other Soil Properties, Soil Sci. Soc. Am. J., 41, 350–352, 1977.
Zeien, H. and Brümmer, G. W.: Chemische Extraktion zur Bestimmung der Schwermetallbindungsformen in Böden, Mitteilungen der Deutsche Bodenkundliche Gesellschaft, Sonderheft 59/I, 505–515, 1989.