Daniel Martin-Ramos

Carbonate and Phosphate Precipitation by Chromohalobacter marismortui

The ability of Chromohalobacter marismortui to precipitate carbonate and phosphate minerals has been demonstrated for the first time. Mineral precipitation in both solid and liquid media at different salts concentrations and different magnesium/calcium ratios occurred whereas crystal formation was not observed in the control. The precipitated minerals were studied by X-ray diffraction, scanning electron microscopy and EDX, and were different in liquid and solid media. In liquid media aragonite, struvite, vaterite and monohydrocalcite were precipitated forming crystals and bioliths. Bioliths accreted preferentially close to organic pellicles, whereas struvite preferentially grows in microenvironments free of such pellicles. Magnesian calcite, calcian-magnesian kutnahorite, “proto-dolomite” and huntite were formed in solid media. The Mg content of the magnesian calcite and of Ca-Mg kutnahorite also varied depending on the salt concentration of the culture media. This is the first report on bacterial precipitation of Ca-Mg kutnahorite and huntite in laboratory cultures. The results of this research show the active role played by C. marismortui in mineral precipitation, and allow us to compare them with those obtained previously using other taxonomic groups of moderately halophilic bacteria.

Ca–Mg kutnahorite and struvite production by Idiomarina strains at modern seawater salinities

The production of Mg-rich carbonates by Idiomarina bacteria at modern seawater salinities has been investigated. With this objective, four strains: Idiomarina abyssalis (strain ATCC BAA-312), Idiomarina baltica (strain DSM 15154), Idiomarina loihiensis (strains DSM 15497 and MAH1) were used. The strain I. loihiensis MAH1 is a new isolate, identified in the scope of this work. The four moderately halophilic strains precipitated struvite (NH4MgPO4 x 6H2O) crystals that appear encased by small Ca-Mg kutnahorite [CaMg(CO3)2] spheres and dumbbells, which are also regularly distributed in the bacterial colonies. The proportion of Ca-Mg kutnahorite produced by the bacteria assayed ranged from 50% to 20%, and I. abyssalis also produced monohydrocalcite. All precipitated minerals appeared to be related to the bacterial metabolism and, consequently, can be considered biologically induced. Amino acid metabolism resulted in a release of ammonia and CO2 that increase the pH and CO(3)(2-) concentration of the culture medium, creating an alkaline environment that favoured carbonate and struvite precipitation. This precipitation may be also related to heterogeneous nucleation on negatively charged points of biological structures. Because the nature of the organic matrix determines which ion is preferentially adsorbed and, consequently, which mineral phase is formed, the uniquely high content in odd-iso-branched fatty acids of the Idiomarina suggests that their particular membrane characteristics could induce Ca-Mg kutnahorite production. The Ca-Mg kutnahorite, a mineral with a dolomite-ordered structure, production at seawater salinities is noticeable. To date, such precipitation in laboratory cultures, has only been described in hypersaline conditions. It has also been the first time that biomineralization processes have been related to Idiomarina bacteria.

Crystal structure and magnetic properties of [Cu(ox)(py)2](py = pyridine): a ferromagnetic oxalate-bridged zigzag chain complex

The compound [Cu(ox)(py)2](ox = oxalate, py = pyridine) was obtained as a breakdown oxidized product of [Cu(epgly)2](Hepgly =N-2-ethylphenylglycine), and has been characterized by means of structural and magnetic measurements. The crystals are monoclinic, space group C2/c, with a= 14.088(3), b= 11.023(2), c= 8.689(2)A, β= 92.23(3)° and Z= 4. The structure was solved and refined to R= 0.039 and R′= 0.040. The structure consists of [Cu(py)2]2+ units bridged sequentially by centrosymmetric oxalate anions to form zigzag polymeric chains parallel to the c axis, with a copper–copper distance of 5.463(1)A. The copper ion is in distorted-octahedral environment and the equatorial co-ordination sites are occupied by N,N′ and O,O′ donors from two oxalate and two pyridine molecules at ca. 2.0 A. Two weaker axial bonds are formed with O″ and O″′ atoms from two oxalate anions, with a O(1″)–Cu–O(1″′) angle of 162.9(1)°. From the magnetic susceptibility measurements, the complex is found to exhibit weak ferromagnetic exchange interaction between nearest-neighbour copper(II) ions.

Carbonate Precipitation of Bacterial Strains Isolated from Sediments and Seawater: Formation Mechanisms

This article presents a research study on carbonate formation in solid and liquid media by Thalassospira sp., Halomonas sp., Bacillus pumilus, and Pseudomonas grimontii, four bacterial strains isolated from sediments and deep seawater. As part of this study, we analyzed carbonic anhydrase activity, pH, adsorption of calcium and magnesium ions, and total organic and inorganic carbon. The geochemical program PHREEQC was also used to calculate the mineral saturation indexes in all the cultures. The minerals formed were studied with X-ray diffraction, X-ray dispersive energy microanalysis, and scanning electron microscopy. In addition, all four bacterial strains were found to induce carbonate precipitation and to have carbonic anhydrase activity. Sterile control experiments did not precipitate carbonate. In solid M1 and B4 media, all of the strains precipitated magnesium calcite, whereas in the liquid media, they precipitated different percentages of magnesium calcite, aragonite, and monohydrocalcite. In both cases, small amounts of amorphous precipitates were also produced. This article discusses carbonate formation and the possible role played by metabolic activity, bacterial surfaces and carbonic anhydrase in this process. Finally, the results obtained lead to a hypothesis regarding the importance of carbonate precipitation for the survival of bacteria populations in certain habitats.

Examining Hydrated Minerals Using Optically Stimulated X-Ray Diffraction, an Inexpensive Modification of Traditional Diffractometers

Optically stimulated X-ray diffraction (OSXRD) modifies a traditional powder XRD by attaching a thermocouple, a precision temperature controller (PID control), and a thyristor power regulator firing a halogen lamp (75 w, 220 V, red-infrared) that provides up to 210°C to the sample. The included OSXRD software allows the diffractometer to be controlled and sequential profiles (ASCII files) to be obtained. These profiles are subsequently processed, obtaining new files: (1) Three-dimensional (cps versus 2θ versus time-temperature), (2) peak areas and (3) maximum 2θ positions. The automatic temperature control loop, using the proportional-integral-derivative control (PID) method, and the modifications of the XRD chamber are described. Some examples of hydrated minerals were examined in the OSXRD prototype: (1) the epsomite-hexahedrite phase transition in different isothermal analyses (28°C, 30°C, 32°C) and (2) the dehydration of the interfaces of a fibrous aragonite. Three-dimensional plots show the epsomite-hexahedrite phase transition in detail. However, in the case of aragonite (no phase transition) the 3D plot does not show visible changes, but the graph of peak-areas distribution versus temperature increases in sinusoidal shape, suggesting steps during the dehydration processes.

Precipitation of Phosphate Minerals by Microorganisms Isolated from a Fixed-Biofilm Reactor Used for the Treatment of Domestic Wastewater

The ability of bacteria isolated from a fixed-film bioreactor to precipitate phosphate crystals for the treatment of domestic wastewater in both artificial and natural media was studied. When this was demonstrated in artificial solid media for crystal formation, precipitation took place rapidly, and crystal formation began 3 days after inoculation. The percentage of phosphate-forming bacteria was slightly higher than 75%. Twelve major colonies with phosphate precipitation capacity were the dominant heterotrophic platable bacteria growing aerobically in artificial media. According to their taxonomic affiliations (based on partial sequencing of the 16S rRNA), the 12 strains belonged to the following genera of Gram-negative bacteria: Rhodobacter, Pseudoxanthobacter, Escherichia, Alcaligenes, Roseobacter, Ochrobactrum, Agromyce, Sphingomonas and Paracoccus. The phylogenetic tree shows that most of the identified populations were evolutionarily related to the Alphaproteobacteria (91.66% of sequences). The minerals formed were studied by X-ray diffraction, scanning electron microscopy (SEM), and energy dispersive X-ray microanalysis (EDX). All of these strains formed phosphate crystals and precipitated struvite (MgNH4PO4·6H2O), bobierrite [Mg3(PO4)2·8H2O] and baricite [(MgFe)3(PO4)2·8H2O]. The results obtained in this study show that struvite and spherulite crystals did not show any cell marks. Moreover, phosphate precipitation was observed in the bacterial mass but also near the colonies. Our results suggest that the microbial population contributed to phosphate precipitation by changing the media as a consequence of their metabolic activity. Moreover, the results of this research suggest that bacteria play an active role in the mineral precipitation of soluble phosphate from urban wastewater in submerged fixed-film bioreactors.

A novel example of a direct interaction between the carbonyl oxygen, O(6), of a N(7)-bonded 6-oxopurine and copper(II). Preparation, spectroscopic study and crystal structure of bis(8-methylthiotheophyllinato)bis(pyridine)copper(II)

Abstract The preparation, spectroscopic study and crystal structure of the complex bis(8-methylthiotheophyllinato) bis(pyridine)copper(II), [Cu(L)2(py)2], are reported. The complex crystallizes in the monoclinic system, space group P21/c with a=7.502(2), b=20.352(4), c=9.757(2) A, β=98.67(3)° and Z=2. The structure was solved for 4056 non-zero Mo Kα reflections (R=0.040). The structure consists of discrete [Cu(L)2(py)2] molecules with the copper(II) atom located on a center of symmetry. Each molecule includes two trans N(7)/O(6) bidentate ligands and two trans pyridine molecules. The copper ligand environment can be described as a highly elongated octahedron with four strong CuN bonds forming an exact basal plane (CuN(7)=1.999(2); CuN(15)=2.032 A) and two weak axial bonds (2.825(2) A) to O(6) and O(6′) carbonyl oxygen atoms. This CuO(6) distance is the shortest observed in a copper(II) complex with a 6-oxopurine. Owing to the N(7)/O(6) bite of the theophyllinato chelate, the CuN(7) bond does not lie as the expected lone-pair direction of N(7) (C(8)N(7)Cu=141.8(2); CuN(7)C(5)=114.9(2)°) and the O(6)O(6′) axis is tilted 15.6° from the normal to the basal plane. The ESR and electronic spectra of the complex are consistent with the same structure being retained in CH2Cl2 solution. The ESR spectra of the complex in CH2Cl2 solution show nine lines of nitrogen superhyperfine splitting indicating clearly the coordination of four nitrogen atoms toward copper(II).

Crystal and molecular structure of methyl α-d-galactopyranoside 3-(sodium sulfate) monohydrate

Abstract The crystal and molecular structure of methyl α- d -galactopyranoside 3-(sodium sulfate) monohydrate has been determined by X-ray diffraction. The molecular structure has a distorted chair conformation 4C1. The conformation of the hydroxymethyl group is gauche-cis and the methyl group is gauche-trans with respect to the pyranoid ring. The distorted sodium ion environment has seven closest oxygens of two different molecules. Coordination with (O-5, O-4, O-6) and (O-1, O-2), related by translational symmetry along the a axis, together with water oxygen O-1W and O-9 of the sulfate group, complete the first coordination sphere of sodium. A complex hydrogen-bond pattern involves all oxygens of the sulfate group as acceptors, linking molecules in [100] through O-7. The hydroxyl groups on C-2 and C-4 also participate in the bonding pattern. The complex packing by hydrogen bonds and ion coordination results in relevant differences with respect to the structure of other surface pyranosides.

Examining Hydrated Minerals Using Optically Stimulated X-Ray Diffraction, an Inexpensive Modification of Traditional Diffractometers: RESEARCH METHODS PAPERS

ABSTRACT Optically stimulated X-ray diffraction (OSXRD) modifies a traditional powder XRD by attaching a thermocouple, a precision temperature controller (PID control), and a thyristor power regulator firing a halogen lamp (75 w, 220 V, red-infrared) that provides up to 210°C to the sample. The included OSXRD software allows the diffractometer to be controlled and sequential profiles (ASCII files) to be obtained. These profiles are subsequently processed, obtaining new files: (1) Three-dimensional (cps versus 2 versus time-temperature), (2) peak areas and (3) maximum 2 positions. The automatic temperature control loop, using the proportional-integral-derivative control (PID) method, and the modifications of the XRD chamber are described. Some examples of hydrated minerals were examined in the OSXRD prototype: (1) the epsomite-hexahedrite phase transition in different isothermal analyses (28°C, 30°C, 32°C) and (2) the dehydration of the interfaces of a fibrous aragonite. Three-dimensional plots show the epsomite-hexahedrite phase transition in detail. However, in the case of aragonite (no phase transition) the 3D plot does not show visible changes, but the graph of peak-areas distribution versus temperature increases in sinusoidal shape, suggesting steps during the dehydration processes.