ALBERT

Description: Archaea belonging to the phylum Bathyarchaeota are the predominant archaeal species in cold, anoxic marine sediments and additionally occur in a variety of habitats, both natural and man-made. Metagenomic and single-cell sequencing studies suggest that Bathyarchaeota may have a significant impact on the emissions of greenhouse gases into the atmosphere, either through direct production of methane or through the degradation of complex organic matter that can subsequently be converted into methane. This is especially relevant in permafrost regions where climate change leads to thawing of permafrost, making high amounts of stored carbon bioavailable. Here we present the analysis of nineteen draft genomes recovered from a sediment core metagenome of the Polar Fox Lagoon, a thermokarst lake located on the Bykovsky Peninsula in Siberia, Russia, which is connected to the brackish Tiksi Bay. We show that the Bathyarchaeota in this lake are predominantly peptide degraders, producing reduced ferredoxin from the fermentation of peptides, while degradation pathways for plant-derived polymers were found to be incomplete. Several genomes encoded the potential for acetogenesis through the Wood-Ljungdahl pathway, but methanogenesis was determined to be unlikely due to the lack of genes encoding the key enzyme in methanogenesis, methyl-CoM reductase. Many genomes lacked a clear pathway for recycling reduced ferredoxin. Hydrogen metabolism was also hardly found: one type 4e [NiFe] hydrogenase was annotated in a single MAG and no [FeFe] hydrogenases were detected. Little evidence was found for syntrophy through formate or direct interspecies electron transfer, leaving a significant gap in our understanding of the metabolism of these organisms.

Description: Using high-resolution angle-resolved photoemission spectroscopy and scanning tunneling microscopy/spectroscopy, the atomic and low energy electronic structure of the Sr-doped superconducting topological insulators (Sr x Bi 2 Se 3 ) was studied. Scanning tunneling microscopy shows that most of the Sr atoms are not in the van der Waals gap. After Sr doping, the Fermi level was found to move further upwards when compared with the parent compound Bi 2 Se 3 , which is consistent with the low carrier density in this system. The topological surface state was clearly observed, and the position of the Dirac point was determined in all doped samples. The surface state is well separated from the bulk conduction bands in the momentum space. The persistence of separated topological surface state combined with small Fermi energy makes this superconducting material a very promising candidate for the time reversal invariant topological superconductor.

Description: The crystal structures of two autunite-group minerals have been solved recently. The crystal structure of bassetite, Fe 2+ [(UO 2 )(PO 4 )] 2 (H 2 O) 10 , from the type locality in Cornwall, United Kingdom (Basset Mines) was solved for the first time. Bassetite is monoclinic, space group P 2 1 /n, a = 6.961(1), b = 20.039(2), c = 6.974(1) Å and β = 90.46(1)°. The crystal structure of saléeite, Mg[(UO 2 )(PO 4 )] 2 (H 2 O) 10 , from Shinkolobwe, Democratic Republic of Congo, was also solved. Saléeite is monoclinic, space group P 2 1 /n, a = 6.951(1), b = 19.942(1), c = 6.967(1) Å and β = 90.58(1)°. The crystal structure investigation of bassetite ( R 1 = 0.0658 for 1879 observed reflections with | F o | ≥ 4 F ) and saléeite ( R 1 = 0.0307 for 1990 observed reflections with | F o | ≥ 4 F ) confirms that both minerals are topologically identical and that bassetite contains ten water molecules per formula unit. Their structure contains autunite-type sheets, [(UO 2 )(PO 4 )] – , consisting of corner-sharing UO 6 square bipyramids and PO 4 tetrahedra. Iron and magnesium are surrounded by water molecules to form Fe(H 2 O) 6 or Mg(H 2 O) 6 octahedra located in interlayer, between the autunite-type sheets. Two isolated independent water molecules are also located in interlayer. Energy-dispersive X-ray spectroscopy analysis confirmed the chemical composition obtained from structure refinement. These new data prompt a re-assessment of minerals of the autunite and meta-autunite groups.

Description: The crystal structure of the natural aluminium uranyl arsenate hydrate arsenuranospathite, ideally Al[(UO 2 )(AsO 4 )] 2 F(H 2 O) 20 , from the Rabejac deposit, Lodève, France, was solved for the first time. Arsenuranospathite is orthorhombic, space group Pnn 2, Z =2, a =29.9262(7), b = 7.1323(1), c = 7.1864(1) Å, and V = 1533.9(1) Å 3 . The crystal structure was refined from single-crystal X-ray diffraction data to R 1 = 0.0373 for 3348 unique observed reflections, and to wR 2 =0.0768 for all 3833 unique reflections. The mineral is isostructural with its P-analogue uranospathite, Al[(UO 2 )(PO 4 )] 2 F(H 2 O) 20 ; both minerals contain the autunite-type sheet [(UO 2 )((As,P)O 4 )]– constituted by corner-sharing UO 6 square bipyramids and (As,P)O 4 tetrahedra. Aluminium is linked with water molecules to form an Al(H 2 O) 6 octahedron located in the interlayer of the structure. Eight independent and isolated water molecules are also located in the interlayer. A very complex network of H-bonds links the water molecules together, to the Al octahedra and to the uranyl-arsenate sheets. Fluorine was not accurately located by the current structure model and is supposed to replace some of the H 2 O molecules in the Al(H 2 O) 6 octahedron. The crystal-chemical formula, calculated on the basis of (As + P + Si + S) = 2 cations per formula unit is (Al 1.02 Cu 0.01 )[(U 0.98 O 2 )(As 0.89 P 0.08 Si 0.02 S 0.01 )O 4 ] 2 (F 0.77 OH 0.05 )(H 2 O) 20.18 .

Description: Strontiohurlbutite, ideally SrBe 2 (PO 4 ) 2 , is a new member of hurlbutite group discovered in the Nanping No. 31 pegmatite, Fujian province, southeastern China. Crystals are mainly found in zones I, II, and IV; they are platy, subhedral-to-anhedral, with a length from 5 μm to 1.5 mm. Associated minerals mainly include quartz, muscovite, beryl, hurlbutite, hydroxylherderite, apatite-group minerals, and phenakite. Strontiohurlbutite crystals are light blue, translucent-to-transparent, and have vitreous luster. The Mohs hardness is about 6, and the tenacity is brittle. Optically, strontiohurlbutite is biaxial (–), α = 1.563(3), β = 1.569(2), = 1.572(3) (white light), 2 V meas = 68.5(5)°, and exhibits weak dispersion, r 〉 v. The optical orientation is X = b , Y c . Electron-microprobe and SIMS analyses (average of 16) give SrO 29.30, P 2 O 5 51.05, CaO 0.91, BaO 0.64, and BeO 17.71 wt%; total 99.61 wt%. The empirical formula, based on 8 O apfu, is (Sr 0.81 Ca 0.05 Ba 0.01 ) 0.87 Be 2.02 P 2.05 O 8 . The stronger eight lines of the measured X-ray powder-diffraction pattern [ d in Å( I )( hkl )] are: 3.554(100)(121); 3.355(51)(211); 3.073(38)(022); 2.542(67)(113); 2.230(42)(213); 2.215(87)(32); 2.046(54)(223); 1.714(32)(143). Strontiohurlbutite is monoclinic, space group P 2 1 / c ; unit-cell parameters refined from single-crystal X-ray diffraction data are: a = 7.997(3), b = 8.979(2), c = 8.420(7) Å, β = 90.18(6)°, V = 604.7(1) Å 3 ( Z = 4, calculated density = 3.101 g/cm 3 ). The mineral is isostructural with hurlbutite, CaBe 2 (PO 4 ) 2 , and with paracelsian, BaAl 2 Si 2 O 8 . The formation of strontiohurlbutite is related to the hydrothermal alteration of primary beryl by late Sr- and P-rich fluids.

Description: Four beryllophosphates with general formula M 2+ Be 2 P 2 O 8 ( M 2+ = Ca, Sr, Pb, Ba) have been synthesized under hydrothermal conditions at 200 °C. Their crystal structures were solved by direct methods and refined by full-matrix least-squares techniques on the basis of F 2 for all unique reflections to agreement indices R 1 of 2.3, 4.8, 1.5, and 2.1%, respectively. CaBe 2 P 2 O 8 is monoclinic, space group P 2 1 / c , Z = 4, a 7.809(1), b 8.799(1), c 8.309(1) Å, β 90.51(1)°, V 570.98(2) ų. SrBe 2 P 2 O 8 is monoclinic, space group P 2 1 / c , Z = 4, a 8.000(1), b 8.986(1), c 8.418(1) Å, β 90.22(1)°, V 605.10(6) ų. PbBe 2 P 2 O 8 is monoclinic, space group P 2 1 / c , Z = 4, a 8.088(1), b 9.019(1), c 8.391(1) Å, β 90.12(1)°, V 612.22(1) ų. BaBe 2 P 2 O 8 is hexagonal, space group P 6/ mmm , Z = 1, a 5.028(1), c 7.466(1) Å, V 162.51(1) ų. The three first compounds are isostructural and show a paracelsian-type structure composed of a framework of corner-sharing BeO 4 and PO 4 tetrahedra. These tetrahedra are assembled in four- and eight-membered rings showing the typical UUDD and DDUDUUDU patterns, respectively. The M 2+ (Ca, Sr, Pb) cation occurs in a distorted 7+3-coordinated polyhedron located in the eight-membered ring. CaBe 2 P 2 O 8 and SrBe 2 P 2 O 8 are isostructural with the minerals hurlbutite and strontiohurlbutite, respectively. The structure of BaBe 2 P 2 O 8 consists of double layers of tetrahedra, which contain both Be and P in a 1:1 ratio. Inside the layers, the (Be,P)O 4 tetrahedra form six-membered rings by sharing corners. The Ba atoms are located in very regular 12-coordinated polyhedra and connect two successive double layers. This Ba beryllophosphate is the synthetic counterpart of minjiangite, and shows similarities with the mineral dmisteinbergite, CaAl 2 Si 2 O 8 , a hexagonal polymorph of anorthite. Other hydrothermal experiments were performed in order to establish the stability of these M 2+ Be 2 P 2 O 8 compounds as a function of temperature and pH; the results show that synthetic hurlbutite can crystallize in acidic as well as in basic conditions. Furthermore, these experiments show that the four title compounds are stable at high temperatures and pressures (600 °C, 1 kbar).

Description: In order to assess the stability of Fe-rich alluaudites in pegmatites, we performed hydrothermal experiments between 400 and 700 °C (1 kbar), in the Na–Fe 2+ –Fe 3+ (+PO 4 ) ternary system. These experiments produced several new phosphate minerals, among which was Na 2 Fe 3+ (HPO 4 )(PO 4 )·H 2 O [ a 15.5004(8), b 7.1465(5), c 29.239(2)Å, V 3238.9(3)Å 3 , Pnma ], which shows a crystal structure based on chains of corner-sharing FeO 6 octahedra, similar to those occurring in the jahnsite-group minerals. Alluaudite-type phosphate minerals occupy a large stability field in the center of the Na–Fe 2+ –Fe 3+ (+PO 4 ) system; this stability field covers between 5.8 (500 °C) and 21.1% (700 °C) of the diagram surface. A comparison of the chemical composition of natural Fe-rich alluaudite-type phosphate minerals with the experimental data obtained herein indicates that these minerals crystallized below ca . 450 °C in pegmatites. This temperature value is in good agreement with the secondary Na-metasomatic origin of these phosphate minerals. Moreover, a structural classification of phosphates occurring in the Na–Fe 2+ –Fe 3+ (+PO 4 ) diagram has been established, taking into account the connectivity between FeO 6 octahedra occurring in the crystal structures of the synthesized phases. This classification indicates a variation of the structural complexity of phosphates, characterized by an increasing dilution of FeO 6 octahedra in the structure as the Na content increases.

Description: Mengxianminite, ideally Ca 2 Sn 2 Mg 3 Al 8 [(BO 3 )(BeO 4 )O 6 ] 2 , is a new borate mineral from Xianghualing skarn, Hunan Province, southern China. It occurs in the hsianghualite vein of Xianghualing skarn, associated with fluorite, phlogopite, hsianghualite, magnetite, dravite, magnesiotaaffeite-2 N '2 S , and calcite. Mengxianminite forms subhedral to euhedral green crystals from 20 to 200 μm long, translucent to transparent, with a vitreous luster. The crystals show perfect cleavage on {100} and good cleavage on {010}, and do not fluoresce in long- or short-wave ultraviolet light. The estimated Mohs hardness is 8, and the tenacity is brittle with irregular fracture. The calculated density is 4.170 g/cm 3 . Optically, mengxianminite is biaxial (–), with α = 1.80(2), β = 1.83(2), = 1.84(2) (589 nm). The mean chemical composition of mengxianminite is Al 2 O 3 40.00, SnO 2 25.96, MgO 6.57, CaO 8.56, FeO 4.83, B 2 O 3 6.53, BeO 4.37, ZnO 1.81, MnO 1.23, Na 2 O 1.13, TiO 2 0.10, SiO 2 0.04, sum 101.12 with a corresponding empirical formula calculated on the basis of 26 O atoms of (Ca 1.64 ,Na 0.39 ) 2.03 (Sn 1.85 ,Zn 0.24 ) 2.09 (Mg 1.75 , Fe 0.72 ,Al 0.42 ,Mn 0.19 ,Ti 0.01 ) 3.09 Al 8 [(B 1.01 O 3 )(Be 0.94 O 4 )O 6 ] 2 . (Be and B were measured by secondary ion mass spectrometry, average of six electron microprobe analyze points and in wt%.) The strongest eight lines of the powder XRD pattern [ d in Å ( I )( hkl )] are: 3.000 (35)(16.2.0); 2.931 (100)(17.1.1); 2.475 (29)(022); 2.430 (30)(13.3.1); 2.375 (100)(14.0.2/640); 2.028 (52)(21.3.1); 1.807 (35)(913); 1.530 (98)(14.6.0/15.3.3). Mengxianminite is orthorhombic, space group Fdd 2; unit-cell parameters refined from single-crystal X-ray diffraction data are: a = 60.699(4), b = 9.914(1), c = 5.745(1) Å, V = 3457.4(4) Å 3 , and Z = 8. The structure of mengxianminite is characterized by the alternating O-T1-O-T2-O'-T2 layers stacked along the a axis, which are equal to two alternating modules: the module A (O-T1-O) corresponding to the spinel module with an additional O layer (AlO 6 octahedra layer), and the module B (T2-O'-T2) showing the simplified formula CaSnAl(BeO 4 )(BO 3 ), where SnO 6 octahedra are isolated in the T2 layers, connected via BeO 4 and CaO 11 groups, and AlO 6 edge-sharing octahedra in the O' layer form chains running along the {011} or {01} direction, connected in the c direction by the BO 3 triangular groups. Mengxianminite is the first borate mineral with both Sn and Be, likely crystallized under F-rich conditions at late stages of the Xianghualing skarn.

Description: The Jocão pegmatite (or Cigana) is located in the well-known Eastern Brazilian Pegmatitic Province (EBPP), Minas Gerais, Brazil. According to their macroscopic textures, three different kinds of phosphate mineral masses were collected from the dumps of the pegmatite: association I is composed of dendritic triphylite, forming intergrowths with silicate minerals (spessartine garnet or albite); association II forms blocky nodules of triphylite-ferrisicklerite-heterosite; and association III shows exsolution lamellae of ferrisicklerite-heterosite in massive beusite. The primary textures and the Fe/(Fe+Mn) ratios of primary triphylite make it possible to establish the crystallization sequence of the primary phases; the petrogenesis of primary intergrowths between garnet and triphylite of association I is also discussed. In the three associations, these primary minerals are hydrothermally altered and secondary species are produced. In association I, the first hydrothermal alteration event was a weakly oxidizing hydroxylation stage, during which triphylite was only replaced by hureaulite (rarely associated with barbosalite) along its cleavage planes. The final stage affecting association I corresponds to meteoric processes during which ludlamite and then vivianite progressively replaced triphylite. Association II evolved under more oxidizing conditions and the first alteration stage corresponds to the progressive oxidation of triphylite accompanied by Li-leaching, leading to ferrisicklerite and heterosite. The second hydrothermal stage corresponds to a hydroxylation event, and the secondary species depend on the phosphate mineral that they replace: triphylite is only altered to Fe 2+ -Mn 2+ -bearing hydrated species (colorless hureaulite); ferrisicklerite is altered to Fe 2+ -, Mn 2+ -, and Fe 3+ -bearing phosphate minerals such as jahnsite s.l. , frondelite s.l., and orange hureaulite; heterosite is replaced by Fe 3+ -bearing species such as ferristrunzite. Consequently, it appears that the secondary phosphate minerals, which crystallize during this second hydrothermal stage, strongly depend on the cations which are locally available in the sample zone. The final stage forms the meteoric species: leucophosphite and phosphosiderite directly replace heterosite, whereas vivianite, a ferrous meteoric species, only appears in the triphylite core. In association III, exsolution lamellae are formed at the expense of a high-temperature homogenous Ca-Li-bearing graftonite-beusite-like phase; when the temperature decreased, Li migrated into triphylite and Ca to the larger M1 site of beusite. During the high-temperature hydrothermal alteration processes, triphylite transforms into ferrisicklerite and heterosite, like in association II; however, beusite is not affected by any transformation process at that stage. During the low temperature hydroxylation stage, ferrisicklerite from the core remains almost unaltered, while beusite is replaced by an intimate mixture of pleochroic Ca-rich hureaulite and tavorite. After this hydroxylation stage, the meteoric stage is characterized by an increase in Ca 2+ and H 2 O activities, responsible for the replacement of hureaulite and tavorite by mitridatite-robertsite. At the nodule border, beusite and heterosite are completely replaced by an intimate mixture mainly composed of frondelite and robertsite-mitridatite. Finally, this study shows that the small phosphate nodules from Jocão are more affected by oxidation than large nodules, thus indicating that the diffusion kinetics of hydrothermal fluids is relatively low in these phosphate nodules. As a consequence, large phosphate nodules show a typical zoning with triphylite (core)–ferrisicklerite-heterosite (rim); this zoning, which preserves the crystal structure of the phosphate minerals, was achieved during the high temperature hydrothermal transformations. The phosphate nodules consequently appear as a relatively closed system compared to the silicate matrix.