Life inhabits rocks: clues to rock erosion from electron microscopy of pisolite at a UNESCO heritage site in Brazil

Rock erosion is attracting increasing attention from scientists worldwide. The area encompassing the Saint John Baptist Church, Saint John Village, XVII century ruins in Rio Grande do Sul at the UNESCO World Heritage Site is considered a Brazilian treasure. However, the risk of damage to this site from rock erosion has recently increased tremendously. Generally, the rocky construction such as fence, wall and tomb stone, seems strong but is actually extremely sensitive to erosion caused by lichens, fungi, molds and bacteria. Because of biological erosion and massive exposure, the fresh rock is dominated by clays and microorganisms. Water-adsorbing clays and microorganisms influence the mechanisms of the rock erosion. In this study, the formation of bio-clay-minerals in porous structure of pisolite was demonstrated using electron microscopy. Bacterial clay mineralization can deform the rock structure and even produce organic materials. Biological activity could easily corrode rocky constructions around the Saint John Baptist Church site. The rocks are pisolitic laterites possibly formed in Tertiary over the Kretaceous Parana flood Basalts. Samples inhabited by lichens and fungi were collected from a collapsed wall in the ancient church. The zonal reddish-brown pisolites are 4 mm in diameter in a matrix of clays associated with porous and empty spaces. Elemental distribution maps from X-ray fluorescence microscopy show iron-rich spherules of pisolite, whereas the matrix is composed of Al, Si, Mn, and Sr; thus producing goethite and kaolinite. Transmission electron microscopic observation showed that various types of bacteria inhabit the spherule and are associated with clay minerals and graphite. STEM elemental analysis confirmed the bio-clay-mineralization with Al, Si, S, and Fe, around bacterial cells. The results presented here will improve our understanding of nm-scale bio-mineralization and bio-erosion in lateritic rocks. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Micro-FTIR spectroscopic signatures of Bacterial lipids in Proterozoic microfossils

Precambrian microbial fossils show carbonaceous cellular structure, which often resemble in shape and size cyanobacteria and other prokaryotes. Morphological taxonomy of these minute, simple, and more or less degraded fossils is, however, often not enough to determine their precise phylogenetic positions. Here we report the results of micro-FTIR spectroscopic analyses of well-preserved microfossils in 850 Ma and 1900 Ma stromatolites, together with those of 8 species of extant prokaryotes and 5 of eukaryotes for comparison. These Proterozoic fossils have low CH₃/CH₂ absorbance ratios (R_3/2 < 0.5) of aliphatic CH moieties, suggesting selective preservation of long, straight, aliphatic carbon chains probably derived from bacterial membrane lipids. All the observed R_3/2 values of coccoids, filaments and amorphous organic matter resemble lipid fractions of extant Bacteria including cyanobacteria, but not Archaea. The results indicate that Proterozoic microfossils belong to Bacteria, which is consistent with the cyanobacterial origin inferred from morphology. Moreover, the R_3/2 value of fossilized cell would reflect chemical composition of its precursor membrane lipid, thus could be a useful new tracer for distinguishing Archaea, Bacteria and possibly Eucarya for fossilized and extant microorganisms.     

Metabolic patterning of biosilicification

Here we show a discernibly unique biosilicification pattern for live, metabolically active Synechococcus cyanobacterial cell surfaces compared to dead Synechococcus cells under identical experimental conditions. The live cell treatments showed signs of cell division and the growth of fimbriae indicating metabolic activity during the 5-day silicification experiment. Live treatment cells were also recultivable after the experiments confirming their continued viability. The metabolically active live cyanobacteria treatment bound twice the amount of colloidal SiO₂ and held it more tightly compared to the dead cell treatment. Further, biosilicification of the live, actively metabolizing bacteria was unipolar, leaving the core surface largely unencrusted. In contrast, biosilicification of the dead cells was heterogeneous, occurring across the entire cell surface with no observable localized pattern. The directed biosilicification localization of live cell surfaces is likely a bacterial strategy to protect the cell functionality against the potentially inhibitory effects of mineral encrustation. Localization of silica biominerals to the polar end of the cell is also consistent with reported bacteria regulated cell polarity, which, under the experimental pH of 3, would enable localized differential attraction between the charged colloidal silica (+) particles and the bacterial cell polar surface (−). Our results show a novel metabolically-linked distinct colloidal SiO₂ biomineralization fingerprint, suggesting a putative biomineralization signature.     

Stability of biological and inorganic hemimorphite: Implications for hemimorphite precipitation in non-sulfide Zn deposits

Hemimorphite, Zn₄Si₂O₇(OH)₂·H₂O, one of the most common minerals in non-sulfide Zn deposits, together with smithsonite and hydrozincite, is one of the most abundant minerals in the “calamine” deposits in SW Sardinia. In spite of their importance for the development of ore genesis models, the stability properties of hemimorphite are poorly known. This paper presents solubility experiments on two different types of hemimorphite: a “geological” hemimorphite from a supergene non-sulfide Zn deposit, of supposed abiotic origin, and a hemimorphite precipitated by bacterial activity. Both specimens were characterized, before and after the experiment, by Synchrotron Radiation X-ray powder diffraction, Scanning Electron Microscopy, and X-ray Absorption Spectroscopy. The calculated solubility product constants (logK_s) are similar for both “geological” and biogenic hemimorphite (30.3 ± 0.4 and 30.5 ± 0.1, respectively). During the solubility experiment, biological hemimorphite undergoes an amorphous to crystalline phase transition, and the distinctive features (mineralized bacterial sheaths and organic filaments), that allowed us to demonstrate its biological origin, are no longer recognizable by Scanning Electron Microscopy.The results of this study may be useful for developing ore genesis models, including evolution in a supergene environment, and in general for performing geochemical speciation and equilibrium calculations. Moreover, our findings open the way for a new interpretation of hemimorphite-forming processes, and suggest the possibility that bacteria may have played a role in the formation of this mineral in ore deposits.     

Microbial primary dolomite from a Norian carbonate platform: northern Calabria, southern Italy

The origin of fine‐grained dolomite in peritidal rocks has been the subject of much debate recently and evidence is presented here for a microbial origin of this dolomite type in the Norian Dolomia Principale of northern Calabria (southern Italy). Microbial carbonates there consist of stromatolites, thrombolites, and aphanitic dolomites. High‐relief thrombolites and stromatolites characterize sub‐tidal facies, and low‐relief and planar stromatolites, with local oncoids, typify the inter‐supratidal facies. Skeletal remains are very rare in the latter, whereas a relatively rich biota of skeletal cyanophycea, red algae and foraminifera is present in the sub‐tidal facies. Some 75% of the succession consists of fabric‐preserving dolomite, especially within the microbial facies, whereas the rest is composed of coarse dolomite with little fabric preservation. Three end‐members of dolomite replacement fabric are distinguished: type 1 and type 2, fabric retentive, with crystal size <5 and 5–60 μm, respectively; and type 3, fabric destructive, with larger crystals, from 60 to several hundred microns. In addition, there are dolomite cements, precipitated in the central parts of primary cavities during later diagenesis. Microbialite textures in stromatolites are generally composed of thin, dark micritic laminae of type 1 dolomite, alternating with thicker lighter‐coloured laminae of the coarser type 2 dolomite. Thrombolites are composed of dark, micritic clotted fabrics with peloids, composed of type 1 dolomite, surrounded by coarser type 2 dolomite. Marine fibrous cement crusts are also present, now composed of type 2 dolomite. Scanning electron microscope observations of the organic‐rich micritic laminae and clots of the inter‐supratidal microbialites reveal the presence of spherical structures which are interpreted as mineralized bacterial remains. These probably derived from the fossilization of micron‐sized coccoid bacteria and spheroidal–ovoidal nanometre‐scale dwarf‐type bacterial forms. Furthermore, there are traces of degraded organic matter, probably also of bacterial origin. The microbial dolomites were precipitated in a hypersaline environment, most likely through evaporative dolomitization, as suggested by the excess Ca in the dolomites, the small crystal size, and the positive δ¹⁸O values. The occurrence of fossilized bacteria and organic matter in the fabric‐preserving dolomite of the microbialites could indicate an involvement of bacteria and organic matter degradation in the precipitation of syn‐sedimentary dolomite.     

The relative contributions of physical and microbiological factors to cohesive sediment stability

The stabilising effects of natural benthic diatom and bacterial assemblages on cohesive sediments were compared with those caused by physico-chemical binding alone. Cohesive sediment beds were reconstructed in 4 annular laboratory miniflumes, using sediment collected at 5–6 m water depth from a local fjord. The sediment was left to stabilise (consolidate) for 1, 2, 5 and 10 days, before being fully resuspended in a series of erosion experiments. The flumes were aerated and subjected to different light/dark conditions; antibiotics were used to isolate diatom from bacteria effects. During consolidation, a constant current velocity was maintained, at a speed well below erosion threshold.     

对虾养殖池水域环境细菌的动态变化

于1990年6月下旬-10月初期间，每隔7－10d在大连市金州区董家沟镇养虾场突池定点采样一次，3h内带回实验室进行细菌培养计数，研究对虾养殖池水域环境中细菌的动态变化。结果表明，对虾养殖池水中异养菌和弧菌的数量变化与水温的变化趋势相同；6—7月末，细菌增长比较缓慢；8月初开始，细菌数量增长较快，8月中旬达到全年的最高值，异养菌为3．4×105cell／ml，弧菌为1．9×105cell／ml；而后随着水温的下降，水中细菌逐渐减少。底记泥浆中，细菌数量一直呈上升趋势，不受水温的影响；异养菌最高达6×107cell／ml，弧菌达1．5×106cell／ml。     

长江口及其附近海域细菌和三磷酸腺苷的分布特征

于1986年1月和7月在长江口及其附近海域进行了细菌的落射荧光直接计数和三磷酸腺苷(ATP)浓度的测定,同时取分样进行了微生物呼吸作用耗氧速率和叶绿素浓度的测定。结果表明,细菌数量和ATP浓度夏季较冬季高,总的分布趋势是,高值区出现在内河段和长江口,向外海逐渐降低;细菌数同悬浮体浓度、硝酸盐浓度和耗氧速率呈正相关,与盐度呈负相关。冬季,在整个海域细菌是ATP的主要贡献者和溶解氧的主要消耗者;夏季,沿冲淡水方向ATP出现两个峰值,第一峰值出现在长江口的最大浊度带,由细菌所贡献;第二个出现在盐度25—30的区域,由浮游植物所贡献。呼吸作用耗氧速率也呈现了与ATP相似的分布特征。     

Carbonate and silicate biomineralization in a hypersaline microbial mat (Mesaieed sabkha,Qatar): Roles of bacteria,extracellular polymeric substances and viruses

In a modern peritidal microbial mat from Qatar, both biomediated carbonates and Mg‐rich clay minerals (palygorskite) were identified. The mat, ca 5 cm thick, shows a clear lamination reflecting different microbial communities. The initial precipitates within the top millimetres of the mat are composed of Ca–Mg–Si–Al–S amorphous nanoparticles (few tens of nanometres) that replace the ultrastructure of extracellular polymeric substances. The extracellular polymeric substances are enriched in the same cations and act as a substrate for mineral nucleation. Successively, crystallites of palygorskite fibres associated with carbonate nanocrystals develop, commonly surrounding bacterial bodies. Micron‐sized crystals of low‐Mg calcite are the most common precipitates, together with subordinate aragonite, very high‐Mg calcite/dolomite and ankerite. Pyrite nanocrystals and framboids are present in the deeper layers of the mat. Calcite crystallites form conical structures, circular to triangular/hexagonal in cross‐section, evolving to crystals with rhombohedral terminations; some crystallite bundles develop into dumb‐bell and stellate forms. Spheroidal organo‐mineral structures are also common within the mat. Nanospheres, a few tens of nanometres in diameter, occur attached to coccoid bacteria and within their cells; these are interpreted as permineralized viruses and could be significant as nuclei for crystallite‐crystal precipitation. Microspheres, 1 to 10 μm in diameter, result from intracellular permineralization within bacteria or the mineralization of the bacteria themselves. Carbonates and clay minerals are commonly aggregated to form peloids, tens of microns in size, surrounded by residual organic matter. Magnesium silicate and carbonate precipitation are likely to have been driven by pH – saturation index – redox changes within the mat, related to microenvironmental chemical changes induced by the microbes – extracellular polymeric substances – viruses and their degradation.     

Coupled trace element and SIMS sulfur isotope geochemistry of sedimentary pyrite:Implications on pyrite growth of Caixiashan Pb-Zn deposit

Colloform pyrite with core-rim texture is commonly deposited in carbonate platforms associated with the sulfide ores such as the Caixiashan Pb-Zn deposit.However,the genesis of colloform pyrite in Pb-Zn deposits,its growth controls and their geological implication are insufficiently understood.Integration of in-situ trace element and SIMS sulfur isotopes has revealed geochemical variations among these pyrite layers.These colloform pyrite occur as residual phases of core-rim aggregates,the cores are made up of very fine-grained anhedral pyrite particles,with some rims being made up of fine-grained and poorlycrystallized pyrite,while the other rims were featured with euhedral cubic pyrite.which are cemented by fine-grained calcite and/or dolomite with minor quartz.Sulfur isotope analysis shows that some wellpreserved rims have negative δ~(34)S values(-28.12‰to-0.49‰),whereas most of the cores and rims have positive δ~(34)S values(0 to+44.28‰;peak at+14.91‰).Integrating with the methane and sulfate were observed in previous fluid inclusion study,we suggest that the ~(34)S depleted rims were initially formed by bacteria sulfate reduction(BSR),whereas the positive δ~(34)S values were resulted from the sulfate reduction driven by anaerobic methane oxidation(AOM).The well-developed authigenic pyrite and calcite may also support the reaction of AOM.Combined with petrographic observations,trace element composition of the colloform pyrite reveals the incorporation and precipitation behavior of those high abundance elements in the pyrite:Pb and Zn were present as mineral inclusion and likely precipitated before Fe,as supported by the time-resolved Pb-Zn signal spikes in most of the analyzed pyrite grains.Other metals,such as Hg,Co and Ni,may have migrated as chloride complexes and entered the pyrite lattice.Arsenic and Sb,generally influenced by complex-forming reactions rather than substitution ones,could also enter the pyrite lattice,or slightly predate the precipitation of colloform pyrite as mineral inclusions,which are controlled by their hydrolysis constant in the ore fluids.The colloform pyrite may have grown inward from the rims.The successive BSR reaction process would enrich H_2~(32)S in the overlying water column but reduce the metal content,the nucleation of these pyrite rims was featured by strongly negative sulfur isotopes.The following AOM process should be activated by deformation like the turbidity sediment of the mudstone as the sulfide deposition are associated with fault activities that caused the emission of methane migration upward and simultaneously replenishing the metal in the column.The higher AOM reaction rate and the higher metal supply(not only Fe.but with minor other metals such as Pb and Zn) caused by sediment movement enhanced the metal concentration within the pyrite lattice.