Biogenic—Abiogenic Interactions in Natural and Anthropogenic Systems

A biological impact on weathering was recognized already at the beginning of the twentieth century, when biochemical influence of the lichen growth on rocks was convincingly demonstrated. Later it was shown that the progress of solid rock weathering initiated by biological colonization was affected by the initial porosity system and sensitivity of mineral association. In the meantime a considerable amount of diverse scientific data confirm the importance of biological rock colonizers (lichens and free-living rock biofilms) in mineral material dynamics as they occur at the atmosphere-exposed rock surfaces on local as well as global scale. Subaerial rock biofilms—microbial ecosystem including free-living heterotrophic and phototrophic settlers of bare rock surfaces—are characteristic for the first stage of primary succession of terrestrial ecosystems on mineral substrates. These cultivable and free-living communities are dominated by fungi and set the stage for the later development of a lichen cover, but in comparison to lichens also represent a new tool for laboratory experimentation and thus open a new stage of work in geomicrobiology. The minerals sensitivity to microbially induced biological weathering can be demonstrated by studies of natural samples as well as by the laboratory mesocosm experiments.

In model tests, the kinetics and the possibility of concoction and biogenesis of ultradisperse forms of Au, Pd, and Pt in different physical and chemical conditions were examined. Studied biosorbents included peat, humic acids, nonhydrolyzed residue, and microscopic fungi in whole extract gold at 86–99 %, palladium at 89–95 % from chloride solutions, and platinum at 73–87 %. The maximum rate of extraction of Pd and Pt from solution by Penicillium canescens Sopp. biomass at different pH values was observed in sour solutions (pH 1–2) to be 16 and 47 mg/g of an element, respectively. The maximum rate of extraction of Au (to 24 mg/g) by fungic biomass was observed in subacidic solutions (pH 4–5). Palladium and platinum from chloride solutions were extracted from microfungi at rate of 87–95 % at optimum acidity of solution, with gold to 99 %. Using scanning electronic microscopy, the Pd and Pt distribution over the entire mycelium surface was established. The sorption process of precious metals by a fungic cell wall proceeded differently: the interaction process of ionic Au with an organic matrix continues up to the formation of metal nanoparticles, on which gold units are further formed, whereas the interaction of Pd and Pt stops at the sorption stage. It is thought that the biomineralization mechanisms of precious metals are caused by several reactions, including ion exchange, complex formation, and oxidation–reduction.

The aim of the study was to investigate the transformations of clay minerals at the laboratory experiments under the growth and fossilization of alkaline cyanobacteria. The clays incubation with cyanobacteria resulted in different trends of their transformations. The direction and intensity of transformation depends on type of clay mineral. The observed processes were fast and completed within the first 10–60 days of experiments. Cyanobacteria most actively influenced the processes of mineral dissolution and the transformations during the stage of their photosynthesis. Formation of carbonate in the experiments with palygorskite, bentonite, and kaolinite was observed at the stage of cyanobacteria fossilization.

Sulfide ores were investigated along with ore-bearing and metalliferous sediments of the hydrothermal fields in the northern near-equatorial Mid-Atlantic Ridge (MAR) zone: Semenov (13°30–31′N), Ashadze-1 (12°58′N), Zenit-Victoria (20°08′N), and Peterburgskoe fields (19°52′N), discovered during legs 26, 32, and 33 of the R/V Professor Logachev FSUE PMGE. Biogenic carbonate and background sediments of this region were also examined. Lithological, biostratigraphic, and geochemical physical-chemical investigations methods were used. Mineragraphic and precision structural and chemical research of typomorphic minerals were carried out at various stages of lithogenesis. It was found out that most sulfide constructions in the Zenit-Victoria and Peterburgskoe fields, as well as the eastern field of the Semenov cluster, are located in biogenic carbonate sediments of the Holocene and Late Pleistocene ages and represent a new type of sulfide mineralization, unknown earlier in the MAR zone. This mineralization was formed by metasomatic replacement of biogenic carbonate sediments by ore minerals, simultaneously with diffuse percolating of hydrothermal solutions through the sediments.

Investigation of biogenic ultramicrotextures in stromatolites is a newer research avenue, which makes it possible to reconstruct this process on the basis of factual evidence and significantly improve current understanding of the stromatolitic system as a whole. New techniques utilizing the electron microscope allowed to establish a variety of mineralized biogenic ultramicroformations, responsible for occurrence of a particular rock microstructure and to determine their elementary composition. Biota significantly affects the development of stromatolitic reefs and their architecture. The cyanobacterial community is a self-learning biological system, flexibly adapting to climatic, geological, atmospheric, and other natural environments. The obtained results present stromatolites as a complexly organized geosystem, with various interacting components constantly exchanging matter, energy, and information.

The top part of a lateritic profile including laterites in sensu stricto, bauxites and even zones of clay minerals (кaolinite, halloysite, montmorillonite), contains plentiful traces and products of interaction of a substratum with live organic substance and mortmasses. The surface of laterites is hidden under the cover of trees and bushes and the dense felt like a film weaved from filamentous fungus, roots of vegetation, and fossilized microorganisms. Dying off, they turned into biofilms, which is replaced with biominerals such as gibbsite-Al (OH)₃, goethite-HFeO₂, hematite-α-Fe₂O₃, and halloysite-Al₄(OH)₁₀[Si₄O₈](OH)₂ · 4H₂O. A zone of a biological pedoturbation is completely processed by the burrowing organisms. Earlier it was represented that they make only mechanical impact on rocks. We revealed that burrowing organisms, including worms, mill all minerals of a substratum, passing it through the digestive path, and satiate it with biochemically active substances. It causes dissolution of all minerals except rutile—TiO₂. Gibbsite, when passed through a digestive path, recrystallizes and forms surprisingly beautiful and perfect idiomorphic crystals filling the burrows of the worms and covering their walls. We managed to find the paradoxical phenomenon: passing of worms through large (2–4 cm) quartz crystals. The entrances are surrounded with a biofilm similar to slimes and turned into units of crystals of hematite. The described phenomena are established on numerous bauxite deposits of India, Guinea, and Brazil of the modern tropic and on the ancient deposits of Siberia.

Nodules of different compositions from Paleozoic sedimentary rocks and those deposited by microbial communities in laboratory-scale experiments were studied by the use of electron paramagnetic resonance, X-ray diffraction, and scanning electron microscopy with energy-dispersive spectrometer. The study of the mineral composition of fossil nodules showed that they have monomineral composition of dolomite or chalcedony, mixed composition of dolomite-chalcedony or of opal-dolomite, and finally nodules can be composed of alternating opal and chalcedony layers cementing fine dispersed dolomite grains or clusters of irregular shape. Similarity in dolomite crystal lattice defects in both the nodules and the host rocks confirms their formation during synsedimentary early diagenesis. Bacterial activity during sedimentary nodules growth is evidenced by the presence of paramagnetic carbon-centered free radicals of fossilized protein substances and findings of fossil bacteria. Experimental laboratory-scale modeling of natural carbonate deposition by microbial communities confirms that bacteria can promote nodules formation.

Information on fossilized resin—a valuable raw material for chemistry, agriculture, and medicine—from the Russian Far East is scarce and insufficient. We studied an extensive collection of samples of amber from beach placers from the mouth of the Najba River to the village of Starodubskoe (South Sakhalin). The sources of amber deposits were erosional local coal deposits from the Paleogene age. The shapes of the wreckage were mostly wrong, squished, flow-like, round and drop-like. The transparency of the samples ranged from perfect to opaque. The textures were solid and flow-sandwich. The color ranged from light yellow to brownish or cherry red. Amber contains numerous microscopic minerals, organic materials, and gaseous inclusions. Based on spectroscopic infrared studies, most amber samples were found to be rumanites, while the rest are an intermediate type between rumanites and retinites. The central part of the sample may have a composition of the rumanite and peripheral-zone retinite. Two main compositional features of these natural resins are the ratio of aromatic to oxygenated hydrocarbons, and the ratio between the ester and the carboxyl groups in the oxygenated compounds. The amber coloration is mainly determined by the distribution of bitumen admixture originating from bitumen crusts of the amber pieces, which also determines the color zoning of the specimens.

The textural, mineralogical, and geochemical features of quartz-hematite rocks associated with Urals VMS deposits indicate that the tube microfossils are responsible for immobilization and accumulation of chemical elements during precipitation of authigenic minerals. The crystallization of authigenic minerals is a result of submarine transformation of mixed hyaloclastitic, sulfide, and carbonate sediments and diagenetic processes, which modify the mineralogy and geochemistry of sediments. The tube microfossils about 100 μm across and up to 1 mm long consist of the external rim made up of fine-disperse hematite or hematite-quartz aggregates and of the internal channel filled with hematite and/or transparent quartz, fine-disperse hematite-quartz aggregates, leucoxene, rare sulfides, apatite, Fe-chlorite, and Mn-calcite. The carbon isotopic composition of calcite from quartz-hematite rocks with tube microfossils (up to −26.2 ‰) indicates its biogenic origin. The habitat conditions of the tube microfossils favored the mineral precipitation. The newly formed apatite, rutile, illite, monazite, dolomite, ankerite, siderite, monheimite, REE carbonates, anatase, leucoxene, Mn-oxides, titanomagnetite, and hematitized framboidal pyrite are observed in quartz-hematite matrix with abundant tube organisms in contrast to quartz-hematite rocks free of tube microfossils. Biomorphic hematite contains high contents of Mn (up to 9393 ppm), As (up to 1872 ppm), V (up to 779 ppm), W (up to 1091 ppm), Mo (up to 40 ppm), and U (up to 8.68 ppm), which are indicative of biological mechanisms of accumulation and conservation of these metals in the system.

For the first time, the quantitative geochemical data are given for urban soils of several groups of cities which differ in population. The content of chemical elements is considered as well as the specific ecological significance of soil contamination by these elements. The figures were established by authors on the base of average concentrations of chemical elements in the soils of more than 300 cities and settlements. The major part of data (sampling, analyses, and their statistical treatment) was obtained directly by authors as a result of special studies conducted for more than 15 years. The sufficiently numerous published materials of different researchers were also used. The greatest elements accumulation comparing with the Earth’s soils (tens of thousands of tons per 1 km2) is associated with an increase in the content of Ca and Mg. Considering the environmental significance of chemical elements accumulation in soils, we note the primary role of Pb and Zn in all groups of cities. Out from the rest pollutants it is necessary, first of all, to note As, Cu, and Cl, which are the main contaminants in four of six cities groups. In two groups of settlements, Cd and Co are important soil pollutants. In three groups, a considerable increase in the Ca content significantly modifies ecological–geochemical state of soils.

Understanding and deciphering the processes proceeding near the surface are the urgent tasks of contemporary mineralogy and geochemistry, which are especially important for resolving ecological challenges and developing principles of rational environmental management. The paper presents our systematized data published about the thermodynamics of selenites, which are formed in the weathering zone of the sulfide ores, and determines approaches to quantitative physicochemical modeling of their formation conditions. The activities of components in natural waters beyond the zones of natural (oxidation zones) and man-made contamination with selenium (a_ΣSe = 10−9, a_ΣFe = 10−5, a_ΣCu = 10−7, a_ΣZn = 5 × 10−7, a_ΣCo = 10−8, a_ΣNi = 6 × 10−8, and a_ΣPb = 10−8) and in waters formed in the oxidation zone (a_ΣSe = 10−5–10−4, a_ΣFe = 10−2, a_ΣCu = 10−2, a_ΣZn = 10−2, a_ΣCo = 10−3, a_ΣNi = 10−2, a_ΣPb = 10−4) have been estimated. Eh–pH diagrams were calculated and plotted using the Geochemist’s Workbench (GMB 7.0) software package. The database comprises the thermodynamic parameters of 46 elements, 47 main particles, 48 redox pairs, 551 particles in solution, 624 solid phases, and 10 gases. The Eh–pH diagrams of the Me–Se–H₂O systems (Me = Cu, Pb, Co, Ni, Fe, Zn) were plotted for the average contents of these elements in underground water and for their contents in oxidation zones of sulfide deposits. The formation of Co, Ni, Fe, Cu, Zn, and Pb selenites and selenates at the surface is discussed.

A notable migration of Cu, Zn, and Cd has been revealed in the soils used under irrigation for a long period of time in Egypt. To describe the distribution of these elements throughout the soil profiles, mathematical models of migration (diffusion and convective-diffusion models) have been tested, their adequacy has been shown, and their parameters have been estimated. The coefficients of diffusion (D) and convective diffusion (D_c) were 10−7–10−5 cm2/c for Cd and 10−7–10−6 cm2/c for Cu and Zn. The value for Cd is equal to the diffusion rate in water solutions, which indicates that its fixation in soil layers is almost absent. Changes in the fractional compositions of these elements in the soils caused by irrigation with different-quality water agree with those in the parameters of migration models for Zn and Cd.

Purpose. The aim of our work was to assess changes in the trace element composition of poplar leaves in large cities and mining centers of Mongolia. The objectives of the study included: (1) to reveal the biogeochemical background features and changes in the trace element composition of poplar leaves in urban and mining landscapes; (2) to determine the degree of technogenic disturbance in the chemical composition of urban vegetation; and (3) to assess the functioning and ecological status of poplars under technogenic impact. Materials and methods. Poplar hybrids, which compose about 75 % of the urban woody plantations, were sampled in Ulaanbaatar (77 samples) in the mid-summer of 2008, Erdenet (30 samples) in 2011, Darkhan (19 samples) in 2011, and Sharyngol (21 samples) in 2013. Bulk concentrations of 54 heavy metals in the samples of the dry plant material were measured by inductively coupled plasma mass spectrometry (ICP-MS) on Elan-6100 and Optima-4300 analyzers. Results and discussion. The local biogeochemical background of the Mongolian cities under consideration differs from the mean global values in the higher concentrations of Cd, Sr, As, and Zn. The concentrations of Be, V, Pb, Cr, and Ni in plants of the background areas are lower than their global values. The maximum coefficients of the biogeochemical transformation, Z _v , were revealed in Ulaanbaatar. In the other cities, the values of Z _v in the industrial zones were higher than those in the residential zones by 1.5–2 times. The trace element ratios characterizing the balance in the provision of metabolic processes confirm the conclusion about the satisfactory state of the urban trees.

Objective The objective was to study the peculiarities of micro-element accumulation in environmental objects (soil, vegetation, human body) in the region of the Southern (Bashkir) Transurals, which lacks large industrial plants. Method The research was conducted throughout 2014 in the area of the Southern (Bashkir) Transurals, which includes the Burzyansky, Zilairsky, and Zianchurinsky administrative districts of the republic of Bashkortostan. Samples were collected from 4 to 5 sample areas in each district. The obtained data were averaged. Results The soils were contaminated by copper and zinc (Zilairsky and Zianchurinsky District), iron (Zianchurinsky, Zilairsky, Burzyansky District), manganese (almost all studied soils), cadmium (most of the studied soils, especially Zilairsky District). Despite the differences in the levels of heavy metals, all the studied soils had an acceptable level of contamination. The heavy metal concentration levels in the dry matter of plants growing in the soils of the Southern Transurals exceeded the acceptable limits in some cases, in particular lead (more than 10 times), cadmium (more than 6 times), and zinc (2 times). The research shows that the level of chemical elements in the soil can affect their accumulation in the bodies of people living in the area.Conclusions The results show the perspectives of related scientific fields (between medicine, geology, and ecology), with an aim to study the elemental “portrait” of the population of biogeochemical provinces to which the Southern Urals belong, with the object of scientific research and the implementation of programs designed for elimination of elemental imbalance in the human body.

A close linear correlation between reducing air pollutant emissions from stationary sources (except emissions from iron ore mining in Kostomuksha) and mortality coefficients (annual number of deaths per 1000 people) was revealed: including mortality coefficients from diseases of the circulatory system (r = 0.98), from external causes (r = 0.97) and the total mortality coefficient (r = 0.97) for 2004–2013. The possible total number of deaths caused by these emissions over a 10-year period was estimated in the interval 12.2–31.6 % using linear statistical models. The spasmodic growth of the mortality coefficient from neoplasms in 2008–2011 could have been the result of a sharp rise in motor transport emissions in 2006–2009.

Microprofiles established due to the activity of endolithic communities inside the solid rocks of East Antarctica were studied with the approaches of soil science. Major products of endolithic rock transformation in situ are the silty-sandy fine earth and abundant organo-mineral films that are formed within the porous space of endolithic system. Such films are the result of interaction between biofilms and mineral surfaces and reflect elemental composition of both components, mainly comprising C, O, Si, Al, Fe, K, Ca, Na, and Mg. Morphology observed on different hierarchical levels and microtomography data indicated that different layers of endolithic system are connected with the fracture network serving for the elements transfer in the subsurface part of solid rocks. Examined profiles in granites with high quartz content had clear eluvial–illuvial differentiation patterns similar to macroprofile of a common Podzol (Spodsol) on loose substrates. It is shown, that subaerial segment of hard rocks is not sealed and is potentially permeable for dissolved products of endolithic weathering and pedogenesis. As a unique result—the soil-like pattern is established inside the massive, crystalline rock. Understanding modern processes in endolithic systems is of fundamental importance to decrypt paleosol record, as such systems may be the closest modern analogues of protosoils that existed on our planet before the higher vascular plants with root systems established.

The weathering of mafic and ultramafic rocks in soil environment was investigated in weakly developed soil profiles in order to determine the origin of phyllosilicate association in the soils formed in humid cold climate of the mountainous tundra of the Polar Urals. The objects of the study are represented by soils formed (i) on and underlain by the ultramafic rock and (ii) on the moraine composed of the mafic rock with an admixture of the ultramafic rock fragments. The minerals found in the clay fraction (<1 µm) of the profiles are the same, characterized by the presence of smectite (saponite), which is absent in both mafic and ultramafic rocks; serpentine and talc identified in ultramafic rock; and chlorite. Chlorite was found in both types of rocks. It was shown that the appearance of smectite (saponite) in the weakly developed soil is not related to pedogenesis. But these soil profiles illustrate the possibility of soil formation on “mature” fine earth formed from a high-sensitive ultramafic rock due to chemical weathering. In cold soil environment the more weatherable ultramafic material plays the more important role as a prerequisite for the weathering trends and soil formation than a mafic rock. The admixture of ultramafic materials mitigates the development of Entic Podzols which were earlier found in the Polar Urals on the pure mafic materials. So, the presence of ultramafic materials either predominating or even in admixture results in the “extreme lithological environment” for a pedogenesis and in the formation of weakly developed soils—Regosols and Leptosols.

In severe climatic and specific landscape conditions of Antarctica birds play an important role in transportation of organic matter of guano to the coastal landscapes. It has been shown that redistribution of guano components affects the speed of soil cover spatial development and formation of new polypedons of soils in environments, surrounding rookeries. Soils development is also affected by flying birds’ transportation activity, while they transport the viable diasporas of plants, material of limpet shells, etc. This affects an initial or additional colonization of rocks being in distance from the coasts, sources of seed, and organic matter. Soils of Antarctica formed under effect of bird activity are the following: the most known typical ornithosols of the current penguin rockeries, post-Ornithosols, developed during post-Ornithogenic succession and organic lithosols formed in the areas of flying sea birds nesting and feeding areas due to limited nitrification and viable plant material and diasporas transportation.

Pioneer plant communities play an important role in the process of parent substrate colonization by biota and a successful restoration of ecosystem as well, especially in the first stages of recovery successions. The aim of the present research is to study the influence of plant communities of the initial stages of primary succession on the mineral composition of substrates from sandy quarries situated in the forest-tundra zone to understand the specificity of substrate transformation initiated by vegetation, Western Siberia close to the town of Labytnangi. Sandy substrate was quarried here in former open woodlands, in communities with spruce, larch, and birch in the overstory and dwarf shrubs, mosses, and lichens in the ground layer. The time of vegetation development in quarries varies from 15 to 40 years. In substrates, pH values decrease simultaneously with the rise of moistening as well as plant canopy closure, which also influences the moistening. Clay size fraction of all samples is characterized by the same mineral association, as follows: highly smectitic clay, minerals of the mica group, chlorite, and kaolinite. In addition, traces of quartz were also identified. According to our findings, the changes in substrate mineralogy affected by the plant community decrease from mosses (reduced proportion of highly smectitic clay and transformation of chlorite into random mixed-layer chlorite-smectite), lichens (reduced proportion of highly smectitic clay), and vascular plants (absence of changes).

This study presents the rare earth elements (REE) and Y concentrations in the main soil forming materials and ploughing horizons of North-West Russia agricultural soils. The study area covers Leningrad region, west part of Novgorod and Pskov regions and southern Karelia. Investigated area (200,000 km2) was subdivided into a net of square cells 50 km on 50 km in size. Eighty-one samples of topsoil (0–25 cm, ploughing layer) and subsoil (C-horizon) were collected. REE and Y concentrations were measured using ICP-MS (Perkin Elmer Sciex Elan 5000). The median concentrations of the investigated elements in the soil forming materials were as follows (mg/kg): Y—15.3, La—21.7, Ce—45.0, Pr—5.5, Nd—20.9, Sm—3.9, Eu—0.8, Gd—3.5, Tb—0.5, Dy—2.7, Ho—0.5, Er—1.5, Tm—0.2, Yb—1.5, Lu—0.2. It was found that the content of REE in northwestern Russia soil forming materials is less than in Earth crust. Varve clays and carbonate moraines are enriched in REE content relatively another soil forming materials of northwestern Russia (non-carbonate moraines, lacustrine-glacial loams, sandy loams and sands, fluvioglacial sands and alluvial sands). Content of REE in soils depends on their concentrations in soil forming materials, therefore, spatial distribution of REE in ploughing horizons of agricultural soils reflects regional abundance of different soil forming materials.

The phytotoxicity of tailings dam of the Dzhidinsky tungsten–molybdenum combine has been studied. It is established that the content of toxic chemical elements (Pb, Zn, As, Cu, Co, Mo, Ni, W) in technogenic sands is extremely dangerous; the total contamination index (Zc) is 425–500. The phytotoxicity of the sands with respect to oats is different: the technogenic sands of the Barun-Naryn tailings refer to II (high) toxicity class, while the technogenic sands of the Modonkul deltoid deposit refer to V (normal) toxicity class. The index of total pollution by toxic elements (Zc) of plant oats grown on technogenic sands and their water extract is consistent to high level (aboveground part of plants—12–69, and underground parts—11–147).

Specific natural and geochemical conditions formed on Vasuygan Mire include a wide variety of vegetation, types of peat deposits, and peats composing them. The study of the Vasyugan Mire’s biospheric functions and elaboration of the scientific bases of regional monitoring are important. Therefore, we investigated mire regimes under field conditions. The examined plot, which includes the biogeocenoses connected geochemically with the landscapes, is the model system for the Vasuygan Mire. According to our data, the age of this plot dates back to 2500–4800 years. Our work revealed peculiarities of biochemical processes that exert influence on the formation of hydrochemical runoff from the paludified territory in the peat deposits of the landscape profile. The chemical composition of mire water and the subsequently migrating stream are formed due to the mixture of atmospheric precipitation with swampy waters. The composition of swampy water is defined by the arrival of movable compounds from the peat deposit, which underwent a regular biochemical transformation. The total runoff of chemical elements during the course of the runoff were as follows: Ca2+—1398, Fe_total—311, SO₄2−—391, NO₃−—236, NO₂−—1, Pb—2.253 × 10−3, Mn—317.29 × 10−3, Zn—41.191 × 10−3, Ni—8.151 × 10−3, and Ti—29.651 × 10−3 kg/km2. The annual runoff losses of dissolved organic matter were equal to 6945 kg/km2. Our study of the concrete water objects and physical, chemical, and biological processes of the transformation of substance and energy flows on the catchment areas provide insight into the chemical constituents of georunoff.

A major focus of this paper is to investigate the environmental fate of chemical pollutants with the amine functionality in soils and its underlying molecular processes. Taking into account a key role of the amine in the structure of chemical pollutant and its reactivity, spin labels with different amine groups were applied to natural soils and investigated by means of electron paramagnetic resonance (EPR) analysis. As spin labels, stable nitroxide radicals modeled chemical pollutants with the amine and, meanwhile, afforded knowledge of the molecular environment of soil where they were located or bound via the amine. The first results of the Spin Labeling EPR investigation showed that chemical pollutants including the amine were differently partitioned among soil sites with the different water–octanol coefficients Kow in dependence on the amine base that allowed for accumulating the amines with a weak base by a non-hydrolysable part of soil organic matter, whereas the amines with a strong base were transformed or bound to small molecules (<5 kDa) of a hydrolysable part of soil organic matter. The uneven partitioning of the amines among soil sites of different hydrophobicity intensified a part of anoxic areas in soil that, in turn, resulted in a restriction of areas fit for soil aerobic microorganisms and a decrease in their magnitude.

This article considers water-migration changes of some biogenic elements in system soil-infiltration waters and the role of organic matter during biogenic elements leaching into high mountain ecosystems. The researches covered alpine (3250 m a.s.l.) and meadow steppe (2085 m a.s.l.) belts of the Aragats mountain massif. To study a water migration flow of biogenic elements, a study was done of peculiarities of their migration in system atmospheric precipitation–soil-infiltration waters. The research was done employing a lysimetric method which provides information about soil infiltration rate, chemical composition, and migration of soil water elements. The research allowed to reveal high contents of biogenic elements in the studied compartments of meadow steppe belt. As indicated, migration intensity of the studied elements and rates of soil biomineralization in meadow steppe versus alpine belt are higher as in cold high mountainous conditions mineralization and humification rates of elements are comparatively lower. Consequently, this phenomenon brings about an increase in the contents of the study of biogenic elements and acceleration of their removal with infiltration runoff. Collation between main migration flows of biogenic elements beginning from their entering (atmospheric precipitation) to leaching into groundwater flow allows to conclude that the highest transformation of a migration flow of elements in the ecosystem of the Aragats mountain massif occurs in meadow steppe belt.

Paleoproterozoic (2.0–2.2 Ga) stromatolites from drill cores of the ICDP Project FAR DEEP were studied by Raman spectroscopy and inductively coupled plasma mass spectrometry with laser ablation (LA-ICP MS) methods. Morphological features of the studied Paleoproterozoic stromatolites together with identification of synsedimentary carbonaceous matter by Raman spectroscopy are strong argument for biogenic origin of these carbonate buildups. Precision geochemical analysis of the stromatolite laminae composition links to sedimentary settings and environmental conditions of the microbialite formation.

Various aspects of the granite destruction in urban environments were studied in cities of Northern Europe (Russia and Finland). Granite is commonly used to create monuments, buildings, and embankments. Rock degradation is associated with physical, chemical, and biological factors. In this chapter, the main forms of granite destruction are described and a classification of biofouling granite is developed. Features of granite biological colonization were established. Rapakivi granite is most strongly subjected to damage by abiotic weathering processes as well as biological colonization, which can be explained by the peculiarities of the mineral composition and texture of this type of rock.

The work is devoted to the research of the interactions between microorganisms, rocks and minerals in simulation experiment conditions. Bacteria and microscopic fungi isolated from different types of rocks were studied as agents of biomineralization processes on the mineral surface in moist chamber and in liquid medium. The formation of calcium oxalates under the influence of fungi (Aspergillus and Penicillium) and bacteria (Bacillus) was observed on the surface of different calcium-bearing minerals: carbonates, phosphates, silicates. The obtained results allow to compare the role of microorganism metabolism, peculiarities of the stone substratum and the experimental conditions (the role of the environment) in calcium oxalate crystallization. It was shown that it is a complicated multifactor process. The metabolic activity of microorganisms affects the morphogenesis of the forming oxalates which can be explained by the difference in solubility of stone substrates in various metabolites. The results of simulation experiments showed that the metabolism of the microbial community is an important factor of secondary mineralization on the surface of rocks and minerals. The present results give a scientific basis for creating new methods for cultural heritage stone monument preservation with the use of modern biotechnologies.

According to the results of screening acidification activity of 24 species of micromycetes in vitro, 18 of them produced organic acids in artificial medium. The fungi from genera Penicillium and strains of Aspergillus niger have the most active production of organic acids. The ratio of acids formed by fungi on a liquid glucose-containing medium changes during ontogenesis: gluconic acid and acids of the Krebs cycle dominated in a log phase of growth; oxalic acid accumulated in a stationary phase while concentrations of other organic acids reduced. Oxalic acid is the main acid produced by fungi in a culture and apparently in a natural habitat. Formation of gluconate improves the efficiency of other carbon substrates consumption by fungi. Citric, succinic, malic, and fumaric acids are produced only at higher concentrations of carbohydrate and high ratio of C/N. Production of oxalic acid by micromycetes increases on the media containing only nitrate nitrogen. Zn in concentration up to 2 mM induces secretion of oxalic acid on nitrate media. Copper has stimulation effect on oxalic acid production only in very low concentration (25 µM). Presence of Zn in culture leads to formation of oxalate Zn crystals on the surface of mycelium. On ammonium-containing culture Zn and Cu does not stimulate oxalic acid production, but induce significant morphological changes.

During the reconstruction of the Summer Garden from 2009 to 2011, all marble statues were moved to the exhibition halls of a Russian museum. Replicas of monuments from artificial marble were installed in the Summer Garden. Artificial marble consists of marble chips and polyester resin. It is known that microorganisms can degrade natural marble, but the influence of microfungi on artificial marble has been less studied. This chapter examines the dynamics of microfungi on different stone materials (granite, artificial marble and natural marble) in local ecosystems of the Summer Garden. We found that the artificial marble was covered by microfungi despite the presence of toxic resins in its composition. During the three time periods (spring–summer–autumn) in the study, 45 microfungi species from 21 genera and 3 subdivisions were identified. Of these, 16 typical rock-inhabiting species were observed on the surface of the statues and pedestals. More than 50 % of the species have dark pigmented mycelium or spores. Microfungi species composition varied at all rocky substrates. The greatest similarity was observed between the artificial and natural marble, and the smallest similarity was found between the artificial marble and granite. Mycobiota had a lower species diversity, whereas natural marble had the highest species diversity. The dynamics of microfungi on artificial marble surfaces were studied, and increases of species diversity were noted during the spring–summer season. There were no changes in the dominant species.

The review of published records of lichens on carbonate stone substrates (marbles, limestones, limestone tufa, and concrete) in Saint Petersburg has been presented. Altogether, 66 species of lichens from 35 genera and 16 families have been found in more than 40 papers. The most diverse genera are Verrucaria, Physcia, and Lecanora. Most of the species inhabiting carbonate stone materials in Saint Petersburg form episubstratic thalli, only the species of genus Verrucaria, often have endolithic or mostly endolithic thalli and could cause pitting of carbonate materials. Other lichen inhabitants of these substrates could be agents of substrate piling. The majority of taxa were not reported in Saint Petersburg from natural carbonate materials (marbles, limestones, or limestone tufa), but only from concrete; species inhabiting exclusively carbonate stones in Saint Petersburg are very few; lichens strictly confined to natural carbonate substrates are almost absent.

Monitoring of the cultural heritage state is significant factor for their preservation, the timely restoration, and conservation. The aim of this work is to develop a system for monitoring cultural heritage using new computer technology. The proposed method of image comparison is based on the spectral characteristics of the studied monument. Photographing of the objects is carried out in visible and invisible spectra. Most information on the biological objects can be obtained, for example, when shooting is in the infrared range. Primary image processing, recognition of weathering features, and assessment of their potential hazards as well as evaluating of the overall state of the monument is made using complex computer programs, and the results are accumulated in a special database. This system works as the expert one. It has been shown that the possibility of classification of the main groups of organisms on monuments and assessment of the biofouling area in time is possible by using this method. This method was tested during the survey of ancient petroglyphs in Republic of Khakassia, Tomsk petroglyphs, as well as on a number of historical monuments in St. Petersburg.

The pattern of ion substitutions and non-stoichiometry of oxalate and phosphate human body minerals (weddellite, whewellite, hydroxyapatite, struvite, and brushite) and their synthetic analogs was investigated by complex X-ray diffraction, spectroscopic, and chemical methods. All the studied biological minerals are characterized by variable non-stoichiometry composition that reflects the non- stationarity of formation conditions. Non-stoichiometry of calcium oxalates results from variations in quantities of disorderly distributed water molecules. The water amount in weddellite significantly influences the crystal structure parameters. In particular, there is positive correlation between the value of a parameter and the occupancy of “zeolitic” water sites. Variations in composition of calcium and magnesium phosphates are caused by substitutions at all the crystallographic sites. Ion replacements in apatite and struvite are more prominent in comparison with those in brushite. Non-stoichiometry of apatite and brushite is due to the presence of vacancies at the Ca-sites, and that of struvite is due to the vacancies at the Mg-site. Two types of non-stoichiometry in carbonated apatites of B-type realize due to replacements PO₄3−← CO₃2− or OH−← H₂O. Maximum concentrations of impurity ions in magnesium and calcium phosphates are mainly limited by the content of these ions in the physiological solution. In case of Mg replacement with Ca in struvite and Ca with K in brushite and apatite, it is also essentially limited by the size differences of the host and admixture ions.

This work examined the protein composition of organic components for different organo-mineral aggregate in the bone tissue of healthy people (without bone disease) and patients with coxarthrosis (arthrosis of the coxofemoral joint), urinary, dental, and salivary calculi. The content of the water-soluble organic substances with a peptide bond in urinary stones depends on the mineral composition of the sample. When monohydrate calcium oxalate crystallizes in the solution in the presence of glutamic acid, the crystal growth is stabilized. When the concentration of amino acid grows, the inhibitory effect grows. Other amino acids (lysine, glycine, aspartic acid) have an inhibitory effect on hydroxyapatite crystal growth in the range of the tested concentrations. By an increase in the electrostatic interaction with non-stoichiometric hydroxyapatite, the tested amino acids can be ranked in order as: lysine > glycine > glutamic acid > aspartic acid. In the course of bone arthrosis, the molecular weight of the organic content was observed to be less than that of collagen. Close packing of the deformed collagen fibers was one of the causes of the increased hardness of arthritic bones. The amino acid composition in the bone tissue of men and women in the age range of 30–79 to 60 years does not depend on the age and gender identity of the samples. After 60 years, the amino acid content varies by age and gender.

Some carbonate apatites were investigated by computer simulation using the General Utility Lattice Program (GULP) with grid techniques. These structures were modeled by a semiempiric method using interatomic potential-based simulation techniques. The supercells of 3 × 3 × 3 elementary cells of carbonate apatite were considered. The arrangement of structural defects (carbonate groups, excess F _x ions, Na ions, Ca vacancies, hydroxyl groups, water molecules H₂O_str fixed in structure) in carbonate fluorapatite (CFA) with the chemical composition near to the synthesized A-B type CFA (2.7 wt% CO₂, 3.3 wt% F) was established. Structural changes in the A type carbonate hydroxylapatite (CHA) due to formation of the CO₂−-radical from the carbonate ion replaced two adjacent hydroxyls in the hydroxylapatite (HA) channel have been studied. The CO₂−-radical formation is accompanied by the appearance of a Ca2 vacancy and results in the considerable rearrangement of ions of the structural environment. The anneal effect on the A type CHA structure with the CO₂−-radical (CHA_r) and possible accompanying defects has been investigated. The CHA_r structure is most stable at the temperatures of T = 298 and 873 K; the CHA structure with the CO₂−-radical and O−-center spaced by one hydroxyl in the same channel (CHA_r–h–r) — at T = 1073 and 1173 K. The obtained data complement and are partly in agreement with experimental and theoretical investigations of CHA.

The influence of chelating agents (organic acids with different structures) on iron oxides and hydroxyapatite nanoparticle (NP) morphology obtained by two different synthetic procedures (precipitation method and hydrothermal synthesis) were studied. The relationship between the synthetic conditions and the nature of the growth limiters or NP morphology regulation agents was considered. The mechanism of the NP growth regulation and the general peculiarities of this process for materials with different chemical natures are also discussed. It was concluded that the use of chelating agents dramatically changes the NP size and shape and the degree of modification is determined by the binding force between chelating agent and ions on NP surfaces.

The paper researches a range of problems related to the peculiarities of calcium oxalate crystallization in the presence of amino acids on the bases of thermodynamic calculations and experimental data. The regularities of phase formation in the system Ca2+–C₂O₄2−–H₂O–amino acid in a widely variable interval of component concentrations and pH are theoretically researched. The influence of pH on the thermodynamic stability of crystalline compounds is considered. The kinetic parameters of crystallization are determined: the induction period, the rate constant, the order of crystals’ growth, and the influence of amino acids on the kinetics of crystallization of calcium oxalate is established.

This chapter presents the results of research on the kinetics of nucleation and crystal growth in solutions simulating the composition of human saliva and plasma. The kinetic characteristics of the processes (order, constant, activation energy, specific surface energy, the size of the critical nucleus) were obtained. The influence of some inorganic (magnesium ions) and organic (protein, alanine and glucose) additives on the kinetics of crystallization is shown.

This paper examines the influence of strontium chloride on the process of crystallization of strontium-substituted carbonated hydroxyapatite from prototype human synovial fluid. Products of synthesis were studied by Fourier transform infrared spectroscopy, X-ray diffraction, and differential thermal analysis. The amount of strontium in the sample using atomic emission analysis was determined. For the synthesized phases, Ca/P-ratio, the parameters of crystallinity, the crystallite size using the formula of Selyakov-Scherrer, and crystal lattice parameters were calculated. It was established that increasing the concentration of strontium ions in the analytical model increases the proportion of brushite in the solid phase. It was found that with increasing formation of a precipitate beneath the mother liquor, the kinetically stable-phase of brushite transforms to the thermodynamically more stable phase (Sr-containing carbonated hydroxyapatite).

The name of V.O. Tauson occupies an important place in the history of Russian school of microbiology. Tauson finished the Moscow University in 1924. His diploma work was linked with the destruction of the paraffin by the mould Aspergillus flavus. This topic was proposed by Prof. E.E. Uspensky (1889–1938), the founder of the Department of microbiology at Moscow University. The pioneer works of Tauson were linked with the microbial oxidation of phenanthrene, naphthalene, saturated, and nonsaturated hydrocarbons, wax, oils. He paid much attention to the role of microorganisms in geological processes, such as weathering of rocks, transformation, and destruction of several caustobioliths (peat, coal, petroleum). Tauson is also the author of some interesting hypotheses on the bioenergy of microbial metabolism, linked with the thermodynamics of anabolic processes.