The biogeochemical cycle of the adsorbed template II: Selective adsorption of mononucleotides on adsorbed polynucleotide templates

Experimental results are presented for the verification of the specific interaction step of the adsorbed template biogeochemical cycle, a simple model for a primitive prebiotic replication system. The experimental system consisted of gypsum as the mineral to which an oligonucleotide template attaches (Poly-C or Poly-U) and 5-AMP, 5-GMP, 5-CMP and 5-UMP as the interacting biomonomers. When Poly-C or Poly-U were used as adsorbed templates, 5-GMP and 5-AMP, respectively were observed to be the most strongly adsorbed species. Moreover, there exists a direct quantitative relationship between the quantity of cytidine or uracil residues in the adsorbed state and the amount of the complementary mononucleotide that is attached to it. NaCl added to the system in order to create conditions of high ionic strength seems to enhance the selectivity of the adsorption of the monmucleotides to these adsorbed templates.     

Microbiological regulation of the biogeochemical nitrogen cycle

Most nitrogen transformations in soil are carried out by micro-organisms. An understanding of the microbiological processes is thus necessary in order for us to devise management practices in agricultural ecosystems, which will optimize plant root uptake of nitrogen and minimize nitrogen losses from the systems. Some aspects of the individual microbiological processes in the nitrogen cycle are discussed and their importance for an efficient management of agroecosystems. In soil various groups of organisms compete for available inorganic nitrogen and quantitative data are needed on the uptake kinetics for these various groups in order to be able to assess their competitive ability under different conditions. The influence of abiotic factors such as oxygen concentration, inorganic nitrogen concentration and pH is discussed in relation to the different processes. The importance of acetylene as a tool in nitrogen cycling studies is discussed briefly.     

生物地球化学锰循环中的微生物胞外电子传递机制

微生物是生物地球化学元素循环的重要驱动者,在锰等变价金属元素的氧化还原过程中起着至关重要的作用。近年来,Mn(Ⅲ)的发现以及在一些环境中的广泛存在,丰富了人们对Mn(Ⅲ)以及自然界锰循环过程的认识。研究发现,锰的生物地球化学循环,尤其是锰还原过程,与微生物胞外电子传递紧密相关,且目前已知的5种胞外电子传递机制均与锰还原有关联。因此,本文综述了锰的生物地球化学循环及其意义,并从微生物胞外电子传递的机制、微生物介导锰氧化、微生物介导锰还原等3个方面来介绍参与锰循环的微生物多样性;以及微生物地球化学锰循环的环境意义。对微生物参与锰循环过程的研究不仅可以进一步丰富相关理论,同时也能推动生物除锰、污染物原位修复及生物冶金等应用领域的发展。     

The biogeochemical cycle of methane in the coastal zone and littoral of the Kandalaksha Bay of the White Sea

Microbiological and biogeochemical investigations of the processes of methane production (MP) and methane oxidation (MO) in the coastal waters and littoral of the Kandalaksha Bay of the White Sea were carried out. The studies were conducted in the coastal zones and in the water areas of the Kandalaksha Preserve, Moscow University White Sea Biological Station, and Zoological Institute (RAS) Biological Station in August, 1999, 2000, and 2001 and in March, 2001. The rate of CO2 assimilation in the shallow and littoral sediments was 35-27800 microg C/(dm3 day) in summer and 32.8-88.9 microg C/(dm3 day) in winter. The maximal rates of MP were observed in the littoral sediments in the zone of macrophyte decomposition, in local depressions, and in the estuary of a freshwater creak (up to 113 microl/(dm3 day)). The maximal level of MO was observed in the shallow estuarine sediments (up to 2450 microl/(dm3 day)). During the winter season, at the temperature of -0.5 to 0.5 degrees C, the MP rate in the littoral sediments was 0.02-0.3 microl/(dm3 day), while MO rate was 0.06-0.7 microl/(dm3 day). The isotopic data obtained indicate that the C(org) of the mats and of the upper sediment layers is enriched with the heavy 13C isotope by 1-4 per thousand as compared to the C(org) of the suspension, comprised on 33.5-34.3% of phytoplankton. A striking difference was found between the levels of methane emission by the typical littoral microlanscapes. In fine sediments, the average emission was 675 microl CH4/(m2 day), in the stormy discharge stretch sediments it was 1670 microl CH4/(m2 day), and under the stones and in silted pits, 1370 microl CH4/(m2 day). The calculation performed with consideration of the microlandscape areas with a high production allowed the CH4 production of 1 km2 of the littoral to be estimated as 192-300 1 CH4/(km2 day).     

Neutrophilic lithotrophic iron-oxidizing prokaryotes and their role in the biogeochemical processes of the iron cycle

Biology of lithotrophic neutrophilic iron-oxidizing prokaryotes and their role in the processes of the biogeochemical cycle of iron are discussed. This group of microorganisms is phylogenetically, taxonomically, and physiologically heterogeneous, comprising three metabolically different groups: aerobes, nitratedependent anaerobes, and phototrophs; the latter two groups have been revealed relatively recently. Their taxonomy and metabolism are described. Materials on the structure and functioning of the electron transport chain in the course of Fe(II) oxidation by members of various physiological groups are discussed. Occurrence of iron oxidizers in freshwater and marine ecosystems, thermal springs, areas of hydrothermal activity, and underwater volcanic areas are considered. Molecular genetic techniques were used to determine the structure of iron-oxidizing microbial communities in various natural ecosystems. Analysis of stable isotope fractionation of ^56/54Fe in pure cultures and model experiments revealed a predominance of biological oxidation over abiotic ones in shallow aquatic habitats and mineral springs, which was especially pronounced under microaerobic conditions at the redox zone boundary. Discovery of anaerobic bacterial Fe(II) oxidation resulted in development of new hypotheses concerning the possible role of microorganisms and the mechanisms of formation of the major iron ore deposits during Precambrian era until the early Proterozoic epoch. Paleobiological data are presented on the microfossils and specific biomarkers retrieved from ancient ore samples and confirming involvement of anaerobic biogenic processes in their formation.     

Precipitation of barite by Myxococcus xanthus: possible implications for the biogeochemical cycle of barium

Bacterial precipitation of barite (BaSO(4)) under laboratory conditions is reported for the first time. The bacterium Myxococcus xanthus was cultivated in a solid medium with a diluted solution of barium chloride. Crystallization occurred as a result of the presence of live bacteria and the bacterial metabolic activity. A phosphorous-rich amorphous phase preceded the more crystalline barite formation. These experiments may indicate the involvement of bacteria in the barium biogeochemical cycle, which is closely related to the carbon cycle.     

Carbon cycle confidence and uncertainty: Exploring variation among soil biogeochemical models

Emerging insights into factors responsible for soil organic matter stabilization and decomposition are being applied in a variety of contexts, but new tools are needed to facilitate the understanding, evaluation, and improvement of soil biogeochemical theory and models at regional to global scales. To isolate the effects of model structural uncertainty on the global distribution of soil carbon stocks and turnover times we developed a soil biogeochemical testbed that forces three different soil models with consistent climate and plant productivity inputs. The models tested here include a first‐order, microbial implicit approach (CASA‐CNP), and two recently developed microbially explicit models that can be run at global scales (MIMICS and CORPSE). When forced with common environmental drivers, the soil models generated similar estimates of initial soil carbon stocks (roughly 1,400 Pg C globally, 0–100 cm), but each model shows a different functional relationship between mean annual temperature and inferred turnover times. Subsequently, the models made divergent projections about the fate of these soil carbon stocks over the 20^th century, with models either gaining or losing over 20 Pg C globally between 1901 and 2010. Single‐forcing experiments with changed inputs, temperature, and moisture suggest that uncertainty associated with freeze‐thaw processes as well as soil textural effects on soil carbon stabilization were larger than direct temperature uncertainties among models. Finally, the models generated distinct projections about the timing and magnitude of seasonal heterotrophic respiration rates, again reflecting structural uncertainties that were related to environmental sensitivities and assumptions about physicochemical stabilization of soil organic matter. By providing a computationally tractable and numerically consistent framework to evaluate models we aim to better understand uncertainties among models and generate insights about factors regulating the turnover of soil organic matter.     

Single-cell determination of iron content in magnetotactic bacteria: implications for the iron biogeochemical cycle

Magnetotactic bacteria (MTB) are ubiquitous aquatic microorganisms that mineralize dissolved iron into intracellular magnetic crystals. After cell death, these crystals are trapped into sediments that remove iron from the soluble pool. MTB may significantly impact the iron biogeochemical cycle, especially in the ocean where dissolved iron limits nitrogen fixation and primary productivity. A thorough assessment of their impact has been hampered by a lack of methodology to measure the amount of, and variability in, their intracellular iron content. We quantified the iron mass contained in single MTB cells of Magnetospirillum magneticum strain AMB-1 using a time-resolved inductively coupled plasma-mass spectrometry methodology. Bacterial iron content depends on the external iron concentration, and reaches a maximum value of ~10⁻⁶ ng of iron per cell. From these results, we calculated the flux of dissolved iron incorporation into environmental MTB populations and conclude that MTB may mineralize a significant fraction of dissolved iron into crystals.     

The biogeochemical heterogeneity of tropical forests

Tropical forests are renowned for their biological diversity, but also harbor variable combinations of soil age, chemistry and susceptibility to erosion or tectonic uplift. Here we contend that the combined effects of this biotic and abiotic diversity promote exceptional biogeochemical heterogeneity at multiple scales. At local levels, high plant diversity creates variation in chemical and structural traits that affect plant production, decomposition and nutrient cycling. At regional levels, myriad combinations of soil age, soil chemistry and landscape dynamics create variation and uncertainty in limiting nutrients that do not exist at higher latitudes. The effects of such heterogeneity are not well captured in large-scale estimates of tropical ecosystem function, but we suggest new developments in remote sensing can help bridge the gap.     

Kinetics of dissolution of Antarctic diatom frustules and the biogeochemical cycle of silicon in the Southern Ocean

Summary In order to simulate the fate of biogenic silica generated in the surface waters of the Southern Ocean, the dissolution of silica frustules was studied for seven natural assemblages of diatoms, collected during summer 1984 in the Indian sector, and two typical Antarctic diatoms (Nitzschia cylindrus and Chaetoceros deflandrei), following the procedure of Kamatani and Riley (1979). For mean summer conditions in the surface waters of the Southern Ocean (2-3d^-1 for the natural assemblages. The silica frustules trapped by fecal pellets and by gelatinous aggregates, and rapidly transported through the cold waters of the Circumpolar Current, reach the sea bottom of either the continental shelves of the abysses without loosing much of the initial amount of silica (less than 10%). A model based on Stokes' law, modified to take in account of non ideal conditions and of the upwelling rate, is used in order to simulate the fate of silica of unaggregated particles settling down in the cold waters of the Antarctic Divergence. It supports the ideas that 1-the cycle of siliceous particles which radii are <2 m (i.e., of a part of the nanoplankton) is completely achieved in the surface layer, 2-although the biogenic silica of large unaggregated particles (radii over 25 m) may reach the seabottom (within one month to a few years) without complete dissolution, the main explanation for the accumulation of biogenic silica on Antarctic abysses remains transport by fecal pellets and gelatinous aggregates.     

Lack of steady-state in the global biogeochemical Si cycle: emerging evidence from lake Si sequestration

Weathering of silicate minerals releases dissolved silicate (DSi) to the soil-vegetation system. Accumulation and recycling of this DSi by terrestrial ecosystems creates a pool of reactive Si on the continents that buffers DSi export to the ocean. Human perturbations to the functioning of the buffer have been a recent research focus, yet a common assumption is that the continental Si cycle is at steady-state. However, we have no good idea of the timescales of ecosystem Si pool equilibration with their environments. A review of modelling and geochemical considerations suggests the modern continental Si cycle is in fact characterised in the long-term by an active accumulation of reactive Si, at least partially attributable to lakes and reservoirs. These lentic systems accumulate Si via biological conversion of DSi to biogenic silica (BSi). An analysis of new and published data for nearly 700 systems is presented to assess their contribution to the accumulating continental pool. Surface sediment BSi concentrations (n = 692) vary between zero and >60 % SiO₂ by weight, apparently independently of lake size, location or water chemistry. Using sediment core BSi accumulation rates (n = 109), still no relationships are found with lake or catchment parameters. However, issues associated with single-core accumulation rates should in any case preclude their use in elemental accumulation calculations. Based on lake/reservoir mass-balances (n = 34), our best global-scale estimate of combined lake and reservoir Si retention is 1.53 TMol year^?1, or 21–27 % of river DSi export. Again, no scalable relationships are apparent, suggesting Si retention is a complex process that varies from catchment to catchment. The lake Si sink has implications for estimation of weathering flux generation from river chemistry. The size of the total continental Si pool is poorly constrained, as is its accumulation rate, but lakes clearly contribute substantially. A corollary to this emerging understanding is that the flux and isotopic composition of DSi delivered to the ocean has likely varied over time, partly mediated by a fluctuating continental pool, including in lakes.     

Glucose metabolism and template synthesis in the mitotic cycle of human diploid fibroblasts

The correlation between the rates of protein and nucleic acid synthesis and the activity of the key enzymes of glycolysis (hexokinase, phosphofructokinase) and pentose phosphate cycle (glucose-6-phosphate dehydrogenase) in the mitotic cycle of human diploid fibroblasts synchronized by double thymidine block was studied. It was found that the removal of the thymidine block is followed by short-term (presumably, non-specific) simultaneous stimulation of matrix syntheses, as well as by glycolytic and pentose phosphate cycle enzyme syntheses. By the beginning of the S-phase, all the processes appear to be inhibited, followed by gradual activation of glycolysis and pentose phosphate cycle reactions. The implementation of the cell cycle is concomitant with stepwise transitions of protein and hexokinase synthesis rates and ATP content to one of the following levels--basal, intermediate or maximal. Changes in the activity of glucose-6-phosphate dehydrogenase in the course of the cell cycle appear as oscillations, those in phosphofructokinase as alternative states. At stage M, the oscillatory processes are temporarily quenched, whereas the ATP content occupies an intermediate level. In contrast with diploid fibroblasts, in transformed T9 cells the enzyme activity is much higher, and the fluctuations in activity throughout the cell cycle are less noticeable. Presumably, in transformed cells the enzyme activity is at the maximum level and is not prone to effector regulation.     

The biogeochemical controls of N2O production and emission in landfill cover soils: the role of methanotrophs in the nitrogen cycle

Emissions of N2O from cover soils of both abandoned (> 30 years) and active landfills greatly exceed the maximum fluxes previously reported for tropical soils, suggesting high microbial activities for N2O production. Low soil matrix potentials (<-0.7 MPa) indicate that nitrification was the most likely mechanism of N2O formation during most of the time of sampling. Soil moisture had a strong influence on N2O emissions. The production of N2O was stimulated by as much as 20 times during laboratory incubations, when moisture was increased from -2.0 MPa to -0.6 MPa. Additional evidence from incubation experiments and delta13C analyses of fatty acids (18:1) diagnostic of methanotrophs suggests that N2O is formed in these soils by nitrification via methanotrophic bacteria. In a NH3(g)-amended landfill soil, the rate of N2O production was significantly increased when incubated with 100 ppmv methane compared with 1.8 ppmv (atmospheric) methane. Preincubation of a landfill soil with 1% CH4 for 2 weeks resulted in higher rates of N2O production when subsequently amended with NH3(g) relative to a control soil preincubated without CH4. At one location, at the soil depth (9-16 cm) of maximum methane consumption and N2O production, we observe elevated concentrations of organic carbon and nitrogen and distinct minima in delta15N (+1.0%) and delta13C (-33.8%) values for organic nitrogen and organic carbon respectively. A delta13C value of -39.3% was measured for 18:1 carbon fatty acids in this soil, diagnostic of type II methanotrophs. The low delta15N value for organic nitrogen is consistent with N2 fixation by type II methanotrophs. These observations all point to a methanotrophic origin for the organic matter at this depth. The results of this study corroborate previous reports of methanotrophic nitrification and N2O formation in aqueous and soil environments and suggest a predominance of type II rather than type I or type X methanotrophs in this landfill soil.     

The coupling of biogeochemical cycles of nutrients

For any element which is incorporated into biomass, the biogeochemical cycle of that element in a given ecosystem will be coupled to that of any other element similarly incorporated. The mutual interaction of two such cycles is examined using a simple model in which each cycle is constrained into four compartments. In each cycle the assimilation rate (primary productivity) is related in a non-linear fashion to the two nutrients and to biomass. The interactions are represented by combining a hyperbolic dependence for each nutrient (involving a "Michaelis constant") with a logistic equation governing the dependence of rate on biomass (involving a "carrying capacity"). The response of the model to perturbation (e.g. mobilization of an abiotic reserve) is strongly governed by the values assigned to these constants. The coupled cycles can exhibit positive feed-back with anomalous responses of the steady state and time-dependent solutions may exhibit complex oscillatory behaviour. Both the steady-state sensitivity and the kinetic behaviour of such coupled systems are simplified if the range of atomic ratios permitted by the assimilation process is restricted. It will therefore be of importance to determine under what conditions the assimilation rates for different elements are governed by mass-action effects (Liebig's Law) or by stoichiometric constraints (Redfield ratios).     

Seasonal evolution of the biogeochemical cycle in the southwest lagoon of New Caledonia. Application of a compartmental model

A biogeochemical box model describing the south-west lagoon of New-Caledonia was developed in order to simulate the seasonal cycle of carbon and nitrogen. We used fluxes generated by a 3D hydrodynamic model to simulate horizontal exchanges between boxes and added freshwater influxes as nitrogen sources from the land. Average residence time proved to be less than 11 days for the lagoon as a whole. Standard simulations showed baseline values of chlorophyll a between 0.2 and 0.4 microgram.L-1. Influences of freshwater influxes proved to be significant (increases up to 1 microgram.L-1) only in shallow areas protected from wind exposure and during short periods of heavy rainfall (tropical depressions). Tropical climatic events have reduced impact in space and time and long-term simulations over decades with increased nutrient inputs did not show any significant process of eutrophication. Hydrodynamics seemed to be one of the major control factors with respect to organic matter cycling in the lagoon.     

稳定碳同位素在滨海湿地碳生物地球化学循环中的应用

碳作为滨海湿地中重要的生命元素,其生物地球化学循环过程是滨海湿地研究的核心内容之一.稳定同位素技术越来越多地被应用到滨海湿地碳生物地球化学循环过程的研究中,提高了其研究水平,并推动了其研究的进程.本文从有机物质生产、土壤有机质来源、食物链传递、温室气体排放以及可溶性有机碳输出5个方面,综述了滨海湿地碳生物地球化学循环过程的稳定同位素研究进展.通过植物及土壤δ13C值的测定进行有机质的生产机理研究及外源追溯,通过对比各生物种群的δ13C值分析碳在生态系统中的流动过程,通过湿地排放温室气体及可溶性有机碳δ13C值的测定揭示影响碳输出的环境因子.最后,文章总结了当前研究中存在的问题,并对其研究前景进行了展望.     

The greening of the Northern Great Plains and its biogeochemical precursors

Vegetation greenness has increased across much of the global land surface over recent decades. This trend is projected to continue—particularly in northern latitudes—but future greening may be constrained by nutrient availability needed for plant carbon (C) assimilation in response to CO₂ enrichment (eCO₂). eCO₂ impacts foliar chemistry and function, yet the relative strengths of these effects versus climate in driving patterns of vegetative greening remain uncertain. Here we combine satellite measurements of greening with a 135 year record of plant C and nitrogen (N) concentrations and stable isotope ratios (δ¹³C and δ¹⁵N) in the Northern Great Plains (NGP) of North America to examine N constraints on greening. We document significant greening over the past two decades with the highest proportional increases in net greening occurring in the dries and warmest areas. In contrast to the climate dependency of greening, we find spatially uniform increases in leaf‐level intercellular CO₂ and intrinsic water use efficiency that track rising atmospheric CO₂. Despite large spatial variation in greening, we find sustained and climate‐independent declines in foliar N over the last century. Parallel declines in foliar δ¹⁵N and increases in C:N ratios point to diminished N availability as the likely cause. The simultaneous increase in greening and decline in foliar N across our study area points to increased N use efficiency (NUE) over the last two decades. However, our results suggest that plant NUE responses are likely insufficient to sustain observed greening trends in NGP grasslands in the future.     

The southwestern South Atlantic continental shelf biogeochemical divide

Biogeochemistry - The structure of the phytoplankton community is strongly influenced by environmental variables linked with variations in sea–air CO2 net fluxes (FCO2). However, compared to...