Marine Benthos in Relation to Pore Water Chemistry and Sediment Geochemistry of Simulated Dredged Material

During the course of study on vertical migration and mortality of benthos in simulated dredged material, changes in pore water chemistry and sediment geochemistry were also examined. Dissolved oxygen, ammonia, and sulfide showed significant changes between overlying water and pore water over the two week experimental period. Chemical effects in dredging operations can be important on infaunal organisms.     

Methane Release through Resuspension of Littoral Sediment

Sediment in the littoral zone of lakes is frequently disturbed by wave action or bioturbation, resulting in sediment resuspension. In undisturbed sediment, methanotrophic bacteria efficiently reduce the diffusive flux of methane into the water column. In a microcosm study, the resuspension of littoral sediment was simulated in sediment cores for a winter (n = 3) and a summer situation (n = 3). The erosion of surface sediment resulted in a large flux of methane into the overlying water (207 ± 176 μmol h⁻¹ m⁻² in winter and 73 ± 18 μmol h⁻¹ m⁻² in summer). Only a minor part (16 ± 7%) of the methane released was oxidized by methanotrophic bacteria, whereas the major part escaped into the water column. Only 6–16% of the littoral zone has to be resuspended to reach the same flux as from undisturbed littoral sediment. For the daily flux, a sediment resuspension has to last 1–4 h to reach the undisturbed daily flux. The study reveals the important role of sediment resuspension in the littoral methane cycle as an intense but variable source of methane of largely unknown magnitude.     

Kinetic Parameters of the Conversion of Methane Precursors to Methane in a Hypereutrophic Lake Sediment

The kinetic parameters K_m, V_max, T_t (turnover time), and v (natural velocity) were determined for H₂ and acetate conversion to methane by Wintergreen Lake sediment, using short-term (a few hours) methods and incubation temperatures of 10 to 14°C. Estimates of the Michaelis-Menten constant, K_m, for both the consumption of hydrogen and the conversion of hydrogen to methane by sediment microflora averaged about 0.024 μmol g⁻¹ of dry sediment. The maximal velocity, V_max, averaged 4.8 μmol of H₂ g⁻¹ h⁻¹ for hydrogen consumption and 0.64 μmol of CH₄ g⁻¹ h⁻¹ for the conversion of hydrogen to methane during the winter. Estimated natural rates of hydrogen consumption and hydrogen conversion to methane could be calculated from the Michaelis-Menten equation and estimates of K_m, V_max, and the in situ dissolved-hydrogen concentration. These results indicate that methane may not be the only fate of hydrogen in the sediment. Among several potential hydrogen donors tested, only formate stimulated the rate of sediment methanogenesis. Formate conversion to methane was so rapid that an accurate estimate of kinetic parameters was not possible. Kinetic experiments using [2-¹⁴C]acetate and sediments collected in the summer indicated that acetate was being converted to methane at or near the maximal rate. A minimum natural rate of acetate conversion to methane was estimated to be about 110 nmol of CH₄ g⁻¹ h⁻¹, which was 66% of the V_max (163 nmol of CH₄ g⁻¹ h⁻¹). A 15-min preincubation of sediment with 5.0 × 10⁻³ atm of hydrogen had a pronounced effect on the kinetic parameters for the conversion of acetate to methane. The acetate pool size, expressed as the term K_m + S_n (S_n is in situ substrate concentration), decreased by 37% and T_t decreased by 43%. The V_max remained relatively constant. A preincubation with hydrogen also caused a 37% decrease in the amount of labeled carbon dioxide produced from the metabolism of [U-¹⁴C]valine by sediment heterotrophs.     

Sediment Core Sectioning and Extraction of Pore Waters under Anoxic Conditions

We demonstrate a method for sectioning sediment cores and extracting pore waters while maintaining oxygen-free conditions. A simple, inexpensive system is built and can be transported to a temporary work space close to field sampling site(s) to facilitate rapid analysis. Cores are extruded into a portable glove bag, where they are sectioned and each 1-3 cm thick section (depending on core diameter) is sealed into 50 ml centrifuge tubes. Pore waters are separated with centrifugation outside of the glove bag and then returned to the glove bag for separation from the sediment. These extracted pore water samples can be analyzed immediately. Immediate analyses of redox sensitive species, such as sulfide, iron speciation, and arsenic speciation indicate that oxidation of pore waters is minimal; some samples show approximately 100% of the reduced species, e.g. 100% Fe(II) with no detectable Fe(III). Both sediment and pore water samples can be preserved to maintain chemical species for further analysis upon return to the laboratory.     

Combined Diffusive and Viscous Transport of Methane in a Carbon Slit Pore

Abstract

The transport of mass through porous materials can occur by essentially two different mechanisms: (1) diffusion and (2) viscous flow. The former occurs when there is a gradient in chemical potential of the pore fluid, while the latter occurs in the presence of a pressure gradient. In general, fluid transport occurs by both of these mechanisms and their respective contributions to the total intra-pore flux are approximately additive. Experimentally, there is no unambiguous way of determining the individual contributions to the total flux of these two modes of transport. Fortunately, molecular simulations does provide a solution.

We present a novel simulation method in which the separate contributions to the total flux are determined. The method involves the use of two non-equilibrium molecular dynamics techniques: dual control volume grand canonical molecular dynamics (DCV GCMD) and an algorithm for simulating planar Poiseuille flow. We apply this technique to study the combined (viscous and diffusive) transport of methane through single slit-shaped graphite pores of width 2.5, 5.0 and 10.0 methane diameters. We find that the viscous contribution to the total intrapore flux through each of these pores is 10%, 15% and 34%, respectively.     

Revealing Sources and Distribution Changes of Dissolved Organic Matter (DOM) in Pore Water of Sediment from the Yangtze Estuary

Dissolved organic matter (DOM) in sediment pore waters from Yangtze estuary of China based on abundance, UV absorbance, molecular weight distribution and fluorescence were investigated using a combination of various parameters of DOM as well as 3D fluorescence excitation emission matrix spectra (F-EEMS) with the parallel factor and principal component analysis (PARAFAC-PCA). The results indicated that DOM in pore water of Yangtze estuary was very variable which mainly composed of low aromaticity and molecular weight materials. Three humic-like substances (C1, C2, C4) and one protein-like substance (C3) were identified by PARAFAC model. C1, C2 and C4 exhibited same trends and were very similar. The separation of samples on both axes of the PCA showed the difference in DOM properties. C1, C2 and C4 concurrently showed higher positive factor 1 loadings, while C3 showed highly positive factor 2 loadings. The PCA analysis showed a combination contribution of microbial DOM signal and terrestrial DOM signal in the Yangtze estuary. Higher and more variable DOM abundance, aromaticity and molecular weight of surface sediment pore water DOM can be found in the southern nearshore than the other regions primarily due to the influence of frequent and intensive human activities and tributaries inflow in this area. The DOM abundance, aromaticity, molecular weight and fluorescence intensity in core of different depth were relative constant and increased gradually with depth. DOM in core was mainly composed of humic-like material, which was due to higher release of the sedimentary organic material into the porewater during early diagenesis.     

Biogeochemical and Molecular Signatures of Anaerobic Methane Oxidation in a Marine Sediment

Anaerobic methane oxidation was investigated in 6-m-long cores of marine sediment from Aarhus Bay, Denmark. Measured concentration profiles for methane and sulfate, as well as in situ rates determined with isotope tracers, indicated that there was a narrow zone of anaerobic methane oxidation about 150 cm below the sediment surface. Methane could account for 52% of the electron donor requirement for the peak sulfate reduction rate detected in the sulfate-methane transition zone. Molecular signatures of organisms present in the transition zone were detected by using selective PCR primers for sulfate-reducing bacteria and for Archaea. One primer pair amplified the dissimilatory sulfite reductase (DSR) gene of sulfate-reducing bacteria, whereas another primer (ANME) was designed to amplify archaeal sequences found in a recent study of sediments from the Eel River Basin, as these bacteria have been suggested to be anaerobic methane oxidizers (K. U. Hinrichs, J. M. Hayes, S. P. Sylva, P. G. Brewer, and E. F. DeLong, Nature 398:802–805, 1999). Amplification with the primer pairs produced more amplificate of both target genes with samples from the sulfate-methane transition zone than with samples from the surrounding sediment. Phylogenetic analysis of the DSR gene sequences retrieved from the transition zone revealed that they all belonged to a novel deeply branching lineage of diverse DSR gene sequences not related to any previously described DSR gene sequence. In contrast, DSR gene sequences found in the top sediment were related to environmental sequences from other estuarine sediments and to sequences of members of the genera Desulfonema, Desulfococcus, and Desulfosarcina. Phylogenetic analysis of 16S rRNA sequences obtained with the primers targeting the archaeal group of possible anaerobic methane oxidizers revealed two clusters of ANME sequences, both of which were affiliated with sequences from the Eel River Basin.     

Identification of Methanoculleus spp. as Active Methanogens during Anoxic Incubations of Swine Manure Storage Tank Samples

Methane emissions represent a major environmental concern associated with manure management in the livestock industry. A more thorough understanding of how microbial communities function in manure storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step. Methanogenic archaea are major contributors to methanogenesis in stored swine manure, and we investigated active methanogenic populations by DNA stable isotope probing (DNA-SIP). Following a preincubation of manure samples under anoxic conditions to induce substrate starvation, [U-¹³C]acetate was added as a labeled substrate. Fingerprint analysis of density-fractionated DNA, using length-heterogeneity analysis of PCR-amplified mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase), showed that the incorporation of ¹³C into DNA was detectable at in situ acetate concentrations (∼7 g/liter). Fingerprints of DNA retrieved from heavy fractions of the ¹³C treatment were primarily enriched in a 483-bp amplicon and, to a lesser extent, in a 481-bp amplicon. Analyses based on clone libraries of the mcrA and 16S rRNA genes revealed that both of these heavy DNA amplicons corresponded to Methanoculleus spp. Our results demonstrate that uncultivated methanogenic archaea related to Methanoculleus spp. were major contributors to acetate-C assimilation during the anoxic incubation of swine manure storage tank samples. Carbon assimilation and dissimilation rate estimations suggested that Methanoculleus spp. were also major contributors to methane emissions and that the hydrogenotrophic pathway predominated during methanogenesis.     

Differential Inhibition by Allylsulfide of Nitrification and Methane Oxidation in Freshwater Sediment

Addition of nitrapyrin, allylthiourea, C(inf2)H(inf2), and CH(inf3)F to freshwater sediment slurries inhibited CH(inf4) oxidation and nitrification to similar extents. Dicyandiamide and allylsulfide were less inhibitory for CH(inf4) oxidation than for nitrification. Allylsulfide was the most potent inhibitor of nitrification, and the estimated 50% inhibitory concentrations for this process and CH(inf4) oxidation were 0.2 and 121 (mu)M, respectively. At a concentration of 2 (mu)M allylsulfide, growth and CH(inf4) oxidation activity of Methylosinus trichosporium OB3b were not inhibited. Allylsulfide at 200 (mu)M inhibited the growth of M. trichosporium by approximately 50% but did not inhibit CH(inf4) oxidation activity. Nitrite production by cells of M. trichosporium was not significantly affected by allylsulfide, except at a concentration of 2 mM, when growth and CH(inf4) oxidation were also inhibited by about 50%. Methane monooxygenase activity present in soluble fractions of M. trichosporium was not inhibited significantly by allylsulfide at either 200 (mu)M or 2 mM. These results suggest that the partial inhibition of CH(inf4) oxidation in sediment slurries by high allylsulfide concentrations may be caused by an inhibition of the growth of methanotrophs rather than an inhibition of methane monooxygenase activity specifically. We conclude that allylsulfide is a promising tool for the study of interactions of methanotrophs and nitrifiers in N cycling and CH(inf4) turnover in natural systems.     

乌梢蛇的人工孵化试验

目的为了提高乌梢蛇的人工繁殖率,更好地保护和利用乌梢蛇的自然资源。方法采用重复实验法、观察法和对比法等方法对乌梢蛇卵进行了人工孵化的研究。结果每年的7月中旬至8月上旬为乌梢蛇的产卵高峰期,每次产卵数量为7～16枚(平均为11枚);最佳孵化温度为28～32℃,孵化环境的相对湿度为70％～85％,乌梢蛇的人工孵化率为75%6～100％,平均为83．84％。结论只要能满足乌梢蛇卵孵化温度和孵化环境的相对湿度等条件,就能够使乌梢蛇的人工孵化率平均达到80％以上。     

Methane flux dynamics during mire succession

Vegetation, temperature and hydrology are major factors controlling wetland methane (CH₄) dynamics. In order to test their importance, we measured CH₄ emissions and environmental characteristics over 2 years from five mires representing a successional sequence, ranging in age from 178 to 2,520 years. We hypothesized CH₄ emissions to be higher from the sedge-dominated fens than from the older bog stage. The more constant hydrological conditions at later successional stages as a consequence of the thicker peat layer appeared to result in lower temporal variation in CH₄ emissions. Accordingly, the other controls, temperature and vegetation, had an effect on CH₄ emissions only when the water table was sufficiently high. The seasonal variation in CH₄ emissions was controlled by temperature only at the oldest study site, which had the lowest variation in water table. Within-season variation in emissions related to plant phenology was highest at the fen stage, which was dominated by aerenchymatous plants with a strong seasonal pattern, namely sedges and forbs. In contrast to our hypothesis, CH₄ emissions increased with mire age towards the bog stage. However, the trend did not emerge during a rainy growing season, due to a rise in CH₄ emissions at the younger stages. The results may imply two different mechanisms during mire succession: while old mires are able to avoid the perturbation associated with variation in the water table and maintain their function as CH₄ emitters, young mires are exposed to perturbation but are able to recover their function.     

Effects of Methane Metabolism on Nitrification and Nitrous Oxide Production in Polluted Freshwater Sediment

We report the effect of CH₄ and of CH₄ oxidation on nitrification in freshwater sediment from Hamilton Harbour, Ontario, Canada, a highly polluted ecosystem. Aerobic slurry experiments showed a high potential for aerobic N₂O production in some sites. It was suppressed by C₂H₂, correlated to NO₃^- production, and stimulated by NH₄⁺ concentration, supporting the hypothesis of a nitrification-dependent source for this N₂O production. Diluted sediment slurries supplemented with CH₄ (1 to 24 μM) showed earlier and enhanced nitrification and N₂O production compared with unsupplemented slurries (≤1 μM CH₄). This suggests that nitrification by methanotrophs may be significant in freshwater sediment under certain conditions. Suppression of nitrification was observed at CH₄ concentrations of 84 μM and greater, possibly through competition for O₂ between methanotrophs and NH₄⁺ -oxidizing bacteria and/or competition for mineral N between these two groups of organisms. In Hamilton Harbour sediment, the very high CH₄ concentrations (1.02 to 6.83 mM) which exist would probably suppress nitrification and favor NH₄⁺ accumulation in the pore water. Indeed, NH₄⁺ concentrations in Hamilton Harbour sediment are higher than those found in other lakes. We conclude that the impact of CH₄ metabolism on N cycling processes in freshwater ecosystems should be given more attention.     

Methane in Water: An Ab Initio Study

Abstract

In preceding publications we discussed some properties of pure water in condensed phases using an ab initio approach. Here this study is used as a basis of comparison for analysing the behaviour of water as a solvent in the presence of an apolar molecule. Our analysis is focused on the process of organization of the hydrogen bonding network around the solute. For this purpose we perform some ab initio calculations for a system of 32 water molecules and one methane molecule at 300 K; in particular, the average molecular dipole moment of water is determined and the result is compared with that of pure water. Next the attention is switched to the methane molecule; related properties such as excluded volume and sphericity of its shape are illustrated and discussed. A comparison with results obtained using classical approaches suggests that some classical models of water can be considered to be still valid when they are used to analyse the water-methane system.     

Denitrification, Acetylene Reduction, and Methane Metabolism in Lake Sediment Exposed to Acetylene

Samples of sediment from Lake St. George, Ontario, Canada, were incubated in the laboratory under an initially aerobic gas phase and under anaerobic conditions. In the absence of added nitrate (NO₃⁻) there was O₂-dependent production of nitrous oxide (N₂O), which was inhibited by acetylene (C₂H₂) and by nitrapyrin, suggesting that coupled nitrification-denitrification was responsible. Denitrification of added NO₃⁻ was almost as rapid under an aerobic gas phase as under anaerobic conditions. The N₂O that accumulated persisted in the presence of 0.4 atm of C₂H₂, but was gradually reduced by some sediment samples at lower C₂H₂ concentrations. Low rates of C₂H₂ reduction were observed in the dark, were maximal at 0.2 atm of C₂H₂, and were decreased in the presence of O₂, NO₃⁻, or both. High rates of light-dependent C₂H₂ reduction occurred under anaerobic conditions. Predictably, methane (CH₄) production, which occurred only under anaerobiosis, was delayed by added NO₃⁻ and inhibited by C₂H₂. Consumption of added CH₄ occurred only under aerobic conditions and was inhibited by C₂H₂.     

Evolution of Volatile Sulfur Compounds during Laboratory-Scale Incubations and Indoor Preparation of Compost Used as a Substrate in Mushroom Cultivation

Volatile sulfur compounds are known to be produced during the preparation of compost used as a substrate in mushroom cultivation. Because they cause odor problems, attempts have been made to reduce the production of these compounds. The influences of temperature and various additions on the production of volatile sulfur compounds from composting material were tested on laboratory-scale preparations. The production of H₂S, COS, CH₃SH, and (CH₃)₂S was proven to be a biological process with an optimal temperature that coincides with the optimal temperature for biological activity. The formation of CS₂ and (CH₃)₂S₂ was shown to be a nonbiological process. The emission of volatile sulfur compounds during the indoor preparation of mushroom compost appeared to be remarkably reduced (about 90%) as compared with the emission during the conventional outdoor process. Introduction of this indoor composting process would result in a significant reduction in environmental pollution.     

Measurement of Mercury Methylation in Lake Water and Sediment Samples

The production of various eremophilane-type sesquiterpenes by Penicillium roqueforti strains has allowed us to propose a biochemical pathway for PR toxin synthesis. A time-course study of P. roqueforti metabolite production by high-performance liquid chromatography was performed to check this hypothetical pathway. The results obtained suggested that eremofortin C was the direct precursor of PR toxin in the P. roqueforti cell. Attempts to determine the amount of PR toxin in the mycelium failed. It was shown that the absence of PR toxin in mycelium was due to its instability during the extraction procedure.     

Distribution and Characteristics of Dissolved Organic Matter in Mangrove Sediment Pore Waters along the Coastline of French Guiana

Mangroves represent a major environment of tropical coasts. They are highly productive, and act both as a source and a sink of organic carbon. Concentrations and characteristics (fluorescence and hydrophobic–hydrophilic fractions) of dissolved organic matter (DOM) were investigated in relation to the organic content of sediments and to the chemistry of pore waters along the coastline of French Guiana. The pore waters studied were extracted (centrifugation, soil moisture sampler) from sediments cored beneath A. germinans mangrove stands representative of development stages: pioneer, mature and senescent. In order to asses the effects of seasonal changes, two cores were performed in each location, just after dry and wet seasons, respectively. Dissolved organic carbon (DOC) concentrations in pore waters of the upper sediment were found to increase, from 0.7 mmol l⁻¹ under the pioneers to 9 under senescent mangroves. The evolution of sedimentary organic carbon (SedOC) in the same sediment paralleled that of DOC, increasing from 0.7 to 28%. On the contrary, in the lower parts of sediment cores SedOC and DOC displayed contrasting vertical trends: SedOC decreased sharply with depth while DOC increased, reaching concentrations up to 30 mmol l⁻¹ at 50 cm in the older, senescent mangroves. In addition, the Fluorescence/DOC ratios and the hydrophobic contents of DOC were higher at greater depths in most cores, expressing changes in the DOC composition. These results suggest that the DOC of the upper layers originated directly from the SedOC of the enclosing sediment, while the hydrophobic and fluorescent DOC accumulated in the anoxic bottom layer. The mechanisms responsible for this accumulation at depth requires additional research to be fully understood. However, the anoxic conditions and high pH values prevailing in the lower sediment, by lessening DOM sorption and enhancing SedOC dissolution, may be partly responsible for the high DOC concentrations and fluorescences at depth. In addition, seasonal variation may be involved. During the rainy season, water sources were mixed resulting in lower DOC concentrations in the upper sediment, whereas during the dry season, increased evapotranspiration concentrate salts and DOC, which are transported vertically with percolating water.     

Conformational Changes during Pore Formation by the Perforin-Related Protein Pleurotolysin

Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis. Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally and mechanistically characterised. Here we present an 11 Å resolution cryo-electron microscopy (cryo-EM) structure of the two-part, fungal toxin Pleurotolysin (Ply), together with crystal structures of both components (the lipid binding PlyA protein and the pore-forming MACPF component PlyB). These data reveal a 13-fold pore 80 Å in diameter and 100 Å in height, with each subunit comprised of a PlyB molecule atop a membrane bound dimer of PlyA. The resolution of the EM map, together with biophysical and computational experiments, allowed confident assignment of subdomains in a MACPF pore assembly. The major conformational changes in PlyB are a ∼70° opening of the bent and distorted central β-sheet of the MACPF domain, accompanied by extrusion and refolding of two α-helical regions into transmembrane β-hairpins (TMH1 and TMH2). We determined the structures of three different disulphide bond-trapped prepore intermediates. Analysis of these data by molecular modelling and flexible fitting allows us to generate a potential trajectory of β-sheet unbending. The results suggest that MACPF conformational change is triggered through disruption of the interface between a conserved helix-turn-helix motif and the top of TMH2. Following their release we propose that the transmembrane regions assemble into β-hairpins via top down zippering of backbone hydrogen bonds to form the membrane-inserted β-barrel. The intermediate structures of the MACPF domain during refolding into the β-barrel pore establish a structural paradigm for the transition from soluble monomer to pore, which may be conserved across the whole superfamily. The TMH2 region is critical for the release of both TMH clusters, suggesting why this region is targeted by endogenous inhibitors of MACPF function.