ALBERT

Description: In general, the complex electrical resistivity in the subsurface is anisotropic. Despite this, algorithms for the tomographic inversion of complex resistivity data commonly assume isotropy, mainly due to the lack of anisotropic modelling and inversion schemes, potentially leading to artefacts in the inversion results in the presence of anisotropy. The development of an effective anisotropic complex resistivity inversion algorithm which utilizes the gradient information of some cost function benefits from understanding the characteristics of the problem's sensitivities, that is, the partial derivative of the impedance forward response with respect to the complex conductivities in the different spatial directions, as well as with respect to the different ratios of complex conductivities, that is, the different anisotropy ratios. We here derive expressions for these sensitivities and, based on a 2.5-D finite-element modelling algorithm, we compute and discuss sensitivity distributions as well as measurement response curves of typical surface and cross-borehole measurement configurations for 2-D subsurface anisotropic complex resistivity distributions. Depending on the electrode layout and measurement configuration, the sensitivity with respect to the conductivity in a particular direction shows a unique pattern, while for other directions sensitivity patterns are qualitatively similar. These sensitivity characteristics translate into important equivalences between impedance responses of local anisotropic and isotropic anomalies, for both magnitude and phase. Accordingly, with collinear surface arrays only the complex conductivity in the direction of the electrode layout can be unambiguously resolved, and with cross-borehole arrays only the conductivity in the vertical direction, provided an in-hole current injection is used. Nevertheless, anisotropy ratios involving these resolvable conductivity components are likewise detectable. The distinct shape of the measurement response curves, reflecting the distinct spatial patterns of the corresponding sensitivity distributions, suggest that optimized measurement configurations can be inferred for specific exploration questions involving electrical anisotropy and given electrode layouts. The gained insight into the characteristics of the sensitivity distributions of complex resistivity measurements in case of subsurface anisotropy should guide the implementation of effective anisotropic complex resistivity inversion schemes and lead to a routine use of such schemes in any resistivity and induced polarization surveys whenever subsurface electrical anisotropy could be encountered.

Description: The streaming potential phenomenon is an electrokinetic effect that occurs in porous media. It is characterized by an electrokinetic (EK) coefficient. The aim of this paper is to simulate the EK coefficient in unsaturated conditions using the Lattice Boltzmann method in a 2-D capillary channel. The multiphase flow is simulated with the model of Shan & Chen. The Poisson–Boltzmann equation is solved by implementing the model of Chai & Shi. The streaming potential response shows a non-monotonous behaviour due to the combination of the increase of charge density and decrease of flow velocity with decreasing water saturation. Using a potential of –20 mV at the air–water interface, an enhancement of a factor 5–30 of the EK coefficient, compared to the saturated state, can be observed due to the positive charge excess at this interface which is magnified by the fluid velocity away from the rock surface. This enhancement is correlated to the fractioning of the bubbles, and to the dynamic state of these bubbles, moving or entrapped in the crevices of the channel.

Description: Animal-associated microbiotas form complex communities, which play crucial functions for their host, including susceptibility to infections. Despite increasing attention to bats as reservoirs of zoonotic pathogens, their microbiota is poorly documented, especially for samples potentially implicated in pathogen transmission such as urine and saliva. Here, using low-biomass individual samples, we examined the composition and structure of bacterial communities excreted by insectivorous bats, focusing on three body habitats (saliva, urine and faeces). We show that niche specialisation occurs as bacterial community composition was distinct across body habitats with the majority of phylotypes being body habitat specific. Our results suggest that urine harbours more diverse bacterial communities than saliva and faeces and reveal potentially zoonotic bacteria such as Leptospira , Rickettsia , Bartonella and Coxiella in all body habitats. Our study emphasised that, in addition to the traditional use of gut-associated samples such as faeces, both urine and saliva are also of interest because of their diverse microbiota and the potential transmission of pathogenic bacteria. Our results represent a critical baseline for future studies investigating the interactions between microbiota and infection dynamics in bats.

Description: R-type bacteriocins are contractile phage tail-like structures that are bactericidal towards related bacterial species. The C-terminal region of the phage tail fiber protein determines target-binding specificity. The mutualistic bacteria Xenorhabdus nematophila and X. bovienii produce R-type bacteriocins (xenorhabdicins) that are selectively active against different Xenorhabdus species. We analyzed the P2-type remnant prophage clusters in draft sequences of nine strains of X. bovienii . The C-terminal tail fiber region in each of the respective strains was unique and consisted of mosaics of modular units. The region between the main tail fiber gene ( xbpH1 ) and the sheath gene ( xbpS1 ) contained a variable number of modules encoding tail fiber fragments. DNA inversion and module exchange between strains was involved in generating tail fiber diversity. Xenorhabdicin-enriched fractions from three different X. bovienii strains isolated from the same nematode species displayed distinct activities against each other. In one set of strains, the strain that produced highly active xenorhabdicin was able to eliminate a sensitive strain. In contrast, xenorhabdicin activity was not a determining factor in the competitive fitness of a second set of strains. These findings suggest that related strains of X. bovienii use xenorhabdicin and additional antagonistic molecules to compete against each other.

Description: Anabaena PCC7120 has two annotated toxin–antitoxin systems: MazEF and HicAB. Overexpression of either of the toxins severely inhibited the growth of Escherichia coli BL21(p lysS )(DE3). Of the two Anabaena toxins, MazF exhibited higher toxicity than HicA as evidenced by (i) 100-fold lower viability upon overexpression of MazF compared to HicA; (ii) complete loss of cell viability within 1 h of induction of MazF expression, as against 〉10 3 colony forming units mL –1 in case of HicA; (iii) inability to maintain the MazF overexpressing plasmid in E. coli cells; and (iv) neutralisation of the toxin was effective at the molar ratio of 1:1.9 for MazF:MazE and 13:1 for HicA:HicB, indicating higher antitoxin requirement for neutralisation of MazF. The growth inhibitory effect of MazF was found to be higher in lag phase cultures compared to mid-logarithmic phase cultures of E. coli , while the reverse was true for HicA. The results suggest possible distinct roles for MazEF and HicAB systems of Anabaena .

Description: Joint inversion that simultaneously inverts multiple geophysical data sets to recover a common Earth model is increasingly being applied to exploration problems. Petrophysical data can serve as an effective constraint to link different physical property models in such inversions. There are two challenges, among others, associated with the petrophysical approach to joint inversion. One is related to the multimodality of petrophysical data because there often exist more than one relationship between different physical properties in a region of study. The other challenge arises from the fact that petrophysical relationships have different characteristics and can exhibit point, linear, quadratic, or exponential forms in a crossplot. The fuzzy c-means (FCM) clustering technique is effective in tackling the first challenge and has been applied successfully. We focus on the second challenge in this paper and develop a joint inversion method based on variations of the FCM clustering technique. To account for the specific shapes of petrophysical relationships, we introduce several different fuzzy clustering algorithms that are capable of handling different shapes of petrophysical relationships. We present two synthetic and one field data examples and demonstrate that, by choosing appropriate distance measures for the clustering component in the joint inversion algorithm, the proposed joint inversion method provides an effective means of handling common petrophysical situations we encounter in practice. The jointly inverted models have both enhanced structural similarity and increased petrophysical correlation, and better represent the subsurface in the spatial domain and the parameter domain of physical properties.

Description: Coal seam fires are a worldwide disaster of both ecological and economic importance. Their remote detection from the ground surface or using airborne techniques is required for developing efficient strategies to extinguish them. We investigate here the use of time-domain-induced polarization to localize coal seam fires. For laboratory experiments, we first introduce a modified time-domain-induced polarization methodology to quickly acquire and invert the secondary voltage distribution mapped after the shutdown of the primary current. A set of sandbox experiments is conducted in which coal is embedded into humidified sand. Raw coal alone generates significant induced polarization anomalies, above those shown by the sand. Even higher induced polarization anomalies are detected in presence of a coal seam fire. We postulate that the higher chargeability is due to the pyrolysis, which may enhance electronic polarization or the polarization associated with the cation exchange capacity (CEC) of the material. The position of the coal seam fire is well recovered inside the tank by inverting the secondary voltages in term of a source current density distribution. We also collected field data over a recognized coal seam fire in Colorado, USA. A chargeability anomaly (~800 mV V –1 ) and a resistivity anomaly (~1 Ohm m) are observed at the position of the coal seam fire. We propose a normalized burning front index (a scaled normalized chargeability) to image and localize, without ambiguity, the position of the coal seam fire in the subsurface. The 3-D reconstructed target is located below a negative self-potential anomaly (similarly to what is observed in laboratory experiments) and a temperature anomaly recorded at a depth of 30 cm.

Description: Rock permeability is an important parameter for the formation evaluation. In this paper, a new method with streaming current is proposed to determine the sample permeability based on the electrokinetic effects, and is proved by the experimental measurements. Corresponding to this method, we have designed an experimental setup and a test system, then performed the streaming current (potential) and electro-osmosis pressure experiments with 23 sandstone samples at 0.05 mol l –1 NaCl solution. The streaming current (potential) coefficient and electro-osmosis pressure coefficient are obtained, respectively, with the experimental data at low frequencies with AC lock-in technique. The electrokinetic permeabilities are further calculated with these coefficients. The results are consistent well with the gas permeability measured with Darcy's law, which verifies the current method for estimating rock permeability. Our measurements are also analysed and compared with previous measurements. The results indicate that our method can reflect the essence of electrokinetic effects better and simplify the electrokinetic measurements as well. In addition, we discuss the influences of experimental artefacts (core holder and confining pressure installation) on the electrokinetic data. The results show that the trough phenomenon, appeared in frequency curves of streaming current (potential) coefficients, is induced by the resonance of the core-holder/vibrator system. This is important for the design of electrokinetic setup and the analysis of low-frequency response of the electrokinetic coupling coefficients.

Description: Four antibiotics (pamamycin, oligomycin A, oligomycin B and echinosporin) were isolated and characterized from the fermentation broth of the marine Streptomyces strains B8496 and B8739. Bioassays revealed that each of these compounds impaired motility and caused subsequent lysis of P. viticola zoospores in a dose- and time-dependent manner. Pamamycin displayed the strongest motility inhibitory and lytic activities (IC 50 0.1 μg mL –1 ) followed by oligomycin B (IC 50 0.15 and 0.2 μg mL –1 ) and oligomycin F (IC 50 0.3 and 0.5 μg mL –1 ). Oligomycin A and echinosporin also showed motility inhibitory activities against the zoospores with IC 50 values of 3.0 and 10.0 μg mL –1 , respectively. This is the first report of motility inhibitory and lytic activities of these antibiotics against zoospores of a phytopathogenic peronosporomycete. Structures of all the isolated compounds were determined based on detailed spectroscopic analysis.

Description: Multiparameter full waveform inversion (FWI) applied to an elastic orthorhombic model description of the subsurface requires in theory a nine-parameter representation of each pixel of the model. Even with optimal acquisition on the Earth surface that includes large offsets, full azimuth, and multicomponent sensors, the potential for trade-off between the elastic orthorhombic parameters are large. The first step to understanding such trade-off is analysing the scattering potential of each parameter, and specifically, its scattering radiation patterns. We investigate such radiation patterns for diffraction and for scattering from a horizontal reflector considering a background isotropic model. The radiation patterns show considerable potential for trade-off between the parameters and the potentially limited resolution in their recovery. The radiation patterns of C 11 , C 22 , and C 33 are well separated so that we expect to recover these parameters with limited trade-offs. However, the resolution of their recovery represented by recovered range of model wavenumbers varies between these parameters. We can only invert for the short wavelength components (reflection) of C 33 while we can mainly invert for the long wavelength components (transmission) of the elastic coefficients C 11 and C 22 if we have large enough offsets. The elastic coefficients C 13 , C 23 , and C 12 suffer from strong trade-offs with C 55 , C 44 , and C 66 , respectively. The trade-offs between C 13 and C 55 , as well as C 23 and C 44 , can be partially mitigated if we acquire P – SV and SV – SV waves. However, to reduce the trade-offs between C 12 and C 66 , we require credible SH – SH waves. The analytical radiation patterns of the elastic constants are supported by numerical gradients of these parameters.

Description: In sulfidic environments, microbes oxidize reduced sulfur compounds via several pathways. We used metagenomics to investigate sulfur metabolic pathways from microbial mat communities in two subterranean sulfidic streams in Lower Kane Cave, WY, USA and from Glenwood Hot Springs, CO, USA. Both unassembled and targeted recA gene assembly analyses revealed that these streams were dominated by Epsilonproteobacteria and Gammaproteobacteria , including groups related to Sulfurovum , Sulfurospirillum , Thiothrix and an epsilonproteobacterial group with no close cultured relatives. Genes encoding sulfide:quinone oxidoreductase (SQR) were abundant at all sites, but the specific SQR type and the taxonomic affiliation of each type differed between sites. The abundance of thiosulfate oxidation pathway genes (Sox) was not consistent between sites, although overall they were less abundant than SQR genes. Furthermore, the Sox pathway appeared to be incomplete in all samples. This work reveals both variations in sulfur metabolism within and between taxonomic groups found in these systems, and the presence of novel epsilonproteobacterial groups.

Description: Pseudomonas aeruginosa is an opportunistic pathogen with high resistance to a wide variety of antimicrobials. The multidrug resistance pump MexAB-OprM promotes the efflux of various antibiotics, mostly when mutations accumulate in the transcriptional regulators MexR, NalC and NalD, thereby causing MexAB-OprM overexpression. In this work, a characterization of 50 P. aeruginosa isolates obtained from Brazilian agricultural soils to determine the reasons of their resistance to aztreonam was done. The majority of the isolates showed higher aztreonam resistance than wild-type strain by MIC method. DNA sequence analysis of mexR , nalC and nalD genes from 13 of these isolates showed the amino acid substitution in NalC for all tested isolates, just one mutation was detected in MexR and none in NalD. Furthermore, an increase in the level of mexA expression by real-time RT-PCR analysis in eight isolates harboring mutations in NalC was found. Although there was not a relationship between MIC of aztreonam and the level of mexA expression, on the other hand, the results presented here suggest that novel mutations in NalC, including Arg 97 -Gly and Ala 186 -Thr, are related to MexAB-OprM overexpression causing aztreonam resistance in P. aeruginosa environmental isolates.

Description: Sedge-dominated wetlands on the Qinghai–Tibetan Plateau are methane emission centers. Methanotrophs at these sites play a role in reducing methane emissions, but relatively little is known about the composition of active methanotrophs in these wetlands. Here, we used DNA stable isotope probing to identify the key active aerobic methanotrophs in three sedge-dominated wetlands on the plateau. We found that Methylocystis species were active in two peatlands, Hongyuan and Dangxiong. Methylobacter species were found to be active only in Dangxiong peat. Hongyuan peat had the highest methane oxidation rate, and cross-feeding of carbon from methanotrophs to methylotrophic Hyphomicrobium species was observed. Owing to a low methane oxidation rate during the incubation, the labeling of methanotrophs in Maduo wetland samples was not detected. Our results indicate that there are large differences in the activity of methanotrophs in the wetlands of this region.

Description: Here we present the generation and function of two sets of bacterial plasmids that harbor fluorescent genes encoding either blue, cyan, yellow or red fluorescent proteins. In the first set, protein expression is controlled by the strong and constitutive nptII promoter whereas in the second set, the strong tac promoter was chosen that underlies LacI q regulation. Furthermore, the plasmids are mobilizable, contain Tn 7 transposons and a temperature-sensitive origin of replication. Using Escherichia coli S17-1 as donor strain, the plasmids allow fast and convenient Tn 7 -transposon delivery into many enterobacterial hosts, such as the here-used E. coli O157:H7. This procedure omits the need of preparing competent recipient cells and antibiotic resistances are only transiently conferred to the recipients. As the fluorescence proteins show little to no overlap in fluorescence emission, the constructs are well suited for the study of multicolored synthetic bacterial communities during biofilm production or in host colonization studies, e.g. of plant surfaces. Furthermore, tac promoter-reporter constructs allow the generation of so-called reproductive success reporters, which allow to estimate past doublings of bacterial individuals after introduction into environments, emphasizing the role of individual cells during colonization.

Description: Typically, seismic data are sparsely and irregularly sampled due to limitations in the survey environment and these cause problems for key seismic processing steps such as surface-related multiple elimination or wave-equation-based migration. Various interpolation techniques have been developed to alleviate the problems caused by sparse and irregular sampling. Among many interpolation techniques, matching pursuit interpolation is a robust tool to interpolate the regularly sampled data with large receiver separation such as crossline data in marine seismic acquisition when both pressure and particle velocity data are used. Multicomponent matching pursuit methods generally used the sinusoidal basis function, which have shown to be effective for interpolating multicomponent marine seismic data in the crossline direction. In this paper, we report the use of wavelet basis functions which further enhances the performance of matching pursuit methods for de-aliasing than sinusoidal basis functions. We also found that the range of the peak wavenumber of the wavelet is critical to the stability of the interpolation results and the de-aliasing performance and that the range should be determined based on Nyquist criteria. In addition, we reduced the computational cost by adopting the inner product of the wavelet and the input data to find the parameters of the wavelet basis function instead of using L-2 norm minimization. Using synthetic data, we illustrate that for aliased data, wavelet-based matching pursuit interpolation yields more stable results than sinusoidal function-based one when we use not only pressure data only but also both pressure and particle velocity together.

Description: Spa -typing and microarray techniques were used to study epidemiological changes in methicillin-resistant Staphylococcus aureus (MRSA) in South-East Austria. The population structure of 327 MRSA isolated between 2002 and 2012 was investigated. MRSA was assigned to 58 different spa types and 14 different MLST CC (multilocus sequence type clonal complexes); in particular, between 2007 and 2012, an increasing diversity in MRSA clones could be observed. The most abundant clonal complex was CC5. On the respective SCC mec cassettes, the CC5 isolates differed clearly within this decade and CC5/SCC mec I, the South German MRSA, predominant in 2002, was replaced by CC5/SCC mec II, the Rhine-Hesse MRSA in 2012. Whereas in many European countries MLST CC22-MRSA (EMRSA 15, the Barnim epidemic MRSA) is predominant, this clone occurred in Austria nearly 10 years later than in neighbouring countries. CC45, the Berlin EMRSA, epidemic in Germany, was only sporadically found in South-East Austria. The Irish ST8-MRSA-II represented by spa -type t190 was frequently found in 2002 and 2007, but disappeared in 2012. Our results demonstrate clonal replacement of MRSA clones within the last years in Austria. Ongoing surveillance is warranted for detection of changes within the MRSA population.

Description: This study aimed to investigate the effects of dietary fibre sources on the gut microbiota in suckling piglets, and to test the hypothesis that a moderate increase of dietary fibre may affect the gut microbiota during the suckling period. Suckling piglets were fed different fibre-containing diets or a control diet from postnatal day 7 to 22. Digesta samples from cecum, proximal colon and distal colon were used for Pig Intestinal Tract Chip analysis. The data showed that the effects of fibre-containing diet on the gut microbiota differed in the fibre source and gut location. The alfalfa diet increased Clostridium cluster XIVb and Sporobacter termitidis in the cecum compared to the pure cellulose diet. Compared to the control diet, the alfalfa diet also increased Coprococcus eutactus in the distal colon, while the pure cellulose diet decreased Eubacterium pyruvativorans in the cecum. The pure cellulose diet increased Prevotella ruminicola compared to the wheat bran diet. Interestingly, the alfalfa group had the lowest abundance of the potential pathogen Streptococcus suis in the cecum and distal colon. These results indicated that a moderate increase in dietary fibres affected the microbial composition in suckling piglets, and that the alfalfa inclusion produced some beneficial effects on the microbial communities.

Description: One function of the gut microbiota gaining recent attention, especially in herbivorous mammals and insects, is the metabolism of plant secondary metabolites (PSMs). We investigated whether this function exists within the gut communities of a specialist avian herbivore. We sequenced the cecal metagenome of the Greater Sage-Grouse ( Centrocercus urophasianus ), which specializes on chemically defended sagebrush ( Artemisia spp.). We predicted that the cecal metagenome of the sage-grouse would be enriched in genes associated with the metabolism of PSMs when compared to the metagenome of the domestic chicken. We found that representation of microbial genes associated with ‘xenobiotic degradation and metabolism’ was 3-fold higher in the sage-grouse cecal metagenomes when compared to that of the domestic chicken. Further, we identified a complete metabolic pathway for the degradation of phenol to pyruvate, which was not detected in the metagenomes of the domestic chicken, bovine rumen or 14 species of mammalian herbivores. Evidence of monoterpene degradation (a major class of PSMs in sagebrush) was less definitive, although we did detect genes for several enzymes associated with this process. Overall, our results suggest that the gut microbiota of specialist avian herbivores plays a similar role to the microbiota of mammalian and insect herbivores in degrading PSMs.

Description: Deep sea pockmarks underlain by chimney-like or pipe structures that contain methane hydrate are abundant along the Norwegian continental margin. In such hydrate provinces the interaction between hydrate formation and fluid flow has significance for benthic ecosystems and possibly climate change. The Nyegga region, situated on the western Norwegian continental slope, is characterized by an extensive pockmark field known to accommodate substantial methane gas hydrate deposits. The aim of this study is to detect and delineate both the gas hydrate and free gas reservoirs at one of Nyegga's pockmarks. In 2012, a marine controlled-source electromagnetic (CSEM) survey was performed at a pockmark in this region, where high-resolution 3-D seismic data were previously collected in 2006. 2-D CSEM inversions were computed using the data acquired by ocean bottom electrical field receivers. Our results, derived from unconstrained and seismically constrained CSEM inversions, suggest the presence of two distinctive resistivity anomalies beneath the pockmark: a shallow vertical anomaly at the underlying pipe structure, likely due to gas hydrate accumulation, and a laterally extensive anomaly attributed to a free gas zone below the base of the gas hydrate stability zone. This work contributes to a robust characterization of gas hydrate deposits within subseafloor fluid flow pipe structures.

Description: Intracellular endosymbiotic bacteria are common and can play a crucial role for insect pathology. Therefore, such bacteria could be a potential key to our understanding of major losses of Western honey bees ( Apis mellifera ) colonies. However, the transmission and potential effects of endosymbiotic bacteria in A. mellifera and other Apis spp. are poorly understood. Here, we explore the prevalence and transmission of the genera Arsenophonus , Wolbachia , Spiroplasma and Rickettsia in Apis spp. Colonies of A. mellifera ( N = 33, with 20 eggs from worker brood cells and 100 adult workers each) as well as mated honey bee queens of A. cerana , A. dorsata and A. florea ( N = 12 each) were screened using PCR. While Wolbachia , Spiroplasma and Rickettsia were not detected, Arsenophonus spp. were found in 24.2% of A. mellifera colonies and respective queens as well as in queens of A. dorsata (8.3%) and A. florea (8.3%), but not in A. cerana . The absence of Arsenophonus spp. from reproductive organs of A. mellifera queens and surface-sterilized eggs does not support transovarial vertical transmission. Instead, horizontal transmission is most likely.

Description: One of the main applications of magnetic field measurements in boreholes is the detection of unexploded ordnance or buried utility structures like pipes or tiebacks. Even though the advantage of fully oriented magnetic vector measurements have long been recognized and could significantly reduce costs and risks, the tools used for those purposes typically measure only the total magnetic field, the vertical and horizontal components or gradients thereof. The Göttingen Bohrloch Magnetometer uses three fibre optic gyros to record its orientation and thus enables us to compute high-quality three-component magnetic vector data regardless of borehole orientation. The measurements described in this paper were run in the scientific borehole Cuxhaven Lüdingworth 1/1A, which was drilled as a part of the ‘Coastal Aquifer Test field’ project to study the dynamics of the saltwater/freshwater interface. As the drill string got stuck during drilling of the first borehole, a second hole was drilled in the immediate vicinity. The drill string lies at a depth between 80 and 114 m at a distance of only 2.5 m southeast of the borehole used for the measurements, making it an ideal target to demonstrate the benefits of vector magnetic surveys. Although the theories to calculate magnetic fields of objects with different shapes is well established and do not need to be tested, they almost exclusively include approximations of the geometry. It is not obvious whether these approximations are suited to describe real data, or whether additional effects or refinements have to be considered. We use both a simplified monopole model and a cylinder model to fit the data and are able to determine the position of the drill string within a statistical error of approximately 10 cm. Additionally, we show that the location of the drill string could not have been determined by measurements of the total field or its horizontal and vertical component alone and that those methods would require the drilling of additional boreholes to obtain an unambiguous result.

Description: Wood-rotting fungi possess remarkably diverse extracellular oxidation mechanisms, including enzymes, such as laccase and peroxidases, and Fenton chemistry. The ability to biologically drive Fenton chemistry by the redox cycling of quinones has previously been reported to be present in both ecologically diverging main groups of wood-rotting basidiomycetes. Therefore, we investigated whether it is even more widespread among fungal organisms. Screening of a diverse selection of a total of 18 ascomycetes and basidiomycetes for reduction of the model compound 2,6-dimethoxy benzoquinone revealed that all investigated strains were capable of reducing it to its corresponding hydroquinone. In a second step, depolymerization of the synthetic polymer polystyrene sulfonate was used as a proxy for quinone-dependent Fenton-based biodegradation capabilities. A diverse subset of the strains, including environmentally ubiquitous molds, white-rot fungi, as well as peatland and aquatic isolates, caused substantial depolymerization indicative for the effective employment of quinone redox cycling as biodegradation tool. Our results may also open up new paths to utilize diverse fungi for the bioremediation of recalcitrant organic pollutants.

Description: Ice-binding proteins (IBPs), such as antifreeze proteins (AFPs) and ice-nucleating proteins (INPs), have been described in diverse cold-adapted organisms, and their potential applications in biotechnology have been recognized in various fields. Currently, both IBPs are being applied to biotechnological processes, primarily in medicine and the food industry. However, our knowledge regarding the diversity of bacterial IBPs is limited; few studies have purified and characterized AFPs and INPs from bacteria. Phenotypically verified IBPs have been described in members belonging to Gammaproteobacteria, Actinobacteria and Flavobacteriia classes, whereas putative IBPs have been found in Gammaproteobacteria, Alphaproteobacteria and Bacilli classes. Thus, the main goal of this minireview is to summarize the current information on bacterial IBPs and their application in biotechnology, emphasizing the potential application in less explored fields such as agriculture. Investigations have suggested the use of INP-producing bacteria antagonists and AFPs-producing bacteria (or their AFPs) as a very attractive strategy to prevent frost damages in crops. UniProt database analyses of reported IBPs (phenotypically verified) and putative IBPs also show the limited information available on bacterial IBPs and indicate that major studies are required.

Description: Triazophos is a broad-spectrum and highly effective insecticide, and the residues of triazophos have been frequently detected in the environment. A triazophos-degrading bacterium, Burkholderia sp. SZL-1, was isolated from a long-term triazophos-polluted soil. Strain SZL-1 could hydrolyze triazophos to 1-phenyl-3-hydroxy-1,2,4-triazole, which was further utilized as the carbon sources for growth. The triazophos hydrolase gene trhA , cloned from strain SZL-1, was expressed and homogenously purified using Ni-nitrilotriacetic acid affinity chromatography. TrhA is 55 kDa and displays maximum activity at 25°C, pH 8.0. This enzyme still has nearly 60% activity at the range of 15°C–50°C for 30 min. TrhA was mutated by sequential error prone PCR and screened for improved activity for triazophos degradation. One purified variant protein (Val89-Gly89) named TrhA-M1 showed up to 3-fold improvement in specific activity against triazophos, and the specificity constants of K cat and K cat / K m for TrhA-M1 were improved up to 2.3- and 8.28-fold, respectively, compared to the wild-type enzyme. The results in this paper provided potential material for the contaminated soil remediation and hydrolase genetic structure research.

Description: The metal mining industry faces many large challenges in future years, among which is the increasing need to process low-grade ores as accessible higher grade ores become depleted. This is against a backdrop of increasing global demands for base and precious metals, and rare earth elements. Typically about 99% of solid material hauled to, and ground at, the land surface currently ends up as waste (rock dumps and mineral tailings). Exposure of these to air and water frequently leads to the formation of acidic, metal-contaminated run-off waters, referred to as acid mine drainage, which constitutes a severe threat to the environment. Formation of acid drainage is a natural phenomenon involving various species of lithotrophic (literally ‘rock-eating’) bacteria and archaea, which oxidize reduced forms of iron and/or sulfur. However, other microorganisms that reduce inorganic sulfur compounds can essentially reverse this process. These microorganisms can be applied on industrial scale to precipitate metals from industrial mineral leachates and acid mine drainage streams, resulting in a net improvement in metal recovery, while minimizing the amounts of leachable metals to the tailings storage dams. Here, we advocate that more extensive exploitation of microorganisms in metal mining operations could be an important way to green up the industry, reducing environmental risks and improving the efficiency and the economy of metal recovery.

Description: Although seismic attenuation measurements have great potential to enhance our knowledge of physical conditions and rock properties, their application is limited because robust methods for improving both the resolution and accuracy of attenuation estimates have not yet been established. We propose attenuation estimation methods for zero-offset vertical seismic profile (VSP) data by combining seismic interferometry (SI) and the modified median frequency shift (MMFS) method developed for attenuation estimation using sonic waveform data. The configuration of zero-offset VSP data is redatumed to that of the sonic logging measurement by adopting two types of SI: deconvolution interferometry and crosscorrelation interferometry (CCI). Then, we can apply the MMFS method to the redatumed VSP data. Although the amplitude information estimated from CCI is biased, we propose a correction method for this bias to correctly estimate attenuation. First, to investigate the performance both in resolution and accuracy, we apply different trace separations to synthetic data with random noise at different signal-to-noise ratio levels. Second, we estimate the influence of residual reflection events after wavefield separation on attenuation estimation. The proposed methods provide more stable attenuation estimates in comparison with the spectral ratio method because the mean-median procedure suppresses random events and characteristic features caused by residual reflection events in spectral domain. Our numerical experiments also imply that the proposed methods can estimate scattering attenuation values even if frequency components are not changed between the two receiver depths. Finally, by preliminarily applying the proposed methods to field VSP data, we demonstrate the advantages of the proposed method in the resolution and stability of attenuation estimates and these observations correlate with those of numerical tests.

Description: Differential inhibitors are important for measuring the relative contributions of microbial groups, such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), to biogeochemical processes in environmental samples. In particular, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) represents a nitric oxide scavenger used for the specific inhibition of AOA, implicating nitric oxide as an intermediate of thaumarchaeotal ammonia oxidation. This study investigated four alternative nitric oxide scavengers for their ability to differentially inhibit AOA and AOB in comparison to PTIO. Caffeic acid, curcumin, methylene blue hydrate and trolox were tested on Nitrosopumilus maritimus , two unpublished AOA representatives (AOA-6f and AOA-G6) as well as the AOB representative Nitrosomonas europaea . All four scavengers inhibited ammonia oxidation by AOA at lower concentrations than for AOB. In particular, differential inhibition of AOA and AOB by caffeic acid (100 μM) and methylene blue hydrate (3 μM) was comparable to carboxy-PTIO (100 μM) in pure and enrichment culture incubations. However, when added to aquarium sponge biofilm microcosms, both scavengers were unable to inhibit ammonia oxidation consistently, likely due to degradation of the inhibitors themselves. This study provides evidence that a variety of nitric oxide scavengers result in differential inhibition of ammonia oxidation in AOA and AOB, and provides support to the proposed role of nitric oxide as a key intermediate in the thaumarchaeotal ammonia oxidation pathway.

Description: Peatlands of all latitudes play an integral role in global climate change by serving as a carbon sink and a primary source of atmospheric methane; however, the microbial ecology of mid-latitude peatlands is vastly understudied. Herein, next generation Illumina amplicon sequencing of small subunit rRNA genes was utilized to elucidate the microbial communities in three southern Appalachian peatlands. In contrast to northern peatlands, Proteobacteria dominated over Acidobacteria in all three sites. An average of 11 bacterial phyla was detected at relative abundance values 〉1%, with three candidate divisions (OP3, WS3 and NC10) represented, indicating high phylogenetic diversity. Physiological traits of isolates within the candidate alphaproteobacterial order, Ellin 329, obtained here and in previous studies indicate that bacteria of this order may be involved in hydrolysis of poly-, di- and monosaccharides. Community analyses indicate that Ellin 329 is the third most abundant order and is most abundant near the surface layers where plant litter decomposition should be primarily occurring. In sum, members of Ellin 329 likely play important roles in organic matter decomposition, in southern Appalachian peatlands and should be investigated further in other peatlands and ecosystem types.

Description: Marine viruses are the most abundant biological entity in the oceans, the majority of which infect bacteria and are known as bacteriophages. Yet, the bulk of bacteriophages form part of the vast uncultured dark matter of the microbial biosphere. In spite of the paucity of cultured marine bacteriophages, it is known that marine bacteriophages have major impacts on microbial population structure and the biogeochemical cycling of key elements. Despite the ecological relevance of marine bacteriophages, there are relatively few isolates with complete genome sequences. This minireview focuses on knowledge gathered from these genomes put in the context of viral metagenomic data and highlights key advances in the field, particularly focusing on genome structure and auxiliary metabolic genes.

Description: The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants ( Erepsia anceps , Phaenocoma prolifera and Leucadendron laureolum ). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera , whereas Deinococcus-Thermus dominated in L. laureolum , revealing species-specific host–bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth.

Description: Capacitively Coupled Resistivity (CCR) is conventionally used to emulate DC resistivity measurements and may provide important information about the ice content of material in periglacial areas. The application of CCR theoretically enables the determination of both electrical parameters, that is, the resistivity and the electrical permittivity, by analysing magnitude and phase shift spectra. The electrical permittivity may dominate the impedance, especially in periglacial areas or regions of hydrogeological interest. However, previous theoretical work suggested that the phase shift may strongly depend on electrode height above ground, implying that electrode height must be known with great accuracy to determine electrical permittivity. Here, we demonstrate with laboratory test measurements, theoretical modelling and by analysing the Jacobian matrix of the inversion that the sensitivity towards electrode height is drastically reduced if the electrical permittivity is frequency dependent in a way that is typical for ice. For the first time, we used a novel broad-band CCR device ‘Chameleon’ for a field test located in one of the ridge galleries beneath the crest of Mount Zugspitze. A permanently ice covered bottom of a tunnel was examined. For the inversion of the measured spectra, the frequency dependence of the electrical parameters was parametrized in three different ways: A Debye Model for pure ices, a Cole–Cole Model for pure ices and a dual Cole–Cole Model including interfacial water additionally. The frequency-dependent resistivity and permittivity spectra obtained from the inversion, including low- and high-frequency limits, agree reasonably well with laboratory and field measurements reported in the literature.

Description: We evaluate the applicability and the effectiveness of GPR attribute analysis for high-resolution glacier imaging and characterization, testing this approach on 4-D GPR multifrequency data collected in a small glacier in the Eastern Alps, by repeating the acquisition along the same profiles in four different periods of the year 2013. The main objectives are to image and characterize the glacier's inner structure and to quantitatively monitor the seasonal thawing of near-surface frozen materials (snow/firn). A multiattribute approach is used to characterize the subsurface through different attribute categories, including instantaneous and textural attributes considering not only amplitude-, phase- and frequency-related attributes, but also other more complex and integrated parameters. We combine information from more than one attribute into a single image with composite displays, using overlays or mixed displays. The results demonstrate that the developed GPR attribute analysis can provide significant improvements in the discrimination of GPR signals, and obtain enhanced and more constrained data interpretations.

Description: Migration velocity analysis aims at automatically updating the large-scale components of the velocity model, called macromodel. Extended Common Image Gathers are panels used to evaluate focusing after imaging and are constructed as a function of a spatial shift introduced in the imaging condition. We investigate how transmitted waves can also be used in migration velocity analysis: instead of back-propagating the residuals associated with reflected waves, we propose to back-propagate the full wavefield. The image function, equivalent to the migrated section for reflected data, does not exhibit localized events in space along horizons but is still sensitive to the choice of the background velocity model and can thus be coupled to the same objective function defined in the image domain. In order to enhance the benefits of direct waves, we consider a cross-well configuration. Direct waves provide a large illumination between two vertical wells. Associated Common Image Gathers present different characteristics than the ones associated with reflected waves in surface acquisition. In particular, energy is spread over up to the maximum penetration depth. We invert cross-well seismic data along two lines. In the first case, the input data contain the full wavefield dominated by transmitted waves. It demonstrates the possibility to handle transmitted waves to determine the velocity model. It appears that the misfit in the data domain is largely reduced after inversion. In the second case, we use the same algorithm, but with reflected observed data only, as in a classical approach. Most of velocity updates are localized around the reflectivity, leading to an incorrect final model. This demonstrates the benefit of transmitted waves for migration velocity analysis in a cross-well configuration.

Description: An integrated approach to interpret Self-Potential (SP) anomalies based on spectral analysis and tomographic methods is presented. The Maximum Entropy Method (MEM) is used for providing accurate estimates of the depth of the anomaly source. The 2-D tomographic inversion technique, based on the underground charge occurrence probability (COP) function, is, then, used to fully characterize the anomalous body, as the MEM is not helpful in delineating the shape of the anomaly source. The proposed integrated approach is applied for the inversion of synthetic SP data generated by geometrically simple anomalous bodies, such as cylinders and inclined sheets. This numerical study has allowed the determination of mathematical relationships between zero lines of the COP distributions, the polarization angles and the positions along the profile of the causative sources, which have been of great help for interpreting the related SP anomalies. Finally, the analysis of field examples shows the high potential applicability of the proposed integrated approach for SP data inversion.

Description: Volcanic and tectonic events are the main processes involved in the generation of the oceanic crust and responsible for the seismicity associated with seafloor spreading. To monitor this activity, usually not or poorly detected by land-based seismological stations, we deployed from February 2012 to February 2013 a network of autonomous hydrophones to compare the behaviour of the ultraslow-spreading Southwest Indian ridge (SWIR) with that of the intermediate-spreading Southeast Indian ridge (SEIR). The rate of seismicity is similar for both ridges, suggesting that there is no systematic relationship between seismicity and spreading rates. The along-axis distribution of the seismic events, however, does differ, reflecting the rate dependence of accretion modes. Earthquakes are sparse and regularly spaced and scattered along the SWIR, reflecting prevailing tectonic processes. By contrast, along the SEIR, events are irregularly distributed and focus at ridge-segment ends and transforms faults, reflecting the ridge segmentation; only two swarms occurred at a segment centre and are probably caused by a magmatic event. This seismicity distribution thus looks controlled by segment-scale crustal heterogeneities along the SEIR and by regional-scale contrasting accretion processes along the SWIR, probably driven by different lithospheric and asthenospheric dynamics on either side of the Melville fracture zone. The comparison of hydroacoustic and teleseismic catalogues shows that, along these spreading ridges, the background seismicity observed in 1 yr by a hydroacoustic network is representative of the seismicity observed over two decades by land-based networks.

Description: The functioning of many natural and engineered environments is dependent on long distance electron transfer mediated through electrical currents. These currents have been observed in exoelectrogenic biofilms and it has been proposed that microbial biofilms can mediate electron transfer via electrical currents on the centimeter scale. However, direct evidence to confirm this hypothesis has not been demonstrated and the longest known electrical transfer distance for single species exoelectrogenic biofilms is limited to 100 μm. In the present study, biofilms were developed on electrodes with electrically non-conductive gaps from 50 μm to 1 mm and the in situ conductance of biofilms was evaluated over time. Results demonstrated that the exoelectrogenic mixed species biofilms in the present study possess the ability to transfer electrons through electrical currents over a distance of up to 1 mm, 10 times further than previously observed. Results indicate the possibility of interspecies interactions playing an important role in the spatial development of exoelectrogenic biofilms, suggesting that these biological networks might remain conductive even at longer distance. These findings have significant implications in regards to future optimization of microbial electrochemical systems.

Description: Bacteriophages are increasingly being used as water quality indicators. Two groups of phages infecting Escherichia coli , somatic and F-specific coliphages, are being considered as indicators of fecal and viral contamination for several types of water around the world. However, some uncertainties remain regarding which coliphages to assess. Recently, E. coli strain CB390 has been reported to be suitable for simultaneous detection of both groups, which seems to be more informative than determining only one of the groups. Here, a significant number of samples from different settings, mostly those where F-specific phages have been reported to outnumber somatic coliphages, are analyzed for somatic coliphages, F-specific RNA phages by standardized methods and coliphages detected by host strain CB390. The results presented here confirm that the numbers of phages counted using CB390 are equivalent to the sum of the somatic and F-specific coliphages counted independently in all settings. Hence the usefulness of this strain for simultaneous detection of somatic and F-specific coliphages is confirmed. Also, sets of data on the presence of coliphages in reclaimed and groundwater are reported.

Description: It is well known that Methylosinus trichosporium OB3b has two forms of methane monooxygenase (MMO) responsible for the initial conversion of methane to methanol, a cytoplasmic (soluble) methane monooxygenase and a membrane-associated (particulate) methane monooxygenase, and that copper strongly regulates expression of these alternative forms of MMO. More recently, it has been discovered that M. trichosporium OB3b has multiple types of the methanol dehydrogenase (MeDH), i.e. the Mxa-type MeDH (Mxa-MeDH) and Xox-type MeDH (Xox-MeDH), and the expression of these two forms is regulated by the availability of the rare earth element (REE), cerium. Here, we extend these studies and show that lanthanum, praseodymium, neodymium and samarium also regulate expression of alternative forms of MeDH. The effect of these REEs on MeDH expression, however, was only observed in the absence of copper. Further, a mutant of M. trichosporium OB3b, where the Mxa-MeDH was knocked out, was able to grow in the presence of lanthanum, praseodymium and neodymium, but was not able to grow in the presence of samarium. Collectively, these data suggest that multiple levels of gene regulation by metals exist in M. trichosporium OB3b, but that copper overrides the effect of other metals by an as yet unknown mechanism.

Description: Geothermal well GRT-1 (Rittershoffen, Alsace) was drilled in 2012. Its open-hole section (extending down to a depth of 2.6 km) penetrated fractured sandstones and granite. In 2013, the well was subjected to Thermal, Chemical and Hydraulic (TCH) stimulation, which improved the injectivity index fivefold. The goal of the study was to assess the impact of the stimulation by comparing pre- and post-stimulation well-logging (acoustic and temperature [ T ] logs) and mud-logging data. This comparison revealed modifications of almost all the natural fractures. However, not all of these fractures are associated with permeability enhancement, and the post-stimulation T logs are important for characterizing this enhancement. Chemical alteration due to mechanical erosion at the tops and bottoms of the fractures was observed in the sandstones. These zones display indications of very small new permeability after the TCH stimulation. Because a major fault zone caved extensively where it crosses the borehole, it was not imaged in the acoustic logs. However, this originally permeable zone was enhanced as demonstrated by the T logs. Based on the natural injectivity of this fault zone, hydraulic erosion and thermal microcracking of its internal quartz veins are associated with this permeability enhancement. Although local changes in the borehole wall observed in the acoustic images cannot be directly linked to the improved injectivity index, the comparison of the acoustic image logs allows for identification of fracture zones impacted by the TCH stimulation.

Description: We investigate the spatial coherence of underwater ambient noise using a yearlong time-series measured off Ascension Island. Qualitative agreement with observed cross-correlations is achieved using a simple range-dependent model, constrained by earlier, active tomographic studies in the area. In particular, the model correctly predicts the existence of two weakly dispersive normal modes in the microseism frequency range, with the group speed of one of the normal modes being smaller than the sound speed in water. The agreement justifies our interpretation of the peaks of the measured cross-correlation function of ambient noise as modal arrivals, with dispersion that is sensitive to crustal velocity structure. Our observations are consistent with Scholte to Moho head wave coupled propagation, with double mode conversion occurring due to the bathymetric variations between receivers. We thus demonstrate the feasibility of interrogating crustal properties using noise interferometry of moored hydrophone data at ranges in excess of 120 km.

Description: Recent tectonic reconstructions of the South Atlantic have partitioned the ocean basin into several segments based upon one or more proposed intraplate South American deformation zones. In several of these reconstructions, opening of the southern segment(s) by seafloor spreading prior to Aptian-Albian time is accompanied by contemporaneous strike-slip motion along an intraplate boundary extending southeastward from the Andean Cochabamba—Santa Cruz bend to the Rio Grande Fracture Zone (RGFZ). We have examined new magnetic data over the Pelotas, Santos and Campos Basins, offshore Argentina and Brazil, acquired by ION-GXT in tandem with long-offset, long record seismic reflection data, and identified seafloor spreading anomalies M4, M3, M2 and M0 (~131, ~129, ~128 and ~125 Ma). Integrating these results with our earlier work, we have been able to correlate magnetochrons M4, M3, M2 and M0 north and south of the RGFZ on the South American margin, and north and south of the Walvis Ridge on the African side. Our results are therefore inconsistent with diachronous opening models that involve substantial continental strike-slip motion north of RGFZ during M4 to M0 time. Although the ocean basin may have opened from south to north, our results indicate that seafloor spreading began north of the RGFZ earlier than previously proposed.

Description: Determining thin layer thickness is very important for reservoir characterization and CO 2 quantification. Given its high time–frequency resolution and robustness, the complex spectral decomposition method was applied on time-lapse 3-D seismic data from the Ketzin pilot site for CO 2 storage to evaluate the frequency-dependent characteristics of thin layers at the injection level. Higher temporal resolution and more stratigraphic details are seen in the all-frequency and monochromatic reflectivity amplitude sections obtained by complex spectral decomposition compared to the stacked sections. The mapped geologic discontinuities within the reservoir are consistent with the preferred orientation of CO 2 propagation. Tuning frequency mapping shows the thicknesses of the reservoir sandstone and gaseous CO 2 is consistent with the measured thickness of the sandstone unit from well logging. An attempt to discriminate between pressure effects and CO 2 saturation using the extracted tuning frequency indicates that CO 2 saturation is the main contributor to the amplitude anomaly at the Ketzin site. On the basis of determined thickness of gaseous CO 2 in the reservoir, quantitative analysis of the amount of CO 2 was performed and shows a discrepancy between the injected and calculated CO 2 mass. This may be explained by several uncertainties, like structural reservoir heterogeneity, a limited understanding of the complex subsurface conditions, error of determined tuning frequency, the presence of ambient noise and ongoing CO 2 dissolution.

Description: Polysulfides (S x 2– ) are sulfide oxidation intermediates that are important for a variety of environmentally relevant processes including pyrite formation, organic matter sulfidization, isotope exchange among reduced sulfur species, and metal chelation. In addition to their chemical reactivity, laboratory experiments with microbial cultures and enzymes indicate both indirect and direct roles for microorganisms in affecting polysulfide chemistry in natural environments through production and consumption. As polysulfides have been detected in a wide array of natural systems ranging from microbial mats to hydrothermal vents, constraining their biogeochemical cycling has broad impacts. However, many questions remain regarding the processes responsible for polysulfide dynamics in these environments and the precise role that microorganisms play in these processes. This review provides a summary of laboratory experiments investigating the role of polysulfides in microbial metabolism, and observations of polysulfides in the environment in order to provide further insight into and highlight open questions about this significant component of the sulfur cycle.

Description: Comprehensive analytical solutions to 3-D axisymmetric problems for static response of multilayered thermoelastic media subjected to surface loads and containing sources are presented in this study. The solution strategy employs Laplace and Hankel transforms to the field variables. The problem is formulated in cylindrical coordinate system and in this coordinate system vector surface harmonics and generalized propagator matrix are introduced to find the solution for the problem for the behaviour of thermoelastic multilayered media subject to surface loads and containing heat sources. A high-order adaptive Gaussian quadrature method with continued fraction expansions is employed to approximate the integral solutions expressed in terms of semi-infinite Hankel-type integrals. It is the first time to apply the proposed solution method to investigate the behaviour of repository for heat-emitting high-level nuclear waste (HLW) in a geological formation where the HLW can be regarded as a decaying with time point heat source.

Description: We present a series of processes for understanding and analysing controlled-source electromagnetic (CSEM) responses for a conductive and permeable earth. To realize the CSEM response, a new 3-D CSEM forward modelling algorithm based on an edge finite element method for both electrically conductive and magnetically permeable heterogeneities is developed. The algorithm shows highly accurate results in validation tests against a semi-analytic solution for stratified earth and an integral form of the scattered field. We describe the vector behaviour of an anomalous magnetic field originating from a conductive and permeable anomaly when the loop sources are deployed over a conductive half-space. The CSEM response of the conductive and permeable anomaly is classified into three effects originating from: conductivity perturbations, permeability perturbations and the coupling of these two effects. The separated individual results and the corresponding integral equation form of the anomalous field help to better understand the physical behaviour. We confirm the characteristic features of the CSEM response from the conductive and permeable anomaly, for example, (1) the general dominance of the induction effect in the out-of-phase response accompanied by a non-negligible magnetization effect from the magnetic anomaly in a conductive half-space and (2) the dominance of near frequency-independent magnetization effects in the in-phase response at relatively low frequencies and change in ruling part of the in-phase response into the induction effect as the frequency increases. We also demonstrate the effect of coupling mode and show that its maximum contribution is limited to a few per cent level of other two modes, induction and magnetization mode, even when the heterogeneity of our model is strong. In our synthetic survey, using examples of land-based profiling surveys of low induction number and intermediate regime, we find that the effect of magnetization can be used as an indicator of the existence of magnetic material. One important point to note from this study is the importance of accurate cancelling-out or estimation of free-space responses, which can mask the magnetic responses to imaging the varying magnetic property.

Description: A total of 65 spore-forming mercury-resistant bacteria were isolated from natural environments worldwide in order to understand the acquisition of additional genes by and dissemination of mercury resistance transposons across related Bacilli genera by horizontal gene movement. PCR amplification using a single primer complementary to the inverted repeat sequence of Tn MERI1 -like transposons showed that 12 of 65 isolates had a transposon-like structure. There were four types of amplified fragments: Tn 5084 , Tn 5085 , Tn d MER3 (a newly identified deleted transposon-like fragment) and Tn 6294 (a newly identified transposon). Tn d MER3 is a 3.5-kb sequence that carries a merRETPA operon with no merB or transposase genes. It is related to the mer operon of Bacillus licheniformis strain FA6-12 from Russia. DNA homology analysis shows that Tn 6294 is an 8.5-kb sequence that is possibly derived from Tn d MER3 by integration of a Tn MERI1 -type transposase and resolvase genes and in addition the merR2 and merB1 genes. Bacteria harboring Tn 6294 exhibited broad-spectrum mercury resistance to organomercurial compounds, although Tn 6294 had only merB1 and did not have the merB2 and merB3 sequences for organomercurial lyases found in Tn 5084 of B. cereus strain RC607. Strains with Tn 6294 encode mercuric reductase (MerA) of less than 600 amino acids in length with a single N-terminal mercury-binding domain, whereas MerA encoded by strains MB1 and RC607 has two tandem domains. Thus, Tn d MER3 and Tn 6294 are shorter prototypes for Tn MERI1 -like transposons. Identification of Tn 6294 in Bacillus sp. from Taiwan and in Paenibacillus sp. from Antarctica indicates the wide horizontal dissemination of Tn MERI1 -like transposons across bacterial species and geographical barriers.

Description: Extraction of fluids from subsurface reservoirs induces changes in pore pressure, leading not only to geomechanical changes, but also perturbations in seismic velocities and hence observable seismic attributes. Time-lapse seismic analysis can be used to estimate changes in subsurface hydromechanical properties and thus act as a monitoring tool for geological reservoirs. The ability to observe and quantify changes in fluid, stress and strain using seismic techniques has important implications for monitoring risk not only for petroleum applications but also for geological storage of CO 2 and nuclear waste scenarios. In this paper, we integrate hydromechanical simulation results with rock physics models and full-waveform seismic modelling to assess time-lapse seismic attribute resolution for dynamic reservoir characterization and hydromechanical model calibration. The time-lapse seismic simulations use a dynamic elastic reservoir model based on a North Sea deep reservoir undergoing large pressure changes. The time-lapse seismic traveltime shifts and time strains calculated from the modelled and processed synthetic data sets (i.e. pre-stack and post-stack data) are in a reasonable agreement with the true earth models, indicating the feasibility of using 1-D strain rock physics transform and time-lapse seismic processing methodology. Estimated vertical traveltime shifts for the overburden and the majority of the reservoir are within ±1 ms of the true earth model values, indicating that the time-lapse technique is sufficiently accurate for predicting overburden velocity changes and hence geomechanical effects. Characterization of deeper structure below the overburden becomes less accurate, where more advanced time-lapse seismic processing and migration is needed to handle the complex geometry and strong lateral induced velocity changes. Nevertheless, both migrated full-offset pre-stack and near-offset post-stack data image the general features of both the overburden and reservoir units. More importantly, the results from this study indicate that integrated seismic and hydromechanical modelling can help constrain time-lapse uncertainty and hence reduce risk due to fluid extraction and injection.

Description: A new plate motions model for the northwest Africa–North America Plate pair during the Oligocene and early Miocene is presented. The model is accompanied by a high-resolution isochron map for the central Atlantic region, resulting from a re-examination of 423 ship tracks from the NGDC data base for the area between the 15°20' FZ and the Azores triple junction. A new digital model of fracture zones for this region and a set of 309 magnetic profiles crossing the Oligocene to recent oceanic crust within the study area allowed to determine accurate finite reconstruction poles for the North America–northwest Africa conjugate plate pair between the early Miocene (Chron 6) and the early Oligocene (Chron 13). For times older than Chron 7 (~25 Ma), the finite reconstruction poles were calculated using a reliable data set coming exclusively from the region south of the Canary Islands FZ (~32°N), which allowed to test the rigidity of the northwest African oceanic lithosphere during the Oligocene–early Miocene phase of Atlas orogeny. A comparison of theoretical magnetic isochrons with observed magnetic lineations systematically shows that anomalously high spreading rates occurred in the area north of the Canary Islands FZ before Chron 7, thereby suggesting that the formation of the Atlas mountain, rather than being a localized intracontinental process, was logically linked to the central Atlantic spreading history. Thus, an independent Moroccan Plate could have existed during the Oligocene–early Miocene time interval, which included both the oceanic lithosphere north of the Canary Islands FZ and the northern Maghrebian areas of Morocco, Algeria and Tunisia. In this eventuality, the Atlas mountain belt should be reinterpreted as a giant flower structure associated with dextral transpression.

Description: Spectral induced polarization measurements are affected by temperature variations due to a variety of temperature-dependent parameters that control the complex electrical conductivity. Most important is the influence of the ion mobility, which increases with increasing temperature. It is responsible for the increase of the conductivity of the fluid in the pores with temperature and influences the electrical double layer on the mineral surface. This work is based on laboratory measurements of 13 sandstone samples from different sources with different geological and petrophysical characteristics. We measured the complex impedance in a frequency range from 0.01 to 100 Hz and a temperature range from 0 to 40 °C. The main observation is a decrease of the characteristic time (defined by the inverse of the frequency, at which the phase shift is maximum) with increasing temperature. The strength of this decrease differs from one sample to another. The temperature dependence of the phase shift magnitude cannot easily be generalized, as it depends on the particular sample. The experimental findings suggest that neglecting the influence of temperature on complex conductivity may lead to significant errors when estimating hydraulic conductivity from relaxation time. We also simulate the temperature dependence with a theoretical model of membrane polarization and review some of the model properties, with an emphasis on the temperature dependence of the parameters. The model reproduces several features characterizing the measured data, including the temperature dependence of the characteristic times. Computed tomography and microscope images of the pore structure of three samples also allow us to associate differences in the geometrical parameters used in the modelling with pore scale parameters of the actual samples.

Description: Knowledge about the pressure dependency of elastic and electrical properties is important for a variety of geophysical applications. We present a technique to invert for the stiff and compliant porosity from velocity measurements made as a function of differential pressure on saturated sandstones. A dual porosity concept is used for dry rock compressibility and a squirt model is employed for the pressure and frequency dependent elastic properties of the rocks when saturated. The total porosity obtained from inversion shows satisfactory agreement with experimental results. The electrical cementation factor was determined using the inverted porosity in combination with measured electrical conductivity. It was found that cementation factor increased exponentially with increasing differential pressure during isostatic loading. Elastic compressibility, electrical cementation factor and electrical conductivity of the saturated rocks correlate linearly with compliant porosity, and electrical cementation factor and electrical conductivity exhibit linear correlations with elastic compressibility of the saturated rocks under loading. The results show that the dual porosity concept is sufficient to explain the pressure dependency of elastic, electrical and joint elastic-electrical properties of saturated porous sandstones.

Description: A new plate motions model for the northwest Africa–North America Plate pair during the Oligocene and early Miocene is presented. The model is accompanied by a high-resolution isochron map for the central Atlantic region, resulting from a re-examination of 423 ship tracks from the NGDC data base for the area between the 15°20' FZ and the Azores triple junction. A new digital model of fracture zones for this region and a set of 309 magnetic profiles crossing the Oligocene to recent oceanic crust within the study area allowed to determine accurate finite reconstruction poles for the North America–northwest Africa conjugate plate pair between the early Miocene (Chron 6) and the early Oligocene (Chron 13). For times older than Chron 7 (~25 Ma), the finite reconstruction poles were calculated using a reliable data set coming exclusively from the region south of the Canary Islands FZ (~32°N), which allowed to test the rigidity of the northwest African oceanic lithosphere during the Oligocene–early Miocene phase of Atlas orogeny. A comparison of theoretical magnetic isochrons with observed magnetic lineations systematically shows that anomalously high spreading rates occurred in the area north of the Canary Islands FZ before Chron 7, thereby suggesting that the formation of the Atlas mountain, rather than being a localized intracontinental process, was logically linked to the central Atlantic spreading history. Thus, an independent Moroccan Plate could have existed during the Oligocene–early Miocene time interval, which included both the oceanic lithosphere north of the Canary Islands FZ and the northern Maghrebian areas of Morocco, Algeria and Tunisia. In this eventuality, the Atlas mountain belt should be reinterpreted as a giant flower structure associated with dextral transpression.

Description: Fungi may play an important role in the production of the greenhouse gas nitrous oxide (N 2 O). Bipolaris sorokiniana is a ubiquitous saprobe found in soils worldwide, yet denitrification by this fungal strain has not previously been reported. We aimed to test if B. sorokiniana would produce N 2 O and CO 2 in the presence of organic and inorganic forms of nitrogen (N) under microaerobic and anaerobic conditions. Nitrogen source (organic-N, inorganic-N, no-N control) significantly affected N 2 O and CO 2 production both in the presence and absence of oxygen, which contrasts with bacterial denitrification. Inorganic N addition increased denitrification of N 2 O (from 0 to 0.3 μg N 2 0-N h –1  g –1 biomass) and reduced respiration of CO 2 (from 0.1 to 0.02 mg CO 2 h –1  g –1 biomass). Isotope analyses indicated that nitrite, rather than ammonium or glutamine, was transformed to N 2 O. Results suggest the source of N may play a larger role in fungal N 2 O production than oxygen status.

Description: Legionella pneumophila is a pathogenic bacterium commonly found in water and responsible for severe pneumonia. Free-living amoebae are protozoa also found in water, which feed on bacteria by phagocytosis. Under favorable conditions, some L. pneumophila are able to resist phagocytic digestion and even multiply within amoebae. However, it is not clear whether L. pneumophila could infect at a same rate a large range of amoebae or if there is some selectivity towards specific amoebal genera or strains. Also, most studies have been performed using collection strains and not with freshly isolated strains. In our study, we assess the permissiveness of freshly isolated environmental strains of amoebae, belonging to three common genera (i.e. Acanthamoeba, Naegleria and Vermamoeba ), for growth of L. pneumophila at three different temperatures. Our results indicated that all the tested strains of amoebae were permissive to L. pneumophila Lens and that there was no significant difference between the strains. Intracellular proliferation was more efficient at a temperature of 40°C. In conclusion, our work suggests that, under favorable conditions, virulent strains of L. pneumophila could equally infect a large number of isolates of common freshwater amoeba genera.

Description: Maximizing vertical resolution is a key objective in seismic data processing. Early deconvolution and spectral balancing algorithms assumed that the seismic source wavelet was temporally invariant, or stationary. In practice, seismic scattering and attenuation give rise to non-stationary seismic source wavelets. To address this issue, most conventional time-varying deconvolution wavelet shaping and spectral modelling techniques using the stationary polynomial fitting assume the wavelet to be locally stationary within a small number of overlapping analysis windows while the fitting coefficients are invariant with all the frequencies. In this paper, we show an improvement obtained by modelling smoothly varying spectra of the seismic wavelet using non-stationary polynomial fitting in the time–frequency domain. We first decompose each seismic trace using a generalized S-transform that provides a good time–frequency distribution for the estimation of the time-varying wavelet spectra. We then model the slowly varying source wavelet spectrum at each time sample by a smooth low-order polynomial. Finally, we spectrally balance the modelled wavelet to flatten the seismic response, thereby increasing vertical resolution. We calibrate the algorithm on a simple synthetic and then apply it to a 3-D land survey acquired in western China, showing the value on both vertical slices through seismic amplitude and attribute time slices. Our new algorithm significantly improves the vertical resolution of the seismic signal, while not increasing the noise.

Description: Knowledge about the pressure dependency of elastic and electrical properties is important for a variety of geophysical applications. We present a technique to invert for the stiff and compliant porosity from velocity measurements made as a function of differential pressure on saturated sandstones. A dual porosity concept is used for dry rock compressibility and a squirt model is employed for the pressure and frequency dependent elastic properties of the rocks when saturated. The total porosity obtained from inversion shows satisfactory agreement with experimental results. The electrical cementation factor was determined using the inverted porosity in combination with measured electrical conductivity. It was found that cementation factor increased exponentially with increasing differential pressure during isostatic loading. Elastic compressibility, electrical cementation factor and electrical conductivity of the saturated rocks correlate linearly with compliant porosity, and electrical cementation factor and electrical conductivity exhibit linear correlations with elastic compressibility of the saturated rocks under loading. The results show that the dual porosity concept is sufficient to explain the pressure dependency of elastic, electrical and joint elastic-electrical properties of saturated porous sandstones.

Description: In order to perform gas exploration and determine the distribution pattern of gas in the Yanchang Oil Field in the eastern part of the North Shaanxi Slope, Ordos Basin, China, gravity and magnetic survey data were systemically collated, processed and interpreted in combination with the drilling data and recent seismic data. The genesis of gravity and magnetic anomalies and the relationship between the characteristics of the gravity and magnetic fields and known gas distribution were explored in order to predict the favourable exploration targets for gas. Gravity anomalies resulted both from the lateral variation in density of the basement rock and lateral lithologic transformation in the sedimentary cover. The regional magnetic anomalies were mainly caused by the basement metamorphic rocks and the residual magnetic anomalies may reflect the amount and general location of the volcanic materials in the overlying strata. The residual gravity and magnetic anomalies generated by high-density sandstone and high content of volcanics in the gas reservoir of the upper Paleozoic distorted and deformed the anomaly curves when they were stacked onto the primary background anomaly. The gas wells were generally found to be located in the anomaly gradient zones, or the distorted part of contour lines, and the flanks of high and low anomalies, or the transitional zones between anomaly highs and lows. The characteristics of gravity and magnetic fields provide significant information that can be used for guidance when exploring the distribution of gas. Based on these characteristics, five favourable areas for gas exploration were identified; these are quasi-equally spaced like a strip extending from the southeast to the northwest.

Description: Spectral induced polarization measurements are affected by temperature variations due to a variety of temperature-dependent parameters that control the complex electrical conductivity. Most important is the influence of the ion mobility, which increases with increasing temperature. It is responsible for the increase of the conductivity of the fluid in the pores with temperature and influences the electrical double layer on the mineral surface. This work is based on laboratory measurements of 13 sandstone samples from different sources with different geological and petrophysical characteristics. We measured the complex impedance in a frequency range from 0.01 to 100 Hz and a temperature range from 0 to 40 °C. The main observation is a decrease of the characteristic time (defined by the inverse of the frequency, at which the phase shift is maximum) with increasing temperature. The strength of this decrease differs from one sample to another. The temperature dependence of the phase shift magnitude cannot easily be generalized, as it depends on the particular sample. The experimental findings suggest that neglecting the influence of temperature on complex conductivity may lead to significant errors when estimating hydraulic conductivity from relaxation time. We also simulate the temperature dependence with a theoretical model of membrane polarization and review some of the model properties, with an emphasis on the temperature dependence of the parameters. The model reproduces several features characterizing the measured data, including the temperature dependence of the characteristic times. Computed tomography and microscope images of the pore structure of three samples also allow us to associate differences in the geometrical parameters used in the modelling with pore scale parameters of the actual samples.

Description: The streaming potential phenomenon is produced by the flow of an electrolyte in a porous medium and is used for geophysical prospecting. It is quantified through an electrokinetic (EK) coefficient. The dependence of the EK coefficient on the conductivity of the electrolyte is described by the Helmholtz–Smoluchowski (HS) equation. This equation provides successful forecasts of the EK coefficient in the standard range of concentration. However, experimental measurements show deviations to this equation at extreme low and extreme high salinities. The aim of this study is to model the EK coefficient using Lattice Boltzmann simulations in a 2-D capillary channel, with a view to understanding these deviations. The effect of the constitutive parameters of the HS equation such as the permittivity and the viscosity is discussed. The validity of the HS equation using strong potentials is assessed. Finally, a model of bulk fluid conductivity is derived. This model allows to take into account the change of local ionic distribution in the vicinity of the mineral. It appears to have a significant impact on the derivation of potentials at low salinities and in the presence of polyvalent counterions.

Description: Extraction of fluids from subsurface reservoirs induces changes in pore pressure, leading not only to geomechanical changes, but also perturbations in seismic velocities and hence observable seismic attributes. Time-lapse seismic analysis can be used to estimate changes in subsurface hydromechanical properties and thus act as a monitoring tool for geological reservoirs. The ability to observe and quantify changes in fluid, stress and strain using seismic techniques has important implications for monitoring risk not only for petroleum applications but also for geological storage of CO 2 and nuclear waste scenarios. In this paper, we integrate hydromechanical simulation results with rock physics models and full-waveform seismic modelling to assess time-lapse seismic attribute resolution for dynamic reservoir characterization and hydromechanical model calibration. The time-lapse seismic simulations use a dynamic elastic reservoir model based on a North Sea deep reservoir undergoing large pressure changes. The time-lapse seismic traveltime shifts and time strains calculated from the modelled and processed synthetic data sets (i.e. pre-stack and post-stack data) are in a reasonable agreement with the true earth models, indicating the feasibility of using 1-D strain rock physics transform and time-lapse seismic processing methodology. Estimated vertical traveltime shifts for the overburden and the majority of the reservoir are within ±1 ms of the true earth model values, indicating that the time-lapse technique is sufficiently accurate for predicting overburden velocity changes and hence geomechanical effects. Characterization of deeper structure below the overburden becomes less accurate, where more advanced time-lapse seismic processing and migration is needed to handle the complex geometry and strong lateral induced velocity changes. Nevertheless, both migrated full-offset pre-stack and near-offset post-stack data image the general features of both the overburden and reservoir units. More importantly, the results from this study indicate that integrated seismic and hydromechanical modelling can help constrain time-lapse uncertainty and hence reduce risk due to fluid extraction and injection.

Description: We study the accuracy and numerical stability of three eigenvector sets for modelling the coupled poroelastic and electromagnetic layered-Earth response. We use a known eigenvector set, its flux-normalized version and a newly derived flux-normalized set. The new set is chosen such that the system is properly uncoupled when the coupling between the poroelastic and electromagnetic fields vanishes. We carry out two different numerical stability tests: the first test focuses on the internal system, eigenvector and eigenvalue consistency; the second test investigates the stability and preciseness of the flux-normalized systems by looking at identity relations. We find that the known set shows the largest deviation for both tests, whereas the new set performs best. In two additional numerical modelling experiments, these numerical inaccuracies are shown to generate numerical noise levels comparable to small signals, such as signals coming from the important interface conversion responses, especially when the coupling coefficient is small. When coupling vanishes completely, the known set does not produce proper results. The new set produces numerically stable and accurate results in all situations. We therefore strongly recommend to use this newly derived set for future layered-Earth seismo-electromagnetic modelling experiments.

Description: The Quaternary Añavieja-Dévanos tufa system is located in the northern sector of the Iberian Chain. It has been previously tackled by means sedimentological studies focused on the available outcrops and some boreholes. They have permitted the proposal of a sedimentary scenario that fits with a pool-barrage fluvial tufa model. However a better knowledge of the characteristics and internal distribution of the usually non-outcropping pool deposits as well as of its relationship with barrage deposits has not been evaluated in detail yet. Palaeoenvironmental studies on tufas are usually biased because tufas are commonly delicate facies exposed to intense erosion during water level fall stages; for this reason outcrops are usually scarce and very often coincide with the most cemented barrage deposits. In order to analyse the internal characteristics of the tufa deposits under study, but also the lateral correlation among different facies, ground penetrating radar (GPR) has been employed both for the evaluation of its applicability in such kind of environments and to improve, if possible, the sedimentary model using geophysical data in sectors without outcrops. A GPR survey including different antennas ranging from 50 to 500 MHz along different sectors and its comparison with natural outcrops has been carried out. GPR results have permitted to deduce clear differences between pool and barrage deposits and to recognise its internal structure and geometrical relationships. The survey also permitted an approach to different scales of heterogeneities in the radarfacies evaluation by using distinct antennas and therefore, reaching different resolutions and penetrations. The resulting integration from different antennas allows three different attenuant and eight reflective radarfacies to be defined permitting a better approach to the real extension of the pool areas. These results have permitted to decipher the horizontal and vertical facies changes and the identification of a scarcer development of pool deposits than expected in the studied system.

Description: Two novel transient controlled source electromagnetic methods called circular electrical dipole (CED) and differential electrical dipole (DED) are theoretically analysed for applications in shallow marine environments. 1-D and 3-D time-domain modelling studies are used to investigate the detectability and applicability of the methods when investigating resistive layers/targets representing hydrocarbon-saturated formations. The results are compared to the conventional time-domain horizontal electrical dipole (HED) and vertical electrical dipole (VED) sources. The applied theoretical modelling studies demonstrate that CED and DED have higher signal detectability towards resistive targets compared to TD-CSEM, but demonstrate significantly poorer signal amplitudes. Future CED/DED applications will have to solve this issue prior to measuring. Furthermore, the two novel methods have very similar detectability characteristics towards 3-D resistive targets embedded in marine sediments as VED while being less susceptible towards non-verticality. Due to the complex transmitter design of CED/DED the systems are prone to geometrical errors. Modelling studies show that even small transmitter inaccuracies have strong effects on the signal characteristics of CED making an actual marine application difficult at the present time. In contrast, the DED signal is less affected by geometrical errors in comparison to CED and may therefore be more adequate for marine applications.

Description: Growth media have been developed to facilitate the enrichment and isolation of acidophilic and acid-tolerant sulfate-reducing bacteria (aSRB) from environmental and industrial samples, and to allow their cultivation in vitro . The main features of the ‘standard’ solid and liquid devised media are as follows: (i) use of glycerol rather than an aliphatic acid as electron donor; (ii) inclusion of stoichiometric concentrations of zinc ions to both buffer pH and to convert potentially harmful hydrogen sulphide produced by the aSRB to insoluble zinc sulphide; (iii) inclusion of Acidocella aromatica (an heterotrophic acidophile that does not metabolize glycerol or yeast extract) in the gel underlayer of double layered (overlay) solid media, to remove acetic acid produced by aSRB that incompletely oxidize glycerol and also aliphatic acids (mostly pyruvic) released by acid hydrolysis of the gelling agent used (agarose). Colonies of aSRB are readily distinguished from those of other anaerobes due to their deposition and accumulation of metal sulphide precipitates. Data presented illustrate the effectiveness of the overlay solid media described for isolating aSRB from acidic anaerobic sediments and low pH sulfidogenic bioreactors.

Description: An L-configured, three-component short period seismic array was deployed on the Ross Ice Shelf, Antarctica during November 2014. Polarization analysis of ambient noise data from these stations shows linearly polarized waves for frequency bands between 0.2 and 2 Hz. A spectral peak at about 1.6 Hz is interpreted as the resonance frequency of the water column and is used to estimate the water layer thickness below the ice shelf. The frequency band from 4 to 18 Hz is dominated by Rayleigh and Love waves propagating from the north that, based on daily temporal variations, we conclude were generated by field camp activity. Frequency–slowness plots were calculated using beamforming. Resulting Love and Rayleigh wave dispersion curves were inverted for the shear wave velocity profile within the firn and ice to ~150 m depth. The derived density profile allows estimation of the pore close-off depth and the firn–air content thickness. Separate inversions of Rayleigh and Love wave dispersion curves give different shear wave velocity profiles within the firn. We attribute this difference to an effective anisotropy due to fine layering. The layered structure of firn, ice, water and the seafloor results in a characteristic dispersion curve below 7 Hz. Forward modelling the observed Rayleigh wave dispersion curves using representative firn, ice, water and sediment structures indicates that Rayleigh waves are observed when wavelengths are long enough to span the distance from the ice shelf surface to the seafloor. The forward modelling shows that analysis of seismic data from an ice shelf provides the possibility of resolving ice shelf thickness, water column thickness and the physical properties of the ice shelf and underlying seafloor using passive-source seismic data.

Description: We present an algorithm to recover the Bayesian posterior model probability density function of subsurface elastic parameters, as required by the full pressure field recorded at an ocean bottom cable due to an impulsive seismic source. Both the data noise and source wavelet are estimated by our algorithm, resulting in robust estimates of subsurface velocity and density. In contrast to purely gradient based approaches, our method avoids model regularization entirely and produces an ensemble of models that can be visualized and queried to provide meaningful information about the sensitivity of the data to the subsurface, and the level of resolution of model parameters. Our algorithm is trans-dimensional and performs model selection, sampling over a wide range of model parametrizations. We follow a frequency domain approach and derive the corresponding likelihood in the frequency domain. We present first a synthetic example of a reservoir at 2 km depth with minimal acoustic impedance contrast, which is difficult to study with conventional seismic amplitude versus offset changes. Finally, we apply our methodology to survey data collected over the Alba field in the North Sea, an area which is known to show very little lateral heterogeneity but nevertheless presents challenges for conventional post migration seismic amplitude versus offset analysis.

Description: A novel application of seismic interferometry (SI) and Marchenko imaging using both surface and borehole data is presented. A series of redatuming schemes is proposed to combine both data sets for robust deep local imaging in the presence of velocity uncertainties. The redatuming schemes create a virtual acquisition geometry where both sources and receivers lie at the horizontal borehole level, thus only a local velocity model near the borehole is needed for imaging, and erroneous velocities in the shallow area have no effect on imaging around the borehole level. By joining the advantages of SI and Marchenko imaging, a macrovelocity model is no longer required and the proposed schemes use only single-component data. Furthermore, the schemes result in a set of virtual data that have fewer spurious events and internal multiples than previous virtual source redatuming methods. Two numerical examples are shown to illustrate the workflow and to demonstrate the benefits of the method. One is a synthetic model and the other is a realistic model of a field in the North Sea. In both tests, improved local images near the boreholes are obtained using the redatumed data without accurate velocities, because the redatumed data are close to the target.

Description: A common dye of prussian blue (PB) as an indicator was used to develop a colorimetric method for detecting the efficacy of the antibiotics in vitro. Considering the electronic production capacity of microbial respiration, ferricyanide was employed in transferring electrons from target microorganism of Escherichia coli ( E. coli ) to produce ferrocyanide. Subsequently, ferrocyanide reacted with ferric ions to form PB. In view of relationship between the PB yield and the bacterial activity, the efficacy of the antibiotics on E. coli was directly detected at 700 nm of PB absorption. When the 5% activity of antibiotics on 20 isolates of E. coli was quantified as 5% efficacy, the applied concentrations of eight antibiotics, such as cefepime, ceftriaxone sodium, cefoperazone sodium, piperacillin sodium, amoxicillin, gentamicin, amikacin and levofloxacin were 2, 2, 4, 4, 10, 4, 8 and 8 μg mL –1 , respectively. To compare with minimum inhibitory concentration results obtained by Clinical and Laboratory Standards Institute broth macrodilution method, the results of PB methods showed good agreements except with gentamicin. Paired t- test result ( P ) also showed that difference between two methods was statistically significant ( P = 0.006).

Description: Metarhizium acridum is an entomopathogenic fungus commonly used as a bioinsecticide. The conidium is the fungal stage normally employed as field inoculum in biological control programs and must survive under field conditions such as high ultraviolet-B (UV-B) exposure. Light, which is an important stimulus for many fungi, has been shown to induce the production of M. robertsii conidia with increased stress tolerance. Here we show that a two-hour exposure to white or blue/UV-A light of fast-growing mycelium induces tolerance to subsequent UV-B irradiation. Red light, however, does not have the same effect. In addition, we established that this induction can take place with as little as 1 min of white-light exposure. This brief illumination scheme could be relevant in future studies of M. acridum photobiology and for the production of UV-B resistant mycelium used in mycelium-based formulations for biological control.

Description: Photorhabdus (Enterobacteriaceae) bacteria are pathogenic to insects and mutualistic with entomopathogenic Heterorhabditis nematodes . Photorhabdus luminescens subsp. akhurstii LN2, associated with Heterorhabditis indica LN2, shows nematicidal activity against H. bacteriophora H06 infective juveniles (IJs). In the present study, an rpoS mutant of P. luminescens LN2 was generated through allelic exchange to examine the effects of rpoS deletion on the nematicidal activity and nematode development. The results showed that P. luminescens LN2 required rpoS for nematicidal activity against H06 nematodes, normal IJ recovery and development of H. indica LN2, however, not for the bacterial colonization in LN2 and H06 IJs. This provides cues for further understanding the role of rpoS in the mutualistic association between entomopathogenic nematodes and their symbionts.

Description: Catechol 2, 3-dioxygenase (C23O) is the key enzyme for aerobic aromatic degradation. Based on clone libraries and quantitative real-time polymerase chain reaction, we characterized diversity and distribution patterns of C23O genes in surface sediments of the Bohai Sea. The results showed that sediments of the Bohai Sea were dominated by genes related to C23O subfamily I.2.A. The samples from wastewater discharge area (DG) and aquaculture farm (KL) showed distinct composition of C23O genes when compared to the samples from Bohai Bay (BH), and total organic carbon was a crucial determinant accounted for the composition variation. C6BH12-38 and C2BH2-35 displayed the highest gene copies and highest ratios to the 16S rRNA genes in KL, and they might prefer biologically labile aromatic hydrocarbons via aquaculture inputs. Meanwhile, C7BH3-48 showed the highest gene copies and highest ratios to the 16S rRNA genes in DG, and this could be selective effect of organic loadings from wastewater discharge. An evident increase in C6BH12-38 and C7BH3-48 gene copies and reduction in diversity of C23O genes in DG and KL indicated composition perturbations of C23O genes and potential loss in functional redundancy. We suggest that ecological habitat and trophic specificity could shape the distribution of C23O genes in the Bohai Sea sediments.

Description: The effect of the selection of different nuclear magnetic resonance (NMR) relaxation times for permeability estimation is investigated for a set of fully brine-saturated rocks acquired from Cretaceous carbonate reservoirs in the North Sea and Middle East. Estimators that are obtained from the relaxation times based on the Pythagorean means are compared with estimators that are obtained from the relaxation times based on the concept of a cumulative saturation cut-off. Select portions of the longitudinal ( T 1 ) and transverse ( T 2 ) relaxation-time distributions are systematically evaluated by applying various cut-offs, analogous to the Winland-Pittman approach for mercury injection capillary pressure (MICP) curves. Finally, different approaches to matching the NMR and MICP distributions using different mean-based scaling factors are validated based on the performance of the related size-scaled estimators. The good results that were obtained demonstrate possible alternatives to the commonly adopted logarithmic mean estimator and reinforce the importance of NMR-MICP integration to improving carbonate permeability estimates.

Description: LysR-type transcriptional regulators (LTTRs) regulate various cellular processes in bacteria. pnpR is an LTTR-encoding gene involved in the regulation of hydroquinone (HQ) degradation, and its effects on the cellular processes of Pseudomonas putida DLL-E4 were investigated at the physiological, biochemical and molecular levels. Reverse transcription polymerase chain reaction revealed that pnpR positively regulated its own expression and that of the pnpC1C2DECX1X2 operon; additionally, pnpR partially regulated the expression of pnpA when P. putida was grown on para -nitrophenol (PNP) or HQ. Strains DLL-E4 and DLL- pnpR exhibited similar cellular morphologies and growth rates. Transcriptome analysis revealed that pnpR regulated the expression of genes in addition to those involved in PNP degradation. A total of 20 genes were upregulated and 19 genes were downregulated by at least 2-fold in strain DLL- pnpR relative to strain DLL-E4. Bioinformatic analysis revealed putative PnpR-binding sites located in the upstream regions of genes involved in PNP degradation, carbon catabolite repression and other cellular processes. The utilization of L-aspartic acid, L-histidine, L-pyroglutamic acid, L-serine, -aminobutyric acid, D,L-lactic acid, D-saccharic acid, succinic acid and L-alaninamide was increased at least 1.3-fold in strain DLL- pnpR as shown by BIOLOG assays, indicating that pnpR plays a potential negative regulation role in the utilization of carbon sources.

Description: Static time-delay corrections are frequency independent and ignore velocity variations away from the assumed vertical ray path through the subsurface. There is therefore a clear potential for improvement if the finite frequency nature of wave propagation can be properly accounted for. Such a method is presented here based on the Born approximation, the assumption of surface consistency and the misfit of instantaneous phase. The concept of instantaneous phase lends itself very well for sweep-like signals, hence these are the focus of this study. Analytical sensitivity kernels are derived that accurately predict frequency-dependent phase shifts due to P -wave anomalies in the near surface. They are quick to compute and robust near the source and receivers. An additional correction is presented that re-introduces the nonlinear relation between model perturbation and phase delay, which becomes relevant for stronger velocity anomalies. The phase shift as function of frequency is a slowly varying signal, its computation therefore does not require fine sampling even for broad-band sweeps. The kernels reveal interesting features of the sensitivity of seismic arrivals to the near surface: small anomalies can have a relative large impact resulting from the medium field term that is dominant near the source and receivers. Furthermore, even simple velocity anomalies can produce a distinct frequency-dependent phase behaviour. Unlike statics, the predicted phase corrections are smooth in space. Verification with spectral element simulations shows an excellent match for the predicted phase shifts over the entire seismic frequency band. Applying the phase shift to the reference sweep corrects for wavelet distortion, making the technique akin to surface consistent deconvolution, even though no division in the spectral domain is involved. As long as multiple scattering is mild, surface consistent finite frequency phase corrections outperform traditional statics for moderately large velocity contrasts, also in the case of a free surface with topography. The kernels could also be used to update the velocity model, if one has knowledge of (wave propagation related only) surface consistent phase operators.

Description: The seislet transform has been demonstrated to have a better compression performance for seismic data compared with other well-known sparsity promoting transforms, thus it can be used to remove random noise by simply applying a thresholding operator in the seislet domain. Since the seislet transform compresses the seismic data along the local structures, the seislet thresholding can be viewed as a simple structural filtering approach. Because of the dependence on a precise local slope estimation, the seislet transform usually suffers from low compression ratio and high reconstruction error for seismic profiles that have dip conflicts. In order to remove the limitation of seislet thresholding in dealing with conflicting-dip data, I propose a dip-separated filtering strategy. In this method, I first use an adaptive empirical mode decomposition based dip filter to separate the seismic data into several dip bands (5 or 6). Next, I apply seislet thresholding to each separated dip component to remove random noise. Then I combine all the denoised components to form the final denoised data. Compared with other dip filters, the empirical mode decomposition based dip filter is data-adaptive. One only needs to specify the number of dip components to be separated. Both complicated synthetic and field data examples show superior performance of my proposed approach than the traditional alternatives. The dip-separated structural filtering is not limited to seislet thresholding, and can also be extended to all those methods that require slope information.

Description: Noise interferometry is the process by which approximations to acoustic Green's functions, which describe sound propagation between two locations, are estimated by cross-correlating time series of ambient noise measured at those locations. Noise-interferometry-based approximations to Green's functions can be used as the basis for a variety of inversion algorithms, thereby providing a purely passive alternative to active-source ocean acoustic remote sensing. In this paper we give an overview of results from noise interferometry experiments conducted in the Florida Straits at 100 m depth in December 2012, and at 600 m depth in September/October 2013. Under good conditions for noise interferometry, estimates of cross-correlation functions are shown to allow one to perform advanced phase-coherent signal processing techniques to perform waveform inversions, estimate currents by exploiting non-reciprocity, perform time-reversal/back-propagation calculations and investigate modal dispersion using time-warping techniques. Conditions which are favourable for noise interferometry are identified and discussed.

Description: In this paper, we consider a new spectral finite volume method (FVM) for the elastic wave equations. Our new FVM is based on a piecewise constant approximation on a fine mesh and a high-order polynomial reconstruction on a coarser mesh. Our new method is constructed based on two existing techniques, the high-order FVM and the spectral FVM. In fact, we will construct a new method to take advantage of both methods. More precisely, our method has two distinctive features. The first one is that the local polynomial reconstructions are performed on the coarse triangles and the reconstruction matrices for all the coarse triangles are the same. This fact enhances the parallelization of our algorithm. We will present a parallel implementation of our method and show excellent efficiency results. The second one is that, by using a suitable number of finer triangles with a coarse triangle, we obtain an overdetermined reconstruction system, which can enhance the robustness of the reconstruction process. To derive our scheme, standard finite volume technique is applied to each fine triangle, and the high-order reconstructed polynomials, computed on coarse triangles, are used to compute numerical fluxes. We will present numerical results to show the performance of our method. Our method is presented for 2-D problems, but the same methodology can be applied to 3-D.

Description: At the heart of the full waveform inversion (FWI) implementation is wavefield extrapolation, and specifically its accuracy and cost. To obtain accurate, dispersion free wavefields, the extrapolation for modelling is often expensive. Combining an efficient extrapolation with a novel gradient preconditioning can render an FWI implementation that efficiently converges to an accurate model. We, specifically, recast the extrapolation part of the inversion in terms of its spectral components for both data and gradient calculation. This admits dispersion free wavefields even at large extrapolation time steps, which improves the efficiency of the inversion. An alternative spectral representation of the depth axis in terms of sine functions allows us to impose a free surface boundary condition, which reflects our medium boundaries more accurately. Using a newly derived perfectly matched layer formulation for this spectral implementation, we can define a finite model with absorbing boundaries. In order to reduce the nonlinearity in FWI, we propose a multiscale conditioning of the objective function through combining the different directional components of the gradient to optimally update the velocity. Through solving a simple optimization problem, it specifically admits the smoothest approximate update while guaranteeing its ascending direction. An application to the Marmousi model demonstrates the capability of the proposed approach and justifies our assertions with respect to cost and convergence.

Description: Spectral induced polarization (SIP) data are commonly analysed using phenomenological models. Among these models the Cole–Cole (CC) model is the most popular choice to describe the strength and frequency dependence of distinct polarization peaks in the data. More flexibility regarding the shape of the spectrum is provided by decomposition schemes. Here the spectral response is decomposed into individual responses of a chosen elementary relaxation model, mathematically acting as kernel in the involved integral, based on a broad range of relaxation times. A frequently used kernel function is the Debye model, but also the CC model with some other a priorly specified frequency dispersion (e.g. Warburg model) has been proposed as kernel in the decomposition. The different decomposition approaches in use, also including conductivity and resistivity formulations, pose the question to which degree the integral spectral parameters typically derived from the obtained relaxation time distribution are biased by the approach itself. Based on synthetic SIP data sampled from an ideal CC response, we here investigate how the two most important integral output parameters deviate from the corresponding CC input parameters. We find that the total chargeability may be underestimated by up to 80 per cent and the mean relaxation time may be off by up to three orders of magnitude relative to the original values, depending on the frequency dispersion of the analysed spectrum and the proximity of its peak to the frequency range limits considered in the decomposition. We conclude that a quantitative comparison of SIP parameters across different studies, or the adoption of parameter relationships from other studies, for example when transferring laboratory results to the field, is only possible on the basis of a consistent spectral analysis procedure. This is particularly important when comparing effective CC parameters with spectral parameters derived from decomposition results.

Description: Viability for the development of an engineered geothermal system (EGS) in the oilsands region near Fort McMurray, Alberta, is investigated by studying the structure of the Precambrian basement rocks with magnetotellurics (MT). MT data were collected at 94 broad-band stations on two east–west profiles. Apparent resistivity and phase data showed little variation along each profile. The short period MT data detected a 1-D resistivity structure that could be identified as the shallow sedimentary basin underlain by crystalline basement rocks to a depth of 4–5 km. At lower frequencies a strong directional dependence, large phase splits, and regions of out-of-quadrant (OOQ) phase were detected. 2-D isotropic inversions of these data failed to produce a realistic resistivity model. A detailed dimensionality analysis found links between large phase tensor skews (~15°), azimuths, OOQ phases and tensor decomposition strike angles at periods greater than 1 s. Low magnitude induction vectors, as well as uniformity of phase splits and phase tensor character between the northern and southern profiles imply that a 3-D analysis is not necessary or appropriate. Therefore, 2-D anisotropic forward modelling was used to generate a resistivity model to interpret the MT data. The preferred model was based on geological observations of outcropping anisotropic mylonitic basement rocks of the Charles Lake shear zone, 150 km to the north, linked to the study area by aeromagnetic and core sample data. This model fits all four impedance tensor elements with an rms misfit of 2.82 on the southern profile, and 3.3 on the northern. The conductive phase causing the anisotropy is interpreted to be interconnected graphite films within the metamorphic basement rocks. Characterizing the anisotropy is important for understanding how artificial fractures, necessary for EGS development, would form. Features of MT data commonly interpreted to be 3-D (e.g. out of OOQ phase and large phase tensor skew) are shown to be interpretable with this 2-D anisotropic model.

Description: Landfills are significant global sources of atmospheric methane, but little is known about the ecology and community structure of methanogens in these sites. Here, we investigated the methanogen community based on methyl coenzyme M reductase A gene amplicons in the vertical profiles of three different sites at a municipal landfill complex in China. Links between methanogen communities and refuse properties were explored using multivariate analysis. Clone library results showed that most clones (92%) were related to the hydrogenotrophic methanogens, Methanomicrobiales. Almost all of the Methanomicrobiales clones retrieved in this study are members of the genus Methanoculleus . Eight clones were affiliated with the genus Methanofollis . The remaining clones were clustered within the genus Methanosarcina . Terminal restriction fragment length polymorphism profiles showed that the landfill was predominated by 22 taxa, making up 69%–96% of the community. Of these, a single taxon comprised 36%–65% of the communities across all sites and depths. Principal components analysis separated the methanogen community into three groups, irrespective of site or depth. Redundancy analysis suggested that total phosphorus and pH play roles in structuring methanogen communities in landfills.

Description: Here we report a newly identified ‘Chalky back’ phenomenon in banana prawns ( Fenneropenaeus merguiensis ) farmed in North Queensland, Australia. This was characterized by localized white discoloured segmentation of the cervical groove, moreover, after cooking the prawns exploded, making them unfit for commercial sale. Histological examination revealed breakdown of gut and abdominal muscle tissue in some moribund specimens. We selectively isolated Vibrio spp., which are known prawn pathogens, from healthy and Chalky back specimens. Isolated bacteria were identified, typed and tested for the presence of eight virulence genes (VGs), biofilm formation, adherence and cytotoxicity to fish cells. In all, 32 isolates were recovered and identified as Vibrio harveyi , V. owensii , V. sinaloensis -like, V. campbellii , V. shilonii , Vibrio sp. and Photobacterium damselae using 16S rRNA gene sequencing. All V. harveyi carried VGs coding for haemolysin, tox R and flagella; formed biofilm; and adhered to both cell lines. This was similar to the V. sinaloensis -like strains that were only isolated from Chalky back specimens. Our data suggest that Vibrio spp. may play a role in the pathogenesis of Chalky back. This study is the first report of Chalky back phenomenon in farmed banana prawns that needs to be closely monitored by the industry.

Description: Deep geological repositories, isolated from the geosphere by an engineered bentonite barrier, are currently considered the safest solution for high-level radioactive waste (HLRW) disposal. As the physical conditions and properties of the bentonite barrier are anticipated to change with time, seismic tomography was suggested as a viable technique to monitor the physical state and integrity of the barrier and to timely detect any unforeseen failure. To do so, the seismic monitoring system needs to be optimized, and this can be achieved by conducting numerical simulations of wave propagation in the repository geometry. Previous studies treated bentonite as an elastic medium, whereas recent experimental investigations indicate its pronounced viscoelastic behaviour. The aims of this contribution are (i) to numerically estimate the effective attenuation of bentonite as a function of temperature T and water content W c , so that synthetic data can accurately reproduce experimental traces and (ii) assess the feasibility and limitation of the HLRW repository monitoring by simulating the propagation of sonic waves in a realistic repository geometry. A finite difference method was utilized to simulate the wave propagation in experimental and repository setups. First, the input of the viscoelastic model was varied to achieve a match between experimental and numerical traces. The routine was repeated for several values of W c and T , so that quality factors Q p ( W c , T ) and Q s ( W c , T ) were obtained. Then, the full-scale monitoring procedure was simulated for six scenarios, representing the evolution of bentonite's physical state. The estimated Q p and Q s exhibited a minimum at W c = 20 per cent and higher sensitivity to W c , rather than T , suggesting that pronounced inelasticity of the clay has to be taken into account in geophysical modelling and analysis. The repository-model traces confirm that active seismic monitoring is, in principle, capable of depicting physical changes in the bentonite barrier. However, the locations of sources and receivers relative to the tunnel need to be optimized to achieve best sensitivity to the changes. It was also observed that first arrivals do not necessarily represent the most informative part of the signal; thus the time windows of the analysis need to be selected, accounting for the geometry of the acquisition system. This contribution should be considered as a next step towards the development of a numerical approach to aid in the design and optimization of a non-intrusive monitoring system in HLRW repositories.

Description: Plant-growth-promoting bacteria belonging to Azospirillum and Pseudomonas genera are major inhabitants of the rhizosphere. Both are increasingly commercialized as crops inoculants. Interspecific interaction in the rhizosphere is critical for inoculants aptness. The objective of this work was to evaluate Azospirillum and Pseudomonas interaction in mixed biofilms by co-cultivation of the model strains Azospirillum brasilense Sp245 and Pseudomonas protegens CHA0. The results revealed enhanced growth of both strains when co-cultured in static conditions. Moreover, Sp245 biofilm formed in plastic surfaces was increased 2-fold in the presence of CHA0. Confocal microscopy revealed highly structured mixed biofilms showing Sp245 mainly on the bottom and CHA0 towards the biofilm surface. In addition, A. brasilense biofilm was thicker and denser when co-cultured with P. protegens. In a colony–colony interaction assay, Sp245 changed nearby CHA0 producing small colony phenotype, which accounts for a diffusible metabolite mediator; though CHA0 spent medium did not affect Sp245 colony phenotype. Altogether, these results point to a cooperative interaction between A. brasilense Sp245 and P. protegens CHA0 in which both strains increase their static growth and produce structured mixed biofilms with a strain-specific distribution.

Description: Knowledge about the factors shaping the rumen microbiota in wild animals is limited. Therefore, the aim of this study was to compare the microbiota from the three cervid species moose ( Alces alces , n = 5), red deer ( Cervus elaphus , n = 4) and roe deer ( Capreolus capreolus , n = 12), sharing the same habitat. Using deep 16S rRNA gene sequencing, we found that the largest species moose had the highest number of unique operational taxonomic units. Furthermore, red deer and moose shared more of the microbiota, compared with the smallest species, roe deer, with Firmicutes and Euryarchaeota being significantly overrepresented for the shared microbiota. These differences could not be explained by diet or range. The animals largely shared the same range, and there are no systematic differences in diet. We therefore believe rumen physiology can be one of the main contributing factors to the observed distribution of the rumen microbiota in cervid species.

Description: Variations in self-potentials (SP) measured at surface during pumping of a heterogeneous confined fractured rock aquifer have been monitored and modelled in order to investigate capabilities and limitations of SP methods in estimating aquifer hydraulic properties. SP variations were recorded around a pumping well using an irregular grid of 31 non-polarizing Pb-PbCl 2 that were referenced to a remote electrode and connected to a commercial multiplexer and digitizer/data logger through a passive lowpass filter on each channel. The lowpass filter reduced noise by a factor of 10 compared to levels obtained using the data logger's integration-based sampling method for powerline noise suppression alone. SP signals showed a linear relationship with water levels observed in the pumping and monitoring wells over the pumping period, with an apparent electrokinetic coupling coefficient of –3.4 mV · m –1 . Following recent developments in SP methodology, variability of the SP response between different electrodes is taken as a proxy for lateral variations in hydraulic head within the aquifer and used to infer lateral variations in the aquifer's apparent transmissivity. In order to demonstrate the viability of this approach, SP is modelled numerically to determine its sensitivity to (i) lateral variations in the hydraulic conductivity of the confined aquifer and (ii) the electrical conductivity of the confining layer and conductive well casing. In all cases, SP simulated on the surface still varies linearly with hydraulic head modelled at the base on the confining layer although the apparent coupling coefficient changes to varying degrees. Using the linear relationship observed in the field, drawdown curves were inferred for each electrode location using SP variations observed over the duration of the pumping period. Transmissivity estimates, obtained by fitting the Theis model to inferred drawdown curves at all 31 electrodes, fell within a narrow range of (2.0–4.2) x 10 –3 m 2 · s –1 and were consistent with values measured in the pumping and monitoring wells. This approach will be of particular interest where monitoring wells are lacking for direct measurement, and SP on the surface can be used to quickly estimate hydraulic properties.

Description: We present a numerical algorithm for 3-D electromagnetic (EM) simulations in conducting media with general electric anisotropy. The algorithm is based on the finite-difference discretization of frequency-domain Maxwell's equations on a Lebedev grid, in which all components of the electric field are collocated but half a spatial step staggered with respect to the magnetic field components, which also are collocated. This leads to a system of linear equations that is solved using a stabilized biconjugate gradient method with a multigrid preconditioner. We validate the accuracy of the numerical results for layered and 3-D tilted transverse isotropic (TTI) earth models representing typical scenarios used in the marine controlled-source EM method. It is then demonstrated that not taking into account the full anisotropy of the conductivity tensor can lead to misleading inversion results. For synthetic data corresponding to a 3-D model with a TTI anticlinal structure, a standard vertical transverse isotropic (VTI) inversion is not able to image a resistor, while for a 3-D model with a TTI synclinal structure it produces a false resistive anomaly. However, if the VTI forward solver used in the inversion is replaced by the proposed TTI solver with perfect knowledge of the strike and dip of the dipping structures, the resulting resistivity images become consistent with the true models.

Description: We develop a procedure to invert time domain induced polarization (IP) data for inductive sources. Our approach is based upon the inversion methodology in conventional electrical IP (EIP), which uses a sensitivity function that is independent of time. However, significant modifications are required for inductive source IP (ISIP) because electric fields in the ground do not achieve a steady state. The time-history for these fields needs to be evaluated and then used to define approximate IP currents. The resultant data, either a magnetic field or its derivative, are evaluated through the Biot-Savart law. This forms the desired linear relationship between data and pseudo-chargeability. Our inversion procedure has three steps: (1) Obtain a 3-D background conductivity model. We advocate, where possible, that this be obtained by inverting early-time data that do not suffer significantly from IP effects. (2) Decouple IP responses embedded in the observations by forward modelling the TEM data due to a background conductivity and subtracting these from the observations. (3) Use the linearized sensitivity function to invert data at each time channel and recover pseudo-chargeability. Post-interpretation of the recovered pseudo-chargeabilities at multiple times allows recovery of intrinsic Cole-Cole parameters such as time constant and chargeability. The procedure is applicable to all inductive source survey geometries but we focus upon airborne time domain EM (ATEM) data with a coincident-loop configuration because of the distinctive negative IP signal that is observed over a chargeable body. Several assumptions are adopted to generate our linearized modelling but we systematically test the capability and accuracy of the linearization for ISIP responses arising from different conductivity structures. On test examples we show: (1) our decoupling procedure enhances the ability to extract information about existence and location of chargeable targets directly from the data maps; (2) the horizontal location of a target body can be well recovered through inversion; (3) the overall geometry of a target body might be recovered but for ATEM data a depth weighting is required in the inversion; (4) we can recover estimates of intrinsic and that may be useful for distinguishing between two chargeable targets.

Description: Mesorhizobium loti MAFF303099 has a functional Type III secretion system (T3SS) that is involved in the determination of competitiveness for legume nodulation. Here we demonstrate that the transcriptional factor TtsI, which positively regulates T3SS genes expression, is involved in a negative regulation of M. loti swimming motility in soft-agar. Conditions that induce T3SS expression affect flagella production. The same conditions also affect promoter activity of M. loti visN gene, a homolog to the positive regulator of flagellar genes that has been described in other rhizobia. Defects in T3SS complex assembly at membranes limited the negative regulation of motility by the expression of TtsI.

Description: Frequent burning is commonly undertaken to maintain diversity in temperate grasslands of southern Australia. How burning affects below-ground fungal community diversity remains unknown. We show, using a fungal rDNA metabarcoding approach (Illumina MiSeq), that the fungal community composition was influenced by fire regime (frequency) but not time-since-fire. Fungal community composition was resilient to direct fire effects, most likely because grassland fires transfer little heat to the soil. Differences in the fungal community composition due to fire regime was likely due to associated changes that occur in vegetation with recurrent fire, via the break up of obligate symbiotic relationships. However, fire history only partially explains the observed dissimilarity in composition among the soil samples, suggesting a distinctiveness in composition in each grassland site. The importance of considering changes in soil microbe communities when managing vegetation with fire is highlighted.

Description: Soil is thought to be important both as a source and a sink of carbonyl sulfide (COS) in the troposphere, but the mechanism affecting COS uptake, especially for fungi, remains uncertain. Fungal isolates that were collected randomly from forest soil showed COS-degrading ability at high frequencies: 38 out of 43 isolates grown on potato dextrose agar showed degradation of 30 ppmv COS within 24 h. Of these isolates, eight degraded 30 ppmv of COS to below the detection limit within 2 h. These isolates also showed an ability to degrade COS included in ambient air (around 500 pptv) and highly concentrated (12 500 ppmv) level, even though the latter is higher than the lethal level for mammals. COS-degrading activity was estimated by using ergosterol as a biomass index for fungi. Trichoderma sp. THIF08 had the highest COS-degrading activity of all the isolates. Interestingly, Umbelopsis/Mortierella spp. THIF09 and THIF13 were unable to degrade 30 ppmv COS within 24 h, and actually emitted COS during the cultivation in ambient air. These results indicate a fungal contribution to the flux of COS between the terrestrial and atmospheric environments.

Description: The extraction of spectral information in the inversion process of time-domain (TD) induced polarization (IP) data is changing the use of the TDIP method. Data interpretation is evolving from a qualitative description of the subsurface, able only to discriminate the presence of contrasts in chargeability parameters, towards a quantitative analysis of the investigated media, which allows for detailed soil- and rock-type characterization. Two major limitations restrict the extraction of the spectral information of TDIP data in the field: (i) the difficulty of acquiring reliable early-time measurements in the millisecond range and (ii) the self-potential background drift in the measured potentials distorting the shape of the late-time IP responses, in the second range. Recent developments in TDIP acquisition equipment have given access to full-waveform recordings of measured potentials and transmitted current, opening for a breakthrough in data processing. For measuring at early times, we developed a new method for removing the significant noise from power lines contained in the data through a model-based approach, localizing the fundamental frequency of the power-line signal in the full-waveform IP recordings. By this, we cancel both the fundamental signal and its harmonics. Furthermore, an efficient processing scheme for identifying and removing spikes in TDIP data was developed. The noise cancellation and the de-spiking allow the use of earlier and narrower gates, down to a few milliseconds after the current turn-off. In addition, tapered windows are used in the final gating of IP data, allowing the use of wider and overlapping gates for higher noise suppression with minimal distortion of the signal. For measuring at late times, we have developed an algorithm for removal of the self-potential drift. Usually constant or linear drift-removal algorithms are used, but these algorithms often fail in removing the background potentials present when the electrodes used for potential readings are previously used for current injection, also for simple contact resistance measurements. We developed a drift-removal scheme that models the polarization effect and efficiently allows for preserving the shape of the IP responses at late times. Uncertainty estimates are essential in the inversion of IP data. Therefore, in the final step of the data processing, we estimate the data standard deviation based on the data variability within the IP gates and the misfit of the background drift removal Overall, the removal of harmonic noise, spikes, self-potential drift, tapered windowing and the uncertainty estimation allows for doubling the usable range of TDIP data to almost four decades in time (corresponding to four decades in frequency), which will significantly advance the applicability of the IP method.

Description: A composite transposon is a mobile genetic element consisting of two insertion sequences (ISs) flanking a segment of cargo DNA often containing antibiotic resistance (AR) genes. Composite transposons can move as a discreet unit. There have been recently several reports on a novel mechanism of movement of an IS 26 -based composite transposon through the formation of a translocatable unit (TU), carrying the internal DNA segment of a composite transposon and one copy of a flanking IS. In this study, we determined the presence of composite transposons and TUs in human oral metagenomic DNA using PCR primers from common IS elements. Analysis of resulting amplicons showed four different IS 1216 composite transposons and one IS 257 composite transposon in our metagenomic sample. As our PCR strategy would also detect TUs, PCR was carried out to detect circular TUs predicted to originate from these composite transposons. We confirmed the presence of two novel TUs, one containing an experimentally proven antiseptic resistance gene and another containing a putative universal stress response protein (UspA) encoding gene. This is the first report of a PCR strategy to amplify the DNA segment on composite transposons and TUs in metagenomic DNA. This can be used to identify AR genes associated with a variety of mobile genetic elements from metagenomes.

Description: Carbonyl sulfide (COS) is an atmospheric trace gas and one of the sources of stratospheric aerosol contributing to climate change. Although one of the major sinks of COS is soil, the distribution of COS degradation ability among bacteria remains unclear. Seventeen out of 20 named bacteria belonging to Actinomycetales had COS degradation activity at mole fractions of 30 parts per million by volume (ppmv) COS. Dietzia maris NBRC 15801 T and Mycobacterium sp. THI405 had the activity comparable to a chemolithoautotroph Thiobacillus thioparus THI115 that degrade COS by COS hydrolase for energy production. Among 12 bacteria manifesting rapid degradation at 30 ppmv COS, D. maris NBRC 15801 T and Streptomyces ambofaciens NBRC 12836 T degraded ambient COS (~500 parts per trillion by volume). Geodermatophilus obscurus NBRC 13315 T and Amycolatopsis orientalis NBRC 12806 T increased COS concentrations. Moreover, six of eight COS-degrading bacteria isolated from soils had partial nucleotide sequences similar to that of the gene encoding clade D of β-class carbonic anhydrase, which included COS hydrolase. These results indicate the potential importance of Actinomycetes in the role of soils as sinks of atmospheric COS.

Description: Surface nuclear magnetic resonance (NMR) is a unique geophysical method due to its direct sensitivity to water. A key limitation to overcome is the difficulty of making surface NMR measurements in environments with anthropogenic electromagnetic noise, particularly constant frequency sources such as powerlines. Here we present a method of removing harmonic noise by utilizing frequency domain symmetry of surface NMR signals to reconstruct portions of the spectrum corrupted by frequency-domain noise peaks. This method supplements the existing NMR processing workflow and is applicable after despiking, coherent noise cancellation, and stacking. The symmetry based correction is simple, grounded in mathematical theory describing NMR signals, does not introduce errors into the data set, and requires no prior knowledge about the harmonics. Modelling and field examples show that symmetry based noise removal reduces the effects of harmonics. In one modelling example, symmetry based noise removal improved signal-to-noise ratio in the data by 10 per cent. This improvement had noticeable effects on inversion parameters including water content and the decay constant T 2 *. Within water content profiles, aquifer boundaries and water content are more accurate after harmonics are removed. Fewer spurious water content spikes appear within aquifers, which is especially useful for resolving multilayered structures. Within T 2 * profiles, estimates are more accurate after harmonics are removed, especially in the lower half of profiles.

Description: In this work, we study seismoelectric conversions generated in the vadose zone, when this region is traversed by a pure SH wave. We assume that the soil is a 1-D partially saturated lossy porous medium and we use the van Genuchten's constitutive model to describe the water saturation profile. Correspondingly, we extend Pride's formulation to deal with partially saturated media. In order to evaluate the influence of different soil textures we perform a numerical analysis considering, among other relevant properties, the electrokinetic coupling, coseismic responses and interface responses (IRs). We propose new analytical transfer functions for the electric and magnetic field as a function of the water saturation, modifying those of Bordes et al. and Garambois & Dietrich, respectively. Further, we introduce two substantially different saturation-dependent functions into the electrokinetic (EK) coupling linking the poroelastic and the electromagnetic wave equations. The numerical results show that the electric field IRs markedly depend on the soil texture and the chosen EK coupling model, and are several orders of magnitude stronger than the electric field coseismic ones. We also found that the IRs of the water table for the silty and clayey soils are stronger than those for the sandy soils, assuming a non-monotonous saturation dependence of the EK coupling, which takes into account the charged air–water interface. These IRs have been interpreted as the result of the jump in the viscous electric current density at the water table. The amplitude of the IR is obtained using a plane SH wave, neglecting both the spherical spreading and the restriction of its origin to the first Fresnel zone, effects that could lower the predicted values. However, we made an estimation of the expected electric field IR amplitudes detectable in the field by means of the analytical transfer functions, accounting for spherical spreading of the SH seismic waves. This prediction yields a value of 15 μV m –1 , which is compatible with reported values.

Description: Neonicotinoids are neurotoxic systemic insecticides used in plant protection worldwide. Unfortunately, application of neonicotinoids affects both beneficial and target insects indiscriminately. Being water soluble and persistent, these pesticides are capable of disrupting both food chains and biogeochemical cycles. This review focuses on the biodegradation of neonicotinoids in soil and water systems by the bacterial community. Several bacterial strains have been isolated and identified as capable of transforming neonicotinoids in the presence of an additional carbon source. Environmental parameters have been established for accelerated transformation in some of these strains. Studies have also indicated that enhanced biotransformation of these pesticides can be accomplished by mixed microbial populations under optimised environmental conditions. Substantial research into the identification of neonicotinoid-mineralising bacterial strains and identification of the genes and enzymes responsible for neonicotinoid degradation is still required to complete the understanding of microbial biodegradation pathways, and advance bioremediation efforts.

Description: In recent years, marine controlled source electromagnetics (CSEM) has found increasing use in hydrocarbon exploration due to its ability to detect thin resistive zones beneath the seafloor. It is the purpose of this paper to evaluate the physics of CSEM for an ocean whose electrical thickness is comparable to or much thinner than that of the overburden using the in-line configuration through examination of the elliptically polarized seafloor electric field, the time-averaged energy flow depicted by the real part of the complex Poynting vector, energy dissipation through Joule heating and the Fréchet derivatives of the seafloor field with respect to the subseafloor conductivity that is assumed to be isotropic. The deep water (ocean layer electrically much thicker than the overburden) seafloor EM response for a model containing a resistive reservoir layer has a greater amplitude and reduced phase as a function of offset compared to that for a half-space, or a stronger and faster response. For an ocean whose electrical thickness is comparable to or much smaller than that of the overburden, the electric field displays a greater amplitude and reduced phase at small offsets, shifting to a stronger amplitude and increased phase at intermediate offsets and a weaker amplitude and enhanced phase at long offsets, or a stronger and faster response that first changes to stronger and slower, and then transitions to weaker and slower. These transitions can be understood by visualizing the energy flow throughout the structure caused by the competing influences of the dipole source and guided energy flow in the reservoir layer, and the air interaction caused by coupling of the entire subseafloor resistivity structure with the sea surface. A stronger and faster response occurs when guided energy flow is dominant, while a weaker and slower response occurs when the air interaction is dominant. However, at intermediate offsets for some models, the air interaction can partially or fully reverse the direction of energy flux in the reservoir layer toward rather than away from the source, resulting in a stronger and slower response. The Fréchet derivatives are dominated by preferential sensitivity to the reservoir layer conductivity for all water depths except at high frequencies, but also display a shift with offset from the galvanic to the inductive mode in the underburden and overburden due to the interplay of guided energy flow and the air interaction. This means that the sensitivity to the horizontal conductivity is almost as strong as to the vertical component in the shallow parts of the subsurface, and in fact is stronger than the vertical sensitivity deeper down. However, the sensitivity to horizontal conductivity is still weak compared to the vertical component within thin resistive regions. The horizontal sensitivity is gradually decreased when the water becomes deep. These observations in part explain the success of shallow towed CSEM using only measurements of the in-line component of the electric field.

Description: Many toxic insecticides used worldwide as well as some chemical warfare agents are phosphotriester derivatives. Therefore, detoxification of organophosphorus compounds has become the subject of many studies and in particular bioremediation, based on the phosphotriesterase catalysed hydrolysis of these compounds, has shown to be an effective and ecological methodology. In order to identify new bacterial phosphotriesterases, a simple and sensitive fluorimetric screening method on solid media was employed that allowed the selection of six strains with phosphotriesterase activity. Since pH and temperature are important parameters for bioremediation of contaminated soils and waters, the influence of these variables on the rate of the enzymatic hydrolysis was assessed. This study afforded notable results, being the most remarkable one the increased activity exhibited by Nocardia asteroides and Streptomyces setonii strains at 50°C, 7 and 30 times higher than at 30°C, respectively. Compared with the results obtained with Brevundimonas diminuta , whose activity is usually considered as reference, an increase of 26 and 75 times is observed, respectively.

Description: Phosphorus (P) is a critical, non-renewable nutrient; yet excess discharges can lead to eutrophication and deterioration of water quality. Thus, P removal from water must be coupled with P recovery to achieve sustainable P management. P-specific proteins provide a novel, promising approach to recover P from water. Bacterial phosphate-binding proteins (PBPs) are able to effectively remove phosphate, achieving extremely low levels in water (i.e. 0.015 mg-P L –1 ). A prerequisite of using PBP for P recovery, however, is not only removal, but also controlled P release, which has not yet been reported. Phosphate release using recombinant PBP-expressing Escherichia coli was explored in this study. Escherichia coli was genetically modified to overexpress PBP in the periplasmic space. The impacts of ionic strength, temperature and pH on phosphate release were assessed. PBP-expressed E. coli demonstrated consistently superior ability to adsorb more phosphate from liquid and release more phosphate under controlled conditions relative to negative controls (unexpressed PBP E. coli and E. coli K12). Lower pH (3.8), higher temperature (35ºC) and higher ionic strength (100 mM KCl) facilitated increased phosphate release, providing a maximum of 2.1% P recovery within 3 h. This study provides proof of concept of the feasibility of using PBP to recover P.

Description: Joint inversion and time-lapse inversion techniques of geophysical data are often implemented in an attempt to improve imaging of complex subsurface structures and dynamic processes by minimizing negative effects of random and uncorrelated spatial and temporal noise in the data. We focus on the structural cross-gradient (SCG) approach (enforcing recovered models to exhibit similar spatial structures) in combination with time-lapse inversion constraints applied to surface-based electrical resistivity and seismic traveltime refraction data. The combination of both techniques is justified by the underlying petrophysical models. We investigate the benefits and trade-offs of SCG and time-lapse constraints. Using a synthetic case study, we show that a combined joint time-lapse inversion approach provides an overall improvement in final recovered models. Additionally, we introduce a new approach to reweighting SCG constraints based on an iteratively updated normalized ratio of model sensitivity distributions at each time-step. We refer to the new technique as the Automatic Joint Constraints (AJC) approach. The relevance of the new joint time-lapse inversion process is demonstrated on the synthetic example. Then, these approaches are applied to real time-lapse monitoring field data collected during a quarter-scale earthen embankment induced-piping failure test. The use of time-lapse joint inversion is justified by the fact that a change of porosity drives concomitant changes in seismic velocities (through its effect on the bulk and shear moduli) and resistivities (through its influence upon the formation factor). Combined with the definition of attributes (i.e. specific characteristics) of the evolving target associated with piping, our approach allows localizing the position of the preferential flow path associated with internal erosion. This is not the case using other approaches.