ALBERT

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: 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: We present two independent, automated methods for estimating the absolute horizontal misorientation of seismic sensors. We apply both methods to 44 free-fall ocean-bottom seismometers (OBSs) of the RHUM-RUM experiment ( http://www.rhum-rum.net/ ). The techniques measure the 3-D directions of particle motion of (1) P -waves and (2) Rayleigh waves of earthquake recordings. For P -waves, we used a principal component analysis to determine the directions of particle motions (polarizations) in multiple frequency passbands. We correct for polarization deviations due to seismic anisotropy and dipping discontinuities using a simple fit equation, which yields significantly more accurate OBS orientations. For Rayleigh waves, we evaluated the degree of elliptical polarization in the vertical plane in the time and frequency domain. The results obtained for the RHUM-RUM OBS stations differed, on average, by 3.1° and 3.7° between the methods, using circular mean and median statistics, which is within the methods’ estimate uncertainties. Using P -waves, we obtained orientation estimates for 31 ocean-bottom seismometers with an average uncertainty (95 per cent confidence interval) of 11° per station. For 7 of these OBS, data coverage was sufficient to correct polarization measurements for underlying seismic anisotropy and dipping discontinuities, improving their average orientation uncertainty from 11° to 6° per station. Using Rayleigh waves, we obtained misorientation estimates for 40 OBS, with an average uncertainty of 16° per station. The good agreement of results obtained using the two methods indicates that they should also be useful for detecting misorientations of terrestrial seismic stations.

Description: We investigate the elastic and anelastic structure of the lowermost mantle at the western edge of the Pacific large low shear velocity province (LLSVP) by inverting a collection of S and ScS waveforms. The transverse component data were obtained from F-net for 31 deep earthquakes beneath Tonga and Fiji, filtered between 12.5 and 200 s. We observe a regional variation of S and ScS arrival times and amplitude ratios, according to which we divide our region of interest into three subregions. For each of these subregions, we then perform 1-D (depth-dependent) waveform inversions simultaneously for radial profiles of shear wave velocity ( V S ) and seismic quality factor ( Q ). Models for all three subregions show low V S and low Q structures from 2000 km depth down to the core–mantle boundary. We further find that V S and Q in the central subregion, sampling the Caroline plume, are substantially lower than in the surrounding regions, whatever the depth. In the central subregion, V S -anomalies with respect to PREM (d V S ) and Q are about –2.5 per cent and 216 at a depth of 2850 km, and –0.6 per cent and 263 at a depth of 2000 km. By contrast, in the two other regions, d V S and Q are –2.2 per cent and 261 at a depth of 2850 km, and –0.3 per cent and 291 at a depth of 2000 km. At depths greater than ~2500 km, these differences may indicate lateral variations in temperature of ~100 K within the Pacific LLSVP. At shallower depths, they may be due to the temperature difference between the Caroline plume and its surroundings, and possibly to a small fraction of iron-rich material entrained by the plume.

Description: We investigated post-seismic velocity changes within the fault zone of the 2008 M 7.9 Wenchuan earthquake using coda wave data of repeating small earthquakes. We employed template matching and grid search methods to identify well-defined repeating earthquakes in order to minimize artefacts induced by variations in source location. We identified a total of 12 isolated patches in the fault zone that ruptured more than twice in a 1 yr period after the M 7.9 earthquake. We applied the coda wave interferometry technique to the waveform data of the 34 identified repeating earthquakes to estimate velocity changes between the first and subsequent events in each cluster. We found that major post-seismic velocity changes occurred in the southwestern part of the rupture area, where the main rupture was initiated and characterized by thrust motion, while the Beichuan area in the northeastern part of the rupture zone appears to experience very little post-seismic velocity changes.

Description: In this study, we demonstrate the feasibility of imaging broad-band (10–150 s) Rayleigh wave phase velocity maps on a continental scale using ambient noise tomography (ANT). We obtain broad-band Rayleigh waves from cross-correlations of ambient noise data between all station pairs of USArray and measure the dispersion curves from these cross-correlations at a period band of 10–150 s. The large-scale dense USArray enables us to obtain over 500 000 surface wave paths which cover the contiguous United States densely. Using these paths, we generate Rayleigh wave phase velocity maps at 10–150 s periods. Our phase velocity maps are similar to other reported phase velocity maps based on ambient noise data at short periods (〈50 s) and based on earthquake data at intermediate/long periods (50–90 s). This study extends ANT from short/intermediate periods (〈50 s) to long periods up to 150 s in a continental scale of the USA. These broad-band phase velocity maps from ANT can be used to construct 3-D lithospheric and asthenospheric velocity structures.

Description: In finite-difference (FD) method, numerical dispersion is the dominant factor influencing the accuracy of seismic modelling. Various optimized FD schemes for scalar wave modelling have been proposed to reduce grid dispersion, while the optimized time–space domain FD schemes for elastic wave modelling have not been fully investigated yet. In this paper, an optimized FD scheme with Equivalent Staggered Grid (ESG) for elastic modelling has been developed. We start from the constant P - and S -wave speed elastic wave equations and then deduce analytical plane wave solutions in the wavenumber domain with eigenvalue decomposition method. Based on the elastic plane wave solutions, three new time–space domain dispersion relations of ESG elastic modelling are obtained, which are represented by three equations corresponding to P -, S - and converted-wave terms in the elastic equations, respectively. By using these new relations, we can study the dispersion errors of different spatial FD terms independently. The dispersion analysis showed that different spatial FD terms have different errors. It is therefore suggested that different FD coefficients to be used to approximate the three spatial derivative terms. In addition, the relative dispersion error in L2-norm is minimized through optimizing FD coefficients using Newton's method. Synthetic examples have demonstrated that this new optimal FD schemes have superior accuracy for elastic wave modelling compared to Taylor-series expansion and optimized space domain FD schemes.

Description: Markov chain Monte-Carlo (McMC) sampling generates correlated random samples such that their distribution would converge to the true distribution only as the number of samples tends to infinity. In practice, McMC is found to be slow to converge, convergence is not guaranteed to be achieved in finite time, and detection of convergence requires the use of subjective criteria. Although McMC has been used for decades as the algorithm of choice for inference in complex probability distributions, there is a need to seek alternative approaches, particularly in high dimensional problems. Walker & Curtis ( 2014 ) developed a method for Bayesian inversion of 2-D spatial data using an exact sampling alternative to McMC which always draws independent samples of the target distribution. Their method thus obviates the need for convergence and removes the concomitant bias exhibited by finite sample sets. Their algorithm is nevertheless computationally intensive and requires large memory. We propose a more efficient method for Bayesian inversion of categorical variables, such as geological facies that requires no sampling at all. The method is based on a 2-D Hidden Markov Model (2D-HMM) over a grid of cells where observations represent localized data constraining each cell. The data in our example application are seismic attributes such as P - and S -wave impedances and rock density; our categorical variables are the hidden states and represent the geological rock types in each cell—facies of distinct subsets of lithology and fluid combinations such as shale, brine-sand and gas-sand. The observations at each location are assumed to be generated from a random function of the hidden state (facies) at that location, and to be distributed according to a certain probability distribution that is independent of hidden states at other locations – an assumption referred to as ‘localized likelihoods’. The hidden state (facies) at a location cannot be determined solely by the observation at that location as it also depends on prior information concerning the spatial distribution of other hidden states elsewhere. The prior information is included in the inversion in the form of a training image which represents a conceptual depiction of local geologies that might be expected, but other forms of prior information can be used in the method as desired. The method provides direct estimates of posterior marginal probability distributions over each variable, so these do not need to be estimated from samples such as in McMC. Nevertheless, in the case that samples are desired, these can be generated. On a 2-D test example the method is shown to outperform previous methods significantly, at a fraction of the computational cost. In many foreseeable applications there are therefore no serious impediments to extending the method to 3-D cases.

Description: A double-correlation method is introduced to locate tremor sources based on stacks of complex, doubly-correlated tremor records of multiple triplets of seismographs back projected to hypothetical source locations in a geographic grid. Peaks in the resulting stack of moduli are inferred source locations. The stack of the moduli is a robust measure of energy radiated from a point source or point sources even when the velocity information is imprecise. Application to real data shows how double correlation focuses the source mapping compared to the common single correlation approach. Synthetic tests demonstrate the robustness of the method and its resolution limitations which are controlled by the station geometry, the finite frequency of the signal, the quality of the used velocity information and noise level. Both random noise and signal or noise correlated at time shifts that are inconsistent with the assumed velocity structure can be effectively suppressed. Assuming a surface wave velocity, we can constrain the source location even if the surface wave component does not dominate. The method can also in principle be used with body waves in 3-D, although this requires more data and seismographs placed near the source for depth resolution.