Change of deep subduction seismicity after a large megathrust earthquake.

Subduction zones are home to the world's largest and deepest earthquakes. Recently, large-scale interactions between shallow (0-60 km) and intermediate (80-150 km) seismicity have been evidenced during the interseismic period but also before and after megathrust earthquakes along with large-scale changes in surface motion. Large-scale deformation transients following major earthquakes have also been observed possibly due to a post-seismic change in slab pull or to a bending/unbending of the plates, which suggests the existence of interactions between the deep and shallow parts of the slab. In this study, we analyze the spatio-temporal variations of the declustered seismicity in Japan from 2000 to 2011/3/11 and from 2011/3/11 to 2013/3/11. We observe that the background rate of the intermediate to deep (150-450 km) seismicity underwent a deceleration of 55% south of the rupture zone and an acceleration of 30% north of it after the Tohoku-oki earthquake, consistent with the GPS surface displacements. This shows how a megathrust earthquake can affect the stress state of the slab over a 2500 km lateral range and a large depth range, demonstrating that earthquakes interact at a much greater scale than the surrounding rupture zone usually considered.

Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale.

Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii ("Iraqibacter") was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment.IMPORTANCE This is the first systematic study about spatial and temporal variation of virioplankton communities in estuaries using deep metagenomics sequencing. It is among the highest-quality viromic data sets to date, showing remarkably consistent sequencing depth and quality across samples. Our results indicate that there exists a large pool of abundant and diverse viruses in estuaries that have not yet been cultivated, their genomes only available thanks to single-cell genomics or single-molecule sequencing, demonstrating the importance of these methods for viral discovery. The spatiotemporal pattern of these abundant uncultivated viruses is more variable than that of cultured viruses. Despite strong environmental gradients, season and location had surprisingly little impact on the viral community within an estuary, but we saw a significant distinction between the two estuaries and also between estuarine and open ocean viromes.

Connecting a broad spectrum of transient slip on the San Andreas fault.

Strain accumulated on the deep extension of some faults is episodically released during transient slow-slip events, which can subsequently load the shallow seismogenic region. At the San Andreas fault, the characteristics of slow-slip events are difficult to constrain geodetically due to their small deformation signal. Slow-slip events (SSEs) are often accompanied by coincident tremor bursts composed of many low-frequency earthquakes. Here, we probabilistically estimate the spatiotemporal clustering properties of low-frequency earthquakes detected along the central San Andreas fault. We find that tremor bursts follow a power-law spatial and temporal decay similar to earthquake aftershock sequences. The low-frequency earthquake clusters reveal that the underlying slow-slip events have two modes of rupture velocity. Compared to regular earthquakes, these slow-slip events have smaller stress drop and rupture velocity but follow similar magnitude-frequency, moment-area, and moment-duration scaling. Our results connect a broad spectrum of transient fault slip that spans several orders of magnitude in rupture velocity.

Complete Genome Sequence of Subcluster 5.2 Synechococcus sp. Strain CB0101, Isolated from the Chesapeake Bay.

Synechococcus sp. strain CB0101 is a model strain for cyanobacteria living in the estuarine environment. It is also a representative member of marine Synechococcus subcluster 5.2. The draft genome sequence of CB0101 was reported in 2014 with 454 sequencing. Here, we report the complete genome sequence of CB0101, obtained with PacBio sequencing. CB0101 contains a specialized array of genes which are involved in sensing, responding to, and persisting in the presence of environmental stress.

Characterizing horizontally-polarized shear and infragravity vibrational modes in the Arctic sea ice cover using correlation methods.

The deployment of three drifting seismic stations on the Arctic sea ice during the winter of 2014-2015 with station inter-spacing between 30 and 80 km enables the characterization of the coherent seismic wavefield at these scales through the use of array methods. Two distinct vibrational modes are observed, corresponding to the fast and non-dispersive horizontally-polarized shear (SH) mode and the slow and dispersive flexural, infragravity mode (ice swell). The excitation of these two modes is not synchronous. The activation of the infragravity mode is linked to the arrival of energetic, dispersive wavetrains that can be readily seen on individual spectrograms, and that, as previous studies have shown, are likely to have their origins in distant storms. In contrast, the SH mode is excited at other time intervals and cannot be isolated on the recording of single stations due to the broadband and emergent nature of these wavetrains; given the horizontal polarization of these waves, the authors hypothesize that SH waves are caused by episodes of rapid SH deformation along major leads located outside the station network. The existence of horizontally-polarized waves propagating over long distances opens the possibility of monitoring ice deformation at the scale of the Arctic basin with unprecedented time resolution.

Optimizing de novo genome assembly from PCR-amplified metagenomes.

BACKGROUND: Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. METHODS: Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. RESULTS: Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. CONCLUSIONS: PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Evaluation of microcystin contamination in blue-green algal dietary supplements using a protein phosphatase inhibition-based test kit.

The cyanobacterium Aphanizomenon flos-aquae (AFA), from Upper-Klamath Lake, Oregon, are used to produce blue-green algal (BGA) dietary supplements. The periodic co-occurrence of hepatotoxin-producing contaminant species prompted the Oregon Health Division to establish a limit of 1 µg/g microcystin (MC) for products sold in Oregon in 1997. At the federal level, the current good manufacturing practice (CGMP) regulations for dietary supplements require manufacturers establish a specification, and test, for limits on contaminants that may adulterate finished products. Despite this, several previous international surveys reported MC in BGA supplements in excess of 1 µg/g. The objectives of this study were (1) identify a reliable, easy to use test kit for the detection of MC in dried BGA materials and (2) use this kit to assess the occurrence of MC contamination in AFA-BGA dietary supplements in the U.S. A commercial protein phosphatase inhibition assay (PPIA), based on the enzyme PP2A, was found to have acceptable relative enzyme inhibition and accuracy for the majority of MC variants tested, including those most commonly identified in commercial samples, making the kit fit for purpose. Using the PPIA kit, 51% (26 of 51) distinct AFA-BGA products had MC ≥0.25 µg/g (the detection limit of the kit), 10 products had MC concentrations between 0.5 and 1.0 µg/g, and 4 products exceeded the limit (1.1-2.8 µg/g). LC-MS/MS confirmed PPIA results ≥0.5 µg/g and determined that MC-LA and MC-LR were the main congeners present. PPIA is a reliable method for the detection of MC contamination in dried BGA dietary supplements produced in the U.S. While the majority of AFA-BGA products contained ≥0.25 µg/g MC, most were at or below 1.0 µg/g, suggesting that manufacturers have adopted this level as a specification in these products; however, variability in recommended serving sizes prevented further analysis of consumer exposure based on the concentrations of MC contamination found.

Monitoring ice thickness and elastic properties from the measurement of leaky guided waves: A laboratory experiment.

The decline of Arctic sea ice extent is one of the most spectacular signatures of global warming, and studies converge to show that this decline has been accelerating over the last four decades, with a rate that is not reproduced by climate models. To improve these models, relying on comprehensive and accurate field data is essential. While sea ice extent and concentration are accurately monitored from microwave imagery, an accurate measure of its thickness is still lacking. Moreover, measuring observables related to the mechanical behavior of the ice (such as Young's modulus, Poisson's ratio, etc.) could provide better insights in the understanding of sea ice decline, by completing current knowledge so far acquired mostly from radar and sonar data. This paper aims at demonstrating on the laboratory scale that these can all be estimated simultaneously by measuring seismic waves guided in the ice layer. The experiment consisted of leaving a water tank in a cold room in order to grow an ice layer at its surface. While its thickness was increasing, ultrasonic guided waves were generated with a piezoelectric source, and measurements were subsequently inverted to infer the thickness and mechanical properties of the ice with very good accuracy.

Toxin-Antitoxin Systems in Estuarine Synechococcus Strain CB0101 and Their Transcriptomic Responses to Environmental Stressors.

Bacterial toxin-antitoxin (TA) systems are genetic elements composed of a toxin gene and its cognate antitoxin, with the ability to regulate growth. TA systems have not previously been reported in marine Synechococcus or Prochlorococcus. Here we report the finding of seven TA system pairs (Type II) in the estuarine Synechococcus CB0101, and their responses of these TA genes to under different stress conditions, which include; nitrogen and phosphate starvation, phage infection, zinc toxicity, and photo-oxidation. Database searches discovered that eight other marine Synechococcus strains also contain at least one TA pair but none were found in Prochlorococcus. We demonstrate that the relB/relE TA pair was active and resulted in RNA degradation when CB0101 was under oxidative stress caused by either zinc toxicity or high light intensities, but the growth inhibition was released when the stress was removed. Having TA systems allows Synechococcus CB0101 to adapt to the low light and highly variable environments in the Chesapeake Bay. We propose that TA systems could be more important for picocyanobacteria living in the freshwater and estuarine environments compared to those living in the open ocean.

Draft Genome Sequence of Synechococcus sp. Strain CB0101, Isolated From the Chesapeake Bay Estuary.

Here, we report the draft genome sequence of the estuarine Synechococcus sp. strain CB0101. The genomics information of this strain will facilitate the study of the poorly understood Synechococcus subcluster 5.2 and how this strain is capable of thriving in a dynamic estuarine system, such as the Chesapeake Bay.

Sea-ice thickness measurement based on the dispersion of ice swell.

The dispersion of flexural waves propagating in the Arctic sea ice cover is exploited in order to locally measure the ice thickness. The observed dispersion, for waves filtered in the 4-20 s period interval, at up to 4 broad-band seismometers deployed in Spring 2007 near the North Pole, is compared to a parameterized model that accounts for a complex wavefield made of a superposition of independent plane waves with different amplitudes and back-azimuth angles. The parameterization, that includes finding the best modeled ice thickness, is performed by using the cross-correlation functions between the seismometers. The ice thickness is estimated to 2.5 ± 0.2 m for the ~1 km-large floe the seismic stations were deployed on, which is coherent with other, independent measurements at this site. This study thus demonstrates the feasibility of using broad-band seismometers deployed on the sea-ice in order to passively measure the ice thickness, without requiring active sources nor human intervention.

Extending earthquakes' reach through cascading.

Earthquakes, whatever their size, can trigger other earthquakes. Mainshocks cause aftershocks to occur, which in turn activate their own local aftershock sequences, resulting in a cascade of triggering that extends the reach of the initial mainshock. A long-lasting difficulty is to determine which earthquakes are connected, either directly or indirectly. Here we show that this causal structure can be found probabilistically, with no a priori model nor parameterization. Large regional earthquakes are found to have a short direct influence in comparison to the overall aftershock sequence duration. Relative to these large mainshocks, small earthquakes collectively have a greater effect on triggering. Hence, cascade triggering is a key component in earthquake interactions.

Scale dependence and localization of the deformation of Arctic sea ice.

A scaling analysis of the deformation of Arctic sea ice over a 3-day time period is performed for scales of 10 to 1000 km. The deformation field is derived from satellite radar data; it allows us to study how a very large solid body-the Arctic sea-ice cover-deforms under the action of heterogeneous forcing winds and ocean currents. The deformation is strongly localized at small scales, and can be characterized as multifractal. This behavior is well known for turbulent flows, and is here also observed for a deforming solid. A multiscaling extrapolation to the meter scale (laboratory scale) shows that, at the 3-day time scale, about 15% of the deformation is larger than 10(-4) s(-1), implying brittle failure, over 0.2% of the total area.

Comment on "Diffusion of epicenters of earthquake aftershocks, Omori's law, and generalized continuous-time random walk models".

Modeling of earthquake sequences using an epidemic-type aftershock sequence model by Phys. Rev. E 66, 061104 (2002)] has led these authors to conclude that previous analyses of apparent earthquake diffusions were flawed. We show here that diffusion analyses based on spatiotemporal correlation measures for earthquake populations are an appropriate method for capturing the space-time coupling present in earthquake triggering processes.

Three-dimensional mapping of dislocation avalanches: clustering and space/time coupling.

There is growing evidence for the complex, intermittent, and heterogeneous character of plastic flow. Here we report a three-dimensional mapping of dislocation avalanches during creep deformation of an ice crystal, from a multiple-transducers acoustic emission analysis. Correlation analysis shows that dislocation avalanches are spatially clustered according to a fractal pattern and that the closer in time two avalanches are, the larger the probability is that they will be closer in space. Such a space/time coupling may contribute to the self-organization of the avalanches into a clustered pattern.