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Detecting and Testing for Structural Error in Computer Models with Application to the Community Atmospheric Model

Bayesian calibration/inversion methods for uncertain input parameters to simulation codes have generated an increasing amount of interest in the climate community in the recent years. This approach uses multiple disparate observational datasets related to the output of the simulator of interest to yield a probabilistic constraint on the uncertain inputs (i.e. probability distribution). A major challenge in applying Bayesian calibration methods to simulation codes is related to the possible presence of a large structural error in the output fields of interest; that is, the presence of discrepancy between the observed and the simulated output that is neither explained by the uncertainty in the inputs nor the observations. We present here methods to test for and visualize structural error in an ensemble of input-perturbed simulations. The methods are based on bootstrap (resmpling) test statistics and well-known metrics to quantify the difference between two probability distributions. The proposed methods are demonstrated using selected precipitation output fields of the Community Atmospheric Model (CAM), which are compared to observations provided by the Global Precipitation Climatology Project (GPCP). The methods are found to be useful in identifying regions and seasons with a large structural error. The proposed structural error detection methodology can be used to screen multiple observational datasets of interest for structural error, making it possible to retain only the datasets with a small structural error for use in Bayesian calibration. In addition, information about the amount of structural error can be valuable to model developers.

58 GEOSCIENCES↗

2018 NISAR Applications Workshop: Forest and Disturbance; Workshop Report

Forest lands cover the globe and are important sources for providing ecosystem services including: carbon sequestration, biodiversity, timber, air and water quality. As such, counties around the world have dedicated programs for managing them. Accurate and timely information concerning the status of these forests (moisture, biomass, disturbance type, etc.) is essential to those Nations’ human and ecological health as well as economy. The joint NASA/US Forest Service workshop focused on arming forest land managers with observations and remote sensing information from the upcoming NASA-ISRO (Indian Space Research Organization) SAR (Synthetic Aperture Radar) (NISAR) satellite mission (expected to launch early 2022). Participants included representatives from different US Federal Agencies, private sector, and non-governmental organizations (NGO) that are key players in facilitating integration of Earth Observations (EO) into forest management and decision support workflows. They included scientists, technicians, and program managers with a responsibility for data acquisition and exploitation such as product development, delivery, and use, and capacity building. Discussions were held over two days to convey the broader forest and disturbance community information needs for various representative participants and programs and to facilitate the delivery of NISAR mission geospatial products and observational capabilities. Case studies were presented to demonstrate the current state of practice in the use of SAR remote sensing for applications of direct importance to forest and disturbance land management community. Eleven organizations presented their information requirements in response to a set of questions provided by the NASA team, then the NASA team responded by describing the degree to which NISAR could meet these requirements. Discussion ensued about needed data product specifications to increase utility (e.g., projection, latency, etc.), tools and capacity building. The general findings of this workshop were that (a) NISAR observations will be particularly useful to the global forest carbon and disturbance monitoring applications, but that certain data product design decisions (projections and radiometric and terrain corrections) need to be considered to increase utility; b) the biomass and disturbance detection algorithms meet many of the community needs, however there are other information products of value (e.g., soil moisture or disturbance classification, not just detection) and all products should be compliant with existing community standards for reporting uncertainty; c) providing SAR education to the community will be key specifically thinking about putting the information first and the SAR theory second, providing a simple guide of standard data processing steps (e.g., dB (decibel) to power conversion and speckle filtering); d) the community needs a user-friendly interface for finding free, archived data over their geographic regions of interest; e) user-friendly tools that connect to open-sources GIS (Global Information System) software (e.g., QGIS (Quantum GIS)) that include a graphical user interface (GUI) for SAR processing that enables both download and cloud processing. To integrate these findings and prepare the community before NISAR launches, it was suggested that there be a dedicated NISAR Forest and Disturbance Applications Working Group (as per the specifications in the NISAR Utilization Plan). After launch, it was decided that the community continue capacity building activities.

Stavros, Natasha↗

Use of VIIRS DNB Data to Monitor Power Outages and Restoration for Significant Weather Events

NASA fs Short-term Prediction Research and Transition (SPoRT) project operates from NASA's Marshall Space Flight Center in Huntsville, Alabama. The team provides unique satellite data to the National Weather Service (NWS) and other agencies and organizations for weather analysis. While much of its work is focused on improving short-term weather forecasting, the SPoRT team supported damage assessment and response to Hurricane Superstorm Sandy by providing imagery that highlighted regions without power. The team used data from the Visible Infrared Imaging Radiometer Suite (VIIRS) on the Suomi National Polar-orbiting Partnership (Suomi NPP) satellite. The VIIRS low-light sensor, known as the day-night-band (DNB), can detect nighttime light from wildfires, urban and rural communities, and other human activity which emits light. It can also detect moonlight reflected from clouds and surface features. Using real time VIIRS data collected by our collaborative partner at the Space Science and Engineering Center of the University of Wisconsin, the SPoRT team created composite imagery to help detect power outages and restoration. This blackout imagery allowed emergency response teams from a variety of agencies to better plan and marshal resources for recovery efforts. The blackout product identified large-scale outages, offering a comprehensive perspective beyond a patchwork GIS mapping of outages that utility companies provide based on customer complaints. To support the relief efforts, the team provided its imagery to the USGS data portal, which the Federal Emergency Management Agency (FEMA) and other agencies used in their relief efforts. The team fs product helped FEMA, the U.S. Army Corps of Engineers, and U.S. Army monitor regions without power as part of their disaster response activities. Disaster responders used the images to identify possible outages and effectively distribute relief resources. An enhanced product is being developed and integrated into a web mapping service (WMS) for dissemination and use by a broader end user community.

Jedlovec, Gary↗

Tracing the Path of Carbon Export in the Ocean though DNA Sequencing of Individual Sinking Particles

Surface phytoplankton communities were linked with the carbon they export into the deep ocean by comparing 18 S rRNA gene sequence communities from surface seawater and individually isolated sinking particles. Particles were collected in sediment traps deployed at locations in the North Pacific subtropical gyre and the California Current. DNA was isolated from individual particles, bulk-collected trap particles, and the surface seawater. The relative sequence abundance of exported phytoplankton taxa in the surface water varied across functional groups and ecosystems. Of the sequences detected in sinking particles, about half were present in large (>300 μm), individually isolated particles and primarily belonged to taxa with small cell sizes (<50 μm). Exported phytoplankton taxa detected only in bulk trap samples, and thus presumably packaged in the smaller sinking size fraction, contained taxa that typically have large cell sizes (>500 m). The effect of particle degradation on the detectable 18 S rRNA gene community differed across taxa, and differences in community composition among individual particles from the same location largely reflected differences in relative degradation state. Using these data and particle imaging, we present an approach that incorporates genetic diversity into mechanistic models of the ocean's biological carbon pump, which will lead to better quantification of the ocean’s carbon cycle.

Carbon Expert↗

‘Flux+Mutability’: a conditional generative approach to one-class classification and anomaly detection

Abstract Anomaly Detection is becoming increasingly popular within the experimental physics community. At experiments such as the Large Hadron Collider, anomaly detection is growing in interest for finding new physics beyond the Standard Model. This paper details the implementation of a novel Machine Learning architecture, called Flux+Mutability, which combines cutting-edge conditional generative models with clustering algorithms. In the ‘flux’ stage we learn the distribution of a reference class. The ‘mutability’ stage at inference addresses if data significantly deviates from the reference class. We demonstrate the validity of our approach and its connection to multiple problems spanning from one-class classification to anomaly detection. In particular, we apply our method to the isolation of neutral showers in an electromagnetic calorimeter and show its performance in detecting anomalous dijets events from standard QCD background. This approach limits assumptions on the reference sample and remains agnostic to the complementary class of objects of a given problem. We describe the possibility of dynamically generating a reference population and defining selection criteria via quantile cuts. Remarkably this flexible architecture can be deployed for a wide range of problems, and applications like multi-class classification or data quality control are left for further exploration.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Extracellular DNA Alters Detection of Subtle Bacterial Responses to Soil Rewetting

Microbial communities are often characterized using DNA-based sequencing, but these approaches also capture extracellular DNA (exDNA) released from dead cells, potentially altering inference about microbial responses to environmental change. This may be especially important during pulse disturbances, such as soil drying–rewetting, which can increase microbial mortality and transient necromass pools. We assessed whether exDNA altered inference about bacterial responses to drying–rewetting (an 80 mm simulated rainfall event following a 28-day drought) in conventionally tilled corn and perennial switchgrass soils. We quantified bacterial abundance (16 S rRNA gene copies), alpha diversity, and community composition in paired soil samples with exDNA included (+ exDNA) and in samples treated with propidium monoazide (PMAxx) to reduce amplification of exDNA (− exDNA). At our level of replication (n = 4), PMAxx treatment did not significantly alter overall temporal response patterns (i.e., no significant main effect of DNA treatment or DNA × time interaction). However, PMAxx treatment increased sensitivity to detect some pairwise temporal changes in bacterial abundance and community composition in corn soils following rewetting. exDNA pools were proportionally highest immediately after rewetting in corn soils, suggesting transient extracellular DNA may contribute to masking during disturbance recovery. In contrast, PMAxx treatment had comparatively small effects in switchgrass soils, which exhibited weaker temporal responses overall. Inclusion of exDNA also changed which taxa appeared most responsive to rewetting. Together, our results suggest that exDNA does not uniformly bias soil microbial inference, but may reduce detectability of subtle disturbance-driven shifts in certain soils. Future studies should advance knowledge of microbial turnover and necromass dynamics, particularly using multiple complementary methods, to help predict when exDNA is most likely to influence ecological inference.

drying-rewetting↗

Quantum-Assisted Variational Segmentation for Image-to-Image Wildfire Detection Using Satellite Data

The quantum computing community has been searching for suitable applications to demonstrate the potential of near-term quantum devices. Quantum machine learning is a potential candidate, particularly using models that cannot be efficiently simulated with classical computers [1, 2]. This work focuses on a transition phase of quantum computers where the quantum machine learning model is still simulable classically but projected not to be simulable as the size of the model grows. Ultimately quantum computers may have advantages for high-dimensional real-world problems. Due to the limited number of qubits in current noisy intermediate-scale quantum (NISQ) devices, the direct application of quantum computers in high dimensional data is not feasible. To remedy this problem, an encoder-decoder architecture can be utilized. The encoder model would transform the high-dimensional data into a compact representation, to a level that small quantum computers can be used today (or in the near future), and the decoder would take the quantum processed outputs back to the high-dimensional space. Addressing the two challenges of quantum machine learning, this work investigates a hybrid supervised generative model with a quantum Ising Born machine embedded as the latent distribution. The model contains four main parts (Figure 1.a.): (1) a U-NET architecture responsible for learning segmentation flow, (2) a Prior network responsible for learning an encoded latent distribution of the input data, (3) a Born machine which represents the latent distribution, and (4) a Posterior network in charge of learning the joint encoded latent distribution of inputs and target data. The initial model, proposed by [3], is optimized by (1) maximizing the overlap of the prior and posterior latent distributions, and (2) minimizing the segmentation loss. The proposed model is designed to be investigated in a simulation environment applied to the real-world application of wildfire segmentation. Specifically, the model is designed to solve the patchy wildfire segmentations of Moderate Resolution Imaging Spectroradiometer (MODIS) by taking the MODIS observations and using Visible Infrared Imaging Radiometer Suite’s (VIIRS) consistent wildfire product as the target. The model solves patchy wildfire segmentations and provides insight into the epistemic errors sourced from model variation. The model utilizes the Born machine as a QUBO solver to represent the latent space as a Bernoulli distribution. The proposed configuration allows the variational segmentation model to leverage the true quantum probabilistic nature and derive a more expressive latent configuration, increasing the model performance in describing wildfire segmentations. The quantum probabilistic information of the Born machine is directly incorporated in the Kullback-Leibler divergence loss in the prior and posterior distributions, forcing the Bernoulli latent distribution to maximize the overlap of input and joint input-target distributions. The proposed model is then trained and compared with a baseline only consisting of direct Bernoulli latent distribution with no Born machine representing the latent space. The models are evaluated based on the segmentation metrics, such as precision, recall, intersect of union, with uncertainty boundaries accounting for the stochastic nature of the model. Our findings show that even in low latent-dimensional space (due to the limit in computational power of the classical quantum simulator), we are able to effectively capture the latent representation and hence the model performs better than the baseline. The findings are a projection for scaling the model into higher dimensional latent space with the Born machine surpassing the baseline performance. Figure 1. Sub-figure (a) demonstrates the architecture for the training phase. The model consists of a Prior and Posterior network that encode inputs and joint input-target data into compact representations, respectively. The Born machine represents the latent distribution, and the U-NET branch learns the segmentation patterns of the data. The stochasticity is introduced to the U-NET through its last layer to create meaningful but stochastic segmentations. Sub-figure (b) represents the inference phase where the model takes the stochastic behavior from the prior network and injects that into the U-NET. Each attempt of inference will generate different but similar segmentations from the same distribution of the wildfire event. REFERENCES [1] Coyle, B., Mills, D., Danos, V., & Kashefi, E. (2020). The Born supremacy: quantum advantage and training of an Ising Born machine. npj Quantum Information, 6(1), 1-11. [2] Liu, J. G., & Wang, L. (2018). Differentiable learning of quantum circuit born machines. Physical Review A, 98(6), 062324. [3] Kohl, S., Romera-Paredes, B., Meyer, C., De Fauw, J., Ledsam, J. R., Maier-Hein, K., ... & Ronneberger, O. (2018). A probabilistic u-net for segmentation of ambiguous images. Advances in neural information processing systems, 31.

quantum machine learning↗

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by current sequencing platforms may fail to recover heterogeneous strain populations and rare organisms. Here we used short (150-bp) and long (multi-kb) synthetic reads to evaluate strain heterogeneity and study microorganisms at low abundance in complex microbial communities from terrestrial sediments. The long-read data revealed multiple (probably dozens of) closely related species and strains from previously undescribed Deltaproteobacteria and Aminicenantes (candidate phylum OP8). Notably, these are the most abundant organisms in the communities, yet short-read assemblies achieved only partial genome coverage, mostly in the form of short scaffolds (N50 = ~2200 bp). Genome architecture and metabolic potential for these lineages were reconstructed using a new synteny-based method. Analysis of long-read data also revealed thousands of species whose abundances were <0.1% in all samples. Most of the organisms in this "long tail" of rare organisms belong to phyla that are also represented by abundant organisms. Genes encoding glycosyl hydrolases are significantly more abundant than expected in rare genomes, suggesting that rare species may augment the capability for carbon turnover and confer resilience to changing environmental conditions. Overall, the study showed that a diversity of closely related strains and rare organisms account for a major portion of the communities. These are probably common features of many microbial communities and can be effectively studied using a combination of long and short reads.

59 BASIC BIOLOGICAL SCIENCES↗

Multi-Detection Events, Probability Density Functions, and Reduced Location Area

Abstract Several efforts have been made in the Comprehensive Nuclear-Test-Ban Treaty (CTBT) community to assess the benefits of combining detections of radionuclides to improve the location estimates available from atmospheric transport modeling (ATM) backtrack calculations. We present a Bayesian estimation approach rather than a simple dilution field of regard approach to allow xenon detections and non-detections to be combined mathematically. This system represents one possible probabilistic approach to radionuclide event formation. Application of this method to a recent interesting radionuclide event shows a substantial reduction in the location uncertainty of that event.

atmospheric modeling↗

Ensuring Interoperability between UAS Detect-and-Avoid and Manned Aircraft Collision Avoidance

The UAS community in the United States has identified the need for a collision avoidance region in which UAS Detect-and-Avoid (DAA) vertical guidance is restricted to preclude interoperability issues with manned aircraft collision avoidance system vertical resolution advisories (RAs). This paper documents the process by which the collision avoidance region was defined. Three candidate definitions were evaluated on 1.3 million simulated pairwise encounters between UAS and manned aircraft covering a wide range of horizontal and vertical closure rates, angles, and miss distances. They were evaluated with regard to UAS DAA interoperability with manned aircraft collision avoidance systems in terms of: 1) the primary objective of restricting DAA vertical guidance before RAs when the aircraft are close, and 2) the secondary objective of avoiding unnecessary restrictions of DAA vertical guidance at a DAA alert when the aircraft are further apart. The collision avoidance region definition that fully achieves the primary objective and best achieves the secondary objective was recommended to and accepted by the UAS community in the United States. By this definition, UAS and manned aircraft are in the collision avoidance region--during which DAA vertical guidance is restricted--when the time to closest point of approach is less than 50 seconds and either the time to co-altitude is less than 50 seconds or the current vertical separation is less than 800 feet.

collision avoidance↗

Assessment of the Utility of the Oral Fluid and Plasma Proteome for Hydrocodone Usage

Non-medical use and abuse of prescription opioids is a growing problem in both the civilian and military communities, with minimal technologies for detecting hydrocodone use. This study explored the proteomic changes that occur in the oral fluid and blood plasma following controlled hydrocodone administration in twenty subjects. The global proteomic profile was determined for samples taken at four time points per subject of pre-exposure and 4, 6, or 168 hours post-exposure. The oral fluid samples analyzed herein provided greater differentiation between “baseline” and “response” time points than was observed with blood plasma, at least partially due to significant person-to-person variability in the plasma proteome. A total of 399 proteins were identified from oral fluid samples, and the abundance of 102 of those proteins was determined to be significantly different upon metabolism of hydrocodone (4 and 6 hour time points) as compared to baseline levels in the oral fluid (pre-dose and 168 hour). This is the first, to our knowledge, assessment of the oral fluid and blood plasma proteome following hydrocodone administration, which demonstrates the potential of oral fluid as a non-invasive sample that may reveal features of hydrocodone or other opioid use and/or misuse.

Kaiser, Brooke LD↗

Interactive Effects of Microbes and Nitrogen on Panicum virgatum Root Functional Traits and Patterns of Phenotypic Selection

Premise of research. Plants in natural and agricultural systems are influenced in myriad ways by their microbial communities, particularly by providing goods and services that change plant functional traits. Microbes are considered an influential part of the environmental context that change plant trait expression, but often, microbe-mediated effects are contingent on local resources, such as nitrogen. Here, we ask how microbes and nitrogen affect belowground functional traits and patterns of phenotypic selection. Methodology. We performed a fully factorial greenhouse experiment with switchgrass (Panicum virgatum), manipulating microbial community composition and nitrogen availability. We measured plant performance and belowground functional traits and performed 16S amplicon sequencing of the root-associated microbial communities. We looked for correlations between microbial taxa and root functional traits, and we performed phenotypic selection analysis on five belowground functional traits to determine how traits affect plant relative performance across biotic and abiotic contexts. Pivotal results. All belowground plant functional traits except root tissue density were affected by adding nitrogen. We found that a microbial taxon (amplicon sequence variant [ASV]) in the genus Micromonospora correlated with shorter root lengths. We also found strong positive selection for longer roots regardless of the abiotic or biotic environment. In contrast, selection favored lower root-to-shoot ratios in high-nitrogen conditions, and selection on root tissue density was highest in treatments that had high nitrogen levels and perturbed microbial communities. Conclusions. We did not detect microbial effects on the expression of plant traits (ecological effects); however, patterns of phenotypic selection (evolutionary effects) on root tissue density differed depending on the biotic and abiotic environment. Additionally, we detected strong selection for increased root length across treatments; we also found that one ASV correlated with decreased root length, indicating potential conflict between root microbiome components and plant fitness. Future work would be to include microbial taxa in phenotypic selection analysis and to conduct manipulations of the microbes correlated with functional traits to determine causality.

59 BASIC BIOLOGICAL SCIENCES↗

Bio‐Imaging quorum sensing signal molecules in a soil‐mimic gel

Rhizosphere, the narrow region surrounding plant roots directly influenced by root exudates and the root associated microbiome, plays an important role in plant productivity and the rhizosphere is well known for stimulating microbial metabolic activities. How microbial communities interact to form stable, metabolically interconnected functional communities is an area of intense interest. The question remains on how microbially produced secreted molecules that function as intercellular communication signals shape the structure and function of microbial communities. Our goal is to detect and quantify signal molecules produced by microbes or plants in the root‐soil environment, spatially and temporarily. As a proof‐of‐concept, we are imaging diffusible extracellular microbial metabolites involved in a bacteria‐bacteria communication process called quorum‐sensing. Quorum‐sensing relies on the accumulation of high concentrations of signal molecules in the environment to control bacterial gene expression, influencing rhizosphere colonization and plant health. Local concentration of quorum sensing molecules are determined using aptamer based sensors. Aptamers that can specifically bind the desired signal molecules are selected through SELEX and immobilized on the surface of nano‐porous membranes. Binding of the signal molecules and aptamer covered surface results in changes in surface charge distribution and steric hinderance and thus modifying the transmembrane ionic transport. Changes in transmembrane impedance can be measured through electrochemical impedance spectroscopy methods to monitor local concentrations of signal molecules. Sensor responses were determined for different concentrations of signal molecules and results showed detection of C4‐HSL in a soil‐mimic solution with K D of 10 nM. We demonstrate that the quorum‐sensing signal molecule C4‐homoserine lactone and (C4‐HSL) can rapidly diffuse in a soil‐mimic gel, providing evidence for our use of a soil‐mimic for further aptasensor development and validation. The sensors were then inserted into soil mimic gel for monitoring C4‐HSL diffusion and the resulted impedance changes were used to determine the C4‐HSL concentration at different positions in the gel. Measurements of local C4‐HSL concentrations variation and numerical solution of diffusion equation were used to create 4D images of C4‐HSL molecule diffusion in the soil‐mimic gel.

Jiang, Nianyu↗

The CommonGround Visual Paradigm for Biosurveillance

Biosurveillance is a critical area in the intelligence community for real-time detection of disease outbreaks. Identifying epidemics enables analysts to detect and monitor disease outbreaks that might be spread from natural causes or from possible biological warfare attacks. Containing these events and disseminating alerts requires the ability to rapidly find, classify and track harmful biological signatures. In this paper, we describe a novel visual paradigm to conduct biosurveillance using an Infectious Disease Weather Map. Our system provides a visual common ground in which users can view, explore and discover emerging concepts and correlations such as symptoms, syndromes, pathogens, and geographic locations.

Livnat, Yarden↗

Cryogenic optical beam steering for superconducting device calibration

We have developed a calibration system based on a micro-electromechanical systems (MEMS) mirror that is capable of delivering an optical beam over a wavelength range of 180 -- 2000 nm (0.62 -- 6.89 eV) in a sub-Kelvin environment. This portable, integrated system can steer the beam over a $\sim$3 cm $\times$ 3 cm area on the surface of any sensor with a precision of $\sim$100 $μ$m, enabling characterization of device response as a function of position. This fills a critical need in the landscape of calibration tools for sub-Kelvin devices, including those used for dark matter detection and quantum computing. These communities have a shared goal of understanding the impact of ionizing radiation on device performance, which can be pursued with our system. This paper describes the design of the first-generation calibration system and the results from successfully testing its performance at room temperature and 20 mK.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Methodological Guidelines for Accurate Detection of Viruses in Wild Plant Species

Here ecological understanding of disease risk, emergence, and dynamics and of the efficacy of control strategies relies heavily on efficient tools for microorganism identification and characterization. Misdetection, such as the misclassification of infected hosts as healthy, can strongly bias estimates of disease prevalence and lead to inaccurate conclusions. In natural plant ecosystems, interest in assessing microbial dynamics is increasing exponentially, but guidelines for detection of microorganisms in wild plants remain limited, particularly so for plant viruses. To address this gap, we explored issues and solutions associated with virus detection by serological and molecular methods in noncrop plant species as applied to the globally important Barley yellow dwarf virus PAV ( Luteoviridae ), which infects wild native plants as well as crops. With enzyme-linked immunosorbent assays (ELISA), we demonstrate how virus detection in a perennial wild plant species may be much greater in stems than in leaves, although leaves are most commonly sampled, and may also vary among tillers within an individual, thereby highlighting the importance of designing effective sampling strategies. With reverse transcription-PCR (RT-PCR), we demonstrate how inhibitors in tissues of perennial wild hosts can suppress virus detection but can be overcome with methods and products that improve isolation and amplification of nucleic acids. These examples demonstrate the paramount importance of testing and validating survey designs and virus detection methods for noncrop plant communities to ensure accurate ecological surveys and reliable assumptions about virus dynamics in wild hosts.

59 BASIC BIOLOGICAL SCIENCES↗

Response of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus × Giganteus Cultivated Soil to Different Nitrogen Fertilization Rates

Miscanthus × giganteus is a promising high-yielding perennial plant to meet growing bioenergy demands; however, the degree to which the soil microbiome affects its nitrogen cycling and subsequently, biomass yield remains unclear. In this study, we hypothesize that contributions of metabolically active soil microbial membership may be underestimated with DNA-based approaches. We assessed the response of the soil microbiome to nitrogen availability in terms of both DNA and RNA soil microbial communities from the Long-term Assessment of Miscanthus Productivity and Sustainability (LAMPS) field trial. DNA and RNA were extracted from 271 samples, and 16S small subunit (SSU) rRNA amplicon sequencing was performed to characterize microbial community structure. Significant differences were observed in the resulting soil microbiomes and were best explained by the sequencing library of origin, either DNA or RNA. Similar numbers of membership were detected in DNA and RNA microbial communities, with more than 90% of membership shared. However, the profile of dominant membership within DNA and RNA differed, with varying proportions of Actinobacteria and Proteobacteria and Firmicutes and Proteobacteria. Only RNA microbial communities showed seasonal responses to nitrogen fertilization, and these differences were associated with nitrogen-cycling bacteria. The relative abundance of bacteria associated with nitrogen cycling was 7-fold higher in RNA than in DNA, and genes associated with denitrifying bacteria were significantly enriched in RNA, suggesting that these bacteria may be underestimated with DNA-only approaches. Our findings indicate that RNA-based SSU characterization can be a significant and complementing resource for understanding the role of soil microbiomes in bioenergy crop production.

59 BASIC BIOLOGICAL SCIENCES↗

Large-Scale Test of Dynamic Correlation Processors: Implications for Correlation-Based Seismic Pipelines

Correlation detectors are of considerable interest to the seismic monitoring communities because they offer reduced detection thresholds and combine detection, location and identification functions into a single operation. They appear to be ideal for applications requiring screening of frequent repeating events. However, questions remain about how broadly empirical correlation methods are applicable. We describe the effectiveness of banks of correlation detectors in a system that combines traditional power detectors with correlation detectors in terms of efficiency, which we define to be the fraction of events detected by the correlators. This paper elaborates and extends the concept of a dynamic correlation detection framework – a system which autonomously creates correlation detectors from event waveforms detected by power detectors; and reports observed performance on a network of arrays in terms of efficiency. We performed a large scale test of dynamic correlation processors on an 11 terabyte global dataset using 25 arrays in the single frequency band 1-3 Hz. The system found over 3.2 million unique signals and produced 459,747 screened detections. A very satisfying result is that, on average, efficiency grows with time and, after nearly 16 years of operation, exceeds 47% for events observed over all distance ranges and approaches 70% for near regional and 90% for local events. This observation suggests that future pipeline architectures should make extensive use of correlation detectors, principally for decluttering observations of local and near-regional events. Our results also suggest that future operations based on correlation detection will require commodity large-scale computing infrastructure, since the numbers of correlators in an autonomous system can grow into the hundreds of thousands.

47 OTHER INSTRUMENTATION↗