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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Panda: A Compiler Framework for Concurrent CPU $+$ GPU Execution of 3D Stencil Computations on GPU-accelerated Supercomputers

We present a new compiler framework for truly heterogeneous 3D stencil computation on GPU clusters. Our framework consists of a simple directive-based programming model and a tightly integrated source-to-source compiler. Annotated with a small number of directives, sequential stencil C codes can be automatically parallelized for large-scale GPU clusters. The most distinctive feature of the compiler is its capability to generate hybrid MPI$+$ CUDA$+$ OpenMP code that uses concurrent CPU$+$ GPU computing to unleash the full potential of powerful GPU clusters. The auto-generated hybrid codes hide the overhead of various data motion by overlapping them with computation. Test results on the Titan supercomputer and the Wilkes cluster show that auto-translated codes can achieve about 90 % of the performance of highly optimized handwritten codes, for both a simple stencil benchmark and a real-world application in cardiac modeling. The user-friendliness and performance of our domain-specific compiler framework allow harnessing the full power of GPU-accelerated supercomputing without painstaking coding effort.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

A high-fidelity method to analyze perturbation evolution in turbulent flows

Small perturbation propagation in fluid flows is usually examined by linearizing the governing equations about a steady basic state. It is often useful, however, to study perturbation evolution in the unsteady evolving turbulent environment. Such analyses can elucidate the role of perturbations in the generation of coherent structures or the production of noise from jet turbulence. The appropriate equations are still the linearized Navier–Stokes equations, except that the linearization must be performed about the instantaneous evolving turbulent state, which forms the coefficients of the linearized equations. This is a far more difficult problem since in addition to the turbulent state, its rate of change and the perturbation field are all required at each instant. In this paper, we develop and use a novel technique for this problem by using a pair (denoted “baseline” and “twin”) of simultaneous synchronized Large-Eddy Simulations (LES). At each time-step, small disturbances whose propagation characteristics are to be studied, are introduced into the twin through a forcing term. At subsequent time steps, the difference between the two simulations is shown to be equivalent to solving the forced Navier–Stokes equations, linearized about the instantaneous turbulent state. The technique does not put constraints on the forcing, which could be arbitrary, e.g., white noise or other stochastic variants. We consider, however, “native” forcing having properties of disturbances that exist naturally in the turbulent environment. The method then isolates the effect of turbulence in a particular region on the rest of the field, which is useful in the study of noise source localization. The synchronized technique is relatively simple to implement into existing codes. In addition to minimizing the storage and retrieval of large time-varying datasets, it avoids the need to explicitly linearize the governing equations, which can be a very complicated task for viscous terms or turbulence closures. The method is illustrated by application to a well-validated Mach 1.3 jet. Specifically, the effects of turbulence on the jet lipline and core collapse regions on the near-acoustic field are isolated. The properties of the method, including linearity and effect of initial transients, are discussed. The results provide insight into how turbulence from different parts of the jet contribute to the observed dominance of low and high frequency content at shallow and sideline angles, respectively.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Implementation of McMurchie–Davidson Algorithm for Gaussian AO Integrals Suited for SIMD Processors

We report an implementation of the McMurchie− Davidson evaluation scheme for 1- and 2-particle Gaussian AO integrals designed for processors with Single Instruction Multiple Data (SIMD) instruction sets. Like in our recent MD implementation for graphical processing units (GPUs) [Asadchev, A.; Valeev, E. F.. J. Chem. Phys. 2024, 160, 244109.], variable-sized batches of shellsets of integrals are evaluated at a time. By optimizing for the floating point instruction throughput rather than minimizing the number of operations, this approach achieves up to 50% of the theoretical hardware peak FP64 performance for many common SIMD-equipped platforms (AVX2, AVX512, NEON), which translates to speedups of up to 30 over the state-of-the-art one-shellset-at-a-time implementation of Obara−Saika-type schemes in Libint for a variety of primitive and contracted integrals. As with our previous work, we rely on the standard C++ programming language such as the std::simd standard library feature to be included in the 2026 ISO C++ standard without any explicit code generation to keep the code base small and portable. The implementation is part of the open source LibintX library freely available at https://github.com/ValeevGroup/libintx.

Basis sets↗
DOE OSTI2014

Simulation of the alpha particle heating and the helium ash source in an International Thermonuclear Experimental Reactor-like tokamak with an internal transport barrier

A guiding center orbit following code, which incorporates a set of non-singular coordinates for orbit integration, was developed and applied to investigate the alpha particle heating in an ITER-like tokamak with an internal transport barrier. It is found that a relatively large q (safety factor) value can significantly broaden the alpha heating profile in comparison with the local heating approximation; this broadening is due to the finite orbit width effects; when the orbit width is much smaller than the scale length of the alpha particle source profile, the heating profile agrees with the source profile, otherwise, the heating profile can be significantly broadened. It is also found that the stagnation particles move to the magnetic axis during the slowing-down process, thus the effect of stagnation orbits is not beneficial to the helium ash removal. The source profile of helium ash is broadened in comparison with the alpha source profile, which is similar to the heating profile.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Design and physics basis for the upcoming DIII-D SAS-VW campaign to quantify tungsten leakage and transport in a new slot divertor geometry

A set of experiments are planned to exploit the high SOL collisionality enabled by a tightly baffled slot divertor geometry to suppress tungsten leakage in DIII-D. A toroidal row of graphite tiles from the Small Angle Slot (SAS) divertor is being coated with 10–15 μ m of tungsten. New spectroscopic viewing chords with in-vacuo optics will measure the W gross erosion source from the divertor surface with high spatial and temporal resolution. In parallel, the bottom of the SAS divertor is changed from a flat to a ‘V’ shape. New SOLPS-ITER/DIVIMP simulations conducted with drifts using the planned ‘V’ shape predict a substantial reduction in W sourcing and SOL accumulation in either B × ∇B direction relative to either the old SAS divertor shape or the open, lower divertor. Dedicated studies are planned to carefully characterize the level of W sourcing, leakage, and scrape-off-layer (SOL) accumulation in DIII-D over a wide range of plasma scenarios. Various actuators will be assessed for their efficacy in further reducing high-Z impurity sources and leakage from the slot divertor geometry. Finally, this coupled code-experiment validation effort will be used to stress-test physics models and build confidence in extrapolations to advanced, high-Z divertor geometries for next-step devices.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

ExaWind: A multifidelity modeling and simulation environment for wind energy

We introduce the open-source ExaWind modeling and simulation environment for wind energy. The primary physics codes of ExaWind are Nalu-Wind and OpenFAST. Nalu-Wind is a wind-focused computational fluid dynamics (CFD) code that is coupled to the whole-turbine simulation code OpenFAST. The ExaWind environment was created under U.S. Department of Energy funding to achieve the highest-fidelity simulations of wind turbines and wind farms to date, with the goal of enabling disruptive changes to turbine and plant design and operation. Innovation will be gleaned through better understanding of the complex flow dynamics in wind farms, including wake evolution and the impact of wakes on downstream turbines and turbulent flow from complex terrain. High-fidelity predictive simulations employ hybrid turbulence models, geometry/boundary-layer-resolving CFD meshes, atmospheric turbulence, nonlinear structural dynamics, and fluid-structure interaction. While there is an emphasis on very high-fidelity simulations (e.g., blade resolved with full fluid-structure coupling), the ExaWind environment supports lower-fidelity modeling capabilities including actuator-line and -disk methods. Important in the development of ExaWind codes is that the codes scale well on today's largest petascale supercomputers and on the next-generation platforms that will enable exascale computing.

17 WIND ENERGY↗
DOE OSTI2025

Towards Automated Reasoning Chains for Verification of LLM-Generated Scientific Code

With the rise of Large Language Model (LLM) generated code, including in domains like scientific computing, ensuring not only syntactical, but also mathematical correctness, has become a critical task. Traditional formal methods approaches often struggle with the ambiguity of floating-point code, and full symbolic execution is extremely costly and limited. We propose a chain-of-reasoning approach that iteratively lifts basic semantics from code into the SPIRAL system and then establishes numerical equivalency to the desired mathematical operation. Here, we leverage the ample mathematical knowledge already formalized in SPIRAL to enable the system to recognize not just different implementations of the same algorithm but fully separate approaches to solving the given problem. The chain establishes tight error bounds on the output of given code with respect to the true continuous solution it approximates, quantifying all sources of error. We demonstrate this approach by establishing the correctness of a pseudospectral solver for a simple 1-dimensional Poisson problem.

Oschatz, Quentin [Carnegie Mellon University,Pitts↗
DOE OSTI2016

OpenACC to FPGA: A Framework for Directive-based High-Performance Reconfigurable Computing

This paper presents a directive-based, high-level programming framework for high-performance reconfigurable computing. It takes a standard, portable OpenACC C program as input and generates a hardware configuration file for execution on FPGAs. We implemented this prototype system using our open-source OpenARC compiler; it performs source-to-source translation and optimization of the input OpenACC program into an OpenCL code, which is further compiled into a FPGA program by the backend Altera Offline OpenCL compiler. Internally, the design of OpenARC uses a high- level intermediate representation that separates concerns of program representation from underlying architectures, which facilitates portability of OpenARC. In fact, this design allowed us to create the OpenACC-to-FPGA translation framework with minimal extensions to our existing system. In addition, we show that our proposed FPGA-specific compiler optimizations and novel OpenACC pragma extensions assist the compiler in generating more efficient FPGA hardware configuration files. Our empirical evaluation on an Altera Stratix V FPGA with eight OpenACC benchmarks demonstrate the benefits of our strategy. To demonstrate the portability of OpenARC, we show results for the same benchmarks executing on other heterogeneous platforms, including NVIDIA GPUs, AMD GPUs, and Intel Xeon Phis. This initial evidence helps support the goal of using a directive-based, high-level programming strategy for performance portability across heterogeneous HPC architectures.

Lee, Seyong↗
DOE OSTI2026

Neural-Network-Enhanced COTSIM: Advancing Predictive Capabilities for Fast DIII-D Simulations

Sustaining fusion reactions in tokamaks requires heating plasma to thermonuclear temperatures while maintaining confinement and stability. Neutral beam injection (NBI) provides heating, current drive, torque, and fueling, while electron cyclotron (EC) waves are widely used for heating and current drive; together, these actuators shape the plasma current, temperature, and density profiles. The control-oriented tokamak simulator (COTSIM), a predictive, control-oriented code, has been enhanced with neural-network surrogates for transport and sources. Turbulent transport is predicted by MMMnet—a neural-network version of the updated multimode model (MMM 9.0.10)—with significantly reduced computation time relative to MMM; neoclassical transport follows the Chang–Hinton model. NUBEAMnet, a surrogate of the Monte Carlo NUBEAM module, predicts beam-driven heating, current, and torque. EC heating and current drive use a control-oriented, empirically scaled source model; plasma resistivity follows the Spitzer formulation; bootstrap current uses the Sauter model. Equilibrium is computed using both prescribed and fixed-boundary solvers (FBSs), and the pedestal structure is modeled with an empirical pedestal model. For a representative DIII-D discharge, COTSIM predicts electron and ion temperature and safety-factor profiles in close agreement with TRANSP predictive and interpretive simulations while extending predictions through the pedestal region to the plasma edge (versus 80% of the minor radius in TRANSP). Furthermore, the equivalent COTSIM simulation runs in under 3 min compared to about 2 h for TRANSP, enabling rapid scenario planning, optimization of tokamak operation, and between-pulse control design.

Control-oriented tokamak simulator (COTSIM)↗
DOE OSTI2022

The Latent Dirichlet Allocation model applied to airborne LiDAR data: A case study on mapping forest degradation associated with fragmentation and fire in the Amazon region

1. LiDAR data are being increasingly used to provide a detailed characterization of the vertical profile of forests. This characterization enables the generation of new insights on the influence of environmental drivers and anthropogenic disturbances on forest structure as well as on how forest structure influences important ecosystem functions and services. Unfortunately, extracting information from LiDAR data in a way that enables the spatial visualization of forest structure, as well as its temporal changes, is challenging due to the high dimensionality of these data. 2. In this study, we show how the Latent Dirichlet Allocation model applied to LiDAR data (LidarLDA) can be used to identify forest structural types and how the relative abundance of these forest types changes throughout the landscape. The code to fit this model is made available through the open-source r package LidarLDA in github. We illustrate the use of LidarLDA both with simulated data and data from a large-scale fire experiment in the Brazilian Amazon region. 3. Using simulated data, we demonstrate that LidarLDA accurately identifies the number of forest types as well as their spatial distribution and absorptance probabilities. For the empirical data, we found that LidarLDA detects both landscape-level patterns in forest structure as well as the strong interacting effect of fire and forest fragmentation on forest structure based on the experimental fire plots. More specifically, LidarLDA reveals that proximity to forest edge exacerbates the impact of fires, and that burned forests remain structurally different from unburned areas for at least 7 years, even when burned only once. Importantly, LidarLDA generates insights on the 3D structure of forest that cannot be obtained using more standard approaches that just focus on top-of-the-canopy information (e.g. canopy height models based on LiDAR data). 4. By enabling the mapping of forest structure and its temporal changes, we believe that LidarLDA will be of broad utility to the ecological research community.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

SU-E-T-314: The Application of Cloud Computing in Pencil Beam Scanning Proton Therapy Monte Carlo Simulation

Purpose: Monte Carlo simulation plays an important role for proton Pencil Beam Scanning (PBS) technique. However, MC simulation demands high computing power and is limited to few large proton centers that can afford a computer cluster. We study the feasibility of utilizing cloud computing in the MC simulation of PBS beams. Methods: A GATE/GEANT4 based MC simulation software was installed on a commercial cloud computing virtual machine (Linux 64-bits, Amazon EC2). Single spot Integral Depth Dose (IDD) curves and in-air transverse profiles were used to tune the source parameters to simulate an IBA machine. With the use of StarCluster software developed at MIT, a Linux cluster with 2–100 nodes can be conveniently launched in the cloud. A proton PBS plan was then exported to the cloud where the MC simulation was run. Results: The simulated PBS plan has a field size of 10×10cm{sup 2}, 20cm range, 10cm modulation, and contains over 10,000 beam spots. EC2 instance type m1.medium was selected considering the CPU/memory requirement and 40 instances were used to form a Linux cluster. To minimize cost, master node was created with on-demand instance and worker nodes were created with spot-instance. The hourly cost for the 40-node cluster was $0.63 and the projected cost for a 100-node cluster was $1.41. Ten million events were simulated to plot PDD and profile, with each job containing 500k events. The simulation completed within 1 hour and an overall statistical uncertainty of < 2% was achieved. Good agreement between MC simulation and measurement was observed. Conclusion: Cloud computing is a cost-effective and easy to maintain platform to run proton PBS MC simulation. When proton MC packages such as GATE and TOPAS are combined with cloud computing, it will greatly facilitate the pursuing of PBS MC studies, especially for newly established proton centers or individual researchers.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2014

SU-E-T-327: The Update of a XML Composing Tool for TrueBeam Developer Mode

Purpose: To introduce a major upgrade of a novel XML beam composing tool to scientists and engineers who strive to translate certain capabilities of TrueBeam Developer Mode to future clinical benefits of radiation therapy. Methods: TrueBeam Developer Mode provides the users with a test bed for unconventional plans utilizing certain unique features not accessible at the clinical mode. To access the full set of capabilities, a XML beam definition file accommodating all parameters including kV/MV imaging triggers in the plan can be locally loaded at this mode, however it is difficult and laborious to compose one in a text editor. In this study, a stand-along interactive XML beam composing application, TrueBeam TeachMod, was developed on Windows platforms to assist users in making their unique plans in a WYSWYG manner. A conventional plan can be imported in a DICOM RT object as the start of the beam editing process in which trajectories of all axes of a TrueBeam machine can be modified to the intended values at any control point. TeachMod also includes libraries of predefined imaging and treatment procedures to further expedite the process. Results: The TeachMod application is a major of the TeachMod module within DICOManTX. It fully supports TrueBeam 2.0. Trajectories of all axes including all MLC leaves can be graphically rendered and edited as needed. The time for XML beam composing has been reduced to a negligible amount regardless the complexity of the plan. A good understanding of XML language and TrueBeam schema is not required though preferred. Conclusion: Creating XML beams manually in a text editor will be a lengthy error-prone process for sophisticated plans. A XML beam composing tool is highly desirable for R and D activities. It will bridge the gap between scopes of TrueBeam capabilities and their clinical application potentials.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2014

SU-E-T-419: Workflow and FMEA in a New Proton Therapy (PT) Facility

Purpose: Workflow is an important component in the operational planning of a new proton facility. By integrating the concept of failure mode and effect analysis (FMEA) and traditional QA requirements, a workflow for a proton therapy treatment course is set up. This workflow serves as the blue print for the planning of computer hardware/software requirements and network flow. A slight modification of the workflow generates a process map(PM) for FMEA and the planning of QA program in PT. Methods: A flowchart is first developed outlining the sequence of processes involved in a PT treatment course. Each process consists of a number of sub-processes to encompass a broad scope of treatment and QA procedures. For each subprocess, the personnel involved, the equipment needed and the computer hardware/software as well as network requirements are defined by a team of clinical staff, administrators and IT personnel. Results: Eleven intermediate processes with a total of 70 sub-processes involved in a PT treatment course are identified. The number of sub-processes varies, ranging from 2-12. The sub-processes within each process are used for the operational planning. For example, in the CT-Sim process, there are 12 sub-processes: three involve data entry/retrieval from a record-and-verify system, two controlled by the CT computer, two require department/hospital network, and the other five are setup procedures. IT then decides the number of computers needed and the software and network requirement. By removing the traditional QA procedures from the workflow, a PM is generated for FMEA analysis to design a QA program for PT. Conclusion: Significant efforts are involved in the development of the workflow in a PT treatment course. Our hybrid model of combining FMEA and traditional QA program serves a duo purpose of efficient operational planning and designing of a QA program in PT.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2014

Poster — Thur Eve — 52: A Web-based Platform for Collaborative Document Management in Radiotherapy

We describe DepDocs, a web-based platform that we have developed to manage the committee meetings, policies, procedures and other documents within our otherwise paperless radiotherapy clinic. DepDocs is essentially a document management system based on the popular Drupal content management software. For security and confidentiality, it is hosted on a linux server internal to our hospital network such that documents are never sent to the cloud or outside of the hospital firewall. We used Drupal's in-built role-based user rights management system to assign a role, and associated document editing rights, to each user. Documents are accessed for viewing using either a simple Google-like search or by generating a list of related documents from a taxonomy of categorization terms. Our system provides document revision tracking and an document review and approval mechanism for all official policies and procedures. Committee meeting schedules, agendas and minutes are maintained by committee chairs and are restricted to committee members. DepDocs has been operational within our department for over six months and has already 45 unique users and an archive of over 1000 documents, mostly policies and procedures. Documents are easily retrievable from the system using any web browser within our hospital's network.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2015

SU-E-J-08: Comparison of Unintended Radiation Doses to Organs at Risk Resulting From the Out-Of-Field Therapeutic Beams and From Image-Guidance X-Ray Procedures

Purpose: The unintended radiation dose to organs at risk (OAR) can be contributed from imaging guidance procedures as well as from leakage and scatter of therapeutic beams. This study compares the imaging dose with the unintended out-of-field therapeutic dose to patient sensitive organs. Methods: The Monte Carlo EGSnrc user codes, BEAMnrc and DOSXYZnrc, were used to simulate kV X-ray sources from imaging devices as well as the therapeutic IMRT/VMAT beams and to calculate doses to target and OARs on patient treatment planning CT images. The accuracy of the Monte Carlo simulations was benchmarked against measurements in phantoms. The dose-volume histogram was utilized in analyzing the patient organ doses. Results: The dose resulting from Standard Head kV-CBCT scans to bone and soft tissues ranges from 0.7 to 1.1 cGy and from 0.03 to 0.3 cGy, respectively. The dose resulting from Thorax scans on the chest to bone and soft tissues ranges from 1.1 to 1.8 cGy and from 0.3 to 0.6 cGy, respectively. The dose resulting from Pelvis scans on the abdomen to bone and soft tissues range from 3.2 to 4.2 cGy and from 1.2 to 2.2 cGy, respectively. The out-of-field doses to OAR are sensitive to the distance between the treated target and the OAR. For a typical Head-and-Neck IMRT/VMAT treatment the out-of-field doses to eyes are 1–3% of the target dose, or 2–6 cGy per fraction. Conclusion: The imaging doses to OAR are predictable based on the imaging protocols used when OARs are within the imaged volume and can be estimated and accounted for by using tabulated values. The unintended out-of-field doses are proportional to the target dose, strongly depend on the distance between the treated target and OAR, and are generally higher comparing to the imaging dose. This work was partially supported by Varian research grant VUMC40590.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

MO-D-213-07: RadShield: Semi- Automated Calculation of Air Kerma Rate and Barrier Thickness

Purpose: To develop the first Java-based semi-automated calculation program intended to aid professional radiation shielding design. Air-kerma rate and barrier thickness calculations are performed by implementing NCRP Report 147 formalism into a Graphical User Interface (GUI). The ultimate aim of this newly created software package is to reduce errors and improve radiographic and fluoroscopic room designs over manual approaches. Methods: Floor plans are first imported as images into the RadShield software program. These plans serve as templates for drawing barriers, occupied regions and x-ray tube locations. We have implemented sub-GUIs that allow the specification in regions and equipment for occupancy factors, design goals, number of patients, primary beam directions, source-to-patient distances and workload distributions. Once the user enters the above parameters, the program automatically calculates air-kerma rate at sampled points beyond all barriers. For each sample point, a corresponding minimum barrier thickness is calculated to meet the design goal. RadShield allows control over preshielding, sample point location and material types. Results: A functional GUI package was developed and tested. Examination of sample walls and source distributions yields a maximum percent difference of less than 0.1% between hand-calculated air-kerma rates and RadShield. Conclusion: The initial results demonstrated that RadShield calculates air-kerma rates and required barrier thicknesses with reliable accuracy and can be used to make radiation shielding design more efficient and accurate. This newly developed approach differs from conventional calculation methods in that it finds air-kerma rates and thickness requirements for many points outside the barriers, stores the information and selects the largest value needed to comply with NCRP Report 147 design goals. Floor plans, parameters, designs and reports can be saved and accessed later for modification and recalculation. We have confirmed that this software accurately calculates air-kerma rates and required barrier thicknesses for diagnostic radiography and fluoroscopic rooms.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2017

Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline

The dinitrogenase reductase gene ( nifH ) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. Furthermore, the developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field. IMPORTANCE: Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. Thus, the utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.

59 BASIC BIOLOGICAL SCIENCES↗