Results for “community detection” — Page 4

DOE OSTI2025

Inter-Kingdom Viral Interactions

Please cite as : Josué A. Rodríguez-Ramos, Amy E. Zimmerman, Ruonan Wu, Sheryl Bell, Trinidad Alfaro, Kirsten Hofmockel, William C. Nelson. 2025. Inter-Kingdom Viral Interactions. [Data Set] PNNL DataHub. This data is published under a CC0 license. The authors encourage data reuse and request attribution by referencing the above citations for the data package and associated manuscript. Deciphering viral ecology in soils is challenging due to their high physiochemical and community complexity. To enhance detection of sub-communities of DNA and RNA viruses, we applied fractionation approaches to soils collected across a moisture gradient from a grassland field experiment. Analyses included metagenomics and metatranscriptomics of size-fractionated extracellular viruses (i.e., DNA and RNA viromes), metagenomics of bacteria/archaea- or eukaryote-enriched samples, and whole soil metatranscriptomes with rRNA-depletion or polyadenylation enrichment. While RNA virome and whole soil RNA methods captured similar viral diversity, RNA viromes identified longer, higher-quality genomes. Further, we showed that significantly more DNA viruses were active in higher moisture than lower moisture samples, whereas responses by overall diversity vary by genome type (DNA versus RNA genomes). Finally, we demonstrate the power of fractionation approaches for identifying distinct viral communities that infect unique hosts, which has significant implications for ecological investigations, particularly related to interkingdom interactions.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1970

Detection and identification of benthic communities and shoreline features in Biscayne Bay

Progress made in the development of a technique for identifying and delinating benthic and shoreline communities using multispectral imagery is described. Images were collected with a multispectral scanner system mounted in a C-47 aircraft. Concurrent with the overflight, ecological ground- and sea-truth information was collected at 19 sites in the bay and on the shore. Preliminary processing of the scanner imagery with a CDC 1604 digital computer provided the optimum channels for discernment among different underwater and coastal objects. Automatic mapping of the benthic plants by multiband imagery and the mapping of isotherms and hydrodynamic parameters by digital model can become an effective predictive ecological tool when coupled together. Using the two systems, it appears possible to predict conditions that could adversely affect the benthic communities. With the advent of the ERTS satellites and space platforms, imagery data could be obtained which, when used in conjunction with water-level and meteorological data, would provide for continuous ecological monitoring.

Kolipinski, M. C.↗

NASA NTRS1975

Factors affecting the noise from small propeller driven aircraft

The factors affecting noise from small propeller driven airplanes are reviewed to quantify their affects where possible, and to indicate the potential for noise reduction. The main sources of external noise are noted to be the propellers and engines; the airframe being of less importance for both aural detection and community annoyance. Propeller noise is a strong function of tip speed and is affected adversely by nonuniform inflows. Reciprocating engine exhausts are noisier than those of comparably rated turboshaft engines, but their noise can be reduced by the use of flight certified exhaust mufflers. Presently, there are no generally accepted engineering methods for development of optimized propellers and exhaust muffler designs from weight and performance penalty standpoints. Flight demonstration results, however, suggest that required noise reductions for future certification should be possible with potentially small penalties.

Maglieri, D. J.↗

NASA NTRS1981

Sound measurements of the MOD-2 wind turbine generator

Sound measurements were made for the MOD-2 wind turbine generator for wind conditions of 7.6 to 13.4 m/sec and for output power ratings of about 1 to 2 NW. Both broad band and narrow band data wre obtained for a range of distances and azimuth angles from the machine. The rotor sound spectra are random in character and peak in the frequency ranges 30 to 50 Hz and 800 to 1300 Hz. Both peaks are predictable from experience with helicopter rotors and propellers. Results suggest that the lower frequency peak is due to the effects of inflow turbulence and the higher frequency peak is due to the interactions of the turbulent boundary layers with the trailing edges of the blades. The boundary layer related sound is the dominant component in the audible frequency range and determines the detectability of the machine. It could be detected at a distance of 1350 m in the upwind direction where the background noise was 30 dB (A) and at distances in excess of 2100 m in the downwind direction. Discrete frequency sound components associated with the power generation equipment are measurable in the direction normal to the axis of rotation but are not believed to be significant for detection or community response.

Hubbard, H. H.↗

NASA NTRSDate not supplied

ISS External Microorganisms: Collecting Planetary Protection Samples During Extravehicular Activity

Introduction: We have designed1, built, and tested a sampling kit (Fig. 1) to aseptically collect microbiological samples from exterior surfaces on the ISS (International Space Station). The kit was flown to ISS as part of the NG-19 commercial cargo mission in August of 2023. Astronauts will use the kit to collect samples from six exterior surfaces on ISS. These samples will be frozen at -80°C after collection and returned to the ground for next generation DNA sequencing. The results of this experiment will help inform planetary protection requirements for crewed missions. We hypothesize that there are detectable microbial communities outside ISS and that these communities originate from inside ISS. Current life support systems do not include any components for reducing microbial leakage. Gases are vented from inside ISS without filtration and there are currently no protocols in place to minimize bioburden on space suit exteriors prior to use. It is important to quantify the bioburden on current vehicles so that achievable limits can be set for crewed missions to astrobiologically relevant locations like Mars. Figure 1: The sampling kit contains eight swab canisters in total (six on the top and two on the bottom). A resuable end effector (1) is used to remove and reinstall the swabs. The kit also contains a handrail (2), tether loop (3), and, bayonet probes(4) to allow easy manipulation during EVA. Methods: We have designed a kit to carry 8 commercially available foam swabs into and out of vacuum without compromising the swabs’ sterility. The specially designed swab canisters contain a 0.2 µm Teflon filter that allows the canister to accommodate pressure changes without introducing unwanted contaminants. The kit meets existing EVA (Extravehicular Activity) safety requirements and has been used by human test subjects in the neutral buoyance lab and at vacuum in test chambers at the Johnson Space Center. In the early part of 2024, astronauts will use this sampling kit to swab six surfaces on the exterior of ISS. We will collect samples from: the airlock vestibule, the interior surface of the airlock thermal cover, an exterior handrail, a vent connected to the CO2 removal system, and a vent connected to the payload vacuum system inside ISS. Approximately 300 cm2 will be swabbed at each location. A seventh swab will be exposed to the vacuum of space without touching any surfaces as a blank. The eighth swab will remain sealed as a process control. After the EVA the swab kit will be frozen at -80°C and returned to earth at the earliest possible opportunity. The samples will remain frozen until they are thawed for next generation DNA sequencing on earth. We will use amplicon sequencing to identify any bacteria, archaea or fungi present in the samples. If there is enough DNA present, we will use shotgun metagenomic sequencing to further characterize the microbial ecology outside ISS. Preliminary Results: Results from ground-based testing demonstrate that the swab kit is capable of cycling in and out of vacuum without contaminating the swabs. Test subjects, wearing flight-like EVA gloves could remove swabs from the canister and sample discrete locations without inadvertently touching any other surfaces. Several types of bacteria and fungi were collected during these ground tests and survived up to 6 hours at vacuum. This includes non-spore forming bacterial like Staphyloccus capitis that are not traditionally considered extremophiles. Shotgun metagenomic sequencing of the ground-test samples revealed bacteria associated with human skin and airways on the exterior of space suits used during these tests 2 In addition to these results we will present preliminary results from our space-flight samples. We will also present lessons learned from attempting to collect microbiological samples during an EVA and describe how our results will affect planetary protection requirements for future crewed missions.

Aaron B. Regberg↗

NASA NTRSDate not supplied

ISS External Microorganisms: Tools and Techniques for Collecting Planetary Protection Samples During Extravehicular Activity

We have designed, built, and tested a sampling kit (Fig. 1) to aseptically collect microbiological samples from exterior surfaces on the ISS (International Space Station). The kit was flown to ISS as part of the NG-19 commercial cargo mission in August of 2023. Astronauts will use the kit to collect samples from six exterior surfaces on ISS. These samples will be frozen at -80°C after collection and returned to the ground for next generation DNA sequencing. The results of this experiment will help inform planetary protection requirements for crewed missions. We hypothesize that there are detectable microbial communities outside ISS and that these communities originate from inside ISS. Current life support systems do not include any components for reducing microbial leakage. Gases are vented from inside ISS without filtration and there are currently no protocols in place to minimize bioburden on space suit exteriors prior to use. It is important to quantify the bioburden on current vehicles so that achievable limits can be set for crewed missions to astrobiologically relevant locations like Mars.

Planetary Protection↗

NASA NTRSDate not supplied

ISS External Microorganisms: Collecting Planetary Protection Samples During Extravehicular Activity

Introduction: We have designed1, built, and tested a sampling kit (Fig. 1) to aseptically collect microbiological samples from exterior surfaces on the ISS (International Space Station). The kit was flown to ISS as part of the NG-19 commercial cargo mission in August of 2023. Astronauts will use the kit to collect samples from six exterior surfaces on ISS. These samples will be frozen at -80°C after collection and returned to the ground for next generation DNA sequencing. The results of this experiment will help inform planetary protection requirements for crewed missions. We hypothesize that there are detectable microbial communities outside ISS and that these communities originate from inside ISS. Current life support systems do not include any components for reducing microbial leakage. Gases are vented from inside ISS without filtration and there are currently no protocols in place to minimize bioburden on space suit exteriors prior to use. It is important to quantify the bioburden on current vehicles so that achievable limits can be set for crewed missions to astrobiologically relevant locations like Mars. Figure 1: The sampling kit contains eight swab canisters in total (six on the top and two on the bottom). A resuable end effector (1) is used to remove and reinstall the swabs. The kit also contains a handrail (2), tether loop (3), and, bayonet probes(4) to allow easy manipulation during EVA. Methods: We have designed a kit to carry 8 commercially available foam swabs into and out of vacuum without compromising the swabs’ sterility. The specially designed swab canisters contain a 0.2 µm Teflon filter that allows the canister to accommodate pressure changes without introducing unwanted contaminants. The kit meets existing EVA (Extravehicular Activity) safety requirements and has been used by human test subjects in the neutral buoyance lab and at vacuum in test chambers at the Johnson Space Center. In the early part of 2024, astronauts will use this sampling kit to swab six surfaces on the exterior of ISS. We will collect samples from: the airlock vestibule, the interior surface of the airlock thermal cover, an exterior handrail, a vent connected to the CO2 removal system, and a vent connected to the payload vacuum system inside ISS. Approximately 300 cm2 will be swabbed at each location. A seventh swab will be exposed to the vacuum of space without touching any surfaces as a blank. The eighth swab will remain sealed as a process control. After the EVA the swab kit will be frozen at -80°C and returned to earth at the earliest possible opportunity. The samples will remain frozen until they are thawed for next generation DNA sequencing on earth. We will use amplicon sequencing to identify any bacteria, archaea or fungi present in the samples. If there is enough DNA present, we will use shotgun metagenomic sequencing to further characterize the microbial ecology outside ISS. Preliminary Results: Results from ground-based testing demonstrate that the swab kit is capable of cycling in and out of vacuum without contaminating the swabs. Test subjects, wearing flight-like EVA gloves could remove swabs from the canister and sample discrete locations without inadvertently touching any other surfaces. Several types of bacteria and fungi were collected during these ground tests and survived up to 6 hours at vacuum. This includes non-spore forming bacterial like Staphyloccus capitis that are not traditionally considered extremophiles. Shotgun metagenomic sequencing of the ground-test samples revealed bacteria associated with human skin and airways on the exterior of space suits used during these tests 2 In addition to these results we will present preliminary results from our space-flight samples. We will also present lessons learned from attempting to collect microbiological samples during an EVA and describe how our results will affect planetary protection requirements for future crewed missions.

Aaron B. Regberg↗

DOE OSTI2020

TriC: Distributed-memory Triangle Counting by Exploiting the Graph Structure

Graph analytics has emerged as an important tool in the analysis of large scale data from diverse application domains such as social networks, cyber security and bioinformatics. Counting the number of triangles in a graph is a fundamental kernel with several applications such as detecting the community structure of a graph or in identifying important vertices in a graph. The ubiquity of massive datasets is driving the need to scale graph analytics on parallel systems. However, numerous challenges exist in efficiently parallelizing graph algorithms, especially on distributed-memory systems. Irregular memory accesses and communication patterns, low computation to communication ratios, and the need for frequent synchronization are some of the leading challenges. In this paper, we present TriC, our distributed-memory implementation of triangle counting in graphs using the Message Passing Interface (MPI), as a submission to the 2020 GraphChallenge competition. Using a set of synthetic and real-world inputs from the challenge, we demonstrate a speedup of up to 90x relative to previous work on 32 processor-cores of a NERSC Cori node. We also provide details from distributed runs with up to8192 processes along with strong scaling results. The observations presented in this work provide an understanding of the system-level bottlenecks at scale that specifically impact sparse-irregular workloads and will therefore benefit other efforts to parallelize graph algorithms.

Halappanavar, Mahantesh↗

DOE OSTI2021

Leveraging Community and Author Context to Explain the Performance and Bias of Text-Based Deception Detection Models

Deceptive news posts shared in online communities can be detected with NLP models, and much recent research has focused on the development of such models. In this work, we use characteristics of online communities and authors --- the context of how and where content is posted --- to explain the performance of a neural network deception detection model and identify sub-populations who are disproportionately affected by model accuracy or failure. We examine who is posting the content, and where the content is posted to. We find that while author characteristics are better predictors of deceptive content than community characteristics, both characteristics are strongly correlated with model performance. Traditional performance metrics such as F1 score may fail to capture poor model performance on isolated sub-populations such as specific authors, and as such, more nuanced evaluation of deception detection models is critical.

machine learning (ML), machine learning explanatio↗

NASA NTRS2001

Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments

A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted-low-dilution communities and the communities regrown from the very dilute (more than 10(-4)) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10(-1)) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.

Non-NASA Center↗

DOE OSTI2024

Specialized protist communities on mycorrhizal fungal hyphae

Abstract Arbuscular mycorrhizal (AM) fungi not only play a crucial role in acquiring nutrients for plants but also serve as a habitat for soil microbes. Recent studies observed that AM fungal hyphae are colonized by specific bacterial communities. However, so far it has not been explored whether fungal hyphae and mycorrhizal networks also harbor specific communities of protists, a key group of microbes in the soil microbiome. Here, we characterized protist communities in soil in a compartment with plant roots and on hyphae collected from hyphal compartments without plant roots. We detected specific protist communities on fungal hyphae. Fourteen protistan amplicon sequences variants (ASVs) were significantly associated with fungal hyphae, half of which belonged to the Cercozoa group. This research, for the first-time detected specific protist ASVs directly associated with abundant AM fungus hyphae, highlighting the complexity of the hyphal food web.

Mycology↗

DOE OSTI2021

Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state

Microbial communities in oxygen minimum zones (OMZs) are known to have significant impacts on global biogeochemical cycles, but viral influence on microbial processes in these regions are much less studied. Here we provide baseline ecological patterns using microscopy and viral metagenomics from the Eastern Tropical North Pacific (ETNP) OMZ region that enhance our understanding of viruses in these climate-critical systems. While extracellular viral abundance decreased below the oxycline, viral diversity and lytic infection frequency remained high within the OMZ, demonstrating that viral influences on microbial communities were still substantial without the detectable presence of oxygen. Viral community composition was strongly related to oxygen concentration, with viral populations in low-oxygen portions of the water column being distinct from their surface layer counterparts. However, this divergence was not accompanied by the expected differences in viral-encoded auxiliary metabolic genes (AMGs) relating to nitrogen and sulfur metabolisms that are known to be performed by microbial communities in these low-oxygen and anoxic regions. Instead, several abundant AMGs were identified in the oxycline and OMZ that may modulate host responses to low-oxygen stress. We hypothesize that this is due to selection for viral-encoded genes that influence host survivability rather than modulating host metabolic reactions within the ETNP OMZ. Together, this study shows that viruses are not only diverse throughout the water column in the ETNP, including the OMZ, but their infection of microorganisms has the potential to alter host physiological state within these biogeochemically important regions of the ocean.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2011

Probability of Detection (POD) Demonstration Transferability

NASA Special Level POD demonstration tests are typically performed on flat plates of a single material containing fatigue cracks with aspect rations between 0.3 and 0.5. Subsequent fracture mechanics analyses consider aspect ratios that range from 0.1 to 0.5. There is debate within the NDE community about the detectability of shallow cracks associated with NASA Special Level penetrant inspections that are routinely performed by propellant tank manufactures. The objective of the task is to investigate effect of crack aspect ratio on POD crack sizes for the penetrant inspection technique.

Parker, Bradford H.↗

DOE OSTI2021

The value of human data annotation for machine learning based anomaly detection in environmental systems

Anomaly detection is the process of identifying unexpected data samples in datasets. Automated anomaly detection is either performed using supervised machine learning models, which require a labelled dataset for their calibration, or unsupervised models, which do not require labels. While academic research has produced a vast array of tools and machine learning models for automated anomaly detection, the research community focused on environmental systems still lacks a comparative analysis that is simultaneously comprehensive, objective, and systematic. This knowledge gap is addressed for the first time in this study, where 15 different supervised and unsupervised anomaly detection models are evaluated on 5 different environmental datasets from engineered and natural aquatic systems. To this end, anomaly detection performance, labelling efforts, as well as the impact of model and algorithm tuning are taken into account. As a result, our analysis reveals the relative strengths and weaknesses of the different approaches in an objective manner without bias for any particular paradigm in machine learning. Most importantly, our results show that expert-based data annotation is extremely valuable for anomaly detection based on machine learning.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Signatures of prescribed fire in the microbial communities of Cornus florida are largely undetectable five months post-fire

Prescribed burn is a management tool that influences the physical structure and composition of forest plant communities and their associated microorganisms. Plant-associated microorganisms aid in host plant disease tolerance and increase nutrient availability. The effects of prescribed burn on microorganisms associated with native ecologically and economically important tree species, such as Cornus florida L. (flowering dogwood), are not well understood, particularly in aboveground plant tissues (e.g., leaf, stem, and bark tissues). The objective of this study was to use 16S rRNA gene and ITS2 region sequencing to evaluate changes in bacterial and fungal communities of five different flowering dogwood-associated niches (soil, roots, bark, stem, and leaves) five months following a prescribed burn treatment. The alpha- and beta-diversity of root bacterial/archaeal communities differed significantly between prescribed burn and unburned control-treated trees. In these bacterial/archaeal root communities, we also detected a significantly higher relative abundance of sequences identified as Acidothermaceae, a family of thermophilic bacteria. No significant differences were detected between prescribed burn-treated and unburned control trees in bulk soils or bark, stem, or leaf tissues. The findings of our study suggest that prescribed burn does not significantly alter the aboveground plant-associated microbial communities of flowering dogwood trees five months following the prescribed burn application. Further studies are required to better understand the short- and long-term effects of prescribed burns on the microbial communities of forest trees.

16S rRNA↗

DOE OSTI2023

Effects of submerged macrophytes (Elodea nuttallii) on water quality and microbial communities of largemouth bass (Micropterus salmoides) ponds

Traditional aquaculture ponds are one of the most vulnerable ecosystems; thus, ecological aquaculture is increasingly valued for its beneficial ecological properties and ecosystem services. However, little is known about ecological aquaculture of largemouth bass with submerged vegetation. Here, we designed three ecological ponds of cultured largemouth bass with submerged macrophytes (the EM group) and three ponds with traditional aquaculture (the M group) to reveal the response of water quality, and phytoplankton and bacterial communities, to submerged macrophyte bioremediation during a 90-day culture period. We observed that Cyanobacterial outbreak occurred in the M group ponds from day 7 to the end of the experiment; however, there were no Cyanobacterial blooms in the EM group ponds throughout the culture period. Compared with the M group ponds, the EM group ponds, which had submerged hydrophytes, had significantly decreased concentrations of TP, TN, and COD Mn , but significantly increased DO concentrations throughout the experimental period. Moreover, ecological aquaculture with submerged macrophytes showed strong effects on the phytoplankton and bacterial community compositions. In particular, the M group ponds had higher phytoplankton density and mainly included Cyanobacteria, whereas the EM group had lower phytoplankton density and mainly included Chlorophyta. Moreover, higher alpha diversity, as determined by Ace and Simpson index values, was detected for bacterial communities in the EM group ponds. Furthermore, PCoA clearly grouped the bacterial communities according to the two culture modes throughout the culture period. These results indicate that ecological aquaculture with submerged macrophytes can improve water quality, control Cyanobacterial blooms, and affect the diversity and composition of bacterial communities. These valuable effects seem to be beneficial and consistent to maintaining aquaculture ecosystem stability.

Nie, Zhijuan↗

DOE OSTI2024

Integrating biological knowledge for mechanistic inference in the host-associated microbiome

Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Locating Seismic Events with Local-Distance Data

As the seismic monitoring community advances toward detecting, identifying, and locating ever-smaller natural and anthropogenic events, the need is constantly increasing for higher resolution, higher fidelity data, models, and methods for accurately characterizing events. Local-distance seismic data provide robust constraints on event locations, but also introduce complexity due to the significant geologic heterogeneity of the Earth’s crust and upper mantle, and the relative sparsity of data that often occurs with small events recorded on regional seismic networks. Identifying the critical characteristics for improving local-scale event locations and the factors that impact location accuracy and reliability is an ongoing challenge for the seismic community. Using Utah as a test case, we examine three data sets of varying duration, finesse, and magnitude to investigate the effects of local earth structure and modeling parameters on local-distance event location precision and accuracy. We observe that the most critical elements controlling relocation precision are azimuthal coverage and local-scale velocity structure, with tradeoffs based on event depth, type, location, and range.

42 ENGINEERING↗