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Results for “PERMANOVA”

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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8 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Comparing gas composition from fast pyrolysis of live foliage measured in bench-scale and fire-scale experiments

Background: Fire models have used pyrolysis data from oxidising and non-oxidising environments for flaming combustion. In wildland fires pyrolysis, flaming and smouldering combustion typically occur in an oxidising environment (the atmosphere). Aims: Using compositional data analysis methods, determine if the composition of pyrolysis gases measured in non-oxidising and ambient (oxidising) atmospheric conditions were similar. Methods: Permanent gases and tars were measured in a fuel-rich (non-oxidising) environment in a flat flame burner (FFB). Permanent and light hydrocarbon gases were measured for the same fuels heated by a fire flame in ambient atmospheric conditions (oxidising environment). Log-ratio balances of the measured gases common to both environments (CO, CO 2 , CH 4 , H 2 , C 6 H 6 O (phenol), and other gases) were examined by principal components analysis (PCA), canonical discriminant analysis (CDA) and permutational multivariate analysis of variance (PERMANOVA). Key results: Mean composition changed between the non-oxidising and ambient atmosphere samples. PCA showed that flat flame burner (FFB) samples were tightly clustered and distinct from the ambient atmosphere samples. CDA found that the difference between environments was defined by the CO-CO 2 log-ratio balance. PERMANOVA and pairwise comparisons found FFB samples differed from the ambient atmosphere samples which did not differ from each other. Conclusion: Relative composition of these pyrolysis gases differed between the oxidising and non-oxidising environments. This comparison was one of the first comparisons made between bench-scale and field scale pyrolysis measurements using compositional data analysis. Implications: These results indicate the need for more fundamental research on the early time-dependent pyrolysis of vegetation in the presence of oxygen.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Transfer of beef bacterial communities onto food-contact surfaces

Introduction Food spoilage and pathogenic bacteria on food-contact surfaces, especially biofilm-forming strains, can transfer to meats during processing. The objectives of this study were to survey the bacterial communities of beef cuts that transfer onto two commonly used food-contact surfaces, stainless steel (SS) and high-density polyethylene (HDPE) and identify potentially biofilm-forming strains. Methods Top round, flank, chuck, and ground beef were purchased from 3 retail stores. SS and HDPE coupons (approximately 2cm × 5cm) were placed on beef portions (3h, 10°C), after which, the coupons were submerged halfway in PBS (24h, 10°C). Bacteria from the beef cuts and coupon surfaces ( n = 3) were collected, plated on tryptic soy agar plates and incubated (5 days, 25°C). Bacterial isolates were identified by 16S rRNA gene amplicon sequencing and assayed for biofilm formation using a crystal violet binding (CV) assay (72h, 10°C). Additionally, beef and coupon samples were collected for bacterial community analysis by 16S rRNA gene amplicon sequencing. Results and discussion Sixty-one of 972 beef isolates, 29 of 204 HDPE isolates, and 30 of 211 SS isolates were strong biofilm-formers (Absorbance>1.000 at 590 nm in the CV assay). Strong-binding isolates identified were of the genera Pseudomonas , Acinetobacter , Psychrobacter , Carnobacterium , and Brochothrix . Coupon bacterial communities among stores and cuts were distinct ( p < 0.001, PERMANOVA), but there was no distinction between the communities found on HDPE or SS coupons ( p > 0.050, PERMANOVA). The bacterial communities identified on the coupons may help determine the communities capable of transferring and colonizing onto surfaces, which can subsequently cross-contaminate foods.

Guron, Giselle K. P.↗
DOE OSTI2021

A cross-sectional study of the nasal and fecal microbiota of sows from different health status within six commercial swine farms

Cull sows are a unique population on swine farms, often representing poor producing or compromised animals, and even though recent studies have reported that the microbiome is associated with susceptibility to diseases, the microbiome of the cull sow population has not been explored. The main objective of this study was to investigate whether there were differences in fecal and upper respiratory tract microbiota composition for groups of sows of different health status (healthy, cull, and compromised/ clinical sows) and from different farms (1 to 6). Six swine farms were visited once. Thirty individual fecal samples and nasal swabs were obtained at each farm and pooled by five across health status and farm. Samples underwent 16S rRNA gene amplicon sequencing and nasal and fecal microbiota were analyzed using QIIME2 v.2021.4. Overall, the diversity of the nasal microbiota was lower than the fecal microbiota (p < 0.01). No significant differences were found in fecal or nasal alpha diversity by sow’s health status or by farm. Furthermore, there were significant differences in nasal microbial composition by farm and health status (PERMANOVA, p < 0.05), and in fecal microbiota by farm (PERMANOVA, p < 0.05), but not by health status. Lastly, at the L7 level, there was one differentially abundant taxa across farms for each nasal and fecal pooled samples. This study provided baseline information for nasal and fecal microbiota of sows under field conditions, and results suggest that farm of origin can affect microbial diversity and composition. Furthermore, sow’s health status may have an impact on the nasal microbiota composition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Microbial community diversity changes during voltage reversal repair in a 12-unit microbial fuel cell

Microbial fuel cell stacks (MFC-Stack) are often confronted with voltage reversals, likely due to an interplay between microbial community dynamics and insufficient electric circuit balancing. Herein, we provide new insight into voltage reversals by examining the microbiomes of twelve MFC units of a 12-liter Pilot-MFC-Stack during repair. Different biofilm repair methods (self-healing, electrostimulation, and re-acclimatization upon cross-inoculation) were used to evaluate the microbial community response. In addition, MFC-Stack simulation was performed based on Kirchhoff’s Second Law to predict values for source potentials and post-evaluate internal resistances. Analysis of the 16S rRNA amplicon sequencing data suggests that the biofilm repair methods could slowly heal damaged biofilms. Notably, severely voltage reversed MFC units had low electrogen relative abundances (18%) and positive anode potentials, while strong bioanodes and contained more than 50% electrogens and had negative anode potentials. Between-community analyses (beta diversity ordination and multinomial regression) of the voltage reversed MFC units revealed differences among biofilms in contrast to healthy/strong MFC units. Permutational multivariate analysis of variance (PERMANOVA) confirmed that reversed biofilms were, indeed, significantly (p < 0.05) different from stronger ones. Overall, these analyses demonstrated the utility of combining electrotechnical and microbial community analyses, especially beta diversity ordination and multinomial regression, to understand problematic MFC units and the potential success of a biofilm repair method. Finally, thicker biofilms were usually healthier and stronger, although thickness was no guarantee for proper structure and power function as all factors were interdependent. There was an evolutionary trend that strong anodes became stronger/healthier and others weaker. This spontaneous trend has to be considered to avoid irreversible voltage reversals and to repair electrogenic biofilms in an MFC-Stack.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Exploring prokaryotic diversity in permafrost-affected soils of Ladakh’s Changthang region and its geochemical drivers

Global warming due to climate change has substantial impact on high-altitude permafrost affected soils. This raises a serious concern that the microbial degradation of sequestered carbon can result in alteration of the biogeochemical cycles. Therefore, the characterization of permafrost affected soil microbiomes, especially of unexplored high-altitude, low oxygen arid region, is important for predicting their response to climate change. This study presents the first report of the bacterial diversity of permafrost-affected soils in the Changthang region of Ladakh. The relationship between soil pH, organic carbon, electrical conductivity, and available micronutrients with the microbial diversity was investigated. Amplicon sequencing of permafrost affected soil samples from Jukti and Tsokar showed that Proteobacteria and Actinobacteria were the dominant phyla in all samples. The genera Brevitalea, Chthoniobacter, Sphingomonas, Hydrogenispora, Clostridium, Gaiella, Gemmatimonas were relatively abundant in the Jukti samples whereas the genera Thiocapsa, Actinotalea, Syntrophotalea, Antracticibcterium, Luteolibacter, Nitrospirillum dominated the Tsokar sample. Correlation analyses highlighted the influence of soil geochemical parameters on the bacterial community structure. PCoA analyses showed that the bacterial beta diversity varied significantly between the sampling locations (PERMANOVA test (F-value: 2.3316; R 2 = 0.466, p = 0.001) and similar results were also obtained while comparing genus abundance data using the ANOSIM test (R = 0.345, p = 0.007).

16S rRNA↗
DOE OSTI2024

Real-time breath analysis towards a healthy human breath profile

Abstract The direct analysis of molecules contained within human breath has had significant implications for clinical and diagnostic applications in recent decades. However, attempts to compare one study to another or to reproduce previous work are hampered by: variability between sampling methodologies, human phenotypic variability, complex interactions between compounds within breath, and confounding signals from comorbidities. Towards this end, we have endeavored to create an averaged healthy human ‘profile’ against which follow-on studies might be compared. Through the use of direct secondary electrospray ionization combined with a high-resolution mass spectrometry and in-house bioinformatics pipeline, we seek to curate an average healthy human profile for breath and use this model to distinguish differences inter- and intra-day for human volunteers. Breath samples were significantly different in PERMANOVA analysis and ANOSIM analysis based on Time of Day, Participant ID, Date of Sample, Sex of Participant, and Age of Participant ( p < 0.001). Optimal binning analysis identify strong associations between specific features and variables. These include 227 breath features identified as unique identifiers for 28 of the 31 participants. Four signals were identified to be strongly associated with female participants and one with male participants. A total of 37 signals were identified to be strongly associated with the time-of-day samples were taken. Threshold indicator taxa analysis indicated a shift in significant breath features across the age gradient of participants with peak disruption of breath metabolites occurring at around age 32. Forty-eight features were identified after filtering from which a healthy human breath profile for all participants was created.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Sphingomonas clade and functional distribution with simulated climate change

Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of Sphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted Sphingomonas clade and functional composition would correspond with site conditions and reflect the Sphingomonas composition of native communities. We extracted Sphingomonas sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major Sphingomonas clades were found at varying relative abundances along the climate gradient, and transplanted Sphingomonas clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; P < 0.001) on the distribution of both Sphingomonas functional (R 2 = 0.465) and clade composition (R 2 = 0.400), suggesting that Sphingomonas composition depends on climate parameters. Additionally, for both Sphingomonas clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native Sphingomonas composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine Sphingomonas clade and functional composition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Amplicon Sequencing Assessment to Measure Microbial Community Response from Heavy Metal Contaminated Soils in Savannah River site, Tims Branch watershed

Long-term presence of heavy metal contamination in soils is correlated with changes in microbial community structures and can lead to the reduction of indigenous species. Tolerance to soil heavy metal toxicity varies among different microbial communities. It remains unclear whether long term effects caused by metal perturbations are associated with soil microbial community dysregulation in Tims Branch watershed. Research Questions: Does heavy metal contamination in Tims Branch soils decrease microbial species diversity significantly compared to non-contaminated soils? Does the species richness decrease in contaminated samples? between samples? Is diversity in low, mid and high contamination soils significantly different compared to control samples? Hypothesis: The relative abundance and diversity of species are significantly altered in soils which are contaminated with heavy metals in the Tims Branch watershed. Objectives: Use amplicon sequencing technology along with bioinformatics to compare bacterial communities between four sites in Tims Branch watershed. Evaluate the percent relative abundance and diversity across the site. Conclusions: All bacterial communities exposed to different heavy metal concentrations were dominated by four major groups (Proteobacteria, Acidobacteria, Chloroflexi and Verrucomicrobia). The dominant phyla Proteobacteria, Acidobacteria and Chloroflexi accounted for 61 % of the relative abundance. Soil bacterial α-diversity, expressed as observed species richness metric and Shannon's diversity index, was the highest in sample location four (high contamination). The lowest observed was at the control location. Species richness increased when concentrations of heavy metals were localized, inferring that the metals can alter microbial community structure. PERMANOVA analysis between contaminated groups tested significant using the Adonis (F (4,29) =1.9712; p < 0.001). There is a 20 percent variation explained between groups (R2 = 0.214). This analysis proves to be beneficial in detecting microbial communities altered by contaminated soils. Moreover, certain concentrations of heavy metals can alter microbial community structures.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗