scholarly journals Microscale and small-scale temporal dynamics of a coastal planktonic microbial community

2005 ◽  
Vol 300 ◽  
pp. 21-37 ◽  
Author(s):  
JR Seymour ◽  
L Seuront ◽  
JG Mitchell
Keyword(s):  
Microbial Community ◽  
Temporal Dynamics ◽  
Small Scale

scholarly journals Multi-Scale Ionospheric Anomalies Monitoring and Spatio-Temporal Analysis during Intense Storm

Atmosphere ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 215
Author(s):  
Na Cheng ◽  
Shuli Song ◽  
Wei Li
Keyword(s):  
Magnetic Storm ◽  
Large Scale ◽  
Temporal Dynamics ◽  
Ionospheric Disturbance ◽  
Ionospheric Scintillation ◽  
Small Scale ◽  
Electron Content ◽  
Total Electron ◽  
Multi Scale ◽  
Intense Storm

The ionosphere is a significant component of the geospace environment. Storm-induced ionospheric anomalies severely affect the performance of Global Navigation Satellite System (GNSS) Positioning, Navigation, and Timing (PNT) and human space activities, e.g., the Earth observation, deep space exploration, and space weather monitoring and prediction. In this study, we present and discuss the multi-scale ionospheric anomalies monitoring over China using the GNSS observations from the Crustal Movement Observation Network of China (CMONOC) during the 2015 St. Patrick’s Day storm. Total Electron Content (TEC), Ionospheric Electron Density (IED), and the ionospheric disturbance index are used to monitor the storm-induced ionospheric anomalies. This study finally reveals the occurrence of the large-scale ionospheric storms and small-scale ionospheric scintillation during the storm. The results show that this magnetic storm was accompanied by a positive phase and a negative phase ionospheric storm. At the beginning of the main phase of the magnetic storm, both TEC and IED were significantly enhanced. There was long-duration depletion in the topside ionospheric TEC during the recovery phase of the storm. This study also reveals the response and variations in regional ionosphere scintillation. The Rate of the TEC Index (ROTI) was exploited to investigate the ionospheric scintillation and compared with the temporal dynamics of vertical TEC. The analysis of the ROTI proved these storm-induced TEC depletions, which suppressed the occurrence of the ionospheric scintillation. To improve the spatial resolution for ionospheric anomalies monitoring, the regional Three-Dimensional (3D) ionospheric model is reconstructed by the Computerized Ionospheric Tomography (CIT) technique. The spatial-temporal dynamics of ionospheric anomalies during the severe geomagnetic storm was reflected in detail. The IED varied with latitude and altitude dramatically; the maximum IED decreased, and the area where IEDs were maximum moved southward.

scholarly journals Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range

2021 ◽  
Vol 11 ◽  
Author(s):  
Janneke Schreuder ◽  
Francisca C. Velkers ◽  
Alex Bossers ◽  
Ruth J. Bouwstra ◽  
Willem F. de Boer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Intestinal Microbiota ◽  
Environmental Changes ◽  
Temporal Dynamics ◽  
Microbial Community Composition ◽  
Sudden Change ◽  
Rrna Gene ◽  
Poultry House ◽  
Over Time

Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.

Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill

2022 ◽  
Author(s):  
Yiqi Cao ◽  
Baiyu Zhang ◽  
Charles W. Greer ◽  
Kenneth Lee ◽  
Qinhong Cai ◽  
...  
Keyword(s):  
Microbial Community ◽  
Late Stage ◽  
Large Scale ◽  
Community Dynamics ◽  
Early Stage ◽  
Small Scale ◽  
Rrna Gene ◽  
Shotgun Metagenomics ◽  
Microcosm Studies ◽  
Over Time

The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1500 mL) microcosms without nutrients addition using low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved into the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic based Metagenome Assembled Genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. Importance In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days) whereas exerting insignificant effects in the late stage (50 days), from both substances removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation, and clarified their degradation and antioxidation mechanisms. The findings would help to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit, and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.

scholarly journals Modeling the temporal dynamics of the gut microbial community in adults and infants

2019 ◽  
Vol 15 (6) ◽  
pp. e1006960 ◽  
Author(s):  
Liat Shenhav ◽  
Ori Furman ◽  
Leah Briscoe ◽  
Mike Thompson ◽  
Justin D. Silverman ◽  
...  
Keyword(s):  
Microbial Community ◽  
Temporal Dynamics ◽  
Gut Microbial Community

scholarly journals The Dimension of Time in Host-Microbiome Interactions

mSystems ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Giulia T. Uhr ◽  
Lenka Dohnalová ◽  
Christoph A. Thaiss
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Temporal Dynamics ◽  
Therapeutic Strategies ◽  
Intestinal Microbiome ◽  
Short Term ◽  
Intestinal Microbial Community ◽  
Intermediate States ◽  
Different Time Scales

ABSTRACT The intestinal microbiota contains trillions of commensal microorganisms that shape multiple aspects of host physiology and disease. In contrast to the host’s genome, the microbiome is amenable to change over the course of an organism’s lifetime, providing an opportunity to therapeutically modulate the microbiome’s impact on human pathophysiology. In this Perspective, we highlight environmental factors that regulate the temporal dynamics of the intestinal microbiome, with a particular focus on the different time scales at which they act. We propose that the identification of transient and intermediate states of microbiome responses to perturbations is essential for understanding the rules that govern the behavior of this ecosystem. The delineation of microbiome dynamics is also helpful for distinguishing cause and effect in microbiome responses to environmental stimuli. Understanding the dimension of time in host-microbiome interactions is therefore critical for therapeutic strategies that aim at short-term or long-term engineering of the intestinal microbial community.

Comparative Analysis of Gut Microbiota Following Changes in Training Volume Among Swimmers

2020 ◽  
Vol 41 (05) ◽  
pp. 292-299 ◽  
Author(s):  
Jarrad Timothy Hampton-Marcell ◽  
Tifani W. Eshoo ◽  
Marc D. Cook ◽  
Jack A. Gilbert ◽  
Craig A. Horswill ◽  
...  
Keyword(s):  
Body Composition ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Temporal Dynamics ◽  
Fecal Microbiota ◽  
Future Research ◽  
Training Volume ◽  
Short Term ◽  
Microbial Composition

AbstractExercise can influence gut microbial community structure and diversity; however, the temporal dynamics of this association have rarely been explored. Here we characterized fecal microbiota in response to short term changes in training volume. Fecal samples, body composition, and training logs were collected from Division I NCAA collegiate swimmers during peak training through their in-season taper in 2016 (n=9) and 2017 (n=7), capturing a systematic reduction in training volume near the conclusion of their athletic season. Fecal microbiota were characterized using 16S rRNA V4 amplicon sequencing and multivariate statistical analysis, Spearman rank correlations, and random forest models. Peak training volume, measured as swimming distance, decreased significantly during the study period from 32.6±4.8 km/wk to 11.3±8.1 km/wk (ANOVA, p<0.05); however, body composition showed no significant changes. Coinciding with the decrease in training volume, the microbial community structure showed a significant decrease in overall microbial diversity, a decrease in microbial community structural similarity, and a decrease in the proportion of the bacterial genera Faecalibacterium and Coprococcus. Together these data demonstrate a significant association between short-term changes in training volume and microbial composition and structure in the gut; future research will establish whether these changes are associated with energy balance or nutrient intake.

scholarly journals Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Paul Carini ◽  
Manuel Delgado-Baquerizo ◽  
Eve-Lyn S. Hinckley ◽  
Hannah Holland‐Moritz ◽  
Tess E. Brewer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Spatial Variability ◽  
Spatial Heterogeneity ◽  
Microbial Communities ◽  
Temporal Variability ◽  
Temporal Dynamics ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Environmental Preferences ◽  
Soil Microbial

ABSTRACT Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes. IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

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