scholarly journals Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

2019 ◽  
Author(s):  
Evan P. Starr ◽  
Erin E. Nuccio ◽  
Jennifer Pett-Ridge ◽  
Jillian F. Banfield ◽  
Mary K. Firestone
Keyword(s):  
Carbon Cycling ◽  
Rna Viruses ◽  
Marker Gene ◽  
Experimental Conditions ◽  
Time Resolved ◽  
Host Cell Death ◽  
Microbial System ◽  
Viral Communities ◽  
Time Signature ◽  
Viral Sequences

AbstractViruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in the most complex microbial system, soil. Here, we assembled 48 individual metatranscriptomes from four habitats within a soil sampled over a 22-day time series: rhizosphere alone, detritosphere alone, a combination of the two, and unamended soil (four time points and three biological replicates per time point). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker gene content. Based on viral phylogeny, much of the diversity wasNarnaviridaethat parasitize fungi orLeviviridaethat infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral communities were structured based on the presence of litter, while putative hosts appeared to be impacted by both the presence of litter and roots. A clear time signature fromLeviviridaeand their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant and active in soil. Their replication causes host cell death, mobilizing carbon in a process that represents a largely overlooked component of carbon cycling in soil.

scholarly journals Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

2019 ◽  
Vol 116 (51) ◽  
pp. 25900-25908 ◽  
Author(s):  
Evan P. Starr ◽  
Erin E. Nuccio ◽  
Jennifer Pett-Ridge ◽  
Jillian F. Banfield ◽  
Mary K. Firestone
Keyword(s):  
Carbon Cycling ◽  
Temporal Dynamics ◽  
Rna Viruses ◽  
Marker Genes ◽  
Experimental Conditions ◽  
Time Resolved ◽  
Host Cell Death ◽  
Root Litter ◽  
Viral Communities ◽  
Microbial Systems

Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity wasNarnaviridaethat may parasitize fungi orLeviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics byLeviviridaeand their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.

scholarly journals Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica)

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 979 ◽  
Author(s):  
Ping Liu ◽  
Wu Chen ◽  
Jin-Ping Chen
Keyword(s):  
De Novo ◽  
Sendai Virus ◽  
Sequence Similarity ◽  
Viral Metagenomics ◽  
Manis Javanica ◽  
Pathogenic Viruses ◽  
Viral Communities ◽  
High Level ◽  
Viral Sequences ◽  
Insight Into

Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.

scholarly journals Novel Viruses Found in Antricola Ticks Collected in Bat Caves in the Western Amazonia of Brazil

Viruses ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 48 ◽  
Author(s):  
Anne-Lie Blomström ◽  
Hermes R. Luz ◽  
Pontus Öhlund ◽  
Matthew Lukenge ◽  
Paulo Eduardo Brandão ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Blood Feeding ◽  
Dominant Group ◽  
Data Set ◽  
Adult Feeding ◽  
Viral Sequences ◽  
Negative Sense ◽  
Bat Guano

In this study, we describe the viral composition of adult Antricola delacruzi ticks collected in a hot bat cave in the state of Rondônia, Western Amazonia, Brazil. A. delacruzi ticks, are special, compared to many other ticks, in that they feed on both bats (larval blood feeding) and bat guano (nymphal and adult feeding) instead of feeding exclusively on vertebrate hosts (blood feeding). Considering this unique life-cycle it is potentially possible that these ticks can pick up/be infected by viruses not only present in the blood of viremic bats but also by virus shed through the bat guano. The viral metagenomic investigation of adult ticks showed that single-stranded negative-sense RNA viruses were the dominant group of viruses identified in the investigated ticks. Out of these, members of the Nairoviridae family were in clear majority constituting 88% of all viral reads in the data set. Genetic and phylogenetic analyses indicate the presence of several different orthonairoviruses in the investigated ticks with only distant relationship to previously described ones. In addition, identification of viral sequences belonging to Orthomyxoviridae, Iflaviridae, Dicistroviridae, Polycipiviridae, Reoviridae and different unclassified RNA viruses showed the presence of viruses with low sequence similarity to previously described viruses.

Round Turbulent Thermals, Puffs, Starting Plumes and Starting Jets in Uniform Crossflow

2003 ◽  
Author(s):  
F. J. Diez ◽  
L. P. Bernal ◽  
G. M. Faeth
Keyword(s):  
Fresh Water ◽  
Salt Water ◽  
Water Channel ◽  
Reynolds Numbers ◽  
Ccd Cameras ◽  
Experimental Conditions ◽  
Time Resolved ◽  
Buoyant Flows ◽  
Video Images ◽  
Density Ratios

The self-preserving properties of round turbulent thermals, puffs, starting plumes and starting jets, in unstratified and uniform crossflow, were investigated experimentally. The experiments involved dye-containing fresh water (for nonbuoyant flows) and salt water (for buoyant flows) sources injected vertically downward into crossflowing fresh water within a water channel. Time-resolved video images of the flows were obtained using CCD cameras. Experimental conditions were as follows: source exit diameters of 3.2 and 6.4 mm, source Reynolds numbers of 2,500–16,000, source/ambient velocity ratios of 4–35, source/ambient density ratios (for buoyant flows) of 1.073 and 1.150, volumes of injected source fluid (for thermals and puffs) comprising 16–318 source diameters, streamwise (vertical) penetration distances of 0–200 source diameters and 0–13 Morton length scales (for buoyant flows) and crosstream (horizontal) penetration distances of 0–620 source diameters. Near-source behavior varied significantly with source properties but the flows generally became turbulent for streamwise distances within 5 source diameters from the source and became self-preserving for streamwise distances from the source greater than 40–50 source diameters. Crosstream motion satisfied the no-slip convection approximation. Streamwise motion for self-preserving conditions satisfied the behavior of corresponding self-preserving flows in still fluids: round thermals and puffs in still fluids for round thermals and puffs in crossflow and two-dimensional line thermals and puffs in still fluids for round starting plumes and jets in crossflow. The no-slip convection approximation for crossflow motion combined with self-preserving approximations for streamwise motion was also effective for predicting flow trajectories at self-preserving conditions for steady round turbulent plumes and jets in crossflow.

A Novel Near-Infrared Fluorescence Sensor for H2O2 Based on N-Acetyl-L-Cysteine-Capped Gold Nanoparticles

2017 ◽  
Vol 46 ◽  
pp. 234-240
Author(s):  
Wen Juan Dong ◽  
Ji Yan Han ◽  
Xin Wu ◽  
Li Fan ◽  
Wen Ting Liang
Keyword(s):  
Hydrogen Peroxide ◽  
Gold Nanoparticles ◽  
Fluorescence Quenching ◽  
Near Infrared ◽  
Fluorescence Probe ◽  
Fluorescence Emission ◽  
Excitation Wavelength ◽  
Experimental Conditions ◽  
Time Resolved ◽  
Near Infrared Fluorescence

A novel near-infrared fluorescence quenching method has been developed for the determination of hydrogen peroxide based on N-acetyl-L-cysteine-capped gold nanoparticles (NAC-AuNPs) as a fluorescence probe. The prepared gold nanoparticles with the size of about 1.91 nm exhibited strong near-infrared fluorescence emission at 693 nm with excitation wavelength at 450 nm in aqueous solution. The fluorescence intensity of NAC-AuNPs was quenched dramatically by adding hydrogen peroxide. Therefore, it could be used to detect hydrogen peroxide based on the fluorescence quenching intensity was linear with the concentration of hydrogen peroxide. Under the optimal experimental conditions, the linear range and detection limit were 1.0×10-6 –3.0×10-2 mol/L and 1.0×10-7 mol/L, respectively. The possible quenching mechanism was investigated by time-resolved fluorescence spectroscopy. The proposed method was simple, sensitive and showed good repeatability and stability.

Detection of amplified HTLV-I/-II viral sequences using time-resolved fluorometry

1992 ◽  
Vol 202 (1) ◽  
pp. 76-81 ◽  
Author(s):  
Antti Iitiä ◽  
Patrik Dahlen ◽  
Michael Nunn ◽  
Veli-Matti Mukkala ◽  
Harri Siitari
Keyword(s):  
Time Resolved ◽  
Viral Sequences

scholarly journals Quantitative sampling and analysis of trace elements in atmospheric aerosols: impactor characterization and Synchrotron-XRF mass calibration

2010 ◽  
Vol 3 (5) ◽  
pp. 1473-1485 ◽  
Author(s):  
A. Richard ◽  
N. Bukowiecki ◽  
P. Lienemann ◽  
M. Furger ◽  
M. Fierz ◽  
...  
Keyword(s):  
Trace Elements ◽  
Atmospheric Aerosols ◽  
Collection Efficiency ◽  
Ambient Air ◽  
Pollution Source ◽  
Data Sets ◽  
Size Segregation ◽  
Ambient Aerosols ◽  
Experimental Conditions ◽  
Time Resolved

Abstract. Identification of trace elements in ambient air can add substantial information to pollution source apportionment studies, although they do not contribute significantly to emissions in terms of mass. A method for quantitative size and time-resolved trace element evaluation in ambient aerosols with a rotating drum impactor and synchrotron radiation based X-ray fluorescence is presented. The impactor collection efficiency curves and size segregation characteristics were investigated in an experiment with oil and salt particles. Cutoff diameters were determined through the ratio of size distributions measured with two particle sizers. Furthermore, an external calibration technique to empirically link fluorescence intensities to ambient concentrations was developed. Solutions of elemental standards were applied with an ink-jet printer on thin films and area concentrations were subsequently evaluated with external wet chemical methods. These customized and reusable reference standards enable quantification of different data sets analyzed under varying experimental conditions.

First-order parallel and consecutive reaction mechanisms — Isosbestic points criterium

2008 ◽  
Vol 86 (9) ◽  
pp. 918-924 ◽  
Author(s):  
A E Croce
Keyword(s):  
Reaction Mechanism ◽  
Absorption Spectra ◽  
Rate Coefficients ◽  
Isosbestic Point ◽  
Experimental Conditions ◽  
Consecutive Reaction ◽  
Time Resolved ◽  
First Order ◽  
Kinetic Information ◽  
First Case

A criterium for the selection of reaction mechanism derived from a condition for isosbestic points occurrence is presented. Analytical relationships involving the molar absorption coefficients of the species, which participate in a mechanism of parallel first-order reactions and the corresponding rate coefficients, are also reported. A model system of four species that present overlapping absorption spectra may correspond to the reactant and products of a system of parallel or consecutive first-order reactions. In the first case, under experimental conditions in which the absorbances are additive, the presence of an isosbestic point in the spectrum of the reaction mixture at a given wavelength leads to a time-independent ratio of the degree of advancement of reaction variables. From this, relevant kinetic information may be extracted, namely, the ratio of the reaction rate coefficients. Moreover, the occurrence of isosbestic points allows discarding the second mechanism. This conclusion is independent of the number of absorbing species. Model calculated examples show the application of the equations here derived. The resolution for the general case of mechanisms of N first-order reactions is provided.Key words: chemical kinetics, time-resolved absorption spectra, reaction mechanism.

Spectrum analysis of plasma produced by pulsed laser ablation of GaAs

2007 ◽  
Vol 73 (2) ◽  
pp. 231-239 ◽  
Author(s):  
AI HUA LIU
Keyword(s):  
Laser Ablation ◽  
Ambient Pressure ◽  
Pulsed Laser ◽  
Emission Spectra ◽  
Diagnostic Technique ◽  
Pulsed Laser Ablation ◽  
Stark Broadening ◽  
Experimental Conditions ◽  
Time Resolved ◽  
Excited Atoms

Abstract.A time-resolved diagnostic technique was used to investigate the emission spectra from the plasmas produced by 1.06 μm, 10 ns pulsed laser ablation of semiconductor GaAs. The characteristics of the species in plasma produced at different ambient pressure were analyzed. The full width at half maximum of the spectral line was measured and analyzed according to obtained spectra of the excited atoms; several line broadening factors were estimated according to our experimental conditions and the results indicate that the Stark broadening is the main broadening mechanism. Under the assumption of local thermodynamic equilibrium, the time evolution of electron number density was deduced from the Stark broadening measurements.

scholarly journals Metagenomic Analysis of the Viral Communities in Fermented Foods

2010 ◽  
Vol 77 (4) ◽  
pp. 1284-1291 ◽  
Author(s):  
Eun-Jin Park ◽  
Kyoung-Ho Kim ◽  
Guy C. J. Abell ◽  
Min-Soo Kim ◽  
Seong Woon Roh ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Fermented Foods ◽  
Human Feces ◽  
Viral Genomes ◽  
Double Stranded Dna ◽  
Viral Communities ◽  
Rrna Gene Sequencing ◽  
Viral Sequences ◽  
Homology Comparison

ABSTRACTViruses are recognized as the most abundant biological components on Earth, and they regulate the structure of microbial communities in many environments. In soil and marine environments, microorganism-infecting phages are the most common type of virus. Although several types of bacteriophage have been isolated from fermented foods, little is known about the overall viral assemblages (viromes) of these environments. In this study, metagenomic analyses were performed on the uncultivated viral communities from three fermented foods, fermented shrimp, kimchi, and sauerkraut. Using a high-throughput pyrosequencing technique, a total of 81,831, 70,591 and 69,464 viral sequences were obtained from fermented shrimp, kimchi and sauerkraut, respectively. Moreover, 37 to 50% of these sequences showed no significant hit against sequences in public databases. There were some discrepancies between the prediction of bacteriophages hosts via homology comparison and bacterial distribution, as determined from 16S rRNA gene sequencing. These discrepancies likely reflect the fact that the viral genomes of fermented foods are poorly represented in public databases. Double-stranded DNA viral communities were amplified from fermented foods by using a linker-amplified shotgun library. These communities were dominated by bacteriophages belonging to the viral orderCaudovirales(i.e.,Myoviridae,Podoviridae, andSiphoviridae). This study indicates that fermented foods contain less complex viral communities than many other environmental habitats, such as seawater, human feces, marine sediment, and soil.

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