scholarly journals Comparing the diversity and relative abundance of free and particle-associated aquatic viruses

2020 ◽  
Author(s):  
Christine N. Palermo ◽  
Dylan W. Shea ◽  
Steven M. Short
Keyword(s):  
Relative Abundance ◽  
Dna Sequences ◽  
Size Fraction ◽  
Metagenomic Data ◽  
Size Fractions ◽  
Small Pore ◽  
Relative Abundances ◽  
Ecological Importance ◽  
Virus Communities ◽  
Virus Size

ABSTRACTMetagenomics has enabled rapid increases in virus discovery, in turn permitting revisions of viral taxonomy and our understanding of the ecology of viruses and their hosts. Inspired by recent discoveries of large viruses prevalent in the environment, we re-assessed the longstanding approach of filtering water through small pore-size filters to separate viruses from cells before sequencing. We studied assembled contigs derived from < 0.45 μm and > 0.45 μm size fractions that were annotated as viral to determine the diversity and relative abundances of virus groups from each fraction. Virus communities were vastly different when comparing the size fractions, indicating that analysis of either fraction alone would provide only a partial perspective of environmental viruses. At the level of virus order/family we observed highly diverse and distinct virus communities in the > 0.45 μm size fractions, whereas the < 0.45 μm size fractions were comprised primarily of highly diverse Caudovirales. The relative abundances of Caudovirales for which hosts could be inferred varied widely between size fractions with higher relative abundances of cyanophages in the > 0.45 μm size fractions potentially indicating replication within cells during ongoing infections. Many of the Mimiviridae and Phycodnaviridae, and all Iridoviridae and Poxviridae were detected exclusively in the often disregarded > 0.45 μm size fractions. In addition to observing unique virus communities associated with each size fraction, we detected viruses common to both fractions and argue that these are candidates for further exploration because they may be the product of ongoing or recent lytic events.IMPORTANCEMost studies of aquatic virus communities analyze DNA sequences derived from the smaller, “free virus” size fraction. Our study demonstrates that analysis of virus communities using only the smaller size fraction can lead to erroneously low diversity estimates for many of the larger viruses such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, whereas analyzing only the larger, > 0.45 μm size fraction can lead to underestimates of Caudovirales diversity and relative abundance. Similarly, our data shows that examining only the smaller size fraction can lead to underestimation of virophage and cyanophage relative abundances that could, in turn, cause researchers to assume their limited ecological importance. Given the considerable differences we observed in this study, we recommend cautious interpretations of environmental virus community assemblages and dynamics when based on metagenomic data derived from different size fractions.

scholarly journals Analysis of different size fractions provides a more complete perspective of viral diversity in a freshwater embayment

2021 ◽  
Author(s):  
Christine N. Palermo ◽  
Dylan W. Shea ◽  
Steven M. Short
Keyword(s):  
Dna Sequences ◽  
Size Fraction ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Size Fractions ◽  
Small Pore ◽  
Relative Abundances ◽  
Ecological Importance ◽  
Virus Communities ◽  
Virus Size

Inspired by recent discoveries of the prevalence of large viruses in the environment, we re-assessed the longstanding approach of filtering water through small pore-size filters to separate viruses from cells before metagenomic analysis. We collected samples from three sites in Hamilton Harbour, an embayment of Lake Ontario, and studied 6 datasets derived from < 0.45 μm and > 0.45 μm size fractions to compare the diversity of viruses in these fractions. At the level of virus order/family we observed highly diverse and distinct virus communities in the > 0.45 μm size fractions, whereas the < 0.45 μm size fractions were comprised primarily of Caudovirales. The relative abundances of Caudovirales for which hosts could be inferred varied widely between size fractions with higher relative abundances of cyanophages in the > 0.45 μm size fractions potentially indicating replication within cells during ongoing infections. Many viruses of eukaryotes, such as Mimiviridae, Phycodnaviridae, Iridoviridae and Poxviridae were detected exclusively in the often disregarded > 0.45 μm size fractions. In addition to observing unique virus communities associated with each size fraction from every site we examined, we detected viruses common to both fractions suggesting that these are candidates for further exploration because they could be the product of ongoing or recent lytic events. Most importantly, our observations indicate that analysis of either fraction alone provides only a partial perspective of dsDNA viruses in the environment, highlighting the need for more comprehensive approaches for analyzing virus communities inferred from metagenomic sequencing. IMPORTANCE Most studies of aquatic virus communities analyze DNA sequences derived from the smaller, “free virus” size fraction. Our study demonstrates that analysis of virus communities using only the smaller size fraction can lead to erroneously low diversity estimates for many of the larger viruses such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, whereas analyzing only the larger, > 0.45 μm size fraction can lead to underestimates of Caudovirales diversity and relative abundance. Similarly, our data shows that examining only the smaller size fraction can lead to underestimations of virophage and cyanophage relative abundances that could, in turn, cause researchers to assume their limited ecological importance. Given the considerable differences we observed in this study, we recommend cautious interpretations of environmental virus community assemblages and dynamics when based on metagenomic data derived from different size fractions.

scholarly journals Metagenomic Analysis of Virus Diversity and Relative Abundance in a Eutrophic Freshwater Harbour

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 792 ◽  
Author(s):  
Christine N. Palermo ◽  
Roberta R. Fulthorpe ◽  
Rosemary Saati ◽  
Steven M. Short
Keyword(s):  
Spatial Scales ◽  
Size Fraction ◽  
Environmental Parameters ◽  
Illumina Hiseq ◽  
Virus Diversity ◽  
Illumina Hiseq Platform ◽  
Ecological Importance ◽  
Virus Communities ◽  
Virus Community ◽  
Insight Into

Aquatic viruses have been extensively studied over the past decade, yet fundamental aspects of freshwater virus communities remain poorly described. Our goal was to characterize virus communities captured in the >0.22 µm size-fraction seasonally and spatially in a freshwater harbour. Community DNA was extracted from water samples and sequenced on an Illumina HiSeq platform. Assembled contigs were annotated as belonging to the virus groups (i.e., order or family) Caudovirales, Mimiviridae, Phycodnaviridae, and virophages (Lavidaviridae), or to other groups of undefined viruses. Virophages were often the most abundant group, and discrete virophage taxa were remarkably stable across sites and dates despite fluctuations in Mimiviridae community composition. Diverse Mimiviridae contigs were detected in the samples and the two sites contained distinct Mimiviridae communities, suggesting that Mimiviridae are important algal viruses in this system. Caudovirales and Phycodnaviridae were present at low abundances in most samples. Of the 18 environmental parameters tested, only chlorophyll a explained the variation in the data at the order or family level of classification. Overall, our findings provide insight into freshwater virus community assemblages by expanding the documented diversity of freshwater virus communities, highlighting the potential ecological importance of virophages, and revealing distinct communities over small spatial scales.

scholarly journals Configuration of flowsheet and reagent dosage for gilsonite flotation towards the ultra-low-ash concentrate

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ataallah Bahrami ◽  
Fatemeh Kazemi ◽  
Mirsaleh Mirmohammadi ◽  
Yousef Ghorbani ◽  
Saghar Farajzadeh
Keyword(s):  
Sulfuric Acid ◽  
Sodium Silicate ◽  
Tannic Acid ◽  
Size Fraction ◽  
Sodium Cyanide ◽  
Ash Content ◽  
Drilling Fluids ◽  
Gas Oil ◽  
Size Fractions ◽  
Process Mineralogy

AbstractGilsonite has a wide variety of applications in the industry, including the manufacture of electrodes, paints and resins, as well as the production of asphalt and roof-waterproofing material. Gilsonite ash is a determining parameter for its application in some industries (e.g., gilsonite with ash content < 5% used as an additive in drilling fluids, resins). Due to the shortage of high grade (low ash) gilsonite reserves, the aim of this study is to develop a processing flowsheet for the production of ultra-low-ash gilsonite (< 5%), based on process mineralogy studies and processing tests. For this purpose, mineralogical studies and flotation tests have been performed on a sample of gilsonite with an average ash content of 15%. According to mineralogical studies, carbonates and clay minerals are the main associated impurities (more than 90 vol.%). Furthermore, sulfur was observed in two forms of mineral (pyrite and marcasite) and organic in the structure of gilsonite. Most of these impurities are interlocked with gilsonite in size fractions smaller than 105 µm. The size fraction of + 105 − 420 µm has a higher pure gilsonite (approximately 90%) than other size fractions. By specifying the gangue minerals with gilsonite and the manner and extent of their interlocking with gilsonite, + 75 − 420 µm size fraction selected to perform flotation tests. Flotation tests were performed using different reagents including collector (Gas oil, Kerosene and Pine oil), frother (MIBC) and depressant (sodium silicate, tannic acid, sulfuric acid and sodium cyanide) in different dosages. Based on the results, the use of kerosene collector, MIBC frother and a mixture of sodium silicate, tannic acid, sulfuric acid and sodium cyanide depressant had the most favorable results in gilsonite flotation in the rougher stage. Cleaner and recleaner flotation stages for the rougher flotation concentrate resulted in a product with an ash content of 4.89%. Due to the interlocking of gilsonite with impurities in size fractions − 105 µm, it is better to re-grinding the concentrate of the rougher stage beforehand flotation in the cleaner and recleaner stages. Finally, based on the results of mineralogical studies and processing tests, a processing flowsheet including crushing and initial granulation of gilsonite, flotation in rougher, cleaner and recleaner stages has been proposed to produce gilsonite concentrate with < 5% ash content.

scholarly journals Long term trends in fertility of soils under continuous cultivation and cereal cropping in southern Queensland. III. Distribution and kinetics of soil organic carbon in particle size fractions

Soil Research ◽  
1986 ◽  
Vol 24 (2) ◽  
pp. 293 ◽  
Author(s):  
RC Dalal ◽  
RJ Mayer
Keyword(s):  
Particle Size ◽  
Organic Matter ◽  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Size Fraction ◽  
Organic C ◽  
Size Fractions ◽  
Particle Size Fractions ◽  
Clay Size Fraction ◽  
Sand Size

Distribution of soil organic carbon in sand-, silt- and clay-size fractions during cultivation for periods ranging from 20 to 70 years was studied in six major soils used for cereal cropping in southern Queensland. Particle-size fractions were obtained by dispersion in water using cation exchange resin, sieving and sedimentation. In the soils' virgin state no single particle-size fraction was found to be consistently enriched as compared to the whole soil in organic C in all six soils, although the largest proportion (48%) of organic C was in the clay-size fraction; silt and sand-size fractions contained remaining organic C in equal amounts. Upon cultivation, the amounts of organic C declined from all particle-size fractions in most soils, although the loss rates differed considerably among different fractions and from the whole soil. The proportion of the sand-size fraction declined rapidly (from 26% to 12% overall), whereas that of the clay-size fraction increased from 48% to 61% overall. The proportion of silt-size organic C was least affected by cultivation in most soils. It was inferred, therefore, that the sand-size organic matter is rapidly lost from soil, through mineralization as well as disintegration into silt-size and clay-size fractions, and that the clay fraction provides protection for the soil organic matter against microbial and enzymic degradation.

scholarly journals Atmospheric trace metals measured at a regional background site (Welgegund) in South Africa

2017 ◽  
Vol 17 (6) ◽  
pp. 4251-4263 ◽  
Author(s):  
Andrew D. Venter ◽  
Pieter G. van Zyl ◽  
Johan P. Beukes ◽  
Micky Josipovic ◽  
Johan Hendriks ◽  
...  
Keyword(s):  
South Africa ◽  
Trace Metals ◽  
Trace Metal ◽  
Size Fraction ◽  
Abundant Species ◽  
Metal Species ◽  
Metal Concentrations ◽  
Igneous Complex ◽  
Size Fractions ◽  
Bushveld Igneous Complex

Abstract. Atmospheric trace metals can cause a variety of health-related and environmental problems. Only a few studies on atmospheric trace metal concentrations have been conducted in South Africa. Therefore the aim of this study was to determine trace metal concentrations in aerosols collected at a regional background site, i.e. Welgegund, South Africa. PM1, PM1–2. 5 and PM2. 5–10 samples were collected for 13 months, and 31 atmospheric trace metal species were detected. Atmospheric iron (Fe) had the highest concentrations in all three size fractions, while calcium (Ca) was the second-most-abundant species. Chromium (Cr) and sodium (Na) concentrations were the third- and fourth-most-abundant species, respectively. The concentrations of the trace metal species in all three size ranges were similar, with the exception of Fe, which had higher concentrations in the PM1 size fraction. With the exception of titanium (Ti), aluminium (Al) and manganese (Mg), 70 % or more of the trace metal species detected were in the smaller size fractions, which indicated the influence of industrial activities. However, the large influence of wind-blown dust was reflected by 30 % or more of trace metals being present in the PM2. 5–10 size fraction. Comparison of trace metals determined at Welgegund to those in the western Bushveld Igneous Complex indicated that at both locations similar species were observed, with Fe being the most abundant. However, concentrations of these trace metal species were significantly higher in the western Bushveld Igneous Complex. Fe concentrations at the Vaal Triangle were similar to levels thereof at Welgegund, while concentrations of species associated with pyrometallurgical smelting were lower. Annual average Ni was 4 times higher, and annual average As was marginally higher than their respective European standard values, which could be attributed to regional influence of pyrometallurgical industries in the western Bushveld Igneous Complex. All three size fractions indicated elevated trace metal concentrations coinciding with the end of the dry season, which could partially be attributed to decreased wet removal and increases in wind generation of particulates. Principal component factor analysis (PCFA) revealed four meaningful factors in the PM1 size fraction, i.e. crustal, pyrometallurgical-related and Au slimes dams. No meaningful factors were determined for the PM1–2. 5 and PM2. 5–10 size fractions, which was attributed to the large influence of wind-blown dust on atmospheric trace metals determined at Welgegund. Pollution roses confirmed the influence of wind-blown dust on trace metal concentrations measured at Welgegund, while the impact of industrial activities was also substantiated.

scholarly journals Pooling size sorted malaise trap fractions to maximise taxon recovery with metabarcoding

2020 ◽  
Author(s):  
Vasco Elbrecht ◽  
Sarah J. Bourlat ◽  
Thomas Hörren ◽  
Angie Lindner ◽  
Adriana Mordente ◽  
...  
Keyword(s):  
Size Fraction ◽  
Sequencing Depth ◽  
List Type ◽  
Malaise Trap ◽  
Size Fractions ◽  
Size Classes ◽  
Size Sorting ◽  
The Individual ◽  
Size Heterogeneity ◽  
Wet Sieving

AbstractSmall and rare specimens can remain undetected when metabarcoding bulk samples with a high size heterogeneity of specimens. This is especially critical for malaise trap samples, where most of the biodiversity is often contributed by small specimens. How to size sort and in which proportions to pool these samples has not been widely explored. We set out to find a size sorting strategy that maximizes taxonomic recovery but remains highly scalable and time efficient.Three 3 malaise trap samples where size sorted into 4 size classes using dry sieving. Each fraction was homogenized and lysed. The corresponding lysates were pooled to simulate samples never sorted, pooled in equal proportions and in 4 different proportions favoring the small size fractions. DNA from the pooled fractions as well as the individual size classes were extracted and metabarcoded using the FwhF2 and Fol-degen-rev primer set. Additionally wet sieving strategies were explored.The small size fractions harbored the highest diversity, and were best represented when pooling in favor of small specimens. Not size sorting a sample leads to a 45-77% decrease in taxon recovery compared to size sorted samples. A size separation into only 2 fractions (below 4 mm and above) can already double taxon recovery compared to not sorting. However, increasing the sequencing depth 3-4 fold can also increase taxon recovery to comparable levels, but remains biased toward biomass rich taxa in the sample.We demonstrate that size fractionizing bulk malaise samples can increase taxon recovery. The most practical approach is wet sieving into two size fractions, and proportional pooling of the lysates in favor of the small size fraction (80-90% volume). However, in large projects with time constraints, increasing sequencing depth can also be an alternative solution.

scholarly journals Towards end-to-end disease prediction from raw metagenomic data

2020 ◽  
Author(s):  
Maxence Queyrel ◽  
Edi Prifti ◽  
Jean-Daniel Zucker
Keyword(s):  
Dna Sequences ◽  
Real Life ◽  
Multiple Instance Learning ◽  
Disease Classification ◽  
Metagenomic Data ◽  
Numerical Representation ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
End To End ◽  
Bioinformatics Workflows

AbstractAnalysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and are stored as fastq files. Conventional processing pipelines consist multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Recent studies have demonstrated that training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimentionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life datasets as well a simulated one, we demonstrated that this original approach reached very high performances, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks.

Mega- and meta-analyses of fecal metagenomic studies in predicting response to immune checkpoint inhibitors.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 2570-2570
Author(s):  
Alya Heirali ◽  
Bo Chen ◽  
Matthew Wong ◽  
Pierre H.H. Schneeberger ◽  
Victor Rey ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Immune Checkpoint ◽  
Statistical Power ◽  
Immune Checkpoint Inhibitors ◽  
Checkpoint Inhibitors ◽  
Bacterial Species ◽  
Metagenomic Data ◽  
Tumor Type ◽  
Meta Analyses ◽  
Clostridium Bolteae

2570 Background: A number of studies have demonstrated that the gut microbiome of responders to immune checkpoint inhibitors (ICI) is compositionally different compared to that of non-responders. However, differences in study design, patient cohorts and bioinformatic analyses make it challenging to identify bacterial species consistently associated with response to ICI across different cohorts and cancer types. Methods: We leveraged the statistical power of mega- and meta-analyses to identify bacterial species consistently associated with response to ICI using data from three published fecal metagenomic studies (Gopalakrishnan et al., Science 2018; Matson et al., Science 2018; Routy et al., Science 2018). Metagenomic data was uniformly processed and analyzed using Metaphlan v2.0. We conducted a two-part modelling approach of bacterial species present in at least 20% of samples to account for both prevalence and relative abundance differences between responders/non-responders. Results: A total of 190 patients (n = 103 responders; n = 87 non-responders) were included from the three studies. Data from Routy et al., was analyzed as subsets based on tumor type for a total of 4 analyzed cohorts. We identified five species including Bacteroides thetaiotaomicron, Clostridium bolteae, Holdemania filiformis, Clostridiaceae bacterium JC118 and Escherichia coli that were concordantly significantly different between responders and non-responders using both meta- and mega-analyses. B. thetaiotaomicron and Clostridium bolteae relative abundance (RA) were independently predictive of non-response to immunotherapy when data sets were combined and analyzed using mega-analyses (AUC 0.59 95% CI 0.51-0.68 and AUC 0.61 95% CI 0.52-0.69, respectively). Conclusions: Despite inter-cohort heterogeneity in tumor type, treatment regimens, and sequencing modalities, meta- and mega analysis of published metagenomic studies identified generalizable bacterial species associated with ICI response or lack thereof. B. thetaiotaomicron and C. bolteae were predictors of non-response to ICI suggesting the clinical potential of narrow spectrum anti-biotics targeting non-response associated bacterial species to improve outcomes in ICI recipients.

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