scholarly journals Pooling size sorted Malaise trap fractions to maximize taxon recovery with metabarcoding

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12177
Author(s):  
Vasco Elbrecht ◽  
Sarah J. Bourlat ◽  
Thomas Hörren ◽  
Angie Lindner ◽  
Adriana Mordente ◽  
...  
Keyword(s):  
Large Scale ◽  
Size Fraction ◽  
Sequencing Depth ◽  
Malaise Trap ◽  
Size Fractions ◽  
Size Classes ◽  
Size Sorting ◽  
The Individual ◽  
Downstream Analysis ◽  
Wet Sieving

Background Small and rare specimens can remain undetected when metabarcoding is applied on bulk samples with a high specimen size heterogeneity. This is especially critical for Malaise trap samples, where most of the biodiversity is contributed by small taxa with low biomass. The separation of samples in different size fractions for downstream analysis is one possibility to increase detection of small and rare taxa. However, experiments systematically testing different size sorting approaches and subsequent proportional pooling of fractions are lacking, but would provide important information for the optimization of metabarcoding protocols. We set out to find a size sorting strategy for Malaise trap samples that maximizes taxonomic recovery but remains scalable and time efficient. Methods Three Malaise trap samples were sorted into four size classes using dry sieving. Each fraction was homogenized and lysed. The corresponding lysates were pooled to simulate unsorted samples. Pooling was additionally conducted in equal proportions and in four different proportions enriching the small size fraction of samples. DNA from the individual size classes as well as the pooled fractions was extracted and metabarcoded using the FwhF2 and Fol-degen-rev primer set. Additionally, alternative wet sieving strategies were explored. Results The small size fractions harboured the highest diversity and were best represented when pooling in favour of small specimens. Metabarcoding of unsorted samples decreases taxon recovery compared to size sorted samples. A size separation into only two fractions (below 4 mm and above) can double taxon recovery compared to not size sorting. However, increasing the sequencing depth 3- to 4-fold can also increase taxon recovery to levels comparable with size sorting, but remains biased towards biomass rich taxa in the sample. Conclusion We demonstrate that size fractionation of Malaise trap bulk samples can increase taxon recovery. While results show distinct patterns, the lack of statistical support due to the limited number of samples processed is a limitation. Due to increased speed and lower risk of cross-contamination as well as specimen damage we recommend wet sieving and proportional pooling of the lysates in favour of the small size fraction (80–90% volume). However, for large-scale projects with time constraints, increasing sequencing depth is an alternative solution.

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 Sorting things out - assessing effects of unequal specimen biomass on DNA metabarcoding

2017 ◽  
Author(s):  
Vasco Elbrecht ◽  
Bianca Peinert ◽  
Florian Leese
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Size Fraction ◽  
Sequencing Depth ◽  
Coi Gene ◽  
Mountain Stream ◽  
Detection Rates ◽  
Size Classes ◽  
Dna Metabarcoding ◽  
Size Sorting

Environmental bulk samples often contain many taxa that vary several orders of magnitude in biomass. This can be problematic in DNA metabarcoding and metagenomic high-throughput sequencing approaches, as large specimens contribute disproportionately high amounts of DNA template. Thus, a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples by specimen size and balancing the amounts of tissue used per size fraction should improve detection rates, but this approach has not been systematically tested. Here we explored the effects of size sorting on taxa detection using two freshwater macroinvertebrate monitoring samples, collected from a low-mountain stream in Germany. Specimens were morphologically identified and sorted into three size classes (body size < 2.5x5, 5x10 and up to 10x20 mm). Tissue from each size category was extracted individually, and pooled to simulate samples that were not sorted by biomass ("Unsorted"). Additionally, size fractions were pooled so that each specimen contributed approximately equal amounts of biomass ("Sorted"). Mock samples were amplified using four different DNA metabarcoding primer sets targeting the Cytochrome c oxidase I (COI) gene. Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification of taxa compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples, at the same sequencing depth. Our results imply that sequencing depth can be decreased approximately five-fold when sorting the samples into three size classes and pooling by specimen abundance. Our study demonstrates that even a coarse size sorting can substantially improve taxa detection using DNA metabarcoding. While high throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass is a simple yet efficient method to reduce current sequencing costs.

scholarly journals Sorting things out - assessing effects of unequal specimen biomass on DNA metabarcoding

2017 ◽  
Author(s):  
Vasco Elbrecht ◽  
Bianca Peinert ◽  
Florian Leese
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Size Fraction ◽  
Sequencing Depth ◽  
West Germany ◽  
Coi Gene ◽  
Mountain Stream ◽  
Size Classes ◽  
Dna Metabarcoding ◽  
Size Sorting

1) Environmental bulk samples often contain many taxa with biomass differences of several orders of magnitude. This can be problematic in DNA metabarcoding and metagenomic high throughput sequencing approaches, as large specimens contribute disproportionate amounts of DNA template. Thus a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples and balancing the amounts of tissue used per size fraction should improve detection rates, but this approach has not been systematically tested. 2) Here we tested the effects of size sorting on taxa detection using freshwater macroinvertebrates. Kick sampling was performed at two locations of a low-mountain stream in West Germany, specimens were morphologically identified and sorted into small, medium and large size classes (< 2.5x5, 5x10 and up to 10x20 mm). Tissue from the 3 size categories was extracted individually, and pooled to simulate samples that were not sorted by biomass and samples that were sorted and then pooled so that each specimen contributed approximately equal amounts of biomass. DNA from all five extractions of samples from both sites was amplified using four different DNA metabarcoding primer sets targeting the Cytochrome c oxidase I (COI) gene. The library was sequenced on a HiSeq Illumina sequencer. 3) Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples, at the same sequencing depth. Our results imply that sequencing depth can be decreased approximately five-fold when sorting the samples into three size classes. 4) Our results demonstrate that even a coarse size sorting can substantially improve detection of taxa using DNA metabarcoding. While high throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass is a simple yet efficient method to reduce current sequencing costs.

scholarly journals Sorting things out - assessing effects of unequal specimen biomass on DNA metabarcoding

2017 ◽  
Author(s):  
Vasco Elbrecht ◽  
Bianca Peinert ◽  
Florian Leese
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Size Fraction ◽  
Sequencing Depth ◽  
Coi Gene ◽  
Mountain Stream ◽  
Detection Rates ◽  
Size Classes ◽  
Dna Metabarcoding ◽  
Size Sorting

Environmental bulk samples often contain many taxa that vary several orders of magnitude in biomass. This can be problematic in DNA metabarcoding and metagenomic high-throughput sequencing approaches, as large specimens contribute disproportionately high amounts of DNA template. Thus, a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples by specimen size and balancing the amounts of tissue used per size fraction should improve detection rates, but this approach has not been systematically tested. Here we explored the effects of size sorting on taxa detection using two freshwater macroinvertebrate monitoring samples, collected from a low-mountain stream in Germany. Specimens were morphologically identified and sorted into three size classes (body size < 2.5x5, 5x10 and up to 10x20 mm). Tissue from each size category was extracted individually, and pooled to simulate samples that were not sorted by biomass ("Unsorted"). Additionally, size fractions were pooled so that each specimen contributed approximately equal amounts of biomass ("Sorted"). Mock samples were amplified using four different DNA metabarcoding primer sets targeting the Cytochrome c oxidase I (COI) gene. Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification of taxa compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples, at the same sequencing depth. Our results imply that sequencing depth can be decreased approximately five-fold when sorting the samples into three size classes and pooling by specimen abundance. Our study demonstrates that even a coarse size sorting can substantially improve taxa detection using DNA metabarcoding. While high throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass is a simple yet efficient method to reduce current sequencing costs.

scholarly journals Sorting things out - assessing effects of unequal specimen biomass on DNA metabarcoding

2016 ◽  
Author(s):  
Vasco Elbrecht ◽  
Bianca Peinert ◽  
Florian Leese
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequencing Depth ◽  
West Germany ◽  
Coi Gene ◽  
Mountain Stream ◽  
Detection Rates ◽  
Size Classes ◽  
Dna Metabarcoding ◽  
Size Sorting

1) Environmental bulk samples often contain many taxa with biomass differences of several orders of magnitude. This can be problematic in DNA metabarcoding and metagenomic high throughput sequencing approaches, as large specimens contribute over proportionally much DNA template. Thus a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples and balancing the amounts of tissue used per size fraction should improve detection rates, but has not been systematically tested. 2) Here we tested the effects of size sorting on taxa detection using freshwater macroinvertebrates. Kick sampling was performed at two locations of a low-mountain stream in West Germany, specimens were morphologically identified and sorted into small, medium and large size classes (< 2.5x5, 5x10 and up to 10x20 mm). Tissue from the 3 size categories was extracted individually, and pooled to simulate bulk samples that were not sorted and samples which were sorted and then pooled proportionately by specimen size. DNA from all 5 extractions of both samples was amplified using 4 different freshwater primer sets for the COI gene and sequenced on a HiSeq Illumina sequencer. 3) Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples, at the same sequencing depth. Our results imply that sequencing depth can be decreased ~ 5 fold when sorting the samples into three size classes. 4) Our results demonstrate that even a coarse size sorting can substantially improve detection rates. While high throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass is a simple yet efficient method to reduce current sequencing costs.

Models, Practices and Methods of Reading: Evolution in Time and Space

2009 ◽  
pp. 59-64
Author(s):  
Yulia P. Melentyeva
Keyword(s):  
Large Scale ◽  
Social Groups ◽  
National Program ◽  
Time And Space ◽  
Lack Of Information ◽  
The Individual

In recent years as public in general and specialist have been showing big interest to the matters of reading. According to discussion and launch of the “Support and Development of Reading National Program”, many Russian libraries are organizing the large-scale events like marathons, lecture cycles, bibliographic trainings etc. which should draw attention of different social groups to reading. The individual forms of attraction to reading are used much rare. To author’s mind the main reason of such an issue has to be the lack of information about forms and methods of attraction to reading.

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.

Flexibility Effects in a Single Link Robotic Manipulator

1993 ◽  
Author(s):  
C. Nataraj
Keyword(s):  
Large Scale ◽  
Robotic Manipulator ◽  
Flexible Beam ◽  
Rotating Speed ◽  
Weighted Residuals ◽  
Individual Interaction ◽  
Single Link ◽  
Rigid Mass ◽  
The Individual ◽  
Future Work

Abstract A single link robotic manipulator is modeled as a rotating flexible beam with a rigid mass at the tip and accurate energy expressions are derived. The resulting partial differential equations are solved using an approximate method of weighted residuals. From the solutions, coupling between axial and flexural deformations and the interactions with rigid body motions are rigorously analyzed. The emphasis in the current paper is not on an exhaustive analysis of existing systems but it is rather intended to compare and highlight the various flexibility effects in a relatively simple system. Hence, a nondimensional parametric analysis is performed to determine the effect of several parameters (including the rotating speed) on the errors and the individual interaction effects are discussed. Comparison with previous work in the field shows important phenomena often ignored or buried in large scale numerical analyses. Future work including application to multi-link robots is outlined.

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.

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