Testing different (e)DNA metabarcoding approaches to assess aquatic oligochaete diversity and the biological quality of sediments

2019 ◽  
Vol 106 ◽  
pp. 105453 ◽  
Author(s):  
Régis Vivien ◽  
Laure Apothéloz-Perret-Gentil ◽  
Jan Pawlowski ◽  
Inge Werner ◽  
Benoit J.D. Ferrari
Keyword(s):  
Biological Quality ◽  
Aquatic Oligochaete ◽  
Dna Metabarcoding

scholarly journals High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes

2021 ◽  
Vol 4 ◽  
Author(s):  
Régis Vivien ◽  
Laure Apothéloz-Perret-Gentil ◽  
Jan Pawlowski ◽  
Inge Werner ◽  
Michel Lafont ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
Genetic Identification ◽  
Dna Barcodes ◽  
Biological Quality ◽  
Dna Metabarcoding ◽  
Morphological Approach

Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.

scholarly journals Spatiotemporal variation of the indoor mycobiome in daycare centers

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Eva Lena F. Estensmo ◽  
Luis Morgado ◽  
Sundy Maurice ◽  
Pedro M. Martin-Sanchez ◽  
Ingeborg B. Engh ◽  
...  
Keyword(s):  
Air Quality ◽  
Indoor Air Quality ◽  
Indoor Air ◽  
Seasonal Pattern ◽  
Spatiotemporal Variation ◽  
Fungal Community Composition ◽  
Daycare Centers ◽  
Outdoor Climate ◽  
Dna Metabarcoding

Abstract Background Children spend considerable time in daycare centers in parts of the world and are exposed to the indoor micro- and mycobiomes of these facilities. The level of exposure to microorganisms varies within and between buildings, depending on occupancy, climate, and season. In order to evaluate indoor air quality, and the effect of usage and seasonality, we investigated the spatiotemporal variation in the indoor mycobiomes of two daycare centers. We collected dust samples from different rooms throughout a year and analyzed their mycobiomes using DNA metabarcoding. Results The fungal community composition in rooms with limited occupancy (auxiliary rooms) was similar to the outdoor samples, and clearly different from the rooms with higher occupancy (main rooms). The main rooms had higher abundance of Ascomycota, while the auxiliary rooms contained comparably more Basidiomycota. We observed a strong seasonal pattern in the mycobiome composition, mainly structured by the outdoor climate. Most markedly, basidiomycetes of the orders Agaricales and Polyporales, mainly reflecting typical outdoor fungi, were more abundant during summer and fall. In contrast, ascomycetes of the orders Saccharomycetales and Capnodiales were dominant during winter and spring. Conclusions Our findings provide clear evidences that the indoor mycobiomes in daycare centers are structured by occupancy as well as outdoor seasonality. We conclude that the temporal variability should be accounted for in indoor mycobiome studies and in the evaluation of indoor air quality of buildings.

scholarly journals Assessment of the effects of wastewater treatment plant effluents on receiving streams using oligochaete communities of the porous matrix

2019 ◽  
pp. 18
Author(s):  
Régis Vivien ◽  
Michel Lafont ◽  
Inge Werner ◽  
Mélanie Laluc ◽  
Benoit J.D. Ferrari
Keyword(s):  
Wastewater Treatment ◽  
Surface Water ◽  
Hyporheic Zone ◽  
Surface Sediments ◽  
Treatment Plant ◽  
Functional Trait ◽  
Porous Matrix ◽  
Biological Quality ◽  
Coarse Surface

Human activities can disturb the natural dynamics of exchanges between surface water and groundwater in rivers. Such exchanges contribute to the self-purification of the environment and an excess of infiltration can lead to contamination of groundwater. In addition, the porous matrix (coarse surface sediments and hyporheic zone), through which water exchanges occur, is a sink for pollutants. For environmental monitoring programs, it is therefore essential to take into account both the dynamics of vertical hydrological exchanges and the biological quality of this matrix. The functional trait (FTR) method, which is based on the study of oligochaete communities in coarse surface sediments and the hyporheic zone, was proposed as a tool to simultaneously assess the dynamics of vertical hydrological exchanges and the effects of pollutants present in the porous matrix. Here, we applied this method during two different periods (in March and September 2016), upstream and downstream of locations affected by discharges from wastewater treatment plants (WWTP) located in Switzerland. The biological quality of surface sediments and the hyporheic zone was shown to be better upstream of the WWTP in both campaigns. In addition, results suggested that the capacity for self-purification was lower downstream of the WWTP, and that groundwater at these locations was vulnerable to pollution by surface water. The FTR method proved valuable as a field method for detecting the effects of point source contamination on receiving streams. In the near future, this community-based approach will benefit from advances in the use of DNA barcodes for oligochaete species identification.

scholarly journals High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Régis Vivien ◽  
Laure Apothéloz-Perret-Gentil ◽  
Jan Pawlowski ◽  
Inge Werner ◽  
Michel Lafont ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
Biological Quality

scholarly journals Modern Methods for Assessing the Quality of Bee Honey and Botanical Origin Identification

Foods ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1028
Author(s):  
Anna Puścion-Jakubik ◽  
Maria Halina Borawska ◽  
Katarzyna Socha
Keyword(s):  
Near Infrared ◽  
Principal Component ◽  
Polyphenol Content ◽  
Chain Reaction ◽  
Dna Metabarcoding ◽  
Modern Methods ◽  
Quality Testing ◽  
Polymerase Chain ◽  
Origin Identification

This paper is a summary of the latest literature on methods for assessing quality of natural bee honey. The publication briefly characterizes methods recommended by the International Honey Commission, published in 2009, as well as newer methods published in the last 10 years. Modern methods of assessing honey quality focus mainly on analyzing markers of individual varieties and classifying them into varieties, using, among others, near infrared spectroscopy techniques (NIR), potentiometric tongue, electronic nose, nuclear magnetic resonance (NMR), zymography, polymerase chain reaction (PCR), DNA metabarcoding, and chemometric techniques including partial least squares (PLS), principal component analysis (PCA) and artificial neural networks (ANN). At the same time, effective techniques for analyzing adulteration, sugar, and water content, hydroxymethylfurfural (HMF), polyphenol content, and diastase activity are being sought. Modern techniques enable the results of honey quality testing to be obtained in a shorter time, using the principles of green chemistry, allowing, at the same time, for high precision and accuracy of determinations. These methods are constantly modified, so that the honey that is on sale is a product of high quality. Prospects for devising methods of honey quality assessment include the development of a fast and accurate alternative to the melissopalynological method as well as quick tests to detect adulteration.

Sea-urchin Embryo Bioassay for in situ Evaluation of the Biological Quality of Coastal Seawater

2001 ◽  
Vol 52 (1) ◽  
pp. 29-32 ◽  
Author(s):  
R. Beiras ◽  
E. Vázquez ◽  
J. Bellas ◽  
J.I. Lorenzo ◽  
N. Fernández ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Coastal Seawater ◽  
Biological Quality ◽  
Sea Urchin Embryo

Wesley Clair Mitchell and the “Illiberal Reformers”

2020 ◽  
pp. 35-56
Author(s):  
Luca Fiorito ◽  
Massimiliano Vatiero
Keyword(s):  
Human Nature ◽  
Progressive Era ◽  
Cultural Milieu ◽  
Biological Quality

The aim of this article is to assess whether Wesley Clair Mitchell, as a reformer, ever expressed concern over the biological quality of individuals and whether he did somehow share the Progressive Era faith in eugenics as an instrument for improving American society’s health, welfare, and morals. Using both published and unpublished evidence, we argue that, as an institutionalist, Mitchell was free from the paternalistic and antidemocratic bent of the progressives described by Thomas Leonard and was ready to accept the new faith in the plasticity of human nature that sustained interwar reformism. At the same time, as someone who had been exposed to the Progressive Era cultural milieu, he could not completely divorce himself from the earlier decades’ preoccupation with the biological quality of individuals.

Biological quality of proteins from three strains of Pleurotus spp.

2006 ◽  
Vol 94 (4) ◽  
pp. 494-497 ◽  
Author(s):  
Gustavo Valencia del Toro ◽  
Rosalía Castelán Vega ◽  
Maria Eugenia Garín-Aguilar ◽  
Hermilo Leal Lara
Keyword(s):  
Biological Quality
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