Search results for "Metabarcoding"

Re-Clustering tool using an Open-Reference method that improves OTU definition

2019

International audience; 1.Environmental microbial communities are now widely studied using metabarcoding approaches, thanks to the democratization of high‐throughput DNA sequencing technologies. The massive number of reads produced with these technologies requires bioinformatic solutions to be treated. A key step in the analysis is to cluster reads into Operational Taxonomic Units (or OTUs) and thus reduce the amount of data for downstream analyses. Due to the important impact of the clustering method on the quantity and quality of OTUs, finding an equilibrium between the reliability and time‐consuming nature of the chosen strategy is a real challenge. The present article proposes a new pos…

Molecular analysis ofPhytophthoradiversity in nursery-grown ornamental and fruit plants

2015

The genetic diversity of Phytophthora spp. was investigated in potted ornamental and fruit tree species. A metabarcoding approach was used, based on a semi-nested PCR with Phytophthora genus-specific primers targeting the ITS1 region of the rDNA. More than 50 ITS1 sequence types representing at least 15 distinct Phytophthora taxa were detected. Nine had ITS sequences that grouped them in defined taxonomic groups (P. nicotianae, P. citrophthora, P. meadii, P. taxon Pgchlamydo, P. cinnamomi, P. parvispora, P. cambivora, P. niederhauserii and P. lateralis) whereas three phylotypes were associated to two or more taxa (P. citricola taxon E or III; P. pseudosyringae, P. ilicis or P. nemorosa; and…

Whither the species? Phytophthora taxa, MOTUs and barcodes in the world of metagenomics

2015

The study of ecosystem diversity is being transformed by high throughput sequencing technology that allows an unparalleled depth of sampling of DNA barcode sequences. The opportunities are great at this fascinating interface of pathology, ecology, taxonomy and molecular biology but there are pitfalls. It is important to consider the potential for bias at all steps in the process from sampling through to data analysis. Increasingly Phytophthora diversity is being examined by metabarcoding of the PCR amplified rDNA ITS regions from soil, water or plant sample DNA. We have applied baiting and isolation, cloning and Sanger sequencing and Illumina MiSeq analysis to a time-series of filtered wate…

Metagenomic strategies to assess genetic diversity in Phytophthora species

ENHANCED BIOREMEDIATION E MONITORAGGIO MICROBIOLOGICO DI ACQUA CONTAMINATA DA SOLVENTI CLORURATI

2023

I solventi clorurati sono composti organici di sintesi appartenenti alla classe degli idrocarburi alifatici clorurati, largamente impiegati in diversi settori industriali e, come conseguenza, ampiamente diffusi nell’ambiente come inquinanti e particolarmente pericolosi anche per la salute umana. Tra i metodi di bonifica di siti contaminati da solventi clorurati, quelli basati sul biorisanamento sfruttano uno dei peculiari metabolismi batterici coinvolti nella biodegradazione di tali composti: la declorurazione riduttiva anaerobia in cui il composto clorurato è utilizzato come accettore terminale di elettroni in un vero e proprio processo di respirazione anaerobia, detta dealorespirazione; i…

Assessing the effect of chromium pollution on benthic foraminiferal community: morphological vs. environmental metabarcoding approaches

The purpose of this experimental study is to assess the impact of different concentrations of chromium (Cr) through time on the diversity of cultured benthic foraminifera combining two morphological approaches for the identification of living specimens that are Rose Bengal (RB) staining and CellTracker Green (CTG) labelling as well as environmental DNA and RNA metabarcoding. Seven tanks/aquaria with different concentrations of Cr in water, namely 100 ppt, 1 ppb, 10 ppb, 100 ppb, 1 ppm and 10 ppm plus the control were used. A mesocosm was extracted from each tank at pre-established time (1 week, 2 weeks, 4 weeks 6 weeks and 8 weeks). Morphological analyses produced 6 datasets based on staini…

Supplementary material 1 from: Lefort M, Wratten S, Cusumano A, Varennes Y, Boyer S (2017) Disentangling higher trophic level interactions in the cab…

2018

OSR aphid mummy collection. Sampling location and size / Amplification success of mummies' DNA extracts by Illumina sequencing.

Supplementary material 3 from: Lefort M, Wratten S, Cusumano A, Varennes Y, Boyer S (2017) Disentangling higher trophic level interactions in the cab…

2018

Exploratory statistics addressing sequencing depth per country and MOTU rarefaction.

Supplementary material 2 from: Lefort M, Wratten S, Cusumano A, Varennes Y, Boyer S (2017) Disentangling higher trophic level interactions in the cab…

2018

Supporting Information 2

Patrones estructurales y funcionales de las comunidades de procariotas en humedales mediterráneos y su relación con el ciclo del carbono

2023

Las zonas húmedas mediterráneas juegan un papel muy importante en los ciclos biogeoquímicos, ya que la presencia de agua, de forma constante o transitoria, favorece unas altas tasas metabólicas. Respecto al ciclo del carbono, los humedales mediterráneos se ven activamente involucrados en la captación o en la emisión de gases de efecto invernadero carbonados (C-GEI) hacia la atmósfera, concretamente el dióxido de carbono y el metano. Esta relevancia de los humedales en el ciclo del carbono se debe, en parte, a la actividad de las comunidades de procariotas que habitan en el agua y en el sedimento de las zonas húmedas, puesto que la abundancia y versatilidad metabólica de los procariotas les …