Search results for "Operational taxonomic unit"
showing 7 items of 7 documents
Further insights in the Tardigrada microbiome: phylogenetic position and prevalence of infection of four new Alphaproteobacteria putative endosymbion…
2019
Abstract Data from a previous study showed that microbiomes of six tardigrade species are species-specific and distinct from associated environmental microbes. We here performed a more in-depth analyses of those data, to identify and characterize new potential symbionts. The most abundant bacterial operational taxonomic units (OTUs) found in tardigrades are classified, and their prevalence in other environments is assessed using public databases. A subset of OTUs was selected for molecular phylogenetic analyses based on their affiliation with host-associated bacterial families in tardigrades. Almost 22.6% of the most abundant OTUs found do not match any sequence at 99% identity in the IMNGS…
Sample Preservation, DNA or RNA Extraction and Data Analysis for High-Throughput Phytoplankton Community Sequencing
2017
Phytoplankton is the basis for aquatic food webs and mirrors the water quality. Conventionally, phytoplankton analysis has been done using time consuming and partly subjective microscopic observations, but next generation sequencing (NGS) technologies provide promising potential for rapid automated examination of environmental samples. Because many phytoplankton species have tough cell walls, methods for cell lysis and DNA or RNA isolation need to be efficient to allow unbiased nucleic acid retrieval. Here, we analyzed how two phytoplankton preservation methods, three commercial DNA extraction kits and their improvements, three RNA extraction methods, and two data analysis procedures affect…
A practical method for barcoding and size-trimming PCR templates for amplicon sequencing
2016
Sample barcoding facilitates the analysis of tens or even hundreds of samples in a single next-generation sequencing (NGS) run, but more efficient methods are needed for high-throughput barcoding and size-trimming of long PCR products. Here we present a two-step PCR approach for barcoding followed by pool shearing, adapter ligation, and 5′ end selection for trimming sets of DNA templates of any size. Our new trimming method offers clear benefits for phylogenetic studies, since targeting exactly the same region maximizes the alignment and enables the use of operational taxonomic unit (OTU)-based algorithms.
Consequences of organ choice in describing bacterial pathogen assemblages in a rodent population
2017
SUMMARYHigh-throughput sequencing technologies now allow for rapid cost-effective surveys of multiple pathogens in many host species including rodents, but it is currently unclear if the organ chosen for screening influences the number and identity of bacteria detected. We used 16S rRNA amplicon sequencing to identify bacterial pathogens in the heart, liver, lungs, kidneys and spleen of 13 water voles (Arvicola terrestris) collected in Franche-Comté, France. We asked if bacterial pathogen assemblages within organs are similar and if all five organs are necessary to detect all of the bacteria present in an individual animal. We identified 24 bacteria representing 17 genera; average bacterial…
Decomposition of Microbial Necromass Is Divergent at the Individual Taxonomic Level in Soil
2021
The turnover of microbial biomass plays an important part in providing a significant source of carbon (C) to soil organic C. However, whether the decomposition of microbial necromass (non-living microbial biomass) in the soil varies at the individual taxa level remains largely unknown. To fill up these gaps, we compared the necromass decomposition of bacterial and archaeal taxa by separating live microbial biomass with 18O-stable isotope probing from dead microbial biomass in soil. Our results showed that most of the microbial necromass at the operational taxonomic unit level (88.51%), which mainly belong to Acidobacteria, Actinobacteria, Gemmatimonadetes, and Proteobacteria, decomposed sig…
Overestimation of the strength of size-assortative pairing in taxa with cryptic diversity: a case of Simpson's paradox.
2015
5 pages; International audience; Size-assortative pairing is one of the most common pairing patterns observed in nature and it probably occurs in many taxa with cryptic diversity. Observed patterns of size-assortative pairing in natural populations may thus be influenced by the co-occurrence of noninterbreeding cryptic groups of individuals living in sympatry. To quantify this potential bias, we sampled amphipods from the Gammarus pulex/Gammarus fossarum crustacean species complex in rivers containing two sympatric and morphologically cryptic groups, i.e. molecular operational taxonomic units (MOTUs). Within each river, MOTUs did not interbreed and differed in mean body size. We measured th…
Phylogenetic diversity and affiliation of tropical African ectomycorrhizal fungi
2022
Ectomycorrhizal fungi form a mutualistic symbiosis with plant roots, and are key for nutrient cycling in many ecosystems. Here we study the ectomycorrhizal fungal communities in the Oueme Superieur reserve forest in Benin (West Africa). We use phylogenetic methods to test if the species from the study site are closer to other tropical African species than to species from other regions. The Oueme Superieur community was represented by nine Operational Taxonomic Units in Amanitaceae, one in Boletaceae, one in Cantharellaceae, one in Cortinariaceae, two in Inocybaceae, fourteen in Russulaceae and three in Sclerodermataceae. Of these thirty-one Operational Taxonomic Units, twenty had no record …