AI Article Synopsis
- DNA-barcoding utilizes small DNA fragments to distinguish species and can effectively identify semi-cryptic species.
- The study analyzed 618 sequences from 114 diatom species and achieved a 99.5% success rate in separating biologically defined species using a specific barcode.
- The proposed barcode is a reliable and cost-effective method for identifying diatom species, outperforming other known molecular markers when reference sequences are available.
Article Abstract
DNA-barcoding is based on the premise that the divergence of a small DNA fragment coincides with biological separation of species. If true, it offers an additional tool for worldwide consistent species recognition even in cases of semi-cryptic species. Our study includes 618 sequences representing 114 diatom species belonging to the two most species-rich classes of diatoms (Mediophyceae and Bacillariophyceae). A 99.5% success rate in separating biologically defined species and a 91% success rate in separating all species tested was obtained when using the proposed barcode starting at the 5' end of 5.8S and ending in the conserved motif of helix III of ITS2 (300 to 400 bp). Including the whole 5.8S+ITS2 region did not significantly improve species resolution. We tested our barcode on 17 unidentified, misidentified or contaminated strains derived mostly from a culture collection, and these were correctly flagged as erroneous by their ITS sequences. We conclude that the proposed barcode represents for the Mediophyceae and Bacillariophyceae a robust, economical, and rapid way to recognize and identify most species (when a reference sequence is available) that is as good as or better than other molecular markers thus far proposed.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.protis.2009.07.001 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
A paradigm shift for evaluating natural attenuation of radioactive iodine in soils and sediments: Species-specific mechanisms and pathways.
J Environ Manage
January 2025
Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA. Electronic address:
The primary approach to assessing monitored natural attenuation (MNA) is currently based on a conceptual model utilizing the total contaminant concentrations, assuming a single aqueous species. However, many contaminants, such as metals and radionuclide - including iodine, can exist in multiple species that behave chemically differently in the environment and can exist simultaneously. For example, radioiodine often occurs concurrently as three major aqueous species: iodide (I), iodate (IO), and organo-I, which undergo distinct attenuation pathways and exhibit markedly different mobility and geochemical behavior.
View Article and Find Full Text PDFCoalescence characteristics of free-living and particle-attached bacteria in a cascade river-reservoir system: A case study of the Jinsha River.
J Environ Manage
January 2025
State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China.
Microbial coalescence plays a crucial role in shaping aquatic ecosystems by facilitating the merging of neighboring microbial communities, thereby influencing ecosystem structure. Although this phenomenon is commonly observed in natural environments, comprehensive quantitative comparative studies on different lifestyle bacteria involved in this process are still lacking. The study focuses on 16S rRNA Amplicon Sequence Variants (ASVs) at the Jinsha River hydropower stations (Wudongde [WDD], Baihetan [BHT], Xiluodu [XLD], Xiangjiaba [XJB]), specifically examining free-living (FL) and particle-attached (PA) bacteria.
View Article and Find Full Text PDFWild bees show local spatial and temporal dynamics in southeastern US blueberry farmscapes.
Environ Entomol
January 2025
Department of Entomology, University of Georgia, Tifton, GA, USA.
Wild bee communities are the target of various conservation and ecological restoration programs. Strategic conservation can influence bee communities visiting fields and help mitigate pollinator limitations in fruit production. However, planning compatible conservation strategies and gauging their effectiveness requires understanding how local communities vary across space and time in crops and adjacent semi-natural areas.
View Article and Find Full Text PDFStudy on the developmental, behavioral toxicity, and toxicological mechanism of the antidepressant drug venlafaxine and its active metabolites in zebrafish.
Environ Toxicol Chem
January 2025
School of Environment and Energy, South China University of Technology, Guangzhou, PR China.
As a representative agent of bicyclic antidepressants, venlafaxine (VEN) has become widely used worldwide and is frequently detected in surface waters with concentrations ranging from ng/L to µg/L. To evaluate the toxicological effects of such medications on aquatic species, studies on environmentally relevant concentrations are essential. Zebrafish were used as a model organism to assess growth and development in larvae and examine tissue accumulation, oxidative stress, and DNA methylation in adults.
View Article and Find Full Text PDFAssessing bioaccumulation with biomagnification factors from dietary bioaccumulation tests.
Integr Environ Assess Manag
January 2025
ExxonMobil Petroleum and Chemical BV, Machelen, Belgium.
Despite the fact that the UN Stockholm Convention on persistent organic pollutants specifically acknowledges that Arctic ecosystems and Indigenous communities are particularly at risk due to biomagnification of contaminants in traditional foods, the bioconcentration factor (BCF) of substances in fish remains the preferred metric for identifying the biomagnification potential of organic substances. The BCF measures uptake of substances from water in water-breathing organisms, but not biomagnification of contaminants from food sources. The purpose of this study is to investigate how the biomagnification factor (BMF) can be used in bioaccumulation assessments.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!