User:David CasMor/sandbox
DNA Metabarcoding[edit]
DNA Metabarcoding is defined as the DNA or eDNA (environmental DNA) based simultaneous identification of many taxa within the same environmental sample. A metabarcode consists of a short variable gene region which is useful for taxonomic assignment flanked by highly conserved gene regions which can be used for primer design[1].
It must be distinguished between DNA barcodes for classical taxonomic identification and DNA metabarcodes for eDNA based biodiversity surveys of mixed samples.
Background[edit]
As early as1971, genetic method as nucleic acid hybridization were used for phylogenetic studies in cultured prokaryotes[2]. Nevertheless, is not until the late 80s where the first environmental DNA (eDNA) protocols for specie identification were proposed[3]. With the development of DNA amplification through PCR, species identification and phylogenetic studies started to be based on sequencing of PCR products[4], which ultimately allowed the first metabarcoding based study at the beginning of the 90s[5].
Methodology[edit]
The standard metabarcoding approach follows, in general, the same workflow that the DNA barcoding. This means, total DNA extraction, PCR amplification, sequencing and data analysis. The main difference between both approaches lies in what the research is interessted in. DNA barcoding looks for a specific species in the sample while DNA metabarcoding looks all the species presents in the sample.
Applications[edit]
In recent years research was focused on the possibilities of using eDNA metabarcoding as a tool for biological monitoring and assessment (such as identification of specific species and analyzing ecosystem function). An overview on metabarcoding studies from the last six years of research can be found in Pawlowski et al. (2018)[6], which propose that in the long term, new molecular indices should be developed based entirely on metabarcoding data. The development of an eDNA metabarcode based bioindicator system for standard monitoring programs has also been suggested by Stoeck et al. (2018c)[7]. Recent paper by Ruppert et al. (2019)[8] provides detailed systematic review of the present applications of eDNA metabarcoding, as well as the future applications (see below). As the authors stated, metabarcoding has the potential to complement biodiversity measures and even replace them in some instances, especially as the technology advances and procedures are optimized, cheaper and more widespread.
DNA metabarcoding applications:
- Ecosystem and biodiversity monitoring:
• Terrestrial monitoring
• Freshwater monitoring
• Estuarine monitoring
• Marine monitoring
- Paleology and ancient ecosystems
- Plant-pollinator interactions
- Diet analysis.
Advantages and Challenges[edit]
While traditional biomonitoring methods commonly include direct observation and capture of targeted organisms, that makes rare, endangered and invasive species to have less chances to be detected. This features make this method time-consuming and dependant of a taxonomy expert. On the other hand, metabarcoding methods are faster, less destructive and more sensitive. With a small amount of eDNA it can reach reliable detection of the different player of the community without depending on a taxonomists[9][10][11]. At the same time, metabarcoding is also time-effective because it requires less tools, volume of samples and experts[12]. Even though metabarcoding seems to be an ideal method, there are still limitations and biases that limits the results. At the same time, researches have not provide consensus considerations of experimental design and bioinformatic criteria that has to be applied to define detections during eDNA metabarcoding[13].
- ^ Pierre,, Taberlet, (2018). Environmental DNA : for biodiversity research and monitoring. Bonin, Aurelie, 1979-. Oxford. ISBN 9780191079993. OCLC 1021883023.
{{cite book}}: CS1 maint: extra punctuation (link) CS1 maint: location missing publisher (link) CS1 maint: multiple names: authors list (link) - ^ Sogin, S. J.; Sogin, M. L.; Woese, C. R. (1972). "Phylogenetic measurement in procaryotes by primary structural characterization". Journal of Molecular Evolution. 1 (2): 173–184. doi:10.1007/bf01659163. ISSN 0022-2844.
- ^ Ogram, Andrew; Sayler, Gary S.; Barkay, Tamar (1987). "The extraction and purification of microbial DNA from sediments". Journal of Microbiological Methods. 7 (2–3): 57–66. doi:10.1016/0167-7012(87)90025-X.
- ^ Cronin, Matthew A.; Palmisciano, Daniel A.; Vyse, Ernest R.; Cameron, David G. (1991). "Mitochondrial DNA in Wildlife Forensic Science: Species Identification of Tissues". Wildlife Society Bulletin (1973-2006). 19 (1): 94–105. ISSN 0091-7648.
- ^ Giovannoni, Stephen J.; Britschgi, Theresa B.; Moyer, Craig L.; Field, Katharine G. (1990). "Genetic diversity in Sargasso Sea bacterioplankton". Nature. 345 (6270): 60–63. doi:10.1038/345060a0. ISSN 0028-0836.
- ^ Pawlowski, Jan; Kelly-Quinn, Mary; Altermatt, Florian; Apothéloz-Perret-Gentil, Laure; Beja, Pedro; Boggero, Angela; Borja, Angel; Bouchez, Agnès; Cordier, Tristan (2018-10). "The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems". Science of The Total Environment. 637–638: 1295–1310. doi:10.1016/j.scitotenv.2018.05.002.
{{cite journal}}: Check date values in:|date=(help) - ^ Stoeck, Thorsten; Frühe, Larissa; Forster, Dominik; Cordier, Tristan; Martins, Catarina I.M.; Pawlowski, Jan (2018-2). "Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture". Marine Pollution Bulletin. 127: 139–149. doi:10.1016/j.marpolbul.2017.11.065.
{{cite journal}}: Check date values in:|date=(help) - ^ Ruppert, Krista M.; Kline, Richard J.; Rahman, Md Saydur (2019-1). "Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA". Global Ecology and Conservation. 17: e00547. doi:10.1016/j.gecco.2019.e00547.
{{cite journal}}: Check date values in:|date=(help) - ^ "ScienceDirect". www.sciencedirect.com. doi:10.1016/j.scitotenv.2018.05.002. Retrieved 2019-03-29.
- ^ Jerde, Christopher L.; Mahon, Andrew R.; Chadderton, W. Lindsay; Lodge, David M. (2011). ""Sight-unseen" detection of rare aquatic species using environmental DNA: eDNA surveillance of rare aquatic species". Conservation Letters. 4 (2): 150–157. doi:10.1111/j.1755-263X.2010.00158.x.
- ^ Goldberg, Caren S.; Turner, Cameron R.; Deiner, Kristy; Klymus, Katy E.; Thomsen, Philip Francis; Murphy, Melanie A.; Spear, Stephen F.; McKee, Anna; Oyler‐McCance, Sara J. (2016). "Critical considerations for the application of environmental DNA methods to detect aquatic species". Methods in Ecology and Evolution. 7 (11): 1299–1307. doi:10.1111/2041-210X.12595. ISSN 2041-210X.
- ^ Evans, Nathan T.; Olds, Brett P.; Renshaw, Mark A.; Turner, Cameron R.; Li, Yiyuan; Jerde, Christopher L.; Mahon, Andrew R.; Pfrender, Michael E.; Lamberti, Gary A. (2016). "Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding". Molecular Ecology Resources. 16 (1): 29–41. doi:10.1111/1755-0998.12433. PMC 4744776. PMID 26032773.
{{cite journal}}: CS1 maint: PMC format (link) - ^ Evans, Darren M.; Kitson, James J. N.; Lunt, David H.; Straw, Nigel A.; Pocock, Michael J. O. (2016). "Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems". Functional Ecology. 30 (12): 1904–1916. doi:10.1111/1365-2435.12659. ISSN 1365-2435.