A panoramic review of DNA barcoding in microalgae: applications and challenge in the urgency of its use in Peru
DOI:
https://doi.org/10.56294/saludcyt20241136Keywords:
Molecular Identification, Taxonomy, Diversity, Ecology, Biotechnology, HABsAbstract
DNA barcoding is a tool for species identification and classification, overcoming traditional limitations; being fundamental for multiple studies and applications. This article will review the progress of the application of DNA barcoding for algal identification; as it presents advantages such as accuracy in species identification, its applicability to various stages and conditions for ecological studies and intraspecific genetic variability, which according to its approach will depend on several factors. DNA barcoding applications in microalgae, such as its molecular identification, is fundamental for diversity and ecology; expanding knowledge about microalgae; being useful in monitoring harmful algae (HABs) that are a danger to aquatic ecosystems; In addition, DNA barcoding of microalgae is used in biotechnology and food industries. In Peru, taxonomic research is of lesser incidence because there is no method that provides precise identification at the species level, among other reasons, but this DNA barcoding technique has proven to be an efficient tool for research in the conservation and management of organisms that are difficult to access or complex to differentiate, such as microalgae. To conclude, DNA barcoding represents an essential tool in modern microalgae research, which should be developed in Peru, as it has significant potential to advance our knowledge and management of these crucial organisms in Peruvian aquatic ecosystems
References
1. De Groot GA, During HJ, Maas JW, Schneider H, Vogel JC, Erkens RHJ. Use of rbcL and trnL-F as a Two-Locus DNA Barcode for Identification of NW-European Ferns: An Ecological Perspective. PLoS ONE 2011;6:e16371. https://doi.org/10.1371/journal.pone.0016371.
2. Hebert PDN, Cywinska A, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proc Biol Sci 2003;270:313–21. https://doi.org/10.1098/rspb.2002.2218.
3. An SS, Friedl T, Hegewald E. Phylogenetic Relationships of Scenedesmus and Scenedesmus‐ like Coccoid Green Algae as Inferred from ITS‐2 rDNA Sequence Comparisons. Plant Biology 1999;1:418–28. https://doi.org/10.1111/j.1438-8677.1999.tb00724.x.
4. Hebert PDN, deWaard JR, Landry J-F. DNA barcodes for 1/1000 of the animal kingdom. Biol Lett 2010;6:359–62. https://doi.org/10.1098/rsbl.2009.0848.
5. Hegewald E, Wolf M. Phylogenetic relationships of Scenedesmus and Acutodesmus (Chlorophyta, Chlorophyceae) as inferred from 18S rDNA and ITS-2 sequence comparisons. Plant Systematics and Evolution 2003;241:185–91. https://doi.org/10.1007/s00606-003-0061-7.
6. Torres MA, Barros MP, Campos SCG, Pinto E, Rajamani S, Sayre RT, et al. Biochemical biomarkers in algae and marine pollution: a review. Ecotoxicol Environ Saf 2008;71:1–15. https://doi.org/10.1016/j.ecoenv.2008.05.009.
7. Becker B, Marin B. Streptophyte algae and the origin of embryophytes. Ann Bot 2009;103:999–1004. https://doi.org/10.1093/aob/mcp044.
8. Amengual-Morro C, Moyà Niell G, Martínez-Taberner A. Phytoplankton as bioindicator for waste stabilization ponds. J Environ Manage 2012;95 Suppl:S71-76. https://doi.org/10.1016/j.jenvman.2011.07.008.
9. Krienitz L, Huss VAR, Bock C. Chlorella: 125 years of the green survivalist. Trends Plant Sci 2015;20:67–9. https://doi.org/10.1016/j.tplants.2014.11.005.
10. Borbor-Córdova MJ, Pozo-Cajas M, Cedeno-Montesdeoca A, Mantilla Saltos G, Kislik C, Espinoza-Celi ME, et al. Risk Perception of Coastal Communities and Authorities on Harmful Algal Blooms in Ecuador. Front Mar Sci 2018;5:365. https://doi.org/10.3389/fmars.2018.00365.
11. Oh J-W, Pushparaj SSC, Muthu M, Gopal J. Review of Harmful Algal Blooms (HABs) Causing Marine Fish Kills: Toxicity and Mitigation. Plants 2023;12:3936. https://doi.org/10.3390/plants12233936.
12. Sharma P, Sharma N. Industrial and Biotechnological Applications of Algae: A Review. JAPB 2017;1:1–25. https://doi.org/10.14302/issn.2638-4469.japb-17-1534.
13. Arora K, Kumar P, Bose D, Li X, Kulshrestha S. Potential applications of algae in biochemical and bioenergy sector. 3 Biotech 2021;11:296. https://doi.org/10.1007/s13205-021-02825-5.
14. Narayanan M, Kandasamy S, He Z, Hemaiswarya S, Raja R, Carvalho IS. Algae biotechnology for nutritional and pharmaceutical applications. Biotechnology in Healthcare, Volume 1, Elsevier; 2022, p. 177–94. https://doi.org/10.1016/B978-0-323-89837-9.00015-2.
15. Eze CN, Onyejiaka CK, Ihim SA, Ayoka TO, Aduba CC, Ndukwe JK, et al. Bioactive compounds by microalgae and potentials for the management of some human disease conditions. AIMSMICRO 2023;9:55–74. https://doi.org/10.3934/microbiol.2023004.
16. Sousa V, Pereira RN, Vicente AA, Dias O, Geada P. Microalgae biomass as an alternative source of biocompounds: New insights and future perspectives of extraction methodologies. Food Research International 2023;173:113282. https://doi.org/10.1016/j.foodres.2023.113282.
17. Dolganyuk V, Belova D, Babich O, Prosekov A, Ivanova S, Katserov D, et al. Microalgae: A Promising Source of Valuable Bioproducts. Biomolecules 2020;10:1153. https://doi.org/10.3390/biom10081153.
18. Díaz-Pillasca HB, Hernández-Amasifuen AD, Machahua M, Pineda-Lázaro AJ, Argüelles-Curaca A, Lugo B. Código de barras de ADN de tres especies de árboles frutales con potencial económico del valle de Huaura, Lima, Perú. RB 2021;3:1992–2000. https://doi.org/10.21931/RB/2021.06.03.18.
19. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics 2007;23:167–72. https://doi.org/10.1016/j.tig.2007.02.001.
20. Bergmann T, Hadrys H, Breves G, Schierwater B. Character-based DNA barcoding: a superior tool for species classification Charakter-basierte DNS Kodierung: ein überlegenes Werkzeug für die Klassifizierung von Arten. Berl Münch Tierärztl Wschr 2009:446–50. https://doi.org/10.2376/0005-9366-122-446.
21. Subhadra B, Grinson-George. Algal biorefinery-based industry: an approach to address fuel and food insecurity for a carbon-smart world. J Sci Food Agric 2011;91:2–13. https://doi.org/10.1002/jsfa.4207.
22. Yanuhar U, Caesar NR, Musa M. Identification of Local Isolate of Microalgae Chlorella Vulgaris using Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large Subunit (rbcL) Gene. IOP Conf Ser: Mater Sci Eng 2019;546:022038. https://doi.org/10.1088/1757-899X/546/2/022038.
23. Buchheim MA, Keller A, Koetschan C, Förster F, Merget B, Wolf M. Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life. PLoS One 2011;6:e16931. https://doi.org/10.1371/journal.pone.0016931.
24. Burja AM, Tamagnini P, Bustard MT, Wright PC. Identification of the green alga, Chlorella vulgaris (SDC1) using cyanobacteria derived 16S rDNA primers: targeting the chloroplast. FEMS Microbiology Letters 2001;202:195–203. https://doi.org/10.1111/j.1574-6968.2001.tb10803.x.
25. Caisová L, Marin B, Melkonian M. A close-up view on ITS2 evolution and speciation - a case study in the Ulvophyceae (Chlorophyta, Viridiplantae). BMC Evol Biol 2011;11:262. https://doi.org/10.1186/1471-2148-11-262.
26. Cecchin M, Marcolungo L, Rossato M, Girolomoni L, Cosentino E, Cuine S, et al. Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions. The Plant Journal 2019;100:1289–305. https://doi.org/10.1111/tpj.14508.
27. Liu M, Zhao Y, Sun Y, Li Y, Wu P, Zhou S, et al. Comparative study on diatom morphology and molecular identification in drowning cases. Forensic Science International 2020;317:110552. https://doi.org/10.1016/j.forsciint.2020.110552.
28. Pombert J-F, Otis C, Lemieux C, Turmel M. The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages. Mol Biol Evol 2005;22:1903–18. https://doi.org/10.1093/molbev/msi182.
29. El-Sheekh M, Abu-Faddan M, Abo-Shady A, Nassar MZA, Labib W. Molecular identification, biomass, and biochemical composition of the marine chlorophyte Chlorella sp. MF1 isolated from Suez Bay. Journal of Genetic Engineering and Biotechnology 2020;18:27. https://doi.org/10.1186/s43141-020-00044-8.
30. CBOL Plant Working Group, Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, et al. A DNA barcode for land plants. Proc Natl Acad Sci USA 2009;106:12794–7. https://doi.org/10.1073/pnas.0905845106.
31. Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, Berney C, et al. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol 2012;10:e1001419. https://doi.org/10.1371/journal.pbio.1001419.
32. Ratnasingham S, Hebert PDN. BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Mol Ecol Notes 2007;7:355–64. https://doi.org/10.1111/j.1471-8286.2007.01678.x.
33. Ballesteros I, Terán P, Guamán-Burneo C, González N, Cruz A, Castillejo P. DNA barcoding approach to characterize microalgae isolated from freshwater systems in Ecuador. Neotropical Biodiversity 2021;7:170–83. https://doi.org/10.1080/23766808.2021.1920296.
34. Fitriyah F, Faramitha Y, Sari DA, Kresnawaty I, Panji T, Santoso D. Molecular identification and phylogenetic analysis of Chlorella isolates from Indonesia using rbcL gene. MP 2021;89. https://doi.org/10.22302/iribb.jur.mp.v89i1.408.
35. Zou S, Li Q, Kong L. Monophyly, Distance and Character–Based Multigene Barcoding Reveal Extraordinary Cryptic Diversity in Nassarius: A Complex and Dangerous Community. PLoS ONE 2012;7:e47276. https://doi.org/10.1371/journal.pone.0047276.
36. Zou S, Fei C, Wang C, Gao Z, Bao Y, He M, et al. How DNA barcoding can be more effective in microalgae identification: a case of cryptic diversity revelation in Scenedesmus (Chlorophyceae). Sci Rep 2016;6:36822. https://doi.org/10.1038/srep36822.
37. Fawley MW, Jameson I, Fawley KP. The phylogeny of the genus Nannochloropsis (Monodopsidaceae, Eustigmatophyceae), with descriptions of N. australis sp. nov . and Microchloropsis gen. nov . Phycologia 2015;54:545–52. https://doi.org/10.2216/15-60.1.
38. Kumar CS, Prabu VA, Kumar CP. DNA Barcode Genes (rbcL, 18s rRNA and ITS Phylogeny) in Skeletonema costatum Grevelli (Cleve, 1873). International Journal of Current Microbiology and Applied Sciences 2015;4:195–203.
39. Gray M, Wawrik B, Paul J, Casper E. Molecular Detection and Quantitation of the Red TideDinoflagellate Karenia brevis in the MarineEnvironment. Appl Environ Microbiol 2003;69:5726–30. https://doi.org/10.1128/AEM.69.9.5726-5730.2003.
40. Crowell RM, Nienow JA, Cahoon AB. The complete chloroplast and mitochondrial genomes of the diatom Nitzschia palea (Bacillariophyceae) demonstrate high sequence similarity to the endosymbiont organelles of the dinotom Durinskia baltica. Journal of Phycology 2019;55:352–64. https://doi.org/10.1111/jpy.12824.
41. Škaloud P, Friedl T, Hallmann C, Beck A, Dal Grande F. Taxonomic revision and species delimitation of coccoid green algae currently assigned to the genus Dictyochloropsis (Trebouxiophyceae, Chlorophyta). Journal of Phycology 2016;52:599–617. https://doi.org/10.1111/jpy.12422.
42. González MA, Aguayo PA, Inostroza IDL, Castro PA, Fuentes GA, Gómez PI. Ultrastructural and molecular characterization of Tetraselmis strains (Chlorodendrophyceae, Chlorophyta) isolated from Chile. Gayana Bot 2015;72:47–57. https://doi.org/10.4067/S0717-66432015000100007.
43. Rad-Menéndez C, Stanley M, Green DH, Cox EJ, Day JG. Exploring cryptic diversity in publicly available strains of the model diatom Thalassiosira pseudonana (Bacillariophyceae). J Mar Biol Ass 2015;95:1081–90. https://doi.org/10.1017/S0025315415000120.
44. Ahn G, Park G-Y, Park D-Y, Jeong OC, Kim Y-H, Ahn J-Y. Microalgae Direct Extract Reagent for Heterocapsa triquetra. Toxicol Environ Health Sci 2019;11:73–8. https://doi.org/10.1007/s13530-019-0390-8.
45. Wang L, Zhuang Y, Zhang H, Lin X, Lin S. DNA barcoding species in Alexandrium tamarense complex using ITS and proposing designation of five species. Harmful Algae 2014;31:100–13. https://doi.org/10.1016/j.hal.2013.10.013.
46. Hoef-Emden K. Pitfalls of Establishing DNA Barcoding Systems in Protists: The Cryptophyceae as a Test Case. PLoS ONE 2012;7:e43652. https://doi.org/10.1371/journal.pone.0043652.
47. Vieira HH, Bagatini IL, Guinart CM, Vieira AAH. tufA gene as molecular marker for freshwater Chlorophyceae. ALGAE 2016;31:155–65. https://doi.org/10.4490/algae.2016.31.4.14.
48. Ermis H, Guven Gulhan U, Akca MS, Cakir T, Altinbas M. Valorization of Human Urine with Mixed Microalgae Examined through Population Dynamics, Nutrient Removal, and Biogas Content. Sustainability 2023;15:6922. https://doi.org/10.3390/su15086922.
49. Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, et al. How genomics can help biodiversity conservation. Trends in Genetics 2023;39:545–59. https://doi.org/10.1016/j.tig.2023.01.005.
50. Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, et al. The era of reference genomes in conservation genomics. Trends in Ecology & Evolution 2022;37:197–202. https://doi.org/10.1016/j.tree.2021.11.008.
51. Famà P, Wysor B, Kooistra WHCF, Zuccarello GC. Molecular phylogeny of the genus Caulerpa (Caulerpales, Chlorophyta) inferred from chloroplast a gene. Journal of Phycology 2002;38:1040–50. https://doi.org/10.1046/j.1529-8817.2002.t01-1-01237.x.
52. Chakraborty C, Doss CGP, Patra BC, Bandyopadhyay S. DNA barcoding to map the microbial communities: current advances and future directions. Appl Microbiol Biotechnol 2014;98:3425–36. https://doi.org/10.1007/s00253-014-5550-9.
53. Collins RA, Armstrong KF, Meier R, Yi Y, Brown SDJ, Cruickshank RH, et al. Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade. PLoS One 2012;7:e28381. https://doi.org/10.1371/journal.pone.0028381.
54. Krohn-Molt I, Wemheuer B, Alawi M, Poehlein A, Güllert S, Schmeisser C, et al. Metagenome Survey of a Multispecies and Alga-Associated Biofilm Revealed Key Elements of Bacterial-Algal Interactions in Photobioreactors. Appl Environ Microbiol 2013;79:6196–206. https://doi.org/10.1128/AEM.01641-13.
55. Gu X, Cao Z, Zhao L, Seswita-Zilda D, Zhang Q, Fu L, et al. Metagenomic Insights Reveal the Microbial Diversity and Associated Algal-Polysaccharide-Degrading Enzymes on the Surface of Red Algae among Remote Regions. IJMS 2023;24:11019. https://doi.org/10.3390/ijms241311019.
56. Toulza E, Blanc-Mathieu R, Gourbière S, Piganeau G. Environmental and Evolutionary Genomics of Microbial Algae: Power and Challenges of Metagenomics. Advances in Botanical Research, vol. 64, Elsevier; 2012, p. 383–427. https://doi.org/10.1016/B978-0-12-391499-6.00010-4.
57. Carnicer O, García-Altares M, Andree KB, Diogène J, Fernández-Tejedor M. First evidence of Ostreopsis cf. ovata in the eastern tropical Pacific Ocean, Ecuadorian coast. Botanica Marina 2016;59:267–74. https://doi.org/10.1515/bot-2016-0022.
58. Yarimizu K, Fujiyoshi S, Kawai M, Norambuena-Subiabre L, Cascales E-K, Rilling J-I, et al. Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile. IJERPH 2020;17:7642. https://doi.org/10.3390/ijerph17207642.
59. Jacobs-Palmer E, Gallego R, Cribari K, Keller AG, Kelly RP. Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae. Front Ecol Evol 2021;9:612107. https://doi.org/10.3389/fevo.2021.612107.
60. Saleem F, Jiang JL, Atrache R, Paschos A, Edge TA, Schellhorn HE. Cyanobacterial Algal Bloom Monitoring: Molecular Methods and Technologies for Freshwater Ecosystems. Microorganisms 2023;11:851. https://doi.org/10.3390/microorganisms11040851.
61. Borowitzka MA. Algal Biotechnology. In: Sahoo D, Seckbach J, editors. The Algae World, vol. 26, Dordrecht: Springer Netherlands; 2015, p. 319–38. https://doi.org/10.1007/978-94-017-7321-8_11.
62. Siozios S, Massa A, Parr CL, Verspoor RL, Hurst GDD. DNA barcoding reveals incorrect labelling of insects sold as food in the UK. PeerJ 2020;8:e8496. https://doi.org/10.7717/peerj.8496.
63. Dawan J, Ahn J. Application of DNA barcoding for ensuring food safety and quality. Food Sci Biotechnol 2022;31:1355–64. https://doi.org/10.1007/s10068-022-01143-7.
64. Stengel DB, Connan S. Marine Algae: a Source of Biomass for Biotechnological Applications. In: Stengel DB, Connan S, editors. Natural Products From Marine Algae, vol. 1308, New York, NY: Springer New York; 2015, p. 1–37. https://doi.org/10.1007/978-1-4939-2684-8_1.
65. Qin S, Wang K, Gao F, Ge B, Cui H, Li W. Biotechnologies for bulk production of microalgal biomass: from mass cultivation to dried biomass acquisition. Biotechnol Biofuels 2023;16:131. https://doi.org/10.1186/s13068-023-02382-4.
66. Cossios E. 2do producto de la consultoria sobre Actualización del perfil de biodiversidad del país Sección VII del 6to Informe Nacional al CDB 2018:1–64.
67. Bellinger EG, Sigee DC. Freshwater Algae: Identification and Use as Bioindicators. 1st ed. Wiley; 2010. https://doi.org/10.1002/9780470689554.
68. Ordinola-Zapata A, Siccha Z, Castillo-Carrillo P, Luque C. Identification by DNA barcode of invading fish in the mangrove of Tumbes (Peru). Manglar 2019;16:91–7. https://doi.org/10.17268/manglar.2019.013.
69. Ekrem T, Willassen E, Stur E. A comprehensive DNA sequence library is essential for identification with DNA barcodes. Molecular Phylogenetics and Evolution 2007;43:530–42. https://doi.org/10.1016/j.ympev.2006.11.021.
70. Altamirano-Benavides M, Yanez-Moretta P. El código de barras de adn (barcoding): una herramienta para la investigación y conservación de la diversidad biológica en Ecuador. Lgr 2016;23. https://doi.org/10.17163/lgr.n23.2016.01.
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