Molecular identification of composting earthworms using DNA barcoding

Authors

DOI:

https://doi.org/10.22201/ib.20078706e.2026.97.5761

Keywords:

Organic waste, Taxonomy, Epigean species

Abstract

Composting earthworms play a key role in the decomposition of organic matter. Epigeic species of the genus Eisenia are widely used both in vermicomposting and as bioindicators in  toxicological studies. However, accurate taxonomic identification of these species remains challenging due to their high morphological similarity, which affects the efficiency and function of vermicomposting processes. In this study, the earthworm species present in 5 vermicomposting facilities located in Veracruz and Quintana Roo, México, were identified through molecular analyses of the mitochondrial COI gene. The results revealed the presence of 2 species: Eisenia andrei and Perionyx excavatus, ruling out Eisenia fetida, which had previously been assumed by facility operators. Genetic distances between the identified specimens were below 1.3%, while divergences from E. fetida exceeded 16%, supporting clear species delimitation. Our results highlight the need to integrate molecular methods into earthworm identification for their use in toxicological studies and to strengthen the sustainable management of organic waste. 

References

Aranda, E. y Barois, I. (2000). Coffee pulp vermicomposting treatment. En T. Sera, C. R. Soccol, A. Pandey y S. Roussos (Eds.), Coffee biotechnology and quality (pp. 489–506). Dordrecht: Kluwer Academic Publishers. https://doi.org/10.1007/978-94-017-1068-8_46

Aranda, E., Barois, I., Arellano, P., Irissón, S., Salazar, T., Rodríguez, J. et al. (1999). Vermicomposting in the Tropics. En P. Lavelle, L. Brussaard y P. Hendrix (Eds.), Earthworm management in tropical agroecosystems (pp. 253–287). Wallingford, United Kingdom: CABI Publishing.

Aranda, E., Barois I., Santos, B. M. y Hernandez-Castellanos, B. (2011). Vermicomposting, research and activities in Mexico. En C. A. Edwards, N. Q. Arancon y R. L. Sherman (Eds.), Vermiculture technology: earthworms, organic wastes, and environmental management (pp. 507–32). Boca Raton, Florida: CRC Press.

Barraux, A., Noël, S., Roy, V. y Dupont, L. (2024). Challenges of molecular barcode-based identification of earthworm specimens for biodiversity assessment. Frontiers in Ecology and Evolution, 12, 1358984. https://doi.org/10.3389/fevo.2024.1358984

Chang, C. H. y James, S. (2011). A critique of earthworm molecular phylogenetics. Pedobiologia, 54, S3–S9. https://doi.org/10.1016/j.pedobi.2011.07.015

Chang, C. H., Rougerie, R. y Chen, J. H. (2009). Identifying earthworms through DNA barcodes: pitfalls and promise. Pedobiologia, 52, 171–80. https://doi.org/10.1016/j.pedobi.2008.08.002

de Waard, J., Ivanova, N., Hajibabaei, M. y Hebert, P. (2008). Assembling DNA barcodes: analytical protocols. En C. C. Martin (Ed.), Methods in Molecular Biology: environmental genomics methods (pp. 275–294). Ottawa: Humana Press https://doi.org/10.1007/978-1-59745-548-0_15

Domínguez, J., Aira, M., Breinholt, J. W., Stojanovic, M., James S. W. y Pérez-Losada, M. (2015). Underground evolution: new roots for the old tree of lumbricid earthworms. Molecular Phylogenetics and Evolution, 83, 7–19. https://doi.org/10.1016/j.ympev.2014.10.024

Domínguez, J. y Edwards, C. A. (2004). Vermicomposting organic wastes: a review. Soil Zoology for Sustainable Development in the 21st Century. Cairo: Geocites Publisher.

Domínguez, J. y Pérez-Losada, M. (2010). Eisenia fetida (Savigny, 1826) y Eisenia andrei Bouché, 1972 son dos especies diferentes de lombrices de tierra. Acta Zoológica Mexicana, 26, 321–31. https://doi.org/10.21829/azm.2010.262897

Domínguez, J., Velando A. y Ferreiro, A. (2005). Are Eisenia fetida (Savigny, 1826) and Eisenia andrei Bouché (1972) different biological species? Pedobiologia, 49, 81–87. https://doi.org/10.1016/j.pedobi.2004.08.005

Fragoso, C. (2011). Lombrices de tierra (Annelida: Oligochaeta). La biodiversidad en Veracruz: estudio de estado (pp. 259–268). México D.F.: Comisión Nacional para el Conocimiento y Uso de la Biodiversidad/ Gobierno del Estado de Veracruz/ Universidad Veracruzana/ Instituto de Ecología A.C.

Fragoso, C. y Rojas, P. (2014). Biodiversidad de lombrices de tierra (Annelida: Oligochaeta: Crassiclitellata) en México. Revista Mexicana de Biodiversidad, 85 (Suplem.), 197–207. https://doi.org/10.7550/rmb.33581

García, S. R., Méndez, G., Velázquez, M. G., Castillo, G. y Retureta, A. (2019). Dinámica poblacional de Eisenia fetida (Savigny, 1826) y Eisenia andrei (Bouché, 1972) en tres sustratos diferentes. Revista Biológico Agropecuaria Tuxpan, 7, 70–78. https://doi.org/10.47808/revistabioagro.v7i2.31

Hebert, P. D. N., Cywinska, A., Ball, S. L. y deWaard, J.R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270, 313–321. https://doi.org/10.1098/rspb.2002.2218

ISO (International Organization for Standardization). (2008). Soil quality: avoidance test for determining the quality of soils and effects of chemicals on behavior. ISO 17512-1. International Organization for Standardization. Disponible en: https://www.iso.org/obp/ui/en/#iso:std:iso:17512:-1:ed-1:v1:en

ISO (International Organization for Standardization). (2012). Soil quality: effects of pollutants on earthworms. ISO 11268-1. International Organization for Standardization. Disponible en: https://www.iso.org/obp/ui/#iso:std:iso:11268:-1:ed-2:v1:en

ISO (International Organization for Standardization). (2019). Soil quality: identification of ecotoxicological test species by DNA barcoding. ISO 21286. International Organization for Standardization. Disponible en: https://www.iso.org/obp/ui/en/#iso:std:iso:21286:ed-1:v1:en

James, S. W., Porco D., Decaëns, T., Richard, B., Rougerie, R. y Erséus, C. (2010). DNA Barcoding reveals cryptic diversity in Lumbricus terrestris L., 1758 (Clitellata): resurrection of L. herculeus (Savigny, 1826). Plos One, 5, 1–8. https://doi.org/10.1371/journal.pone.0015629

King, R. A., Tibble, A. L. y Symondson, W. O. C. (2008). Opening a can of worms: unprecedented sympatric cryptic diversity within British lumbricid earthworms. Molecular Ecology, 17, 4684–4698. https://doi.org/10.1111/j.1365-294X.2008.03931.x

Kumar, S., Stecher, G. y Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874. https://doi.org/10.1093/molbev/msw054

Martínez-Cano, M., Dorantes-Acosta, A. E., Lara-González, R., Salgado-Hernández, E. y Ortiz-Ceballos, A. I. (2024). Effect of sargassum on the behavior and survival of the earthworm Eisenia fetida. Bulletin of Environmental Contamination and Toxicology, 113, 36. https://doi.org/10.1007/s00128-024-03935-5

Misirlioğlu, M., Reynolds, J. W., Stojanović, M., Trakić, T., Sekulić, J., James, S. W. et al. (2023). Earthworms (Clitellata, Megadrili) of the world: an updated checklist of valid species and families, with notes on their distribution. Zootaxa, 5255, 17–438. https://doi.org/10.11646/zootaxa.5255.1.33

Montero-Pau, J., Gómez, A. y Muñoz, J. (2008). Application of an inexpensive and high-throughput genomic DNA extraction method for the molecular ecology of zooplanktonic diapausing eggs. Limnology and Oceanography: Methods, 6, 218–222. https://doi.org/10.4319/lom.2008.6.218

Moreno, A. G. y Borges, S. (2004). Advances in earthworm taxonomy. Madrid: Editorial Complutense.

Prosser, S., Martínez-Arce, A. y Elías-Gutiérrez, M. (2013). A new set of primers for COI amplification from freshwater microcrustaceans. Molecular Ecology Resources, 13, 1151–1155. https://doi.org/10.1111/1755-0998.12132

Ratnasingham, S. y Hebert, P. D. N. (2013). A DNA-based registry for all animal species: The Barcode Index Number (BIN) System. Plos One, 8, e66213. https://doi.org/10.1371/journal.pone.0066213

Römbke, J., Aira, M., Backeljau, T., Breugelmans, K., Domínguez, J., Funke, E. et al. (2016). DNA barcoding of earthworms (Eisenia fetida/andrei complex) from 28 ecotoxicological test laboratories. Applied Soil Ecology, 104, 3–11. https://doi.org/10.1016/j.apsoil.2015.02.010

Saitou, N. y Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

Suthar, S. y Singh, S. (2008). Vermicomposting of domestic waste by using two epigeic earthworms (Perionyx excavatus and Perionyx sansibaricus). International Journal of Environmental Science & Technology, 5, 99–106. https://doi.org/10.1007/BF03326002

Yadav, S. y Mullah, M. (2017). A review on molecular markers as tools to study earthworm diversity. International Journal of Pure and Applied Zoology, 5, 62–69.

Zhang, M., Jouquet, P., Dai, J., Xiao, L., Du, Y., Liu, K. et al. (2022). Assessment of bioremediation potential of metal contaminated soils (Cu, Cd, Pb and Zn) by earthworms from their tolerance, accumulation and impact on metal activation and soil quality: a case study in South China. Science of The Total Environment, 820, 152834. https://doi.org/10.1016/j.scitotenv.2021.152834

Published

2026-05-27

How to Cite

Martínez-Cano, M., Dorantes-Acosta, A. E. ., Martínez-Hernández, S. ., García-Pérez, J. A., Ortiz-Oliveros, H. B. ., & Ortiz-Ceballos, A. I. . (2026). Molecular identification of composting earthworms using DNA barcoding. Revista Mexicana De Biodiversidad, 97, e975761. https://doi.org/10.22201/ib.20078706e.2026.97.5761

Issue

Section

ECOLOGÍA