Publications

Peer-reviewed publications involving members of the EnGeL Research Group, spanning soil biodiversity, molecular ecology, genomics and ecotoxicology.

Peer-reviewed papers

Journals worldwide

Of continuous output (2007–2026)

Papers in flagship venues

Findings appear across leading journals in ecology, evolution and soil science — including Nature Communications, Global Change Biology, Global Ecology & Biogeography, Heredity, Molecular Phylogenetics & Evolution and Soil Biology & Biochemistry — alongside sustained contributions to Zootaxa, Applied Soil Ecology, Geoderma, Science of the Total Environment and Scientific Reports.

What the work has shown

Nearly two decades of research converge on a handful of connected insights about how soil life records, adapts to, and is reshaped by the living and human world.

Humans are written into the soil

Ancient and recent human activity is a defining force on Amazonian soil biodiversity. Our work helped confirm the anthropic origin of Amazonian Dark Earths and showed how these engineered soils still carry a distinctive macroinvertebrate signature today.

Nature Communications · Global Change Biology

Life adapts on the volcanic edge

Earthworms living in active volcanic and geothermal soils show genetic isolation and molecular signatures of adaptation to extreme, multi-stressor environments — making them models for how metazoans persist at the limits of habitability.

Heredity · Life Science Alliance

Invasion has a hidden genealogy

Combining genomics and morphology, we resolved the cryptic diversity, multiple introductions and mixed reproductive strategies of the peregrine earthworm Pontoscolex corethrurus — and formalised its taxonomy with a neotype.

Biological Invasions · Molecular Phylogenetics & Evolution

Soil biodiversity can be read in DNA

We develop and validate DNA-based strategies — barcoding, metabarcoding and integrative morphological–molecular methods — that make soil biodiversity measurable, comparable and ready for continental-scale monitoring.

Ecology & Evolution · Global Ecology & Biogeography

Small animals are early warnings

From metals to microplastics, soil and aquatic invertebrates act as sensitive sentinels of pollution — their cells, microbiomes and reproduction revealing environmental stress before it becomes visible at larger scales.

Science of the Total Environment · European Journal of Soil Biology

Full publication list

2026 Leitão, R.; Ferreira, T.; Ferreira, N. G. C.; Orozco-terWengel, P.; Kille, P.; Brown, G. G.; Cunha, L. Compartment-specific responses of soil, root, and earthworm gut microbiomes to Terra Preta de Índio–inspired amendments in a tropical latosol Applied Soil Ecology, 225, pp. 107278. Link
2026 Leitão, R.; Podpečan, V.; Cunha, L.; Vazquez, C.; David, F.; Imbert, C.; Symanczik, S.; Sousa, J. P.; Bünemann, E. K.; Debeljak, M.; Creamer, R.; Lori, M. Rapid evidence mapping of soil fauna responses to agricultural management assisted by large language models Geoderma, 471, pp. 117890. Link
2026 Barbosa, F. L. A.; Almeida, M. S.; Garcia, K. G. V.; Henrique, G. S.; Moniz, T. C. D.; dos Santos, J. M. R.; Nascimento, Í. V.; et al. Biochar-driven shifts in the soil bacterial community structure of degraded semiarid soils Soil Ecology Letters, 8(6), pp. 260461. Link
2025 Dudas, R. T.; Bartz, M. L. C.; Cunha, L.; Brown, G. G. New species of Glossoscolex and Fimoscolex earthworms (Oligochaeta: Glossoscolecidae) from the Brazilian Atlantic Forest and Cerrado biomes Zootaxa, 5728(1), pp. 79-106. Link
2025 Fraga Dornellas, L.; Mata, V.A.; Mendes, S.; Leitão, R.; Bartz, M.; Nascimento, E.; Costa, J.; Sousa, J.P.; Cunha, L. Establishing DNA‐Based Strategies for Soil Biodiversity Assessment: Insights From Carabid Beetles. Ecology and Evolution, 15(11), p.e72461. Link
2025 Almeida-Azevedo, R.; Acioli, A. N. S.; Heleodoro, R.; Morais, J. W. de; Brown, G. G.; Kille, P.; Cunha, L.; Azevedo, R. A. de Tucupitermes, the largest Apicotermitinae (Isoptera, Termitidae) from the Amazon Rainforest Zootaxa, 5633(1), pp. 186-194. Link
2025 Lori, M.; Leitao, R.; Felix, D.; Imbert, C.; Corti, A.; Cunha, L.; Symanczik, S.; et al. Response of soil biota to agricultural management practices: A systematic quantitative meta-data-analysis and method selection framework Soil Biology and Biochemistry, 207, pp. 109815. Link
2025 Jänsch, S.; Alves, D.; Cunha, L.; Krogh, P. H.; Natal-Da-Luz, T.; Rojo, V.; Römbke, J.; et al. Comparison of Morphological and DNA-Based Identification Methods to Assess Earthworm (Clitellata: Lumbricidae) Diversity at 25 Permanent Soil Monitoring Sites in Germany Ecology and Evolution, 15(4), pp. e71155. Link
2024 Quigley, E.; Silva, A. L. P.; Chelinho, S.; Cunha, L.; Briones, M. J.; Sousa, J. P. Pristine and UV-aged polyethylene microplastics’ impact on gut microbiome and reproduction of earthworm Eisenia andrei European Journal of Soil Biology, 122, pp. 103640. Link
2023 Conrado, A. C.; Demetrio, W. C.; Stanton, D. W.; Bartz, M. L.; James, S. W.; Santos, A.; da Silva, E.; et al. Amazonian earthworm biodiversity is heavily impacted by ancient and recent human disturbance Science of The Total Environment, 895, pp. 165087. Link
2023 Dudas, R. T.; Demetrio, W. C.; Maia, L. S.; Sátiro, J. N.; Silva, K. A.; Nicola, V. B.; Kille, P.; et al. Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil Zootaxa, 5255(1), pp. 347-361. Link
2022 Perry, I.; Hernadi, S. B.; Cunha, L.; Short, S.; Marchbank, A.; Spurgeon, D. J.; Orozco-Terwengel, P.; Kille, P. Molecular insights into high-altitude adaptation and acclimatisation of Aporrectodea caliginosa Life Science Alliance, 5(11), pp. e202201513. Link
2022 Lombardo, U.; Arroyo-Kalin, M.; Schmidt, M.; Huisman, H.; Lima, H. P.; de Paula Moraes, C.; Neves, E. G.; et al. Evidence confirms an anthropic origin of Amazonian Dark Earths Nature Communications, 13, pp. 3444. Link
2022 Ramalho, B.; Dieckow, J.; de Freitas Melo, V.; Gardner Brown, G.; Luzia Simon, P.; Alves Ibarr, M.; Cunha, L.; Kille, P.; Network, T. Carbon and nitrogen storage and stability by mineral-organic association in physical fractions of anthropogenic dark earth and of reference soils in Amazonia CATENA, 213, pp. 106185. Link
2021 Sátiro, J. N. de O.; Motta, A. C. V.; Demetrio, W. C.; Segalla, R. F.; Cremonesi, M. V.; Araújo, E. M.; Falcão, N. P. de S.; et al. Micronutrient availability in Amazonian Dark Earths and adjacent soils Geoderma, 395, pp. 115072. Link
2021 Demetrio, W. C.; Conrado, A. C.; Acioli, A. N.; Casadei Ferreira, A.; Bartz, M. L.; James, S. W.; da Silva, E.; et al. A "Dirty" Footprint: Macroinvertebrate diversity in Amazonian Anthropic Soils Global Change Biology, 27(19), pp. 4575-4591. Link
2021 da Silva, K. A.; Nicola, V. B.; Dudas, R. T.; Demetrio, W. C.; Maia, L. dos S.; Cunha, L.; Bartz, M. L. C.; et al. Pesticides in a case study on no-tillage farming systems and surrounding forest patches in Brazil Scientific Reports, 11(1), pp. 9839. Link
2021 Melo, T. O.; Franciscon, L.; Brown, G.; Kopka, J.; Cunha, L.; Martinez-Seidel, F.; Madureira, L. A. dos S.; Hansel, F. A. Univariate statistical analysis of gas chromatography – mass spectrometry fingerprints analyses Chemical Data Collections, 33, pp. 100719. Link
2021 Santos, A.; Cremonesi, M. V.; Zanatta, J. A.; Cunha, L.; Drake, H. L.; Brown, G. G. Emission of greenhouse gases and soil changes in casts of a giant Brazilian earthworm Biology and Fertility of Soils, 57(5), pp. 617-628. Link
2021 Ferreira, T.; Hansel, F. A.; Maia, C. M.; Guiotoku, M.; Cunha, L.; Brown, G. G. Earthworm-biochar interactions: A laboratory trial using Pontoscolex corethrurus Science of The Total Environment, 777, pp. 146147. Link
2021 Etxabe, A. G.; Pini, J. M.; Short, S.; Cunha, L.; Kille, P.; Watson, G. J. Identifying conserved polychaete molecular markers of metal exposure: Comparative analyses using the Alitta virens (Annelida, Lophotrochozoa) transcriptome. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 240, pp. 108913. Link
2020 White, H. J.; León-Sánchez, L.; Burton, V. J.; Cameron, E. K.; Caruso, T.; Cunha, L.; Dirilgen, T.; et al. Methods and approaches to advance soil macroecology Global Ecology and Biogeography, 29(10), pp. 1674-1690. Link
2020 Ortíz-Gamino, D.; Gregorio, J.; Cunha, L.; Martínez-Romero, E.; Fragoso, C.; Ortíz-Ceballos, Á. I. Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico ZooKeys, 941, pp. 49-69. Link
2020 Taheri, S.; Decaëns, T.; Cunha, L.; Brown, G. G.; da Silva, E.; Bartz, M. L. C.; Baretta, D.; Dupont, L. Genetic evidence of multiple introductions and mixed reproductive strategy in the peregrine earthworm Pontoscolex corethrurus Biological Invasions, 22(8), pp. 2545-2557. Link
2020 Talavera, J.; Cunha, L.; Arévalo, J.; Talavera, I.; Kille, P.; Novo, M. Anthropogenic disturbance and environmental factors drive the diversity and distribution of earthworms in São Miguel Island (Azores, Portugal) Applied Soil Ecology, 145, pp. 103301. Link
2020 Nadolny, H.; Santos, A.; Demetrio, W.; Ferreira, T.; Maia, L. dos S.; Conrado, A. C.; Bartz, M.; et al. Recommendations for assessing earthworm populations in Brazilian ecosystems Pesquisa Agropecuária Brasileira, 55, pp. 01006. Link
2019 Ferreira, N. G.; Morgado, R. G.; Cunha, L.; Novo, M.; Soares, A. M.; Morgan, A. J.; Loureiro, S.; Kille, P. Unravelling the molecular mechanisms of nickel in woodlice. Environmental Research, 176, pp. 108507. Link
2019 James, S. W.; Bartz, M. L. C.; Stanton, D.; Conrado, A. C.; Dupont, L.; Taheri, S.; Silva, E.; Cunha, L.; Brown, G. A neotype for Pontoscolex corethrurus (Müller, 1857) (Clitellata) Zootaxa, 4545(1), pp. 124-132. Link
2018 Taheri, S.; James, S.; Roy, V.; Decaëns, T.; Williams, B.; Anderson, F.; Rougerie, R.; et al. Complex taxonomy of the ‘brush tail’ peregrine earthworm Pontoscolex corethrurus Molecular Phylogenetics and Evolution, 124, pp. 60-70. Link
2017 Anderson, C.; Cunha, L.; Sechi, P.; Kille, P.; Spurgeon, D. Genetic variation in populations of the earthworm, Lumbricus rubellus, across contaminated mine sites BMC Genetics, 18(1), pp. 97. Link
2017 Cunha, L.; Thornber, A.; Kille, P.; Morgan, A.; Novo, M. A large set of microsatellites for the highly invasive earthworm Amynthas corticis predicted from low coverage genomes Applied Soil Ecology, 119, pp. 152-155. Link
2018 Parelho, C.; Rodrigues, A. dos S.; Bernardo, F.; Barreto, M. do C.; Cunha, L.; Poeta, P.; Garcia, P. Biological endpoints in earthworms ( Amynthas gracilis ) as tools for the ecotoxicity assessment of soils from livestock production systems Ecological Indicators, 95, pp. 984-990. Link
2017 Conrado, A. C.; Arruda, H.; Stanton, D. W.; James, S. W.; Kille, P.; Brown, G.; Silva, E.; et al. The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning ZooKeys, 688, pp. 1-13. Link
2016 Rougon-Cardoso, A.; Flores-Ponce, M.; Ramos-Aboites, H.; Martínez-Guerrero, C.; Hao, Y.; Cunha, L.; Rodríguez-Martínez, J.; et al. The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: Evolutionary signatures of a pathogenic lifestyle Scientific Reports, 6, pp. 37536. Link
2016 Cunha, L.; Brown, G.; Stanton, D.; da Silva, E.; Hansel, F.; Jorge, G.; Mckey, D.; et al. Soil animals and pedogenesis: The role of earthworms in anthropogenic soils Soil Science, 181(3-4), pp. 110-125. Link
2016 M, N.; R, F.; Sc, A.; Df, M.; L, C.; Dj, D. C. Phylogenomic analyses of a Mediterranean earthworm family (Annelida: Hormogastridae). Molecular phylogenetics and evolution, 94, pp. 473-478. Link
2015 Novo, M.; Cunha, L.; Maceda-Veiga, A.; Talavera, J.; Hodson, M.; Spurgeon, D.; Bruford, M.; Morgan, A.; Kille, P. Multiple introductions and environmental factors affecting the establishment of invasive species on a volcanic island Soil Biology and Biochemistry, 85, pp. 89-100. Link
2014 Novo, M.; Andre, J.; Cunha, L.; Morgan, A. J.; Spurgeon, D.; Kille, P. The functional ghost in the genome machine: Holistic mapping of environmentally induced changes in the epigenome of a soil sentinel Toxicology Letters, 229(Supplement), pp. S18. Link
2014 Cunha, L.; Montiel, R.; Novo, M.; Orozco-Terwengel, P.; Rodrigues, A.; Morgan, A. J.; Kille, P. Living on a volcano's edge: genetic isolation of an extremophile terrestrial metazoan Heredity, 112(2), pp. 132-142. Link
2011 Cunha, L.; Campos, I.; Montiel, R.; Rodrigues, A.; Morgan, A. J. Morphometry of the epidermis of an invasive megascoelecid earthworm (Amynthas gracilis, Kinberg 1867) inhabiting actively volcanic soils in the Azores archipelago Ecotoxicology and Environmental Safety, 74(1), pp. 25-32. Link
2011 Cunha, L.; Zanon, V.; Amaral, A.; Ferreira, J.; Rodrigues, A. dos S. Altered inorganic composition of enamel and dentin in mice teeth chronically exposed to an enriched mineral environment at Furnas, São Miguel (Azores) Arquipelago. Life and Marine Sciences, 28, pp. 33-37. Link
2009 Ventura Garcia, P.; Cunha, L.; Amaral, A.; Rodrigues, A. Bioavailability of heavy metals and apoptotic effects on the midgut cells of Pseudaletia unipuncta (Lepidoptera: Noctuidae) inhabiting volcanic environments Toxicology Letters, 189(Supplement), pp. S196. Link
2008 Cunha, L.; Mascaro, M.; Chiapa, X.; Costa, A.; Simoes, N. Experimental studies on the effect of food in early larvae of the cleaner shrimp Lysmata amboinensis (De Mann, 1888) (Decapoda : Caridea : Hippolytidae) Aquaculture, 277(1-2), pp. 117-123. Link
2008 Cunha, L.; Amaral, A.; Medeiros, V.; Martins, G. M.; Wallenstein, F. F. M. M.; Couto, R. P.; Neto, A. I.; Rodrigues, A. Bioavailable metals and cellular effects in the digestive gland of marine limpets living close to shallow water hydrothermal vents Chemosphere, 71(7), pp. 1356-1362. Link
2008 Rodrigues, A.; Cunha, L.; Amaral, A.; Medeiros, J.; Garcia, P. Bioavailability of heavy metals and their effects on the midgut cells of a phytopaghous insect inhabiting volcanic environments Science of the Total Environment, 406(1-2), pp. 116-122. Link
2007 Cunha, L.; Martins, G.; Amaral, A.; Rodrigues, A. A case of simultaneous hermaphroditism in the Azorean endemic limpet Patella candei gomesii (Mollusca: Patellogastropoda), a gonochoristic species Invertebrate Reproduction and Development, 50(4), pp. 203-205. Link