*: corresponding author; †: equal contribution

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Fantom N., R.A. Dawson, E. Prondvai, P. Constant, G.M King, H. Schäfer, M. Hernández*. Metabolism of CO and H2 by pioneer bacteria in volcanic soils and the phyllosphere. ISME Journal. 19, wraf053. https://doi.org/10.1093/ismejo/wraf053

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Ding, C., Y. Liu, M. Hernández, H. Sun, S. Jiao, H. Pan, T. Ge, K. Zhao, Q. Zhang, J. Xu, Y. Li. 2025. Coupling soil bacterial and fungal community traits to multifunctionality in grassland ecosystem. Agriculture, Ecosystems and Environment. 388 (2025) 109648.

https://doi.org/10.1016/j.agee.2025.109648

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Dawson, R.A., P. Aguila, T. Martin Pozas, G. King, M. Hernández*. 2025. Carbon monoxide-oxidising Pseudomonadota on volcanic deposits. Environ Microbiome 20:12. https://doi.org/10.1186/s40793-025-00672-y

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Roy S., R.A. Dawson, J.A. Bradley, M. Hernández*. 2025. Antimicrobial resistance in Arctic soils is mediated by competition and facilitation. BMC Microbiol. 25:50. https://doi.org/10.1186/s12866-025-03745-7

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Liu J., M. Zhou, L. Zhou, R. Dang, L. Xiao, Y. Tan, M. Li, J. Yu, P. Zhang, M. Hernández, E. Lichtfouse. 2025. Methane production related to microbiota in dairy cattle feces. Environmental Research. 267:120642. https://doi.org/10.1016/j.envres.2024.120642

 

Liu J., J. Yu, Y. Tan, R. Dang, M. Zhou, M. Hernández, E. Lichtfouse, L. Xiao. 2023. Biomethane is produced by acetate cleavage, not direct interspecies electron transfer: genome-centric view and carbon isotope. Bioresource Technology 387: 129589. https://doi.org/10.1016/j.biortech.2023.129589

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Hernández, M., S. Roy, C.W. Keevil, M. G. Dumont. 2023. Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing combined with high-throughput sequencing. Environmental Microbiome 18, 34.    

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Vera-Gargallo, B., M. Hernández, A. Ventosa, M. G. Dumont. 2023. Thrive or survive: prokaryotic life in hypersaline soils. Environmental Microbiome. 18, 17.

                                                                 

Ding, C., X. Xu, Y. Liu, X. Huang, M. Xi, H. Liu, E. Deyett, M.G. Dumont, H. Di, M. Hernández, J. Xu, Y. Li. 2023. Diversity and assembly of active bacteria and their potential function along soil aggregates in a paddy field. Science of the Total Environment 866:161360. http://dx.doi.org/10.1016/j.scitotenv.2022.161360

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Zhu, X., Y. Deng, M. Hernández, J. Fang, P. Xing, Y. Liu. 2023. Distinct responses of soil methanotrophy in hummocks and hollows to simulated glacier meltwater and temperature rise in Tibetan glacier foreland. Science of the Total Environment 862:160888. https://doi.org/10.1016/j.scitotenv.2022.160888 

 

Ni, G., R. Lappan, M. Hernández, T. Santini, A.G. Tomkins, C. Greening. 2022. Functional basis of primary succession: traits of the pioneer microbes. Environmental Microbiology 1-6. https://doi.org/10.1111/1462-2920.16266 

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Fang, J., Y. Deng, J.M. Adams, X. Zhu, M. Hernández, Y. Liu. 2022. Propagule limitation affects the response of soil methane oxidizer community to increased salinity. Geoderma 426:116082. https://doi.org/10.1016/j.geoderma.2022.116082

 

†*Hernández, M., M. Farhan Ul Haque†, A.T. Crombie, J.C. Murrell. 2022. Identification of active gaseous-alkane degraders at natural gas seeps. ISME Journal. doi: 10.1038/s41396-022-01211-0

 

†*Hernández, M., M. McDaniel†*, M.G. Dumont, L.J. Ingram, and M.A. Adams. 2021. Soil microbial communities, and their links to carbon cycling, along a soil/vegetation gradient in a sub-alpine Australian ecosystem. Microorganisms. 9: 606. doi: 10.3390/microorganisms9030606

 

Islam, T., M. Hernández, A. Gessesse, JC Murrell, L Øvreås. 2021. Methanol oxidation by a moderately thermophilic bacterium within the class Alphaproteobacteria. Microorganisms. 9: 477. doi: 10.3390/microorganisms9030477

 

Zhao, J., D. Chen, W. Gao, Z. Guo, Z. Jia, Hernández, M*. 2021. Resuscitation of soil microbiota after > 70-years of desiccation. European Journal of Soil Biology. 103: 103290. doi: 10.1016/j.ejsobi.2021.103290

 

*Hernández, M., B. Vera, M. Calabi, G.M. King, R. Conrad, C.C. Tebbe. 2020. Reconstructing genomes of carbon monoxide oxidisers in volcanic deposits including members of the class Ktedonobacteria. Microorganisms. 8: 1880. doi: 10.3390/microorganisms8121880

 

*Hernández, M., M. Calabi, R. Conrad and M. Dumont. 2020. Analysis of the microbial communities in soils of different ages following volcanic eruptions. Pedosphere. 30: 126-134. doi: 10.1016/S1002-0160(19)60823-4

 

Lia Y., Y. Liu, H. Pan, M. Hernández, X. Guan, W. Wang, et al. 2020. Impact of grazing on shaping abundance and composition of active methanotrophs and methane oxidation activity in a grassland soil. Biology and Fertility Soils. 56: 799-810. doi: 10.1007/s00374-020-01461-0

 

Hernández, M., M. Klose, P. Claus, A. Enrich-Prast, and R. Conrad. Structure and function of methanogenic microbial communities in temporarily inundated soils of the Amazon rainforest (Cunia Reserve, Rondonia). Environmental Microbiology. 21: 1702-1717. doi: 10.1111/1462-2920.14535

 

McDaniel, M.D., D. Saha, M. G. Dumont, M. Hernández and M.A. Adams. 2019. The effect of land-use change on soil CH4 and N2O fluxes: a meta-analysis. Ecosystems.  22: 1424-1443. doi: 10.1007/s10021-019-00347-z

 

Wu, S., M. Hernández, Y. Deng, C. Han, X. Hong, J. Xu, W. Zhong, and H. Deng. 2019. The voltage signals of microbial fuel cell-based sensors positively correlated with methane emission flux in paddy fields of China. FEMS Microbial Ecology. 95: fiz018. doi: 10.1093/femsec/fiz018

 

Yuan, Q., M. Hernández, M. G. Dumont, J. Rui, A. Fernandez Scavino and R. Conrad. 2018. Soil bacterial community mediates the effect of labile carbon on methanogenic decomposition of soil organic matter. Soil Biology and Biochemistry. 116: 99-109. doi: 10.1016/j.soilbio.2017.10.004

 

Calabi-Floody M., J. Medina, C. Rumpel, L.M. Condron, M. Hernández, M.G. Dumont, and M.L. Mora. 2018. Smart fertilizers as a strategy for sustainable agriculture. Advances in Agronomy. 147: 119-157. doi: 10.1016/bs.agron.2017.10.003

 

*Hernández, M., R. Conrad, M. Klose, K. Ma, and Y. Lu. 2017. Structure and function of methanogenic microbial communities in soils from flooded rice and upland soybean fields from Sanjiang plain, NE China. Soil Biology and Biochemistry. 105: 81-91. doi: 10.1016/j.soilbio.2016.11.010

 

†Hernández, M., A. Reim†, M. Klose, A. Chidthaisong, M. Yuttitham, and R. Conrad. 2017. Response of methanogenic microbial communities to desiccation stress in flooded and rain-fed paddy soil from Thailand. Frontiers in Microbiology. 8: 785. doi: 10.3389/fmicb.2017.00785

 

Méndez, V., S. Fuentes, V. Morgante, M. Hernández, M. González, E. Moore and M. Seeger. 2017. Novel hydrocarbonoclastic and metal-tolerant Acinetobacter and Pseudomonas strains from Aconcagua river oil-polluted soil. Journal of Soil Science and Plant Nutrition. 17: 1074-1087. doi: 10.4067/S0718-95162017000400017

 

Marileo, L.G., M.A. Jorquera, M. Hernández, G. Briceño, M.L. Mora, R. Demanet and G. Palma. 2016. Changes in bacterial communities by post-emergent herbicides in an Andisol fertilized with urea as revealed by DGGE. Applied Soil Ecology. 101: 141-151 doi: 10.1016/j.apsoil.2016.02.003

 

Hernández, M., M.G. Dumont, Q. Yuan and R. Conrad. 2015. Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon. Applied and Environmental Microbiology. 81: 2244-2253 doi: 10.1128/AEM.03209-14

 

*Hernández, M., M. Dumont, M. Calabi, D. Basualto and R. Conrad. 2014. Ammonia oxidizers are pioneer microorganisms in the colonization of new acidic volcanic soils from South of Chile. Environmental Microbiology Reports. 6: 70-79. doi: 10.1111/1758-2229.12109

 

Deng, Y., X. Cui, M. Hernández and M.G. Dumont. 2014. Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan Plateau revealed by 16S rRNA pyrosequencing. Plos One. 9: e103115. doi: 10.1371/journal.pone.0103115

 

Wu Y., X. Ke, M. Hernández, B. Wang, M. Dumont, Z. Jia and R. Conrad. 2013. Autotrophic growth of bacterial and archaeal ammonia oxidizers in freshwater sediment microcosms incubated at different temperatures. Applied and Environmental Microbiology. 79: 3076-3084. doi: 10.1128/AEM.00061-13

 

Morgante, V., C. Flores, X. Fadic, M. González, M. Hernández, F. Cereceda-Balic and M. Seeger. 2012. Influence of microorganisms and leaching on simazine attenuation in agricultural soils. Journal of Environmental Management. 95: S300-S305. doi: 10.1016/j.jenvman.2011.06.045

 

Hernández, M., Z. Jia, M. Seeger and R. Conrad. 2011. Simazine application inhibits nitrification and changes the ammonia-oxidizing bacterial communities in a fertilized agricultural soil. FEMS Microbiology and Ecology. 78: 511-519. doi: 10.1111/j.1574-6941.2011.01180.x

 

Seeger, M., M. Hernández, V. Méndez, B. Ponce, M. Córdova and M. González. 2010. Bacterial degradation and bioremediation of chlorinated herbicides and biphenyls. Journal of Soil Science and Plant Nutrition. 10: 320-332. doi: 10.4067/S0718-95162010000100007

 

Méndez, V., S. Fuentes, M. Hernández, V. Morgante, M. González, and M. Seeger. 2010. Isolation of hydrocarbon-degrading heavy-metal-resistant bacteria from crude oil-contaminated soil in central Chile. Journal of Biotechnology. 150: S287. doi: 10.1016/j.jbiotec.2010.09.225

 

Jorquera, M. A., M. Hernández, O. Martínez, P. Marschner, and M. L. Mora. 2010. Detection of aluminium tolerance plasmids and microbial diversity in the rhizosphere of plants grown in acidic volcanic soil. European Journal of Soil Biology. 46: 255-263. doi: 10.1016/j.ejsobi.2010.03.005

 

Hernández, M., V. Morgante, M. Ávila, P. Moralles, M. González, and M. Seeger. 2008. Novel s-triazine-degrading bacteria isolated from agricultural soils of central Chile for herbicide bioremediation. Electronic Journal of Biotechnology. 11: 5-6. doi: 10.2225/vol11-issue5-fulltext-4

 

Hernández, M., V. Morgante, C. Flores, P. Villalobos, M. González, P. Miralles, M. A. Dinamarca and M. Seeger. 2008. Modern approaches for the study of bioremediation of s-triazine herbicides in agricultural soils. Journal of Soil Science and Plant Nutrition. 8:19-30. doi: 10.4067/S0718-27912008000200004

 

Hernández, M., P. Villalobos, V. Morgante, M. González, C. Reiff, E. Moore and M. Seeger. 2008. Isolation and characterization of a novel simazine-degrading bacterium from agricultural soil of central Chile, Pseudomonas sp. MHP41. FEMS Microbiology Letters. 286: 184-190. doi: 10.1111/j.1574-6968.2008.01274.x

 

Jorquera, M. A., M. Hernández, Z. Rengel, P. Marschner, and M. L. Mora. 2008. Isolation of culturable phosphobacteria with both phytate-mineralization and phosphate-solubilization activity from the rhizosphere of plants grown in a volcanic soil. Biology and Fertility Soils. 44: 1025-1034. doi: 10.1007/s00374-008-0288-0

 

Martínez, P., L. Agulló, M. Hernández, and M. Seeger. 2007. Chlorobenzoate inhibits growth and induces stress proteins in the PCB-degrading bacterium Burkholderia xenovorans LB400. Archives in Microbiology. 188: 289-297. doi: 10.1007/s00203-007-0247-4                                                                        

 

 

OTHER PUBLICATIONS

 

Hernández, M. 2020. COVID-19 and the gender gap in science: a mother’s perspective. Microbiologist magazine (Society for Applied Microbiology), Pages 34-35. September issue.

 

 

BOOK

 

Dumont, M.G., and M. Hernández. 2019. Stable Isotope Probing: Methods in Molecular Biology. Springer Nature. Vol. 2016. 247 pp. doi: 10.1007/978-1-4939-9721-3

 

 

BOOK CHAPTERS

 

Cao, W, M. Hernández and Z. Jia. 2019. DNA Stable Isotope Probing. In: Stable Isotope Probing: Methods in Molecular Biology (Dumont, M.G. and M. Hernández, eds). Springer Nature. 2046: 17-29. doi: 10.1007/978-1-4939-9721-3_2

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Hu, A., Y. Lu, M. Hernández and M.G. Dumont. 2019. Targeted metatranscriptomics of soil microbial communities with stable isotope probing. In: Stable Isotope Probing: Methods in Molecular Biology (Dumont, M.G. and M. Hernández, eds). Springer Nature. 2046: 163-174. doi: 10.1007/978-1-4939-9721-3_13

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Hernández, M., J.D. Neufeld and M.G. Dumont. 2017. Enhancing functional metagenomics of complex microbial communities using stable isotopes. In: Functional Metagenomics: Tools and Applications (Charles, T.C., M.R. Liles and A. Sessitsch, eds), pp. 139-150, Springer Nature. doi: 10.1007/978-3-319-61510-3_8       

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Seeger, M., V. Morgante, and M. Hernández. 2009. Bacterial degradation of herbicides in soils. In: Microbial Populations: Structure and Evolution (Lodeiro, A., ed.), Vol 1, Editorial Research Signpost, Kerala, India.

 

 

PATENT

 

Hernández, M., V. Morgante, P. Villalobos, C. Flores, M. González, and M. Seeger. (2007-2009): s-Triazine herbicide-degrading bacteria, product for the bioremediation and method of bioremediation. Chilean Patent, No 1982-2007 dated 06.07.2007. American Patent, No 12/166,961 dated 02.07.08. Canadian Patent, No 2,636,856 dated 07.07.08. Columbian Patent, No 0806 8859 dated 04.07.08. Argentinian Patent, No 08 01 02903 dated 04.07.09.

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