Geomicrobiology and Biogeochemistry

The Geomicrobiology and Biogeochemistry research group aims at studying the microbial diversity and the interactions between microorganisms, minerals and organic matter in complex ecosystems, such as subterranean environments (caves and mines), stone cultural heritage, soils and sediments. We implement novel approaches to blending classical microbiology, molecular biology, metagenomics, advanced microscopy, mineralogy and biogeochemistry in a holistic effort to understand the role of microorganisms and their interactions with geological substrates.

Due to the achievements and contributions of the group in the field of geomicrobiology, it actively collaborates with internationally recognized researchers from Portugal, Spain, Italy, Germany, Austria and the United States. In addition, it collaborates with the European Space Agency in the organization of the cave astronaut training course (PANGAEA and CAVES) for future human missions to the Moon and Mars.


Geomicrobiología de cuevas volcánicas
Estudio de la diversidad, función y dinámica de las comunidades microbianas.
Caracterización morfológica de los sustratos basálticos colonizados por los microorganismos.
Caracterización geoquímica para identificar cambios ambientales
Reconocimiento de biominerales y microfósiles almacenados en el registro mineral plausibles para la comprensión del origen de la vida en la Tierra.
Colaboración con la Agencia Espacial Europea (ESA) en el programa de entrenamiento de astronautas en geología planetaria y astrobiología en cuevas (PANGAEA y CAVES).



Ana Zelia Miller

Beatriz Cubero

Juana Muñoz

The main goal of the Geomicrobiology and Biogeochemistry research group consists in investigating the diversity, function and dynamics of microbial communities from complex ecosystems to understand which microorganisms grow in these harsh environments, how do they do it (i.e. which metabolic mechanisms and pathways are utilized), and what is their role in biogeochemistry cycling.

The specific objectives for addressing this investigation involve:

  1. Morphological and mineralogical characterization of solid substrates colonized by microorganisms.
  2. Study of microbial diversity, function and dynamics using metagenomics.
  3. Isolation, culture and characterization of isolated microorganisms, and potential description of novel species.
  4. Characterization and screening of antimicrobial and enzymatic activities of the isolated microorganisms.
  5. Recognition of microbe-mineral interactions and biosignatures preserved in the rock record plausible for the understanding of the origin of life on Earth and to help life-detection on other planets, based on a wide range of microscopy and chemical analyses.
  6. In-depth organic geochemical characterization of secondary mineral deposits to establish their biogenicity and provide information on past environmental changes preserved in minerals.

This multidisciplinary approach allows us to understand the role of microorganisms in the formation and dissolution of minerals, the erosion and alteration of rocks, the mobilization of metals from soil and sediments, the bioremediation of metal-contaminated soils and waters, fossilization mechanisms, as well as the biotransformation of elements. In addition, by studying microbe-mineral interactions and the molecular characterization of the organic fraction preserved in speleothems, we aim to contribute to the understanding of the origin of life on Earth and possibly on other planets, as well as to reconstruct environmental changes registered in minerals. Due to the increasing demand in the discovery of new bioactive compounds of interest for the pharmaceutical industry or the recovery of the environment, our group also investigates extremophilic microorganisms, and their secondary metabolites, isolated from pristine environments, such as volcanic and salt caves.

To carry out these investigations, we apply a wide range of analytical and imaging techniques including next generation sequencing, classical microbiology, mineralogy, organic geochemistry and advanced microscopy (FESEM, FIB-SEM, TEM, CLSM, Epifluorescence, micro-CT) in order to advance scientific knowledge on the role of microorganisms and their interactions with geological substrates.


El grupo estudia la diversidad microbiana y las interacciones entre microorganismos, minerales y materia orgánica en ecosistemas complejos (ambientes subterráneos, patrimonio cultural, suelos y sedimentos), aplicando enfoques novedosos que combinan microbiología clásica, biología molecular, metagenómica, microscopía avanzada, mineralogía y biogeoquímica.


Miller AZ, De la Rosa JM, Jiménez-Morillo NT, Pereira MFC, González-Pérez JA, Knicker H, Saiz-Jimenez C. 2020. Impact of wildfires on subsurface volcanic environments: New insights into speleothem chemistry. Science Total Environ 698, 134321.

D’Angeli IM, (…), Miller AZ, et al. 2019. Geomicrobiology of a seawater-influenced Garcia-Sanchez AM, Machado-Moreira B, Freire M, Santos R, Monteiro S, Dias D,

Neves O, Dionísio A, Miller AZ* (2019) Characterization of microbial communities associated with ceramic raw materials as potential contributors for the improvement of ceramic rheological properties. Minerals 9, sulfuric acid cave. PLOS ONE 14, e0220706.

Dominguez-Moñino I, Jurado V, Gonzalez-Pimentel JL, Miller AZ et al. 2018. Bacillus onubensis sp. nov., isolated from the air of two Andalusian caves. Syst Appl Microbiol 41, 167-172.

Gonzalez-Pimentel JL, Miller AZ*, Jurado V, Laiz L, Pereira MFC, Saiz-Jimenez C. 2018. Yellow coloured mats from lava tubes of La Palma (Canary Islands, Spain) are dominated by metabolically active Actinobacteria. Scientific Reports 8: 1944.

Miller AZ et al. 2018. Origin of abundant moonmilk deposits in a subsurface granitic environment. Sedimentology 65, 1482-1503.

Miller AZ, Gonzalez-Pimentel JL, Stahl S, Castro-Wallace S, Sauro F, Pozzobon R, Massironi M, Maurer M, Bessone L, Martínez-Frìas J. 2018. Exploring possible Mars- like microbial life in a lava tube from Lanzarote:preliminary results of in-situ DNA-based analysis as part of the PANGAEA-X Test Campaign. EGU 2018, pp. EGU2018-1258.

Sasso S, Miller AZ, Rogerio-Candelera MA, Cubero B, Coutinho ML, Scrano L, Bufo SA. 2016. Potential of natural biocides for biocontrolling phototrophic colonization on limestone. Int Biodeter Biodegr 107, 102-110.

Miller AZ , De la Rosa JM et al. 2016. Analytical pyrolysis and light stable isotope analyses reveal environmental changes in coralloid speleothems from Easter Island. Journal of Chromatography A 1461, 144–152.

Miller AZ et al. 2015. Ana Heva lava tube (Easter Island): Preliminary characterization of the internal layers of coralloid-type speleothems. Microsc Microanal 21, 68-69.

Riquelme C, Hathaway JJM, Dapkevicius M, Miller AZ. et al. 2015. Actinobacterial diversity in volcanic caves and associated geomicrobiological interactions. Front. Microbiol. 6:1342. Riquelme C, Dapkevicius M.D., Miller AZ, Charlop-Powers Z, Brady S, Mason CT, Cheeptham N. 2017. Biotechnological potential of Actinobacteria from Canadian and Azorean volcanic caves. Appl Microbiol Biotechnol 101, 843-857.

Miller AZ et al. 2014. Siliceous speleothems and associated microbe-mineral interactions from Ana Heva lava tube in Easter Island (Chile). Geomicrobiol. J. 31, 236–245.

Miller AZ et al. 2012. Biogenic Mn oxide minerals coating in a subsurface granite environment. Chem Geol 322-323, 181-191.

Miller AZ et al. 2012. Enigmatic reticulated filaments in subsurface granite. Environ. Microbiol. Rep. 4, 596-603.

Saiz-Jimenez C, Miller AZ, et al. 2012. Uncovering the origin of the black stains in Lascaux Cave in France. Environ. Microbiol. 14, 3220-3231.

Sasso S, Miller AZ*, Rogerio-Candelera MA, Cubero B, Coutinho ML, Scrano L, Bufo SA. 2016. Potential of natural biocides for biocontrolling phototrophic colonization on limestone. Int Biodeter Biodegr 107, 102-110.

Laiz L, Miller AZ, et al. 2009. Isolation of five Rubrobacter strains from biodeteriorated monuments. Naturwissenschaften 96, 71-79.

2020 – 2023: Project title: “Discovering subsurface microbiota and biominerogenesis in lava tubes from Lanzarote (TUBOLAN)”, Spanish Ministry for Science Innovation and Universities, PID2019-108672RJ-I00 (Programa Estatal de I+D+i Orientada a los Retos de la Sociedad). PI: Ana Z. Miller. Total amount: 234.740,00€.

2021 – 2024: Project title: “Microbial biocenosis in volcanic caves from pristine islands: potential for Astrobiology, Biotechnology and Paleoenvironmental Research (MICROCENO)”, Portuguese Foundation for Science and Technology (FCT), PTDC/CTA-AMB/0608/2020. PI: Ana Z. Miller. Total amount: 249.965,60€