microscopio cabeceras

Biogeochemistry and Microbial Ecology


Head of Department:

Asunción de los Ríos Murillo



Biogeochemistry at MNCN-CSIC


 General description  

- Research lines        

- On-going research projects        

- Past research projects








General description


This department is dedicated to the study of the effects of global change and extreme environments on ecosystem structure and functioning, including the ecological implications of microbes in biogeochemical cycling and organic compound degradation. Our ultimate goal is to develop a mechanistic view of ecosystems to model biogeochemical process under global change drivers. The department is comprised of a multidisciplinary group of scientists with expertise on biogeochemistry, aquatic ecology, terrestrial ecology, microbial ecology and geomicrobiology.


Left: Professor Walter L. Kubiena (edaphologist from Austria) in a lecture at the Institute of Edaphology in 1940s; right: building where both the Institute of Edaphology and Plant Biology and the Center for Environmental Sciences were located and where the department is situated since its founding. 


This department has its origins in a Department of Biology formed during 1967 in the historic Institute of Edaphology and Plant Biology founded by Jose Maria Albareda (founder of CSIC), in which were enrolled or trained both several renowned scientists and academics in the field of Spanish natural sciences (F. Velasco, F. González Bernáldez, F. García Novo, T. Mendizabal, P. Montserrat, A. Gómez Sal, among many others). Later, the Deparment was renamed Environmental Biology in 1977 and, subsequently, it remained as such in the now extinct Center for Environmental Sciences (CCMA) until 2010, the year when it was moved as a whole to the National Museum of Natural Sciences. Since 2013 acquired its current denomination, according with the scientific activity carried out during the last 10 years, while retaining the fundamentals of multidisciplinarity which motivated its fundation for the study of ecology and conservation biology in Spain.


Particularly, our research starts from the premise that human pressure modifies the flows between the compartments of an ecosystem, significantly altering its function and structure. These changes are studied from different organizational levels (macroscopic, microscopic and molecular) in order to cover all processes operating in an ecosystem and their interactions at different scales. To do this, ecosystem studies are conducted from pristine to disturbed, including those developed in extreme environments, considering a wide range of human-induced disturbances. The results are allowing to quantify how the various biotic and abiotic compartments are changing their contributions to the ecosystem biogeochemical fluxes and therefore to the ecosystem functioning, and are allowing to model their responses global change scenarios. Our results contribute to improve the scientific knowledge on the functioning of ecosystems, key for both the development of strategies for environmental conservation to the medium and long-term and to conduct reasonable ecological restorations, with the ultimate goal of contributing to the sustainable development of our society.





Upper: Atacama Expedition-2013

- camp close to the Andes;

middle: an experiment to measure

methane emission by a wetland

in Central Spain; lower: laboratory

of biogeochemistry



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Research lines



The department develops three interrelated research lines: one dedicated to the study of the biogeochemistry of ecosystems (macroscopic), other devoted to the study of microbial ecology and geomicrobiology (microscopic) and another dedicated to the chemistry of organic matter (molecular):



The line Ecosystem Biogeochemistry studies the functionality of continental ecosystems considering how characteristics and evolution are changing as induced by human activity. Ecosystems are analyzed by quantifying the biogeochemical fluxes between compartments at different time scales (from minutes to millennia), with emphasis on processes related to the transformations of C, N and P and their interconnections with the structure of the biotic compartment (food webs). The ultimate goal of the line is to model processes that drive the biogeochemical cycles -which sustain the activity of ecosystems- in relation to global change.


Left: mangroves of the Estero de Santa Maria in Sinaloa (Mexico); middle: waterfall on a travertine barrier in Ruidera chain lakes during February 2010; right: Altillo chica playa lake in Central Spain (La Mancha Húmeda Biosphere Reserve).



The line on Microbial Ecology and Geomicrobiology is centered on the in situ investigation of the microorganisms that colonize the lithic substrate and their relationships with the abiotic environment, including the ecological and biogeomorphological implications and their involvement in the biogeochemical cycling as well ability to respond to global change. The lithic substrate is mainly analyzed as the habitat of microorganisms living in extreme environments. In addition, we are doing the diagnosis of the biodeterioration of monumental stone related to the presence and activity of microbial communities, as well as possible biocontrol strategies.


Left: image obtained in LTSEM of colonization by cyanobacteria in halite of Yungay (Atacama Desert Chile), asterisks are Cyanobacteria, stars are extracellular polymeric substances (EPS) and arrows salt crystals; middle: Pioneer lichen comunnity from Ward Hurd glacier foreland (Livingston Island, Antarctica); right: Microbial endolithic colonization of ignimbrite from the Atacama Desert.


The line Chemistry of the Organic Matter on Soils and Sediments studies the spatial variability of the humus composition from a ecological perspective with the aim to provide comprehensive models determining the functional relationship of the humus in the environment and their bearing on the carbon balance and biogeochemical processes. The so-called humic substances are widely distributed in soil, water and fossil organic resources and represent the greatest reservoir of organic carbon on the surface of the Earth. They include complex mixtures of altered biosynthetic materials in addition to newly-formed macromolecules. Consequently, the research on humic substances can be carried out using perspectives typical of Pedology, Ecology and Soil Microbiology, Organic Geochemistry or Macromolecular Chemistry. .



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On-going research projects


Adaptation and geomicrobiology of lithobiontic microbial communities in hyperarid environments and their metabolites: resources in biotechnology. MINECO, Dirección General de Investigación. 2015-2017. 85,000 €


PI: Jacek Wierzchos


The Atacama Desert is among the oldest and driest deserts in the world and its hyperarid core is described as "the most barren region imaginable". This desert is becoming increasingly appealing for studies that seek to understand all aspects of the adaptation strategies of microorganisms to extreme environmental conditions. In two prior PN projects, we identified and described endolithic microbial communities colonizing five different rock substrates of evaporite, volcanic and sedimentary origin in the hyperarid zone of the Atacama Desert. Up until 2006, this region was thought to be the limit for photosynthetic life - we are now beginning to understand how these microorganisms optimize their access to scarce water and use it for their physiological requirements. The next logical step is to further our knowledge on adaptation strategies used by lithobiontic microbial communities and identify and constrain the abiotic factors that control lithobiontic colonization in a range of substrates and climate regimes in the Atacama Desert. We will also characterize the physiological state of lithobiontic communities in their natural habitat and bioreceptivity of lithic substrates and how desertification processes could impact their survival. We postulate that the resistance of these communities to the hostile climate conditions of the Atacama Desert depends as much on their ability to avoid exposure to multiple adverse factors as it does on their ability to adapt to such factors. Besides looking at adaptive strategies, we will address the use of lithobiontic microbial ecosystems as indicators of future climate regimes. A harsh climate will give rise to specific adaptation processes such as the build-up of antioxidant and UV-protective metabolites. These biomolecules (carotenoids, scytonemin and PUFAs) may have biotechnological applications. We will analyse these communities at (1) the molecular level using high-throughput barcoded 16S rRNA gene sequencing, (2) the micro-morphological level using electron and photon microscopy, and (3) the substrate level by analysing the rocks' physical, chemical, and mineralogical properties. Using ecological models we will identify processes that influence microbial assemblages and build a model to determine parameters for the "dry edge" for colonization. The multiphase and interdisciplinary approach will be used to determine substrate characteristics, identify bioweathering processes, characterize biosignatures and develop ways to induce the production of intracellular metabolites. These investigation lines will also provide us with a more solid background for speculations regarding the habitability of other planets. Our team members are all highly experienced and we already have significant preliminary data to confirm the feasibility of this project. In addition, through our collaborations with international partners in previous projects, we have substantial information on several aspects of the lithobiontic colonization of extremely arid environments. Image 3D-CLSM showing an aggregate of endolithic cyanobacteria from Atacama's halite (red signal) involved by scytonemin (UV protective pigment - white signal).


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Lithic microbial ecosystems developed in exposed areas after glacial retreat. Ecological succession, phylodiversity and geomicrobiology. MINECO, Dirección General de Investigación. 2013-2015. 173,000 €


PI: Asunción de los Ríos


Primary succession is a fundamental process in macroecosystems; however, how these processes occur in the development of microbial ecosystems and the influence of environmental changes on microbial community structure is poorly understood. We focus on pioneer microbial communities because they have the potential to kickstart the succession. Rock mineral weathering, mediated by lithobiontic microorganisms (rock colonizers), enhances ecosystem development because it triggers soil development and plant biocenosis. Our investigation looks at changes in the microbial communities along chronosequencies of different glacier forelands from Northern and Southern Hemispheres. The differences in succession between hemispheres could be related to retreat rates, environmental (climate and lithic substrate) conditions, and the availability of a pool of effectively dispersed species. Therefore, the development of lithobiontic ecosystems may not only be the result of deterministic trajectory but could be strongly influenced by a stochastic interplay of biotic interactions and assembly processes, and different physical and chemical environmental factors. The phylodiversity and the phylogenetic structure of the microbial communities (with especial emphasis on symbiotic microbial associations), together with the geomicrobiological study of the microbial biofilms (i.e. microbial communities and colonized lithic substrate), will be used to characterize the changes along the chronosequencies. In addition, the study of functional genes will help us to understand the drivers of these changes along the glacier forelands. The synthesis of these results will allow us to understand the differences in ecological succession between northern and southern Polar Regions. 

Left: Breioamerkurjökull glacier in southeast Iceland, which is receding due to climate change and where it is analyzing the sequence of microbial colonization in soils and rocks of the area uncovered by the receding; right: Asunción de los Ríos collecting soil samples in the exposed area by the retreat of Hurd Glacier on Livingston Island (Antarctica). 


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Sustainability and Conservation of Built Heritage Geomaterials (GEOMATERIALES-2). Comunidad de Madrid. 2014-2017. 49,000 €


PI-subproject: Carmen Ascaso


The program outlined in this proposal focuses on conservation technology of geomaterials used in built heritage and any other cultural asset. A geomaterial is defined as any material from a geological source that after undergoing a process is utilized in different sectors such as civil engineering materials, construction, advanced materials, heritage conservation, environment, etc.This program follows GEOMATERIALES Programme (S2009/MAT_1629) and this proposal includes new technology based objectives. The consortium has been modified and new research groups, national and international, are incorporated. Besides, related sector and industry companies are directly involved. From a technological scope, the program is focused on providing solutions to different aspects affecting geomaterials conservation. Relevant issues such as nanomaterials development applied to heritage conservation, design of new treatments for the consolidation and protection of contemporary heritage geomaterials, new restoration mortars formulation or sensors and monitoring systems development that allow the environmental conditions control that will affect the interior and exterior preservation of the buildings and their materials (fittingout for use and comfort), which in turn will allow preventive conservation, are addressed. A fundamental and essential topic in heritage conservation technology is the validation and improvement of portable and nondestructive techniques that enable and make easier the data collection, without material damage, in order to explain the processes that are affecting heritage asset conservation and to carry out decision making with a scientific and technological approach. The program will conduct its activities taking into account different aggressive environments and special attention is paid to underwater heritage conservation. One of the objectives pursued is to control risks, both natural and anthropogenic, in heritage conservation. Therefore, it is expected to solve moisture problems, to determine the effects of urine from social activity ("bottle effect"), or the damage due to fire action, as the result of climate change, etc. Another objective, not studied hitherto conveniently, is the effectiveness and sustainability analysis of interventions performed in ancient heritage. These studies will reveal and assess the evolution of such interventions over time and they will entail guidelines on current and future conservation operations. Objectives directly focused on technological aspects are proposed, such as Information and Communication Technologies (ICT), in order to establish the procedures and techniques for the processing, storage and transmission of information. This issue entails an essential tool to coordinate the results achieved in the entire program, and will make easier the interpretation and definition of the actions to accomplish. The new technologies incorporation that can be put at the industry disposal is also proposed, both related with new materials development and monitoring techniques implementation or equipment validation. Industry and companies can be highly benefited with the results of this program. Potential impact forwards industrial, business and technological sector focused on heritage conservation, besides construction and new construction sectors, is expected. The program has a social value as it is aimed to improve the knowledge as well as the study and intervention techniques for heritage conservation. This issue affects people quality of life, their identity as citizens, social profitability and its historical and technological conception maintenance. This gives advantage to a stable economic attraction as entails improvements on monumental tourism and museum resources. Ultimately, the scientific and technological knowledge transfer is addressed, and current research and innovation that can support the different sectors involved are disseminated, in order to increase their competitiveness and to promote the economic attraction of the region.


Left: experimental plots where biocide and laser treatment are applied; right: SEM-BSE image showing the effect of biocide treatment on liquen colonization.


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Life at the dry limit: Cyanobacteria inside halite pinnacles in the Atacama Desert. NASA Astrobiology: Exobiology and Evolutionary Biology Program. 2011-2015. 210,000 USD.


PI: A.F. Dávila (Co-investigator: J. Wierzchos)


We want to demonstrate that the limit for photosynthesis on Earth can be expanded if we consider the habitability of hygroscopic minerals. Given the similarities between the Atacama Desert and Mars, our work could potentially reveal an environment on Mars (where evaporitic deposits have already been found) with conditions close to the habitability limits proposed by COSPAR. This would re-define current maps of special regions on Mars and could potentially re-direct the focus of future life detection missions. The proposed research focuses on the adaptation of life to extreme dry environments (applicable to Earth and Mars), as well as on assessing the habitability of hygroscopic minerals (found both on Earth and Mars), and therefore addresses one of the main areas of research emphasis stated in the Astrobiology program. 


Image of the interior of halite rock colonized by endolithic microorganisms (green bands).





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Environmental impacts assessment through the molecular characterization of resilient forms of organic matter in soils. Ministerio de Ciencia e Innovación, Plan Nacional I+D+i. CGL2008-04926. 2009-2014.


PI: Gonzalo Almendros


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Sustainable local management in the field of water policy. Contract by Las Rozas de Madrid Municipality. 2014. 20,000 €


PI: Miguel Álvarez-Cobelas


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Proyectos de investigación finalizados (últimos 5 años) / Past research projects (last 5 years)


Mitigación del cambio global por las Lagunas y Humedales de la Reserva de la Biosfera de La Mancha Húmeda. Obra Social La Caixa-EINTAM. 2011-2012. 30.000€. IP: Salvador Sánchez-Carrillo.


Informe de actuaciones preceptivas para la restauración ecológica del lavajo de las Lavanderas de Carpio (Valladolid) así como para la realización del estudio limnológico de la misma. Fundación Patrimonio Natural de Castilla y León. 2011-2012. 30.000 €. IP: Santos Cirujano y Salvador Sánchez-Carrillo.


Biogeoquímica isotópica de nutrientes aplicada al metabolismo de lagos (BIOMET). Plan Nacional I+D+i (CGL2009-10408). 2010-2013. 120.000 €. IP: Salvador Sánchez-Carrillo.


Estudios limnológicos para la aplicación del Marco Comunitario de Actuación en el ámbito de la Política de Aguas. Ayuntamiento de Las Rozas de Madrid. 2010-2013. 160.000 €. IP: Miguel Álvarez-Cobelas.


Efectos del cambio global en la ecología y la biogeoquímica de Las Tablas de Daimiel (DECAMERON). Organismo Autónomo Parques Nacionales (2008/001). 2009-2013. 123.000 €. IP: Salvador Sánchez-Carrillo. (


Programa de seguimiento científico del proyecto de restauración y puesta en valor de las Lagunas de Cantalejo (Segovia). Fundación Patrimonio Natural de Castilla y León. 2009. 30.000 €. IP: Santos Cirujano y Salvador Sánchez-Carrillo.


Seguimiento y monitoreo ambiental del PN Tablas de Daimiel. Parque Nacional Tablas de Daimiel. 2008-2013. 360.000 €. IP: Miguel Álvarez-Cobelas y Santos Cirujano.


Estudio integral de la cantidad y la calidad del agua superficial y subterránea en el Alto Guadiana, en relación con los usos pasados y presentes del territorio, enfocado hacia la restauración de los ecosistemas acuáticos. Contrato con la Confederación Hidrográfica del Guadiana. 2008-2011. 750.000 €. IP: Miguel Álvarez-Cobelas.


Estrategias de colonización de microorganismos endolíticos en ambientes áridos e hiperáridos y búsqueda de sus biomarcadores: estudio de desiertos extremos análogos de Marte. MICINN, Dirección General de Investigación. 2011-2013. 107.000 €. IP: J. Wierzchos.


Durabilidad y conservación de geomateriales del patrimonio construido (Geomateriales). Comunidad de Madrid S 2009/MAT-1629. 2010-2013. 61.122 €. IP-subproyecto: Carmen Ascaso.


Ecosistemas microbianos litobionticos en gradientes antárticos ambientales: biodiversidad, fisiología y geomicrobiología. Plan Nacional I+D+i (CTM2009-12838-CO4-O3). 2010-12. 103.000€. IP: Asunción de los Ríos.


Estudios Sobre Machu Picchu: cooperación cultural y científica Perú-España para su conservación y preservación como recurso al desarrollo. Fundación Carolina. 2010-11. IP: Asunción de los Ríos.


Estrategias de adaptación de microorganismos endoevaporiticos colonizadores de halitas en las hiper-áridas zonas del Desierto de Atacama, Chile. Proyecto Intramural Especial CSIC. 2009. 30.000 €. IP: J. Wierzchos.


Lichens and Fungi Experiment (LIFE). EXPOSE-E Program (ESA) en la Estación Espacial Internacional (ISS). 2009-2010. IP: Silvano Onofri (Co-investigador: Carmen Ascaso).


Ecología microbiana y geomicrobiología de hábitats litobiónticos en ambientes extremos: desiertos de Atacama y Negev. MEC, Dirección General de Investigación. 2007-2010. 100.000 €. IP: J. Wierzchos.


Bases científicas para la restauración de ecosistemas degradados en el contexto de los bienes y servicios ambientales que proporcionan los suelos y la vegetación de Castilla la Mancha, POII11-0267-4154. Junta de Castilla-La Mancha. 2011-2012. IP: G. Almendros.


Evaluación agroecológica de las características organo-minerales de los suelos volcánicos que influyen en la calidad de los suelos y los mostos en los viñedos de las Islas Canarias, Agencia Canaria de Investigación, Innovación y Sociedad de la Información. Gobierno de Canarias [Bodegas Viñátigo e Instituto Canario de la Uva y el Vino, IDT-TF-09/044]. 2010-2013. IP: J.P. Pérez Trujillo (Co-investigador: G. Almendros).


Biochar application to soils: can cattle do it for us? Massey University, New Zealand. PROP-20453-SLMACC-MAU.2009-2010. IP: Marta Camps (Co-investigador: G. Almendros).


La biofumigación como alternativa no química en la replantación y reconversión en suelos de viñedo. Junta de Comunidades de Castilla-La Mancha, PAI09-0010-4701. 2009-2011. IP: J.A. López Pérez (Co-investigador: G. Almendros).


Focos rojos en emisión de gases de invernadero en México. CONACyT - SEMARNAT. 2006-2009. IP: Norma E. García Calderón & G. Almendros.


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Personal científico

Ministerio de Ciencia, Innovación y UniversidadesConsejo Superior de Investigaciones Científicas

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