Ricardo Amils

Ricardo Amils
Centro de Astrobiología | CAB · Planetology and Habitability

PhD on Science U. Autónoma de Barcelona

About

712
Publications
74,007
Reads
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10,317
Citations
Introduction
Ricardo Amils currently works at the Planetology and Habitability Department at Centro de Astrobiología (INTA-CSIC) and the Virology and Microbiology Department at the Centro de Biología Molecular Severo Ochoa (CSIC-UAM). Ricardo does research in Microbial Ecology of extreme environments (Río Tinto, Uyuny salt lake, Dallol). Current research interest: study of the deep subsurface geomicrobiolog using fluorescence in situ hybridization techniques.
Additional affiliations
July 1997 - present
Centro de Astrobiología
Position
  • Senior Researcher
September 1977 - present
Universidad Autónoma de Madrid
Position
  • Full Professor of Microbiology
Description
  • Microbiology, Environmental Biotechnology, Early evolution of life, Extremophiles and its applications
September 1977 - present
Centro De Biología Molecular Severo Ochoa
Position
  • Full Professor of Microbiology
Education
October 1965 - July 1969
Universidad de Barcelona
Field of study
  • Chemistry

Publications

Publications (712)
Poster
Full-text available
Water is structurally and functionally essential to life. Liquid water was detected in different places in the Solar System, albeit the presence of liquid water is not indicative of the habitability of these locations, given that water is not always available for life1. Water stress is caused by the lack of bioavailable water. Desiccation is theref...
Article
Full-text available
The Iberian Pyrite Belt (IPB) is one of the largest deposits of sulphidic minerals on Earth. Río Tinto raises from its core, presenting low a pH and high metal concentration. Several drilling cores were extracted from the IPB's subsurface, and strain T2.3D-1.1 was isolated from a core at 121.8 m depth. We aimed to characterize this subterranean mic...
Preprint
Orbital missions have shown that some regions of the ancient Martian crust contain hundreds of discrete terrains covered by chloride evaporites. In terrestrial evaporitic systems, aqueous precipitation typically begins with the deposition of carbonates, followed by sulfates, and finally chlorides, a depositional sequence that has not yet been found...
Preprint
Tirez was a small and seasonal endorheic athalassohaline lagoon that was located in central Spain. In recent years, the lagoon has totally dried out, offering for the first time the opportunity to analyze its evolution to hyperaridity as an analog to similar processes in Meridiani Planum, Mars. In Meridiani, an early period of water ponding within...
Article
Full-text available
The Chiquini and Galaxias caves contain speleothems that are templated by long fungal structures. They have been associated with the carbonate lacustrine deposits in the margins of the Coipasa and Uyuni Salar basins. During a wetter episode, such carbonates formed at the end of the last glaciation raising the lake level to more than 100 m in the Ta...
Article
Full-text available
The identification of reliable biomarkers, such as amino acids, is key for the search of extraterrestrial life. A large number of microorganisms metabolize, synthesize, take up and excrete amino acids as part of the amino acid metabolism during aerobic and/or anaerobic respiration or in fermentation. In this work, we investigated whether the anaero...
Article
Salar de Uyuni (SdU), with a geological history that reflects 50 000 years of climate change, is the largest hypersaline salt flat on Earth and is estimated to be the biggest lithium reservoir in the world. Its salinity reaches saturation levels for NaCl, a kosmotropic salt, and high concentrations of MgCL2 and LiCl both salts considered important...
Article
Full-text available
In the mining-impacted Rio Tinto, Spain, Fe-cycling microorganisms influence the transport of heavy metals (HMs) into the Atlantic Ocean. However, it remains largely unknown how spatial and temporal hydrogeochemical gradients along the Rio Tinto shape the composition of Fe-cycling microbial communities and how this in turn affects HM mobility. Usin...
Article
Full-text available
The preservation of biosignatures on Mars is largely associated with extensive deposits of clays formed under mild early Noachian conditions (> 3.9 Ga). They were followed by widespread precipitation of acidic sulfates considered adverse for biomolecule preservation. In this paper, an exhaustive mass spectrometry investigation of ferric subsurface...
Article
Full-text available
Peña de Hierro, located in southwest Spain, encompasses the springs and headwaters for the Rio Tinto River that emerge above normal faults and has been mined for its rich sulfide ore since 2500 BC. The springs are typically characterized by an orange coloration, typical pH of ~2.33, and contain elevated concentrations of heavy metals that are produ...
Article
Full-text available
In the subsurface, the interplay between microbial communities and the surrounding mineral substrate, potentially used as an energy source, results in different mineralized structures. The molecular composition of such structures can record and preserve information about the metabolic pathways that have produced them. To characterize the molecular...
Conference Paper
Full-text available
Palabras claves: Microorganismo endolíticos, basaltos, Marte, bajas temperaturas, radiación UV, análogo. Resumen: A pesar de las condiciones favorables para la vida en Marte, como es la presencia de agua en forma de vapor en la atmósfera y congelada en el subsuelo, su existencia es todavía un enigma. Aunque misiones espaciales, como el Perseverance...
Article
Full-text available
The drilling of the Rio Tinto basement has provided evidence of an underground microbial community primarily sustained by the Fe and S metabolism through the biooxidation of pyrite orebodies. Although the gossan is the microbial activity product, which dates back to the Oligocene (25 Ma), no molecular evidence of such activity in the past has been...
Article
Full-text available
The Dallol geothermal area originated as a result of seismic activity and the presence of a shallow underground volcano, both due to the divergence of two tectonic plates. In its ascent, hot water dissolves and drags away the subsurface salts. The temperature of the water that comes out of the chimneys is higher than 100 °C, with a pH close to zero...
Article
Full-text available
NGS long-reads sequencing technologies (or third generation) such as Pacific BioSciences (PacBio) have revolutionized the sequencing field over the last decade improving multiple genomic applications like de novo genome assemblies. However, their error rate, mostly involving insertions and deletions (indels), is currently an important concern that...
Article
Most of the terrestrial deep subsurfaces are oligotrophic environments in which some gases, mainly H2, CH4, and CO2, play an important role as energy and/or carbon sources. In this work, we assessed their biotic and abiotic origin in samples from subsurface hard‐rock cores of the Iberian Pyrite Belt (IPB) at three different depths (414, 497, and 52...
Article
Full-text available
The exploration of extreme environments has led to the discovery of numerous environments that were, until recently, considered uninhabitable [...]
Article
Full-text available
Astrobiology is often regarded as the study of life beyond Earth, but here we consider life on Earth through an astrobiological lens. Microbiology has historically focused on various anthropocentric sub‐fields (such as fermented foods or commensals and pathogens of crop plants, livestock, and humans), but addressing key biological questions via ast...
Article
Full-text available
Background Extreme terrestrial, analogue environments are widely used models to study the limits of life and to infer habitability of extraterrestrial settings. In contrast to Earth’s ecosystems, potential extraterrestrial biotopes are usually characterized by a lack of oxygen. Methods In the MASE project (Mars Analogues for Space Exploration), we...
Article
Full-text available
Salar de Uyuni is the biggest athalosaline environment on Earth, holding a high percentage of the known world Li reserves. Due to its hypersalinity, temperature and humidity fluctuations, high exposure to UV radiation, and its elevated concentration of chaotropic agents like MgCl2, LiCl and NaBr, Salar de Uyuni is considered a polyextreme environme...
Article
Full-text available
We report the draft genome of Pseudomonas sp. strain T2.31D-1, which was isolated from a drilling core sample obtained 414 m below surface in the Iberian Pyrite Belt. The genome consists of a 4.7-Mb chromosome with 4,428 coding sequences, 1 rRNA operon, 59 tRNA genes, and a 31.8-kb plasmid.
Chapter
Among extremophiles, acidophiles are of special interest because their chemolithotrophic metabolism obtains energy from reduced minerals, thus creating the extreme acidic conditions in which they thrive. Rio Tinto is a 92 km long extreme acidic environment, which is the product of the metabolic activity of chemolithotrophic microorganisms thriving...
Article
Full-text available
Despite being considered an extreme environment, several studies have shown that life in the deep subsurface is abundant and diverse. Microorganisms inhabiting these systems live within the rock pores and, therefore, the geochemical and geohydrological characteristics of this matrix may influence the distribution of underground biodiversity. In thi...
Article
Full-text available
Shewanella sp. strain T2.3D-1.1 was isolated from the deep subsurface of the Iberian Pyrite Belt. We report its draft genome sequence, consisting of 49 scaffolds, with a chromosome of ≈4.6 Mb and a 23.8-kb plasmid. The chromosome annotation identified 4,068 coding DNA sequences, 1 rRNA operon, and 108 tRNA genes.
Article
Full-text available
The influence of the particle size distribution of a petroleum coke sample compared to its sulfur content was investigated. For this matrix, an optimization procedure of the Suspension Assisted Analysis (SAA) by Total-reflection X-Ray Fluorescence (TXRF) quantitative method was developed. SAA-TXRF sulfur recoveries were evaluated for three particle...
Preprint
Full-text available
The influence of the particle size distribution of a petroleum coke sample compared to its sulfur content was investigated. For this matrix, an optimization procedure of the Suspension Assisted Analysis (SAA) by Total-reflection X-Ray Fluorescence (TXRF) quantitative method was developed. SAA-TXRF sulfur recoveries were evaluated for three particle...
Conference Paper
Full-text available
Salar de Uyuni (SdU) is the biggest athalassohaline system on the Earth located in the southern endorheic basin of the Bolivian Altiplano. SdU is part of the well-known Lithium Triangle and is considered the largest reserve of lithium. It is characterized by extreme conditions such as high salinity, high UV and albedo radiation, extreme daily tempe...
Article
Full-text available
The study of plants adapted to an extreme environment with a high concentration of iron such as Río Tinto allowed the study of important elements for the development and control of plant growth including their localization, management, and storage. The absorption, transport, and accumulation of iron were studied in different species of dicotyledons...
Chapter
Full-text available
Five bacterial (facultatively) anaerobic strains, namely Buttiauxella sp. MASE-IM-9, Clostridium sp. MASE-IM-4, Halanaerobium sp. MASE-BB-1, Trichococcus sp. MASE-IM-5, and Yersinia intermedia MASE-LG-1 isolated from different extreme natural environments were subjected to Mars relevant environmental stress factors in the laboratory under controlle...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Oxidation of sulfide ores in the Iberian Pyrite Belt region leads to the presence of extremely high concentration of dissolved heavy metals (HMs) in the acidic water of the Rio Tinto. Fe(II) is microbially oxidized resulting in the formation of suspended particulate matter (SPM) consisting of microbial cells and Fe(III) minerals with co-precipitate...
Article
Five bacterial (facultatively) anaerobic strains, namely Buttiauxella sp. MASE-IM-9, Clostridium sp. MASE-IM-4, Halanaerobium sp. MASE-BB-1, Trichococcus sp. MASE-IM-5, and Yersinia intermedia MASE-LG-1 isolated from different extreme natural environments were subjected to Mars relevant environmental stress factors in the laboratory under controlle...
Poster
Full-text available
1. ARAMIS is a new tool to correct indel errors in long-reads genome assemblies combining different software in just one step with less memory usage, obtaining better results than other published correction tools. 2. Using ARAMIS on PacBio assembled genomes we have found:-Indel errors are mainly located in homopolymeric regions but not all homopoly...
Article
Full-text available
One of the main objectives for astrobiology is to unravel and explore the habitability of environments beyond Earth, paying special attention to Mars. If the combined environmental stress factors on Mars are compatible with life or if they were less harsh in the past, to investigate the traces of past or present life is critical to understand its p...
Article
Full-text available
Effluents from petroleum refineries contain a toxic mixture of sulfide, nitrogen, and phenolic compounds that require adequate treatment for their removal. Biological denitrification processes are a cost-effective option for the treatment of these effluents, but the knowledge on the microbial interactions in simultaneous sulfide and phenol oxidatio...
Article
Full-text available
The draft genome of Brevundimonas sp. strain T2.26MG-97, isolated at a depth of 492.6 m in the subsurface of the Iberian Pyrite Belt, is reported here. It consists of 262 scaffolds with a total genome length of 3.68 Mbp, where 3,549 coding DNA sequences have been annotated.
Article
Full-text available
The Dallol geothermal area in the northern part of the Danakil Depression (up to 124–155 meter below sea level) is deemed one of the most extreme environments on Earth. The area is notable for being part of the Afar Depression, an incipient seafloor-spreading center located at the triple junction, between Nubian, Somali and Arabian plates, and for...
Article
Full-text available
Rhodoplanes sp. strain T2.26MG-98 was isolated from the deep subsurface of the Iberian Pyrite Belt. We report its draft genome, consisting of 214 contigs with a chromosome of ∼5.6 Mb and a 53.7-kb plasmid. The chromosome annotation identified 4,994 coding DNA sequences, 1 rRNA operon, and 57 tRNA genes.
Article
The formation of secondary copper deposits, the source of more than half of the world's production, is usually interpreted as abiogenic. In this study of the Las Cruces deposit (southwestern Spain), in situ hybridization and scanning electron microscopy analysis together with integrated genomic and bioinformatic studies on cultures provide compelli...
Article
Full-text available
Although biomineralization in plants is an important area of research, there is very limited information. In this work, we report the location of Na, K, Ca, Mg and Fe biominerals in Sarcocornia pruinosa (Chenopodiacaeae), a halophyte species growing in the estuarine area of Río Tinto, an extreme acidic environment. The estuarine soils of the Tinto...
Article
Full-text available
Rhizobium sp. strain T2.30D-1.1 was isolated from the deep subsurface of the Iberian Pyrite Belt. We report its draft genome, consisting of 60 contigs with a chromosome of ≈4.6 Mb and a plasmid of 179 kb. The annotation revealed 4,526 coding DNA sequences, 45 tRNA genes, and 1 rRNA operon.
Article
Full-text available
Cyanobacteria are ecologically versatile microorganisms inhabiting most environments, ranging from marine systems to arid deserts. Although they possess several pathways for light-independent energy generation, until now their ecological range appeared to be restricted to environments with at least occasional exposure to sunlight. Here we present m...
Presentation
Full-text available
Pyrite oxidation in the Iberian Pyrite Belt mines leads to a high input of dissolved heavy metals into the Rio Tinto. Despite of these potentially harmful and toxic conditions, the Rio Tinto is inhabited by acidophilic Fe(II)-oxidizing microorganisms enriching the acidic water with dissolved Fe(III). However, the hydrochemistry of the river is dram...
Article
Full-text available
Dalangtan Playa is the second largest salt playa in the Qaidam Basin, north-western China. The hyper saline deposition, extremely arid climate and high UV radiation make Dalangtan a Mars analogue both for geomorphology and life preservation. To better understand microbial life at Dalangtan, both culture-dependent and culture-independent methods wer...
Data
Ingredients of Arq medium used for archaeal isolation in this study. (DOCX)
Data
SEM images of bacterial isolates from Dalangtan Playa cultured in the modified growth media (MGM) with salinities of 18% (a, c, d, e, and f) and 3% (b). (TIF)
Conference Paper
During the project “Mars Analogues for Space Exploration” (MASE) several microbial isolates were obtained from extreme terrestrial environments. Some of these strains were subjected to Mars relevant environmental stress factors in the laboratory under controlled conditions; e.g. radiation, low water activity, high salt concentrations, or oxidizing...
Article
Full-text available
Although information from devoted geomicrobiological drilling studies is limited, it is clear that the results obtained so far call for a systematic exploration of the deep continental subsurface, similar to what has been accomplished in recent years by the Ocean Drilling Initiatives. In addition to devoted drillings from the surface, much of the c...
Article
Full-text available
Two deep boreholes were drilled at 320 and 620 meters below surface in the Iberian Pyritic Belt (IPB) at Peña de Hierro (Huelva, Southwestern Spain). Cores were sampled and used for the establishment of enrichment cultures with methanogenic activity. The cultivable diversity of these enrichments was accessed using different cultivation techniques a...
Article
Soda lakes are inhabited by important haloalkaliphilic microbial communities that are well adapted to these extreme characteristics. The surface waters of the haloalkaline Mono Lake (CA, USA) are alkaline but, in contrast to its bottom waters, do not present high salinity. We have studied the microbiota present in the shoreline sediments of Mono La...
Article
The search for extinct and extant life on Mars is based on the study of biosignatures that could be preserved under Mars-like, extreme conditions that are replicated in different terrestrial analog environments. The mineral record in the subsurface of the Río Tinto system is one example of a Mars analog site that has been exposed to weathering cond...
Article
Full-text available
Growth in sodium chloride (NaCl) is known to induce stress in non-halophilic microorganisms leading to effects on the microbial metabolism and cell structure. Microorganisms have evolved a number of adaptations, both structural and metabolic, to counteract osmotic stress. These strategies are well-understood for organisms in NaCl-rich brines such a...
Data
Principal Component Analysis (PCA) plot showing the multivariate variation among the three sample sets (control, NaCl stressed and MgSO4 stressed; n = 3) in terms of the obtained peaks.
Data
List of identified and putatively identified lipids. Metabolite levels for each experimental group are shown. Levels are expressed as mean peak intensity relative to the mean peak intensity of the control group. Numbers indicated in bold indicates statistically significance (p < 0.05).