Microbial Ecology in the Atmosphere: The Last Extreme Environment

The atmosphere is an extreme environment where organisms are subject to low temperatures and high radiation. Many of the microorganisms detected there appear in resistant forms or show mechanisms of adaptation designed to withstand these extreme conditions. Airborne microorganisms may play an important role in the global climate system, biogeochemical cycling, and health. Dust storms are the atmospheric phenomenon that move more topsoil through the Earth’s atmosphere, and numerous microorganisms attached to dust particles are thus transported. The Iberian Peninsula is periodically affected by this phenomenon as African dust frequently reaches southern Europe and the Mediterranean basin. There are numerous methods for sampling airborne microbes, but factors such as low biomass and high variability of the atmosphere render them not yet sufficiently efficient. Very few studies have been conducted directly in the atmosphere via sampling using airborne platforms. The National Institute for Aerospace Technology has two CASA C-212-200 aircraft that have been suitably modified to operate as airborne research platforms. These aircraft are a unique tool for the study of atmospheric microbial diversity and the different environments where they can be found. A study of the airborne microbial diversity in a Saharan dust event from four aerobiology sampling flights is provided in advance

Integration of an Optical Ring Resonator Biosensor into a Self-Contained Microfluidic Cartridge with Active, Single-Shot Micropumps

While there have been huge advances in the field of biosensors during the last decade, their integration into a microfluidic environment avoiding external tubing and pumping is still neglected. Herein, we show a new microfluidic design that integrates multiple reservoirs for reagent storage and single-use electrochemical pumps for time-controlled delivery of the liquids. The cartridge has been tested and validated with a silicon nitride-based photonic biosensor incorporating multiple optical ring resonators as sensing elements and an immunoassay as a potential target application. Based on experimental results obtained with a demonstration model, subcomponents were designed and existing protocols were adapted. The newly-designed microfluidic cartridges and photonic sensors were separately characterized on a technical basis and performed well. Afterwards, the sensor was functionalized for a protein detection. The microfluidic cartridge was loaded with the necessary assay reagents. The integrated pumps were programmed to drive the single process steps of an immunoassay. The prototype worked selectively, but only with a low sensitivity. Further work must be carried out to optimize biofunctionalization of the optical ring resonators and to have a more suitable flow velocity progression to enhance the system’s reproducibility.The authors would like to thank the European Union for their funding of the project PBSA “Photonic Biosensor for Space Application” within the FP7-program (FP7 program Grant Agreement No. 312942-PBSA. We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI

Impacts of Saharan dust intrusions on bacterial communities of the low troposphere

We have analyzed the bacterial community of a large Saharan dust event in the Iberian Peninsula and, for the frst time, we ofer new insights regarding the bacterial distribution at diferent altitudes of the lower troposphere and the replacement of the microbial airborne structure as the dust event receeds. Samples from diferent open-air altitudes (surface, 100m and 3km), were obtained onboard the National Institute for Aerospace Technology (INTA) C-212 aircrafts. Samples were collected during dust and dust-free air masses as well two weeks after the dust event. Samples related in height or time scale seems to show more similar community composition patterns compared with unrelated samples. The most abundant bacterial species during the dust event, grouped in three diferent phyla: (a) Proteobacteria: Rhizobiales, Sphingomonadales, Rhodobacterales, (b) Actinobacteria: Geodermatophilaceae; (c) Firmicutes: Bacillaceae. Most of these taxa are well known for being extremely stress-resistant. After the dust intrusion, Rhizobium was the most abundant genus, (40–90% total sequences). Samples taken during the fights carried out 15 days after the dust event were much more similar to the dust event samples compared with the remaining samples. In this case, Brevundimonas, and Methylobacterium as well as Cupriavidus and Mesorizobium were the most abundant genera

Occurrence and transport of microplastics sampled within and above the planetary boundary layer

Nowadays, there is no direct evidence about the presence of microplastics (MPs) in the atmosphere above ground level. Here, we investigated the occurrence, chemical composition, shape, and size of MPs in aircraft sampling campaigns flying within and above the planetary boundary layer (PBL). The results showed that MPs were present with concentrations ranging from 1.5 MPs m−3 above rural areas to 13.9 MPs m−3 above urban areas. MPs represented up to almost one third of the total amount of microparticles collected. Fourier Transform Infrared Spectroscopy allowed identifying seven types of MPs with the highest diversity corresponding to urban areas. Atmospheric transport and deposition simulations were performed using the HYbrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model. Air mass trajectory analyses showed that MPs could be transported more than 1000 km before being deposited. This pioneer study is the first evidence of the microplastic presence above PBL and their potential long-range transport from their point of release even crossing distant bordersWe also acknowledge support from the EnviroPlaNet Network Thematic Newtork of Micro- and Nanoplastics in the Environment (RED2018-102345-T; Ministerio de Ciencia, Innovación y Universidades). We thank the financial support provided by the Spanish Ministerio de Ciencia, Innovación y Universidades (CTM2016-74927-C2-1-R/2-R, CGL2015-69758-P, CGL2017-92086-EXP, RTI2018-094867-B-I00) and National Institute for Aerospace Technology (PAI/APL/001/09

Occurrence and transport of microplastics sampled within and above the planetary boundary layer.

Nowadays, there is no direct evidence about the presence of microplastics (MPs) in the atmosphere above ground level. Here, we investigated the occurrence, chemical composition, shape, and size of MPs in aircraft sampling campaigns flying within and above the planetary boundary layer (PBL). The results showed that MPs were present with concentrations ranging from 1.5 MPs m−3 above rural areas to 13.9 MPs m−3 above urban areas. MPs represented up to almost one third of the total amount of microparticles collected. Fourier Transform Infrared Spectroscopy allowed identifying seven types of MPs with the highest diversity corresponding to urban areas. Atmospheric transport and deposition simulations were performed using the HYbrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model. Air mass trajectory analyses showed that MPs could be transported more than 1000 km before being deposited. This pioneer study is the first evidence of the microplastic presence above PBL and their potential long-range transport from their point of release even crossing distant borders.We also acknowledge support from the EnviroPlaNet Network Thematic Newtork of Micro- and Nanoplastics in the Environment (RED2018-102345-T; Ministerio de Ciencia, Innovación y Universidades). We thank the financial support provided by the Spanish Ministerio de Ciencia, Innovación y Universidades (CTM2016-74927-C2-1-R/2-R, CGL2015-69758-P, CGL2017-92086-EXP, RTI2018-094867-B-I00) and National Institute for Aerospace Technology (PAI/APL/001/09)

Biomarker Profiling of Microbial Mats in the Geothermal Band of Cerro Caliente, Deception Island (Antarctica): Life at the Edge of Heat and Cold

© María Ángeles Lezcano et al. 2019.Substrate–atmosphere interfaces in Antarctic geothermal environments are hot–cold regions that constitute thin habitable niches for microorganisms with possible counterparts in ancient Mars. Cerro Caliente hill in Deception Island (active volcano in the South Shetland Islands) is affected by ascending hydrothermal fluids that form a band of warm substrates buffered by low air temperatures. We investigated the influence of temperature on the community structure and metabolism of three microbial mats collected along the geothermal band of Cerro Caliente registering 88°C, 8°C, and 2°C at the time of collection. High-throughput sequencing of small subunit ribosomal ribonucleic acid (SSU rRNA) genes and Life Detector Chip (LDChip) microarray immunoassays revealed different bacterial, archaeal, and eukaryotic composition in the three mats. The mat at 88°C showed the less diverse microbial community and a higher proportion of thermophiles (e.g., Thermales). In contrast, microbial communities in the mats at 2°C and 8°C showed relatively higher diversity and higher proportion of psychrophiles (e.g., Flavobacteriales). Despite this overall association, similar microbial structures at the phylum level (particularly the presence of Cyanobacteria) and certain hot- and cold-tolerant microorganisms were identified in the three mats. Daily thermal oscillations recorded in the substrate over the year (4.5–76°C) may explain the coexistence of microbial fingerprints with different thermal tolerances. Stable isotope composition also revealed metabolic differences among the microbial mats. Carbon isotopic ratios suggested the Calvin–Benson–Bassham cycle as the major pathway for carbon dioxide fixation in the mats at 2°C and 8°C, and the reductive tricarboxylic acid cycle and/or the 3-hydroxypropionate bicycle for the mat at 88°C, indicating different metabolisms as a function of the prevailing temperature of each mat. The comprehensive biomarker profile on the three microbial mats from Cerro Caliente contributes to unravel the diversity, composition, and metabolism in geothermal polar sites and highlights the relevance of geothermal-cold environments to create habitable niches with interest in other planetary environments.This study has been funded by the Spanish Research Agency (AEI) from the Ministry of Science Innovation and Universities and the European FEDER Grants Nos. ESP2015-69540-R, RYC2014-19446, and CGL2015-74254-JIN; the AEI Project No. MDM-2017-0737 Unidad de Excelencia ‘‘Marı´a de Maeztu,’’ and the European Research Council Starting Grant (ERC StG) No. 307496. M.A´ . Lezcano and M.A´ . Fernández Martínez were supported by a postdoctoral fellowship by the Youth Employment Initiative from the European Union and implanted in Comunidad de Madrid

Inmunoensayos para exploración planetaria: implementación en instrumentación para análisis “in situ”

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 21-11-2016Esta tesis tiene embargado el acceso al texto completo hasta el 21-05-2018Uno de los mayores retos de la astrobiología es la búsqueda de señales de vida en otros cuerpos planetarios. Con el objetivo de detectar biomarcadores moleculares, se desarrolló en el Centro de Astrobiología el instrumento denominado SOLID, por ‘‘Signs Of LIfe Detector’’, provisto del biosensor inmunológico LDChip (por “Life Detector Chip”), un microarray de anticuerpos capaz de detectar multitud de analitos de muestras sólidas o líquidas. El concepto SOLID-LDChip es novedoso en exploración planetaria y, para aumentar su madurez y nivel tecnológico, es un requisito imprescindible que sus componentes más críticos soporten las duras condiciones a las que se verán expuestos en una misión. Uno de esos componentes es el corazón biosensor LDChip y los anticuerpos. En esta tesis se ha testado y evaluado la estabilidad de los componentes bioquímicos de LDChip (anticuerpos capturadores inmovilizados en el microarray y anticuerpos trazadores marcados con fluorescencia) sometiéndolos a condiciones relevantes para el espacio (radiación ionizante, temperaturas extremas fluctuantes, o diferentes tipos y tiempos de almacenaje). Los resultados mostraron que, en las condiciones de protección y conservación adecuadas, los anticuerpos, fluorocromos y el inmunoensayo en general serían funcionales bajo las dosis de radiación y temperaturas fluctuantes en una misión a Marte de al menos 2 años de duración. Asimismo, se ha testado y validado la versión de campo de SOLIDv3.0 y LDChip con 300 anticuerpos para la detección de biomarcadores microbianos en ambientes análogos terrestres de Marte, como son los depósitos salinos evaporíticos del Desierto de Atacama (Chile) y el permafrost y ambiente hidrotermal de Isla Decepción (Antártida). Se demostró la sensibilidad de SOLID-LDChip en el entorno de ng mL-1 o 103-105 células o esporas por mL en los extractos y su capacidad para detectar biomarcadores moleculares en muestras del subsuelo de Atacama obtenidas a más de 2 m de profundidad. La información proporcionada por SOLID-LDChip es rica y permite identificar en el campo en pocas horas los elementos principales de las comunidades microbianas.The search for signs of life in other planetary bodies is one of the main challenges for astrobiology. With the aim of detecting molecular biomarkers, the instrument SOLID (“Signs Of LIfe Detector”) has been developed in Centro de Astrobiología. It contains the immunologic biosensor LDChip (“Life Detector Chip”), a microarray able to detect multiple analytes from liquid and solid samples. The concept SOLID-LDChip is a novelty in planetary exploration, and therefore it is mandatory, in order to increase its maturity and technological level, that its most critical components are able to bear the tough conditions to which they will be exposed in a mission. One of such components is its core biosensor LDChip and the antibodies. In this thesis the stability of LDChip biological components (tracer antibodies, labeled with fluorescence, as well as capturing antibodies) was tested under conditions of radiation, temperature, storage techniques and times that apply to a planetary exploration mission. Results show that, under proper storage and protection conditions, antibodies, fluorochromes and the immunoassay in general would be functional under the doses of radiation and fluctuant temperatures that would exist in a 2-year-or-more mission to Mars. Furthermore, the field version of SOLID v3.0 and LDChip with 300 antibodies has been tested and validated for the detection of microbial biomarkers extreme environments that are considered analogous of Mars: arid hypersaline environments in Atacama Desert (Chile), and permafrost and hydrothermal environment in Deception Island (Antarctica). SOLID-LDChip sensitivity was assessed to the range of ng mL-1 or 103-105 cells or spores per mL, as well as its ability to detect molecular biomarkers in Atacama subsoil samples obtained at 2m depth. SOLID-LDChip provides rich information, which allows on-field identification of the main component of microbial communities in a few hours

Impacts of Saharan Dust Intrusions on Bacterial Communities of the Low Troposphere

© The Author(s) 2020.We have analyzed the bacterial community of a large Saharan dust event in the Iberian Peninsula and, for the first time, we offer new insights regarding the bacterial distribution at different altitudes of the lower troposphere and the replacement of the microbial airborne structure as the dust event receeds. Samples from different open-air altitudes (surface, 100 m and 3 km), were obtained onboard the National Institute for Aerospace Technology (INTA) C-212 aircrafts. Samples were collected during dust and dust-free air masses as well two weeks after the dust event. Samples related in height or time scale seems to show more similar community composition patterns compared with unrelated samples. The most abundant bacterial species during the dust event, grouped in three different phyla: (a) Proteobacteria: Rhizobiales, Sphingomonadales, Rhodobacterales, (b) Actinobacteria: Geodermatophilaceae; (c) Firmicutes: Bacillaceae. Most of these taxa are well known for being extremely stress-resistant. After the dust intrusion, Rhizobium was the most abundant genus, (40–90% total sequences). Samples taken during the flights carried out 15 days after the dust event were much more similar to the dust event samples compared with the remaining samples. In this case, Brevundimonas, and Methylobacterium as well as Cupriavidus and Mesorizobium were the most abundant genera.This work was funded by the Spanish Economy and Competitiveness Ministry (MINECO) grants CGL2015-69758-P, CGL2017-92086-EXP, ESP2016-79612-C3-1-R, RTI2018-094867-BI00 and i-LINK 1151 grant founded by the Council for Scientific Research (CSIC). FPS was supported by the MINECO grant CTM2016-80095-C2-1-R

A microbial oasis in the hypersaline atacama subsurface discovered by a life detector chip:Implications for the search for life on mars

The Atacama Desert has long been considered a good Mars analogue for testing instrumentation for planetary exploration, but very few data (if any) have been reported about the geomicrobiology of its salt-rich subsurface. We performed a Mars analogue drilling campaign next to the Salar Grande (Atacama, Chile) in July 2009, and several cores and powder samples from up to 5m deep were analyzed in situ with LDChip300 (a Life Detector Chip containing 300 antibodies). Here, we show the discovery of a hypersaline subsurface microbial habitat associated with halite-, nitrate-, and perchlorate-containing salts at 2m deep. LDChip300 detected bacteria, archaea, and other biological material (DNA, exopolysaccharides, some peptides) from the analysis of less than 0.5g of ground core sample. The results were supported by oligonucleotide microarray hybridization in the field and finally confirmed by molecular phylogenetic analysis and direct visualization of microbial cells bound to halite crystals in the laboratory. Geochemical analyses revealed a habitat with abundant hygroscopic salts like halite (up to 260g kg -1) and perchlorate (41.13μg g -1 maximum), which allow deliquescence events at low relative humidity. Thin liquid water films would permit microbes to proliferate by using detected organic acids like acetate (19.14μg g -1) or formate (76.06μg g -1) as electron donors, and sulfate (15875μg g -1), nitrate (13490μg g -1), or perchlorate as acceptors. Our results correlate with the discovery of similar hygroscopic salts and possible deliquescence processes on Mars, and open new search strategies for subsurface martian biota. The performance demonstrated by our LDChip300 validates this technology for planetary exploration, particularly for the search for life on Mars