Soil Particles and Phenanthrene Interact in Defining the Metabolic Profile of Pseudomonas putida G7: A Vibrational Spectroscopy Approach

In soil, organic matter and mineral particles (soil particles; SPs) strongly influence the bio-available fraction of organic pollutants, such as polycyclic aromatic hydrocarbons (PAHs), and the metabolic activity of bacteria. However, the effect of SPs as well as comparative approaches to discriminate the metabolic responses to PAHs from those to simple carbon sources are seldom considered in mineralization experiments, limiting our knowledge concerning the dynamics of contaminants in soil. In this study, the metabolic profile of a model PAH-degrading bacterium, Pseudomonas putida G7, grown in the absence and presence of different SPs (i.e., sand, clays and humic acids), using either phenanthrene or glucose as the sole carbon and energy source, was characterized using vibrational spectroscopy (i.e., FT-Raman and FT-IR spectroscopy) and multivariate classification analysis (i.e., PLS-DA). The different type of SPs specifically altered the metabolic profile of P. putida, especially in combination with phenanthrene. In comparison to the cells grown in the absence of SPs, sand induced no remarkable change in the metabolic profile of the cells, whereas clays and humic acids affected it the most, as revealed by the higher discriminative accuracy (R2, RMSEP and sensitivity) of the PLS-DA for those conditions. With respect to the carbon-source (phenanthrene vs. glucose), no effect on the metabolic profile was evident in the absence of SPs or in the presence of sand. On the other hand, with clays and humic acids, more pronounced spectral clusters between cells grown on glucose or on phenanthrene were evident, suggesting that these SPs modify the way cells access and metabolize PAHs. The macromolecular changes regarded mainly protein secondary structures (a shift from α-helices to β-sheets), amino acid levels, nucleic acid conformation and cell wall carbohydrates. Our results provide new interesting evidences that SPs specifically interact with PAHs in defining bacteria metabolic profiles and further emphasize the importance of studying the interaction of bacteria with their surrounding matrix to deeply understand PAHs degradation in soils

Planetary protection: an international concern and responsibility

Planetary protection is a set of measures agreed upon at an international level to ensure the protection of scientific investigation during space exploration. As space becomes more accessible with traditional and new actors launching complex and innovative projects that involve robotics (including sample return) and human exploration, we have the responsibility to protect the pristine environments that we explore and our own biosphere. In this sense, the Committee on Space Research (COSPAR) provides the international standard for planetary protection as well as a forum for international consultation. COSPAR has formulated a Planetary Protection Policy with associated requirements for responsible space exploration. Although not legally binding under international law, the standard offered by the Policy with its associated requirements is internationally endorsed along with implementation guidelines supplied for reference in support States’ compliance with Article IX of the United Nations Outer Space Treaty of 1967. Indeed, States parties to the Outer Space Treaty (under Article VI) are responsible for any space activities in their countries, governmental and non-governmental. The main goal of this Policy is to avoid compromising the search for any lifeforms on other celestial bodies and to protect the Earth from a potential threat posed by extraterrestrial samples returned by an interplanetary mission. The COSPAR Planetary Protection Policy has defined five categories, depending on the target and objective of the specific space mission. Associated to these categories are requirements are various degrees of rigor in the contamination control applied. The Policy is assessed regularly and updated with input from new scientific findings and in conjunction with the fast-evolving space exploration milieu. The COSPAR Panel on Planetary Protection (PPP) is a designated international committee composed of scientists, agency representatives and space experts. Its role is to support and revise the COSPAR Policy and its related requirements (https://cosparhq.cnes.fr/scientific-structure/panels/panel-on-planetary-protection-ppp/). The Panel’s activities deal with the individual needs of a space mission while exercising swift care and expertise to ensure sustainable exploration of the Solar System

The COSPAR planetary protection requirements for space missions to Venus

The Committee on Space Research's (COSPAR) Planetary Protection Policy states that all types of missions to Venus are classified as Category II, as the planet has significant research interest relative to the processes of chemical evolution and the origin of life, but there is only a remote chance that terrestrial contamination can proliferate and compromise future investigations. "Remote chance" essentially implies the absence of environments where terrestrial organisms could survive and replicate. Hence, Category II missions only require simplified planetary protection documentation, including a planetary protection plan that outlines the intended or potential impact targets, brief Pre- and Post-launch analyses detailing impact strategies, and a Post-encounter and End-of-Mission Report. These requirements were applied in previous missions and are foreseen for the numerous new international missions planned for the exploration of Venus, which include NASA's VERITAS and DAVINCI missions, and ESA's EnVision mission. There are also several proposed missions including India's Shukrayaan-1, and Russia's Venera-D. These multiple plans for spacecraft coincide with a recent interest within the scientific community regarding the cloud layers of Venus, which have been suggested by some to be habitable environments. The proposed, privately funded, MIT/Rocket Lab Venus Life Finder mission is specifically designed to assess the habitability of the Venusian clouds and to search for signs of life. It includes up to three atmospheric probes, the first one targeting a launch in 2023. The COSPAR Panel on Planetary Protection evaluated scientific data that underpins the planetary protection requirements for Venus and the implications of this on the current policy. The Panel has done a thorough review of the current knowledge of the planet's conditions prevailing in the clouds. Based on the existing literature, we conclude that the environmental conditions within the Venusian clouds are orders of magnitude drier and more acidic than the tolerated survival limits of any known terrestrial extremophile organism. Because of this future orbital, landed or entry probe missions to Venus do not require extra planetary protection measures. This recommendation may be revised in the future if new observations or reanalysis of past data show any significant increment, of orders of magnitude, in the water content and the pH of the cloud layer

COSPAR Sample Safety Assessment Framework (SSAF)

The Committee on Space Research (COSPAR) Sample Safety Assessment Framework (SSAF) has been developed by a COSPAR appointed Working Group. The objective of the sample safety assessment would be to evaluate whether samples returned from Mars could be harmful for Earth's systems (e.g., environment, biosphere, geochemical cycles). During the Working Group's deliberations, it became clear that a comprehensive assessment to predict the effects of introducing life in new environments or ecologies is difficult and practically impossible, even for terrestrial life and certainly more so for unknown extraterrestrial life. To manage expectations, the scope of the SSAF was adjusted to evaluate only whether the presence of martian life can be excluded in samples returned from Mars. If the presence of martian life cannot be excluded, a Hold & Critical Review must be established to evaluate the risk management measures and decide on the next steps. The SSAF starts from a positive hypothesis (there is martian life in the samples), which is complementary to the null-hypothesis (there is no martian life in the samples) typically used for science. Testing the positive hypothesis includes four elements: (1) Bayesian statistics, (2) subsampling strategy, (3) test sequence, and (4) decision criteria. The test sequence capability covers self-replicating and non-self-replicating biology and biologically active molecules. Most of the investigations associated with the SSAF would need to be carried out within biological containment. The SSAF is described in sufficient detail to support planning activities for a Sample Receiving Facility (SRF) and for preparing science announcements, while at the same time acknowledging that further work is required before a detailed Sample Safety Assessment Protocol (SSAP) can be developed. The three major open issues to be addressed to optimize and implement the SSAF are (1) setting a value for the level of assurance to effectively exclude the presence of martian life in the samples, (2) carrying out an analogue test program, and (3) acquiring relevant contamination knowledge from all Mars Sample Return (MSR) flight and ground elements. Although the SSAF was developed specifically for assessing samples from Mars in the context of the currently planned NASA-ESA MSR Campaign, this framework and the basic safety approach are applicable to any other Mars sample return mission concept, with minor adjustments in the execution part related to the specific nature of the samples to be returned. The SSAF is also considered a sound basis for other COSPAR Planetary Protection Category V, restricted Earth return missions beyond Mars. It is anticipated that the SSAF will be subject to future review by the various MSR stakeholders

Indirect amperometric detection of non-electroactive species. towards an electrochemical bioasay of mineral weathering?

Ion exchange polymers doped with a suitable electroactive mediator (i.e., Cu2+ or Fe(CN)63-) have been used to modify carbon paste electrodes that have been further applied to the indirect amperometric detection of non-redox cations or anions in flow injection analysis. The detection mechanism involves ion exchange between the non-redox ionic analyte and the electroactive mediator, in the polymer particles located at the electrode surface, followed by the electrochemical transformation of the mediator species leached out of the polymer at the electrode/solution interface. Operating in the absence of added supporting electrolyte led to peak currents made of a major faradic component that is added to a capacitive contribution due to the conductivity jump occurring upon the analyte passing the electrode surface. The method can be applied to the detection of non-electroactive mineral cations and anions, as well as poorly-dissociated organic acids, which are usually involved in mineral weathering. After having characterized and discussed the main parameters affecting the sensitivity of the detection (with respect to analyte charge, size and degree of dissociation), the electrochemical device was evaluated as a possible test to monitor mineral weathering in a simple case (zeolite dissolution in acidic medium) and in a more sophisticated one (biomediated olivine dissolution by fungi)

Décomposition tensorielle de signaux luminescents émis par des biosenseurs bactériens pour l'identification de Systèmes Métaux-Bactéries

La disponibilité et la persistance à l'échelle locale des métaux lourds pourraient être critiques notamment pour l'usage futur des zones agricoles ou urbaines, au droit desquelles de nombreux sites industriels se sont installés dans le passé. La gestion de ces situations environnementales complexes nécessitent le développement de nouvelles méthodes d'analyse peu invasives (capteurs environnementaux), comme celles utilisant des biosenseurs bactériens, afin d'identifier et d'évaluer directement l'effet biologique et la disponibilité chimique des métaux. Ainsi dans ce travail de thèse, nous avons cherché à identifier, à l'aide d'outils mathématiques de l'algèbre multilinéaire, les réponses de senseurs bactériens fluorescents dans des conditions environnementales variées, qu'il s'agisse d'un stress engendré par la présence à forte dose d'un métal ou d'une carence nutritive engendrée par son absence. Cette identification est fondée sur l'analyse quantitative à l'échelle d'une population bactérienne de signaux multidimensionnels. Elle repose en particulier sur (i) l'acquisition de données spectrales (fluorescence) multi-variées sur des suspensions de biosenseurs multicolores interagissant avec des métaux et sur (ii) le développement d'algorithme de décomposition tensoriels. Les méthodes proposées, développées et utilisées dans ce travail s'efforcent d'identifier sans a priori a minima, la réponse fonctionnelle de biosenseurs sous différentes conditions environnementales, par des méthodes de décomposition de tenseurs sous contraintes des signaux spectraux observables. Elles tirent parti de la variabilité des réponses systémiques et permettent de déterminer les sources élémentaires identifiant le système et leur comportement en fonction des paramètres extérieurs. Elles sont inspirées des méthodes CP et PARALIND . L'avantage de ce type d'approche, par rapport aux approches classiques, est l'identification unique des réponses des biosenseurs sous de faibles contraintes. Le travail a consisté à développer des algorithmes efficaces de séparations de sources pour les signaux fluorescents émis par des senseurs bactériens, garantissant la séparabilité des sources fluorescentes et l'unicité de la décomposition. Le point original de la thèse est la prise en compte des contraintes liées à la physique des phénomènes analysés telles que (i) la parcimonie des coefficients de mélange ou la positivité des signaux source, afin de réduire au maximum l'usage d'a priori ou (ii) la détermination non empirique de l'ordre de la décomposition (nombre de sources). Cette posture a permis aussi d'améliorer l'identification en optimisant les mesures physiques par l'utilisation de spectres synchrones ou en apportant une diversité suffisante aux plans d'expériences. L'usage des spectres synchrones s'est avéré déterminant à la fois pour améliorer la séparation des sources de fluorescence, mais aussi pour augmenter le rapport signal sur bruit des biosenseurs les plus faibles. Cette méthode d'analyse spectrale originale permet d'élargir fortement la gamme chromatique des biosenseurs fluorescents multicolores utilisables simultanément. Enfin, une nouvelle méthode d'estimation de la concentration de polluants métalliques présents dans un échantillon à partir de la réponse spectrale d'un mélange de biosenseurs non-spécifiques a été développéeAvailability and persistence of heavy metals could be critical for future use of agricultural or urban areas, on which many industrial sites have installed in the past. The management of these complex environmental situations requiring the development of new analytical methods minimally invasive, such as bacterial biosensors, to identify and directly assess the biological effects and the chemical availability of metals. The aims of this thesis was to identify the responses of fluorescent bacterial sensors various environmental conditions, using mathematical tools of algebra multi-linear, whether stress caused by the presence of high dose of a metal or a nutrient deficiency caused by his absence. This identification is based on quantitative analysis of multidimensional signals at the bacterial population-scale. It is based in particular on (i) the acquisition of multivariate spectral data on suspensions of multicolored biosensors interacting with metals and (ii) the development of algorithms for tensor decomposition. The proposed methods, developed and used in this study attempt to identify functional response of biosensors without \textsl{a priori} by decomposition of tensor containing the spectral signals. These methods take advantage of the variability of systemic responses and allow to determine the basic sources identifying the system and their behavior to external factors. They are inspired by the CP and PARALIND methods. The advantage of this approach, compared to conventional approaches, is the unique identification of the responses of biosensors at low constraints. The work was to develop efficient algorithms for the source separation of fluorescent signals emitted by bacterial sensors, ensuring the sources separability and the uniqueness of the decomposition. The original point of this thesis is the consideration of the physical constraints of analyzed phenomena such as (i) the sparsity of mixing coefficients or positivity of sources signals in order to minimize the use of a priori or (ii) the non-empirical determination of the order of decomposition (number of sources).This posture has also improved the identification optimizing physical measurements by the use of synchronous spectra or providing sufficient diversity in design of experiments. The use of synchronous spectra proved crucial both to improve the separation of fluorescent sources, but also to increase the signal to noise ratio of the lowest biosensors. This original method of spectral analysis can greatly expand the color range of multicolored fluorescent biosensors used simultaneously. Finally, a new method of estimating the concentration of metal pollutants present in a sample from the spectral response of a mixture of non-specific biosensor was developedMETZ-SCD (574632105) / SudocNANCY1-Bib. numérique (543959902) / SudocNANCY2-Bibliotheque electronique (543959901) / SudocNANCY-INPL-Bib. électronique (545479901) / SudocSudocFranceF

Traces de vie présente ou passée : quels indices, signatures ou marqueurs ?

SCOPUS: ed.jinfo:eu-repo/semantics/publishe

Gels de silice hybrides dopés en particules colloïdales de smectites pour l'étude des interactions bactérie/silicate

Ce travail concerne l'étude des interactions bactéries /silicates grâce à de nouveaux matériaux ou gels de silice hybrides dopés en particules colloïdales de smectites (GSH). Les deux objectifs principaux sont la caractérisation physicochimique des GSH et l'amélioration des connaissances sur les mécanismes de l'altération minérale grâce aux GSH. Dans le premier volet de la thèse, nous avons ainsi pu mettre en évidence que le gel est constitué d'une matrice siliceuse particulaire de nature fractale dans laquelle les particules minérales sont dispersées. La structure des GSH est stabilisée par le traitement hydrothermal choisi (type autoclave). Dans le second volet de la thèse, l'altération minérale est étudiée pour des GSH à concentration variable en particules minérales, à teneur élevée (NAu-2) ou basse (SWy-2) en fer. Il est ainsi montré que la diffusion des acides organiques et des sidérophores dans le GSH, hors adhésion ou formation d'un biofilm en surface des minéraux, est suffisante pour altérer efficacement les particules minérales. La mise en évidence de gradients de protons locaux produits par la bactérie en interaction avec les GSH peut également expliquer l'efficacité biotique de la dissolution minérale par rapport à des conditions abiotiques. En conclusion, les points forts et les limites de l'utilisation d'un matériau hybride type GSH pour cibler les interactions minéral/microorganismes sont discutésThis work deals with the study of bacteria/silicate interactions by using new hybrid materials, i.e. hybrid silica gel dopped with colloidal smectite particles (HSG). The aims are (1) to characterize HSG physicochemical properties and (2) to get a better knowledge about mineral/bacteria interactions. In a first part of the thesis, it is shown that HSG is a fractal silica network containing well-dispersed mineral particles. Hydrothermal treatment is necessary to stabilize the HSG structure. In the second part, it is shown that diffusion of organic acids and siderophores is sufficient to explain the high efficiency of bacterial action compared to abiotic treatments. Preventing bacterial adhesion or biofilm formation at the mineral surface permits to enhance the influence of metabolites diffusion. To conclude, the advantages and limits of using HSG in environmental studies are discussedMETZ-SCD (574632105) / SudocNANCY1-Bib. numérique (543959902) / SudocNANCY2-Bibliotheque electronique (543959901) / SudocNANCY-INPL-Bib. électronique (545479901) / SudocSudocFranceF

Experimental Study on the Phlogopite Weathering Potential of Bacterial Communities Isolated from Different Soil Profiles

International audienc

Soil particles alter the metabolic profile of Pseudomonas putida grown in the presence of phenanthrene: A vibrationalSpectroscopy approach

International audienc