M. Ji, Atmospheric trace gases support primary production in Antarctic desert surface soil, Nature, vol.552, pp.400-403, 2017.

T. P. Makhalanyane, Microbial ecology of hot desert edaphic systems, FEMS microbiology reviews, vol.39, pp.203-221, 2015.

J. W. Neilson, Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Extremophiles: life under extreme conditions, vol.16, pp.553-566, 2012.

R. C. Lynch, J. L. Darcy, N. C. Kane, D. R. Nemergut, and S. K. Schmidt, Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria, Frontiers in microbiology, vol.5, 2014.

D. Mandakovic, Complete genome sequence of Microbacterium sp. CGR1, bacterium tolerant to wide abiotic conditions isolated from the Atacama Desert, Journal of biotechnology, vol.216, pp.149-150, 2015.

Z. W. Yang, Microbacterium album sp. nov. and Microbacterium deserti sp. nov., two halotolerant actinobacteria isolated from desert soil, International journal of systematic and evolutionary microbiology, vol.68, pp.217-222, 2018.

D. Mandakovic, Microbiome analysis and bacterial isolation from Lejia Lake soil in Atacama Desert, Extremophiles: life under extreme conditions, vol.22, pp.665-673, 2018.

C. Demergasso, Prokaryotic diversity pattern in high-altitude ecosystems of the Chilean Altiplano, vol.115, 2010.

E. J. O'brien, J. M. Monk, and B. O. Palsson, Using Genome-scale Models to Predict Biological Capabilities, Cell, vol.161, pp.971-987, 2015.

S. Noack, A. Wahl, E. Qeli, and W. Wiechert, Visualizing regulatory interactions in metabolic networks, BMC biology, vol.5, 2007.

M. Durot, P. Y. Bourguignon, and V. Schachter, Genome-scale models of bacterial metabolism: reconstruction and applications, FEMS microbiology reviews, vol.33, pp.164-190, 2009.

W. J. Kim, H. U. Kim, and S. Y. Lee, Current state and applications of microbial genome-scale metabolic models, Current Opinion in Systems Biology, vol.2, pp.10-18, 2017.

G. Plata, C. S. Henry, and D. Vitkup, Long-term phenotypic evolution of bacteria, Nature, vol.517, pp.369-372, 2015.

J. L. Reed, T. D. Vo, C. H. Schilling, and B. O. Palsson, An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/ GPR), Genome biology, vol.4, 2003.

C. S. Henry, J. F. Zinner, M. P. Cohoon, and R. L. Stevens, iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations, Genome biology, vol.10, 2009.

M. T. Alam, M. H. Medema, E. Takano, and R. Breitling, Comparative genome-scale metabolic modeling of actinomycetes: the topology of essential core metabolism, FEBS letters, vol.585, pp.2389-2394, 2011.

V. Razmilic, J. F. Castro, F. Marchant, J. A. Asenjo, and B. Andrews, Metabolic modelling and flux analysis of microorganisms from the Atacama Desert used in biotechnological processes, Antonie van Leeuwenhoek, vol.111, pp.1479-1491, 2018.

M. W. Henson, Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment, PeerJ, vol.3, 1395.

D. Mandakovic, Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience, Scientific reports, vol.8, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01774624

K. Katoh, K. Misawa, K. Kuma, and T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Res, vol.30, pp.3059-3066, 2002.

K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution, vol.30, pp.772-780, 2013.

K. Tamura, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Molecular biology and evolution, vol.28, pp.2731-2739, 2011.

K. Tamura, G. Stecher, D. Peterson, A. Filipski, S. Kumar et al., Molecular Evolutionary Genetics Analysis version 6.0. Molecular biology and evolution, vol.30, pp.2725-2729, 2013.

I. Letunic and P. Bork, Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, vol.44, pp.242-245, 2016.

T. Tatusova, NCBI prokaryotic genome annotation pipeline, Nucleic Acids Res, vol.44, pp.6614-6624, 2016.

R. K. Aziz, The RAST Server: rapid annotations using subsystems technology, BMC Genomics, vol.9, 2008.

T. M. Lowe and S. R. Eddy, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res, vol.25, pp.955-964, 1997.

A. L. Delcher, K. A. Bratke, E. C. Powers, and S. L. Salzberg, Identifying bacterial genes and endosymbiont DNA with Glimmer, Bioinformatics, vol.23, pp.673-679, 2007.

M. Aite, Traceability, reproducibility and wiki-exploration for "a-la-carte" reconstructions of genome-scale metabolic models, PLoS computational biology, vol.14, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01807842

P. D. Karp, Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology, Briefings in bioinformatics, vol.17, pp.877-890, 2016.

J. Schellenberger, Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0, Nature protocols, vol.6, pp.1290-1307, 2011.

N. Loira, A. Zhukova, D. J. Sherman, and . Pantograph, A template-based method for genome-scale metabolic model reconstruction, Journal of bioinformatics and computational biology, vol.13, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01123733

P. D. Karp, S. Paley, and P. Romero, The Pathway Tools software, Bioinformatics, vol.18, issue.1, pp.225-232, 2002.

N. Jamshidi and B. O. Palsson, Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets, BMC systems biology, vol.1, 2007.

M. Kim, Reconstruction of a high-quality metabolic model enables the identification of gene overexpression targets for enhanced antibiotic production in Streptomyces coelicolor A3(2), Biotechnology journal, vol.9, pp.1185-1194, 2014.

A. D. Rovira and J. R. Harris, Plant root excretions in relation to the rhizosphere effect: v. The exudation of b-group vitamins, Plant and Soil, vol.14, pp.199-214, 1961.

S. Roje, Vitamin B biosynthesis in plants, Phytochemistry, vol.68, 1904.

Z. A. King, BiGG Models: A platform for integrating, standardizing and sharing genome-scale models, Nucleic Acids Res, vol.44, pp.515-522, 2016.

J. Lopez, Production of beta-ionone by combined expression of carotenogenic and plant CCD1 genes in Saccharomyces cerevisiae, Microb Cell Fact, vol.14, 2015.

W. Xie, Construction of a controllable beta-carotene biosynthetic pathway by decentralized assembly strategy in Saccharomyces cerevisiae, Biotechnol Bioeng, vol.111, pp.125-133, 2014.

A. T. Bull, B. A. Andrews, C. Dorador, and M. Goodfellow, Introducing the Atacama Desert, Antonie van Leeuwenhoek, vol.111, pp.1269-1272, 2018.

C. L. Lauber, M. Hamady, R. Knight, and N. Fierer, Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale, Appl Environ Microbiol, vol.75, pp.5111-5120, 2009.

J. Rousk, Soil bacterial and fungal communities across a pH gradient in an arable soil, The ISME journal, vol.4, pp.1340-1351, 2010.

U. Behrendt, A. Ulrich, and P. Schumann, Description of Microbacterium foliorum sp. nov. and Microbacterium phyllosphaerae sp. nov., isolated from the phyllosphere of grasses and the surface litter after mulching the sward, and reclassification of Aureobacterium resistens (Funke et al. 1998) as Microbacterium resistens comb, International journal of systematic and evolutionary microbiology, vol.51, pp.1267-1276, 2001.

C. A. Lozupone and R. Knight, Global patterns in bacterial diversity, Proc Natl Acad Sci, vol.104, pp.11436-11440, 2007.

A. Ventosa, J. J. Nieto, and A. Oren, Biology of moderately halophilic aerobic bacteria. Microbiology and molecular biology reviews: MMBR 62, pp.504-544, 1998.

S. Orla-jensen, The Lactic Acid Bacteria. Copenhagen: Høst and Søn, 1919.

M. Takeuchi and K. Hatano, Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium, International journal of systematic bacteriology, vol.48, pp.739-747, 1998.

M. D. Collins, D. Jones, and R. M. Kroppenstedt, Reclassification of Brevibacterium imperiale (Steinhaus) and "Corynebacterium laevaniformans, as Microbacterium imperiale comb. nov. and Microbacterium laevaniformans nom. rev.; comb. nov. Systematic and applied microbiology, vol.4, pp.80034-80038, 1983.

J. Liu, Genome sequence of the biocontrol agent Microbacterium barkeri strain 2011-R4, J Bacteriol, vol.194, pp.6666-6667, 2012.

A. Kageyama, Microbacterium sediminicola sp. nov. and Microbacterium marinilacus sp. nov., isolated from marine environments, International journal of systematic and evolutionary microbiology, vol.57, pp.2355-2359, 2007.

M. Madhaiyan, Microbacterium azadirachtae sp. nov., a plant-growth-promoting actinobacterium isolated from the rhizoplane of neem seedlings, International journal of systematic and evolutionary microbiology, vol.60, pp.1687-1692, 2010.

X. F. Sheng, J. J. Xia, C. Y. Jiang, L. Y. He, and M. Qian, Characterization of heavy metal-resistant endophytic bacteria from rape (Brassica napus) roots and their potential in promoting the growth and lead accumulation of rape, Environmental pollution, vol.156, pp.1164-1170, 2008.

K. Gneiding, R. Frodl, and G. Funke, Identities of Microbacterium spp. encountered in human clinical specimens, Journal of clinical microbiology, vol.46, pp.3646-3652, 2008.

A. J. Mccarthy and S. T. Williams, Actinomycetes as agents of biodegradation in the environment-a review, Gene, vol.115, pp.189-192, 1992.

H. Yurimoto, N. Kato, and Y. Sakai, Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism, Chemical record, vol.5, pp.367-375, 2005.

E. Diaz, Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility, International microbiology: the official journal of the Spanish Society for Microbiology, vol.7, pp.173-180, 2004.

L. P. Wackett, Pseudomonas putida-a versatile biocatalyst, Nat Biotechnol, vol.21, pp.136-138, 2003.

H. Santos and M. S. Da-costa, Compatible solutes of organisms that live in hot saline environments, Environ Microbiol, vol.4, pp.501-509, 2002.

W. L. Hung, W. G. Wade, R. Boden, D. P. Kelly, and A. P. Wood, Facultative methylotrophs from the human oral cavity and methylotrophy in strains of Gordonia, Leifsonia, and Microbacterium, Archives of microbiology, vol.193, pp.407-417, 2011.

C. Lieven, A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase. Frontiers in microbiology 9, 2018.

J. Nogales, High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities, Environ Microbiol, vol.22, pp.255-269, 2020.

Y. K. Oh, B. O. Palsson, S. M. Park, C. H. Schilling, and R. Mahadevan, Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data, J Biol Chem, vol.282, pp.28791-28799, 2007.

R. Mahadevan and B. O. Palsson, Properties of metabolic networks: structure versus function, Biophysical journal, vol.88, pp.7-09, 2005.

R. Mahadevan, B. O. Palsson, and D. R. Lovley, In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling, Nat Rev Microbiol, vol.9, pp.39-50, 2011.

O. Ates, E. T. Oner, and K. Y. Arga, Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043. BMC systems biology 5, vol.12, 2011.

A. De-la-torre, Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1), vol.188, 2015.

H. He, C. Edlich-muth, and S. N. Lindner, & Bar-Even, A. Ribulose Monophosphate Shunt Provides Nearly All Biomass and Energy Required for Growth of E. coli, ACS synthetic biology, vol.7, pp.1601-1611, 2018.

M. B. Burg and J. D. Ferraris, Intracellular organic osmolytes: function and regulation, J Biol Chem, vol.283, pp.7309-7313, 2008.

S. Ma and H. J. Bohnert, Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression, Genome biology, vol.8, 2007.

G. Zhang, Importance and regulation of inositol biosynthesis during growth and differentiation of Streptomyces, Mol Microbiol, vol.83, pp.1178-1194, 2012.

A. Klanchui, C. Khannapho, A. Phodee, S. Cheevadhanarak, and A. Meechai, iAK692: a genome-scale metabolic model of Spirulina platensis C1, BMC systems biology, vol.6, 2012.

T. A. Krulwich, G. Sachs, and E. Padan, Molecular aspects of bacterial pH sensing and homeostasis, Nat Rev Microbiol, vol.9, pp.330-343, 2011.

J. P. Viala, Sensing and adaptation to low pH mediated by inducible amino acid decarboxylases in Salmonella, PLoS One, vol.6, 2011.

E. Padan, E. Bibi, M. Ito, and T. A. Krulwich, Alkaline pH homeostasis in bacteria: new insights, Biochim Biophys Acta, vol.1717, pp.67-88, 2005.

R. Orij, Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pH(c) in Saccharomyces cerevisiae, Genome biology, vol.13, 2012.

A. Oren, Salinibacter: an extremely halophilic bacterium with archaeal properties, FEMS Microbiol Lett, vol.342, pp.1-9, 2013.

M. M. Caldwell, J. F. Bornman, C. L. Ballare, S. D. Flint, and G. Kulandaivelu, Terrestrial ecosystems, increased solar ultraviolet radiation, and interactions with other climate change factors. Photochemical & photobiological sciences: Official journal of the European Photochemistry Association and the, European Society for Photobiology, vol.6, pp.252-266, 2007.

D. L. Jones and B. K. Baxter, DNA Repair and Photoprotection: Mechanisms of Overcoming Environmental Ultraviolet Radiation Exposure in Halophilic, Archaea. Frontiers in microbiology, vol.8, 1882.

D. Gotz, Responses of hyperthermophilic crenarchaea to UV irradiation, Genome biology, vol.8, 2007.

R. W. Tuveson, R. A. Larson, and J. Kagan, Role of cloned carotenoid genes expressed in Escherichia coli in protecting against inactivation by near-UV light and specific phototoxic molecules, J Bacteriol, vol.170, pp.4675-4680, 1988.

M. Dieser, M. Greenwood, and C. M. Foreman, Carotenoid Pigmentation in Antarctic Heterotrophic Bacteria as a Strategy to Withstand Environmental Stresses, Arctic, Antarctic, and Alpine Research, vol.42, pp.396-405, 2010.

M. Mohammadi, L. Burbank, and M. C. Roper, Biological role of pigment production for the bacterial phytopathogen Pantoea stewartii subsp. stewartii, Appl Environ Microbiol, vol.78, pp.6859-6865, 2012.

O. F. Ordonez, M. R. Flores, J. R. Dib, A. Paz, and M. E. Farias, Extremophile culture collection from Andean lakes: extreme pristine environments that host a wide diversity of microorganisms with tolerance to UV radiation, Microbial ecology, vol.58, pp.461-473, 2009.

G. Sandmann, Carotenoids of biotechnological importance, Advances in biochemical engineering/biotechnology, vol.148, pp.449-467, 2015.

M. Rodriguez-concepcion and A. Boronat, Elucidation of the methylerythritol phosphate pathway for isoprenoid biosynthesis in bacteria and plastids. A metabolic milestone achieved through genomics, Plant physiology, vol.130, p.7138, 2002.

P. C. Lee and C. Schmidt-dannert, Metabolic engineering towards biotechnological production of carotenoids in microorganisms, Appl Microbiol Biotechnol, vol.60, pp.1-11, 2002.

V. Perez, Bacterial Survival under Extreme UV Radiation: A Comparative Proteomics Study of Rhodobacter sp., Isolated from High Altitude Wetlands in Chile, Frontiers in microbiology, vol.8, 1173.