Perspectivas metagenómicas y taxonómicas de poblaciones metilótrofas del Golfo de México

Tito David, Peña Montenegro; Juan David, Sanchez Calderón

2024

UniLibre Repository (Universidad Libre Colombia)

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Fawzy, S., Osman, A. I., Doran, J. & Rooney, D. W. Strategies for mitigation of climate change: a review. Environ Chem Lett 18, 2069–2094 (2020).; Pratt, C. & Tate, K. Mitigating methane: emerging technologies to combat climate change’s second leading contributor. Environ Sci Technol 52, 6084–6097 (2018).; Wuebbles, D. J. & Hayhoe, K. Atmospheric methane and global change. Earth Sci Rev 57, 177–210 (2002).; Chistoserdova, L. & Kalyuzhnaya, M. G. Current trends in methylotrophy. Trends Microbiol 26, 703–714 (2018).; Chistoserdova, L. Methylotrophs in natural habitats: current insights through metagenomics. Appl Microbiol Biotechnol 99, 5763–5779 (2015).; Kumar, M., Tomar, R. S., Lade, H. & Paul, D. Methylotrophic bacteria in sustainable agriculture. World J Microbiol Biotechnol 32, 1–9 (2016).; Epstein, S. S. The phenomenon of microbial uncultivability. Curr Opin Microbiol 16, 636–642 (2013).; Murrell, J. C. & Radajewski, S. Cultivation-independent techniques for studying methanotroph ecology. Res Microbiol 151, 807–814 (2000).; Setubal, J. C. Metagenome-assembled genomes: concepts, analogies, and challenges. Biophys Rev 13, 905–909 (2021).; Chen, L.-X., Anantharaman, K., Shaiber, A., Eren, A. M. & Banfield, J. F. Accurate and complete genomes from metagenomes. Genome Res 30, 315–333 (2020).; Montzka, S. A., Dlugokencky, E. J. & Butler, J. H. Non-CO2 greenhouse gases and climate change. Nature 476, 43–50 (2011).; Udara Willhelm Abeydeera, L. H., Wadu Mesthrige, J. & Samarasinghalage, T. I. Global research on carbon emissions: A scientometric review. Sustainability 11, 3972 (2019).; Jeffry, L. et al. Greenhouse gases utilization: A review. Fuel 301, 121017 (2021).; Houghton, J. Global warming. Reports on progress in physics 68, 1343 (2005).; Shakoor, A. et al. Biogeochemical transformation of greenhouse gas emissions from terrestrial to atmospheric environment and potential feedback to climate forcing. Environmental Science and Pollution Research 27, 38513–38536 (2020).; Pecl, G. T. et al. Biodiversity redistribution under climate change: Impacts on ecosystems and human well-being. Science (1979) 355, eaai9214 (2017).; Malhi, G. S., Kaur, M. & Kaushik, P. Impact of climate change on agriculture and its mitigation strategies: A review. Sustainability 13, 1318 (2021).; Organización de las Naciones Unidas. Informe de Los Objetivos de Desarrollo Sostenible 2023: Edición Especial. (2023).; Masson-Delmotte, V. et al. Global Warming of 1.5 C: IPCC Special Report on Impacts of Global Warming of 1.5 C above Pre-Industrial Levels in Context of Strengthening Response to Climate Change, Sustainable Development, and Efforts to Eradicate Poverty. (Cambridge University Press, 2022).; Söllinger, A. & Urich, T. Methylotrophic methanogens everywhere—physiology and ecology of novel players in global methane cycling. Biochem Soc Trans 47, 1895–1907 (2019).; Kumar, M. et al. Novel methanotrophic and methanogenic bacterial communities from diverse ecosystems and their impact on environment. Biocatal Agric Biotechnol 33, 102005 (2021).; Picone, N. et al. Metagenome assembled genome of a novel verrucomicrobial methanotroph from Pantelleria Island. Front Microbiol 12, 666929 (2021).; Nazir, R. & Zaffar, R. Climate Change Extenuation by Greenhouse Gas Quenching Microflora. Microbiomes and the Global Climate Change 31–41 (2021).; Kumar, M., Saxena, R., Tomar, R. S., Rai, P. K. & Paul, D. Role of methylotrophic bacteria in climate change mitigation. Microbes for climate resilient agriculture 149–164 (2018).; Chistoserdova, L., Kalyuzhnaya, M. G. & Lidstrom, M. E. The expanding world of methylotrophic metabolism. Annu Rev Microbiol 63, 477–499 (2009).; Chistoserdova, L. Modularity of methylotrophy, revisited. Environ Microbiol 13, 2603–2622 (2011).; Dedysh, S. N., Knief, C. & Dunfield, P. F. Methylocella species are facultatively methanotrophic. J Bacteriol 187, 4665–4670 (2005).; Dedysh, S. N. & Dunfield, P. F. Facultative and obligate methanotrophs: how to identify and differentiate them. in Methods in enzymology vol. 495 31–44 (Elsevier, 2011).; Bajpai, A. et al. Prospect of pink pigmented facultative methylotrophs in mitigating abiotic stress and climate change. J Basic Microbiol 62, 889–899 (2022).; Masood, F., Ahmad, S. & Malik, A. Role of methanotrophs in mitigating global warming. Microbiomes and the Global Climate Change 43–60 (2021).; Rani, V. et al. Synergistic interaction of methanotrophs and methylotrophs in regulating methane emission. Microbial technology for sustainable environment 419–437 (2021).; Rodriguez-r, L. M. & Konstantinidis, K. T. Estimating coverage in metagenomic data sets and why it matters. ISME J 8, 2349–2351 (2014).; Hiraoka, S., Yang, C. & Iwasaki, W. Metagenomics and bioinformatics in microbial ecology: current status and beyond. Microbes Environ 31, 204–212 (2016).; Streit, W. R. & Schmitz, R. A. Metagenomics–the key to the uncultured microbes. Curr Opin Microbiol 7, 492–498 (2004).; Singh, J. et al. Metagenomics: Concept, methodology, ecological inference and recent advances. Biotechnology Journal: Healthcare Nutrition Technology 4, 480–494 (2009).; Lapidus, A. L. & Korobeynikov, A. I. Metagenomic data assembly–the way of decoding unknown microorganisms. Front Microbiol 12, 613791 (2021).; Taş, N. et al. Metagenomic tools in microbial ecology research. Curr Opin Biotechnol 67, 184–191 (2021).; Grossart, H., Massana, R., McMahon, K. D. & Walsh, D. A. Linking metagenomics to aquatic microbial ecology and biogeochemical cycles. Limnol Oceanogr 65, S2–S20 (2020).; Hug, L. A. et al. A new view of the tree of life. Nat Microbiol 1, 1–6 (2016).; Yang, C. et al. A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. Comput Struct Biotechnol J 19, 6301–6314 (2021).; Grettenberger, C. L. & Hamilton, T. L. Metagenome-assembled genomes of novel taxa from an acid mine drainage environment. Appl Environ Microbiol 87, e00772-21 (2021).; Dueholm, M. K. D. et al. Genetic potential for exopolysaccharide synthesis in activated sludge bacteria uncovered by genome-resolved metagenomics. Water Res 229, 119485 (2023).; Liu, Y.-F. et al. Anaerobic hydrocarbon degradation in candidate phylum ‘Atribacteria’(JS1) inferred from genomics. ISME J 13, 2377–2390 (2019).; Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 35, 725–731 (2017).; Albertsen, M. et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31, 533–538 (2013).; Voskoboynik, A. et al. The genome sequence of the colonial chordate, Botryllus schlosseri. Elife 2, e00569 (2013).; Chistoserdova, L. Methanotrophy: An evolving field. Methane Biocatalysis: Paving the Way to Sustainability 1–15 (2018).; Tuyishime, P. & Sinumvayo, J. P. Novel outlook in engineering synthetic methylotrophs and formatotrophs: a course for advancing C1-based chemicals production. World J Microbiol Biotechnol 36, 118 (2020).; Matsen, J. B., Yang, S., Stein, L. Y., Beck, D. A. & Kalyuzhanaya, M. G. Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: transcriptomic study. Front Microbiol 4, 43697 (2013).; Evans, P. N. et al. An evolving view of methane metabolism in the Archaea. Nat Rev Microbiol 17, 219–232 (2019).; Ho, A., Kwon, M., Horn, M. A. & Yoon, S. Environmental applications of methanotrophs. Methanotrophs: Microbiology Fundamentals and Biotechnological Applications 231–255 (2019).; Hakemian, A. S. & Rosenzweig, A. C. The biochemistry of methane oxidation. Annu. Rev. Biochem. 76, 223–241 (2007).; Dumont, M. G. & Murrell, J. C. Community‐level analysis: key genes of aerobic methane oxidation. Methods Enzymol 397, 413–427 (2005).; Sirajuddin, S. & Rosenzweig, A. C. Enzymatic oxidation of methane. Biochemistry 54, 2283–2294 (2015).; Jones, J. C., Banerjee, R., Shi, K., Semonis, M. M., Aihara, H., Pomerantz, W. C., & Lipscomb, J. D. (2021). Soluble methane monooxygenase component interactions monitored by 19F NMR. Biochemistry, 60(25), 1995-2010.; Samanta, D. et al. Genetical and Biochemical Basis of Methane Monooxygenases of Methylosinus trichosporium OB3b in Response to Copper. Methane 3, 103–121 (2024).; Taubert, M. et al. Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy. Environ Microbiol 21, 3780–3795 (2019).; van Grinsven, S., Sinninghe Damsté, J. S., Harrison, J., Polerecky, L. & Villanueva, L. Nitrate promotes the transfer of methane‐derived carbon from the methanotroph Methylobacter sp. to the methylotroph Methylotenera sp. in eutrophic lake water. Limnol Oceanogr 66, 878–891 (2021).; Gwak, J. H., Awala, S. I., Nguyen, N. L., Yu, W. J., Yang, H. Y., von Bergen, M., . & Rhee, S. K. (2022). Sulfur and methane oxidation by a single microorganism. Proceedings of the National Academy of Sciences, 119(32), e2114799119.; Sharon, I. & Banfield, J. F. Genomes from metagenomics. Science (1979) 342, 1057–1058 (2013).; Ghurye, J. S., Cepeda-Espinoza, V. & Pop, M. Focus: microbiome: metagenomic assembly: overview, challenges and applications. Yale J Biol Med 89, 353 (2016).; Suzuki, Y. & Myers, G. Accurate k-mer classification using read profiles. in 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022) (Schloss Dagstuhl-Leibniz-Zentrum für Informatik, 2022).; Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).; Pérez-Cobas, A. E., Gomez-Valero, L. & Buchrieser, C. Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. Microb Genom 6, e000409 (2020).; Sangwan, N., Xia, F. & Gilbert, J. A. Recovering complete and draft population genomes from metagenome datasets. Microbiome 4, 1–11 (2016).; Hickl, O., Queirós, P., Wilmes, P., May, P. & Heintz-Buschart, A. binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets. Brief Bioinform 23, bbac431 (2022).; Haryono, M. A. S. et al. Recovery of high quality metagenome-assembled genomes from full-scale activated sludge microbial communities in a tropical climate using longitudinal metagenome sampling. Front Microbiol 13: 869135. Preprint at (2022).; Singleton, C. M. et al. Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing. Nat Commun 12, 2009 (2021).; Zhu, J. et al. Over 50,000 metagenomically assembled draft genomes for the human oral microbiome reveal new taxa. Genomics Proteomics Bioinformatics 20, 246–259 (2022).; Zhang, C. et al. Evolving paradigms in biological carbon cycling in the ocean. Natl Sci Rev 5, 481–499 (2018).; Li, M. et al. Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea. Nat Commun 6, 8933 (2015).; Wang, L. Microbial control of the carbon cycle in the ocean. Natl Sci Rev 5, 287–291 (2018).; Sun, J. et al. One carbon metabolism in SAR11 pelagic marine bacteria. PLoS One 6, e23973 (2011).; Halsey, K. H., Carter, A. E. & Giovannoni, S. J. Synergistic metabolism of a broad range of C1 compounds in the marine methylotrophic bacterium HTCC2181. Environ Microbiol 14, 630–640 (2012).; Sammarco, P. W. et al. Distribution and concentrations of petroleum hydrocarbons associated with the BP/Deepwater Horizon Oil Spill, Gulf of Mexico. Mar Pollut Bull 73, 129–143 (2013).; Hu, L., Yvon‐Lewis, S. A., Kessler, J. D. & MacDonald, I. R. Methane fluxes to the atmosphere from deepwater hydrocarbon seeps in the northern Gulf of Mexico. J Geophys Res Oceans 117, (2012).; Rakowski, C. V et al. Methane and microbial dynamics in the Gulf of Mexico water column. Front Mar Sci 2, 69 (2015).; Zhuang, G., Peña‐Montenegro, T. D., Montgomery, A., Hunter, K. S. & Joye, S. B. Microbial metabolism of methanol and methylamine in the Gulf of Mexico: insight into marine carbon and nitrogen cycling. Environ Microbiol 20, 4543–4554 (2018).; Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004).; Riesenfeld, C. S., Schloss, P. D. & Handelsman, J. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38, 525–552 (2004).; Kingsford, C., Schatz, M. C. & Pop, M. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11, 1–11 (2010).; Paszkiewicz, K. & Studholme, D. J. De novo assembly of short sequence reads. Brief Bioinform 11, 457–472 (2010).; Olson, N. D. et al. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Brief Bioinform 20, 1140–1150 (2019).; Forster, S. C. et al. A human gut bacterial genome and culture collection for improved metagenomic analyses. Nat Biotechnol 37, (2019).; Lin, L. et al. Genome-centric investigation of bile acid metabolizing microbiota of dairy cows and associated diet-induced functional implications. ISME J 17, 172–184 (2023).; Xie, F., Xu, L., Wang, Y. & Mao, S. Metagenomic sequencing reveals that high-grain feeding alters the composition and metabolism of cecal microbiota and induces cecal mucosal injury in sheep. mSystems 6, 10–1128 (2021).; Nelkner, J. et al. Effect of long-term farming practices on agricultural soil microbiome members represented by metagenomically assembled genomes (MAGs) and their predicted plant-beneficial genes. Genes (Basel) 10, 424 (2019).; Handelsman, J. Metagenomics: application of genomics to uncultured microorganisms. Microbiology and molecular biology reviews 68, 669–685 (2004).; Dhamodharan, R. & Rajasekar, A. Isolation and characterization of methylotrophic bacteria from Western Ghats. Int J Eng Tech Res 2, 1752–1756 (2013).; Zhao, D. et al. Members of the class Candidatus Ordosarchaeia imply an alternative evolutionary scenario from methanogens to haloarchaea. ISME J 18, wrad033 (2024).; von Arx, J. N. et al. Methylphosphonate-driven methane formation and its link to primary production in the oligotrophic North Atlantic. Nat Commun 14, 6529 (2023).; Orata, F. D., Meier-Kolthoff, J. P., Sauvageau, D. & Stein, L. Y. Phylogenomic analysis of the gammaproteobacterial methanotrophs (order Methylococcales) calls for the reclassification of members at the genus and species levels. Front Microbiol 9, 3162 (2018).; Dunfield, P. F. et al. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450, 879–882 (2007).; Toulza, E., Tagliabue, A., Blain, S. & Piganeau, G. Analysis of the global ocean sampling (GOS) project for trends in iron uptake by surface ocean microbes. PLoS One 7, e30931 (2012).; Gwak, J.-H. et al. Sulfur and methane oxidation by a single microorganism. Proceedings of the National Academy of Sciences 119, e2114799119 (2022).; Kop, L. F. M., Koch, H., Jetten, M. S. M., Daims, H. & Lücker, S. Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses. ISME communications 4, ycad017 (2024).; Friedrich, C. G., Rother, D., Bardischewsky, F., Quentmeier, A. & Fischer, J. Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism? Appl Environ Microbiol 67, 2873–2882 (2001).; Schmitz, R. A. et al. Simultaneous sulfide and methane oxidation by an extremophile. Nat Commun 14, 2974 (2023).; Eren, A. M. et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3, e1319 (2015).; Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25, 1043–1055 (2015).; Shaiber, A. & Eren, A. M. Composite metagenome-assembled genomes reduce the quality of public genome repositories. mBio 10, 10–1128 (2019).; Tørresen, O. K. et al. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res 47, 10994–11006 (2019).; Chen, Q. et al. Quality matters: biocuration experts on the impact of duplication and other data quality issues in biological databases. Genomics Proteomics Bioinformatics 18, 91–103 (2020).; Hugenholtz, P., Chuvochina, M., Oren, A., Parks, D. H. & Soo, R. M. Prokaryotic taxonomy and nomenclature in the age of big sequence data. ISME J 15, 1879–1892 (2021).; Tripp, H. J. The unique metabolism of SAR11 aquatic bacteria. Journal of Microbiology 51, 147–153 (2013).; Singer, E. et al. Genomic potential of Marinobacter aquaeolei, a biogeochemical “opportunitroph”. Appl Environ Microbiol 77, 2763–2771 (2011).; Amin, S. A., Green, D. H., Al Waheeb, D., Gärdes, A. & Carrano, C. J. Iron transport in the genus Marinobacter. Biometals 25, 135–147 (2012).; Barbeau, K., Zhang, G., Live, D. H. & Butler, A. Petrobactin, a photoreactive siderophore produced by the oil-degrading marine bacterium Marinobacter hydrocarbonoclasticus. J Am Chem Soc 124, 378–379 (2002).; Peña-Montenegro, T. D. et al. Species-specific responses of marine bacteria to environmental perturbation. ISME communications 3, 99 (2023).; Gauglitz, J. M., Zhou, H. & Butler, A. A suite of citrate-derived siderophores from a marine Vibrio species isolated following the Deepwater Horizon oil spill. J Inorg Biochem 107, 90–95 (2012).; Amin, S. A. et al. Siderophore-mediated iron uptake in two clades of Marinobacter spp. associated with phytoplankton: the role of light. Biometals 25, 181–192 (2012).; https://hdl.handle.net/10901/31522

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