Bioprospección in silico de Archaeas en el metagenoma de un tapete microbiano halófilo
Palabras clave:
Archaea, Tapete microbiano hipersalino, Bioprospección, In silico, Metataxonomía
Resumen
Los ambientes hipersalinos son fuentes de organismos de alto interés para la bioprospección. Los tapetes microbianos halófilos son comunidades metabólicamente interdependientes adaptadas a la alta salinidad. El dominio Archaea es característico de estos ambientes, representando una alta variedad de funciones dentro de los ciclos biogeoquímicos, entre ellas, el reciclaje de nutrientes. En México, la bioprospección de Archaeas halófilas se encuentra en etapas tempranas, en consecuencia, existe un gran potencial de investigación en diferentes partes del país. Yucatán posee una gran variedad de ambientes hipersalinos, por lo que son sitios atractivos para la identificación de Archaeas halófilas novedosas. El objetivo de este trabajo fue identificar las secuencias de Archaeas presentes en el tapete microbiano de una charca salina en Santa Clara, Yucatán; utilizando herramientas in silico para la identificación y análisis de su metataxonomía. Con base en los resultados, se observó la presencia de Archaeas (5.83%) del total de secuencias del metagenoma obtenido. Halobacteria es la clase más abundante de las Archaeas encontradas en el metagenoma y es una clase característica de las Archaeas halófilas. En porcentajes menores al 1% se presentaron los grupos termófilos TACK y DPANN, así como varios géneros con presencia de especies desconocidas. La bioprospección de Archaeas en la región, marca la pauta a estudios más profundos que permitan identificar la participación ecológica de cada género dentro de los ecosistemas de estudios, así como nichos de aprovechamiento biotecnológico.
Citas
Ali Fazıl YENİDÜNYA Aydemir BARIŞ Betül AYDIN Cenk YÜCEL Meryem Burcu KÜLAHCI Nebahat Aytuna ÇERÇİ Neslihan BAL Özgür KEBABCI Pınar CAGLAYAN Serap ÇETİNKAYA, A. (2022). DEPTHS OF SCIENCE EDITOR Cenk YÜCEL. www.iksadyayinevi.com
Antunes, A., Simões, M. F., Grötzinger, S. W., Eppinger, J., Bragança, J., & Bajic, V. B. (2017). Bioprospecting Archaea: Focus on Extreme Halophiles. 81–112. https://doi.org/10.1007/978-3-319-47935-4_5
Baker, B. J., De Anda, V., Seitz, K. W., Dombrowski, N., Santoro, A. E., & Lloyd, K. G. (2020). Diversity, ecology and evolution of Archaea. Nature Microbiology 2020 5:7, 5(7), 887–900. https://doi.org/10.1038/s41564-020-0715-z
Bueno de Mesquita, C. P., Zhou, J., Theroux, S. M., & Tringe, S. G. (2021). Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern. Genes 2021, Vol. 12, Page 1609, 12(10), 1609. https://doi.org/10.3390/GENES12101609
Campbell, M. A., Grice, K., Visscher, P. T., Morris, T., Wong, H. L., White, R. A., Burns, B. P., & Coolen, M. J. L. (2020). Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses. Frontiers in Microbiology, 11, 2741. https://doi.org/10.3389/FMICB.2020.560336/BIBTEX
Castro‐Fernandez, V., Zamora, R., Morande, A. H., Vallejos, G., Gonzalez‐Ordenes, F., & Guixé, V. (2017). Evolution, Metabolism and Molecular Mechanisms Underlying Extreme Adaptation of Euryarchaeota and Its Biotechnological Potential. Archaea - New Biocatalysts, Novel Pharmaceuticals and Various Biotechnological Applications. https://doi.org/10.5772/INTECHOPEN.69943
Chao, A., Chiu, C.-H., Jost, L., Chao, A., Chiu, C.-H., & Jost, L. (2016). Phylogenetic Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers. Topics in Biodiversity and Conservation, 14, 141–172. https://doi.org/10.1007/978-3-319-22461-9_8
Chen, S., Xu, Y., Sun, S., & Chen, F. (2019). Haloterrigena salifodinae sp. nov., an extremely halophilic archaeon isolated from a subterranean rock salt. Antonie van Leeuwenhoek 2019 112:9, 112(9), 1317–1329. https://doi.org/10.1007/S10482-019-01264-W
Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884–i890. https://doi.org/10.1093/BIOINFORMATICS/BTY560
Cui, H. L., & Dyall-Smith, M. L. (2021). Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments. Marine Life Science & Technology 2021 3:2, 3(2), 243–251. https://doi.org/10.1007/S42995-020-00087-3
DasSarma, S., & DasSarma, P. (2017). Halophiles. ELS, 1–13. https://doi.org/10.1002/9780470015902.A0000394.PUB4
Dombrowski, N., Lee, J. H., Williams, T. A., Offre, P., & Spang, A. (2019). Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiology Letters, 366(2), 8. https://doi.org/10.1093/FEMSLE/FNZ008
García-Maldonado, J. Q., Escobar-Zepeda, A., Raggi, · Luciana, Bebout, B. M., Sanchez-Flores, A., & Alejandro López-Cortés, ·. (2018). Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments. 22, 903–916. https://doi.org/10.1007/s00792-018-1047-2
Gerba, C. P. (2015). Indicator Microorganisms. In Environmental Microbiology: Third Edition. Elsevier Inc. https://doi.org/10.1016/B978-0-12-394626-3.00023-5
Gonzalez, O., Oberwinkler, T., Mansueto, L., Pfeiffer, F., Mendoza, E., Zimmer, R., & Oesterhelt, D. (2010). Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis. PLOS Computational Biology, 6(6), e1000799. https://doi.org/10.1371/JOURNAL.PCBI.1000799
Grant, W. D. (2015). Halobacterium. Bergey’s Manual of Systematics of Archaea and Bacteria, 1–11. https://doi.org/10.1002/9781118960608.GBM00482
Han, S. B., Hou, X. J., Wu, C., Zhao, Z., Ju, Z., Zhang, R., Cui, H. L., Keen, L. J., Xu, L., & Wu, M. (2019). Complete genome sequence of Salinigranum rubrum GX10T, an extremely halophilic archaeon isolated from a marine solar saltern. Marine Genomics, 44, 57–60. https://doi.org/10.1016/J.MARGEN.2018.09.004
Huson, D. H., Beier, S., Flade, I., Górska, A., El-Hadidi, M., Mitra, S., Ruscheweyh, H. J., & Tappu, R. (2016). MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLOS Computational Biology, 12(6), e1004957. https://doi.org/10.1371/JOURNAL.PCBI.1004957
Kemp, B. L., Tabish, E. M., Wolford, A. J., Jones, D. L., Butler, J. K., & Baxter, B. K. (2018). The Biogeography of Great Salt Lake Halophilic Archaea: Testing the Hypothesis of Avian Mechanical Carriers. Diversity 2018, Vol. 10, Page 124, 10(4), 124. https://doi.org/10.3390/D10040124
Kulkarni, S., Dhakar, K., & Joshi, A. (2019). Alkaliphiles: Diversity and Bioprospection. Microbial Diversity in the Genomic Era, 239–263. https://doi.org/10.1016/B978-0-12-814849-5.00015-0
Lima, J., Manning, T., Rutherford, K. M., Baima, E. T., Dewhurst, R. J., Walsh, P., & Roehe, R. (2021). Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions. Journal of Microbiological Methods, 186. https://doi.org/10.1016/j.mimet.2021.106235
Littlechild, J. A. (2015). Archaeal Enzymes and Applications in Industrial Biocatalysts. Archaea, 2015. https://doi.org/10.1155/2015/147671
Mani, K., Taib, N., Hugoni, M., Bronner, G., Bragança, J. M., & Debroas, D. (2020). Transient dynamics of archaea and bacteria in sediments and brine across a salinity gradient in a solar saltern of Goa, India. Frontiers in Microbiology, 11, 1891. https://doi.org/10.3389/FMICB.2020.01891/BIBTEX
Menasria, T., Aguilera, M., Hocine, H., Benammar, L., Ayachi, A., Si Bachir, A., Dekak, A., & Monteoliva-Sánchez, M. (2018). Diversity and bioprospecting of extremely halophilic archaea isolated from Algerian arid and semi-arid wetland ecosystems for halophilic-active hydrolytic enzymes. Microbiological Research, 207, 289–298. https://doi.org/10.1016/J.MICRES.2017.12.011
Moissl-Eichinger, C., Pausan, M., Taffner, J., Berg, G., Bang, C., & Schmitz, R. A. (2018). Archaea Are Interactive Components of Complex Microbiomes. Trends in Microbiology, 26(1), 70–85. https://doi.org/10.1016/J.TIM.2017.07.004
Mongodin, E. F., Nelson, K. E., Daugherty, S., DeBoy, R. T., Wister, J., Khouri, H., Weidman, J., Walsh, D. A., Papke, R. T., Perez, G. S., Sharma, A. K., Nesbø, C. L., MacLeod, D., Bapteste, E., Doolittle, W. F., Charlebois, R. L., Legault, B., & Rodriguez-Valera, F. (2005). The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea. Proceedings of the National Academy of Sciences of the United States of America, 102(50), 18147–18152. https://doi.org/10.1073/PNAS.0509073102/SUPPL_FILE/09073TABLE1.PDF
Najjari, A., Stathopoulou, P., Elmnasri, K., Hasnaoui, F., Zidi, I., Sghaier, H., Ouzari, H. I., Cherif, A., & Tsiamis, G. (2021). Assessment of 16s rrna gene-based phylogenetic diversity of archaeal communities in halite-crystal salts processed from natural saharan saline systems of Southern Tunisia. Biology, 10(5). https://doi.org/10.3390/BIOLOGY10050397
Nancy, D., Luna, C., & Xoxocotlán, S. C. (2021). Identificación de bacterias y arqueas halófilas con capacidad para capturar NaCl in vitro. http://literatura.ciidiroaxaca.ipn.mx:8080/xmlui/handle/LITER_CIIDIROAX/510
Olin, M. C. N., Mariette, V. J., Gabriela, O. Á., Eguiarte Luis, E., Valeria, S., & Susana De La, T. Z. (2019). Diversity of Archaea Domain in Cuatro Cienegas Basin: Archaean Domes. BioRxiv, 766709. https://doi.org/10.1101/766709
Oren, A. (2013). Salinibacter: an extremely halophilic bacterium with archaeal properties. FEMS Microbiology Letters, 342(1), 1–9. https://doi.org/10.1111/1574-6968.12094
Oren, A. (2015). Halophilic microbial communities and their environments. Current Opinion in Biotechnology, 33, 119–124. https://doi.org/10.1016/J.COPBIO.2015.02.005
Oueriaghli, N. (2014). Estudio de la diversidad procariota en ambientes salinos empleando técnicas moleculares. Editorial de la Universidad de Granada.
Pinto, N. G. (2017). FILOGENIA DE LOS SERES VIVOS: DOMINIO ARCHAEA.
Ramos-Barbero, M. D., Martin-Cuadrado, A. B., Viver, T., Santos, F., Martinez-Garcia, M., & Antón, J. (2019). Recovering microbial genomes from metagenomes in hypersaline environments: The Good, the Bad and the Ugly. Systematic and Applied Microbiology, 42(1), 30–40. https://doi.org/10.1016/J.SYAPM.2018.11.001
Richardson, L., Allen, B., Baldi, G., Beracochea, M., Bileschi, M. L., Burdett, T., Burgin, J., Caballero-Pérez, J., Cochrane, G., Colwell, L. J., Curtis, T., Escobar-Zepeda, A., Gurbich, T. A., Kale, V., Korobeynikov, A., Raj, S., Rogers, A. B., Sakharova, E., Sanchez, S., … Finn, R. D. (2023). MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Research, 51(D1), D753–D759. https://doi.org/10.1093/NAR/GKAC1080
Rinke, C., Chuvochina, M., Mussig, A. J., Chaumeil, P. A., Davín, A. A., Waite, D. W., Whitman, W. B., Parks, D. H., & Hugenholtz, P. (2021). A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature Microbiology 2021 6:7, 6(7), 946–959. https://doi.org/10.1038/s41564-021-00918-8
Rojas-Herrera, R., Narváez-Zapata, J., Zamudio-Maya, M., & Mena-Martínez, M. E. (2008). A simple silica-based method for metagenomic DNA extraction from soil and sediments. Molecular Biotechnology, 40(1), 13–17. https://doi.org/10.1007/S12033-008-9061-8/TABLES/3
Wong, H. L., MacLeod, F. I., White, R. A., Visscher, P. T., & Burns, B. P. (2020). Microbial dark matter filling the niche in hypersaline microbial mats. Microbiome 2020 8:1, 8(1), 1–14. https://doi.org/10.1186/S40168-020-00910-0
Wong, H. L., Visscher, P. T., White, R. A., Smith, D. L., Patterson, M. M., & Burns, B. P. (2017). Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes. Scientific Reports 2017 7:1, 7(1), 1–12. https://doi.org/10.1038/srep46160
Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1). https://doi.org/10.1186/S13059-019-1891-0
Ximena, C., & Ortiz, R. (2016). Biology and population ecology of uncultured Archaea in natural environments analyzed by taxon-specific molecular markers = Biología y ecología poblacional de Archaeas no cultivadas en ambientes naturales analizadas mediante marcadores moleculares específicos. TDX (Tesis Doctorals En Xarxa). https://www.tdx.cat/handle/10803/386392
Antunes, A., Simões, M. F., Grötzinger, S. W., Eppinger, J., Bragança, J., & Bajic, V. B. (2017). Bioprospecting Archaea: Focus on Extreme Halophiles. 81–112. https://doi.org/10.1007/978-3-319-47935-4_5
Baker, B. J., De Anda, V., Seitz, K. W., Dombrowski, N., Santoro, A. E., & Lloyd, K. G. (2020). Diversity, ecology and evolution of Archaea. Nature Microbiology 2020 5:7, 5(7), 887–900. https://doi.org/10.1038/s41564-020-0715-z
Bueno de Mesquita, C. P., Zhou, J., Theroux, S. M., & Tringe, S. G. (2021). Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern. Genes 2021, Vol. 12, Page 1609, 12(10), 1609. https://doi.org/10.3390/GENES12101609
Campbell, M. A., Grice, K., Visscher, P. T., Morris, T., Wong, H. L., White, R. A., Burns, B. P., & Coolen, M. J. L. (2020). Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses. Frontiers in Microbiology, 11, 2741. https://doi.org/10.3389/FMICB.2020.560336/BIBTEX
Castro‐Fernandez, V., Zamora, R., Morande, A. H., Vallejos, G., Gonzalez‐Ordenes, F., & Guixé, V. (2017). Evolution, Metabolism and Molecular Mechanisms Underlying Extreme Adaptation of Euryarchaeota and Its Biotechnological Potential. Archaea - New Biocatalysts, Novel Pharmaceuticals and Various Biotechnological Applications. https://doi.org/10.5772/INTECHOPEN.69943
Chao, A., Chiu, C.-H., Jost, L., Chao, A., Chiu, C.-H., & Jost, L. (2016). Phylogenetic Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers. Topics in Biodiversity and Conservation, 14, 141–172. https://doi.org/10.1007/978-3-319-22461-9_8
Chen, S., Xu, Y., Sun, S., & Chen, F. (2019). Haloterrigena salifodinae sp. nov., an extremely halophilic archaeon isolated from a subterranean rock salt. Antonie van Leeuwenhoek 2019 112:9, 112(9), 1317–1329. https://doi.org/10.1007/S10482-019-01264-W
Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884–i890. https://doi.org/10.1093/BIOINFORMATICS/BTY560
Cui, H. L., & Dyall-Smith, M. L. (2021). Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments. Marine Life Science & Technology 2021 3:2, 3(2), 243–251. https://doi.org/10.1007/S42995-020-00087-3
DasSarma, S., & DasSarma, P. (2017). Halophiles. ELS, 1–13. https://doi.org/10.1002/9780470015902.A0000394.PUB4
Dombrowski, N., Lee, J. H., Williams, T. A., Offre, P., & Spang, A. (2019). Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiology Letters, 366(2), 8. https://doi.org/10.1093/FEMSLE/FNZ008
García-Maldonado, J. Q., Escobar-Zepeda, A., Raggi, · Luciana, Bebout, B. M., Sanchez-Flores, A., & Alejandro López-Cortés, ·. (2018). Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments. 22, 903–916. https://doi.org/10.1007/s00792-018-1047-2
Gerba, C. P. (2015). Indicator Microorganisms. In Environmental Microbiology: Third Edition. Elsevier Inc. https://doi.org/10.1016/B978-0-12-394626-3.00023-5
Gonzalez, O., Oberwinkler, T., Mansueto, L., Pfeiffer, F., Mendoza, E., Zimmer, R., & Oesterhelt, D. (2010). Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis. PLOS Computational Biology, 6(6), e1000799. https://doi.org/10.1371/JOURNAL.PCBI.1000799
Grant, W. D. (2015). Halobacterium. Bergey’s Manual of Systematics of Archaea and Bacteria, 1–11. https://doi.org/10.1002/9781118960608.GBM00482
Han, S. B., Hou, X. J., Wu, C., Zhao, Z., Ju, Z., Zhang, R., Cui, H. L., Keen, L. J., Xu, L., & Wu, M. (2019). Complete genome sequence of Salinigranum rubrum GX10T, an extremely halophilic archaeon isolated from a marine solar saltern. Marine Genomics, 44, 57–60. https://doi.org/10.1016/J.MARGEN.2018.09.004
Huson, D. H., Beier, S., Flade, I., Górska, A., El-Hadidi, M., Mitra, S., Ruscheweyh, H. J., & Tappu, R. (2016). MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLOS Computational Biology, 12(6), e1004957. https://doi.org/10.1371/JOURNAL.PCBI.1004957
Kemp, B. L., Tabish, E. M., Wolford, A. J., Jones, D. L., Butler, J. K., & Baxter, B. K. (2018). The Biogeography of Great Salt Lake Halophilic Archaea: Testing the Hypothesis of Avian Mechanical Carriers. Diversity 2018, Vol. 10, Page 124, 10(4), 124. https://doi.org/10.3390/D10040124
Kulkarni, S., Dhakar, K., & Joshi, A. (2019). Alkaliphiles: Diversity and Bioprospection. Microbial Diversity in the Genomic Era, 239–263. https://doi.org/10.1016/B978-0-12-814849-5.00015-0
Lima, J., Manning, T., Rutherford, K. M., Baima, E. T., Dewhurst, R. J., Walsh, P., & Roehe, R. (2021). Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions. Journal of Microbiological Methods, 186. https://doi.org/10.1016/j.mimet.2021.106235
Littlechild, J. A. (2015). Archaeal Enzymes and Applications in Industrial Biocatalysts. Archaea, 2015. https://doi.org/10.1155/2015/147671
Mani, K., Taib, N., Hugoni, M., Bronner, G., Bragança, J. M., & Debroas, D. (2020). Transient dynamics of archaea and bacteria in sediments and brine across a salinity gradient in a solar saltern of Goa, India. Frontiers in Microbiology, 11, 1891. https://doi.org/10.3389/FMICB.2020.01891/BIBTEX
Menasria, T., Aguilera, M., Hocine, H., Benammar, L., Ayachi, A., Si Bachir, A., Dekak, A., & Monteoliva-Sánchez, M. (2018). Diversity and bioprospecting of extremely halophilic archaea isolated from Algerian arid and semi-arid wetland ecosystems for halophilic-active hydrolytic enzymes. Microbiological Research, 207, 289–298. https://doi.org/10.1016/J.MICRES.2017.12.011
Moissl-Eichinger, C., Pausan, M., Taffner, J., Berg, G., Bang, C., & Schmitz, R. A. (2018). Archaea Are Interactive Components of Complex Microbiomes. Trends in Microbiology, 26(1), 70–85. https://doi.org/10.1016/J.TIM.2017.07.004
Mongodin, E. F., Nelson, K. E., Daugherty, S., DeBoy, R. T., Wister, J., Khouri, H., Weidman, J., Walsh, D. A., Papke, R. T., Perez, G. S., Sharma, A. K., Nesbø, C. L., MacLeod, D., Bapteste, E., Doolittle, W. F., Charlebois, R. L., Legault, B., & Rodriguez-Valera, F. (2005). The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea. Proceedings of the National Academy of Sciences of the United States of America, 102(50), 18147–18152. https://doi.org/10.1073/PNAS.0509073102/SUPPL_FILE/09073TABLE1.PDF
Najjari, A., Stathopoulou, P., Elmnasri, K., Hasnaoui, F., Zidi, I., Sghaier, H., Ouzari, H. I., Cherif, A., & Tsiamis, G. (2021). Assessment of 16s rrna gene-based phylogenetic diversity of archaeal communities in halite-crystal salts processed from natural saharan saline systems of Southern Tunisia. Biology, 10(5). https://doi.org/10.3390/BIOLOGY10050397
Nancy, D., Luna, C., & Xoxocotlán, S. C. (2021). Identificación de bacterias y arqueas halófilas con capacidad para capturar NaCl in vitro. http://literatura.ciidiroaxaca.ipn.mx:8080/xmlui/handle/LITER_CIIDIROAX/510
Olin, M. C. N., Mariette, V. J., Gabriela, O. Á., Eguiarte Luis, E., Valeria, S., & Susana De La, T. Z. (2019). Diversity of Archaea Domain in Cuatro Cienegas Basin: Archaean Domes. BioRxiv, 766709. https://doi.org/10.1101/766709
Oren, A. (2013). Salinibacter: an extremely halophilic bacterium with archaeal properties. FEMS Microbiology Letters, 342(1), 1–9. https://doi.org/10.1111/1574-6968.12094
Oren, A. (2015). Halophilic microbial communities and their environments. Current Opinion in Biotechnology, 33, 119–124. https://doi.org/10.1016/J.COPBIO.2015.02.005
Oueriaghli, N. (2014). Estudio de la diversidad procariota en ambientes salinos empleando técnicas moleculares. Editorial de la Universidad de Granada.
Pinto, N. G. (2017). FILOGENIA DE LOS SERES VIVOS: DOMINIO ARCHAEA.
Ramos-Barbero, M. D., Martin-Cuadrado, A. B., Viver, T., Santos, F., Martinez-Garcia, M., & Antón, J. (2019). Recovering microbial genomes from metagenomes in hypersaline environments: The Good, the Bad and the Ugly. Systematic and Applied Microbiology, 42(1), 30–40. https://doi.org/10.1016/J.SYAPM.2018.11.001
Richardson, L., Allen, B., Baldi, G., Beracochea, M., Bileschi, M. L., Burdett, T., Burgin, J., Caballero-Pérez, J., Cochrane, G., Colwell, L. J., Curtis, T., Escobar-Zepeda, A., Gurbich, T. A., Kale, V., Korobeynikov, A., Raj, S., Rogers, A. B., Sakharova, E., Sanchez, S., … Finn, R. D. (2023). MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Research, 51(D1), D753–D759. https://doi.org/10.1093/NAR/GKAC1080
Rinke, C., Chuvochina, M., Mussig, A. J., Chaumeil, P. A., Davín, A. A., Waite, D. W., Whitman, W. B., Parks, D. H., & Hugenholtz, P. (2021). A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature Microbiology 2021 6:7, 6(7), 946–959. https://doi.org/10.1038/s41564-021-00918-8
Rojas-Herrera, R., Narváez-Zapata, J., Zamudio-Maya, M., & Mena-Martínez, M. E. (2008). A simple silica-based method for metagenomic DNA extraction from soil and sediments. Molecular Biotechnology, 40(1), 13–17. https://doi.org/10.1007/S12033-008-9061-8/TABLES/3
Wong, H. L., MacLeod, F. I., White, R. A., Visscher, P. T., & Burns, B. P. (2020). Microbial dark matter filling the niche in hypersaline microbial mats. Microbiome 2020 8:1, 8(1), 1–14. https://doi.org/10.1186/S40168-020-00910-0
Wong, H. L., Visscher, P. T., White, R. A., Smith, D. L., Patterson, M. M., & Burns, B. P. (2017). Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes. Scientific Reports 2017 7:1, 7(1), 1–12. https://doi.org/10.1038/srep46160
Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1). https://doi.org/10.1186/S13059-019-1891-0
Ximena, C., & Ortiz, R. (2016). Biology and population ecology of uncultured Archaea in natural environments analyzed by taxon-specific molecular markers = Biología y ecología poblacional de Archaeas no cultivadas en ambientes naturales analizadas mediante marcadores moleculares específicos. TDX (Tesis Doctorals En Xarxa). https://www.tdx.cat/handle/10803/386392
Publicado
2023-08-24
Sección
Artículos de Investigación
Esta obra está bajo licencia internacional Creative Commons Reconocimiento-NoComercial 4.0.
Avisos de derechos de autor propuestos por Creative Commons
1. Política propuesta para revistas que ofrecen acceso abierto
Aquellos autores/as que tengan publicaciones con esta revista, aceptan los términos siguientes:
- Los autores/as conservarán sus derechos de autor y garantizarán a la revista el derecho de primera publicación de su obra, el cuál estará simultáneamente sujeto a la Licencia de reconocimiento de Creative Commons que permite a terceros compartir la obra siempre que se indique su autor y su primera publicación esta revista.
- Los autores/as podrán adoptar otros acuerdos de licencia no exclusiva de distribución de la versión de la obra publicada (p. ej.: depositarla en un archivo telemático institucional o publicarla en un volumen monográfico) siempre que se indique la publicación inicial en esta revista.
- Se permite y recomienda a los autores/as difundir su obra a través de Internet (p. ej.: en archivos telemáticos institucionales o en su página web) antes y durante el proceso de envío, lo cual puede producir intercambios interesantes y aumentar las citas de la obra publicada. (Véase El efecto del acceso abierto).
