“Diversidad y estructura comunitaria de ensambles microbianos de pozas de evaporación del Noroeste de México”

Autores

  • Carla M Centeno Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México
  • Anidia Blanco Jarvio Programa de Bioingeniería y Ciencias Ambientales, Departamento Académico de Ingeniería en Pesquerías, Universidad Autónoma de Baja California Sur, Unidad Pichilingue, La Paz, Baja California Sur, México
  • Andrea Bautista García Programa de Bioingeniería y Ciencias Ambientales, Departamento Académico de Ingeniería en Pesquerías, Universidad Autónoma de Baja California Sur, Unidad Pichilingue, La Paz, Baja California Sur, México
  • Yislem Beltrán Instituto de Ecología, Campus Yucatán, Ucú, 97357, México
  • Omar Mejía

Palavras-chave:

Illumina, teoría neutral, 16seRNA, salinidad, Vizcaíno

Resumo

Antecedentes. Los ambientes evaporiticos representan hábitats extremos por el efecto combinado de una serie de factores tales como temperatura y salinidad, a pesar de ello, alojan una gran diversidad de organismos procariontes, la mayoría poco estudiados pero con un gran potencial biotecnológico. La región del Vizcaíno en el Noroeste de México representa un área ideal para la exploración de ambientes salinos, los cuales son el resultado de su historia geológica y contemporánea, en particular, las pozas conocidas como “Las Charcas” representan un excelente modelo de estudio por su nula perturbación antrópica. Objetivo. Explorar los factores que determinan la estructura comunitaria de las bacterias y arqueas que residen en los sedimentos de pozas de evaporación con diferentes niveles de salinidad. Método. Seis pozas de evaporación fueron muestreadas durante enero de 2018, posteriormente, se amplificó y secuenció un fragmento de la fracción 16S rRNA mediante SNG. Se calcularon estimadores de diversidad alfa y beta, por otro lado, las métricas NTI y NRI descritas por Webb se utilizaron para discriminar los factores que determinan la estructura filogenética de las comunidades en cada poza, finalmente, para estimar que taxa podrian estar sujetos a presiones selectivas se realizó un modelo neutral. Resultados. Los niveles de diversidad mostraron una correlación positiva con la salinidad y la materia orgánica, sin embargo, ninguno de los parámetros biogeoquímicos evaluados permitió explicar las diferencias significativas encontradas al comparar las pozas. Conclusiones. La estructura de las comunidades que residen en los sedimentos de las pozas analizadas está determinada por factores tanto determinísticos como estocáticos, incluyendo selección homogenizadora, dispersión y deriva ecológica.

Downloads

Referências

Baati, H., S. Guermazi, R. Amdouni, N. Gharsallah, A. Sghir & E. Ammar. 2008. Prokaryotic diversity of a Tunisian multipond solar saltern. Extremophiles 12: 5-518. DOI:10.1007/s00792-008-0154-x

Benlloch, S., A. López‐López, E.O. Casamayor, L. Øvreås, V. Goddard, F.L. Daae & F. Rodríguez‐Valera. 2002. Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. Environmental Microbiology, 4, 349-360. DOI: 10.1046/j.1462-2920.2002.00306.x

Bowen, J.L., H. G. Morrison, J.E. Hobbie & M.L. Sogin. 2012. Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates. The ISME Journal, 6, 2014-2023. DOI: 10.1038/ismej.2012.47

Brandt, K. K., B.P. Patel & K. Ingvorsen. 1999. Desulfocella halophila gen. nov., sp. nov., a halophilic, fatty-acid-oxidizing, sulfate-reducing bacterium isolated from sediments of the Great Salt Lake. International Journal of Systematic and Evolutionary Microbiology, 49, 193-200. DOI: 10.1099/00207713-49-1-193

Brenner, K, L. You & F.H. Arnold. 2008. Engineering microbial consortia: a new frontier in synthetic biology. Trends in Biotechnology, 26: 483-489. DOI: 10.1016/j.tibtech.2008.05.004

Brigmon, R. L., P. Morris & G. Smith. 2008. Evaporite microbial films, mats, microbialites and stromatolites. In : Dilek, Y., H. Furnes & K. Muehlenbachs (eds.), Links between Geological Processes, Microbial Activities, Evolution of Life. Springer Netherlands, pp. 197-235.

Brito-Castillo, L., L. C. Méndez-Rodríguez, S. Chávez-López & B. Acosta-Vargas. 2010. Groundwater differentiation of the aquifer in the Vizcaino Biosphere Reserve, Baja California Peninsula, Mexico. Geofísica Internacional, 49, 167-179. DOI: 10.22201/igeof.00167169p.2010.49.4.126

Burns, A. R., W. Z. Stephens, K. Stagaman, S. Wong, J.F. Rawls, K. Guillemin & B.J. Bohannan. 2016. Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. The ISME journal, 10, 655-664. DOI: 10.1038/ismej.2015.142

Callahan, B.J., P.J. McMurdie, M.J. Rosen, A.W. Han, A.J.A. Johnson & S.P. Holmes. 2016. “DADA2: High-resolution sample inference from Illumina amplicon data.” Nature Methods, 13, 581-583. DOI: 10.1038/nmeth.3869

Cameron, E. S., P.J. Schmidt, B.J.M. Tremblay, M.B. Emelko & K.M. Müller. 2021. Enhancing diversity analysis by repeatedly rarefying next generation sequencing data describing microbial communities. Scientific reports, 11, 1-13. DOI: 10.1038/s41598-021-01636-1

Caporaso, J. G., C.L. Lauber, W.A. Walters, D. Berg-Lyons, C.A. Lozupone, P.J. Turnbaugh & R. Knight. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the national academy of sciences, 108(supplement_1), 4516-4522. DOI: 10.1073/pnas.1000080107

Casamayor, E. O., J.I. Calderón-Paz & C. Pedrós-Alió. 2000. 5S rRNA fingerprints of marine bacteria, halophilic archaea and natural prokaryotic assemblages along a salinity gradient. FEMS microbiology ecology, 34, 113-119.

DOI: 10.1111/j.1574-6941.2000.tb00760.x

Cowan D.A, J.B. Ramond, T.P. Makhalanyane & P. De Maayer. 2015. Metagenomics of extreme environments. Current Opinion in Microbiology, 25, 97-102. DOI: 10.1016/j.mib.2015.05.005

DasSarma, S. and P. DasSarma. 2017. Halophiles. In: eLS, John Wiley & Sons, Ltd (ed.). DOI: 10.1002/9780470015902.a0000394.pub4

Dillon, J.G., M. Carlin, A. Gutierrez, V. Nguyen & N. McLain. 2013. Patterns of microbial diversity along a salinity gradient in the Guerrero Negro solar saltern, Baja CA Sur, Mexico. Frontiers in microbiology, 4, 399. DOI: 10.3389/fmicb.2013.00399

Eriksson, P. G., S. Banerjee, O. Catuneanu, S. Sarkar, A.J. Bumby & M.N. Mtimkulu. 2007. Prime controls on Archaean–Palaeoproterozoic sedimentation: change over time. Gondwana Research, 12, 550-559. DOI: 10.1016/j.gr.2007.04.004

Finstad, K. M., A.J. Probst, B.C. Thomas, G.L. Andersen, C. Demergasso, A. Echeverría & J.F. Banfield. 2017. Microbial community structure and the persistence of cyanobacterial populations in salt crusts of the hyperarid Atacama Desert from genome-resolved metagenomics. Frontiers in microbiology, 8, 1435. DOI: 10.3389/fmicb.2017.01435

García-Maldonado, J. Q., B.M. Bebout, R.C. Everroad & A. López-Cortés. 2015. Evidence of novel phylogenetic lineages of methanogenic archaea from hypersaline microbial mats. Microbial ecology, 69, 106-117. DOI: 10.1007/s00248-014-0473-7

García-Maldonado, J. Q., A. Escobar-Zepeda, L. Raggi, B.M. Bebout, A. Sanchez-Flores & A. López-Cortés. 2018. Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments. Extremophiles, 22, 903-916. DOI: 10.1007/s00792-018-1047-2

García-Maldonado, J. Q., H. Latisnere-Barragán, A. Escobar-Zepeda, S. Cadena, P.J. Ramírez-Arenas, R. Vázquez-Juárez & A. López-Cortés. 2023. Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities. Microorganisms, 11, 812. DOI: 10.21203/rs.3.rs-2281927/v1

Gittel, A., M. Seidel, J. Kuever, A.S. Galushko, H. Cypionka & M. Könneke. 2010. Desulfopila inferna sp. nov., a sulfate-reducing bacterium isolated from the subsurface of a tidal sand-flat. International journal of systematic and evolutionary microbiology, 60, 1626-1630. DOI: 10.1099/ijs.0.015644-0

Gouy, M., S. Guindon & O. Gascuel. 2010. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular biology and evolution, 27, 221-224. DOI: 10.1093/molbev/msp259

Harris, J.K., J. Caporaso, J.J. Walker, J.R. Spear, N.J. Gold, C.E. Robertson & N.R. Pace. 2013. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. The ISME journal, 7, 50-60. DOI: 10.1038/ismej.2012.79

Hollister E. B., A.S. Engledow, A.J. Hammett, T.L. Provin, H.H. Wilkinson & T.J. Gentry. 2010. Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. ISME J, 4: 829. DOI: 10.1038/ismej.2010.3

Huang, L, J. Bai, J. Wang, G. Zhang, W. Wang, X. Wang & B. Cui. 2022. Different stochastic processes regulate bacterial and fungal community assembly in estuarine wetland soils. Soil Biology and Biochemistry, 167, 108586. DOI: 10.1016/j.soilbio.2022.108586

Ikenaga, M., R. Guevara, A.L. Dean, C. Pisani & J.N. Boyer. 2010. Changes in community structure of sediment bacteria along the Florida coastal everglades marsh–mangrove–seagrass salinity gradient. Microbial ecology, 59, 284-295. DOI: 10.1007/s00248-009-9572-2

Javor, B. 2012. Hypersaline environments: microbiology and biogeochemistry. Springer Science & Business Media, Berlin. 328 p.

Jia, X., F. Dini-Andreote & J.F. Salles. 2018. Community assembly processes of the microbial rare biosphere. Trends in microbiology, 26, 738-747. DOI: 10.1016/j.tim.2018.02.011

Kouzuma, A, S. Kato S & K. Watanabe. 2015. Microbial interspecies interactions: recent findings in syntrophic consortia. Frontiers in Microbiology, 6: 477. DOI: 10.3389/fmicb.2015.00477

Legendre, P. & E. D. Gallagher. 2001. Ecologically meaningful transformations for ordination of species data. Oecologia 129, 271-280. 10.1007/s004420100716

Ley, R. E., J.K. Harris, J. Wilcox, J.R. Spear, S.R. Miller, B.M. Bebout & N.R. Pace. 2006. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Applied and environmental microbiology 72, 3685-3695. 10.1128/aem.72.5.3685-3695.2006

Li, S. J., Z.S. Hua, L.N. Huang, J. Li, S.H. Shi, L.X. Chen & W.S. Shu. 2014. Microbial communities evolve faster in extreme environments. Scientific Reports 4: 6205. DOI: 10.1038/srep06205

Liu, J. & M.M. Häggblom. 2018. Genome-guided identification of organohalide-respiring Deltaproteobacteria from the marine environment. MBio, 9, 10-1128. DOI: 10.1128/mbio.02471-18

Liu, C., Y. Cui, X. Li & M. Yao. 2021. microeco: an R package for data mining in microbial community ecology. FEMS Microbiology Ecology 97, fiaa255. DOI: 10.1093/femsec/fiaa255

Liu,X., Y. Wang, Y & D.J. Gu. 2021b. Ecological distribution and potential roles of Woesearcheota in anaerobic biogeochemical cycling unveiled by genomic analysis. Computational and Structural Biotechnology Journal 19, 794-800. DOI: 10.1016/j.csbj.2021.01.013

Locey, K. J. & J.T. Lennon. 2016. Scaling laws predict global microbial diversity. Proceedings of the National Academy of Sciences 113, 5970-5975. DOI: 10.1073/pnas.1521291113

Logares, R., S.V.M. Tesson, B. Canbäck, M. Pontarp, K. Hedlund K & K. Rengefors. 2018. Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes. Environmental Microbiology 20, 2231-2240. DOI: 10.1111/1462-2920.14265

Marty, B., G. Avice, D.V. Bekaert & M.W. Broadley. 2018. Salinity of the Archaean oceans from analysis of fluid inclusions in quartz. Comptes Rendus Geoscience 350, 154-163. DOI: 10.1016/j.crte.2017.12.002

McMurdie, P. J., & S. Holmes. 2013. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PloS one 8, e61217. DOI: 10.1371/journal.pone.0061217

McMurdie, P. J., & S. Holmes, S. 2014. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Computational Biology, 10, e1003531. DOI: 10.1371/journal.pcbi.1003531

Medina-Chávez, N. O. & M. Travisano. 2022. Archaeal Communities: The Microbial Phylogenomic Frontier. Frontiers in Genetics, 12, 693193. DOI: 10.3389/fgene.2021.693193

Menéndez-Serra, M., V.J. Ontiveros, X. Triadó-Margarit, D. Alonso & E.O. Casamayor. 2020. Dynamics and ecological distributions of the Archaea microbiome from inland saline lakes (Monegros Desert, Spain). FEMS Microbiology Ecology, 96, fiaa019. DOI: 10.1093/femsec/fiaa019

Menéndez-Serra, M., X. Triadó-Margarit & E. Casamayor. 2021. Ecological and Metabolic thresholds in the Bacterial, Protist, and Fungal microbiome of Ephemeral saline lakes (Monegros Desert, Spain). Microbial Ecology, 82: 885-896. DOI: 10.1007/s00248-021-01732-9

Ning, D., Y. Deng, J.M. Tiedje & J. Zhou. 2019. A general framework for quantitatively assessing ecological stochasticity. Proceedings of the National Academy of Sciences 116, 16892-16898. DOI: 10.1073/pnas.1904623116

Oksanen, J., R. Kindt, P. Legendre, B. O’Hara, M.H.H. Stevens, M.J. Oksanen & M.A.S.S Suggests. 2007. The vegan package. Community ecology package 10, 719. DOI: 10.1658/11009233(2003)014[0927:vaporf]2.0.co;2

Oren, A. 1999. Bioenergetic aspects of halophilism. Microbial and Molecular Biology Reviews, 63:334–348. DOI: 10.1128/mmbr.63.2.334-348.1999

Oren, A. 2002. Diversity of halophilic microorganisms: environments, phylogeny, physiology, and applications. Journal of Industrial Microbiology and Biotechnology, 28, 56-63. DOI: 10.1038/sj.jim.7000176

Oren, A. 2016. Probing Saltern Brines with an Oxygen Electrode: What Can We Learn about the Community Metabolism in Hypersaline Systems? Life 6:,23. DOI: 10.3390/life6020023

Paerl H. W. & J.L. Pinckney. 1996. A mini-review of microbial consortia: their roles in aquatic production and biogeochemical cycling. Microbial Ecology, 31, 225-247. DOI: 10.1007/bf00171569

Pedrós-Alió, C. 2012. The rare bacterial biosphere. Annual review of marine science, 4, 449-466. DOI: 10.1146/annurev-marine-120710-100948

Schmidt, P. J., E.S. Cameron, K.M. Müller, & M.B. Emelko. 2022. Ensuring that fundamentals of quantitative microbiology are reflected in microbial diversity analyses based on next-generation sequencing. Frontiers in microbiology, 13, 258. DOI: 10.3389/fmicb.2022.728146

Shade, A., S.E. Jones, J.G. Caporaso, J. Handelsman, R. Knight, N. Fierer & J.A. Gilbert. 2014. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. MBio, 5, e01371-14. DOI: 10.1128/mbio.01371-14

Sloan, W. T., M. Lunn, S. Woodcock, I.M. Head, S. Nee & T.P. Curtis. 2006. Quantifying the roles of immigration and chance in shaping prokaryote community structure. Environmental microbiology, 8, 732-740. DOI: 10.1111/j.1462-2920.2005.00956.x

Stamatakis, A. 2015. Using RAxML to infer phylogenies. Current protocols in bioinformatics, 51, 6-14. DOI: 10.1002/0471250953.bi0614s51

Stegen, J.C., X. Lin, J.K. Fredrickson, X. Chen, D.W. Kennedy, C.J. Murray & A. Konopka. 2013. Quantifying community assembly processes and identifying features that impose them. The ISME journal, 7, 2069-2079. DOI: 10.1038/ismej.2013.93

Stegen, J. C., X. Lin, J.K. Fredrickson & A.E. Konopka. 2015. Estimating and mapping ecological processes influencing microbial community assembly. Frontiers in microbiology, 6, 370. DOI: 10.3389/fmicb.2015.00370

Uritskiy, G., A. Munn, M. Dailey, D.R. Gelsinger, S. Getsin, A. Davila & J. DiRuggiero. 2020. Environmental factors driving spatial heterogeneity in desert halophile microbial communities. Frontiers in Microbiology, 11, 578669. DOI: 10.3389/fmicb.2020.578669

Violle, C., W. Thuiller, N. Mouquet, F. Munoz, N.J. Kraft, M.W. Cadotte & D. Mouillot. 2017. Functional rarity: the ecology of outliers. Trends in Ecology and Evolution, 32, 356-367. DOI: 10.1016/j.tree.2017.02.002

Vogt, J. C., R.M. Abed, D.C. Albach & K.A. Palinska. 2018. Bacterial and archaeal diversity in hypersaline cyanobacterial mats along a transect in the intertidal flats of the Sultanate of Oman. Microbial ecology, 75, 331-347. DOI: 10.1007/s00248-017-1040-9

Wang, Z., K. Feng, G. Lu, H. Yu, S. Wang, Z. Wei & Y. Deng. 2022. Homogeneous Selection and Dispersal Limitation Dominate the Effect of Soil Strata Under Warming Condition. Frontiers in Microbiology, 13, 338. DOI: 10.3389/fmicb.2022.801083

WEBB, C. O. 2000. Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. The American Naturalist, 156, 145-155. DOI: 10.2307/3079215

Yang, J., L.A. Ma, H. Jiang, G. Wu & H. Dong. 2016. Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes. Scientific reports, 6, 25078. DOI: 10.1038/srep25078

Yilmaz P., L.W. Parfrey, P. Yarza, J. Gerken, E. Pruesse & C. Quast. 2014. The SILVA and “all-species living tree project (LTP)” taxonomic frameworks. Nucleic acids research 42(D1) D643-D648. DOI: 10.1093/nar/gkt120

Zhou, J. & D. Ning. 2017. Stochastic community assembly: does it matter in microbial ecology? Microbiology and Molecular Biology Reviews, 81, e00002-17. DOI: 10.1128/mmbr.00002-17

Zhou, Z., J. Pan, F. Wang, J.D. Gu & M. Li. 2018. Bathyarcheota: globally distributed metabolic generalists in anoxic environments. Fems Microbiology Reviews 42, 639-655. DOI: 10.1093/femsre/fu

Downloads

Publicado

2025-04-01

Como Citar

M Centeno, C., Blanco Jarvio, A., Bautista García, A., Beltrán, Y., & Mejía, O. (2025). “Diversidad y estructura comunitaria de ensambles microbianos de pozas de evaporación del Noroeste de México”. HIDROBIOLÓGICA, 35(1). Recuperado de https://hidrobiologica.izt.uam.mx/index.php/revHidro/article/view/1846

Edição

Seção

Material suplementario

Artigos mais lidos pelo mesmo(s) autor(es)