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Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments

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Abstract

Bacterial and archaeal community structure of five microbial communities, developing at different salinities in Baja California Sur, Mexico, were characterized by 16S rRNA sequencing. The response of the microbial community to artificial changes in salinity–sulfate concentrations and to addition of trimethylamine was also evaluated in microcosm experiments. Ordination analyses of the microbial community structure showed that microbial composition was distinctive for each hypersaline site. Members of bacteria were dominated by Bacteroidetes and Proteobacteria phyla, while Halobacteria of the Euryarchaeota phylum was the most represented class of archaea for all the environmental samples. At a higher phylogenetic resolution, methanogenic communities were dominated by members of the Methanosarcinales, Methanobacteriales and Methanococcales orders. Incubation experiments showed that putative hydrogenotrophic methanogens of the Methanomicrobiales increased in abundance only under lowest salinity and sulfate concentrations. Trimethylamine addition effectively increased the abundance of methylotrophic members from the Methanosarcinales, but also increased the relative abundance of the Thermoplasmata class, suggesting the potential capability of these microorganisms to use trimethylamine in hypersaline environments. These results contribute to the knowledge of microbial diversity in hypersaline environments from Baja California Sur, Mexico, and expand upon the available information for uncultured methanogenic archaea in these ecosystems.

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Acknowledgements

This project was supported by CONACYT grant 105969-Z (2008–2014) to ALC and by grants to BMB by NASA’s Exobiology program. We are grateful with Exportadora de Sal, S.A. for access to the Guerrero Negro field site. We thank to Adrian Mungia for technical assistance in the library prep and 454 pyrosequencing. We thank ‘Unidad de Secuenciación Masiva y Bioinformática’ at the ‘Laboratorio Nacional de Apoyo Tecnológico a las Ciencias Genómicas’, CONACyT #260481, Instituto de Biotecnología/UNAM for computational resources used for the bioinformatics analyses. We are thankful to Santiago Cadena Rodríguez for lab assistance and for his contributions on the interpretations of the results. We are very appreciative of many helpful discussions with Cheryl Kelley and for the field assistance of Angela M. Detweiler.

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Authors and Affiliations

  1. CONACYT - Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Antigua Carretera a Progreso Km. 6, Yucatán, 97310, Mexico

    José Q. García-Maldonado

  2. Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico, Mexico

    Alejandra Escobar-Zepeda & Alejandro Sanchez-Flores

  3. CONACYT - Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana San Nicolás de Hidalgo, Morelia, Michoacán, Mexico

    Luciana Raggi

  4. Exobiology Branch, Ames Research Center, National Aeronautics and Space Administration, Moffett Field, CA, USA

    Brad M. Bebout

  5. Laboratorio de Geomicrobiología y Biotecnología, Instituto Politécnico Nacional 195, Centro de Investigaciones Biológicas del Noroeste, Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, 23096, Mexico

    Alejandro López-Cortés

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  1. José Q. García-Maldonado
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  3. Luciana Raggi
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Correspondence to José Q. García-Maldonado or Alejandro López-Cortés.

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Communicated by A. Oren.

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792_2018_1047_MOESM1_ESM.png

Supplementary Figure S1. Composition of the methanogenic archaeal community in relative abundance at genus level. The environmental samples from natural hypersaline microbial mats and endovaporitic communities from Laguna San Ignacio (LSI) and Exportadora de Sal S.A. de C.V. (ESSA) in Guerrero Negro, are intercalated with the samples from the microcosms experiments with a decreased salinity–sulfate concentrations (LOW suffix) or trimethylamine additions (TMA suffix). Notably, sample ESSA-A9-LOW was completely absent from methanogenic archaea. Sample LSI-S3-TMA was discarded because of low sequencing yield. (PNG 232 kb)

792_2018_1047_MOESM2_ESM.html

Supplementary Material S2. Interactive abundance charts showing the relative abundance of bacteria at the genus level. A different Krona chart is displayed separately for the environmental samples from natural hypersaline microbial mats and endovaporitic communities from Laguna San Ignacio (LSI) and Exportadora de Sal S.A. de C.V. (ESSA) in Guerrero Negro, and for the samples in microcosm experiments incubated 23 days in a low salinity (LOW suffix) or trimethylamine (TMA suffix). Sample LSI-S3-TMA was discarded because of low sequencing yield. (HTML 434 kb)

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García-Maldonado, J.Q., Escobar-Zepeda, A., Raggi, L. et al. Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments. Extremophiles 22, 903–916 (2018). https://doi.org/10.1007/s00792-018-1047-2

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