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Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene

  • Environmental Microbiology
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Abstract

This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.

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Acknowledgments

We are thankful to Gregory Arjona and Francisco Puc for sample collection, and to Abril Gamboa-Muñoz and Victor Ceja for lab assistance. Computational resources used for all bioinformatics analyses were provided by Emanuel Hernández-Núñez. We also are thankful to the anonymous reviewers that help to improve the present manuscript.

Funding

This research has been funded by the Mexican National Council for Science and Technology-Mexican Ministry of Energy Hydrocarbon Fund, project 201441 and CONACYT 251622-2015 received by JQGM. This research was also supported by grants of the “Biotechnology of marine organisms” awarded by the National Council of Science and Technology of Mexico (CONACYT) project 15689-2014. CONACYT awarded MFSSJ with a Ph.D. scholarship. This is a contribution of the Gulf of Mexico Research Consortium (CIGoM).

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Authors and Affiliations

  1. Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico

    Ma. Fernanda Sánchez-Soto & Ma. Leopoldina Aguirre-Macedo

  2. Consorcio de Investigación del Golfo de México (CIGOM), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico

    Daniel Cerqueda-García

  3. Instituto de Geología, Universidad Nacional Autónoma de México, Mexico City, Mexico

    Rocío J. Alcántara-Hernández

  4. Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Mexico

    Luisa I. Falcón

  5. Laboratorio de Biodiversidad Marina y Cambio Climático, El Colegio de la Frontera Sur, Campeche, Mexico

    Daniel Pech

  6. Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico

    Flor Árcega-Cabrera

  7. CONACYT-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México

    José Q. García-Maldonado

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  1. Ma. Fernanda Sánchez-Soto
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  2. Daniel Cerqueda-García
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  3. Rocío J. Alcántara-Hernández
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  7. Ma. Leopoldina Aguirre-Macedo
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  8. José Q. García-Maldonado
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Contributions

Ma. Fernanda Sánchez-Soto generated and designed the experiments, performed the experiments, analyzed the data, prepared the figures and/or tables, authored/reviewed drafts of the paper, and approved the final draft. Daniel Cerqueda-García analyzed the data, prepared the figures and/or tables, authored/reviewed drafts of the paper, and approved the final draft. Rocío J. Alcántara-Hernández and Luisa I. Falcón analyzed the data, contributed to the discussion of the obtained results, authored/reviewed drafts of the paper, and approved the final draft. Daniel Pech and Flor Árcega-Cabrera led the physicochemical analyses, authored/reviewed drafts of the paper, and approved the final draft. Ma. Leopoldina Aguirre-Macedo and José Q. García-Maldonado conceived the research, secured funding, contributed to the discussion of the results, authored contribute to the discussion of the results, reviewed drafts of the paper, and approved the final draft.

Corresponding authors

Correspondence to Ma. Leopoldina Aguirre-Macedo or José Q. García-Maldonado.

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Sánchez-Soto, M.F., Cerqueda-García, D., Alcántara-Hernández, R.J. et al. Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene. Microb Ecol 81, 908–921 (2021). https://doi.org/10.1007/s00248-020-01631-5

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