The microbial community in an alkaline saline sediment of a former maar lake bed



The “Hoya del Rincón de Parangueo (HRP)” is a maar that contained a perennial alkaline lake that drained in the 1980s so that a sediment with high pH and extreme salinity remained. The aim of this work was to determine how the bacterial and archaeal community was controlled by these extreme conditions.

Materials and methods

Sediment samples were collected from the 0–20-cm layer along a crater-wide transect. Physicochemical characteristics and the archaeal and bacterial community were determined by analysis of the 16S rRNA through Illumina sequencing.

Results and discussion

The sediment samples had a pH 10 and an electrolytic conductivity (EC) that ranged from 29.8 to 74.4 dS m−1. Three archaeal and 37 bacterial phyla were detected with Euryarchaeota (relative abundance 62.7 ± 17.6%) dominating the Archaea, and Proteobacteria (28.2 ± 10.7%) and Actinobacteria (21.1 ± 6.4%) the Bacteria. The most abundant archaeal genus was Candidatus Nitrososphaera while Euzebya, Halomonas, KSA1 and Planctomycetes dominated the bacterial gene. Thaumarchaeota were enriched in sediment samples with a higher Pb content and Euryarchaeota in sediment with a higher Mg content, while Crenarchaeota and Candidatus Nitrososphaera were enriched in sediment with a higher sand, total N and organic C content. Proteobacteria were enriched in sediment with a higher organic C and total N, Si and sand content, while Bacteroidetes and Planctomycetes in sediment with a higher water holding capacity and clay and Mg content. Members of KSA1 and Euzebya were enriched in sediment with a lower EC, organic C and total N content. Although a large number of bacterial and archaeal groups were correlated significantly with a range of sediment characteristics, the sediment characteristics explained the variation of only two bacterial groups > 50% (TM6 and Desulfonatronospira) using the machine learning tool randomForest and none of the archaeal groups. Archaeal and bacterial functional guilds were dominated by ammonium oxidation and nitrite reduction.


Although the different sediment samples were dominated often by similar bacterial and archaeal groups, the measured sediment characteristics explained little of the variation found between the sampling points. The high bacterial and archaeal diversity indicated that the site might be a source of unclassified species and phylotypes with specific metabolic capacities involved in the N and S cycles.

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We thank Procuraduría Ambiental y de Ordenamiento Territorial del Estado de Guanajuato for access to the sampling site La Hoya del Rincón de Parangueo.

Funding information

This research was funded by Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN, Mexico), and Apoyo Especial para Fortalecimiento de Doctorado PNPC 2013, 2014 and project Infraestructura 205945 from Consejo Nacional de Ciencia y Tecnología (CONACyT, Mexico) and project CB 2014-236674-Z from CONACyT. C.L. I.-S., and S. G.-A. received grant-aided support from CONACyT.

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Correspondence to Elizabeth Selene Gomez-Acata.

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Fig. S1

Rarefication curves of the number of sequences versus the number of OTU’s for a) Bacteria and b) Archaea (PDF 65 kb)

Fig. S2

Heat map with the significant Spearman correlations between sediment characteristics, and alpha diversity indexes, number of OTUs and Good coverage of a) Bacteria and b) Archaea in the sediment of “La Hoya del Rincón de Parangueo”. Data were not normalized and the bacterial/archaeal groups were ordered from those with the highest to the lowest relative abundance (PDF 58 kb)

Fig. S3

Heat map with the significant Spearman correlations between sediment characteristics, and the relative abundance (%) of the bacterial a) phyla and b) genera in the sediment of “La Hoya del Rincón de Parangueo”. Data were not normalized and the bacterial groups were ordered from those with the highest to the lowest relative abundance (PDF 118 kb)

Fig. S4

Heat map with the significant Spearman correlations between sediment characteristics and the relative abundance (%) of archaeal a) phyla, b) orders and c) genera in the sediment of “La Hoya del Rincón de Parangueo”. Data were not normalized and the archaeal groups were ordered from those with the highest to the lowest relative abundance (PDF 122 kb)

Fig. S5

Canonical analysis of principal coordinates (CAP) with the functions of a) Archaea and b) Bacteria of the sediment of “La Hoya del Rincón de Parangueo” (PDF 68 kb)

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Ibarra-Sánchez, C.L., Prince, L., Aguirre-Noyola, J.L. et al. The microbial community in an alkaline saline sediment of a former maar lake bed. J Soils Sediments 20, 542–555 (2020).

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  • Alpha diversity
  • Diversity analysis
  • Illumina sequencing
  • Maar
  • Microbial communities
  • Transect