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Single‐cell sequencing unveils the lifestyle and CRISPR‐based population history of Hydrotalea sp. in acid mine drainage
Author(s) -
Medeiros J. D.,
Leite L. R.,
Pylro V. S.,
Oliveira F. S.,
Almeida V. M.,
Fernandes G. R.,
Salim A. C. M.,
Araújo F. M. G.,
Volpini A. C.,
Oliveira G.,
CuadrosOrellana S.
Publication year - 2017
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.14294
Subject(s) - biology , crispr , genome , population , phylogenetic tree , clade , evolutionary biology , genetics , ecology , gene , demography , sociology
Acid mine drainage ( AMD ) is characterized by an acid and metal‐rich run‐off that originates from mining systems. Despite having been studied for many decades, much remains unknown about the microbial community dynamics in AMD sites, especially during their early development, when the acidity is moderate. Here, we describe draft genome assemblies from single cells retrieved from an early‐stage AMD sample. These cells belong to the genus Hydrotalea and are closely related to Hydrotalea flava . The phylogeny and average nucleotide identity analysis suggest that all single amplified genomes ( SAG s) form two clades that may represent different strains. These cells have the genomic potential for denitrification, copper and other metal resistance. Two coexisting CRISPR‐Cas loci were recovered across SAG s, and we observed heterogeneity in the population with regard to the spacer sequences, together with the loss of trailer‐end spacers. Our results suggest that the genomes of Hydrotalea sp. strains studied here are adjusting to a quickly changing selective pressure at the microhabitat scale, and an important form of this selective pressure is infection by foreign DNA .