Single‐cell sequencing unveils the lifestyle and CRISPR‐based population history of Hydrotalea sp. in acid mine drainage

Abstract

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 (SAGs) 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 SAGs, 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.

Genomic signatures and co‐occurrence patterns of the ultra‐small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle

“…genome from our metagenome data set. In doing so, we found our data to closely align with that of Medeiros et al (). Detailed information on the obtained Hydrotalea sp.…”

“…However, stronger correlations were found with Hydrotalea spp. Following this line of reasoning, the genus Hydrotalea was also previously reported to occur at a high relative abundance in the same AMD system (Medeiros et al, 2017). In addition, by using single-cell genomics, Medeiros et al…”

“…The AMD system sampled in this study was at an early stage of formation, with a pH ~ 5 and enriched with copper (previously described in details by Medeiros et al, 2017). High concentrations of copper are known to be toxic to cells, leading to the inactivation of enzymes and intracellular oxidative damage (Macomber & Imlay, 2009).…”

Root renovation: how an improved understanding of basic root biology could inform the development of elite crops that foster sustainable soil health

“…Given that it is often challenging to culture the majority of uncharacterised microbial species, single cell sequencing enables culture-free sequencing of genomes for these organisms (Stepanauskas 2015;Woyke et al 2017). Several studies have demonstrated the use of single-cell sequencing directly on environmental samples to study uncharacterised microbial species in atypical microbial communities, including Oceanospirillales in oil spillcontaminated sea water (Mason et al 2012), Hydrotalea in highly acidic mine drainage (Medeiros et al 2017) and Poribacteria, endosymbionts in marine sponges (Siegl et al 2011). However, the application of single-cell sequencing is restricted to a microbial community where cells can be isolated relatively easily (Woyke et al 2017).…”

Translational Bioinformatics for Cholangiocarcinoma: Opportunities and Challenges

“…Many bio-techniques like deep sequencing, single cell sequencing, CRISPR, etc . 24 - 26 are developed as efficient tools for the deep investigation of the complex mechanisms of complex disease like CCA. The accumulation of big sequencing data and other clinical data provides the opportunity, but also the challenge, to build bioinformatics models for early diagnosis and personalized treatment, even prevention of cancers like CCA and others.…”