DNA uptake from a laboratory environment drives unexpected adaptation of a thermophile to a minor medium component

Abstract

DNA uptake is widespread among microorganisms and considered a strategy for rapid adaptation to new conditions. While both DNA uptake and adaptation are referred to in the context of natural environments, they are often studied in laboratories under defined conditions. For example, a strain of the thermophile Thermoanaerobacter kivui had been adapted to growth on high concentrations of carbon monoxide (CO). Unusual phenotypes of the CO-adapted strain prompted us to examine it more closely, revealing a horizontal gene transfer (HGT) event from another thermophile, Thermoanaerobacter sp. strain X514, being cultured in the same laboratory. The transferred genes conferred on T. kivui the ability to utilize trehalose, a trace component of the yeast-extract added to the media during CO-adaptation. This same HGT event simultaneously deleted a native operon for thiamine biosynthesis, which likely explains why the CO-adapted strain grows poorly without added vitamins. Attempts to replicate this HGT by providing T. kivui with genomic DNA from Thermoanaerobacter sp. strain X514 revealed that it is easily reproducible in the lab. This subtle form of “genome contamination” is difficult to detect, since the genome remains predominantly T. kivui, and no living cells from the original contamination remain. Unexpected HGT between two microorganisms as well as simultaneous adaptation to several conditions may occur often and unrecognized in laboratory environments, requiring caution and careful monitoring of phenotype and genotype of microorganisms that are naturally-competent for DNA uptake.

Adaptive laboratory evolution of a thermophile toward a reduced growth temperature optimum

“…Two more are located in transcriptional regulators that have relatively low expression levels at 66°C (unpublished data), but may be of importance in cold adaptation. Since T. kivui easily takes up and integrates environmental DNA at 66°C (Basen et al, 2018 ; Zeldes et al, 2023 ), the SNP in Cas6-1, a CRISPR RNA maturation endonuclease (Jesser et al, 2019 ), may modulate the ability to acquire foreign DNA as a strategy for the adaptation of the environment. Another SNP was detected in the gene encoding the potassium ATPase kdpC N146K (AAT → AAG).…”

“…On a shorter time scale, it may be conceivable that thermophiles profit from HGT events in adaptation to lower temperatures. T. kivui , the organism used in this study, has recently been shown to efficiently take up and integrate foreign DNA from a laboratory environment into its genome, which allowed the strain to adapt to a certain medium type (Zeldes et al, 2023 ).…”

“…Cell morphology was documented using a Nikon Eclipse Ni-U microscope equipped with a Nikon DSFi3 camera (Nikon, Tokyo, Japan). Glucose and organic acid concentrations were determined by HPLC as described previously (Zeldes et al, 2023 ).…”

“…The genomes of adapted strains were analyzed for single-nucleotide polymorphisms as recently described (Zeldes et al, 2023 ).…”

Obligate autotrophy at the thermodynamic limit of life in a new acetogenic bacterium

“…Certain differences between the topologies of particular trees are likely to result from subsequent gene replacements via HGT across shorter phylogenetic distances. The members of the TTC group seem prone to ready acquisition of genetic information, as evidenced by demonstration of wide occurrence of natural competence among Thermoanaerobacter and Thermoanaerobacterium species (Shaw et al, 2010;Zeldes et al, 2023).…”