Biology subjects

Farrell, A. A.

Publications and source records attributed to Farrell, A. A..

2 recordsLinked to original sources

bioRxiv2024

Bacterial growth temperature as a horizontally acquired polygenic trait

Evolutionary events leading to organismal preference for a specific growth temperature, as well as genes whose products are needed for a proper function at that temperature, are poorly understood. Using 64 bacteria from phylum Thermotogota as a model system, we examined how optimal growth temperature changed throughout Thermotogota history. We inferred that Thermotogotas last common ancestor was a thermophile and that some Thermotogota evolved the mesophilic and hyperthermophilic lifestyles secondarily. By modeling gain and loss of genes throughout Thermotogota history and by reconstructing their phylogenies, we demonstrated that adaptations to lower and higher growth temperature require both the acquisition of necessary genes and loss of unnecessary genes. Via a pangenome-wide association study, we correlated presence/absence of 68 gene families with specific optimal growth temperature intervals. While some of these genes are poorly characterized, most are involved in metabolism of amino acids, nucleotides, carbohydrates, and lipids, as well as in signal transduction and regulation of transcription. Most of the 68 genes have a history of horizontal gene transfer to/from other bacteria and archaea, suggesting that parallel acquisitions of genes likely promote independent adaptations of different Thermotogota species to specific growth temperatures. SignificanceWhile the currently known range of life-permitting temperatures spans from -15{degrees}C to +122{degrees}C, most living organisms, including microbes, can grow only in a narrow temperature interval around their optimal growth temperature. The genetic and genomic determinants of such preference remain poorly understood. Using genomes from Thermotogota, a group of bacteria that collectively can grow between 20{degrees} and 90{degrees}C, we detected 68 genes, presence of which strongly correlates with growth at specific optimal growth temperature. Our findings dramatically expand a list of genes that are likely important for both lowering and increasing preferred growth temperature of a microorganism. We also demonstrated that these genes were usually horizontally acquired from other bacteria and archaea that likely share environment with Thermotogota, highlighting the importance of gene exchange in microbial adaptation.

evolutionary biology↗

bioRxiv2023

Early divergence and gene exchange highways in the evolutionary history of Mesoaciditogales

The placement of a non-hyperthermophilic order Mesoaciditogales at the base of Thermotogota tree challenges the prevailing hypothesis that the last common ancestor of Thermotogota was a hyperthermophile. Yet, given the long branch leading to the only two Mesoaciditogales described to-date, the phylogenetic position of the order may be due to the long branch attraction artifact. By testing various models and applying data recoding in phylogenetic reconstructions, we observed that Mesoaciditogales basal placement is strongly supported by the conserved marker genes assumed to be vertically inherited. However, based on the taxonomic content of 1,181 gene families and a phylogenetic analysis of 721 gene family trees, we also found that a substantial number of Mesoaciditogales genes are more closely related to species from the order Petrotogales. These genes contribute to coenzyme transport and metabolism, fatty acid biosynthesis, genes known to respond to heat and cold stressors, and include many genes of unknown functions. The Petrotogales comprise moderately thermophilic and mesophilic species with similar temperature tolerances to that of Mesoaciditogales. Our findings hint at extensive horizontal gene transfer between, or parallel independent gene gains by, the two ecologically similar lineages, and suggest that the exchanged genes may be important for adaptation to comparable temperature niches. SignificanceThe high-temperature phenotype is often referenced when conjecturing about characteristics of the last common ancestor of all present-day organisms. Such inferences rely on accuracy of phylogenetic trees, especially with respect to lineages that branch closest to the last common ancestor. Here, we examined evolutionary history of Mesoaciditogales, an early-branching lineage within Thermotogota phylum, which is one of the early-diverging groups of bacteria. Thermotogota is composed of thermophiles, hyperthermophiles and mesophiles, who collectively can grow between 20 to 90 degrees Celsius, making it challenging to infer the growth temperature of their common ancestor. Our analysis revealed a complex evolutionary history of Mesoaciditogales genome content impacted by horizontal gene transfer, highlighting the challenges of ancestral phenotype inferences using present-day genomes.

evolutionary biology↗