Biology subjects

Louyakis, A. S.

Publications and source records attributed to Louyakis, A. S..

5 recordsLinked to original sources

bioRxiv2023

Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense

In this study, we use pan-genomics to characterize the organized variability from the widely dispersed halophilic archaeal species Halorubrum ezzemoulense. We include a multi-regional sampling of newly sequenced, high-quality draft genomes. Using the pan-genome graph of the species, we discover 50 genomic islands which represent rare accessory genetic capabilities available to members of the species. 19 of these islands are likely the remnant of mobile genetic elements and are enriched for genomic dark matter. 10 islands encode for niche adapting solute transporters, with a cosmopolitan but limited distribution throughout the strains. We also observe rearrangements which have led to the insertion/recombination/replacement of mutually exclusive genomic islands in equivalent genome positions ("homeocassettes"). These conflicting islands encode for similar functions, but homologs from islands located between the same core genes exhibit extreme divergence on the amino acid level. Homeocasettes provide variations for a homologous function, which may confer a greater range of adaptability to the species group. We observe some islands that appear geographically restricted; however, we also observe the coexistence of genomes, in a single geographic region, with and without certain genomic islands, demonstrating the retention and spread of rare genes in the pan-genome. ImportanceUnderstanding the evolution of genome content is a key puzzle in evolutionary biology. Despite its importance, this area hasnt received thorough investigation. This is especially true of Archaeal organisms, which constitute a large fraction of Earths diversity, but are often referred to as the "forgotten" or "third" domain of life. This study dives into those questions by finding rare genes amongst a group of closely related Archaeal species, and describes how their transfer, utilization and persistence may contribute to the speciation and specialization of the group.

microbiology↗

bioRxiv2022

Functional and compositional changes in the fecal microbiome of a shorebird during pre-migratory weight gain

Shorebirds migrate long distances twice annually, which requires intense physiological and morphological adaptations, including the ability to rapidly gain weight via fat deposition at stopover locations. The role of the microbiome in weight gain in avian hosts is unresolved, but there is substantial evidence to support the hypothesis that the microbiome is involved with host weight from mammalian microbiome literature. Here, we collected 100 fecal samples of Ruddy Turnstones to investigate microbiome composition and function during stopover weight gain in Delaware Bay, USA. Using 16S rRNA sequencing on 90 of these samples and metatranscriptomic sequencing on 22, we show that taxonomic composition of the microbiome shifts during weight gain, as do functional aspects of the metatranscriptome. We identified ten genes that are associated with weight class and polyunsaturated fatty acid biosynthesis in the microbiota is significantly increasing as birds gain weight. Our results support that the microbiome is a dynamic feature of host biology that interacts with both the host and the environment and may be involved in the rapid weight gain of shorebirds.

microbiology↗

bioRxiv2020

Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model Archaeon

Horizontal gene transfer is a means by which bacteria, archaea, and eukaryotes are able to trade DNA within and between species. While there are a variety of mechanisms through which this genetic exchange can take place, one means prevalent in the archaeon Haloferax volcanii involves the transient formation of cytoplasmic bridges between cells and is referred to as mating. This process can result in the exchange of very large fragments of DNA between the participating cells. Genes governing the process of mating, including triggers to initiate mating, mechanisms of cell fusion, and DNA exchange, have yet to be characterized. We used a transcriptomic approach to gain a more detailed knowledge of how mating might transpire. By examining the differential expression of genes expressed in cells harvested from mating conditions on a filter over time and comparing them to those expressed in a shaking culture, we were able to identify genes and pathways potentially associated with mating. These analyses provide new insights into both the mechanisms and barriers of mating in Hfx. volcanii.

microbiology↗

bioRxiv2020

The Impact of Restriction-Modification Systems on Mating in Haloferax volcanii

Halobacteria have been observed to be highly recombinogenic, frequently exchanging genetic material. Several barriers to mating in the Halobacteria have been examined, such as CRISPR-Cas, glycosylation, and archaeosortases, but these are low barriers that do not drastically reduce the recombination frequency. Another potential barrier could be restriction-modification (RM) systems, which cleave DNA that is not properly methylated, thus limiting the exchange of genetic material between cells which do not have compatible RM systems. In order to examine the role of RM systems on limiting recombination in the Halobacteria, the impact of RM systems on cell-to-cell mating in Haloferax volcanii, a well-characterized method of genetic exchange and recombination in a halobacterial species, was examined. Strains which possessed all naturally-occurring RM system genes in H. volcanii (RM+) and strains without these RM systems ({Delta}RM) were mated together to compare the efficiency of gene transfer between RM-compatible strains and RM-incompatible strains. The results indicated that mating RM-incompatible strains together resulted in a decrease in gene transfer efficiency compared to mating RM-compatible strains together, suggesting that RM systems limit mating in H. volcanii, but do not act as absolute barriers to recombination. Therefore, RM systems are low barriers to recombination in the Halobacteria, with RM-incompatible strains exchanging genetic material at a lower frequency than those with compatible RM systems, similar to other low recombination barriers in the Halobacteria.

evolutionary biology↗

bioRxiv2019

Reconstructing the evolutionary origins of extreme halophilic Archaeal lineages

Interest and controversy surrounding the evolutionary origins of extremely halophilic Archaea has increased in recent years, due to the discovery and characterization of the Nanohaloarchaea and the Methanonatronarchaeia. Initial attempts in explaining the evolutionary placement of the two new lineages in relation to the classical Halobacteria (also referred to as Haloarchaea) resulted in hypotheses that imply the new groups share a common ancestor with the Haloarchaea. However, more recent analyses have led to a shift: the Nanohaloarchaea have been largely accepted as being a member of the DPANN superphylum, outside of the euryarchaeota; while the Methanonatronarchaeia have been placed near the base of the Methanotecta (composed of the class II methanogens, the Halobacteriales, and Archaeoglobales). These opposing hypotheses have far-reaching implications on the concepts of convergent evolution (unrelated groups evolve similar strategies for survival), genome reduction, and gene transfer. In this work, we attempt to resolve these conflicts with phylogenetic and phylogenomic data. We provide a robust taxonomic sampling of Archaeal genomes that spans the Asgardarchaea, TACK Group, euryarchaeota, and the DPANN superphylum. In addition, we assembled draft genomes from seven new representatives of the Nanohaloarchaea from distinct geographic locations. Phylogenies derived from these data imply that the highly conserved ATP synthase catalytic/non-catalytic subunits of Nanohaloarchaea share a sisterhood relationship with the Haloarchaea. We also employ a novel gene family distance clustering strategy which shows this sisterhood relationship is not likely the result of a recent gene transfer. In addition, we present and evaluate data that argue for and against the monophyly of the DPANN superphylum, in particular, the inclusion of the Nanohaloarchaea in DPANN. Significance StatementMany recent analyses have considered large groups of Bacteria and Archaea composed exclusively of environmentally assembled genomes as deep branching taxonomic groups in their respective domains. These groups display characteristics distinct from other members of their domain, which can attract unrelated lineages into those groups. This manuscript evaluates the case of the Nanohaloarchaea, and their inclusion in the DPANN Archaea, through careful analysis of the genes that compose the core of the Nanohaloarchaea. Analyses without inspection of the genes that compose a phylogenomic marker set increases the potential for the inclusion of artifacts and confuses the tree/web of life. Due to horizontal gene transfer and phylogenetic reconstruction artifacts, the placement of divergent archaeal classes into larger groups remains uncertain.

microbiology↗