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Microorganisms
Special Issues
Systematics, Evolution and Distribution of Archaea and Their Mobilomes
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Systematics, Evolution and Distribution of Archaea and Their Mobilomes

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Systems Microbiology".

Deadline for manuscript submissions: closed (15 December 2023) | Viewed by 3054

Special Issue Editors

Prof. Dr. Patrick Forterre

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Guest Editor
Department of Microbiology, Institut Pasteur, Paris, France
Interests: giant viruses; co-evolution of viruses and archaea
Dr. Violette Da Cunha

E-Mail Website
Guest Editor
Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
Interests: evolution of archaxea and bacteria; genomic and metagenomics; phylogenetic analysis

Special Issue Information

Dear Colleagues,

The discovery of Archaea by Carl Woese and his colleagues has been one of the most important breakthroughs in biology in the last century. Whereas the first identified archaea were limited to a small number of phenotypes, mainly extremophiles, works in molecular ecology first based on 16r RNA screening and later metagenomics led to a spectucalar expansion of archaeal diversity. We know now that Archaea are present here, there and everywhere and exhibit a plethora of phenotypes. In the meantime, interesting new archaea continue to be isolated and characterized. The description and characterization of archaeal viruses and plasmids are also on the rise. Notably, whereas Archaea are evolutionary tightly linked to eukaryotes, part of their mobilome is typically “bacterial”, whereas another part is unique to this domain. This Special Issue will cover the description of archaea and their mobilome diversity based on a variety of approaches and possibly tackle fundamental evolutionary questions that remain open such as the topology of the archaeal tree, the position of the root and the position of DPANN and other fast-evolving species. The nomenclature of Archaea is also in turmoil, and papers discussing this issue will be welcome.

Prof. Dr. Patrick Forterre
Dr. Violette Da Cunha
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • archaea
  • metagenomic
  • evolution and distribution

Published Papers (2 papers)

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Research

16 pages, 2597 KiB  
Article
Distribution and Implications of Haloarchaeal Plasmids Disseminated in Self-Encoded Plasmid Vesicles
by Dominik Lücking, Tomás Alarcón-Schumacher and Susanne Erdmann
Microorganisms 2024, 12(1), 5; https://doi.org/10.3390/microorganisms12010005 - 19 Dec 2023
Viewed by 1182
Abstract
Even though viruses and plasmids are both drivers of horizontal gene transfer, they differ fundamentally in their mode of transfer. Virus genomes are enclosed in virus capsids and are not dependent on cell-to-cell contacts for their dissemination. In contrast, the transfer of plasmids [...] Read more.
Even though viruses and plasmids are both drivers of horizontal gene transfer, they differ fundamentally in their mode of transfer. Virus genomes are enclosed in virus capsids and are not dependent on cell-to-cell contacts for their dissemination. In contrast, the transfer of plasmids most often requires physical contact between cells. However, plasmid pR1SE of Halorubrum lacusprofundi is disseminated between cells, independent of cell-cell contacts, in specialized membrane vesicles that contain plasmid proteins. In this study, we searched for pR1SE-like elements in public databases and a metagenomics dataset from Australian salt lakes and identified 40 additional pR1SE-like elements in hypersaline environments worldwide. Herein, these elements are named apHPVs (archaeal plasmids of haloarchaea potentially transferred in plasmid vesicles). They share two sets of closely related proteins with conserved synteny, strongly indicating an organization into different functional clusters. We find that apHPVs, besides transferring themselves, have the potential to transfer large fragments of DNA between host cells, including virus defense systems. Most interestingly, apHPVs likely play an important role in the evolution of viruses and plasmids in haloarchaea, as they appear to recombine with both of them. This further supports the idea that plasmids and viruses are not distinct but closely related mobile genetic elements. Full article
(This article belongs to the Special Issue Systematics, Evolution and Distribution of Archaea and Their Mobilomes)
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14 pages, 3335 KiB  
Article
Fast-Evolving Alignment Sites Are Highly Informative for Reconstructions of Deep Tree of Life Phylogenies
by L. Thibério Rangel and Gregory P. Fournier
Microorganisms 2023, 11(10), 2499; https://doi.org/10.3390/microorganisms11102499 - 5 Oct 2023
Cited by 2 | Viewed by 1398
Abstract
The trimming of fast-evolving sites, often known as “slow–fast” analysis, is broadly used in microbial phylogenetic reconstruction under the assumption that fast-evolving sites do not retain an accurate phylogenetic signal due to substitution saturation. Therefore, removing sites that have experienced multiple substitutions would [...] Read more.
The trimming of fast-evolving sites, often known as “slow–fast” analysis, is broadly used in microbial phylogenetic reconstruction under the assumption that fast-evolving sites do not retain an accurate phylogenetic signal due to substitution saturation. Therefore, removing sites that have experienced multiple substitutions would improve the signal-to-noise ratio in phylogenetic analyses, with the remaining slower-evolving sites preserving a more reliable record of evolutionary relationships. Here, we show that, contrary to this assumption, even the fastest-evolving sites present in the conserved proteins often used in Tree of Life studies contain reliable and valuable phylogenetic information, and that the trimming of such sites can negatively impact the accuracy of phylogenetic reconstruction. Simulated alignments modeled after ribosomal protein datasets used in Tree of Life studies consistently show that slow-evolving sites are less likely to recover true bipartitions than even the fastest-evolving sites. Furthermore, site-specific substitution rates are positively correlated with the frequency of accurately recovered short-branched bipartitions, as slowly evolving sites are less likely to have experienced substitutions along these intervals. Using published Tree of Life sequence alignment datasets, we also show that both slow- and fast-evolving sites contain similarly inconsistent phylogenetic signals, and that, for fast-evolving sites, this inconsistency can be attributed to poor alignment quality. Furthermore, trimming fast sites, slow sites, or both is shown to have a substantial impact on phylogenetic reconstruction across multiple evolutionary models. This is perhaps most evident in the resulting placements of the Eukarya and Asgardarchaeota groups, which are especially sensitive to the implementation of different trimming schemes. Full article
(This article belongs to the Special Issue Systematics, Evolution and Distribution of Archaea and Their Mobilomes)
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