The final, formatted version of the article will be published soon.
ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Biology of Archaea
Volume 15 - 2024 |
doi: 10.3389/fmicb.2024.1433224
Navigating the Archaeal Frontier: Insights and Projections from Bioinformatic Pipelines
Provisionally accepted- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Vienna, Austria
Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5% to 25%, and less studied lineages being comparable to archaea with the range of 35-40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes. environments make archaea indispensable for maintaining the equilibrium of these elemental cycles, impacting nutrient availability, greenhouse gas emissions, and overall ecosystem health (Falkowski et
Keywords: Archaea, Energy Metabolism, microbial dark matter, microbial ecology, Microbial Diversity
Received: 15 May 2024; Accepted: 28 Aug 2024.
Copyright: © 2024 Karavaeva and Sousa. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Filipa L. Sousa, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, 1090, Vienna, Austria
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.