Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation
- 16 March 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Science China Life Sciences
- Vol. 63 (6), 886-897
- https://doi.org/10.1007/s11427-020-1679-1
Abstract
Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the “Gerdarchaeota”. Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood—Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.Keywords
This publication has 81 references indexed in Scilit:
- Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regionsNucleic Acids Research, 2013
- SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genesBioinformatics, 2012
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell SequencingJournal of Computational Biology, 2012
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depthBioinformatics, 2012
- Accelerated Profile HMM SearchesPLoS Computational Biology, 2011
- PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotesBioinformatics, 2010
- Prodigal: prokaryotic gene recognition and translation initiation site identificationBMC Bioinformatics, 2010
- BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignmentsBMC Evolutionary Biology, 2010
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome DatabasesNucleic Acids Research, 2007