Seasonality of archaeal proteorhodopsin and associated Marine Group IIb ecotypes (Ca. Poseidoniales) in the North Western Mediterranean Sea
- 7 December 2020
- journal article
- research article
- Published by Oxford University Press (OUP) in The ISME Journal
- Vol. 15 (5), 1302-1316
- https://doi.org/10.1038/s41396-020-00851-4
Abstract
The Archaea Marine Group II (MGII) is widespread in the world’s ocean where it plays an important role in the carbon cycle. Despite recent discoveries on the group’s metabolisms, the ecology of this newly proposed order (Candidatus Poseidoniales) remains poorly understood. Here we used a combination of time-series metagenome-assembled genomes (MAGs) and high-frequency 16S rRNA data from the NW Mediterranean Sea to test if the taxonomic diversity within the MGIIb family (Candidatus Thalassarchaeaceae) reflects the presence of different ecotypes. The MAGs’ seasonality revealed a MGIIb family composed of different subclades that have distinct lifestyles and physiologies. The vitamin metabolisms were notably different between ecotypes with, in some, a possible link to sunlight’s energy. Diverse archaeal proteorhodopsin variants, with unusual signature in key amino acid residues, had distinct seasonal patterns corresponding to changing day length. In addition, we show that in summer, archaea, as opposed to bacteria, disappeared completely from surface waters. Our results shed light on the diversity and the distribution of the euryarchaeotal proteorhodopsin, and highlight that MGIIb is a diverse ecological group. The work shows that time-series based studies of the taxonomy, seasonality, and metabolisms of marine prokaryotes is critical to uncover their diverse role in the ocean.Keywords
Funding Information
- Agence Nationale de la Recherche (ANR-14-CE02-0004-01)
- Agence Nationale de la Recherche (ANR-14-CE02-0004-01)
This publication has 65 references indexed in Scilit:
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depthBioinformatics, 2012
- Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine EuryarchaeotaScience, 2012
- Easyfig: a genome comparison visualizerBioinformatics, 2011
- Constitutive Expression of the Proteorhodopsin Gene by a Flavobacterium Strain Representative of the Proteorhodopsin-Producing Microbial Community in the North SeaApplied and Environmental Microbiology, 2010
- Prodigal: prokaryotic gene recognition and translation initiation site identificationBMC Bioinformatics, 2010
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage GenomesDNA Research, 2008
- SOAP: short oligonucleotide alignment programBioinformatics, 2008
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997