Seasonality of archaeal proteorhodopsin and associated Marine Group IIb ecotypes (Ca. Poseidoniales) in the North Western Mediterranean Sea

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.

Vertical Niche Partitioning of Archaea and Bacteria Linked to Shifts in Dissolved Organic Matter Quality and Hydrography in North Atlantic Waters

“…The observed differences on the link between intermediate and subsurface assemblages with hydrography and DOM quality indicators suggest an important disparity between Archaea and Bacteria domains. This disconnection was also found by Pereira et al (2021), who found that Archaea completely disappeared from superficial waters in the NW Mediterranean Sea during low-productive summer, contrarily to Bacteria that were present all year round. In our study area, archaeal upper subsurface communities were dominated by MarG.II, particularly MarG.II_2 and MarG.II_others.…”

Seasonality of biogeochemically relevant microbial genes in a coastal ocean microbiome

“…The seasonal trends of specific groups such as photosynthetic bacteria (Paerl et al, 2012), ammonia oxidizing bacteria (Galand et al, 2010), and photoheterotrophic groups (Auladell et al, 2019; Ferrera et al, 2014; Nguyen et al, 2015) have been described through amplicon analyses. In addition, some temporal metagenomic analyses have focused on studying specific taxonomic groups through the generation of metagenome assembled genomes (MAGs; Kashtan et al, 2014; Pereira et al, 2021). Despite the potential of MAGs for the analysis of functional groups, they usually miss the contribution of rare groups as well as groups without a good genome recovery due to repetitive regions or high microdiversity (Haro‐Moreno et al, 2020).…”

Seasonal microbial dynamics in the ocean inferred from assembled and unassembled data: a view on the unknown biosphere

“…Furthermore, Euryarchaeota was also found to have a key role. The CAG built in this study does not allow for a precise taxonomy; however, a previous study on the same site highlighted the presence of the MGII clade [ 17 , 61 ] now defined as an order lineage. The ecological success of the MGII group could be due to the presence of light-harvesting proteins (i.e.…”

“…The ecological success of the MGII group could be due to the presence of lightharvesting proteins (i.e. proteorhodopsin) [61][62][63]. Recently, the partially reconstructed MGIIa genome revealed the presence of glycoside hydrolases that are possibly involved in algal substrate breakdown [64,65].…”