Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean

Abstract

Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re‐analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co‐occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene‐coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.

Prokaryotic Diversity and Distribution Along Physical and Nutrient Gradients in the Tunisian Coastal Waters (South Mediterranean Sea)

“…Archaea were well represented in all Tunisian coastal seawater samples (>10% of the prokaryotes) and were mainly composed of the candidate order "Poseidoniales" (MGII), as observed in coastal northwest Mediterranean Sea and in surface waters of different marine areas around the world (Galand et al, 2010;Hugoni et al, 2013;Pereira et al, 2019;Rinke et al, 2019;Santoro et al, 2019). In our winter study, the MGIIb group (Candidatus Thalassarchaeaceae, represented by the ASVs 3, 21, 29, 40) was more abundant that the MGIIa (represented by the ASVs 28 and 41) in seawaters.…”

Mesozooplankton taurine production and prokaryotic uptake in the northern Adriatic Sea

“…Thaumarchaeota MG I and Euryarchaeota MGIIb in the winter and Euryarchaeota MGIIa in the summer exist in various ecotypes in the coastal surface waters of the western Mediterranean Sea, characterized by different activity patterns (Hugoni et al 2013). Furthermore, several recent studies on the Euryarchaeota MGII group in coastal and open ocean systems identified diverse subclades with different ecological niches and lifestyles including members able to utilize taurine (Orellana et al 2019; Pereira et al 2019). Alteromonas phylo‐ and ecotypes also drastically differ in their utilization efficiencies of specific C‐compounds (Gómez‐Consarnau et al 2012; Sarmento and Gasol 2012).…”

Exploring Marine Planktonic Archaea: Then and Now

“…Several excellent reviews and articles focussed on marine planktonic Archaea have recently been published ( Stahl and de la Torre, 2012 ; Zhang et al, 2015 ; Haro-Moreno et al, 2017 ; Pereira et al, 2019 ; Santoro et al, 2019 ; Baker et al, 2020 ), so readers are referred to those for more comprehensive overviews. This short Perspective deliberately focuses on a brief historical account of own my lab’s adventures in studying marine planktonic Archaea over the past 30 years.…”