New insights into marine group III Euryarchaeota, from dark to light

Abstract

Marine Euryarchaeota remain among the least understood major components of marine microbial communities. Marine group II Euryarchaeota (MG-II) are more abundant in surface waters (4-20% of the total prokaryotic community), whereas marine group III Euryarchaeota (MG-III) are generally considered low-abundance members of deep mesopelagic and bathypelagic communities. Using genome assembly from direct metagenome reads and metagenomic fosmid clones, we have identified six novel MG-III genome sequence bins from the photic zone (Epi1-6) and two novel bins from deep-sea samples (Bathy1-2). Genome completeness in those genome bins varies from 44% to 85%. Photic-zone MG-III bins corresponded to novel groups with no similarity, and significantly lower GC content, when compared with previously described deep-MG-III genome bins. As found in many other epipelagic microorganisms, photic-zone MG-III bins contained numerous photolyase and rhodopsin genes, as well as genes for peptide and lipid uptake and degradation, suggesting a photoheterotrophic lifestyle. Phylogenetic analysis of these photolyases and rhodopsins as well as their genomic context suggests that these genes are of bacterial origin, supporting the hypothesis of an MG-III ancestor that lived in the dark ocean. Epipelagic MG-III occur sporadically and in relatively small proportions in marine plankton, representing only up to 0.6% of the total microbial community reads in metagenomes. None of the reconstructed epipelagic MG-III genomes were present in metagenomes from aphotic zone depths or from high latitude regions. Most low-GC bins were highly enriched at the deep chlorophyll maximum zones, with the exception of Epi1, which appeared evenly distributed throughout the photic zone worldwide.

Fine stratification of microbial communities through a metagenomic profile of the photic zone

“…All the assembled rhodopsin genes clustered with previously described groups indicating that surveys may have be saturating the 500 extant diversity of rhodopsins, at least in the oligotrophic ocean photic zone. Rhodopsin sequences clustered primarily by phylum, with the exception of euryarchaeal rhodopsins as previously reported (Iverson et al, 2012;Haro-Moreno et al, 2017). Within the proteorhodopsin cluster, we could clearly differentiate another bacterial cluster including only Bacteroidetes sequences (Figure 4a).…”

“…Further analysis confirmed that all of them belonged to the same cluster ( Supplementary Figure 10), marine group II Euryarchaeota, known to be prevalent throughout the photic zone (Martin-Cuadrado et al, 2014). Whereas MED-G33 was closely 470 related to MG2-GG3 (Iverson et al, 2012), assembled from an estuary in the North Pacific, the remaining bins MED-G34 to MED-G38 were related with the recently described Thalassoarchaea Although we could not assign any contig to the marine group III Euryarchaeota, the recruitment of the previously described EUIII-Epi2 and EUIII-Epi6 (Haro-Moreno et al, 2017) showed that they were also present at the DCM. Ca.…”

A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column

“…Members of the MGII reside mainly in the marine photic zone although other ecotypes have been detected in deeper water columns (see Zhang, Xie, Martin-Cuadrado, & Rodriguez-Valera, 2015 for a review). MGIII archaea have been mainly detected in deep mesopelagic and bathypelagic, and most recently also in epipelagic waters, but their physiology is essentially unknown (Bano, Ruffin, Ransom, & Hollibaugh, 2004;Haro-Moreno, Rodriguez-Valera, López-García, Moreira, & Martin-Cuadrado, 2017; López-García, Moreira, López-López, & Rodriguez-Valera, 2001;Massana, DeLong, & Pedros-Alio, 2000), also because they remain uncultured. In addition, the presence of members of the archaeal superphylum DPANN in marine settings, mainly in microbial mats, sediments, plankton, and hydrothermal vents, is increasingly reported (Pachiadaki, Kallionaki, Dählmann, De Lange, & Kormas, 2011;Robertson, Spear, Harris, & Pace, 2009).…”

Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation

“…While MGII are more abundant in surface waters (Fuhrman and Davis, 1997;Massana et al, 2000;L opez-García et al, 2001;Mincer et al, 2007) and were also found in deep-sea water (Deschamps et al, 2014;Li et al, 2015;Liu et al, 2017), marine Thaumarchaeota are more abundant in meso-and bathypelagic waters (Karner et al, 2001;Herndl et al, 2005;Mincer et al, 2007;Teira et al, 2008;Varela et al, 2008). MGIII are generally considered to be more restricted to deeper waters (Massana et al, 2000;Galand et al, 2009) and, to a lesser extent, the photic zone (Haro-Moreno et al, 2017). Two major MGII groups, MGIIa and MGIIb , have been identified by their 16S rRNA gene (Massana et al, 2000;Martin-Cuadrado et al, 2008).…”