Pangenome Evidence for Extensive Interdomain Horizontal Transfer Affecting Lineage Core and Shell Genes in Uncultured Planktonic Thaumarchaeota and Euryarchaeota

Abstract

Horizontal gene transfer (HGT) is an important force in evolution, which may lead, among other things, to the adaptation to new environments by the import of new metabolic functions. Recent studies based on phylogenetic analyses of a few genome fragments containing archaeal 16S rRNA genes and fosmid-end sequences from deep-sea metagenomic libraries have suggested that marine planktonic archaea could be affected by high HGT frequency. Likewise, a composite genome of an uncultured marine euryarchaeote showed high levels of gene sequence similarity to bacterial genes. In this work, we ask whether HGT is frequent and widespread in genomes of these marine archaea, and whether HGT is an ancient and/or recurrent phenomenon. To answer these questions, we sequenced 997 fosmid archaeal clones from metagenomic libraries of deep-Mediterranean waters (1,000 and 3,000 m depth) and built comprehensive pangenomes for planktonic Thaumarchaeota (Group I archaea) and Euryarchaeota belonging to the uncultured Groups II and III Euryarchaeota (GII/III-Euryarchaeota). Comparison with available reference genomes of Thaumarchaeota and a composite marine surface euryarchaeote genome allowed us to define sets of core, lineage-specific core, and shell gene ortholog clusters for the two archaeal lineages. Molecular phylogenetic analyses of all gene clusters showed that 23.9% of marine Thaumarchaeota genes and 29.7% of GII/III-Euryarchaeota genes had been horizontally acquired from bacteria. HGT is not only extensive and directional but also ongoing, with high HGT levels in lineage-specific core (ancient transfers) and shell (recent transfers) genes. Many of the acquired genes are related to metabolism and membrane biogenesis, suggesting an adaptive value for life in cold, oligotrophic oceans. We hypothesize that the acquisition of an important amount of foreign genes by the ancestors of these archaeal groups significantly contributed to their divergence and ecological success.

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

“…For the second, a pyruvate phosphate dikinase was found that could operate in the catabolic direction, as have been described in some archaea (Tjaden et al, 2006). Similar proteins were also found among the fosmids from the deep Mediterranean libraries (Deschamps et al, 2014) but they were absent in the MG2-GG3 or any other MGII genomic fragment. Therefore, further investigations must be performed in this direction to clarify if the EMP functions in the gluconeogenic direction rather than the glycolytic pathway, as has been proposed for other Archaea (Hutchins et al, 2001;Hallam et al, 2006).…”

“…During a systematic search of a Mediterranean DCM metagenomic fosmid library (Ghai et al, 2010) for rRNA genes, we identified four fosmids (6.2 to 36 to kb in size) containing rRNA sequences classified as MGII, two of them containing 16S rRNA and the other two 23S rRNA genes (Supplementary Figure 1). Interestingly, they had an atypical low GC content (34-40%) compared with the 52% of the assembled MG2-GG3 genome (Iverson et al, 2012) or the MGII fosmids previously described (DeLong et al, 1999;Moreira et al, 2004;Frigaard et al, 2006;Martin-Cuadrado et al, 2008;Rich et al, 2008;Ghai et al, 2010;Deschamps et al, 2014). MGII have the two rRNA genes separated in the genome (Moreira et al, 2004;Martin-Cuadrado et al, 2008), a feature observed also in the Thermoplasmatales and in A. boonei (Ruepp et al, 2000;Moreira et al, 2004).…”

“…The SAG SCGC-AAA-288-C18 from 700 m deep in the central North Pacific also had a low similarity (average 70%). The highest similarities were found with the proteins of the large set of MGII fosmids retrieved from bathypelagic Mediterranean samples (Ionian Sea 3000 m, 324 fosmids; and Adriatic Sea 1000 m, 139 fosmids) (Deschamps et al, 2014). Of the nonredundant thalassoarchaeal proteins 1599 had a hit with Adriatic (38% of their total) and 1850 with the Ionian fosmids.…”

“…This set of proteins was compared separately to the proteins of the MG2-GG3 (1698), A. boonei T469 (1544) and SCGC_AAA288-C18 (398) genomes using a reciprocal best blast hit analysis to identify putative homologs. The same set was also compared with the proteins detected in the bathypelagic fosmids from the KM3 (9946 proteins), AD1000 (4215) and SAT1000 (1301) collections (Deschamps et al, 2014). Previously, all the sequences used in the comparison were annotated using the same methodology as the thalassoarchaeal contigs to avoid methodological discrepancies.…”

“…Sequencing large metagenomic clones provides a powerful strategy for obtaining valuable information about the structure and ecology of uncultured microorganisms (Martin-Cuadrado et al, 2008;Ghai et al, 2013;Deschamps et al, 2014). From a metagenomic library constructed from the biomass recovered at the DCM in the Mediterranean, we sequenced about 7000 fosmid clones (Ghai et al, 2010Mizuno et al, 2013) and we have analyzed the MGII genome fragments present in these fosmids.…”