Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea

Abstract

Archaebacterial halophiles (Haloarchaea) are oxygen-respiring heterotrophs that derive from methanogens--strictly anaerobic, hydrogen-dependent autotrophs. Haloarchaeal genomes are known to have acquired, via lateral gene transfer (LGT), several genes from eubacteria, but it is yet unknown how many genes the Haloarchaea acquired in total and, more importantly, whether independent haloarchaeal lineages acquired their genes in parallel, or as a single acquisition at the origin of the group. Here we have studied 10 haloarchaeal and 1,143 reference genomes and have identified 1,089 haloarchaeal gene families that were acquired by a methanogenic recipient from eubacteria. The data suggest that these genes were acquired in the haloarchaeal common ancestor, not in parallel in independent haloarchaeal lineages, nor in the common ancestor of haloarchaeans and methanosarcinales. The 1,089 acquisitions include genes for catabolic carbon metabolism, membrane transporters, menaquinone biosynthesis, and complexes I-IV of the eubacterial respiratory chain that functions in the haloarchaeal membrane consisting of diphytanyl isoprene ether lipids. LGT on a massive scale transformed a strictly anaerobic, chemolithoautotrophic methanogen into the heterotrophic, oxygen-respiring, and bacteriorhodopsin-photosynthetic haloarchaeal common ancestor.

Fig. 1.

(A) Number of shared genes between 1,078 bacterial genomes and 75 archaebacterial genomes. (B) Types of phylogenetic trees obtained with respect to the relationship of Haloarchaea, nonhalophilic archaea, and eubacterial genes. (C) Types of phylogenetic trees detailed by the number of haloarchaeal taxa.

Fig. 2.

Eubacterial genes in Haloarchaea. (A) Distribution of eubacterial imports present in at least two Haloarchaea. (B) Histogram of phylogenetic splits in imported and recipient trees. (Inset) Statistical test supporting single acquisition of imported eubacterial genes into the haloarchaeal common ancestor (Methods). df, degrees of freedom. Note that incompatible split frequency correlates with topological distance to the reference tree (P = 7·10⁻¹³ for recipient genes, r = 0.76; P = 7·10⁻¹⁹ for the imports), as expected for phylogenetic errors but not for competing biological signals (SI Text). (C) Numbers of eubacterial acquisitions and replacements in the ancestors of haloarchaea (Ha), methanosarcinales (Ms), methanomicrobiales (Mm), and methanocellales (Mc) shown for the reference topology in Fig. 1A and for the alternative topologies with respect to the Ms/Mm/Mc branching order (for unlabeled branches, the number of imports is identical with that shown for the reference topology; numbers of acquisitions and replacements are given in SI Text). Note that the uncultured methanogenic archaeon RC-I is not classified with methanocellales in GenBank taxonomy, but it branched with Methanocella paludicola SANAE in our reference topology, for which reason it was treated as an Mc member here. The frequency distributions of eubacterial imports across genomes and functional categories for haloarchaea is given in Table S1. The numbers of acquisitions and replacements, respectively, for the numbers of imports shown in C are 4: (4, 0); 124: (101, 23); 30: (22, 8); 418: (373, 45); 211: (141, 70); 40: (30, 10); 1,089: (952, 137); 72: (58, 14); and 32: (17, 15). For the methanogens in C, all species names and corresponding frequency distributions for functional categories are given in Table S3.

Fig. 3.

Eubacterial respiratory chain components in Haloarchaea. Green boxes indicate presence of the gene in the corresponding Haloarchaea genome and that the gene is more similar to eubacterial than to archaebacterial homologs in the corresponding phylogenetic trees. Gray boxes indicate that homologs can be detected in the corresponding genome by blast searches, but that the clustering procedure did not included them within the 16,061 archaeal clusters. White boxes indicate that no homolog was detected. (A) Haloarchaeal nuoL sequences are monophyletic but an additional paralogous copy is present in Halorhabdus. (B) Salinibacter has acquired a copy of ndhF from Haloarchaea, which are otherwise monophyletic. (C) Haloarchaeal sdhA sequences are monophyletic but additional paralogous copies of eubacterial origin are present in several genomes (see also Table S4).