Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions

Abstract

Marine planktonic archaea are widespread and abundant in deep oceanic waters but, despite their obvious ecological importance, little is known about them. Metagenomic analyses of large genome fragments allow access to both gene content and genome structure from single individuals of these cultivation-reluctant organisms. We present the comparative analysis of 22 archaeal genomic clones containing 16S rRNA genes that were selected from four metagenomic libraries constructed from meso- and bathypelagic plankton of different oceanic regions (South Atlantic, Antarctic Polar Front, Adriatic and Ionian Sea; depths from 500 to 3000 m). We sequenced clones of the divergent archaeal lineages Group 1A (Crenarchaeota) and Group III (Euryarchaeota) as well as clones from the more frequent Group I Crenarchaeota and Group II Euryarchaeota. Whenever possible, we analysed clones that had identical or nearly identical 16S rRNA genes and that were retrieved from distant geographical locations, that is, that defined pan-oceanic operational taxonomic units (OTUs). We detected genes involved in nitrogen fixation in Group 1A Crenarchaeota, and genes involved in carbon fixation pathways and oligopeptide importers in Group I Crenarchaeota, which could confirm the idea that these are mixotrophic. A two-component system resembling that found in ammonia-oxidizing bacteria was found in Group III Euryarchaeota, while genes for anaerobic respiratory chains were detected in Group II Euryarchaeota. Whereas gene sequence conservation was high, and recombination and gene shuffling extensive within and between OTUs in Group I Crenarchaeota, gene sequence conservation was low and global synteny maintained in Group II Euryarchaeota. This implies remarkable differences in genome dynamics in Group I Crenarchaeota and Group II Euryarchaeota with recombination and mutation being, respectively, the dominant genome-shaping forces. These observations, along with variations in GC content, led us to hypothesize that the two groups of organisms have fundamentally different lifestyles.

Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea

“…Phylogenetic analysis of complete fosmid sequences The 21 archaeal fosmids containing 16S rRNA genes used for our analysis are those recently described by Martín-Cuadrado et al (2008). Twenty of them were retrieved by phylogenetic screening of three fosmid libraries constructed from deep-sea planktonic samples: AD1000 (Adriatic Sea, 1000 m depth, seven fosmids), KM3 (Ionian Sea, 3000 m depth, eight fosmids) and SAT1000 (South Atlantic, 1000 m depth, five fosmids).…”

“…In contrast with Thaumarchaeota, these euryarchaeotal groups lack any cultured representative and their metabolic capabilities remain unknown, except for the indication of a possible phototrophic metabolism in group II archaea from surface waters . Group II Euryarchaeota usually appear to be relatively more abundant in surface waters compared with Thaumarchaeota (Karner et al, 2001;Ghai et al, 2010), but they may be abundant in deep-sea waters as well, reaching in some oceanic regions even higher proportions than Thaumarchaeota (Martín-Cuadrado et al, 2008). The much more enigmatic group III Euryarchaeota have been almost exclusively detected in deep-sea plankton, and are found in general in lower abundance than Thaumarchaeota and group II Euryarchaeota (Fuhrman and Davis, 1997;Martín-Cuadrado et al, 2008).…”

“…16S rDNA-containing complete fosmid sequences Archaeal fosmids containing 16S rRNA genes in the different deep-sea metagenomic libraries were identified in a previous work by PCR using specific archaeal primers and fully sequenced (Martín-Cuadrado et al, 2008). Twelve fosmids belonged to Thaumarchaeota and nine to Euryarchaeota (seven to group II and two to group III).…”

“…Phylogenetic analysis of ORF sequences from complete fosmid sequences For each ORF of the 21 archaeal fosmids containing 16S rRNA genes (Martín-Cuadrado et al, 2008), we retrieved its homologues in two steps. First, we carried out a BLASTp (Altschul et al, 1997) search on the non-redundant database at NCBI (http:// www.ncbi.nlm.nih.gov/) with default parameters, except for the max-target-sequences threshold, which was fixed at 1000.…”

“…Taxonomic ascription and phylogenetic analysis of fosmid-end sequences Each fosmid-end DNA sequence was queried using BLASTx (Altschul et al, 1997) against a local sequence database containing all protein sequences encoded by 291 bacterial, 50 archaeal and 53 eukaryotic complete annotated genomes as well as 12 813 amino-acid ORFs predicted from environmental oceanic archaeal BAC and fosmid sequences from various previous works (Béjá et al, 2000b;Hallam et al, 2004;Ló pez-García et al, 2004;Moreira et al, 2004;Martín-Cuadrado et al, 2008). An automated analysis of the 15 best BLASTx hits (counting only one result per species) allowed us to determine the most probable taxonomic origin of the corresponding fosmid-end sequence.…”