Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences

Abstract

ABSTRACT. Marine microbial diversity is important yet poorly-known, due to low culturability and undersampling. However, 16s rRNA gene sequences cloned directly from biomass allow us to know what microbial types are present, irrespective of culturing, and to create probes suitable for biodiversity studies. Many sequences are needed for good probe design. Here we report on sequences from 57 deep sea clones, obtained by the polymerase chain reaction with 'universal' primers, from 500 m and 3000 m depths in the northeast Pacific and 1000 m depth in the subtropical Atlantic. The most common group, with 19 of the new sequences (10 Atlantic), was a recently reported crenarchaeal cluster, Group I. We also found 6 sequences in 2 other archaeal groups in the broad methanogen-halophile lineage; 2 of these were in a distinct lineage not previously reported. The bacterial sequences included 22 dispersed among the a and y Proteobacteria (8 related to SAR 1 l), 5 related to a previously reported broad group (Group A) of marine clones poorly affiliated with known (cultured and sequenced) major bacterial divisions, 6 in a second group with little affiliation to any previously reported division (we call this Group B), 1 In a third possible major novel group, 2 deeply branched with~n the 'Green Nonsulfur' lineage, and 1 branching with a soil clone. In contrast to the vast majority of the sequences, a cluster of 5 sequences was very close to a cultured marine proteobacterium, Alterornonas macleod~j. It appeared that 5 of the clones were chimeric, although this label is difficult to apply when sequences are only distantly related to those in the database, as was common. We conclude that the deep sea contains numerous novel and widespread major prokaryotic lineages. Given the huge volume of this habitat and typical bacteria.1 abundances, it appears that the previously unknown archaeal and bacterial groups may be the most abundant organisms on Earth.

Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing

“…This is the first time group III is reported as dominating an archaeal assemblage. Group III Euryarchaeota were first identified in the Northeast Pacific (Fuhrman and Davis 1997) and was later detected in different parts of the Mediterranean Sea (Massana et al, 2000;Martin-Cuadrado et al, 2007, the South Atlantic (Martin-Cuadrado et al, 2007;Ló pez-García et al, 2001) and in the North Pacific Ocean . However, group III is usually rarely represented in marine ecosystems, in which MGI Crenarchaeota and group II Euryarchaeota are the most abundant groups (Massana et al, 2000).…”

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

“…Genome fragments from Group III Euryarchaeota Euryarchaeota Group III was first identified from environmental 16S rRNA gene libraries by Fuhrman and Davis (1997) in samples retrieved from the Northeast Pacific at 500 and 300 m depth, and was later detected at 941 m depth in the Alboran Sea (Mediterranean) (Massana et al, 2000) and at 3000 m depth in the Antarctic Polar Front (Ló pez-García et al, 2001), suggesting that they were specific inhabitants of the deep ocean. Group III members were also detected in metagenomic libraries throughout the ALOHA water column in the Pacific, although at lower frequencies in surface waters .…”

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

“…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).…”

“…The other two groups of marine planktonic archaea, groups II and III are phylogenetically related and branch as sister-group of the Thermoplasmatales within the Euryarchaeota in 16S rDNA phylogenetic trees (DeLong, 1992;Fuhrman and Davis, 1997). 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 .…”