Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin

• Published in: Environmental microbiology 2009-09, Vol.11 (9), p.2446-2462
• Main Authors: Roussel, Erwan G, Sauvadet, Anne-Laure, Chaduteau, Carine, Fouquet, Yves, Charlou, Jean-Luc, Prieur, Daniel, Cambon Bonavita, Marie-Anne
• Format: Article
• Language: English
• Subjects: Archaea; Archaea - classification; Archaea - genetics; Base Sequence; Biodiversity; Biomass; Electrophoresis; Electrophoresis - methods; Geography; Geologic Sediments; Geologic Sediments - chemistry; Geologic Sediments - microbiology; Life Sciences; Microbiology and Parasitology; Molecular Sequence Data; New Caledonia; Oceans and Seas; Oxidoreductases; Oxidoreductases - genetics; Oxidoreductases - metabolism; Pacific Ocean; Phylogeny; RNA, Ribosomal, 16S; RNA, Ribosomal, 16S - analysis; Seawater; Seawater - chemistry; Seawater - microbiology
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/j.1462-2920.2009.01976.x

The distribution of the archaeal communities in deep subseafloor sediments [0-36 m below the seafloor (mbsf)] from the New Caledonia and Fairway Basins was investigated using DNA- and RNA-derived 16S rRNA clone libraries, functional genes and denaturing gradient gel electrophoresis (DGGE). A new method, Co-Migration DGGE (CM-DGGE), was developed to access selectively the active archaeal diversity. Prokaryotic cell abundances at the open-ocean sites were on average ~3.5 times lower than at a site under terrestrial influence. The sediment surface archaeal community (0-1.5 mbsf) was characterized by active Marine Group 1 (MG-1) Archaea that co-occurred with ammonia monooxygenase gene (amoA) sequences affiliated to a group of uncultured sedimentary Crenarchaeota. However, the anoxic subsurface methane-poor sediments (below 1.5 mbsf) were dominated by less active archaeal communities, such as the Thermoplasmatales, Marine Benthic Group D and other lineages probably involved in the methane cycle (Methanosarcinales, ANME-2 and DSAG/MBG-B). Moreover, the archaeal diversity of some sediment layers was restricted to only one lineage (Uncultured Euryarchaeota, DHVE6, MBG-B, MG-1 and SAGMEG). Sequences forming two clusters within the Thermococcales order were also present in these cold subseafloor sediments, suggesting that these uncultured putative thermophilic archaeal communities might have originated from a different environment. This study shows a transition between surface and subsurface sediment archaeal communities.