Phylogenetic Characterization of Marine Benthic Archaea in Organic-Poor Sediments of the Eastern Equatorial Pacific Ocean (ODP Site 1225)

Antje Lauer,Ketil Sørensen,Andreas Teske

doi:10.3390/microorganisms4030032

Abstract

Sequencing surveys of microbial communities in marine subsurface sediments have focused on organic-rich, continental margins; the database for organic-lean deep-sea sediments from mid-ocean regions is underdeveloped. The archaeal community in subsurface sediments of ODP Site 1225 in the eastern equatorial Pacific (3760 m water depth; 1.1 and 7.8 m sediment depth) was analyzed by PCR, cloning and sequencing, and by denaturant gradient gel electrophoresis (DGGE) of 16S rRNA genes. Three uncultured archaeal lineages with different depth distributions were found: Marine Group I (MG-I) within the Thaumarchaeota, its sister lineage Marine Benthic Group A (MBG-A), the phylum-level archaeal lineage Marine Benthic Group B (also known as Deep-Sea Archaeal Group or Lokiarchaeota), and the Deep-Sea Euryarchaeotal Group 3. The MG-I phylotypes included representatives of sediment clusters that are distinct from the pelagic members of this phylum. On the scale from fully oxidized, extremely organic carbon-depleted sediments (for example, those the South Pacific Gyre) to fully reduced, organic carbon-rich marine subsurface sediments (such as those of the Peru Margin), Ocean Drilling Program (ODP) Site 1225 falls into the non-extreme organic carbon-lean category, and harbors archaeal communities from both ends of the spectrum.

Highlights

Molecular surveys of microbial communities in marine subsurface sediments have detected distinct archaeal populations in deep-sea sediments of the central oceanic basins, and near-shore or continental margin locations; these differences most likely reflect the contrasting redox states and organic carbon content of organic-lean, oxidized open-ocean sediments with low sedimentation rates, and organic carbon-rich, reduced coastal and continental margin sediments that receive primary production from the water column and terrestrial input [1,2]
The first Ocean Drilling Program (ODP) expedition dedicated to the study of life deep beneath the seafloor, ODP Leg 201, combined detailed geochemical analyses, cell counts, cultivations, and molecular screening of subsurface microbial communities [7], and succeeded in a comprehensive census of subsurface microbial life in the context of geochemical controls that shape microbial community composition, abundance, and activity [8,9,10,11,12,13,14]
The majority of the clones from the first DNA extraction are affiliated with different subgroups of Marine Group 1 (MG-I), whereas most clones from the second DNA extraction were members of Deep-Sea Archaeal Group/Marine Benthic Group B (DSAG/MBG-B) (Table 2)

Summary

Introduction

Molecular surveys of microbial communities in marine subsurface sediments have detected distinct archaeal populations in deep-sea sediments of the central oceanic basins, and near-shore or continental margin locations; these differences most likely reflect the contrasting redox states and organic carbon content of organic-lean, oxidized open-ocean sediments with low sedimentation rates, and organic carbon-rich, reduced coastal and continental margin sediments that receive primary production from the water column and terrestrial input [1,2]. Subsurface sediment cores were obtained from open ocean sites with organic-poor sediments in the eastern equatorial Pacific (Sites 1225 and 1226) and in the Peru Basin (Site 1231) These sites had cell densities in the range of 105 to 5 × 106 cells/cm below the upper few meters of the sediment column, low organic C content (1%–2% for ODP Site 1226;

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Results

Conclusion