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PALEOCEANOGRAPHY, VOL. 22, PA2211, doi:10.1029/2006PA001309, 2007

Identification of organic matter sources in sulfidic late Holocene Antarctic fjord sediments from fossil rDNA sequence analysis

Marco J. L. Coolen

Department of Marine Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands


John K. Volkman

CSIRO Marine and Atmospheric Research, Hobart, Tasmania, Australia


Ben Abbas

Department of Marine Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands


Gerard Muyzer

Department of Marine Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands


Stefan Schouten

Department of Marine Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands


Jaap S. Sinninghe Damsté

Department of Marine Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands


Abstract

The 18S ribosomal DNA (rDNA) isolated from sulfidic Holocene sediments and particulate organic matter in the water column of the stratified Small Meromictic Basin (SMB) in Ellis Fjord (eastern Antarctica) was analyzed to identify possible biological sources of organic matter. Previous work had shown that the sediments contained numerous diatom frustules and high contents of a highly branched isoprenoid (HBI) C25:2 alkene (which is a specific biomarker of certain species of the diatom genera Navicula, Haslea, Pleurosigma, or Rhizosolenia), so we focused our search on preserved fossil 18S rDNA of diatoms using sensitive polymerase chain reaction (PCR) approaches. We did not find diatom-derived fossil 18S rDNA using general eukaryotic primers, and even when we used primers selective for diatom 18S rDNA, we only identified a Chaetoceros phylotype, which is known to form cysts in the SMB but is not a likely source of the C25:2 HBI. When we used PCR/denaturing gradient gel electrophoresis methods specific to phylotypes within the HBI-biosynthesizing genera, we were able to identify three phylotypes in the sediments related to HBI-producing strains of the genera Haslea and Navicula. The ancient DNA data thus provided a limited, but valuable, view of the diversity of late Holocene primary producers with a particular bias to specific components of the biota that were better preserved such as the Chaetoceros cysts. This use of paleogenetics also revealed unexpected possible sources of organic matter such as novel stramenopiles for which no specific lipid biomarkers are known and thus would not have been identified based on traditional lipid stratigraphy alone.

Received 27 April 2006; accepted 19 November 2006; published 9 May 2007.

Keywords: ancient DNA; diatoms; Ellis Fjord.

Index Terms: 0424 Biogeosciences: Biosignatures and proxies; 0404 Biogeosciences: Anoxic and hypoxic environments (4802, 4834); 1055 Geochemistry: Organic and biogenic geochemistry; 9310 Geographic Location: Antarctica (4207); 4950 Paleoceanography: Paleoecology.

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Citation: Coolen, M. J. L., J. K. Volkman, B. Abbas, G. Muyzer, S. Schouten, and J. S. Sinninghe Damsté (2007), Identification of organic matter sources in sulfidic late Holocene Antarctic fjord sediments from fossil rDNA sequence analysis, Paleoceanography, 22, PA2211, doi:10.1029/2006PA001309.