Bacterial and Archaeal 16S rRNA Genes in Late Pleistocene to Holocene Muddy Sediments from the Kanto Plain of Japan

Abstract

Microbial communities in ancient marine sediments composed of clay and silt obtained from the terrestrial subsurface were phylogenetically analyzed based on their 16S rRNA gene sequences. Chloroflexi and Miscellaneous Crenarchaeotic Group were predominant in bacterial and archaeal clone libraries, respectively. Of 44 operational taxonomic units (OTUs) that had close relatives in the database, 30 were close to sequences obtained from marine environments. Some sequences belonged to the candidate groups JS1, ANME-I, and Marine Benthic Group-C, which are typically found in marine sediments. Low chloride concentrations in the sediments suggest that these marine-affiliated sequences may not reflect currently active microbial communities. Our results indicate the existence of long-term preserved DNA or descendants of ancient oceanic microbial components in subsurface muddy sediments in a temperate region, which may reflect indigenous population of paleoenvironments.

Keywords:

• microbial community
• 16S rRNA gene
• Holocene sediments
• muddy sediments
• extra cellular DNA

This research was partially supported by a grant from the Ministry of Education, Science, Sports and Culture of Japan, Grant-in-Aid for Young Scientists (B), 19740315, 2007. We thank Maki Sugihara and Haruka Urakawa for their technical assistance, and we deeply appreciate the kind cooperation of Dr. Yuji Sekiguchi, AIST for phylogenetic analysis.

Notes

∗Not determined.

∗∗No PCR product was obtained.