Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis

Rochelle, Paul A., Cragg, Barry Andrew, Fry, John Christopher, Parkes, Ronald John and Weightman, Andrew John ORCID: https://orcid.org/0000-0002-6671-2209 1994. Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiology Ecology 15 (1-2) , pp. 215-225. 10.1111/j.1574-6941.1994.tb00245.x

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Abstract

The diversity of bacterial communities in deep marine sediments, up to 503 metres below the sea floor of the Japan Sea, was investigated by sequence analysis of amplified 16S rRNA genes. The use of different sample handling procedures greatly affected the types and diversity of sequences obtained. DNA from sediment samples stored aerobically for up to 24 h before freezing was dominated by sequences belonging to the β- and γ-proteobacteria, many of which appeared to originate from aerobic bacteria. Sub-samples equilibrated anaerobically at 16°C, were then injected with a radiotracer and immediately frozen, to simulate the conditions of a typical control sample from a radiotracer based activity assay, contained mostly α-proteobacterial sequences. Pristine sediment samples taken anaerobically and frozen within 2 h contained the widest diversity of sequences from α-, γ-, δ-proteobacteria and Gram-positive bacteria, which appeared to have originated from predominantly anaerobic or facultative bacteria. It was clear that both samples that were not frozen immediately (within 2 h) showed signs of enrichment of specific bacterial groups. Our results strongly suggest that immediate freezing should always be employed when sediment samples are to be used to assess bacterial diversity by molecular methods.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Biosciences Earth and Environmental Sciences
Subjects:	Q Science > QR Microbiology
Uncontrolled Keywords:	Community diversity; 16S rRNA gene; Marine sediment; Sequence diversity
Publisher:	Wiley-Blackwell
ISSN:	0168-6496
Last Modified:	18 Oct 2022 12:18
URI:	https://orca.cardiff.ac.uk/id/eprint/9308

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