Preservation of microbial DNA in marine sediments: insights from extracellular DNA pools

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Preservation of microbial DNA in marine sediments : insights from extracellular DNA pools. / Torti, Andrea; Jorgensen, Bo Barker; Lever, Mark Alexander.

In: Environmental Microbiology, Vol. 20, No. 12, 12.2018, p. 4526-4542.

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@article{2ecaddbb2bd74e7881ccc6c00aec6c9f,
title = "Preservation of microbial DNA in marine sediments: insights from extracellular DNA pools",
abstract = "Marine sediments harbour extracellular DNA (exDNA) not associated with currently living organisms. Including this exDNA in genetic surveys may distort abundance and diversity estimates of living prokaryotic communities. We separately extract exDNA and intracellular DNA (inDNA) from 11 horizons in a 10-m deep sediment core from Aarhus Bay (Denmark) that spans > 9000 years of Holocene sedimentation. We compare depth profiles of bacterial and archaeal 16S rRNA gene compositions to those of macrofaunal activity (bioturbation), sulfate and methane concentrations, sediment age and lithology. Among these variables, bioturbation shows the strongest relationship with the two DNA pools. In bioturbated surface sediments, the majority of Operational Taxonomic Units (OTUs) present in exDNA is absent from inDNA, thus belonging to microorganisms that were not alive at the time of sampling. Below the bioturbation zone, the two DNA pools display a much higher phylogenetic similarity. At all depths, the majority of exDNA and inDNA sequences show highest sequence similarities to sediment microorganisms, a finding that is additionally supported by separate analyses on low- and high-molecular weight exDNA. Our results indicate that in Aarhus Bay the vast majority of prokaryotic exDNA is turned over, thus not contributing to a genetic archive of past environmental change.",
keywords = "ORGANIC-MATTER, INTRACELLULAR DNA, ARENICOLA-MARINA, BACTERIAL, SEA, RNA, DEGRADATION, EVOLUTION, SURVIVAL, RATES",
author = "Andrea Torti and Jorgensen, {Bo Barker} and Lever, {Mark Alexander}",
year = "2018",
month = "12",
doi = "10.1111/1462-2920.14401",
language = "English",
volume = "20",
pages = "4526--4542",
journal = "Environmental Microbiology",
issn = "1462-2912",
publisher = "Wiley-Blackwell Publishing Ltd",
number = "12",

}

RIS

TY - JOUR

T1 - Preservation of microbial DNA in marine sediments

T2 - insights from extracellular DNA pools

AU - Torti, Andrea

AU - Jorgensen, Bo Barker

AU - Lever, Mark Alexander

PY - 2018/12

Y1 - 2018/12

N2 - Marine sediments harbour extracellular DNA (exDNA) not associated with currently living organisms. Including this exDNA in genetic surveys may distort abundance and diversity estimates of living prokaryotic communities. We separately extract exDNA and intracellular DNA (inDNA) from 11 horizons in a 10-m deep sediment core from Aarhus Bay (Denmark) that spans > 9000 years of Holocene sedimentation. We compare depth profiles of bacterial and archaeal 16S rRNA gene compositions to those of macrofaunal activity (bioturbation), sulfate and methane concentrations, sediment age and lithology. Among these variables, bioturbation shows the strongest relationship with the two DNA pools. In bioturbated surface sediments, the majority of Operational Taxonomic Units (OTUs) present in exDNA is absent from inDNA, thus belonging to microorganisms that were not alive at the time of sampling. Below the bioturbation zone, the two DNA pools display a much higher phylogenetic similarity. At all depths, the majority of exDNA and inDNA sequences show highest sequence similarities to sediment microorganisms, a finding that is additionally supported by separate analyses on low- and high-molecular weight exDNA. Our results indicate that in Aarhus Bay the vast majority of prokaryotic exDNA is turned over, thus not contributing to a genetic archive of past environmental change.

AB - Marine sediments harbour extracellular DNA (exDNA) not associated with currently living organisms. Including this exDNA in genetic surveys may distort abundance and diversity estimates of living prokaryotic communities. We separately extract exDNA and intracellular DNA (inDNA) from 11 horizons in a 10-m deep sediment core from Aarhus Bay (Denmark) that spans > 9000 years of Holocene sedimentation. We compare depth profiles of bacterial and archaeal 16S rRNA gene compositions to those of macrofaunal activity (bioturbation), sulfate and methane concentrations, sediment age and lithology. Among these variables, bioturbation shows the strongest relationship with the two DNA pools. In bioturbated surface sediments, the majority of Operational Taxonomic Units (OTUs) present in exDNA is absent from inDNA, thus belonging to microorganisms that were not alive at the time of sampling. Below the bioturbation zone, the two DNA pools display a much higher phylogenetic similarity. At all depths, the majority of exDNA and inDNA sequences show highest sequence similarities to sediment microorganisms, a finding that is additionally supported by separate analyses on low- and high-molecular weight exDNA. Our results indicate that in Aarhus Bay the vast majority of prokaryotic exDNA is turned over, thus not contributing to a genetic archive of past environmental change.

KW - ORGANIC-MATTER

KW - INTRACELLULAR DNA

KW - ARENICOLA-MARINA

KW - BACTERIAL

KW - SEA

KW - RNA

KW - DEGRADATION

KW - EVOLUTION

KW - SURVIVAL

KW - RATES

U2 - 10.1111/1462-2920.14401

DO - 10.1111/1462-2920.14401

M3 - Journal article

VL - 20

SP - 4526

EP - 4542

JO - Environmental Microbiology

JF - Environmental Microbiology

SN - 1462-2912

IS - 12

ER -