Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments

被引:110
作者
Corinaldesi, C. [1 ]
Barucca, M. [2 ]
Luna, G. M. [1 ]
Dell'Anno, A. [1 ]
机构
[1] Polytech Univ Marche, Dept Marine Sci, Fac Sci, I-60131 Ancona, Italy
[2] Polytech Univ Marche, Dept Biochem Biol & Genet, Fac Sci, I-60131 Ancona, Italy
关键词
extracellular DNA; marine sediments; preserved gene sequences; GREEN SULFUR BACTERIA; BLACK-SEA; MARINE-SEDIMENTS; MICROBIAL COMMUNITIES; EUKARYOTIC DIVERSITY; CONTINENTAL-MARGIN; NUCLEIC-ACIDS; HOLOCENE; QUANTIFICATION; OXIDATION;
D O I
10.1111/j.1365-294X.2010.04958.x
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Molecular approaches that target the total DNA pool recovered from permanently anoxic marine ecosystems have revealed an extraordinary diversity of prokaryotes and unicellular eukaryotes. However, the presence of gene sequences contained within the extracellular DNA pool is still largely neglected. We have investigated the preservation, origin and genetic imprint of extracellular DNA recovered from permanently anoxic deep-sea sediments of the Black Sea. Despite high DNase activities, huge amounts of total extracellular DNA were found in both the surface and subsurface sediment layers, suggesting reduced availability of the extracellular DNA pool to nuclease degradation. The reduced degradation of the total extracellular DNA was confirmed by its low decay rate and the high accumulation in the deeper sediment layers. The copy numbers of 16S and 18S rDNA contained within the extracellular DNA pool in both the surface and subsurface sediment layers was very high, indicating that permanently anoxic sediments of the deep Black Sea are hot spots of preserved extracellular gene sequences. The extracellular DNA recovered from these sediment layers also contained highly diversified 18S rDNA sequences. These were not only representative of the major protistan lineages, but also of new very divergent lineages, branching as independent clades at the base of the tree. Our findings indicate that the extracellular DNA pool is a major archive of present/past eukaryotic gene sequences, and they highlight the importance of integrating molecular cell-oriented approaches with molecular analyses of the extracellular DNA pool, for a better assessment of microbial diversity and temporal changes in marine benthic ecosystems.
引用
收藏
页码:642 / 654
页数:13
相关论文
共 57 条
[1]   Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA [J].
Agnelli, A ;
Ascher, J ;
Corti, G ;
Ceccherini, MT ;
Nannipieri, P ;
Pietramellara, G .
SOIL BIOLOGY & BIOCHEMISTRY, 2004, 36 (05) :859-868
[2]   An endobiont-bearing allogromiid from the Santa Barbara Basin: Implications for the early diversification of foraminifera [J].
Bernhard, Joan M. ;
Habura, Andrea ;
Bowser, Samuel S. .
JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, 2006, 111 (G3)
[3]   A marine microbial consortium apparently mediating anaerobic oxidation of methane [J].
Boetius, A ;
Ravenschlag, K ;
Schubert, CJ ;
Rickert, D ;
Widdel, F ;
Gieseke, A ;
Amann, R ;
Jorgensen, BB ;
Witte, U ;
Pfannkuche, O .
NATURE, 2000, 407 (6804) :623-626
[4]  
Calvert SE, 1998, GEOLOGY, V26, P107, DOI 10.1130/0091-7613(1998)026<0107:OCAITH>2.3.CO
[5]  
2
[6]   BINDING OF RECA PROTEIN TO SINGLE-STRANDED NUCLEIC-ACIDS - SPECTROSCOPIC STUDIES USING FLUORESCENT POLYNUCLEOTIDES [J].
CAZENAVE, C ;
TOULME, JJ ;
HELENE, C .
EMBO JOURNAL, 1983, 2 (12) :2247-2251
[7]   217 000-year-old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment [J].
Coolen, Marco J. L. ;
Overmann, Joerg .
ENVIRONMENTAL MICROBIOLOGY, 2007, 9 (01) :238-249
[8]   Vertical distribution of metabolically active eukaryotes in the water column and sediments of the Black Sea [J].
Coolen, Marco J. L. ;
Shtereva, Galina .
FEMS MICROBIOLOGY ECOLOGY, 2009, 70 (03) :525-539
[9]   DNA and lipid molecular stratigraphic records of haptophyte succession in the Black Sea during the Holocene [J].
Coolen, Marco J. L. ;
Saenz, James P. ;
Giosan, Liviu ;
Trowbridge, Nan Y. ;
Dimitrov, Petko ;
Dimitrov, Dimitar ;
Eglinton, Timothy I. .
EARTH AND PLANETARY SCIENCE LETTERS, 2009, 284 (3-4) :610-621
[10]   Identification of organic matter sources in sulfidic late Holocene Antarctic fjord sediments from fossil rDNA sequence analysis [J].
Coolen, Marco J. L. ;
Volkman, John K. ;
Abbas, Ben ;
Muyzer, Gerard ;
Schouten, Stefan ;
Damste, Jaap S. Sinninghe .
PALEOCEANOGRAPHY, 2007, 22 (02)