Bacterial gene transfer by natural genetic transformation in the environment.

Lorenz, Michael G.; Wackernagel, Wilfried

doi:10.1128/mmbr.58.3.563-602.1994

Cited by 864 publications

(577 citation statements)

References 230 publications

(436 reference statements)

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“…Adsorptive binding to hydroxyapatite retards the spontaneous decay of DNA (Lindahl, 1993). In addition to spontaneous hydrolysis, microbial DNase activity leads to rapid degradation of free DNA in water and sediments (Lorenz and Wackernagel, 1994), but is also effectively prevented by adsorption even in sandy sediments which bind DNA much less efficiently than the sapropels (Romanowski et al, 1991;Crecchio and Stotzky, 1998). Based on our results, the outstanding adsorption capacity of eastern Mediterranean sediments, in particular of the sapropel matrix, represents the major reason for the efficient preservation of fossil DNA of green sulfur bacteria.…”

Section: Authenticity Of the Green Sulfur Bacterial Dnamentioning

confidence: 99%

217 000‐year‐old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment

Coolen

Overmann

2006

Environmental Microbiology

110

113

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Summary Deep‐sea sediments of the eastern Mediterranean harbour a series of dark, organic carbon‐rich layers, so‐called sapropels. Within these layers, the carotenoid isorenieratene was detected. Since it is specific for the obligately anaerobic phototrophic green sulfur bacteria, the presence of isorenieratene may suggest that extended water column anoxia occurred in the ancient Mediterranean Sea during periods of sapropel formation. Only three carotenoids (isorenieratene, β‐isorenieratene and chlorobactene) are typical for green sulfur bacteria and thus do not permit to differentiate between the ∼80 known phylotypes. In order to reconstruct the paleoecological conditions in more detail, we searched for fossil 16S rRNA gene sequences of green sulfur bacteria employing ancient DNA methodology. 540 bp‐long fossil sequences could indeed be amplified from up to 217 000‐year‐old sapropels. In addition, such sequences were also recovered from carbon‐lean intermediate sediment layers deposited during times of an entirely oxic water column. Unexpectedly, however, all the recovered 16S rRNA gene sequences grouped with freshwater or brackish, rather than truly marine, types of green sulfur bacteria. It is therefore feasible that the molecular remains of green sulfur bacteria originated from populations which thrived in adjacent freshwater or estuarine coastal environments rather than from an indigenous pelagic population.

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Section: Authenticity Of the Green Sulfur Bacterial Dnamentioning

confidence: 99%

217 000‐year‐old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment

Coolen

Overmann

2006

Environmental Microbiology

110

113

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“…The biotic mediated decay conducted by microbial communities in marine ecosystems play a large part in the turnover of DNA, a process known as natural transformation (Lorenz & Wackernagel, 1994;Pietramellara et al, 2009). A broad variety of microorganisms in marine ecosystems have the physiological ability to take up DNA during normal growth, including both free extracellular DNA, DNA associated with particles, cellular debris, inactivated and even living cells (Paul, Jeffrey, & DeFlaun, 1987;Pietramellara et al, 2009).…”

Section: Degradationmentioning

confidence: 99%

The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries

et al. 2018

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Application of environmental DNA (eDNA) analysis has attracted the attention of researchers, advisors and managers of living marine resources and biodiversity. The apparent simplicity and cost‐effectiveness of eDNA analysis make it highly attractive as species distributions can be revealed from water samples. Further, species‐specific analyses indicate that eDNA concentrations correlate with biomass and abundance, suggesting the possibility for quantitative applications estimating abundance and biomass of specific organisms in marine ecosystems, such as for stock assessment. However, the path from detecting occurrence of an organism to quantitative estimates is long and indirect, not least as eDNA concentration depends on several physical, chemical and biological factors which influence its production, persistence and transport in marine ecosystems. Here, we provide an overview of basic principles in relation to eDNA analysis with potential for marine fisheries application. We describe fundamental processes governing eDNA generation, breakdown and transport and summarize current uncertainties about these processes. We describe five major challenges in relation to application in fisheries assessment, where there is immediate need for knowledge building in marine systems, and point to apparent weaknesses of eDNA compared to established marine fisheries monitoring methods. We provide an overview of emerging applications of interest to fisheries management and point to recent technological advances, which could improve analysis efficiency. We advise precaution against exaggerating the present scope for application of eDNA analysis in fisheries monitoring, but also argue that with informed insights into strengths and limitations, eDNA analysis can become an integrated tool in fisheries assessment and management.

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“…Little is known about the mechanisms for natural gene transfer in cyanobacteria, which may enable genetic recombination in M. chthonoplastes. For cyanobacteria mainly the uptake of free DNA through natural transformation has been studied in detail (Lorenz and Wackernagel, 1994). Cyanophages common in the marine environment (Mann, 2003) may shuttle DNA through transduction and promote cyanobacterial diversification (Weinbauer and Rassoulzadegan, 2004).…”

Section: Recombination Within M Chthonoplastesmentioning

confidence: 99%

Frequent genetic recombination in natural populations of the marine cyanobacterium Microcoleus chthonoplastes

Lodders

Stackebrandt

Nübel

2005

Environmental Microbiology

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A culture-independent method for multilocus sequence typing of Microcoleus chthonoplastes was developed based on mechanical separation of individual cyanobacterial filaments from natural microbial mat populations through micromanipulation, subsequent polymerase chain reaction (PCR) amplification and sequence analysis of three genetic loci (kaiC, petB/D, rDNA-ITS). Among 81 individuals sampled from intertidal sand flats of the North Sea and Baltic Sea, we found 8-14 different sequences (alleles) per genetic locus, resulting in 36 distinct genotypes with unique allele profiles. Non-congruent phylogenetic gene trees for the three loci analysed and split decomposition analysis indicated the occurrence of horizontal genetic exchange. The index of association determined for the entire population was 0.096, indicating that recombination occurs frequently enough to cause almost random association (linkage equilibrium) among alleles. Analysing individuals from three different locations in the North Sea and Baltic Sea, we did not find evidence for geographic subdivisions between populations.

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Bacterial gene transfer by natural genetic transformation in the environment.

Cited by 864 publications

References 230 publications

217 000‐year‐old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment

217 000‐year‐old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment

The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries

Frequent genetic recombination in natural populations of the marine cyanobacterium Microcoleus chthonoplastes

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