Microbial Sources of Exocellular DNA in the Ocean

Linney, Morgan D.; Eppley, John M.; Romano, Anna E.; Luo, Elaine; DeLong, Edward F.; Karl, David M.

doi:10.1128/aem.02093-21

Cited by 12 publications

(7 citation statements)

References 69 publications

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“…“Tara Oceans virome”: <0.2 µm fraction purified by size filtrations and DNase treatment [ 17 ]. “Heligoland phage Isolates”: DNA extracted from virus isolates, purified by 0.2 µm size filtration [ 41 ]. …”

Section: Resultsmentioning

confidence: 99%

Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

Lücking,

Mercier,

Alarcón-Schumacher

et al. 2023

ISME Communications

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Environmental virus metagenomes, commonly referred to as “viromes”, are typically generated by physically separating virus-like particles (VLPs) from the microbial fraction based on their size and mass. However, most methods used to purify VLPs, enrich extracellular vesicles (EVs) and gene transfer agents (GTAs) simultaneously. Consequently, the sequence space traditionally referred to as a “virome” contains host-associated sequences, transported via EVs or GTAs. We therefore propose to call the genetic material isolated from size-fractionated (0.22 µm) and DNase-treated samples protected environmental DNA (peDNA). This sequence space contains viral genomes, DNA transduced by viruses and DNA transported in EVs and GTAs. Since there is no genetic signature for peDNA transported in EVs, GTAs and virus particles, we rely on the successful removal of contaminating remaining cellular and free DNA when analyzing peDNA. Using marine samples collected from the North Sea, we generated a thoroughly purified peDNA dataset and developed a bioinformatic pipeline to determine the potential origin of the purified DNA. This pipeline was applied to our dataset as well as existing global marine “viromes”. Through this pipeline, we identified known GTA and EV producers, as well as organisms with actively transducing proviruses as the source of the peDNA, thus confirming the reliability of our approach. Additionally, we identified novel and widespread EV producers, and found quantitative evidence suggesting that EV-mediated gene transfer plays a significant role in driving horizontal gene transfer (HGT) in the world’s oceans.

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Section: Resultsmentioning

confidence: 99%

Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

Lücking,

Mercier,

Alarcón-Schumacher

et al. 2023

ISME Communications

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“…The presence of extracellular DNA is an evolutionarily conserved phenomenon that has been observed across diverse life forms, including but not limited to humans 8,101,125,126 , cyanobacteria 127 , plants 128 , and social amoeba, D. discoideum 129 . While the excessive presence of secreted DNA/NETs has been mostly associated with adverse outcomes during various infections and hyper-inflammatory disorders 8 , recent studies suggest otherwise for certain conditions 13,14,16 .…”

Section: Discussionmentioning

confidence: 99%

Neutrophils secrete exosome-associated DNA to resolve sterile acute inflammation

Arya,

Collie,

et al. 2024

Preprint

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Acute inflammation, characterized by a rapid influx of neutrophils, is a protective response that can lead to chronic inflammatory diseases when left unresolved. Secretion of LTB4-containing exosomes is required for effective neutrophil infiltration during inflammation. In this study, we show that neutrophils release nuclear DNA in a non-lytic, rapid, and repetitive manner, via a mechanism distinct from suicidal NET release and cell death. The packaging of nuclear DNA occurs in the lumen of nuclear envelope (NE)-derived multivesicular bodies (MVBs) that harbor the LTB4 synthesizing machinery and is mediated by the lamin B receptor (LBR) and chromatin decondensation. Disruption of secreted exosome-associated DNA (SEAD) in a model of sterile inflammation in mouse skin amplifies and prolongs the presence of neutrophils, impeding the onset of resolution. Together, these findings advance our understanding of neutrophil functions during inflammation and the physiological significance of NETs, with implications for novel treatments for inflammatory disorders.

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“…Alpha diversity indices indicated that sediment samples were richer and more diverse compared to seawater samples (Table 1), possibly due to challenges in extracting sufficient DNA from seawater. While 1 L of seawater was filtered in this study, the yield might have been influenced by the presence of exocellular DNA from viruses and vesicles [27] [28] [29]. A new PCA analysis excluding Chloroplast-related OTUs and seawater samples revealed further differences between the Dutch North Sea and the Danish site in terms of microbial composition.…”

Section: Comparative Analysis Of the Site Distributionmentioning

confidence: 99%

Characterisation of the Bacteria and Archaea Community Associated with Wild Oysters, at Three Possible Restoration Sites in the North Sea

Juste-Poinapen,

Lu,

De Hoyos

et al. 2024

OJMS

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With 85% of the global oyster reefs destroyed, there is an urgent need for large scale restoration to benefit from the ecosystem services provided by biogenic oyster reefs and their associated biodiversity, including microorganisms that drive marine biogeochemical cycles. This experiment established a baseline for the monitoring of the bacterial and archaeal community associated with wild oysters, using samples from their immediate environment of the Voordelta, with cohabiting Crassostrea gigas and Ostrea edulis, Duikplaats with only C. gigas attached to rocks, and the Dansk Skaldyrcentre, with no onsite oysters. The microbial profiling was carried out through DNA analysis of samples collected from the surfaces of oyster shells and their substrate, the sediment and seawater. Following 16S rRNA amplicon sequencing and bioinformatics, alpha indices implied high species abundance and diversity in sediment but low abundance in seawater. As expected, Proteobacteria, Bacteroidetes, Firmicutes and Thaumarchaeota dominated the top 20 OTUs.

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Microbial Sources of Exocellular DNA in the Ocean

Cited by 12 publications

References 69 publications

Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

Neutrophils secrete exosome-associated DNA to resolve sterile acute inflammation

Characterisation of the Bacteria and Archaea Community Associated with Wild Oysters, at Three Possible Restoration Sites in the North Sea

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