Brierley AS, Kingsford MJ. Impacts of climate change on marine organisms and ecosystems. Curr Biol. 2009;19:R602–R614.
Google Scholar
Gissi E, Manea E, Mazaris AD, Fraschetti S, Almpanidou V, Bevilacqua S, et al. A review of the combined effects of climate change and other local human stressors on the marine environment. Sci Total Environ. 2021;755:142564.
Google Scholar
Carella F, Antuofermo E, Farina S, Salati F, Mandas D, Prado P, et al. In the wake of the ongoing mass mortality events: co-occurrence of Mycobacterium, Haplosporidium and other pathogens in Pinna nobilis collected in Italy and Spain (Mediterranean Sea). Front Mar Sci. 2020;7:48.
Google Scholar
Seuront L, Nicastro KR, Zardi GI, Goberville E. Decreased thermal tolerance under recurrent heat stress conditions explains summer mass mortality of the blue mussel Mytilus edulis. Sci Rep. 2019;9:17498.
Google Scholar
Fey SB, Siepielski AM, Nussle S, Cervantes-Yoshida K, Hwan JL, Huber ER, et al. Recent shifts in the occurrence, cause, and magnitude of animal mass mortality events. Proc Natl Acad Sci USA. 2015;112:1083–8.
Google Scholar
Scarpa F, Sanna D, Azzena I, Mugetti D, Cerruti F, Hosseini S, et al. Multiple non-species-specific pathogens possibly triggered the mass mortality in Pinna nobilis. Life. 2020;10:238.
Google Scholar
Bradley M, Kutz SJ, Jenkins E, O’Hara TM. The potential impact of climate change on infectious diseases of Arctic fauna. Int J Circumpolar Health. 2005;64:468–77.
Google Scholar
Beyer J, Green NW, Brooks S, Allan IJ, Ruus A, Gomes T, et al. Blue mussels (Mytilus edulis spp.) as sentinel organisms in coastal pollution monitoring: a review. Mar Environ Res. 2017;130:338–65.
Google Scholar
Siravegna G, Marsoni S, Siena S, Bardelli A. Integrating liquid biopsies into the management of cancer. Nat Rev Clin Oncol. 2017;14:531–48.
Google Scholar
Wan JCM, Massie C, Garcia-Corbacho J, Mouliere F, Brenton JD, Caldas C, et al. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer. 2017;17:223–38.
Google Scholar
Mandel P, Metais P. Nuclear acids in human blood plasma. Comptes Rendus Séances Soc Biol Filiales. 1948;142:241–3.
Google Scholar
Bronkhorst AJ, Ungerer V, Holdenrieder S. The emerging role of cell-free DNA as a molecular marker for cancer management. Biomol Detect Quantif. 2019;17:100087.
Google Scholar
Ignatiadis M, Sledge GW, Jeffrey SS. Liquid biopsy enters the clinic – implementation issues and future challenges. Nat Rev Clin Oncol. 2021;18:297–312.
Google Scholar
Lo YM, Corbetta N, Chamberlain PF, Rai V, Sargent IL, Redman CW, et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997;350:485–7.
Google Scholar
Moufarrej MN, Wong RJ, Shaw GM, Stevenson DK, Quake SR. Investigating pregnancy and its complications using circulating cell-free RNA in women’s blood during gestation. Front Pediatr. 2020;8:605219.
Google Scholar
Oellerich M, Sherwood K, Keown P, Schutz E, Beck J, Stegbauer J, et al. Liquid biopsies: donor-derived cell-free DNA for the detection of kidney allograft injury. Nat Rev Nephrol. 2021;17:591–603.
Google Scholar
Wong FC, Lo YM. Prenatal diagnosis innovation: genome sequencing of maternal plasma. Annu Rev Med. 2016;67:419–32.
Google Scholar
Gu W, Deng X, Lee M, Sucu YD, Arevalo S, Stryke D, et al. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nat Med. 2021;27:115–24.
Google Scholar
Huang YF, Chen YJ, Fan TC, Chang NC, Chen YJ, Midha MK, et al. Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females. BMC Med Genom. 2018;11:16.
Google Scholar
Goggs R, Jeffery U, LeVine DN, Li RHL. Neutrophil-extracellular traps, cell-free DNA, and immunothrombosis in companion animals: a review. Vet Pathol. 2020;57:6–23.
Google Scholar
Kowarsky M, De Vlaminck I, Okamoto J, Neff NF, LeBreton M, Nwobegabay J, et al. Cell-free DNA reveals potential zoonotic reservoirs in non-human primates. BioRxiv. 2018;481093.
Caza F, Bernet E, Veyrier FJ, Betoulle S, St-Pierre Y. Hemocytes released in seawater act as Trojan horses for spreading of bacterial infections in mussels. Sci Rep. 2020;10:19696.
Google Scholar
Andrew S. FastQC: a quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Google Scholar
Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27:2957–63.
Google Scholar
Morgulis A, Gertz EM, Schäffer AA, Agarwala R. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. Comput Biol. 2006;13:1028–40.
Google Scholar
Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.
Google Scholar
Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15:R46.
Google Scholar
Cuccuru G, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, et al. Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics. 2014;30:1928–9.
Google Scholar
Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinform. 2011;12:385.
Google Scholar
Lüskow F, Riisgård H. In situ filtration rates of blue mussels (Mytilus edulis) measured by an open-top chamber method. OJMS. 2018;8:395–406.
Google Scholar
Szpechcinski A, Struniawska R, Zaleska J, Chabowski M, Orlowski T, Roszkowski K, et al. Evaluation of fluorescence-based methods for total vs. amplifiable DNA quantification in plasma of lung cancer patients. J Physiol Pharmacol. 2008;59:675–81.
Google Scholar
Tissot C, Toffart AC, Villar S, Souquet PJ, Merle P, Moro-Sibilot D, et al. Circulating free DNA concentration is an independent prognostic biomarker in lung cancer. Eur Respir J. 2015;46:1773–80.
Google Scholar
Kustanovich A, Schwartz R, Peretz T, Grinshpun A. Life and death of circulating cell-free DNA. Cancer Biol Ther. 2019;20:1057–67.
Google Scholar
Prouteau A, Denis JA, De Fornel P, Cadieu E, Derrien T, Kergal C, et al. Circulating tumor DNA is detectable in canine histiocytic sarcoma, oral malignant melanoma, and multicentric lymphoma. Sci Rep. 2021;11:877.
Google Scholar
Vandewoestyne M, Van Hoofstat D, Franssen A, Van Nieuwerburgh F, Deforce D. Presence and potential of cell free DNA in different types of forensic samples. For Sci Int Genet. 2013;7:316–20.
Google Scholar
Kowarsky M, Camunas-Soler J, Kertesz M, De Vlaminck I, Koh W, Pan W, et al. Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA. Proc Natl Acad Sci USA. 2017;114:9623–8.
Google Scholar
Meddeb R, Dache ZAA, Thezenas S, Otandault A, Tanos R, Pastor B, et al. Quantifying circulating cell-free DNA in humans. Sci Rep. 2019;9:5220.
Google Scholar
Li YF, Yang N, Liang X, Yoshida A, Osatomi K, Power D, et al. Elevated seawater temperatures decrease microbial diversity in the gut of Mytilus coruscus. Front Physiol. 2018;9:839.
Google Scholar
Musella M, Wathsala R, Tavella T, Rampelli S, Barone M, Palladino G, et al. Tissue-scale microbiota of the Mediterranean mussel (Mytilus galloprovincialis) and its relationship with the environment. Sci Total Environ. 2020;717:137209.
Google Scholar
Thompson JR, Randa MA, Marcelino LA, Tomita-Mitchell A, Lim E, Polz MF. Diversity and dynamics of a north atlantic coastal Vibrio community. Appl Environ Microbiol. 2004;70:4103–10.
Google Scholar
Pfister CA, Meyer F, Antonopoulos DA. Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling. PLoS One. 2010;5:e10518.
Google Scholar
Galand PE, Casamayor EO, Kirchman DL, Potvin M, Lovejoy C. Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing. ISME J. 2009;3:860–9.
Google Scholar
Korzhenkov AA, Toshchakov SV, Bargiela R, Gibbard H, Ferrer M, Teplyuk AV, et al. Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity. Microbiome. 2019;7:11.
Google Scholar
Spain EA, Johnson SC, Hutton B, Whittaker JM, Lucieer V, Watson SJ, et al. Shallow seafloor gas emissions near Heard and McDonald Islands on the Kerguelen Plateau, southern Indian Ocean. Earth Space Sci. 2020;7:e2019EA000695.
Google Scholar
Farías L, Florez-Leiva L, Besoain V, Sarthou G, Fernández C. Dissolved greenhouse gases (nitrous oxide and methane) associated with the naturally iron-fertilized Kerguelen region (KEOPS 2 cruise) in the Southern Ocean. Biogeosciences. 2015;12:1925–40.
Google Scholar
Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, et al. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc Natl Acad Sci USA. 2014;111:4274–9.
Google Scholar
Levasseur A, Andreani J, Delerce J, Bou Khalil J, Robert C, La Scola B, et al. Comparison of a modern and fossil pithovirus reveals its genetic conservation and evolution. Genome Biol Evol. 2016;8:2333–9.
Google Scholar
Kelley JL, Brown AP, Therkildsen NO, Foote AD. The life aquatic: advances in marine vertebrate genomics. Nat Rev Genet. 2016;17:523–34.
Google Scholar
Colmer SF, Luethy D, Abraham M, Stefanovski D, Hurcombe SD. Utility of cell-free DNA concentrations and illness severity scores to predict survival in critically ill neonatal foals. PLoS One. 2021;16:e0242635.
Google Scholar
Rushton JG, Ertl R, Klein D, Tichy A, Nell B. Circulating cell-free DNA does not harbour a diagnostic benefit in cats with feline diffuse iris melanomas. J Feline Med Surg. 2019;21:124–32.
Google Scholar
Tagawa M, Shimbo G, Inokuma H, Miyahara K. Quantification of plasma cell-free DNA levels in dogs with various tumors. J Vet Diagn Investig. 2019;31:836–43.
Google Scholar
Shi J, Zhang R, Li J, Zhang R. Size profile of cell-free DNA: a beacon guiding the practice and innovation of clinical testing. Theranostics. 2020;10:4737–48.
Google Scholar
Fernando MR, Jiang C, Krzyzanowski GD, Ryan WL. Analysis of human blood plasma cell-free DNA fragment size distribution using EvaGreen chemistry based droplet digital PCR assays. Clin Chim Acta. 2018;483:39–47.
Google Scholar
Findlay AJ. Microbial impact on polysulfide dynamics in the environment. FEMS Microbiol Lett. 2016;363:fnw103.
Google Scholar
Jørgensen BB, Findlay AJ, Pellerin A. The biogeochemical sulfur cycle of marine sediments. Front Microbiol. 2019;10:849.
Google Scholar
Teske A, Brinkhoff T, Muyzer G, Moser DP, Rethmeier J, Jannasch HW. Diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents. Appl Environ Microbiol. 2000;66:3125–33.
Google Scholar
Zhang X, Du Z, Zheng R, Luan Z, Qi F, Cheng K, et al. Development of a new deep-sea hybrid Raman insertion probe and its application to the geochemistry of hydrothermal vent and cold seep fluids. Deep Sea Res Part I Oceanogr Res Pap. 2017;123:1–12.
Google Scholar
Egger M, Riedinger N, Mogollón JM, Jørgensen BB. Global diffusive fluxes of methane in marine sediments. Nat Geosci. 2018;11:421–5.
Google Scholar
Ansorge R, Romano S, Sayavedra L, Kupczok A, Tegetmeyer HE, Dubilier N, et al. Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels. Nat Microbiol. 2019;4:2487–97.
Google Scholar
Russell SL, Pepper-Tunick E, Svedberg J, Byrne A, Ruelas Castillo J, Vollmers C, et al. Horizontal transmission and recombination maintain forever young bacterial symbiont genomes. PLoS Genet. 2020;16:e1008935.
Google Scholar
Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, et al. The marine viromes of four oceanic regions. PLoS Biol. 2006;4:e368.
Google Scholar
Li Z, Pan D, Wei G, Pi W, Zhang C, Wang JH, et al. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. ISME J. 2021;15:2366–78.
Google Scholar
Thongsripong P, Chandler JA, Kittayapong P, Wilcox BA, Kapan DD, Bennett SN. Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes. Sci Rep. 2021;11:8448.
Google Scholar
Koonin EV, Krupovic M, Agol VI. The Baltimore classification of viruses 50 years later: how does it stand in the light of virus evolution? Microbiol Mol Biol Rev. 2021;85:e0005321.
Google Scholar
Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, et al. Global organization and proposed megataxonomy of the virus world. Microbiol Mol Biol Rev. 2020;84:e00061–19.
Google Scholar
Breitbach S, Tug S, Simon P. Circulating cell-free DNA: an up-coming molecular marker in exercise physiology. Sports Med. 2012;42:565–86.
Google Scholar
Preissner KT, Herwald H. Extracellular nucleic acids in immunity and cardiovascular responses: between alert and disease. Thromb Haemost. 2017;117:1272–82.
Google Scholar
Schwarzenbach H. Circulating nucleic acids as biomarkers in breast cancer. Breast Cancer Res. 2013;15:211.
Google Scholar
Murphy DJ. Freezing resistance in intertidal invertebrates. Annu Rev Physiol. 1983;45:289–99.
Google Scholar
Robledo JAF, Yadavalli R, Allam B, Espinosa EP, Gerdol M, Greco S, et al. From the raw bar to the bench: bivalves as models for human health. Dev Comp Immunol. 2019;92:260–82.
Google Scholar
Cowart DA, Murphy KR, Cheng CC. Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula. Mar Genom. 2018;37:148–60.
Google Scholar
Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, et al. Ancient plant DNA in lake sediments. New Phytol. 2017;214:924–42.
Google Scholar
Mariani S, Baillie C, Giuliano C, Riesgo A. Sponges as natural environmental DNA samplers. Curr Biol. 2019;29:R401–R402.
Google Scholar
Weber S, Brink L, Wörner M, Künzel S, Veith M, Teubner D, et al. Molecular diet analysis in zebra and quagga mussels (Dreissena spp.) and an assessment of the utility of aquatic filter feeders as biological eDNA filters. BioRxiv. 2021; 432951.
Caza F, Joly de Boissel PG, Villemur R, Betoulle S, St-Pierre Y. Liquid biopsies for omics-based analysis in sentinel mussels. Plos One. 2019;14:e0223525.
Google Scholar
Hunter ME, Ferrante JA, Meigs-Friend G, Ulmer A. Improving eDNA yield and inhibitor reduction through increased water volumes and multi-filter isolation techniques. Sci Rep. 2019;9:5259.
Google Scholar
Burkhardt W III, Calci KR. Selective accumulation may account for shellfish-associated viral illness. Appl Environ Microbiol. 2000;66:1375–8.
Google Scholar
Di Girolamo R, Liston J, Matches J. Ionic bonding, the mechanism of viral uptake by shellfish mucus. Appl Environ Microbiol. 1977;33:19–25.
Google Scholar
Metzger MJ, Reinisch C, Sherry J, Goff SP. Horizontal transmission of clonal cancer cells causes leukemia in soft-shell clams. Cell. 2015;161:255–63.
Google Scholar
Metzger MJ, Villalba A, Carballal MJ, Iglesias D, Sherry J, Reinisch C, et al. Widespread transmission of independent cancer lineages within multiple bivalve species. Nature. 2016;534:705–9.
Google Scholar
Canesi L, Gallo G, Gavioli M, Pruzzo C. Bacteria–hemocyte interactions and phagocytosis in marine bivalves. Microsc Res Tech. 2002;57:469–76.
Google Scholar
Andruszkiewicz EA, Koseff JR, Fringer OB, Ouellette NT, Lowe AB, Edwards CA, et al. Modeling environmental DNA transport in the coastal ocean using Lagrangian particle tracking. Front Mar Sci. 2019;6:477.
Google Scholar
Wood ZT, Lacoursière-Roussel A, LeBlanc F, Trudel M, Kinnison MT, Garry McBrine C, et al. Spatial heterogeneity of eDNA transport improves stream assessment of threatened salmon presence, abundance, and location. Front Ecol Evol. 2021;9:650717.
Google Scholar
Rand AC, Jain M, Eizenga JM, Musselman-Brown A, Olsen HE, Akeson M, et al. Mapping DNA methylation with high-throughput nanopore sequencing. Nat Methods. 2017;14:411–3.
Google Scholar
Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W. Detecting DNA cytosine methylation using nanopore sequencing. Nat Methods. 2017;14:407–10.
Google Scholar
Cavalli G, Heard E. Advances in epigenetics link genetics to the environment and disease. Nature. 2019;571:489–99.
Google Scholar
Fan G, Song Y, Yang L, Huang X, Zhang S, Zhang M, et al. Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K). Gigascience. 2020;9:giaa080.
Google Scholar
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