Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments

Willerslev, Eske; Hansen, Anders J.; Binladen, Jonas; Brand, Tina B.; Gilbert, M. Thomas P.; Shapiro, Beth; Bunce, Michael; Wiuf, Carsten; Gilichinsky, D.; Cooper, Alan

doi:10.1126/science.1084114

Cited by 559 publications

(491 citation statements)

References 19 publications

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“…Short DNA sequences can persist for long time periods mainly in cold environments with reduced exposure or absence of light (Willerslev et al 2003). This has been observed in studies conducted in old sediments and ice cores (Hofreiter, Mead, Martin, & Poinar, 2003;Willerslev, Capellini, Boomsman, & Nielsen, 2007).…”

Section: Trophic Interactions and Dietary Studiesmentioning

confidence: 83%

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

Díaz-Ferguson

Moyer

2014

RBT

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Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980's and phytoplankton communities in the water column since the early-1990's. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist with an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments. Rev. Biol. Trop. 62 (4): 1273-1284. Epub 2014 December 01.Key words: environmental DNA (eDNA), detection probability, occupancy models, persistence, metabarcode, minibarcode.In order to understand distributions, patterns, and abundances for populations or species, the collection (detection) and identification of individuals from their physical origins must be undertaken. Thus, species detection is fundamental to scientific disciplines such as phylogenetics, conservation biology, and ecology. However, species detection is sometimes extremely difficult especially in marine and aquatic environments where organisms have complex life cycles, and direct observation of early development stages is almost impossible (Ficetola, Miaud, Pompanon, & Taberlet, 2008). Species detection in these environments has been conducted using traditional direct observation methods (visual or acoustic) (Thomsen et al., 2012a). Nonetheless, traditional detection methods can have logistic limitations, be time consuming, expensive, and in some cases, harmful to the environment (e.g., marine bottom trawls, electrofishing and rotenone poisoning) (Thomsen et al., 2012b). The advent of novel molecular and forensic methods have provided innovative tools for detecting marine and aquatic organisms that may circumvent the aforementioned limitations (Darling & Blum, 2007;valentini, Pompano, & Taberlet, 2009;Lodge et al., 2012).One such tool is the detection of an organism's environmental DNA (eDNA). Defined as short DNA fragments that an organism leaves behind in non-living components of the ecosystem (i.e., water, air or sediments), eDNA is derived from either cellular DNA present in epithelial cells released by organisms to the environment through skin, urine, feces or mucus or extracellular DNA that is the DNA in the environment resulting from cell death and subsequent destruction of cell structure (Foote, Thomsen, Sveegaard, Wahlberg, Kielgast, Kyhn, Salling, Galatius, Orlando, & Gilbert, 2012;Taberlet, Coissac, Hajibabaei, & Rieseberg, 2012a). Methodologically, eDNA d...

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Section: Trophic Interactions and Dietary Studiesmentioning

confidence: 83%

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

Díaz-Ferguson

Moyer

2014

RBT

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“…The problem is compounded by the fact that calibration rates are ultimately based on a known fossil record (Doolittle, 1997;Doolittle et al, 1996;Feng et al, 1997;Lee, 1999), and even then rates may vary between lineages (Ochman et al, 1999;Soltis et al, 2002). In addition, there are no reliable reports of 'molecular fossils' that are more than 50-100 million years old (Poinar et al, 1996;Willerslev et al, 2003). Such problems have been highlighted by Sneath (1974) and are beginning to be discussed again.…”

Section: Genome Of R Balticamentioning

confidence: 99%

Taxonomic heterogeneity within the Planctomycetales as derived by DNA–DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emended description of the genus Pirellula

Schlesner

Rensmann

Tindall

et al. 2004

International Journal of Systematic and Evolutionary Microbiology

173

120

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Ninety-seven strains of budding bacteria originating from various aquatic habitats and morphologically resembling planctomycetes were investigated taxonomically. Taxonomic differentiation was based on DNA–DNA hybridization, physiological properties and chemotaxonomic tests. Nineteen hybridization groups, containing 79 of the tested strains, were established. Eighteen strains, however, did not fit into any of these groups. Rhodopirellula baltica gen. nov., sp. nov. is described, with strain SH 1T (=IFAM 1310T=DSM 10527T=NCIMB 13988T) as the type strain. Pirellula marina is transferred to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov., with strain SH 106T (=IFAM 1313T=DSM 3645T=ATCC 49069T) as the type strain. An emended description of the genus Pirellula is also provided. Differentiation between R. baltica, B. marina and Pirellula staleyi was achieved by the integration of morphological, physiological, chemotaxonomic and genetic characteristics.

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“…Soils and sediments often contain DNA that can be amplified by PCR (Hofreiter et al 2003;Willerslev et al 2003) and bacterial DNA sequences have been found in sediments that go back over half a million years (Willerslev et al 2004). Therefore, there is the possibility that DNA bound to minerals (Cleaves et al 2010;Lyon et al 2010) could exist on the Martian surface (Fajardo-Cavazos et al 2010) and be accessible for analysis.…”

Section: Introductionmentioning

confidence: 99%

PCR-based analysis of microbial communities during the EuroGeoMars campaign at Mars Desert Research Station, Utah

Thiel

Ehrenfreund

Foing

et al. 2011

International Journal of Astrobiology

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Abstract:The search for evidence of past or present life on Mars will require the detection of markers that indicate the presence of life. Because deoxyribonucleic acid (DNA) is found in all known living organisms, it is considered to be a 'biosignature' of life. The main function of DNA is the long-term storage of genetic information, which is passed on from generation to generation as hereditary material. The Polymerase Chain Reaction (PCR) is a revolutionary technique which allows a single fragment or a small number of fragments of a DNA molecule to be amplified millions of times, making it possible to detect minimal traces of DNA. The compactness of the contemporary PCR instruments makes routine sample analysis possible with a minimum amount of laboratory space. Furthermore the technique is effective, robust and straightforward. Our goal was to establish a routine for the detection of DNA from micro-organisms using the PCR technique during the EuroGeoMars simulation campaign. This took place at the Mars Society's Mars Desert Research Station (MDRS) in Utah in February 2009 (organized with the support of the International Lunar Exploration Working Group (ILEWG), NASA Ames and the European Space Research and Technology Centre (ESTEC)). During the MDRS simulation, we showed that it is possible to establish a minimal molecular biology lab in the habitat for the immediate on-site analysis of samples by PCR after sample collection. Soil and water samples were taken at different locations and soil depths. The sample analysis was started immediately after the crew returned to the habitat laboratory. DNA was isolated from micro-organisms and used as a template for PCR analysis of the highly conserved ribosomal DNA to identify representatives of the different groups of micro-organisms (bacteria, archaea and eukarya). The PCR products were visualized by agarose gel electrophoresis and documented by transillumination and digital imaging. The microbial diversity in the collected samples was analysed with respect to sampling depth and the presence or absence of vegetation. For the first time, we have demonstrated that it is possible to perform direct on-site DNA analysis by PCR at MDRS, a simulated planetary habitat in an extreme environment that serves as a model for preparation and optimization of techniques to be used for future Mars exploration.

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Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments

Cited by 559 publications

References 19 publications

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

PCR-based analysis of microbial communities during the EuroGeoMars campaign at Mars Desert Research Station, Utah

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