Contamination Control for Scientific Drilling Operations

Kallmeyer, Jens

doi:10.1016/bs.aambs.2016.09.003

Cited by 27 publications

(25 citation statements)

References 41 publications

(15 reference statements)

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“…Deep subsurface microbiology studies have demonstrated the importance of contamination detection through the use of tracers (18, 49). Fluorescent latex beads similar in size to microbes have been used extensively in deep subsurface microbiology (e.g.…”

Section: Discussionmentioning

confidence: 99%

“…Applying the tracer to the wrong sampling component or at the wrong time may lead to a false negative, i.e. the presumption that decontamination is complete when the lack of detection of the tracer is actually due to loss during handling (12, 18, 51). Based on our observations, tracer should be applied both to the drilling apparatus and cores in the field and again in the laboratory; application solely in the field led to inconsistent detection of tracer even before decontamination.…”

Section: Discussionmentioning

confidence: 99%

“…Such studies have formalized highly stringent sampling and decontamination protocols, with protocols to minimize contamination and controls to monitor contamination at all stages from sampling to downstream analyses (e.g. (18-24)). Similar approaches may be beneficial for permafrost studies.…”

Section: Introductionmentioning

confidence: 99%

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Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples

Saidi‐Mehrabad

Neuberger

Cavaco

et al. 2020

Preprint

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25This study aims to act as a methodological guide for contamination monitoring, 26 decontamination, and DNA extraction for peaty and silty permafrost samples with low 27 biomass or difficult to extract DNA. We applied a biological tracer, either only in the 28 field or both in the field and in the lab, via either spraying or painting. Spraying in the 29 field followed by painting in the lab resulted in a uniform layer of the tracer on the core 30 sections. A combination of bleaching, washing, and scraping resulted in complete 31 removal of the tracer leaving sufficient material for DNA extraction, while other widely 32 used decontamination methods did not remove all detectable tracer. In addition, of four 33 widely used commercially available DNA extraction kits, only a modified 34ZymoBIOMICS TM DNA Microprep kit was able to acquire PCR amplifiable DNA. 35Permafrost chemical parameters, age, and soil texture did not have an effect on 36 decontamination efficacy; however, the permafrost type did influence DNA extraction. 37Based on these findings, we developed recommendations for permafrost microbiologists 38 to acquire contaminant-free DNA from permafrost with low biomass. 39 IMPORTANCE: 40Permafrost has the capacity to preserve microbial and non-microbial genomic material for 41 millennia; however, major challenges are associated with permafrost samples, including 42 decontamination of samples and acquiring pure DNA. Contamination of samples during 43 coring and post coring handling and processing could affect downstream analyses and 44 interpretations. Despite the use of multiple different decontamination and DNA extraction 45 methods in studies of permafrost, the efficacy of these methods is not well known. We 46 used a biological tracer to test the efficacy of previously published decontamination 47 methods, as well as a bleach-based method we devised, on two chemically and 48 structurally different permafrost core sections. Our method was the only one that 49 removed all detectable tracer. In addition, we tested multiple DNA extraction kits and 50 modified one that is able to acquire pure, PCR amplifiable DNA from silty, and to some 51 extent from peaty, permafrost samples. 52 53 54 55

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples

Saidi‐Mehrabad

Neuberger

Cavaco

et al. 2020

Preprint

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“…Applying the tracer to the wrong sampling component or at the wrong time may lead to a false negative, i.e. the presumption that decontamination is complete when the lack of detection of the tracer is actually due to loss during handling 14,20,53 . Based on our observations, tracer should be applied both to the drilling apparatus and cores in the field and again in the laboratory; application solely in the field led to inconsistent detection of tracer even before decontamination.…”

Section: Discussionmentioning

confidence: 99%

“…Such studies have formalized highly stringent sampling and decontamination protocols, with protocols to minimize contamination and controls to monitor contamination at all stages from sampling to downstream analyses (e.g. 20 – 26 ). Similar approaches may be beneficial for permafrost studies.…”

Section: Introductionmentioning

confidence: 99%

Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples

Saidi‐Mehrabad

Neuberger

Cavaco

et al. 2020

Sci Rep

View full text Add to dashboard Cite

this study aims to act as a methodological guide for contamination monitoring, decontamination, and DNA extraction for peaty and silty permafrost samples with low biomass or difficult to extract DNA. We applied a biological tracer, either only in the field or both in the field and in the lab, via either spraying or painting. Spraying in the field followed by painting in the lab resulted in a uniform layer of the tracer on the core sections. A combination of bleaching, washing, and scraping resulted in complete removal of the tracer leaving sufficient material for DNA extraction, while other widely used decontamination methods did not remove all detectable tracer. in addition, of four widely used commercially available DNA extraction kits, only a modified ZymoBIOMICS DNA Microprep kit was able to acquire PCR amplifiable DNA. Permafrost chemical parameters, age, and soil texture did not have an effect on decontamination efficacy; however, the permafrost type did influence DNA extraction. Based on these findings, we developed recommendations for permafrost researchers to acquire contaminant-free DnA from permafrost with low biomass. Permafrost, i.e. Earth materials below 0 °C for at least two years and up to millions of years, acts as an archive of past environments and ecosystems, preserving biological material as a result of its isolation from atmospheric inputs, low temperatures, and low water activity 1. Ancient DNA derived from long-dead organisms is an important example of such material and has been used for a variety of purposes, ranging from reconstructing human migration patterns to reconstituting the genomes of extinct organisms such as the woolly mammoth and North American horses 2-6. Furthermore, permafrost-dwelling microbes may also play important roles in carbon cycling by conversion of permafrost organic carbon to methane and carbon dioxide, both important greenhouse gasses 7-10. The use of high-throughput sequencing technologies has enriched our understanding of microbial communities in permafrost and ancient DNA. However, these technologies require the extraction of high yields of DNA devoid of contaminants 11. External contamination is particularly problematic in DNA-based approaches due to the high sensitivity in detecting, amplifying and sequencing of DNA. The nature of these contaminants are primarily DNA from humans and background or exogenous DNA of microorganisms 12,13. Obtaining DNA devoid of contaminants from environmental samples, especially from those with low biomass such as permafrost, is often challenging. Such samples are prone to external contamination during drilling and collection in the field and handling in the laboratory, which could lead to misinterpretation of microbial diversity, activity, or ancient DNA studies 14-16. Several methods have been used for permafrost decontamination, such as scraping the outer surface of cores, fracturing of cores followed by clean subsampling from the interior of the core sections (i.e. "disk sampling"), or washing the cores with DNase (e.g. 17...

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