Contamination tracer testing with seabed drills:  IODP Expedition 357

Orcutt, Beth N.; Bergenthal, Markus; Freudenthal, Tim; Smith, David C.; Lilley, Marvin D.; Schnieders, Luzie; Green, Sophie M.; Früh-Green, Gretchen L.

doi:10.5194/sd-23-39-2017

Cited by 15 publications

(28 citation statements)

References 16 publications

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“…Many precautions were taken during handling of the rock core samples to minimize, eliminate, and detect contamination, and our results agree with previous reports that these efforts were generally successful (20,57,58). 295…”

Section: Serpentinite Samples Have Minimal Environmental Contaminationsupporting

confidence: 92%

“…The contribution of seawater DNA sequences into the serpentinites was minimal (Figure 3), further demonstrating that the sampling-handling precautions on the ship and at the Kochi Core Center were successful in eliminating environmental contamination that must have occurred at some level during core recovery on the seafloor. In addition, our 315 results agree with those of Orcutt et al (57) that there was no noticeable difference in contamination levels between rocks whose outer surfaces had been subjected to flame sterilization compared to those that were not flamed.…”

Section: Serpentinite Samples Have Minimal Environmental Contaminationsupporting

confidence: 91%

“…To assess environmental contamination of the cores, perfluoromethylcyclohexane (PFC) was injected into the seabed drilling fluids during coring. Orcutt et al (57) reported that the interior zones of rocks whose outer surfaces had been shaved off with a sterile rock saw had greatly reduced levels of PFC. Only one sample in our 300 study (0AMRd073), whose exterior had been shaved, contained detectable levels of PFC.…”

Section: Serpentinite Samples Have Minimal Environmental Contaminationmentioning

confidence: 99%

“…Two additional samples (0AMRd030, 0AMRd036), which were too rubbly to be shaved with the rock saw and were instead washed with ultrapure water, contained detectable PFC. In general, however, washing rubbly samples with ultrapure water was largely effective in reducing the level of PFC, and presumably of any other 305 surface contamination (57). The PFC tracer, however, was not designed to track any seawater contamination that might have occurred after drilling or any contamination that might have resulted from handling the rock cores shipboard or in the laboratory.…”

Section: Serpentinite Samples Have Minimal Environmental Contaminationmentioning

confidence: 99%

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Microbial residents of the Atlantis Massif’s shallow serpentinite subsurface

Motamedi

Orcutt

Früh-Green

et al. 2019

Preprint

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The Atlantis Massif rises 4,000 m above the seafloor near the Mid-Atlantic Ridge and consists of rocks uplifted from Earth's upper mantle. Exposure of the mantle rocks to seawater leads to their alteration into serpentinites. These aqueous geochemical 25 reactions, collectively known as the process of serpentinization, are exothermic and are associated with the release of hydrogen gas (H 2 ), methane (CH 4 ), and small organic molecules. The biological consequences of this flux of energy and organic compounds from the Atlantis Massif were explored by International Ocean Discovery Program (IODP) Expedition 357, which used seabed drills to collect continuous 30 sequences of shallow (<16 meters below seafloor) marine serpentinites and mafic assemblages. Here, we report the first census of microbial diversity in samples of the drill cores, as measured by environmental 16S rRNA gene amplicon sequencing.The problem of contamination of subsurface samples was a primary concern during all stages of this project, starting from the initial study design, continuing to the 35 collection of samples from the seafloor, handling the samples shipboard and in the lab, preparing the samples for DNA extraction, and analyzing the DNA sequence data. To distinguish endemic microbial taxa of serpentinite subsurface rocks from seawater residents and other potential contaminants, the distributions of individual 16S rRNA gene sequences among all samples were evaluated, taking into 40 consideration both presence/absence as well as relative abundances. Our results highlight a few candidate residents of the shallow serpentinite subsurface, including uncultured representatives of the Thermoplasmata, Acidobacteria, Acidimicrobiia, and Chloroflexi. 3 45 Importance International Ocean Discovery Program Expedition 357: "Serpentinization and Life" utilized seabed drills for the first time to collect rocks from the oceanic crust. The recovered rock cores represent the shallow serpentinite subsurface of the Atlantis Massif, where reactions between uplifted mantle rocks and water, collectively known 50 as serpentinization, produce environmental conditions that can stimulate biological activity and are thought to be analogous to environments that were prevalent on the early Earth and perhaps other planets. The methodology and results of this project have implications for life detection experiments, including sample return missions, and provide the first window into the diversity of microbial communities inhabiting 55 subseafloor serpentinites.

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Section: Serpentinite Samples Have Minimal Environmental Contaminationsupporting

confidence: 92%

Section: Serpentinite Samples Have Minimal Environmental Contaminationsupporting

confidence: 91%

Section: Serpentinite Samples Have Minimal Environmental Contaminationmentioning

confidence: 99%

Section: Serpentinite Samples Have Minimal Environmental Contaminationmentioning

confidence: 99%

See 2 more Smart Citations

Microbial residents of the Atlantis Massif’s shallow serpentinite subsurface

Motamedi

Orcutt

Früh-Green

et al. 2019

Preprint

Self Cite

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“…Sequencing of environmental DNA from seafloor rocks is challenging due to their very low biomass and their abundance of minerals (e.g. phyllosilicates) that inhibit Many precautions were taken during handling of the rock core samples to minimize, eliminate, and detect contamination, and our results agree with previous reports that these efforts were generally successful (20,59,60).…”

Section: Serpentinite Samples Have Minimal Environmental Contaminationsupporting

confidence: 88%

Microbial Residents of the Atlantis Massif’s Shallow Serpentinite Subsurface

Motamedi

Orcutt

Früh-Green

et al. 2020

Appl Environ Microbiol

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The Atlantis Massif rises 4,000 m above the seafloor near the Mid-Atlantic Ridge and consists of rocks uplifted from Earth’s lower crust and upper mantle. Exposure of the mantle rocks to seawater leads to their alteration into serpentinites. These aqueous geochemical reactions, collectively known as the process of serpentinization, are exothermic and are associated with the release of hydrogen gas (H2), methane (CH4), and small organic molecules. The biological consequences of this flux of energy and organic compounds from the Atlantis Massif were explored by International Ocean Discovery Program (IODP) Expedition 357, which used seabed drills to collect continuous sequences of shallow (<16 m below seafloor) marine serpentinites and mafic assemblages. Here, we report the census of microbial diversity in samples of the drill cores, as measured by environmental 16S rRNA gene amplicon sequencing. The problem of contamination of subsurface samples was a primary concern during all stages of this project, starting from the initial study design, continuing to the collection of samples from the seafloor, handling the samples shipboard and in the lab, preparing the samples for DNA extraction, and analyzing the DNA sequence data. To distinguish endemic microbial taxa of serpentinite subsurface rocks from seawater residents and other potential contaminants, the distributions of individual 16S rRNA gene sequences among all samples were evaluated, taking into consideration both presence/absence and relative abundances. Our results highlight a few candidate residents of the shallow serpentinite subsurface, including uncultured representatives of the Thermoplasmata, Acidobacteria, Acidimicrobia, and Chloroflexi. IMPORTANCE The International Ocean Discovery Program Expedition 357—“Serpentinization and Life”—utilized seabed drills to collect rocks from the oceanic crust. The recovered rock cores represent the shallow serpentinite subsurface of the Atlantis Massif, where reactions between uplifted mantle rocks and water, collectively known as serpentinization, produce environmental conditions that can stimulate biological activity and are thought to be analogous to environments that were prevalent on the early Earth and perhaps other planets. The methodology and results of this project have implications for life detection experiments, including sample return missions, and provide a window into the diversity of microbial communities inhabiting subseafloor serpentinites.

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Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation

Armbrecht

Coolen

Lejzerowicz

et al. 2019

Earth-Science Reviews

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The study of ancient DNA (aDNA) from sediments (sedaDNA) offers great potential for paleoclimate interpretation, and has recently been applied as a tool to characterise past marine life and environments from deep ocean sediments over geological timescales. Using sedaDNA, palaeo-communities have been detected, including prokaryotes and eukaryotes that do not fossilise, thereby revolutionising the scope of marine micropalaeontological research. However, many studies to date have not reported on the measures taken to prove the authenticity of sedaDNA-derived data from which conclusions are drawn. aDNA is highly fragmented and degraded and extremely sensitive to contamination by non-target environmental DNA. Contamination risks are particularly high on research vessels, drilling ships and platforms, where logistics and facilities do not yet allow for sterile sediment coring, and due consideration needs to be given to sample processing and analysis following aDNA guidelines. This review clarifies the use of aDNA terminology, discusses common pitfalls and highlights the urgency behind adopting new standards for marine sedaDNA research, with a focus on sampling optimisation to facilitate the incorporation of routine sedaDNA research into International Ocean Discovery Program (IODP) operations. Currently available installations aboard drilling ships and platforms are reviewed, improvements suggested, analytical approaches detailed, and the controls and documentation necessary to support the authenticity of aDNA retrieved from deep-sea sediment cores is outlined. Beyond practical considerations, concepts relevant to the study of past marine biodiversity based on aDNA, and the applicability of the new guidelines to the study of other contamination-susceptible environments (permafrost and outer space) are discussed.

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Contamination tracer testing with seabed drills: IODP Expedition 357

Cited by 15 publications

References 16 publications

Microbial residents of the Atlantis Massif’s shallow serpentinite subsurface

Microbial residents of the Atlantis Massif’s shallow serpentinite subsurface

Microbial Residents of the Atlantis Massif’s Shallow Serpentinite Subsurface

Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation

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