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Akondi RN, Trexler RV, Pfiffner SM, Mouser PJ, Sharma S. Modified Lipid Extraction Methods for Deep Subsurface Shale. Front Microbiol 2017; 8:1408. [PMID: 28790998 PMCID: PMC5524817 DOI: 10.3389/fmicb.2017.01408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 07/11/2017] [Indexed: 01/12/2023] Open
Abstract
Growing interest in the utilization of black shales for hydrocarbon development and environmental applications has spurred investigations of microbial functional diversity in the deep subsurface shale ecosystem. Lipid biomarker analyses including phospholipid fatty acids (PLFAs) and diglyceride fatty acids (DGFAs) represent sensitive tools for estimating biomass and characterizing the diversity of microbial communities. However, complex shale matrix properties create immense challenges for microbial lipid extraction procedures. Here, we test three different lipid extraction methods: modified Bligh and Dyer (mBD), Folch (FOL), and microwave assisted extraction (MAE), to examine their ability in the recovery and reproducibility of lipid biomarkers in deeply buried shales. The lipid biomarkers were analyzed as fatty acid methyl esters (FAMEs) with the GC-MS, and the average PL-FAME yield ranged from 67 to 400 pmol/g, while the average DG-FAME yield ranged from 600 to 3,000 pmol/g. The biomarker yields in the intact phospholipid Bligh and Dyer treatment (mBD + Phos + POPC), the Folch, the Bligh and Dyer citrate buffer (mBD-Cit), and the MAE treatments were all relatively higher and statistically similar compared to the other extraction treatments for both PLFAs and DGFAs. The biomarker yields were however highly variable within replicates for most extraction treatments, although the mBD + Phos + POPC treatment had relatively better reproducibility in the consistent fatty acid profiles. This variability across treatments which is associated with the highly complex nature of deeply buried shale matrix, further necessitates customized methodological developments for the improvement of lipid biomarker recovery.
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Affiliation(s)
- Rawlings N Akondi
- Department of Geology and Geography, West Virginia UniversityMorgantown, WV, United States
| | - Ryan V Trexler
- Civil, Environmental and Geodetic Engineering, The Ohio State UniversityColumbus, OH, United States
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, United States
| | - Paula J Mouser
- Civil, Environmental and Geodetic Engineering, The Ohio State UniversityColumbus, OH, United States
| | - Shikha Sharma
- Department of Geology and Geography, West Virginia UniversityMorgantown, WV, United States
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Wilkins MJ, Daly RA, Mouser PJ, Trexler R, Sharma S, Cole DR, Wrighton KC, Biddle JF, Denis EH, Fredrickson JK, Kieft TL, Onstott TC, Peterson L, Pfiffner SM, Phelps TJ, Schrenk MO. Trends and future challenges in sampling the deep terrestrial biosphere. Front Microbiol 2014; 5:481. [PMID: 25309520 PMCID: PMC4162470 DOI: 10.3389/fmicb.2014.00481] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 08/27/2014] [Indexed: 11/28/2022] Open
Abstract
Research in the deep terrestrial biosphere is driven by interest in novel biodiversity and metabolisms, biogeochemical cycling, and the impact of human activities on this ecosystem. As this interest continues to grow, it is important to ensure that when subsurface investigations are proposed, materials recovered from the subsurface are sampled and preserved in an appropriate manner to limit contamination and ensure preservation of accurate microbial, geochemical, and mineralogical signatures. On February 20th, 2014, a workshop on "Trends and Future Challenges in Sampling The Deep Subsurface" was coordinated in Columbus, Ohio by The Ohio State University and West Virginia University faculty, and sponsored by The Ohio State University and the Sloan Foundation's Deep Carbon Observatory. The workshop aims were to identify and develop best practices for the collection, preservation, and analysis of terrestrial deep rock samples. This document summarizes the information shared during this workshop.
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Affiliation(s)
- Michael J. Wilkins
- School of Earth Sciences, The Ohio State UniversityColumbus, OH, USA
- Department of Microbiology, The Ohio State UniversityColumbus, OH, USA
| | - Rebecca A. Daly
- Department of Microbiology, The Ohio State UniversityColumbus, OH, USA
| | - Paula J. Mouser
- Department of Engineering, The Ohio State UniversityColumbus, OH, USA
| | - Ryan Trexler
- Department of Engineering, The Ohio State UniversityColumbus, OH, USA
| | - Shihka Sharma
- Department of Geology and Geography, West Virginia UniversityMorgantown, WV, USA
| | - David R. Cole
- School of Earth Sciences, The Ohio State UniversityColumbus, OH, USA
| | - Kelly C. Wrighton
- Department of Microbiology, The Ohio State UniversityColumbus, OH, USA
| | - Jennifer F. Biddle
- College of Earth, Ocean, and Environment, University of DelawareLewes, DE, USA
| | | | - Jim K. Fredrickson
- Biological Sciences Division, Pacific Northwest National LaboratoryRichland, WA, USA
| | | | | | | | - Susan M. Pfiffner
- Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA
| | - Tommy J. Phelps
- Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA
| | - Matthew O. Schrenk
- Department of Geological Sciences, Michigan State UniversityEast Lansing, MI, USA
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Fajardo-Cavazos P, Langenhorst F, Melosh HJ, Nicholson WL. Bacterial spores in granite survive hypervelocity launch by spallation: implications for lithopanspermia. ASTROBIOLOGY 2009; 9:647-57. [PMID: 19778276 DOI: 10.1089/ast.2008.0326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Bacterial spores are considered good candidates for endolithic life-forms that could survive interplanetary transport by natural impact processes, i.e., lithopanspermia. Organisms within rock can only embark on an interplanetary journey if they survive ejection from the surface of the donor planet and the associated extremes of compressional shock, heating, and acceleration. Previous simulation experiments have measured each of these three stresses more or less in isolation of one another, and results to date indicate that spores of the model organism Bacillus subtilis can survive each stress applied singly. Few simulations, however, have combined all three stresses simultaneously. Because considerable experimental and theoretical evidence supports a spallation mechanism for launch, we devised an experimental simulation of launch by spallation using the Ames Vertical Gun Range (AVGR). B. subtilis spores were applied to the surface of a granite target that was impacted from above by an aluminum projectile fired at 5.4 km/s. Granite spall fragments were captured in a foam recovery fixture and then recovered and assayed for shock damage by transmission electron microscopy and for spore survival by viability assays. Peak shock pressure at the impact site was calculated to be 57.1 GPa, though recovered spall fragments were only very lightly shocked at pressures of 5-7 GPa. Spore survival was calculated to be on the order of 10(-5), which is in agreement with results of previous static compressional shock experiments. These results demonstrate that endolithic spores can survive launch by spallation from a hypervelocity impact, which lends further evidence in favor of lithopanspermia theory.
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Affiliation(s)
- Patricia Fajardo-Cavazos
- Department of Microbiology and Cell Science, University of Florida , Space Life Sciences Laboratory, Kennedy Space Center, Florida 32899, USA
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Nicholson WL. Ancient micronauts: interplanetary transport of microbes by cosmic impacts. Trends Microbiol 2009; 17:243-50. [PMID: 19464895 DOI: 10.1016/j.tim.2009.03.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Revised: 03/17/2009] [Accepted: 03/23/2009] [Indexed: 10/20/2022]
Abstract
Recent developments in microbiology, geophysics and planetary sciences raise the possibility that the planets in our solar system might not be biologically isolated. Hence, the possibility of lithopanspermia (the interplanetary transport of microbial passengers inside rocks) is presently being re-evaluated, with implications for the origin and evolution of life on Earth and within our solar system. Here, I summarize our current understanding of the physics of impacts, space transport of meteorites, and the potentiality of microorganisms to undergo and survive interplanetary transfer.
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Affiliation(s)
- Wayne L Nicholson
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Laboratory, Building M6-1025, Room 201-B, Kennedy Space Center, FL 32899, USA.
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Mitchell KR, Takacs-Vesbach CD. A comparison of methods for total community DNA preservation and extraction from various thermal environments. J Ind Microbiol Biotechnol 2008; 35:1139-47. [DOI: 10.1007/s10295-008-0393-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Accepted: 07/02/2008] [Indexed: 10/21/2022]
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Kieft TL, Kovacik WP, Ringelberg DB, White DC, Haldeman DL, Amy PS, Hersman LE. Factors limiting microbial growth and activity at a proposed high-level nuclear repository, yucca mountain, nevada. Appl Environ Microbiol 1997; 63:3128-33. [PMID: 16535670 PMCID: PMC1389225 DOI: 10.1128/aem.63.8.3128-3133.1997] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As part of the characterization of Yucca Mountain, Nev., as a potential repository for high-level nuclear waste, volcanic tuff was analyzed for microbial abundance and activity. Tuff was collected aseptically from nine sites along a tunnel in Yucca Mountain. Microbial abundance was generally low: direct microscopic cell counts were near detection limits at all sites (3.2 x 10(sup4) to 2.0 x 10(sup5) cells g(sup-1) [dry weight]); plate counts of aerobic heterotrophs ranged from 1.0 x 10(sup1) to 3.2 x 10(sup3) CFU g(sup-1) (dry weight). Phospholipid fatty acid concentrations (0.1 to 3.7 pmol g(sup-1)) also indicated low microbial biomasses; diglyceride fatty acid concentrations, indicative of dead cells, were in a similar range (0.2 to 2.3 pmol g(sup-1)). Potential microbial activity was quantified as (sup14)CO(inf2) production in microcosms containing radiolabeled substrates (glucose, acetate, and glutamic acid); amendments with water and nutrient solutions (N and P) were used to test factors potentially limiting this activity. Similarly, the potential for microbial growth and the factors limiting growth were determined by performing plate counts before and after incubating volcanic tuff samples for 24 h under various conditions: ambient moisture, water-amended, and amended with various nutrient solutions (N, P, and organic C). A high potential for microbial activity was demonstrated by high rates of substrate mineralization (as much as 70% of added organic C in 3 weeks). Water was the major limiting factor to growth and microbial activity, while amendments with N and P resulted in little further stimulation. Organic C amendments stimulated growth more than water alone.
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Chandler DP, Brockman FJ, Fredrickson JK. Use of 16S rDNA clone libraries to study changes in a microbial community resulting from ex situ perturbation of a subsurface sediment. FEMS Microbiol Rev 1997. [DOI: 10.1111/j.1574-6976.1997.tb00310.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Lindahl V, Aa K, Olsen RA. Effects on microbial activity by extraction of indigenous cells from soil slurries. FEMS Microbiol Ecol 1996. [DOI: 10.1111/j.1574-6941.1996.tb00349.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Chandler DP, Brockman FJ. Estimating biodegradative gene numbers at a JP-5 contaminated site using PCR. Appl Biochem Biotechnol 1996; 57-58:971-82. [PMID: 8669924 DOI: 10.1007/bf02941777] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We have utilized a most-probable-number polymerase chain reaction (MPN-PCR) procedure to estimate gene numbers and biodegradative potential at a jet fuel (JP-5) contaminated site undergoing the first phase of bioremediation. Nucleic acid analysis was used to determine whether a lack of genetic potential for bioremediation was responsible for low levels of oxygen utilization at the site. Total community DNA was extracted and analyzed by PCR for genes (nahAc,alkB, and xylE) known to be involved in the degradation of certain JP-5 constituents. Results indicate that significant aromatic biodegradative potential exists at the site and outlying areas not subjected to engineered remediation, suggesting that physical and/or chemical factors are inhibiting oxygen delivery. xylE and nahAc were often present in significant portions of the microbial community, whereas alkB was rarely detected. This study illustrates the utility of molecular techniques in evaluating biodegradative potential in the field during active bioremediation.
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Affiliation(s)
- D P Chandler
- Battelle Laboratories, Environmental Microbiology, Richland, WA 99352, USA
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Haldeman DL, Amy PS, Ringelberg D, White DC, Garen RE, Ghiorse WC. Microbial growth and resuscitation alter community structure after perturbation. FEMS Microbiol Ecol 1995. [DOI: 10.1111/j.1574-6941.1995.tb00124.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Haldeman D, Amy P, Russell C, Jacobson R. Comparison of drilling and mining as methods for obtaining microbiological samples from the deep subsurface. J Microbiol Methods 1995. [DOI: 10.1016/0167-7012(94)00057-e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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