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Bartak D, Bedrníková E, Kašpar V, Říha J, Hlaváčková V, Večerník P, Šachlová Š, Černá K. Survivability and proliferation of microorganisms in bentonite with implication to radioactive waste geological disposal: strong effect of temperature and negligible effect of pressure. World J Microbiol Biotechnol 2023; 40:41. [PMID: 38071262 PMCID: PMC10710388 DOI: 10.1007/s11274-023-03849-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023]
Abstract
As bentonite hosts a diverse spectrum of indigenous microorganisms with the potential to influence the long-term stability of deep geological repositories, it is essential to understand the factors influencing microbial activity under repository conditions. Here, we focus on two factors, i.e., temperature and swelling pressure, using a suspension of Cerny Vrch bentonite to boost microbial activity and evaluate microbial response. Suspensions were exposed either to different pressures (10, 12 and 15 MPa; to simulate the effect of swelling pressure) or elevated temperatures (60, 70, 80 and 90 °C; to simulate the effect of cannister heating) for four weeks. Each treatment was followed by a period of anaerobic incubation at atmospheric pressure/laboratory temperature to assess microbial recovery after treatment. Microbial load and community structure were then estimated using molecular-genetic methods, with presence of living cells confirmed through microscopic analysis. Our study demonstrated that discrete application of pressure did not influence on overall microbial activity or proliferation, implying that pressure evolution during bentonite swelling is not the critical factor responsible for microbial suppression in saturated bentonites. However, pressure treatment caused significant shifts in microbial community structure. We also demonstrated that microbial activity decreased with increasing temperature, and that heat treatment strongly influenced bentonite microbial community structure, with several thermophilic taxa identified. A temperature of 90 °C proved to be limiting for microbial activity and proliferation in all bentonite suspensions. Our study emphasizes the crucial role of a deep understanding of microbial activity under repository-relevant conditions in identifying possible strategies to mitigate the microbial potential within the deep geological repository and increase its long-term stability and safety.
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Affiliation(s)
- Deepa Bartak
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, 460 01, Liberec, Czech Republic
| | - Eva Bedrníková
- Disposal processes and safety, ÚJV Řež, a. s., Hlavní 130, 250 68, Husinec, Czech Republic
| | - Vlastislav Kašpar
- Disposal processes and safety, ÚJV Řež, a. s., Hlavní 130, 250 68, Husinec, Czech Republic
| | - Jakub Říha
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, 460 01, Liberec, Czech Republic
| | - Veronika Hlaváčková
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, 460 01, Liberec, Czech Republic
| | - Petr Večerník
- Disposal processes and safety, ÚJV Řež, a. s., Hlavní 130, 250 68, Husinec, Czech Republic
| | - Šárka Šachlová
- Disposal processes and safety, ÚJV Řež, a. s., Hlavní 130, 250 68, Husinec, Czech Republic
| | - Kateřina Černá
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, 460 01, Liberec, Czech Republic.
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Bachman P, Fischer J, Song Z, Urbanczyk-Wochniak E, Watson G. Environmental Fate and Dissipation of Applied dsRNA in Soil, Aquatic Systems, and Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:21. [PMID: 32117368 PMCID: PMC7016216 DOI: 10.3389/fpls.2020.00021] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/10/2020] [Indexed: 05/10/2023]
Abstract
Two primary use patterns exist for dsRNA-based products for crop protection: in planta produced dsRNA such as in a genetically engineered (GE) crop; and topically applied dsRNA such as a spray application. To enable effective environmental risk assessments for these products, dsRNA must be successfully measured in relevant environmental compartments (soil, sediment, surface water) to provide information on potential exposure. This perspective reviews results from numerous environmental fate and degradation studies with topically applied unformulated dsRNAs to demonstrate the high lability of these molecules and low potential for persistence in the environment. Additionally, we report on results of a pilot study of topically applied dsRNA on soybean plants demonstrating similar rapid degradation under field conditions. Microbial degradation of nucleic acids in environmental compartments has been shown to be a key driver for this lack of persistence. In fact, the instability of dsRNA in the environment has posed a challenge for the development of commercial topically-applied products. Formulations or other approaches that mitigate environmental degradation may lead to development of commercially successful products but may change the known degradation kinetics of dsRNAs. The formulation of these products and the resultant impacts on the stability of the dsRNA in environmental compartments will need to be addressed using problem formulation and product formulation testing may be required on a case by case basis to ensure an effective risk assessment.
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Affiliation(s)
- Pamela Bachman
- Science Organization, The Climate Corporation, Creve Coeur, MO, United States
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, United States
| | - Joshua Fischer
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, United States
| | - Zihong Song
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, United States
| | | | - Greg Watson
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, United States
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Mojarro A, Hachey J, Bailey R, Brown M, Doebler R, Ruvkun G, Zuber MT, Carr CE. Nucleic Acid Extraction and Sequencing from Low-Biomass Synthetic Mars Analog Soils for In Situ Life Detection. ASTROBIOLOGY 2019; 19:1139-1152. [PMID: 31204862 PMCID: PMC6708270 DOI: 10.1089/ast.2018.1929] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Recent studies regarding the origins of life and Mars-Earth meteorite transfer simulations suggest that biological informational polymers, such as nucleic acids (DNA and RNA), have the potential to provide unambiguous evidence of life on Mars. To this end, we are developing a metagenomics-based life-detection instrument which integrates nucleic acid extraction and nanopore sequencing: the Search for Extra-Terrestrial Genomes (SETG). Our goal is to isolate and sequence nucleic acids from extant or preserved life on Mars in order to determine if a particular genetic sequence (1) is distantly related to life on Earth, indicating a shared ancestry due to lithological exchange, or (2) is unrelated to life on Earth, suggesting convergent origins of life on Mars. In this study, we validate prior work on nucleic acid extraction from cells deposited in Mars analog soils down to microbial concentrations (i.e., 104 cells in 50 mg of soil) observed in the driest and coldest regions on Earth. In addition, we report low-input nanopore sequencing results from 2 pg of purified Bacillus subtilis spore DNA simulating ideal extraction yields equivalent to 1 ppb life-detection sensitivity. We achieve this by employing carrier sequencing, a method of sequencing sub-nanogram DNA in the background of a genomic carrier. After filtering of carrier, low-quality, and low-complexity reads we detected 5 B. subtilis reads, 18 contamination reads (including Homo sapiens), and 6 high-quality noise reads believed to be sequencing artifacts.
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Affiliation(s)
- Angel Mojarro
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Address correspondence to: Angel Mojarro, Massachusetts Institute of Technology, 77 Massachusetts Ave, Room E25-647, Cambridge, MA 02139
| | | | - Ryan Bailey
- Claremont Biosolutions, LLC, Upland, California
| | - Mark Brown
- Claremont Biosolutions, LLC, Upland, California
| | | | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Maria T. Zuber
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christopher E. Carr
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
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Prosser CM, Hedgpeth BM. Effects of bioturbation on environmental DNA migration through soil media. PLoS One 2018; 13:e0196430. [PMID: 29689092 PMCID: PMC5915775 DOI: 10.1371/journal.pone.0196430] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/12/2018] [Indexed: 01/03/2023] Open
Abstract
Extracting and identifying genetic material from environmental media (i.e. water and soil) presents a unique opportunity for researchers to assess biotic diversity and ecosystem health with increased speed and decreased cost as compared to traditional methods (e.g. trapping). The heterogeneity of soil mineralogy, spatial and temporal variations however present unique challenges to sampling and interpreting results. Specifically, fate/transport of genetic material in the terrestrial environment represents a substantial data gap. Here we investigate to what degree, benthic fauna transport genetic material through soil. Using the red worm (Eisenia fetida), we investigate how natural movement through artificial soil affect the transport of genetic material. All experiments were run in Frabill® Habitat® II worm systems with approximately 5 cm depth of artificial soil. We selected an “exotic” source of DNA not expected to be present in soil, zebrafish (Danio rerio) tissue. Experiment groups contained homogenized zebrafish tissue placed in a defined location combined with a varying number of worms (10, 30 or 50 worms per experimental group). Experimental groups comprised two controls and three treatment groups (representing different worm biomass) in triplicate. A total of 210 soil samples were randomly collected over the course of 15 days to investigate the degree of genetic transfer, and the rate of detection. Positive detections were identified in 14% - 38% of samples across treatment groups, with an overall detection rate of 25%. These findings highlight two important issues when utilizing environmental DNA for biologic assessments. First, benthic fauna are capable of redistributing genetic material through a soil matrix. Second, despite a defined sample container and abundance of worm biomass, as many as 86% of the samples were negative. This has substantial implications for researchers and managers who wish to interpret environmental DNA results from terrestrial systems. Studies such as these will aid in future study protocol design and sample collection methodology.
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Affiliation(s)
- Christopher M. Prosser
- ExxonMobil Biomedical Sciences Incorporated, Annandale, NJ, United States of America
- * E-mail:
| | - Bryan M. Hedgpeth
- ExxonMobil Biomedical Sciences Incorporated, Annandale, NJ, United States of America
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Mojarro A, Ruvkun G, Zuber MT, Carr CE. Nucleic Acid Extraction from Synthetic Mars Analog Soils for in situ Life Detection. ASTROBIOLOGY 2017; 17:747-760. [PMID: 28704064 PMCID: PMC5567878 DOI: 10.1089/ast.2016.1535] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Biological informational polymers such as nucleic acids have the potential to provide unambiguous evidence of life beyond Earth. To this end, we are developing an automated in situ life-detection instrument that integrates nucleic acid extraction and nanopore sequencing: the Search for Extra-Terrestrial Genomes (SETG) instrument. Our goal is to isolate and determine the sequence of nucleic acids from extant or preserved life on Mars, if, for example, there is common ancestry to life on Mars and Earth. As is true of metagenomic analysis of terrestrial environmental samples, the SETG instrument must isolate nucleic acids from crude samples and then determine the DNA sequence of the unknown nucleic acids. Our initial DNA extraction experiments resulted in low to undetectable amounts of DNA due to soil chemistry-dependent soil-DNA interactions, namely adsorption to mineral surfaces, binding to divalent/trivalent cations, destruction by iron redox cycling, and acidic conditions. Subsequently, we developed soil-specific extraction protocols that increase DNA yields through a combination of desalting, utilization of competitive binders, and promotion of anaerobic conditions. Our results suggest that a combination of desalting and utilizing competitive binders may establish a "universal" nucleic acid extraction protocol suitable for analyzing samples from diverse soils on Mars. Key Words: Life-detection instruments-Nucleic acids-Mars-Panspermia. Astrobiology 17, 747-760.
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Affiliation(s)
- Angel Mojarro
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Maria T. Zuber
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christopher E. Carr
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
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Gumpenberger T, Vorkapic D, Zingl FG, Pressler K, Lackner S, Seper A, Reidl J, Schild S. Nucleoside uptake in Vibrio cholerae and its role in the transition fitness from host to environment. Mol Microbiol 2015. [PMID: 26202476 DOI: 10.1111/mmi.13143] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
As it became evident recently, extracellular DNA could be a versatile nutrient source of the facultative pathogen Vibrio cholerae along the different stages of its life cycle. By the use of two extracellular nucleases and periplasmic phosphatases, V. cholerae degrades extracellular DNA to nucleosides. In this study, we investigated the nucleoside uptake via identification and characterization of VCA0179, VC1953 and VC2352 representing the three nucleoside transport systems in V. cholerae. Based on our results VC2352 seems to be the dominant nucleoside transporter. Nevertheless, all three transporters are functional and can contribute to the utilization of nucleosides as a sole source of carbon or nitrogen. We found that the transcriptional activity of these three distal genes is equally promoted or antagonized by CRP or CytR respectively. Finally, mutants impaired for nucleoside uptake exhibit decreased transition fitness from the host into low carbon environments along the life cycle of V. cholerae.
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Affiliation(s)
- Tanja Gumpenberger
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50, Graz, 8010, Austria
| | - Dina Vorkapic
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50, Graz, 8010, Austria
| | - Franz G Zingl
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50, Graz, 8010, Austria
| | - Katharina Pressler
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50, Graz, 8010, Austria
| | - Stefanie Lackner
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50, Graz, 8010, Austria
| | - Andrea Seper
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50, Graz, 8010, Austria
| | - Joachim Reidl
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50, Graz, 8010, Austria
| | - Stefan Schild
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50, Graz, 8010, Austria
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Gryndler M, Trilčová J, Hršelová H, Streiblová E, Gryndlerová H, Jansa J. Tuber aestivum Vittad. mycelium quantified: advantages and limitations of a qPCR approach. MYCORRHIZA 2013; 23:341-348. [PMID: 23271632 DOI: 10.1007/s00572-012-0475-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 12/17/2012] [Indexed: 06/01/2023]
Abstract
A quantitative real-time PCR (qPCR) marker Ta0 with hydrolysis probe ("TaqMan"), targeted to the internal transcribed spacer region of the ribosomal DNA, has been developed for quantification of summer truffle (Tuber aestivum) mycelium. Gene copy concentrations determined by the qPCR were calibrated against pure culture mycelium of T. aestivum, enabling quantification of the mycelium in soil and in host roots from the fields. Significant concentrations of the fungus were observed not only in the finest roots with ectomycorrhizae but also in other root types, indicating that the fungus is an important component of the microbial film at the root surface. The concentration of T. aestivum in soil is relatively high compared to other ectomycorrhizal fungi. To evaluate the reliability of the measurement of the soil mycelium density using qPCR, the steady basal extracellular concentration of the stabilized T. aestivum DNA should be known and taken into account. Therefore, we addressed the stability of the qPCR signal in soil subjected to different treatments. After the field soil was sieved, regardless of whether it was dried/rewetted or not, the T. aestivum DNA was quickly decomposed. It took just about 4 days to reach a steady concentration. This represents a conserved pool of T. aestivum DNA and determines detection limit of the qPCR quantification in our case. When the soil was autoclaved and recolonized by saprotrophic microorganisms, this conserved DNA pool was eliminated and the soil became free of T. aestivum DNA.
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Affiliation(s)
- Milan Gryndler
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220 Prague 4, Czech Republic.
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Bellemain E, Davey ML, Kauserud H, Epp LS, Boessenkool S, Coissac E, Geml J, Edwards M, Willerslev E, Gussarova G, Taberlet P, Brochmann C. Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost. Environ Microbiol 2012; 15:1176-89. [DOI: 10.1111/1462-2920.12020] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 10/04/2012] [Indexed: 01/28/2023]
Affiliation(s)
- Eva Bellemain
- National Centre for Biosystematics; Natural History Museum; University of Oslo; P.O. Box 117 Blindern; NO-0318; Oslo; Norway
| | | | - Håvard Kauserud
- Microbial Evolution Research Group (MERG); Department of Biology; University of Oslo; P.O. Box 1066 Blindern; N-0316; Oslo; Norway
| | - Laura S. Epp
- National Centre for Biosystematics; Natural History Museum; University of Oslo; P.O. Box 117 Blindern; NO-0318; Oslo; Norway
| | - Sanne Boessenkool
- National Centre for Biosystematics; Natural History Museum; University of Oslo; P.O. Box 117 Blindern; NO-0318; Oslo; Norway
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine CNRS UMR 5553; Univ. Joseph Fourier; BP 53; 38041 Grenoble Cedex 9; France
| | - Jozsef Geml
- Kits van Waveren Foundation; Nationaal Herbarium Nederland; Universiteit Leiden; P.O. Box 9514; 2300 RA; Leiden; The Netherlands
| | - Mary Edwards
- Geography and Environment; University of Southampton; University Road; Southampton; UK
| | - Eske Willerslev
- Centre for GeoGenetics; Natural History Museum of Denmark; Øster Voldgade 5-7; 1350; Copenhagen K; Denmark
| | - Galina Gussarova
- National Centre for Biosystematics; Natural History Museum; University of Oslo; P.O. Box 117 Blindern; NO-0318; Oslo; Norway
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine CNRS UMR 5553; Univ. Joseph Fourier; BP 53; 38041 Grenoble Cedex 9; France
| | - Christian Brochmann
- National Centre for Biosystematics; Natural History Museum; University of Oslo; P.O. Box 117 Blindern; NO-0318; Oslo; Norway
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Wang Y, Hayatsu M, Fujii T. Extraction of bacterial RNA from soil: challenges and solutions. Microbes Environ 2012; 27:111-21. [PMID: 22791042 PMCID: PMC4036013 DOI: 10.1264/jsme2.me11304] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Detection of bacterial gene expression in soil emerged in the early 1990s and provided information on bacterial responses in their original soil environments. As a key procedure in the detection, extraction of bacterial RNA from soil has attracted much interest, and many methods of soil RNA extraction have been reported in the past 20 years. In addition to various RT-PCR-based technologies, new technologies for gene expression analysis, such as microarrays and high-throughput sequencing technologies, have recently been applied to examine bacterial gene expression in soil. These technologies are driving improvements in RNA extraction protocols. In this mini-review, progress in the extraction of bacterial RNA from soil is summarized with emphasis on the major difficulties in the development of methodologies and corresponding strategies to overcome them.
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Affiliation(s)
- Yong Wang
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan.
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Abstract
Anthropogenic activities are having a deleterious effect on biodiversity. To understand the magnitude of this issue, and ultimately temper its pace, requires reproducible biodiversity measurements at suitable spatio-temporal scales. Procuring such data solely by existing approaches is unachievable because of the costs, time and the taxonomic expertise required. High-throughput molecular biodiversity analysis shows great promise, increasing the breadth of biota sampled and accelerating the rate of data collection. In this issue of Molecular Ecology, Yoccoz et al. (2012) use short informative DNA product 'meta-barcodes' to provide an insight into above-ground vascular plant diversity from boreal, temperate and tropical environments. Interestingly, their molecular analysis was derived from the soils and not the plants themselves, with the molecular signatures of the soils not only strongly reflecting current diversity, but also traces of crops not sown for up to one hundred years. Importantly, the research examines the complexities associated with deriving biomass estimates from molecular data and the need to consider biomass turnover. The use of soil-derived meta-barcodes extends beyond estimating vascular plant diversity, with the approach being suited to the range of ecological applications, especially scenarios where DNA may be degraded.
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Ahn J, Byun JY, Shin YB, Kim MG. Photoactivated immobilization of single-stranded DNAs on a psoralen-functionalized surface under low pH conditions. BIOCHIP JOURNAL 2012. [DOI: 10.1007/s13206-012-6210-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Direito SOL, Marees A, Röling WFM. Sensitive life detection strategies for low-biomass environments: optimizing extraction of nucleic acids adsorbing to terrestrial and Mars analogue minerals. FEMS Microbiol Ecol 2012; 81:111-23. [PMID: 22329626 DOI: 10.1111/j.1574-6941.2012.01325.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 01/19/2012] [Accepted: 01/31/2012] [Indexed: 11/29/2022] Open
Abstract
The adsorption of nucleic acids to mineral matrixes can result in low extraction yields and negatively influences molecular microbial ecology studies, in particular for low-biomass environments on Earth and Mars. We determined the recovery of nucleic acids from a range of minerals relevant to Earth and Mars. Clay minerals, but also other silicates and nonsilicates, showed very low recovery (< 1%). Consequently, optimization of DNA extraction was directed towards clays. The high temperatures and acidic conditions used in some methods to dissolve mineral matrices proved to destruct DNA. The most efficient method comprised a high phosphate solution (P/EtOH; 1 M phosphate, 15% ethanol buffer at pH 8) introduced at the cell-lysing step in DNA extraction, to promote chemical competition with DNA for adsorption sites. This solution increased DNA yield from clay samples spiked with known quantities of cells up to nearly 100-fold. DNA recovery was also enhanced from several mineral samples retrieved from an aquifer, while maintaining reproducible DGGE profiles. DGGE profiles were obtained for a clay sample for which no profile could be generated with the standard DNA isolation protocol. Mineralogy influenced microbial community composition. The method also proved suitable for the recovery of low molecular weight DNA (< 1.5 kb).
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Affiliation(s)
- Susana O L Direito
- Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Netherlands
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13
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Seper A, Fengler VHI, Roier S, Wolinski H, Kohlwein SD, Bishop AL, Camilli A, Reidl J, Schild S. Extracellular nucleases and extracellular DNA play important roles in Vibrio cholerae biofilm formation. Mol Microbiol 2011; 82:1015-37. [PMID: 22032623 PMCID: PMC3212620 DOI: 10.1111/j.1365-2958.2011.07867.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biofilms are a preferred mode of survival for many microorganisms including Vibrio cholerae, the causative agent of the severe secretory diarrhoeal disease cholera. The ability of the facultative human pathogen V. cholerae to form biofilms is a key factor for persistence in aquatic ecosystems and biofilms act as a source for new outbreaks. Thus, a better understanding of biofilm formation and transmission of V. cholerae is an important target to control the disease. So far the Vibrio exopolysaccharide was the only known constituent of the biofilm matrix. In this study we identify and characterize extracellular DNA as a component of the Vibrio biofilm matrix. Furthermore, we show that extracellular DNA is modulated and controlled by the two extracellular nucleases Dns and Xds. Our results indicate that extracellular DNA and the extracellular nucleases are involved in diverse processes including the development of a typical biofilm architecture, nutrient acquisition, detachment from biofilms and the colonization fitness of biofilm clumps after ingestion by the host. This study provides new insights into biofilm development and transmission of biofilm-derived V. cholerae.
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Affiliation(s)
- Andrea Seper
- Institut fuer Molekulare Biowissenschaften, Karl-Franzens-Universitaet Graz, Humboldtstrasse 50, 8010 Graz, Austria
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Cleaves HJ, Crapster-Pregont E, Jonsson CM, Jonsson CL, Sverjensky DA, Hazen RA. The adsorption of short single-stranded DNA oligomers to mineral surfaces. CHEMOSPHERE 2011; 83:1560-7. [PMID: 21316734 DOI: 10.1016/j.chemosphere.2011.01.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 01/10/2011] [Accepted: 01/11/2011] [Indexed: 05/19/2023]
Abstract
We studied the adsorption of short single-stranded deoxyribonucleic acid (ssDNA) oligomers, of approximately 30 nucleotides (nt) in length, of varying sequence, adenine+guanine+cytosine (AGC) content, and propensity to form secondary structure, to equal surface area samples of olivine, pyrite, calcite, hematite, and rutile in 0.1M NaCl, 0.05M pH 8.1 KHCO(3) buffer. Although the mineral surfaces have widely varying points of zero charge, under these conditions they show remarkably similar adsorption of ssDNA regardless of oligomer characteristics. Mineral surfaces appear to accommodate ssDNA comparably, or ssDNA oligomers of this length are able to find binding sites of comparable strength and density due to their flexibility, despite the disparate surface properties of the different minerals. This may partially be due charge shielding by the ionic strength of the solutions tested, which are typical of many natural environments. These results may have some bearing on the adsorption and accumulation of biologically derived nucleic acids in sediments as well as the abiotic synthesis of nucleic acids before the origin of life.
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Affiliation(s)
- H James Cleaves
- Geophysical Laboratory, the Carnegie Institution of Washington, 5251 Broad Branch Road NW, Washington, DC 20015, USA
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Bryksin AV, Matsumura I. Rational design of a plasmid origin that replicates efficiently in both gram-positive and gram-negative bacteria. PLoS One 2010; 5:e13244. [PMID: 20949038 PMCID: PMC2951906 DOI: 10.1371/journal.pone.0013244] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Accepted: 09/08/2010] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Most plasmids replicate only within a particular genus or family. METHODOLOGY/PRINCIPAL FINDINGS Here we describe an engineered high copy number expression vector, pBAV1K-T5, that produces varying quantities of active reporter proteins in Escherichia coli, Acinetobacter baylyi ADP1, Agrobacterium tumefaciens, (all gram-negative), Streptococcus pneumoniae, Leifsonia shinshuensis, Peanibacillus sp. S18-36 and Bacillus subtilis (gram-positive). CONCLUSIONS/SIGNIFICANCE Our results demonstrate the efficiency of pBAV1K-T5 replication in different bacterial species, thereby facilitating the study of proteins that don't fold well in E. coli and pathogens not amenable to existing genetic tools.
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Affiliation(s)
- Anton V. Bryksin
- Center for Fundamental and Applied Molecular Evolution, Department of Biochemistry, Emory University, Atlanta, Georgia, United States of America
| | - Ichiro Matsumura
- Center for Fundamental and Applied Molecular Evolution, Department of Biochemistry, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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Campbell JH, Clark JS, Zak JC. PCR-DGGE comparison of bacterial community structure in fresh and archived soils sampled along a Chihuahuan Desert elevational gradient. MICROBIAL ECOLOGY 2009; 57:261-266. [PMID: 19107315 DOI: 10.1007/s00248-008-9479-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 11/19/2008] [Indexed: 05/27/2023]
Abstract
The polymerase chain reaction coupled with denaturing gradient gel electrophoresis (PCR-DGGE) has been used widely to determine species richness and structure of microbial communities in a variety of environments. Researchers commonly archive soil samples after routine chemical or microbial analyses, and applying PCR-DGGE technology to these historical samples offers evaluation of long-term patterns in bacterial species richness and community structure that was not available with previous technology. However, use of PCR-DGGE to analyze microbial communities of archived soils has been largely unexplored. To evaluate the stability of DGGE patterns in archived soils in comparison with fresh soils, fresh and archived soils from five sites along an elevational gradient in the Chihuahuan Desert were compared using PCR-DGGE of 16S rDNA. DNA from all archived samples was extracted reliably, but DNA in archived soils collected from a closed-canopy oak forest site could not be amplified. DNA extraction yields were lower for most archived soils, but minimal changes in bacterial species richness and structure due to archiving were noted in bacterial community profiles from four sites. Use of archived soils to determine long-term changes in bacterial community structure via PCR-DGGE appears to be a viable option for addressing microbial community dynamics for particular ecosystems or landscapes.
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Affiliation(s)
- James H Campbell
- Department of Biological Sciences, Texas Tech University, P.O. Box 43131, Lubbock, TX 79409-3131, USA.
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18
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Abstract
The role of extracellular DNA in the maintenance of biofilms formed by gram-positive and gram-negative bacteria was studied. This study evaluated all the bacterial strains that were tested for the presence of extracellular DNA with an average size of 30 kb in the matrix. Our results indicate changes in community biomass, architecture, morphology, and the numbers of CFU in the presence of DNase. This effect seems to be common to biofilms established by various unrelated gram-positive and gram-negative bacteria. The cleavage of extracellular DNA leads to the formation of an altered biofilm that permits the increased penetration of antibiotics. Thus, the addition of DNase enhances the effect of antibiotics, resulting in decreased biofilm biomass and numbers of CFU.
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Rajendhran J, Gunasekaran P. Strategies for accessing soil metagenome for desired applications. Biotechnol Adv 2008; 26:576-90. [PMID: 18786627 DOI: 10.1016/j.biotechadv.2008.08.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 08/03/2008] [Accepted: 08/05/2008] [Indexed: 11/27/2022]
Abstract
Most of the microorganisms in nature are inaccessible as they are uncultivable in the laboratory. Metagenomic approaches promise the accessibility of the genetic resources and their potential applications. Genetic resources from terrestrial environments can be accessed by exploring the soil metagenome. Soil metagenomic analyses are usually initiated by the isolation of environmental DNAs. Several methods have been described for the direct isolation of environmental DNAs from soil and sediments. Application of metagenomics largely depends on the construction of genomic DNA libraries and subsequent high-throughput sequencing or library screening. Thus, obtaining large quantities of pure cloneable DNA from the environment is a prerequisite. This review discusses the recent developments related to efficient extraction and purification of soil metagenome highlighting the considerations for various metagenomic applications.
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Affiliation(s)
- J Rajendhran
- Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai-625 021, India
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20
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Popp N, Schlömann M, Mau M. Bacterial diversity in the active stage of a bioremediation system for mineral oil hydrocarbon-contaminated soils. Microbiology (Reading) 2006; 152:3291-3304. [PMID: 17074900 DOI: 10.1099/mic.0.29054-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Soils contaminated with mineral oil hydrocarbons are often cleaned in off-site bioremediation systems. In order to find out which bacteria are active during the degradation phase in such systems, the diversity of the active microflora in a degrading soil remediation system was investigated by small-subunit (SSU) rRNA analysis. Two sequential RNA extracts from one soil sample were generated by a procedure incorporating bead beating. Both extracts were analysed separately by generating individual SSU rDNA clone libraries from cDNA of the two extracts. The sequencing results showed moderate diversity. The two clone libraries were dominated by Gammaproteobacteria, especially Pseudomonas spp. Alphaproteobacteria and Betaproteobacteria were two other large groups in the clone libraries. Actinobacteria, Firmicutes, Bacteroidetes and Epsilonproteobacteria were detected in lower numbers. The obtained sequences were predominantly related to genera for which cultivated representatives have been described, but were often clustered together in the phylogenetic tree, and the sequences that were most similar were originally obtained from soils and not from pure cultures. Most of the dominant genera in the clone libraries, e.g. Pseudomonas, Acinetobacter, Sphingomonas, Acidovorax and Thiobacillus, had already been detected in (mineral oil hydrocarbon) contaminated environmental samples. The occurrence of the genera Zymomonas and Rhodoferax was novel in mineral oil hydrocarbon-contaminated soil.
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Affiliation(s)
- Nicole Popp
- Interdisziplinäres Ökologisches Zentrum, TU Bergakademie Freiberg, Leipziger Str. 29, D-09599 Freiberg, Germany
| | - Michael Schlömann
- Interdisziplinäres Ökologisches Zentrum, TU Bergakademie Freiberg, Leipziger Str. 29, D-09599 Freiberg, Germany
| | - Margit Mau
- Interdisziplinäres Ökologisches Zentrum, TU Bergakademie Freiberg, Leipziger Str. 29, D-09599 Freiberg, Germany
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21
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Assessing Bacterial and Fungal Community Structure in Soil Using Ribosomal RNA and Other Structural Gene Markers. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/3-540-29449-x_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Weinbauer MG. Ecology of prokaryotic viruses. FEMS Microbiol Rev 2004; 28:127-81. [PMID: 15109783 DOI: 10.1016/j.femsre.2003.08.001] [Citation(s) in RCA: 912] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2002] [Revised: 07/22/2003] [Accepted: 08/05/2003] [Indexed: 11/24/2022] Open
Abstract
The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with phages in aquatic systems has stimulated research on the ecology of prokaryotic viruses and their role in ecosystems. This review treats the ecology of prokaryotic viruses ('phages') in marine, freshwater and soil systems from a 'virus point of view'. The abundance of viruses varies strongly in different environments and is related to bacterial abundance or activity suggesting that the majority of the viruses found in the environment are typically phages. Data on phage diversity are sparse but indicate that phages are extremely diverse in natural systems. Lytic phages are predators of prokaryotes, whereas lysogenic and chronic infections represent a parasitic interaction. Some forms of lysogeny might be described best as mutualism. The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies. The host cell is the main resource for phages and the resource quality, i.e., the metabolic state of the host cell, is a critical factor in all steps of the phage life cycle. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.g., by 'killing the winner' and keeping in check competitively dominant species or populations. Moreover, they mediate gene transfer between prokaryotes, but this remains largely unknown in the environment. Genomics or proteomics are providing us now with powerful tools in phage ecology, but final testing will have to be performed in the environment.
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Affiliation(s)
- Markus G Weinbauer
- Department of Biological Oceanography, Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands.
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Wang PH, Chang CW. Detection of the low-germination-rate resting oospores of Pythium myriotylum from soil by PCR. Lett Appl Microbiol 2003; 36:157-61. [PMID: 12581375 DOI: 10.1046/j.1472-765x.2003.01287.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To establish a sensitive and specific polymerase chain reaction (PCR)-based method for detecting Pythium myriotylum in soils. METHODS AND RESULTS Oospores of P. myriotylum were separated from large soil particles by flotation in sucrose solution. The thick-walled oospores were disrupted by vortex with sea sand and its DNA was extracted by the Cetyl trimethyl Ammonium Bromide (CTAB) method. The recovered DNA was verified by PCR amplification of a 150-bp target sequence of P. myriotylum. Samples of 10 g of soil were assayed; thus, the detection limit by PCR-based method was 10 oospores per gram soil. The method was successfully applied for the detection of P. myriotylum in soils collected in March, prior to planting of ginger crops. CONCLUSIONS A PCR-based method for detecting P. myriotylum from soil was achieved. SIGNIFICANCE AND IMPACT OF THE STUDY The PCR method has allowed us to monitor the presence of P. myriotylum in soil prior planting season as a way of reducing or eliminating disease.
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Affiliation(s)
- P H Wang
- Department of Microbiology, Soochow University, Taipei, Taiwan, 11102, Republic of China.
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Boye M, Baloda SB, Leser TD, Møller K. Survival of Brachyspira hyodysenteriae and B. pilosicoli in terrestrial microcosms. Vet Microbiol 2001; 81:33-40. [PMID: 11356316 DOI: 10.1016/s0378-1135(01)00328-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The survival of Brachyspira hyodysenteriae and Brachyspira pilosicoli was investigated at 10 degrees C in laboratory microcosms consisting of soil, porcine faeces, and in soil mixed with 10% porcine faeces, respectively. By plate spreading, survival of B. hyodysenteriae was found to be 10, 78 and 112 days in soil, soil mixed with 10% faeces, and in porcine faeces, respectively. The identities of the colonies on the plates were confirmed using PCR targeting 23S rDNA for specific detection of B. hyodysenteriae. A positive PCR signal could be obtained up to 112 days in all microcosms by direct extraction of DNA from microcosms followed by PCR. The survival time for B. pilosicoli was 119 days in pure soil and 210 days in soil mixed with 10% porcine faeces and in pure faeces, respectively, as determined by plate spreading followed by PCR. On the other hand, by direct extraction of DNA followed by specific detection by PCR. B. pilosicoli could be detected up to 330 days in all microcosms.Dot blot hybridisation with digoxigenin-labelled specific oligonucleotide probe targeting rDNA could not be used for direct detection of Brachyspira spp. from microcosms due to low sensitivity. However, it was used for confirmation of the identity of colonies and proved to be a useful technique. These results show that the two Brachyspira species may survive in outdoor environment for the times shown in these investigations using laboratory microcosms.
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Affiliation(s)
- M Boye
- Danish Veterinary Laboratory, Bülowsvej 27, DK-1790 V, Copenhagen, Denmark.
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Demanèche S, Kay E, Gourbière F, Simonet P. Natural transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in soil. Appl Environ Microbiol 2001; 67:2617-21. [PMID: 11375171 PMCID: PMC92915 DOI: 10.1128/aem.67.6.2617-2621.2001] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2000] [Accepted: 03/07/2001] [Indexed: 11/20/2022] Open
Abstract
Little information is available concerning the occurrence of natural transformation of bacteria in soil, the frequency of such events, and the actual role of this process on bacterial evolution. This is because few bacteria are known to possess the genes required to develop competence and because the tested bacteria are unable to reach this physiological state in situ. In this study we found that two soil bacteria, Agrobacterium tumefaciens and Pseudomonas fluorescens, can undergo transformation in soil microcosms without any specific physical or chemical treatment. Moreover, P. fluorescens produced transformants in both sterile and nonsterile soil microcosms but failed to do so in the various in vitro conditions we tested. A. tumefaciens could be transformed in vitro and in sterile soil samples. These results indicate that the number of transformable bacteria could be higher than previously thought and that these bacteria could find the conditions necessary for uptake of extracellular DNA in soil.
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Affiliation(s)
- S Demanèche
- Laboratoire d'Ecologie Microbienne, UMR 5557, Université Lyon I, 69622 Villeurbanne Cedex, France
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Demanèche S, Jocteur-Monrozier L, Quiquampoix H, Simonet P. Evaluation of biological and physical protection against nuclease degradation of clay-bound plasmid DNA. Appl Environ Microbiol 2001; 67:293-9. [PMID: 11133458 PMCID: PMC92568 DOI: 10.1128/aem.67.1.293-299.2001] [Citation(s) in RCA: 166] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to determine the mechanisms involved in the persistence of extracellular DNA in soils and to monitor whether bacterial transformation could occur in such an environment, we developed artificial models composed of plasmid DNA adsorbed on clay particles. We determined that clay-bound DNA submitted to an increasing range of nuclease concentrations was physically protected. The protection mechanism was mainly related to the adsorption of the nuclease on the clay mineral. The biological potential of the resulting DNA was monitored by transforming the naturally competent proteobacterium Acinetobacter sp. strain BD413, allowing us to demonstrate that adsorbed DNA was only partially available for transformation. This part of the clay-bound DNA which was available for bacteria, was also accessible to nucleases, while the remaining fraction escaped both transformation and degradation. Finally, transformation efficiency was related to the perpetuation mechanism, with homologous recombination being less sensitive to nucleases than autonomous replication, which requires intact molecules.
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Affiliation(s)
- S Demanèche
- Laboratoire d'Ecologie Microbienne, UMR 5557, Université Claude Bernard Lyon I, 69622 Villeurbanne Cedex, France
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Wernegreen JJ, Moran NA. Vertical transmission of biosynthetic plasmids in aphid endosymbionts (Buchnera). J Bacteriol 2001; 183:785-90. [PMID: 11133977 PMCID: PMC94939 DOI: 10.1128/jb.183.2.785-790.2001] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2000] [Accepted: 10/16/2000] [Indexed: 11/20/2022] Open
Abstract
This study tested for horizontal transfer of plasmids among Buchnera aphidicola strains associated with ecologically and phylogenetically related aphid hosts (Uroleucon species). Phylogenetic congruence of Buchnera plasmid (trpEG and leuABC) and chromosomal (dnaN and trpB) genes supports strictly vertical long-term transmission of plasmids, which persist due to their contributions to host nutrition rather than capacity for infectious transfer. Synonymous divergences indicate elevated mutation on plasmids relative to chromosomal genes.
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Affiliation(s)
- J J Wernegreen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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29
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Bruce KD, Hughes MR. Terminal restriction fragment length polymorphism monitoring of genes amplified directly from bacterial communities in soils and sediments. Mol Biotechnol 2000; 16:261-9. [PMID: 11252810 DOI: 10.1385/mb:16:3:261] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Terminal Restriction Fragment Length Polymorphism (T-RFLP) or Fluorescent Polymerase Chain Reaction/Restriction Fragment Length Polymorphism (FluRFLP) have made a significant impact on the way in which PCR products amplified from mixed community DNA extracts have been assessed. Technically, these approaches are essentially the same. PCR products are generated that contain at one 5' end label, typically a fluorescent moiety, that will be detected by a DNA sequencing machine. Upon digestion using a specific restriction endonuclease, labeled and unlabeled fragments are generated. This restriction endonuclease is chosen such that following this digestion, each labeled fragment corresponds to a different sequence variant. During electrophoretic separation, the DNA sequencing machine detects only these labeled fragments and therefore detects only the sequence variants. The aim of this article is to describe the protocols and demonstrate that this profiling can be performed using different DNA sequencing machines. The analysis and applications of this approach are also discussed.
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Affiliation(s)
- K D Bruce
- Division of Life Sciences, Franklin-Wilkins Building, 150 Stamford Street, King's College, London, SE1 8WA, UK.
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Abstract
Molecular methods for studying microbial communities are still under development. Enormous sequence catalogues can be collected; they must now be related to microbial activities. Messenger RNA detection, fluorescent in situ hybridization, cell sorting, and oligonucleotide array technology are currently being explored. Biases are associated with all these methods, but combined approaches offer checks and balances.
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Abstract
Molecular evolution in bacteria is examined with an emphasis on the self-assembly of cells capable of primitive division and growth during early molecular evolution. Also, the possibility that some type of encapsulation structure preceeded biochemical pathways and the assembly of genetic material is examined. These aspects will be considered from an evolutionary perspective.
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Trevors J. Molecular evolution in bacteria: genome size, cell size, restriction-modification and recognition. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0020-2452(98)80026-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Bräutigam M, Hertel C, Hammes WP. Evidence for natural transformation of Bacillus subtilis in foodstuffs. FEMS Microbiol Lett 1997; 155:93-8. [PMID: 9345769 DOI: 10.1111/j.1574-6968.1997.tb12691.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The effect of foodstuffs on the natural transformation of Bacillus subtilis was investigated. As examples of complex food matrices milk with various fat contents as well as chocolate milk were used. The frequencies of transformation varied with the fat content and ranged between 3.8 X 10(-4) and 1.4 X 10(-3). Highest frequencies of about 3 X 10(-3) were observed in chocolate milk with 1.5% fat. Development of competence was observed in chocolate milk, resulting in maximal transformation frequencies upon incubation for 10-12 h at 37 degrees C.
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Affiliation(s)
- M Bräutigam
- Institut für Lebensmitteltechnologie, Universität Hohenheim, Stuttgart, Germany
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Abstract
The past year has witnessed several excellent advances in basic and applied research on nucleic acids in the environment. Improved methods for extracting nucleic acids from environmental samples have been published, as well as information on the use of reporter genes in bacteria, natural genetic transformation in soil and DNA adsorption to soil. These advances will have a significant impact on both future research and the way in which we view nucleic acids in the environment.
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Affiliation(s)
- J T Trevors
- Department of Environmental Biology, University of Guelph, Ontario, Canada.
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