1
|
Abstract
Bacteria thrive in environments rich in fluid flow, such as the gastrointestinal tract, bloodstream, aquatic systems, and the urinary tract. Despite the importance of flow, how flow affects bacterial life is underappreciated. In recent years, the combination of approaches from biology, physics, and engineering has led to a deeper understanding of how bacteria interact with flow. Here, we highlight the wide range of bacterial responses to flow, including changes in surface adhesion, motility, surface colonization, quorum sensing, virulence factor production, and gene expression. To emphasize the diversity of flow responses, we focus our review on how flow affects four ecologically distinct bacterial species: Escherichia coli, Staphylococcus aureus, Caulobacter crescentus, and Pseudomonas aeruginosa. Additionally, we present experimental approaches to precisely study bacteria in flow, discuss how only some flow responses are triggered by shear force, and provide perspective on flow-sensitive bacterial signaling.
Collapse
Affiliation(s)
- Gilberto C. Padron
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alexander M. Shuppara
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jessica-Jae S. Palalay
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Anuradha Sharma
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joseph E. Sanfilippo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
2
|
Ahn SY, Liu J, Vellampatti S, Wu Y, Um SH. DNA Transformations for Diagnosis and Therapy. ADVANCED FUNCTIONAL MATERIALS 2021; 31:2008279. [PMID: 33613148 PMCID: PMC7883235 DOI: 10.1002/adfm.202008279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/22/2020] [Indexed: 05/03/2023]
Abstract
Due to its unique physical and chemical characteristics, DNA, which is known only as genetic information, has been identified and utilized as a new material at an astonishing rate. The role of DNA has increased dramatically with the advent of various DNA derivatives such as DNA-RNA, DNA-metal hybrids, and PNA, which can be organized into 2D or 3D structures by exploiting their complementary recognition. Due to its intrinsic biocompatibility, self-assembly, tunable immunogenicity, structural programmability, long stability, and electron-rich nature, DNA has generated major interest in electronic and catalytic applications. Based on its advantages, DNA and its derivatives are utilized in several fields where the traditional methodologies are ineffective. Here, the present challenges and opportunities of DNA transformations are demonstrated, especially in biomedical applications that include diagnosis and therapy. Natural DNAs previously utilized and transformed into patterns are not found in nature due to lack of multiplexing, resulting in low sensitivity and high error frequency in multi-targeted therapeutics. More recently, new platforms have advanced the diagnostic ability and therapeutic efficacy of DNA in biomedicine. There is confidence that DNA will play a strong role in next-generation clinical technology and can be used in multifaceted applications.
Collapse
Affiliation(s)
- So Yeon Ahn
- School of Chemical EngineeringSungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
| | - Jin Liu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaSchool of Chemistry and Chemical Engineering Huazhong University of Science and Technology1037 Luoyu LoadWuhan430074China
| | - Srivithya Vellampatti
- Institute of Convergent Chemical Engineering and TechnologySungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
- Present address:
Progeneer, Inc.#1002, 12, Digital‐ro 31‐gil, Guro‐guSeoul08380Korea
| | - Yuzhou Wu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaSchool of Chemistry and Chemical Engineering Huazhong University of Science and Technology1037 Luoyu LoadWuhan430074China
| | - Soong Ho Um
- School of Chemical EngineeringSKKU Advanced Institute of Nanotechnology (SAINT)Biomedical Institute for Convergence at SKKU (BICS) and Institute of Quantum Biophysics (IQB)Sungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
- Progeneer Inc.#1002, 12, Digital‐ro 31‐gil, Guro‐guSeoul08380Korea
| |
Collapse
|
3
|
Anissi J, El Hassouni M, Ouardaoui A, Sendide K. A simple method for large-scale purification of nucleic acids from plants using calcium phosphate-type monetite. Process Biochem 2017. [DOI: 10.1016/j.procbio.2016.09.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
4
|
Whyte LG, Schultz A, Beilen JB, Luz AP, Pellizari V, Labbé D, Greer CW. Prevalence of alkane monooxygenase genes in Arctic and Antarctic hydrocarbon-contaminated and pristine soils. FEMS Microbiol Ecol 2012; 41:141-50. [PMID: 19709248 DOI: 10.1111/j.1574-6941.2002.tb00975.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Abstract The prevalence of four alkane monooxygenase genotypes (Pseudomonas putida GPo1, Pp alkB; Rhodococcus sp. strain Q15, Rh alkB1 and Rh alkB2; and Acinetobacter sp. strain ADP-1, Ac alkM) in hydrocarbon-contaminated and pristine soils from the Arctic and Antarctica were determined by both culture-independent (PCR hybridization analyses) and culture-dependent (colony hybridization analyses) molecular methods, using oligonucleotide primers and DNA probes specific for each of the alk genotypes. PCR hybridization of total soil community DNA detected the rhodococcal alkB genotypes in most of the contaminated (Rh alkB1, 18/20 soils; Rh alkB2, 13/20) and many pristine soils (Rh alkB1, 9/10 soils; Rh alkB2, 7/10), while Pp alkB was generally detected in the contaminated soils (15/20) but less often in pristine soils (5/10). Ac alkM was rarely detected in the soils (1/30). The colony hybridization technique was used to determine the prevalence of each of the alk genes and determine their relative abundance in culturable cold-adapted (5 degrees C) and mesophilic populations (37 degrees C) from eight of the polar soils. The cold-adapted populations, in general, possessed relatively higher percentages of the Rh alkB genotypes (Rh alkB1, 1.9% (0.55); Rh alkB2, 2.47% (0.89)), followed by the Pp alkB (1.13% (0.50)), and then the Ac alkM (0.53% (0.36)). The Rh alkB1 genotype was clearly more prevalent in culturable cold-adapted bacteria (1.9% (0.55)) than in culturable mesophiles (0.41 (0.55)), suggesting that cold-adapted bacteria are the predominant organisms possessing this genotype. Overall, these results indicated that (i) Acinetobacter spp. are not predominant members of polar alkane degradative microbial communities, (ii) Pseudomonas spp. may become enriched in polar soils following contamination events, and (iii) Rhodococcus spp. may be the predominant alkane-degradative bacteria in both pristine and contaminated polar soils.
Collapse
Affiliation(s)
- L G Whyte
- Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, QC, Canada H4P 2R2
| | | | | | | | | | | | | |
Collapse
|
5
|
Tuson HH, Auer GK, Renner LD, Hasebe M, Tropini C, Salick M, Crone WC, Gopinathan A, Huang KC, Weibel DB. Measuring the stiffness of bacterial cells from growth rates in hydrogels of tunable elasticity. Mol Microbiol 2012; 84:874-91. [PMID: 22548341 DOI: 10.1111/j.1365-2958.2012.08063.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although bacterial cells are known to experience large forces from osmotic pressure differences and their local microenvironment, quantitative measurements of the mechanical properties of growing bacterial cells have been limited. We provide an experimental approach and theoretical framework for measuring the mechanical properties of live bacteria. We encapsulated bacteria in agarose with a user-defined stiffness, measured the growth rate of individual cells and fit data to a thin-shell mechanical model to extract the effective longitudinal Young's modulus of the cell envelope of Escherichia coli (50-150 MPa), Bacillus subtilis (100-200 MPa) and Pseudomonas aeruginosa (100-200 MPa). Our data provide estimates of cell wall stiffness similar to values obtained via the more labour-intensive technique of atomic force microscopy. To address physiological perturbations that produce changes in cellular mechanical properties, we tested the effect of A22-induced MreB depolymerization on the stiffness of E. coli. The effective longitudinal Young's modulus was not significantly affected by A22 treatment at short time scales, supporting a model in which the interactions between MreB and the cell wall persist on the same time scale as growth. Our technique therefore enables the rapid determination of how changes in genotype and biochemistry affect the mechanical properties of the bacterial envelope.
Collapse
Affiliation(s)
- Hannah H Tuson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Satpute SK, Bhuyan SS, Pardesi KR, Mujumdar SS, Dhakephalkar PK, Shete AM, Chopade BA. Molecular Genetics of Biosurfactant Synthesis in Microorganisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 672:14-41. [DOI: 10.1007/978-1-4419-5979-9_2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
7
|
Evaluation of oil recovery by rhamnolipid produced with isolated strain from Iranian oil wells. ANN MICROBIOL 2009. [DOI: 10.1007/bf03175148] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
8
|
Errampalli D, Trevors JT, Lee H, Leung K, Cassidy M, Knoke K, Marwood T, Shaw K, Blears M, Chung E. Bioremediation: A perspective. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/15320389709383560] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- D. Errampalli
- a Department of Environmental Biology , University of Guelph , Guelph, Ontario, N1G 2W1, Canada
| | - J. T. Trevors
- a Department of Environmental Biology , University of Guelph , Guelph, Ontario, N1G 2W1, Canada
| | - H. Lee
- a Department of Environmental Biology , University of Guelph , Guelph, Ontario, N1G 2W1, Canada
| | - K. Leung
- a Department of Environmental Biology , University of Guelph , Guelph, Ontario, N1G 2W1, Canada
| | - M. Cassidy
- a Department of Environmental Biology , University of Guelph , Guelph, Ontario, N1G 2W1, Canada
| | - K. Knoke
- a Department of Environmental Biology , University of Guelph , Guelph, Ontario, N1G 2W1, Canada
| | - T. Marwood
- a Department of Environmental Biology , University of Guelph , Guelph, Ontario, N1G 2W1, Canada
| | - K. Shaw
- a Department of Environmental Biology , University of Guelph , Guelph, Ontario, N1G 2W1, Canada
| | - M. Blears
- a Department of Environmental Biology , University of Guelph , Guelph, Ontario, N1G 2W1, Canada
| | - E. Chung
- a Department of Environmental Biology , University of Guelph , Guelph, Ontario, N1G 2W1, Canada
| |
Collapse
|
9
|
Weir SC, Lee H, Trevors JT. Survival of free and alginate-encapsulatedPseudomonas aeruginosaUG2Lr in soil treated with disinfectants. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1365-2672.1996.tb03184.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
10
|
Puławska J, Sobiczewski P. Development of a semi-nested PCR based method for sensitive detection of tumorigenic Agrobacterium in soil. J Appl Microbiol 2005; 98:710-21. [PMID: 15715875 DOI: 10.1111/j.1365-2672.2004.02503.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To develop a specific, sensitive and rapid PCR-based method for detection of tumorigenic Agrobacterium in soil. METHODS AND RESULTS Three newly designed primers complementary to tms2 gene amplified DNA of only the tumor-inducing agrobacteria of 113 strains tested, resulting in 617 bp and 458 bp products in the first and second rounds of semi-nested PCR respectively. As optimized method of pre-incubation of soil suspensions on selective medium, DNA isolation and two-round semi-nested PCR enabled detection of 1-2 bacterial cells in 1 g of soil. Using this method tumour-inducing Agrobacterium was detected in 67 of 69 samples of naturally infested soil originating from the field, where plants with crown gall symptoms occurred. The pathogen was detected only in two samples of 15 tested, collected from a nursery where crown gall symptoms were not observed. CONCLUSIONS The semi-nested PCR-based method allowed for sensitive and rapid detection of tumorigenic agrobacteria in soil. SIGNIFICANCE AND IMPACT OF THE STUDY The method is proposed for testing of soil in fields intended for nursery production of fruit trees, roses or other plants susceptible to crown gall, as well as a tool for ecological studies.
Collapse
Affiliation(s)
- J Puławska
- Research Institute of Pomology and Floriculture, Skierniewice, Poland.
| | | |
Collapse
|
11
|
England LS, Vincent ML, Trevors JT, Holmes SB. Extraction, detection and persistence of extracellular DNA in forest litter microcosms. Mol Cell Probes 2004; 18:313-9. [PMID: 15294319 DOI: 10.1016/j.mcp.2004.05.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2004] [Accepted: 05/04/2004] [Indexed: 10/26/2022]
Abstract
A DNA extraction method was developed that preferentially extracted extracellular DNA rather than intracellular DNA from forest litter. The method purposely avoided the use of harsh chemicals and physical disruption steps used in total DNA extraction to release DNA from cells. The detection limit of PCR, determined by spiking forest litter samples with a dilution series of Choristoneura fumiferana MNPVegt(-)/lacZ(+) genomic DNA, was about 1 ng DNA or 6.85 x 10(6) target copies 0.5 g(-1) moist forest litter or 0.14 g(-1) dry forest litter. In this study, outdoor terrestrial microcosms, each spiked with 49.2 microg of genomic DNA (from the baculovirus CfMNPVegt(-)/lacZ(+)), were exposed to summer conditions. A 530 bp DNA fragment from the genome of the baculovirus CfMNPVegt(-)/lacZ(+) was detected in these microcosms for about 3 months. The DNA may have persisted for a longer period but was below the detection limit of the PCR analysis.
Collapse
Affiliation(s)
- L S England
- Laboratory of Microbial Technology, Department of Environmental Biology, University of Guelph, Room 3220, Bovey Building, Guelph, Ont., Canada N1G 2W1
| | | | | | | |
Collapse
|
12
|
Mishra S, Sarma PM, Lal B. Crude oil degradation efficiency of a recombinantAcinetobacter baumanniistrain and its survival in crude oil-contaminated soil microcosm. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09606.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
13
|
Margesin R, Labbé D, Schinner F, Greer CW, Whyte LG. Characterization of hydrocarbon-degrading microbial populations in contaminated and pristine Alpine soils. Appl Environ Microbiol 2003; 69:3085-92. [PMID: 12788702 PMCID: PMC161509 DOI: 10.1128/aem.69.6.3085-3092.2003] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biodegradation of petroleum hydrocarbons in cold environments, including Alpine soils, is a result of indigenous cold-adapted microorganisms able to degrade these contaminants. In the present study, the prevalence of seven genotypes involved in the degradation of n-alkanes (Pseudomonas putida GPo1 alkB; Acinetobacter spp. alkM; Rhodococcus spp. alkB1, and Rhodococcus spp. alkB2), aromatic hydrocarbons (P. putida xylE), and polycyclic aromatic hydrocarbons (P. putida ndoB and Mycobacterium sp. strain PYR-1 nidA) was determined in 12 oil-contaminated (428 to 30,644 mg of total petroleum hydrocarbons [TPH]/kg of soil) and 8 pristine Alpine soils from Tyrol (Austria) by PCR hybridization analyses of total soil community DNA, using oligonucleotide primers and DNA probes specific for each genotype. The soils investigated were also analyzed for various physical, chemical, and microbiological parameters, and statistical correlations between all parameters were determined. Genotypes containing genes from gram-negative bacteria (P. putida alkB, xylE, and ndoB and Acinetobacter alkM) were detected to a significantly higher percentage in the contaminated (50 to 75%) than in the pristine (0 to 12.5%) soils, indicating that these organisms had been enriched in soils following contamination. There was a highly significant positive correlation (P < 0.001) between the level of contamination and the number of genotypes containing genes from P. putida and Acinetobacter sp. but no significant correlation between the TPH content and the number of genotypes containing genes from gram-positive bacteria (Rhodococcus alkB1 and alkB2 and Mycobacterium nidA). These genotypes were detected at a high frequency in both contaminated (41.7 to 75%) and pristine (37.5 to 50%) soils, indicating that they are already present in substantial numbers before a contamination event. No correlation was found between the prevalence of hydrocarbon-degradative genotypes and biological activities (respiration, fluorescein diacetate hydrolysis, lipase activity) or numbers of culturable hydrocarbon-degrading soil microorganisms; there also was no correlation between the numbers of hydrocarbon degraders and the contamination level. The measured biological activities showed significant positive correlation with each other, with the organic matter content, and partially with the TPH content and a significant negative correlation with the soil dry-mass content (P < 0.05 to 0.001).
Collapse
Affiliation(s)
- R Margesin
- Institute of Microbiology, University of Innsbruck, A-6020 Innsbruck, Austria.
| | | | | | | | | |
Collapse
|
14
|
Boyandin AN, Lobova TI, Popova LY, Pechurkin NS. Survival and alteration of the plasmid-containing microorganism Escherichia coli Z905/pPHL7 introduced into manmade closed aquatic microcosms. ADVANCES IN SPACE RESEARCH : THE OFFICIAL JOURNAL OF THE COMMITTEE ON SPACE RESEARCH (COSPAR) 2003; 31:1763-1768. [PMID: 14503515 DOI: 10.1016/s0273-1177(03)00118-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
It has been demonstrated that the transgenic microorganism Escherichia coli Z905/pPHL7 (AprLux+) can exist for a long time at an elevated concentration of mineral salts. The microorganism was introduced into microcosms with sterile brackish water (salinity variable from 21 to 22 g l-1) taken from Lake Shira (Khakasia, Russia). The survival of the microorganism was estimated both by measuring the growth of the colonies on solid nutrient media and by the bioluminescence exhibited by the transgenic strain in samples from the microcosms and in the enrichment culture with the added selective factor-ampicillin (50 micrograms/ml). In the enrichment culture, the bioluminescent signal was registered through the 160-day experiment. It has been shown that in the closed microcosms with brackish water the E. coli strain becomes heterogeneous in its ampicillin resistance. The populations of the transgenic strain were mainly represented by isolates able to persist in the medium containing 50 micrograms/ml, but there were also the cells (about 10%) with the threshold of ampicillin resistance not more than 0.05 micrograms/ml. Thus, it was shown that in the microcosms with brackish water and in the absence of the selective factor the transgenic strain survives and retails the recombinant plasmid.
Collapse
Affiliation(s)
- A N Boyandin
- Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Akademgorodok, Krasnoyarsk, Russia.
| | | | | | | |
Collapse
|
15
|
Yarwood RR, Rockhold ML, Niemet MR, Selker JS, Bottomley PJ. Noninvasive quantitative measurement of bacterial growth in porous media under unsaturated-flow conditions. Appl Environ Microbiol 2002; 68:3597-605. [PMID: 12089048 PMCID: PMC126793 DOI: 10.1128/aem.68.7.3597-3605.2002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glucose-dependent growth of the luxCDABE reporter bacterium Pseudomonas fluorescens HK44 was monitored noninvasively in quartz sand under unsaturated-flow conditions within a 45- by 56- by 1-cm two-dimensional light transmission chamber. The spatial and temporal development of growth were mapped daily over 7 days by quantifying salicylate-induced bioluminescence. A nonlinear model relating the rate of increase in light emission after salicylate exposure to microbial density successfully predicted growth over 4 orders of magnitude (r(2) = 0.95). Total model-predicted growth agreed with growth calculated from the mass balance of the system by using previously established growth parameters of HK44 (predicted, 1.2 x 10(12) cells; calculated, 1.7 x 10(12) cells). Colonization expanded in all directions from the inoculation region, including upward migration against the liquid flow. Both the daily rate of expansion of the colonized zone and the population density of the first day's growth in each newly colonized region remained relatively constant throughout the experiment. Nonetheless, substantial growth continued to occur on subsequent days in the older regions of the colonized zone. The proportion of daily potential growth that remained within the chamber declined progressively between days 2 and 7 (from 97 to 13%). A densely populated, anoxic region developed in the interior of the colonized zone even though the sand was unsaturated and fresh growth medium continued to flow through the colonized zone. These data illustrate the potential of a light transmission chamber, bioluminescent bacteria, and sensitive digital camera technology to noninvasively study real-time hydrology-microbiology interactions associated with unsaturated flow in porous media.
Collapse
Affiliation(s)
- R R Yarwood
- Department of Microbiolog, Oregon State University, Corvallis, OR 97331-3804, USA
| | | | | | | | | |
Collapse
|
16
|
Pacheco-Oliver M, McDonald IR, Groleau D, Murrell JC, Miguez CB. Detection of methanotrophs with highly divergent pmoA genes from Arctic soils. FEMS Microbiol Lett 2002; 209:313-9. [PMID: 12007824 DOI: 10.1111/j.1574-6968.2002.tb11150.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Tundra soil samples from the Canadian Arctic community, Kuujjuaq, were analyzed for the presence of the soluble (sMMO) and particulate (pMMO) methane monooxygenase genes. Total genomic DNA extracted from these soils was used as template for PCR using sMMO- and pMMO-specific primers, mmoX1-mmoX2 and A189-A682, respectively. pMMO and sMMO genes were detected in the Kuujjuaq soil samples. Isolation of sMMO-possessing methanotrophic microorganisms from the three soils, as determined by the colony naphthalene oxidation assay, was carried out using direct plating (5 degrees C) and methane enrichment studies (5 degrees C and 25 degrees C). Direct plating did not yield sMMO-possessing methanotrophic bacteria, whereas methane enrichments yielded isolates possessing and expressing sMMO activity. Analysis of derived amino acid sequences of pmoA genes and partial 16S rRNA genes obtained by PCR, using DNA isolated directly from this environment and from isolates, revealed the presence of highly divergent PmoA/AmoA sequences and 16S rRNA sequences that cluster closely with but are distinct from the genes from the genera Methylosinus and Methylocystis.
Collapse
Affiliation(s)
- Maria Pacheco-Oliver
- Microbial and Enzyme Technology Group, Bioprocess Sector, Biotechnology Research Institute, National Research Council, 6100 Royalmount Ave., Montreal, QC H4P 2R2, Canada
| | | | | | | | | |
Collapse
|
17
|
England LS, Trevors JT, Holmes SB. Extraction and detection of baculoviral DNA from lake water, detritus and forest litter. J Appl Microbiol 2001; 90:630-6. [PMID: 11309076 DOI: 10.1046/j.1365-2672.2001.01289.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS This paper describes a quick, reproducible, sensitive method for baculoviral DNA extraction, purification and detection from freshwater and forest litter environments. METHODS AND RESULTS The extraction protocol utilizes enzymatic and chemical lysis and physical disruption. To assess the efficiency of the extraction and purification protocol, PCR was used to detect a 530 bp DNA fragment from the genome of a genetically-modified baculovirus, Choristoneura fumiferana NPVegt-/lacZ+. The detection limit of PCR amplification was routinely about 4.1 x 102 occlusion bodies (OBs) 450 microl-1 lake water. Template DNA from the detritus and forest litter samples required 100-fold dilutions before use in PCR reactions. The detection limits for detritus and forest litter samples were routinely about 7.41 x 103 and 2.08 x 104 OBs 0.5 g-1 dry weight, respectively. CONCLUSION The DNA extraction and purification methodology is reproducible, sensitive and can be used in lieu of, or in conjunction with, insect bioassays. SIGNIFICANCE AND IMPACT OF THE STUDY The DNA extraction and purification protocol described in this paper will facilitate risk assessment and ecological studies of both wild-type and genetically-modified baculoviruses.
Collapse
Affiliation(s)
- L S England
- Department of Natural Resources, Canadian Forest Service, Great Lakes Forestry Centre, Sault Ste Marie, Ontario, Canada
| | | | | |
Collapse
|
18
|
Elväng AM, Westerberg K, Jernberg C, Jansson JK. Use of green fluorescent protein and luciferase biomarkers to monitor survival and activity of Arthrobacter chlorophenolicus A6 cells during degradation of 4-chlorophenol in soil. Environ Microbiol 2001; 3:32-42. [PMID: 11225721 DOI: 10.1046/j.1462-2920.2001.00156.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The recently isolated novel species Arthrobacter chlorophenolicus A6 is capable of growth on and degradation of high concentrations of 4-chlorophenol (up to 350 microg ml(-1)) as the sole carbon and energy source. This strain shows promise for bioremediation of environmental sites contaminated with high levels of chlorophenols. In this study, green fluorescent protein (gfp) or luciferase (luc) genes were used as biomarkers for monitoring cell number and activity, respectively, during degradation of 4-chlorophenol by A. chlorophenolicus cells. The individual marked strains, Arthrobacter chlorophenolicus A6L (luc-tagged) and Arthrobacter chlorophenolicus A6G (gfp-tagged), were monitored during degradation of 250 microg ml(-1) 4-chlorophenol in pure culture and 175 microg g(-1) 4-chlorophenol in soil microcosms. Both gene-tagged strains were capable of cleaning up the contaminated soil during 9 d incubation. During the bioremediation experiments, the luc-tagged cells were monitored using luminometry and the gfp-tagged cells using flow cytometry, in addition to selective plate counting for both strains. The cells remained at high population levels in the soil (evidenced by GFP-fluorescent cell counts) and the A. chlorophenolicus A6L population was metabolically active (evidenced by luciferase activity measurements). These results demonstrate that the Arthrobacter chlorophenolicus A6 inoculum is effective for cleaning-up soil containing high concentrations of 4-chlorophenol.
Collapse
Affiliation(s)
- A M Elväng
- Department of Biochemistry, Arrhenius Laboratories, Stockholm University, Sweden
| | | | | | | |
Collapse
|
19
|
Lowder M, Unge A, Maraha N, Jansson JK, Swiggett J, Oliver JD. Effect of starvation and the viable-but-nonculturable state on green fluorescent protein (GFP) fluorescence in GFP-tagged Pseudomonas fluorescens A506. Appl Environ Microbiol 2000; 66:3160-5. [PMID: 10919764 PMCID: PMC92128 DOI: 10.1128/aem.66.8.3160-3165.2000] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The green fluorescent protein (GFP) gene, gfp, of the jellyfish Aequorea victoria is being used as a reporter system for gene expression and as a marker for tracking prokaryotes and eukaryotes. Cells that have been genetically altered with the gfp gene produce a protein that fluoresces when it is excited by UV light. This unique phenotype allows gfp-tagged cells to be specifically monitored by nondestructive means. In this study we determined whether a gfp-tagged strain of Pseudomonas fluorescens continued to fluoresce under conditions under which the cells were starved, viable but nonculturable (VBNC), or dead. Epifluorescent microscopy, flow cytometry, and spectrofluorometry were used to measure fluorescence intensity in starved, VBNC, and dead or dying cells. Results obtained by using flow cytometry indicated that microcosms containing VBNC cells, which were obtained by incubation under stress conditions (starvation at 37.5 degrees C), fluoresced at an intensity that was at least 80% of the intensity of nonstressed cultures. Similarly, microcosms containing starved cells incubated at 5 and 30 degrees C had fluorescence intensities that were 90 to 110% of the intensity of nonstressed cells. VBNC cells remained fluorescent during the entire 6-month incubation period. In addition, cells starved at 5 or 30 degrees C remained fluorescent for at least 11 months. Treatment of the cells with UV light or incubation at 39 or 50 degrees C resulted in a loss of GFP from the cells. There was a strong correlation between cell death and leakage of GFP from the cells, although the extent of leakage varied depending on the treatment. Most dead cells were not GFP fluorescent, but a small proportion of the dead cells retained some GFP at a lower concentration than the concentration in live cells. Our results suggest that gfp-tagged cells remain fluorescent following starvation and entry into the VBNC state but that fluorescence is lost when the cells die, presumably because membrane integrity is lost.
Collapse
Affiliation(s)
- M Lowder
- Department of Biology, University of North Carolina at Charlotte, 28223, USA
| | | | | | | | | | | |
Collapse
|
20
|
Thomas JC, St-Pierre Y, Beaudet R, Villemur R. Monitoring by laser-flow-cytometry of the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. strain 107 during biotreatment of a contaminated soil. Can J Microbiol 2000; 46:433-40. [PMID: 10872079 DOI: 10.1139/w00-008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A flow cytometric method (FCM) was used to detect and accurately enumerate a polycyclic aromatic hydrocarbon-degrading bacterial strain, Sphingomonas sp. 107, inoculated into a soil sample artificially contaminated with pyrene. To compare the FCM method with colony forming unit (CFU) assays, a rifampicin-resistant Sphingomonas sp. 107 was obtained which could be distinguished from the indigenous microflora, since there was no organism resistant to rifampicin in the soil that could transform indole to indigo (naphthalene dioxygenase activity). By combining light-scattering profiles (i.e., morphological properties), ethidium bromide influx (i.e., cell wall permeability), and fluorescence in situ hybridization against the 16S rRNA (i.e., detection specificity), we could enumerate the bacterial population of interest from the indigenous microflora and soil debris during the biotreatment. The FCM technique revealed that the number of inoculated Sphingomonas cells decreased gradually for 15 days of incubation before reaching a steady level of 7 to 12 x 10(5) cells.g-1 of soil. Similar values were obtained with the CFU assay. During this period, pyrene concentration decreased from 632 to 26 mg.kg-1 of dry soil. The FCM detection was improved by adding blocking reagent to the hybridization buffer to minimize the non-specific attachment of the fluorescent probe to soil particles. Combined with the improvements in probe technology, FCM detection was shown to be a good alternative to the conventional culture methods for the analysis of bacterial populations in environmental samples. This technique could be potentially useful for the detection of microorganisms that grow poorly in culture.
Collapse
Affiliation(s)
- J C Thomas
- INRS, Institut Armand-Frappier, Microbiologie et Biotechnologie, Laval, Canada
| | | | | | | |
Collapse
|
21
|
Cassidy MB, Leung KT, Lee H, Trevors JT. A comparison of enumeration methods for culturable Pseudomonas fluorescens cells marked with green fluorescent protein. J Microbiol Methods 2000; 40:135-45. [PMID: 10699669 DOI: 10.1016/s0167-7012(99)00131-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The detection of bacteria in environmental samples using genetic markers is valuable in microbial ecology. The green fluorescent protein (GFP) reporter gene was studied under nutrient starvation conditions at 4 degrees C, 23 degrees C and 30 degrees C in Pseudomonas fluorescens R2fG1 cells tagged with a red-shifted gfp. Fluorescence intensity was not significantly different in cells maintained in a buffer for at least 48 days at all the tested temperatures. gfp-Tagged R2fG1 cells were introduced into bulk soil microcosms and soil microcosms with wheat seedlings. GFP-marked cells were enumerated immediately after inoculation into soil and again in soil and root samples after 10 days. Counts of culturable colonies were obtained from drop plates using 5-microl aliquots of serial dilutions viewed with an epifluorescent microscope. Traditional spread plates (using 100-microl aliquots) and the most-probable-number (MPN) method using a spectrofluorometer were also used to enumerate the GFP-marked Pseudomonas cells in soil, rhizosphere and rhizoplane samples. Microcolonies were visualized on root surfaces under the epifluorescent microscope after immobilizing in agar and incubation for 24 h. Counts from traditional spread plates were significantly higher (P<0.05) than the population estimates of the MPN method for all treatments at any sampling time. Counts using the drop plate method, however, were not significantly different (P<0.05) except in one treatment, and provided similar estimates in half the time of spread plates and at an estimated third of the cost.
Collapse
Affiliation(s)
- M B Cassidy
- Department of Environmental Biology, University of Guelph, Guelph, Canada
| | | | | | | |
Collapse
|
22
|
Jansson JK, Björklöf K, Elvang AM, Jørgensen KS. Biomarkers for monitoring efficacy of bioremediation by microbial inoculants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2000; 107:217-223. [PMID: 15092998 DOI: 10.1016/s0269-7491(99)00140-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/1998] [Accepted: 05/22/1999] [Indexed: 05/24/2023]
Abstract
Bioaugmentation of contaminated sites with microbes that are adapted or genetically engineered for degradation of specific toxic compounds is an area that is currently being explored as a clean-up option. Biomarkers have been developed to track the survival and efficacy of specific bacteria that are used as inocula for bioremediation of contaminated soil. Examples of biomarkers include the luc gene, encoding firefly luciferase and the gfp gene, encoding the green fluorescent protein (GFP). The luc gene was used to tag different bacteria used for bioremediation of gasoline or chlorophenols. The bacteria were monitored on the basis of luciferase activity in cell extracts from soil. The gfp gene was also used to monitor bacteria during degradation of chlorophenol in soil, based on fluorescence of the GFP protein. Other biomarkers can also be used for monitoring of microbial inocula used for bioaugmentation of contaminated sites. The choice of biomarker and monitoring system depends on the particular site, bacterial strain and sensitivity and specificity of detection required.
Collapse
Affiliation(s)
- J K Jansson
- Department of Biochemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, S-10691 Stockholm, Sweden.
| | | | | | | |
Collapse
|
23
|
Errampalli D, Okamura H, Lee H, Trevors JT, Elsas J. Green fluorescent protein as a marker to monitor survival of phenanthrene-mineralizing Pseudomonas sp. UG14Gr in creosote-contaminated soil. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb00504.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|
24
|
Hall BM, McLoughlin AJ, Leung KT, Trevors JT, Lee H. Transport and survival of alginate-encapsulated and free lux-lac marked Pseudomonas aeruginosa UG2Lr cells in soil. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb01561.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
25
|
Dyke M, Prosser J. Effect of cell density and attachment on resuscitation in soil of starved Pseudomonas fluorescens MON787. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb01562.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
26
|
Tin Leung K, Watt A, Lee* H, Trevors JT. Quantitative detection of pentachlorophenol-degrading Sphingomonas sp. UG30 in soil by a most-probable-number/polymerase chain reaction protocol. J Microbiol Methods 1997. [DOI: 10.1016/s0167-7012(97)00082-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
27
|
Rotthauwe JH, Witzel KP, Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol 1997; 63:4704-12. [PMID: 9406389 PMCID: PMC168793 DOI: 10.1128/aem.63.12.4704-4712.1997] [Citation(s) in RCA: 1362] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The naturally occurring genetic heterogeneity of autotrophic ammonia-oxidizing populations belonging to the beta subclass of the Proteobacteria was studied by using a newly developed PCR-based assay targeting a partial stretch of the gene which encodes the active-site polypeptide of ammonia monooxygenase (amoA). The PCR yielded a specific 491-bp fragment with all of the nitrifiers tested, but not with the homologous stretch of the particulate methane monooxygenase, a key enzyme of methane-oxidizing bacteria. The assay also specifically detected amoA in DNA extracted from various aquatic and terrestrial environments. The resulting PCR products retrieved from rice roots, activated sludge, a freshwater sample, and an enrichment culture were used for the generation of amoA gene libraries. No false positives were detected in a set of 47 randomly selected clone sequences that were analyzed further. The majority of the environmental sequences retrieved from rice roots and activated sludge grouped within the phylogenetic radiation defined by cultured strains of the genera Nitrosomonas and Nitrosospira. The comparative analysis identified members of both of these genera in activated sludge; however, only Nitrosospira-like sequences with very similar amino acid patterns were found on rice roots. Further differentiation of these molecular isolates was clearly possible on the nucleic acid level due to the accumulation of synonymous mutations, suggesting that several closely related but distinct Nitrosospira-like populations are the main colonizers of the rhizosphere of rice. Each of the amoA gene libraries obtained from the freshwater sample and the enrichment culture was dominated by a novel lineage that shared a branch with the Nitrosospira cluster but could not be assigned to any of the known pure cultures. Our data suggest that amoA represents a very powerful molecular tool for analyzing indigenous ammonia-oxidizing communities due to (i) its specificity, (ii) its fine-scale resolution of closely related populations, and (iii) the fact that a functional trait rather than a phylogenetic trait is detected.
Collapse
Affiliation(s)
- J H Rotthauwe
- Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany
| | | | | |
Collapse
|
28
|
Vahjen W, Munch JC, Tebbe CC. Fate of three genetically engineered, biotechnologically important microorganism species in soil: impact of soil properties and intraspecies competition with nonengineered strains. Can J Microbiol 1997. [DOI: 10.1139/m97-120] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The fate of a bacterium and two yeast species genetically engineered by insertion of a nucleotide sequence encoding for aprotinin was studied in three different soils. Corynebacterium glutamicum carried the recombinant gene on plasmid pUN1, Saccharomyces cerevisiae carried the gene on plasmid p707, and in Pichia angusta (formerly Hansenula polymoropha) LR9-Apr8, the gene was chromosomally inserted with eight tandem repeats. Corynebacterium glutamicum persisted longer than both yeast strains. In a sandy loam of pH 5.9, recovery rates of cultured cells were lower than in a clay silt or a silty sand, with pH values of 7.1 and 6.7, respectively. Generally, persistence at 10 °C was higher than at 20 °C. An adaptation of the genetically engineered strains resulting in higher soil persistence was not observed for any of the three species tested. Competition experiments between nonengineered and genetically engineered strains in presterilized soils revealed a reduced fitness of the engineered strains. However, a more competitive C. glutamicum pUN1 evolved after reinoculation of cells, preselected by a preceding competition experiment.Key words: ecological risk assessment, genetic engineering, nondeliberate release, soil inoculation, aprotinin.
Collapse
|
29
|
Cassidy M, Lee H, Trevors* J. Survival and activity of lac-lux marked Pseudomonas aeruginosa UG2Lr cells encapsulated in κ-carrageenan over four years at 4°C. J Microbiol Methods 1997. [DOI: 10.1016/s0167-7012(97)00059-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
30
|
Jansson JK, Prosser JI. Quantification of the presence and activity of specific microorganisms in nature. Mol Biotechnol 1997; 7:103-20. [PMID: 9219225 DOI: 10.1007/bf02761746] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Traditional techniques for assessment of microbial numbers and activity generally lack the specificity required for risk assessment following environmental release of genetically engineered microbial inocula. Immunological and molecular-based techniques, such as DNA probing and genetic tagging, were initially used to determine the presence or absence of microorganisms in environmental samples. Increasingly they are being developed for quantification of populations of specific organisms, either indigenous or introduced, in the environment. In addition, they are being used to quantify the activity of particular organisms or groups of organisms, greatly extending the range of techniques available to the microbial ecologist. This article reviews the use of traditional techniques for the quantification of microbial population size and activity and the application of molecular techniques, including DNA probing, genetic marking, use of fluorescent probes, and quantitative PCR, in combination with advanced cell detection techniques such as confocal laser scanning microscopy and flow cytometry.
Collapse
Affiliation(s)
- J K Jansson
- Department of Biochemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden.
| | | |
Collapse
|
31
|
|
32
|
Weir SC, Lee H, Trevors JT. Effect of Selected Disinfectants on the Persistence and Movement of a Genetically Engineered Pseudomonas sp. in Soil. Syst Appl Microbiol 1996. [DOI: 10.1016/s0723-2020(96)80072-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
33
|
Trevors JT. DNA in soil: adsorption, genetic transformation, molecular evolution and genetic microchip. Antonie Van Leeuwenhoek 1996; 70:1-10. [PMID: 8836436 DOI: 10.1007/bf00393564] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This review examines interactions between DNA and soil with an emphasis on the persistence and stability of DNA in soil. The role of DNA in genetic transformation in soil microorganisms will also be discussed. In addition, a postulated mechanism for stabilization and elongation/assembly of primitive genetic material and the role of soil particles, salt concentrations, temperature cycling and crystal formation is examined.
Collapse
Affiliation(s)
- J T Trevors
- Department of Environmental Biology, University of Guelph, Ontario, Canada.
| |
Collapse
|
34
|
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.
Collapse
Affiliation(s)
- J T Trevors
- Department of Environmental Biology, University of Guelph, Ontario, Canada.
| |
Collapse
|
35
|
Kozdrój J. Survival of lux-marked bacteria introduced into soil and the rhizosphere of bean (Phaseolus vulgaris L.). World J Microbiol Biotechnol 1996; 12:261-5. [PMID: 24415235 DOI: 10.1007/bf00360925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/27/1995] [Accepted: 11/27/1995] [Indexed: 10/26/2022]
Abstract
The survival of lux-marked recombinants of Escherichia coli and Bacillus subtilis was studied in the rhizosphere of bean (Phaseolus vulgaris L.) and in bulk soil. The number of E. coli (pSB343) containing a complete lux operon did not differ significantly according to whether they were introduced into soil separately or together with a non-luminescent mutant Pseudomonas fluorescens R2fN. When genetically altered strains of E. coli and B. subtilis bearing a complete or an incomplete lux-reporter system were introduced into soil, the numbers of surviving cells were the same both in the rhizosphere and bulk soil. The insertion of lux genes into bacterial strains therefore does not affect their competitiveness and survival in the rhizosphere and bulk soil.
Collapse
|
36
|
Berthelet M, Whyte LG, Greer CW. Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns. FEMS Microbiol Lett 1996; 138:17-22. [PMID: 8674967 DOI: 10.1111/j.1574-6968.1996.tb08128.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Polyvinylpolypyrrolidone spin columns were used to rapidly purify crude soil DNA extracts from humic materials for polymerase chain reaction (PCR) analysis. The PCR detection limit for the tfdC gene, encoding chlorocatechol dioxygenase from the 2,4-dichlorophenoxyacetic acid degradation pathway, was 10(1)-10(2) cells/g soil in inoculated soils. The procedure could be applied to the amplification of biodegradative genes from indigenous microbial populations from a wide variety of soil types, and the entire analysis could be performed within 8 h.
Collapse
Affiliation(s)
- M Berthelet
- National Research Council of Canada, Biotechnology Research Institute, Montréal, Québec, Canada
| | | | | |
Collapse
|
37
|
Fedi S, Brazil D, Dowling DN, O'Gara F. Construction of a modified mini-Tn5 lacZY non-antibiotic marker cassette: ecological evaluation of a lacZY marked Pseudomonas strain in the sugarbeet rhizosphere. FEMS Microbiol Lett 1996; 135:251-7. [PMID: 8595865 DOI: 10.1111/j.1574-6968.1996.tb07997.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
In order to monitor the fate of genetically manipulated fluorescent pseudomonads following release into the environment, a lacZY transposable cassette, lacking antibiotic resistance genes, was constructed using a pUT suicide plasmid delivery system. The resulting plasmid, pUTLacZY, can be easily used to generate lacZY marked pseudomonads without having to use antibiotic resistance determinants. The lacZY transposon generates random, stable transcriptional/translational fusions on integration into the target genome. Pseudomonas fluorescens strain F113 was marked with lacZY and was unaltered with respect to ecological fitness in the rhizosphere. Although lateral gene transfer of the chromosomally integrated lacZY marker could be detected in vitro, it was not detected in rhizosphere microcosms.
Collapse
Affiliation(s)
- S Fedi
- Department of Microbiology, University College, Cork, Ireland
| | | | | | | |
Collapse
|
38
|
Weir SC, Providenti MA, Lee H, Trevors JT. Effect of alginate encapsulation and selected disinfectants on survival of and phenanthrene mineralization byPseudomonas sp UG14Lr in creosote-contaminated soil. ACTA ACUST UNITED AC 1996. [DOI: 10.1007/bf01569923] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
39
|
Prosser JI, Killham K, Glover LA, Rattray EA. Luminescence-based systems for detection of bacteria in the environment. Crit Rev Biotechnol 1996; 16:157-83. [PMID: 8635199 DOI: 10.3109/07388559609147420] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The development of techniques for detection and tracking of microorganisms in natural environments has been accelerated by the requirement for assessment of the risks associated with environmental release of genetically engineered microbial inocula. Molecular marker systems are particularly appropriate for such studies and luminescence-based markers have the broadest range of applications, involving the introduction of prokaryotic (lux) or eukaryotic (luc) genes for the enzyme luciferase. Lux or luc genes can be detected on the basis of unique DNA sequences by gene probing and PCR amplification, but the major advantage of luminescence-based systems is the ability to detect light emitted by marked organisms or by luciferase activity in cell-free extracts. Luminescent colonies can be detected by eye, providing distinction from colonies of indigenous organisms, and the sensitivity of plate counting can be increased greatly by CCD imaging. Single cells or microcolonies of luminescent organisms can also be detected in environmental samples by CCD image-enhanced microscopy, facilitating study of their spatial distribution. The metabolic activity of luminescence-marked populations can be quantified by luminometry and does not require extraction of cells or laboratory growth. Metabolic activity, and potential activity, of marked organisms therefore can be measured during colonization of soil particles and plant material in real time without disturbing the colonization process. In comparison with traditional activity techniques, luminometry provides significant increases in sensitivity, accuracy, and, most importantly, selectivity, as activity can be measured in the presence of indigenous microbial communities. The sensitivity, speed, and convenience of luminescence measurements make this a powerful technique that is being applied to the study of an increasingly wide range of ecological problems. These include microbial survival and recovery, microbial predation, plant pathogenicity, phylloplane and rhizosphere colonization and reporting of gene expression in environmental samples.
Collapse
Affiliation(s)
- J I Prosser
- Department of Molecular and Cell Biology, University of Aberdeen, Marischal College, Scotland
| | | | | | | |
Collapse
|
40
|
Chatterjee J, Meighen EA. BIOTECHNOLOGICAL APPLICATIONS OF BACTERIAL BIOLUMINESCENCE (lux) GENES. Photochem Photobiol 1995. [DOI: 10.1111/j.1751-1097.1995.tb08711.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
41
|
Weir SC, Dupuis SP, Providenti MA, Lee H, Trevors JT. Nutrient-enhanced survival of and phenanthrene mineralization by alginate-encapsulated and free Pseudomonas sp. UG14Lr cells in creosote-contaminated soil slurries. Appl Microbiol Biotechnol 1995; 43:946-51. [PMID: 7576562 DOI: 10.1007/bf02431932] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The effects of nutrient amendment and alginate encapsulation on survival of and phenanthrene mineralization by the bioluminescent Pseudomonas sp. UG14Lr in creosote-contaminated soil slurries were examined. UG14Lr was inoculated into creosote-contaminated soil slurries either as a free cell suspension or encapsulated in alginate beads prepared with montmorillonite clay and skim milk. Additional treatments were free-cell-inoculated slurries amended with sterile alginate beads, free-cell-inoculated and uninoculated slurries amended with skim milk only, and uninoculated, unamended slurries. Mineralization was determined by measuring 14CO2 released from radiolabelled phenanthrene. Survival was measured by selective plating and bioluminescence. Inclusion of skim milk was found to enhance both survival of and phenanthrene mineralization by free and encapsulated UG14Lr cells.
Collapse
Affiliation(s)
- S C Weir
- Department of Environmental Biology, University of Guelph, Ontario, Canada
| | | | | | | | | |
Collapse
|
42
|
Survival of lac-lux marked Pseudomonas aeruginosa UG2Lr cells encapsulated in κ-carrageenan and alginate. J Microbiol Methods 1995. [DOI: 10.1016/0167-7012(95)00038-m] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
43
|
Providenti MA, Flemming CA, Lee H, Trevors JT. Effect of addition of rhamnolipid biosurfactants or rhamnolipid-producing Pseudomonas aeruginosa on phenanthrene mineralization in soil slurries. FEMS Microbiol Ecol 1995. [DOI: 10.1111/j.1574-6941.1995.tb00123.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
44
|
Survival and Transport of lac-lux Marked Pseudomonas fluorescens Strain in Uncontaminated and Chemically Contaminated Soils. Syst Appl Microbiol 1995. [DOI: 10.1016/s0723-2020(11)80079-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
45
|
Leung K, Cassidy MB, Holmes SB, Lee H, Trevors JT. Survival of κ-carrageenan-encapsulated and unencapsulated Pseudomonas aeruginosa UG2Lr cells in forest soil monitored by polymerase chain reaction and spread plating. FEMS Microbiol Ecol 1995. [DOI: 10.1111/j.1574-6941.1995.tb00270.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
|
46
|
Schraft H, Griffiths MW. Specific oligonucleotide primers for detection of lecithinase-positive Bacillus spp. by PCR. Appl Environ Microbiol 1995; 61:98-102. [PMID: 7887632 PMCID: PMC167265 DOI: 10.1128/aem.61.1.98-102.1995] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
An assay based on the PCR has been developed to facilitate detection and identification of Bacillus cereus in foods. Three primers for the PCR have been designed within the sequence for cereolysin AB, a cytolytic determinant that encodes lecithin-hydrolyzing and hemolytic activities of B. cereus. With the PCR and hybridization, the specificity of the primers was tested with 39 isolates of the B. cereus group, with 17 other Bacillus spp., and with 21 non-Bacillus strains. Results demonstrate a high specificity of the three oligonucleotides for isolates of the B. cereus group. With a combined PCR-hybridization assay, the detection limit for B. cereus in artificially contaminated milk was 1 CFU/ml of milk.
Collapse
Affiliation(s)
- H Schraft
- Department of Food Science, University of Guelph, Ontario, Canada
| | | |
Collapse
|
47
|
Abstract
Recent advances in microbiology and molecular biology have a unifying influence on our understanding of genetic diversity/similarity and evolutionary relationships in microorganisms. This article attempts to unify information from diverse areas such as microbiology, molecular biology, microbial physiology, clay crystal genes, metals-microbe-clay interactions and bacterial DNA restriction-modification systems (R-M) as they may apply to molecular evolution of bacteria. The possibility is discussed that the first informational molecules may have been catalytic RNA (micro-assembler) not DNA (now the master copy) and these first micro-assemblers may have been precursors of ribosomes.
Collapse
Affiliation(s)
- J T Trevors
- Department of Environmental Biology, University of Guelph, Ontario, Canada
| |
Collapse
|
48
|
Flemming CA, Lee H, Trevors JT. Bioluminescent Most-Probable-Number Method To Enumerate
lux
-Marked
Pseudomonas aeruginosa
UG2Lr in Soil. Appl Environ Microbiol 1994; 60:3458-61. [PMID: 16349396 PMCID: PMC201832 DOI: 10.1128/aem.60.9.3458-3461.1994] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bioluminescence measured with a luminometer and charge-coupled device was an effective marker in most-probable-number assays for
luxAB
-marked
Pseudomonas aeruginosa
UG2Lr in soil. Most-probable-number assays with microtiter plate wells and luminometer tubes gave estimates for UG2Lr that were similar to viable colony counts. Both methods detected five cells per g of soil.
Collapse
Affiliation(s)
- C A Flemming
- Department of Environmental Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | | | | |
Collapse
|
49
|
LEUNG K, ENGLAND LS, CASSIDY MB, TREVORS JT, WEIR S. Microbial diversity in soil: effect of releasing genetically engineered micro-organisms. Mol Ecol 1994. [DOI: 10.1111/j.1365-294x.1994.tb00081.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|