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Jang HB, Chittick L, Li YF, Zablocki O, Sanderson CM, Carrillo A, van den Engh G, Sullivan MB. Viral tag and grow: a scalable approach to capture and characterize infectious virus-host pairs. ISME COMMUNICATIONS 2022; 2:12. [PMID: 37938680 PMCID: PMC9723727 DOI: 10.1038/s43705-022-00093-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/06/2022] [Accepted: 01/13/2022] [Indexed: 04/27/2023]
Abstract
Viral metagenomics (viromics) has reshaped our understanding of DNA viral diversity, ecology, and evolution across Earth's ecosystems. However, viromics now needs approaches to link newly discovered viruses to their host cells and characterize them at scale. This study adapts one such method, sequencing-enabled viral tagging (VT), to establish "Viral Tag and Grow" (VT + Grow) to rapidly capture and characterize viruses that infect a cultivated target bacterium, Pseudoalteromonas. First, baseline cytometric and microscopy data improved understanding of how infection conditions and host physiology impact populations in VT flow cytograms. Next, we extensively evaluated "and grow" capability to assess where VT signals reflect adsorption alone or wholly successful infections that lead to lysis. Third, we applied VT + Grow to a clonal virus stock, which, coupled to traditional plaque assays, revealed significant variability in burst size-findings that hint at a viral "individuality" parallel to the microbial phenotypic heterogeneity literature. Finally, we established a live protocol for public comment and improvement via protocols.io to maximally empower the research community. Together these efforts provide a robust foundation for VT researchers, and establish VT + Grow as a promising scalable technology to capture and characterize viruses from mixed community source samples that infect cultivable bacteria.
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Affiliation(s)
- Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Lauren Chittick
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Yueh-Fen Li
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Olivier Zablocki
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Alfonso Carrillo
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
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Fabrication of a new all-in-one microfluidic dielectrophoresis integrated chip and living cell separation. iScience 2022; 25:103776. [PMID: 35146391 PMCID: PMC8819401 DOI: 10.1016/j.isci.2022.103776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/16/2021] [Accepted: 01/11/2022] [Indexed: 11/22/2022] Open
Abstract
Microfluidic dielectrophoresis (DEP) technology has been applied to many devices to perform label-free target cell separation. Cells separated by these devices are used in laboratories, mainly for medical research. The present study designed a microfluidic DEP device to fabricate a rapid and semiautomated cell separation system in conjunction with microscopy to enumerate the separated cells. With this device, we efficiently segregated bacterial cells from liquid products and enriched one cell type from two mixed eukaryotic cell types. The device eliminated sample pretreatment and established cell separation by all-in-one operation in a lab-on-chip, requiring only a small sample volume (0.5–1 mL) to enumerate the target cells and completing the entire separation process within 30 min. Such a rapid cell separation technique is in high demand by many researchers to promptly characterize the target cells. A new all-in-one microfluidic dielectrophoresis integrated chip is fabricated Simultaneous operation of buffer exchange and continuous cell separation on a chip Chip’s cell separation performance is evaluated with bacterial and eukaryotic cells
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Advances and applications of isomotive dielectrophoresis for cell analysis. Anal Bioanal Chem 2020; 412:3813-3833. [DOI: 10.1007/s00216-020-02590-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/03/2020] [Accepted: 03/09/2020] [Indexed: 01/31/2023]
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He S, Hong X, Huang T, Zhang W, Zhou Y, Wu L, Yan X. Rapid quantification of live/dead lactic acid bacteria in probiotic products using high-sensitivity flow cytometry. Methods Appl Fluoresc 2017; 5:024002. [DOI: 10.1088/2050-6120/aa64e4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Lee D, Hwang B, Kim B. The potential of a dielectrophoresis activated cell sorter (DACS) as a next generation cell sorter. MICRO AND NANO SYSTEMS LETTERS 2016. [DOI: 10.1186/s40486-016-0028-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Tejerizo GT, Bañuelos LA, Cervantes L, Gaytán P, Pistorio M, Romero D, Brom S. Development of molecular tools to monitor conjugative transfer in rhizobia. J Microbiol Methods 2015; 117:155-63. [PMID: 26272377 DOI: 10.1016/j.mimet.2015.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 01/26/2023]
Abstract
Evolution of bacterial populations has been extensively driven by horizontal transfer events. Conjugative plasmid transfer is considered the principal contributor to gene exchange among bacteria. Several conjugative and mobilizable plasmids have been identified in rhizobia, and two major molecular mechanisms that regulate their transfer have been described, under laboratory conditions. The knowledge of rhizobial plasmid transfer regulation in natural environments is very poor. In this work we developed molecular tools to easily monitor the conjugative plasmid transfer in rhizobia by flow cytometry (FC) or microscopy. 24 cassettes were constructed by combining a variety of promotors, fluorescent proteins and antibiotic resistance genes, and used to tag plasmids and chromosome of donor strains. We were able to detect plasmid transfer after conversion of non-fluorescent recipients into fluorescent transconjugants. Flow cytometry (FC) was optimized to count donor, recipient and transconjugant strains to determine conjugative transfer frequencies. Results were similar, when determined either by FC or by viable counts. Our constructions also allowed the visualization of transconjugants in crosses performed on bean roots. The tools presented here may also be used for other purposes, such as analysis of transcriptional fusions or single-cell tagging. Application of the system will allow the survey of how different environmental conditions or other regulators modulate plasmid transfer in rhizobia.
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Affiliation(s)
- Gonzalo Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata-CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.
| | - Luis Alfredo Bañuelos
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Laura Cervantes
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata-CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - David Romero
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
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Altamore I, Lanzano L, Gratton E. Dual channel detection of ultra low concentration of bacteria in real time by scanning FCS. MEASUREMENT SCIENCE & TECHNOLOGY 2013; 24:65702. [PMID: 24039347 PMCID: PMC3770197 DOI: 10.1088/0957-0233/24/6/065702] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We describe a novel method to detect very low concentrations of bacteria in water. Our device consists of a portable horizontal geometry small confocal microscope with large pinhole and a holder for cylindrical cuvettes containing the sample. Two motors provide a fast rotational and slow vertical motion of the cuvette so the device looks like a simplified flow cytometer without flow. To achieve high sensitivity the design has two detection channels. Bacteria are stained by two different nucleic acid dyes and excited with two different lasers. Data are analyzed with a correlation filter based on particle passage pattern recognition. The passage of a particle through the illumination volume is compared with a Gaussian pattern in both channels. The width of the Gaussian correlates with the time of passage of the particle so one particle is counted when the algorithm finds a match with a Gaussian in both channels. The concentration of particles in the sample is deduced from the total number of coincident hits and the total volume scanned. This portable setup provides higher sensitivity, low cost and it could have a wide use ranging from clinical applications to pollution monitors and water and air quality control.
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Cell sorting enriches Escherichia coli mutants that rely on peptidoglycan endopeptidases to suppress highly aberrant morphologies. J Bacteriol 2012; 195:855-66. [PMID: 23243305 DOI: 10.1128/jb.01450-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial morphology imparts physiological advantages to cells in different environments and, judging by the fidelity with which shape is passed to daughter cells, is a tightly regulated characteristic. Surprisingly, only in the past 10 to 15 years has significant headway been made in identifying the mechanisms by which cells create and maintain particular shapes. One reason for this is that the relevant discoveries have relied heavily on the arduous, somewhat subjective process of manual microscopy. Here, we show that flow cytometry, coupled with the sorting capability of fluorescence-activated cell sorting (FACS), can detect, quantify, and enrich bacteria with morphological alterations. The light scattering properties of several highly aberrant morphological mutants of Escherichia coli were characterized by flow cytometry. Cells from a region that overlapped the distribution of normal rod-shaped cells were collected by FACS and reincubated. After 4 to 15 iterations of this enrichment process, suppressor mutants were isolated that returned almost all the population to a near-normal shape. Suppressors were successfully isolated from strains lacking three or four penicillin binding proteins (PBPs) but not from a mutant lacking a total of seven PBPs. The peptidoglycan endopeptidase, AmpH, was identified as being important for the suppression process, as was a related endopeptidase, MepA. The results validate the use of cell sorting as a means for studying bacterial morphology and identify at least one new class of enzymes required for the suppression of cell shape defects.
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Vorobjev IA, Buchholz K, Prabhat P, Ketman K, Egan ES, Marti M, Duraisingh MT, Barteneva NS. Optimization of flow cytometric detection and cell sorting of transgenic Plasmodium parasites using interchangeable optical filters. Malar J 2012; 11:312. [PMID: 22950515 PMCID: PMC3544587 DOI: 10.1186/1475-2875-11-312] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 08/29/2012] [Indexed: 12/05/2022] Open
Abstract
Background Malaria remains a major cause of morbidity and mortality worldwide. Flow cytometry-based assays that take advantage of fluorescent protein (FP)-expressing malaria parasites have proven to be valuable tools for quantification and sorting of specific subpopulations of parasite-infected red blood cells. However, identification of rare subpopulations of parasites using green fluorescent protein (GFP) labelling is complicated by autofluorescence (AF) of red blood cells and low signal from transgenic parasites. It has been suggested that cell sorting yield could be improved by using filters that precisely match the emission spectrum of GFP. Methods Detection of transgenic Plasmodium falciparum parasites expressing either tdTomato or GFP was performed using a flow cytometer with interchangeable optical filters. Parasitaemia was evaluated using different optical filters and, after optimization of optics, the GFP-expressing parasites were sorted and analysed by microscopy after cytospin preparation and by imaging cytometry. Results A new approach to evaluate filter performance in flow cytometry using two-dimensional dot blot was developed. By selecting optical filters with narrow bandpass (BP) and maximum position of filter emission close to GFP maximum emission in the FL1 channel (510/20, 512/20 and 517/20; dichroics 502LP and 466LP), AF was markedly decreased and signal-background improve dramatically. Sorting of GFP-expressing parasite populations in infected red blood cells at 90 or 95% purity with these filters resulted in 50-150% increased yield when compared to the standard filter set-up. The purity of the sorted population was confirmed using imaging cytometry and microscopy of cytospin preparations of sorted red blood cells infected with transgenic malaria parasites. Discussion Filter optimization is particularly important for applications where the FP signal and percentage of positive events are relatively low, such as analysis of parasite-infected samples with in the intention of gene-expression profiling and analysis. The approach outlined here results in substantially improved yield of GFP-expressing parasites, and requires decreased sorting time in comparison to standard methods. It is anticipated that this protocol will be useful for a wide range of applications involving rare events.
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Affiliation(s)
- Ivan A Vorobjev
- Immune Disease Institute and Program in Cellular and Molecular Medicine, Children's Hospital, D-239, 200 Longwood Avenue, 02115, Boston, MA, USA
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Rapid detection of the top six non-O157 Shiga toxin-producing Escherichia coli O groups in ground beef by flow cytometry. J Clin Microbiol 2012; 50:2137-9. [PMID: 22493328 DOI: 10.1128/jcm.00137-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid, sensitive, and highly specific flow-cytometric assays were developed for the detection of the top six non-O157 Shiga toxin-producing Escherichia coli (STEC) O groups in ground beef. The analytical sensitivity of the assays was 2 × 10(3) target cells in a bacterial mixture of 10(5) CFU/ml, and the limit of detection in ground beef was 1 to 10 CFU following 8 h of enrichment. The assays may be utilized for rapid detection of STEC O groups in meat.
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11
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He X, Zhou L, He D, Wang K, Cao J. Rapid and ultrasensitive E. coli O157:H7 quantitation by combination of ligandmagnetic nanoparticles enrichment with fluorescent nanoparticles based two-color flow cytometry. Analyst 2011; 136:4183-91. [PMID: 21858380 DOI: 10.1039/c1an15413c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A novel, fast and sensitive determination strategy for E. coli O157:H7 has been developed by combination of ligandmagnetic nanoparticles (LMNPs) enrichment with a fluorescent silica nanoparticles (FSiNPs) based two-color flow cytometry assay (LMNPs@FSiNPs-FCM). E. coli O157:H7 was first captured and enriched through the lectin concanavalin A (Con A) favored strong adhesion of E. coli O157:H7 to the mannose-conjugated magnetic nanoparticles. The enriched E. coli O157:H7 was further specially labeled with goat anti-E. coli O157:H7 antibody modified RuBpy-doped FSiNPs, and then stained with a nucleic acid dye SYBR Green I (SYBR-I). After dual-labeling with FSiNPs and SYBR-I, the enriched E. coli O157:H7 was determined using multiparameter FCM analysis. With this method, the detection sensitivity was greatly improved due to the LMNPs enrichment and the signal amplification of the FSiNPs labelling method. Furthermore, the false positives caused by aggregates of FSiNPs conjugates and nonspecific binding of FSiNPs to background debris could be significantly decreased. This assay allowed the detection of E. coli O157:H7 in PB buffer at levels as low as 7 cells mL(-1). The total assay time including E. coli O157:H7 sample enrichment and detection was less than 4 h. An artificially contaminated bottled mineral water sample with a concentration of 6 cells mL(-1) can be detected by this method. It is believed that the proposed method will find wide applications in biomedical fields demanding higher sensitive bacterial identification.
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Affiliation(s)
- Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
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12
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Cd-specific mutants of mercury-sensing regulatory protein MerR, generated by directed evolution. Appl Environ Microbiol 2011; 77:6215-24. [PMID: 21764963 DOI: 10.1128/aem.00662-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mercury-sensing regulatory protein, MerR (Tn21), which regulates mercury resistance operons in Gram-negative bacteria, was subjected to directed evolution in an effort to generate a MerR mutant that responds to Cd but not Hg. Oligonucleotide-directed mutagenesis was used to introduce random mutations into the key metal-binding regions of MerR. The effects of these mutations were assessed using a vector in which MerR controlled the expression of green fluorescent protein (GFP) and luciferase via the mer operator/promoter. An Escherichia coli cell library was screened by fluorescence-activated cell sorting, using a fluorescence-based dual screening strategy that selected for MerR mutants that showed GFP repression when cells were induced with Hg but GFP activation in the presence of Cd. Two Cd-responsive MerR mutants with decreased responses toward Hg were identified through the first mutagenesis/selection round. These mutants were used for a second mutagenesis/selection round, which yielded eight Cd-specific mutants that had no significant response to Hg, Zn, or the other tested metal(loid)s. Seven of the eight Cd-specific MerR mutants showed repressor activities equal to that of wild-type (wt) MerR. These Cd-specific mutants harbored multiple mutations (12 to 22) in MerR, indicating that the alteration of metal specificity with maintenance of repressor function was due to the combined effect of many mutations rather than just a few amino acid changes. The amino acid changes were studied by alignment against the sequences of MerR and other metal-responsive MerR family proteins. The analysis indicated that the generated Cd-specific MerR mutants appear to be unique among the MerR family members characterized to date.
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Hammes F, Egli T. Cytometric methods for measuring bacteria in water: advantages, pitfalls and applications. Anal Bioanal Chem 2010; 397:1083-95. [DOI: 10.1007/s00216-010-3646-3] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Revised: 03/05/2010] [Accepted: 03/08/2010] [Indexed: 11/30/2022]
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Single-cell analysis and isolation for microbiology and biotechnology: methods and applications. Appl Microbiol Biotechnol 2010; 86:1281-92. [DOI: 10.1007/s00253-010-2524-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 02/23/2010] [Accepted: 02/24/2010] [Indexed: 01/14/2023]
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Yang L, Wu L, Zhu S, Long Y, Hang W, Yan X. Rapid, Absolute, and Simultaneous Quantification of Specific Pathogenic Strain and Total Bacterial Cells Using an Ultrasensitive Dual-Color Flow Cytometer. Anal Chem 2009; 82:1109-16. [DOI: 10.1021/ac902524a] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Lingling Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, The Key Laboratory of Analytical Science, Xiamen University, Xiamen 361005, China
| | - Lina Wu
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, The Key Laboratory of Analytical Science, Xiamen University, Xiamen 361005, China
| | - Shaobin Zhu
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, The Key Laboratory of Analytical Science, Xiamen University, Xiamen 361005, China
| | - Yao Long
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, The Key Laboratory of Analytical Science, Xiamen University, Xiamen 361005, China
| | - Wei Hang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, The Key Laboratory of Analytical Science, Xiamen University, Xiamen 361005, China
| | - Xiaomei Yan
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, The Key Laboratory of Analytical Science, Xiamen University, Xiamen 361005, China
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Abstract
Over the last few decades, advances in cultivation-independent methods have significantly contributed to our understanding of microbial diversity and community composition in the environment. At the same time, cultivation-dependent methods have thrived, and the growing number of organisms obtained thereby have allowed for detailed studies of their physiology and genetics. Still, most microorganisms are recalcitrant to cultivation. This review not only conveys current knowledge about different isolation and cultivation strategies but also discusses what implications can be drawn from pure culture work for studies in microbial ecology. Specifically, in the light of single-cell individuality and genome heterogeneity, it becomes important to evaluate population-wide measurements carefully. An overview of various approaches in microbial ecology is given, and the cell as a central unit for understanding processes on a community level is discussed.
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Affiliation(s)
- Karsten Zengler
- Bioengineering Department, University of California, San Diego, La Jolla, California 92093, USA.
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17
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Bergquist PL, Hardiman EM, Ferrari BC, Winsley T. Applications of flow cytometry in environmental microbiology and biotechnology. Extremophiles 2009; 13:389-401. [PMID: 19301090 DOI: 10.1007/s00792-009-0236-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 02/26/2009] [Indexed: 10/21/2022]
Abstract
Flow cytometry (FCM) is a technique for counting, examining and sorting microscopic particles suspended in a stream of fluid. It uses the principles of light scattering, light excitation and the emission from fluorescent molecules to generate specific multiparameter data from particles and cells. The cells are hydrodynamically focussed in a sheath solution before being intercepted by a focused light source provided by a laser. FCM has been used primarily in medical applications but is being used increasingly for the examination of individual cells from environmental samples. It has found uses in the isolation of both culturable and hitherto non-culturable bacteria present infrequently in environmental samples using appropriate growth conditions. FCM lends itself to high-throughput applications in directed evolution for the analysis of single cells or cell populations carrying mutant genes. It is also suitable for encapsulation studies where individual bacteria are compartmentalised with substrate in water-in-oil-in-water emulsions or with individual genes in transcriptional/translational mixtures for the production of mutant enzymes. The sensitivity of the technique has allowed the examination of gene optimisation by a procedure known as random or neutral drift where screening and selection is based on the retention of some predetermined level of activity through multiple rounds of mutagenesis.
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Affiliation(s)
- Peter L Bergquist
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia.
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Pothier JF, Wisniewski-Dyé F, Weiss-Gayet M, Moënne-Loccoz Y, Prigent-Combaret C. Promoter-trap identification of wheat seed extract-induced genes in the plant-growth-promoting rhizobacterium Azospirillum brasilense Sp245. MICROBIOLOGY (READING, ENGLAND) 2007; 153:3608-3622. [PMID: 17906157 DOI: 10.1099/mic.0.2007/009381-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Azospirillum strains have been used as plant-growth-promoting rhizobacteria (PGPR) of cereal crops, but their adaptation to the root remains poorly understood. Here, we used a global approach based on differential fluorescence induction (DFI) promoter trapping to identify genes of the wheat isolate Azospirillum brasilense Sp245 that are induced in the presence of spring wheat seed extracts. Fluorescence-based flow cytometry sorting of Sp245 cells was validated using PlacZ, PsbpA and PnifH promoters and egfp. A random promoter library was constructed by cloning 1-3 kb Sp245 fragments upstream of a promoterless version of egfp in the promoter-trap plasmid pOT1e (genome coverage estimated at threefold). Exposure to spring wheat seed extracts obtained using a methanol solution led to the detection of 300 induced DFI clones, and upregulation by seed extracts was confirmed in vitro for 46 clones. Sequencing of 21 clones enabled identification of seven promoter regions. Five of them displayed upregulation once inoculated onto spring wheat seedlings. Their downstream sequence was similar to (i) a predicted transcriptional regulator, (ii) a serine/threonine protein kinase, (iii) two conserved hypothetical proteins, or (iv) the copper-containing dissimilatory nitrite reductase NirK. Two of them were also upregulated when inoculated on winter wheat and pea but not on maize, whereas the three others (including PnirK) were upregulated on the three hosts. The amounts of nitrate and/or nitrite present in spring wheat seed extracts were sufficient for PnirK upregulation. Overall, DFI promoter trapping was useful to reveal Azospirillum genes involved in the interaction with the plant.
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Affiliation(s)
- Joël F Pothier
- CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, F-69622, France
- Université Lyon 1, Lyon, F-69003, France
- Université de Lyon, Lyon, F-69003, France
| | - Florence Wisniewski-Dyé
- CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, F-69622, France
- Université Lyon 1, Lyon, F-69003, France
- Université de Lyon, Lyon, F-69003, France
| | - Michèle Weiss-Gayet
- CNRS, UMR 5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
- Université Lyon 1, Lyon, F-69003, France
- Université de Lyon, Lyon, F-69003, France
| | - Yvan Moënne-Loccoz
- CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, F-69622, France
- Université Lyon 1, Lyon, F-69003, France
- Université de Lyon, Lyon, F-69003, France
| | - Claire Prigent-Combaret
- CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, F-69622, France
- Université Lyon 1, Lyon, F-69003, France
- Université de Lyon, Lyon, F-69003, France
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Musovic S, Oregaard G, Kroer N, Sørensen SJ. Cultivation-independent examination of horizontal transfer and host range of an IncP-1 plasmid among gram-positive and gram-negative bacteria indigenous to the barley rhizosphere. Appl Environ Microbiol 2006; 72:6687-92. [PMID: 17021220 PMCID: PMC1610302 DOI: 10.1128/aem.00013-06] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The host range and transfer frequency of an IncP-1 plasmid (pKJK10) among indigenous bacteria in the barley rhizosphere was investigated. A new flow cytometry-based cultivation-independent method for enumeration and sorting of transconjugants for subsequent 16S rRNA gene classification was used. Indigenous transconjugant rhizosphere bacteria were collected by fluorescence-activated cell sorting and identified by cloning and sequencing of 16S rRNA genes from the sorted cells. The host range of the pKJK10 plasmid was exceptionally broad, as it included not only bacteria belonging to the alpha, beta, and gamma subclasses of the Proteobacteria, but also Arthrobacter sp., a gram-positive member of the Actinobacteria. The transfer frequency (transconjugants per donor) from the Pseudomonas putida donor to the indigenous bacteria was 7.03 x 10(-2) +/- 3.84 x 10(-2). This is the first direct documentation of conjugal transfer between gram-negative donor and gram-positive recipient bacteria in situ.
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Affiliation(s)
- Sanin Musovic
- Dept. of Microbiology, University of Copenhagen, Institute of Biology, Sølvgade 83H, 1307K Copenhagen K, Denmark
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Longnecker K, Sherr BF, Sherr EB. Activity and phylogenetic diversity of bacterial cells with high and low nucleic acid content and electron transport system activity in an upwelling ecosystem. Appl Environ Microbiol 2006; 71:7737-49. [PMID: 16332746 PMCID: PMC1317353 DOI: 10.1128/aem.71.12.7737-7749.2005] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated whether bacteria with higher cell-specific nucleic acid content (HNA) or an active electron transport system, i.e., positive for reduction of 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), were responsible for the bulk of bacterioplankton metabolic activity. We also examined whether the phylogenetic diversity of HNA and CTC-positive cells differed from the diversity of Bacteria with low nucleic acid content (LNA). Bacterial assemblages were sampled both in eutrophic shelf waters and in mesotrophic offshore waters in the Oregon coastal upwelling region. Cytometrically sorted HNA, LNA, and CTC-positive cells were assayed for their cell-specific [3H]leucine incorporation rates. Phylogenetic diversity in sorted non-radioactively labeled samples was assayed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes. Cell-specific rates of leucine incorporation of HNA and CTC-positive cells were on average only slightly greater than the cell-specific rates of LNA cells. HNA cells accounted for most bacterioplankton substrate incorporation due to high abundances, while the low abundances of CTC-positive cells resulted in only a small contribution by these cells to total bacterial activity. The proportion of the total bacterial leucine incorporation attributable to LNA cells was higher in offshore regions than in shelf waters. Sequence data obtained from DGGE bands showed broadly similar phylogenetic diversity across HNA, LNA, and CTC-positive cells, with between-sample and between-region variability in the distribution of phylotypes. Our results suggest that LNA bacteria are not substantially different from HNA bacteria in either cell-specific rates of substrate incorporation or phylogenetic composition and that they can be significant contributors to bacterial metabolism in the sea.
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Affiliation(s)
- K Longnecker
- OSU/COAS, 104 COAS Admin Bldg., Corvallis, OR 97331-5503, USA.
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Ferrari BC, Stoner K, Bergquist PL. Applying fluorescence based technology to the recovery and isolation of Cryptosporidium and Giardia from industrial wastewater streams. WATER RESEARCH 2006; 40:541-8. [PMID: 16426657 DOI: 10.1016/j.watres.2005.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 11/21/2005] [Accepted: 11/25/2005] [Indexed: 05/06/2023]
Abstract
As increasing water shortages continue, water re-use is posing new challenges with treated wastewater becoming a significant source of non-potable water. Rapid detection strategies that target waterborne pathogens of concern to industry are gaining importance in the assessment of water quality. This study reports on the ability to recover spiked Cryptosporidium and Giardia from a variety of industrial wastewater streams of varied water quality. Incorporation of an internal quality control used commonly in finished water-enabled quantitative assessments of pathogen loads and we describe successful analysis of pre- and part-treated wastewater samples from four industrial sites. The method used combined calcium carbonate flocculation followed by flow cytometry and epifluorescence microscopy. Our focus will now aim at characterising the ambient parasites isolated from industrial wastewater with the objective of developing a suite of highly specific platform detection technologies targeted to industrial needs.
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Affiliation(s)
- B C Ferrari
- Department of Chemistry and Biomolecular Sciences, Environmental Biotechnology CRC and Biotechnology Research Institute, Macquarie University Sydney, NSW 2109, Australia.
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