A dispersion and differential centrifugation technique for representatively sampling microorganisms from soil

Hopkins, D. W.; Macnaughton, Sarah J.; O'Donnell, Anthony G.

doi:10.1016/0038-0717(91)90055-o

Cited by 153 publications

(73 citation statements)

References 27 publications

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“…Procedures used to promote the dissociation of microorganisms from particulate matter include the use of buffered diluents (348), chelating agents (300), elutriation (219), mild ultrasonication (379), and repeated homogenization of soil in several buffers followed by separation of extract from residue (122); these procedures address the problems outlined above to varying degrees. Several of these physicochemical procedures were incorporated into a multistage dispersion and differential centrifugation procedure (220) that was shown to be effective for representative sampling of bacteria, including actinomycetes, from soils with different textures (220,300).…”

Section: Selective Isolation and Characterization Of Novel Microorganmentioning

confidence: 99%

Search and Discovery Strategies for Biotechnology: the Paradigm Shift

Bull

Ward

Goodfellow

2000

Microbiol Mol Biol Rev

418

250

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SUMMARY Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology.

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Section: Selective Isolation and Characterization Of Novel Microorganmentioning

confidence: 99%

Search and Discovery Strategies for Biotechnology: the Paradigm Shift

Bull

Ward

Goodfellow

2000

Microbiol Mol Biol Rev

418

250

View full text Add to dashboard Cite

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“…Pioneer methods for soil DNA isolation used ex situ methodologies that included long incubations of soils in a solution made of sodium cholate and Chelex 100 resin, followed by centrifugation and passage through a Percoll gradient to separate the most dense soil particles from the floating organic matter and microorganisms [48,117]. Further breakage of the cells by sonication and differential centrifugation allowed DNA extraction.…”

Section: Initial Attempts For Dna Isolationmentioning

confidence: 99%

Determination of Denitrification Genes Abundance in Environmental Samples

Correa‐Galeote¹,

Tortosa²,

Bedmar³

2013

Metagenomics

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Diversity of microorganisms involved in the biogeochemical N cycle is of fundamental interest in microbial ecology. Denitrification is a key step in the cycle by which nitrate is reduced to dinitrogen gas via the soluble nitrite and the gaseous compounds nitric oxide and nitrous oxide. The process is carried out by the sequential activity of the nitrate, nitrite, nitric oxide, and nitrous oxide reductase enzyme, respectively. The fluorescence-based quantitative real-time polymerase chain reaction (qPCR) is widely used for quantification of nucleic acids in samples obtained from numerous, diverse sources. Here, we provide a well-proven methodology for isolation of DNA from environmental samples and describe relevant experimental conditions for utilization of qPCR to assay the 16S rRNA and nar/nap, nirK/nirS, c-nor/qnor, and nos denitrification genes that encode synthesis of denitrifying enzymes. The ISO 11063 standard method and MIQUE guidelines are considered with the aim to increase experimental transparency.

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“…An alternative approach to that of direct DNA extraction is to remove the microorganisms from the soil matrix prior to nucleic acid extraction. Such indirect methods rely on the efficient recovery of microorganisms from soil (25) and are now used less often. However, indirect methods offer the possibility of selectively recovering the bacterial fraction and of cleaning up the cell preparation prior to nucleic acid extraction.…”

Section: Dna Extractionmentioning

confidence: 99%

The use of 16s rDNA methods in soil microbial ecology

Macrae¹

2000

Braz. J. Microbiol.

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New and exciting molecular methods, many using the 16S small sub-unit ribosomal nucleic acid molecule, are opening the microbial black box in soil. These studies have added much to our knowledge of microbial diversity in soils, and are beginning to advance our understanding of the relationship between this diversity and its function in soil processes. Over the next few years, the knowledge gained from molecular studies will, we hope, lead to improvements in sustainable land management and sustainable exploitation of soil genetic resources. As we enter the third millenium, it is appropriate to review the application of 16S rDNA methods to soil microbiology. This review examines 16S ribosomal DNA (rDNA) methods and their application to soil. It mentions their limits and suggests how they may be applied in the future.

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A dispersion and differential centrifugation technique for representatively sampling microorganisms from soil

Cited by 153 publications

References 27 publications

Search and Discovery Strategies for Biotechnology: the Paradigm Shift

Search and Discovery Strategies for Biotechnology: the Paradigm Shift

Determination of Denitrification Genes Abundance in Environmental Samples

The use of 16s rDNA methods in soil microbial ecology

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