Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis

LaMontagne, Michael G.; Michel, Frederick C.; Holden, Patricia A.; Reddy, C. A.

doi:10.1016/s0167-7012(01)00377-3

Cited by 186 publications

(107 citation statements)

References 35 publications

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“…Recent publications (La Montagne et al 2002) comparing the methods according to Zhou and Porteous (Porteous et al 1994) show a lower DNA yield is obtained by the method of Porteous (ultrasonic, lysozyme) than with the method of Zhou, but the lower yield does not introduce a bias towards lower community diversity. However, the two methods that were compared here differ strongly in the kind of extraction procedure (freeze-thaw-cycles, enzymatically vs. bead beating), whereas the methods compared by La Montagne (La Montagne et al 2002) …”

Section: Comparison Of Different Dna-extraction Methodsmentioning

confidence: 99%

DNA isolation from soil samples for cloning in different hosts

Kauffmann

Schmitt

Schmid

2004

Applied Microbiology and Biotechnology

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Many protocols to extract DNA directly from soil samples have been developed in recent years. We employed two extraction methods which differed in the method of lysis and compared these methods with respect to yield, purity and degree of shearing. The main focus was on the specific isolation of DNA from different microorganisms, especially DNA from actinomycetes, as these cells are very difficult to lyse in contrast to non-actinomycetes. Thus, we used both methods to isolate DNA from Pseudomonas (Entcheva et al. 2001), Arthrobacter and Rhodococcus (Borneman et al. 1996) and from soil spiked with the respective microorganisms. Both methods rendered high DNA yields with a low degree of shearing but differed in the type of cells that were lysed. By one protocol (utilizing enzymatic lysis) only DNA from the Gram-negative Pseudomonas strain could be obtained whereas by the other protocol (utilizing mechanical lysis), all microorganisms that were used could be lysed and DNA from them extracted. Using a combination of both protocols, DNA from those organisms could be obtained selectively. Furthermore, one of the protocols was modified, resulting in higher DNA yield and purity.3

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Section: Comparison Of Different Dna-extraction Methodsmentioning

confidence: 99%

DNA isolation from soil samples for cloning in different hosts

Kauffmann

Schmitt

Schmid

2004

Applied Microbiology and Biotechnology

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“…In either case, contaminants that tend to copurify with DNA from samples high in organic matter can be removed by methods such as agarose gel electrophoresis or column chromatography 6,7 . Direct isolation may also capture DNA from virus particles or free DNA from dead cells; when these noncellular DNAs are the intended target, they can be directly solubilized and concentrated without lysis of cells in the sample 8,9 .…”

Section: Environmental Nucleic Acid Analysismentioning

confidence: 99%

Metagenomics: DNA sequencing of environmental samples

2005

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“…Clone libraries of 16S rRNA genes and DGGE analyses have been widely used to investigate microbial communities of different habitats, but these approaches suffer from specific limitations that have been elaborated on previously (LaMontagne et al 2002;von Wintzingerode et al 1997). Because this study does not aim to describe diversity in general, but focuses on specific changes in microbial diversity, the use of identical tools on different mesocosms minimizes variance in methodological biases.…”

Section: Perception Of Diversitymentioning

confidence: 99%

Effects of Deposition of Heavy-Metal-Polluted Harbor Mud on Microbial Diversity and Metal Resistance in Sandy Marine Sediments

Toes

Finke

Kuenen

et al. 2008

Arch Environ Contam Toxicol

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Deposition of dredged harbor sediments in relatively undisturbed ecosystems is often considered a viable option for confinement of pollutants and possible natural attenuation. This study investigated the effects of deposition of heavy-metal-polluted sludge on the microbial diversity of sandy sediments during 12 months of mesocosm incubation. Geochemical analyses showed an initial increase in pore-water metal concentrations, which subsided after 3 months of incubation. No influence of the deposited sediment was observed in denaturing gradient gel electrophoresis (DGGE) profiles of bacterial 16S rRNA genes, whereas a minor, transient impact on the archaeal community was revealed. Phylogenetic analyses of bacterial 16S rRNA clone libraries showed an abundance of members of the Flavobacteriaceae, the a-and c-Proteobacteria, in both the muddy and the sandy sediments. Despite the finding that some groups of clones were shared between the metal-impacted sandy sediment and the harbor control, comparative analyses showed that the two sediments were significantly different in community composition. Consequences of redeposition of metalpolluted sediment were primarily underlined with cultivation-dependent techniques. Toxicity tests showed that the percentage of Cd-and Cu-tolerant aerobic heterotrophs was highest among isolates from the sandy sediment with metal-polluted mud on top.

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Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis

Cited by 186 publications

References 35 publications

DNA isolation from soil samples for cloning in different hosts

DNA isolation from soil samples for cloning in different hosts

Metagenomics: DNA sequencing of environmental samples

Effects of Deposition of Heavy-Metal-Polluted Harbor Mud on Microbial Diversity and Metal Resistance in Sandy Marine Sediments

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