DNA Extraction from Soils: Old Bias for New Microbial Diversity Analysis Methods

Martin-Laurent, Fabrice; Philippot, Laurent; Hallet, Stéphanie; Chaussod, Rémi; Germon, Jean-Claude; Soulas, Guy; Catroux, Gérard

doi:10.1128/aem.67.9.4397-4397.2001

Cited by 94 publications

(115 citation statements)

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“…The results described herein corroborate earlier reports that DNA isolation methods introduce bias into studies of microbial ecology (Martin‐Laurent et al. 2001; Webster et al.…”

Section: Discussionsupporting

confidence: 90%

“…The apparent discrepancy in the SSU quantification (significantly greater than all other methods) and species richness results (average bacterial richness, low fungal richness) seen for method MS may be a result of residual contaminants in the DNA preparations. Martin‐Laurent et al determined that, depending on primer set (16S Universal or 16S‐23S intergenic Universal), PCR efficiency was affected by either the extraction method or the soil composition (Martin‐Laurent et al. 2001).…”

Section: Discussionmentioning

confidence: 99%

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Comparison of DNA extraction methods for analysis of turkey cecal microbiota

2007

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Aim: As a prelude to long‐term studies to characterize the microbiota of the turkey ceca, 14 DNA isolation protocols were evaluated for their ability to reproducibly characterize microbial diversity. Methods and Results: Eight commercially available DNA extraction kits were assessed. DNA quantity and quality were assessed and competitive PCR was used to quantify the 16S bacterial rRNA genes. The Invitrogen Easy‐DNA Kit extraction method for large samples yielded over eight times more DNA than any other method (3144 ± 873 μg g−1 of sample, P < 0·05). Bacterial and fungal species richness was estimated by Automated Ribosomal Intergenic Spacer Analysis. The Invitrogen Easy‐DNA Kit generated the greatest bacterial species richness (46 ± 7 peaks) while Bio‐Rad Aquapure yielded the highest fungal species richness (71 ± 9·5 peaks). Conclusion: Cluster analysis indicated different DNA extraction methods generated different microbial community compositions using the same cecal matrix from a single donor bird. Significance and Impact of the Study: Optimized DNA extraction protocols Invitrogen Easy‐DNA Kit extraction method for large samples and Bio‐Rad Aquapure outperform other methods for extraction of DNA from poultry fecal samples, although these methods do not necessarily recover all available DNA. They will be used in future studies to monitor the dynamics of microbial communities of the avian ceca.

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“…The results described herein corroborate earlier reports that DNA isolation methods introduce bias into studies of microbial ecology (Martin‐Laurent et al. 2001; Webster et al.…”

Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Comparison of DNA extraction methods for analysis of turkey cecal microbiota

2007

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“…The fluid obtained from both potato cultivars from 13 CO 2 ‐labeled plants as well as from control plants were further used for DNA isolation according to Martin‐Laurent et al . (2001).…”

Section: Methodsmentioning

confidence: 99%

DNA‐based stable isotope probing enables the identification of active bacterial endophytes in potatoes

et al. 2008

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Summary• A 13 CO 2 (99 atom-%, 350 ppm) incubation experiment was performed to identify active bacterial endophytes in two cultivars of Solanum tuberosum, cultivars Desirée and Merkur. We showed that after the assimilation and photosynthetic transformation of 13 CO 2 into 13 C-labeled metabolites by the plant, the most directly active, cultivarspecific heterotrophic endophytic bacteria that consume these labeled metabolites can be identified by DNA stable isotope probing (DNA-SIP).• Density-resolved DNA fractions obtained from SIP were subjected to 16S rRNA gene-based community analysis using terminal restriction fragment length polymorphism analysis and sequencing of generated gene libraries.• Community profiling revealed community compositions that were dominated by plant chloroplast and mitochondrial 16S rRNA genes for the 'light' fractions of 13 CO 2 -incubated potato cultivars and of potato cultivars not incubated with 13 CO 2 . In the 'heavy' fractions of the 13 CO 2 -incubated endophyte DNA, a bacterial 492-bp terminal restriction fragment became abundant, which could be clearly identified as Acinetobacter and Acidovorax spp. in cultivars Merkur and Desirée, respectively, indicating cultivar-dependent distinctions in 13 C-label flow. These two species represent two common potato endophytes with known plant-beneficial activities.• The approach demonstrated the successful detection of active bacterial endophytes in potato. DNA-SIP therefore offers new opportunities for exploring the complex nature of plant-microbe interactions and plant-dependent microbial metabolisms within the endosphere.

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“…Many procedures have been recently developed that rely on culture‐independent and molecular approaches (Veum, Lorenz, & Kremer, 2019). These genomic and lipid techniques include (i) molecular DNA methods (Martin‐Laurent et al., 2001), (ii) fatty acid methyl ester analysis (FAME) (Cavigelli, Robertson, & Klug, 1995), (iii) phospholipid‐linked FAME analysis (Pankhurst, Yu, Hawke, & Harch, 2001), and (iv) phospholipid fatty acid analysis (PLFA) (Buyer & Sasser, 2012; Helgason, Walley, & Germida, 2010; Hill et al., 2000).…”

Section: Introductionmentioning

confidence: 99%

Long‐term perennial management and cropping effects on soil microbial biomass for claypan watersheds

et al. 2020

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Sustainable vegetative management plays a significant role in improving soil quality in degraded agricultural landscapes by enhancing soil microbial biomass. This study investigated the effects of grass buffers (GBs), biomass crops (BCs), grass waterways (GWWs), and agroforestry buffers (ABs) on soil microbial biomass and soil organic C (SOC) compared with continuous corn (Zea mays L.)-soybean [Glycine max (L.)Merr.] rotation (row crop [RC]) on claypan soils. The RC, AB, GB, GWW, and BC treatments were established in 10-cm depth at summit, backslope, and footslope landscape positions. Within AB treatment, soils were collected from the 50-cm and 150-cm tree distance. Total microbial biomass and biomass of gram-positive bacteria, gram-negative bacteria, actinomycetes, rhizobia, fungi, arbuscular mycorrhizae, saprophytes, and protozoa were determined by phospholipid fatty acid (PLFA) analysis. Results showed that soil microbial biomass and SOC across all microbial groups were significantly higher (P < .01) under perennial vegetation treatments compared with RC. The footslope position exhibited the highest total microbial biomass compared with the summit and backslope positions. The sampling distance of 50 cm from the tree base demonstrated 16% greater total microbial biomass and 15% higher SOC compared with 150 cm. These findings highlight the influence of landscape on soil biological properties and show that perennial vegetation systems have the potential to increase soil microbial biomass and enhance agricultural sustainability in degraded RC systems.Abbreviations: AB, agroforestry buffer; AC, active carbon; AB150, agroforestry buffer at 150 cm distance; AB50, agroforestry buffer at 50 cm

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DNA Extraction from Soils: Old Bias for New Microbial Diversity Analysis Methods

Cited by 94 publications

References 0 publications

Comparison of DNA extraction methods for analysis of turkey cecal microbiota

Comparison of DNA extraction methods for analysis of turkey cecal microbiota

DNA‐based stable isotope probing enables the identification of active bacterial endophytes in potatoes

Long‐term perennial management and cropping effects on soil microbial biomass for claypan watersheds

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