Soil microbial diversity: an ISO standard for soil DNA extraction

Philippot, Laurent; Abbate, Cristina; Bispo, Antonio; Chesnot, Thierry; Hallin, Sara; Lemanceau, Philippe; Lindström, Kristina; Pandard, Pascal; Romero, Esperanza; Schloter, Michael; Simonet, Pascal; Smalla, Kornelia; Wilke, Berndt‐Michael; Petric, Imes; Martin-Laurent, Fabrice

doi:10.1007/s11368-010-0265-8

Cited by 16 publications

(15 citation statements)

References 12 publications

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“…Finally, nucleic acids were precipitated by adding 1 volume of ice-cold isopropanol. The DNA pellets obtained after centrifugation (14,000 g for 5 min at 4°C) were washed with 70% ethanol (full details are described in (Martin-Laurent et al ., 2001 ; Philippot et al ., 2010 ; Petric et al ., 2011 ).…”

Section: Methodsmentioning

confidence: 99%

“…In this context, a standardized ‘ISO-11063: Soil quality – Method to directly extract DNA from soil’ was developed and validated by independent laboratories to efficiently recover bacterial DNA from various soil samples (Philippot et al ., 2010 ; Petric et al ., 2011 ). However, archaeal and fungal groups also constitute a significant proportion of the soil microbial biodiversity and are key organisms for soil processes.…”

Section: Introductionmentioning

confidence: 99%

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Meta‐barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition

Terrat

Plassart

Bourgeois

et al. 2014

Microbial Biotechnology

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This study was designed to assess the influence of three soil DNA extraction procedures, namely the International Organization for Standardization (ISO-11063, GnS-GII and modified ISO procedure (ISOm), on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico-chemical characteristics and land use. A meta-barcoded pyrosequencing approach targeting 16S and 18S rRNA genes was applied to characterize soil microbial communities. We first observed that the GnS-GII introduced some heterogeneity in bacterial composition between replicates. Then, although no major difference was observed between extraction procedures for soil bacterial diversity, we saw that the number of fungal genera could be underestimated by the ISO-11063. In particular, this procedure underestimated the detection in several soils of the genera Cryptococcus, Pseudallescheria, Hypocrea and Plectosphaerella, which are of ecological interest. Based on these results, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities. Indeed, the ISOm procedure provides a better evaluation of bacterial and fungal communities and is limited to the modification of the mechanical lysis step of the existing ISO-11063 standard.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Meta‐barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition

Terrat

Plassart

Bourgeois

et al. 2014

Microbial Biotechnology

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“…However, we note that the assessment of microbial biodegradation potential of synthetic pesticides using radiorespirometry is lengthy (generally several weeks) and is not always easy to implement, especially when using radiolabeled pesticides, which require specific authorization delivered by national radioprotection agencies, such as Agence de Sureté Nucléaire (ASN) in France, special laboratories and appropriate treatment of radioactive wastes. One alternative to this method could be the use of molecular approaches based on direct extraction of nucleic acids from environmental matrices and their subsequent analysis by PCR-based approaches to quantify the abundance of pesticide-degrading communities (Philippot et al, 2010). Specific information on the potential of biodegradation can be obtained by examining functional genes encoding enzymes involved in degradation pathways (Smith andOsborn, 2008 andBombach et al, 2010).…”

Section: Did the Ban Of Diuron Lead To A Decrease In The Exposure Levmentioning

confidence: 99%

Freshwater sediment pesticide biodegradation potential as an ecological indicator of microbial recovery following a decrease in chronic pesticide exposure: A case study with the herbicide diuron

Pesce¹,

Margoum²,

Rouard³

et al. 2013

Ecological Indicators

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The aim of this study was to evaluate the use of freshwater sediment biodegradation potential as an ecological indicator for monitoring microbial recovery following a decrease in chronic pesticide exposure. For this purpose, a four-year case study (2008)(2009)(2010)(2011) was conducted in a small stream (Morcille river) long exposed to high diuron concentrations, increasing from upstream to downstream. Our results show that the ban on diuron in December 2008 resulted in a progressive decrease in its concentrations in the Morcille river over the survey period. However, diuron remained present in the water three years after the ban. The spatio-temporal variations in the sediment biodegradation potential were assessed by radiorespirometry using [ring-U-14C] diuron to estimate diuron mineralization potentials. Between autumn 2008 and autumn 2011, mean diuron mineralization percentage after 15 weeks of incubation decreased by 65% downstream and by 82% in the intermediate sector, and mean 10% diuron dissipation time values increased between 143% (downstream) and 210% (intermediate). Thus the decrease in the level of chronic diuron exposure in the river also caused a fall in sediment diuron-mineralizing capacities, revealing a corresponding recovery of microbial communities. Our results show that the use of freshwater sediment biodegradation potential may be useful for assessing microbial recovery after a decrease in chronic exposure to pollutants, opening prospects for developing a new class of ecological indicator to monitor the recovery of biological quality of water resources. In this way, the use of molecular approaches based on direct extraction of nucleic acids from environmental matrices and their subsequent analysis by PCR-based approaches to quantify the abundance of pesticide-degrading communities could represent a promising alternative. Highlights► We performed a 4-year survey in a river long exposed to diuron. ► The ban on diuron resulted in a gradual fall in its concentrations in the river. ► Sediment diuron biodegradation potential decreased throughout the survey. ► Degradation capacities can be an ecological indicator to gauge microbial recovery.

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“…Humus, contaminants, salts, and many other substances made DNA extraction a crucial and challenging procedure in soil metagenomic studies ( Steffan et al, 1988 ; Tebbe and Vahjen, 1993 ). Soil DNA extraction methods can be divided into direct methods and indirect methods ( Daniel, 2005 ) with the former being more widely used ( Zhou et al, 1996 ; Robe et al, 2003 ; Philippot et al, 2010 ). Moreover, DNA solutions achieved with manual methods were often contaminated by the humus, which would interfere with further PCR amplification and sequencing ( Zhou et al, 1996 ; Arbeli and Fuentes, 2007 ).…”

Section: Introductionmentioning

confidence: 99%

“…The widely used DNA extraction methods, which also included many commercial kits, usually contained bead-beating lysis steps before further DNA extraction ( Philippot et al, 2010 ; Natarajan et al, 2016 ). Previous studies ( Leff et al, 1995 ; Kauffmann et al, 2004 ; Lakay et al, 2007 ; Purohit and Singh, 2009 ) have reported that higher DNA yield and quality were achieved with the bead beating step than other physical steps, such as freezing and thawing, microwave heating, and liquid nitrogen grinding.…”

Section: Introductionmentioning

confidence: 99%

Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil

et al. 2018

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High-throughput amplicon sequencing technology has been widely used in soil microbiome studies. Here, we estimated the bias of amplicon sequencing data affected by DNA extraction methods in a saline soil, and a non-saline normal soil was used as a control. Compared with the normal soil, several unique points were observed in the saline soil. The soil washing pretreatment can improve not only DNA quantity and quality but also microbial diversities in the saline soil; therefore, we recommend the soil washing pretreatment for saline soils especially hypersaline soils that cannot be achieved with detectable DNA amounts without the pretreatment. Also, evenness indices were more easily affected by DNA extraction methods than richness indices in the saline soil. Moreover, proportions of Gram-positive bacteria had significant positive correlations with the achieved microbial diversities within replicates of the saline soil. Though DNA extraction methods can bias the microbial diversity or community and relative abundances of some phyla/classes can vary by a factor of more than five, soil types were still the most important factor of the whole community. We confirmed good comparability in the whole community, but more attention should be paid when concentrating on an exact diversity value or the exact relative abundance of a certain taxon. Our study can provide references for the DNA extraction from saline and non-saline soils and comparing sequencing data across studies who may employ different DNA extraction methods.

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Soil microbial diversity: an ISO standard for soil DNA extraction

Cited by 16 publications

References 12 publications

Meta‐barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition

Meta‐barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition

Freshwater sediment pesticide biodegradation potential as an ecological indicator of microbial recovery following a decrease in chronic pesticide exposure: A case study with the herbicide diuron

Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil

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