Inter-laboratory evaluation of the ISO standard 11063 “Soil quality — Method to directly extract DNA from soil samples”

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

doi:10.1016/j.mimet.2011.01.016

Cited by 99 publications

(64 citation statements)

References 32 publications

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“…DNA extraction DNA was extracted from 250 mg dry-weight soil samples according to ISO standard 11063 'Soil quality-Method to directly extract DNA from soil samples' (Petric et al, 2011). In brief, samples were homogenized in 1 ml extraction buffer (1 M Tris-HCl pH = 8, 0.5 M ethylenediaminetetraacetic acid pH = 8, 1 M NaCl, 20% polyvinylpyrrolidone, 20% sodium dodecyl sulfate) for 30 s at 1600 rpm in a mini-bead beater cell disrupter Mikro-DismembratorS (B. Braun, Biotech International, Germany) and incubated at 70°C for 15 min with vortexing every 5 min.…”

Section: Nitrogen Cyclingmentioning

confidence: 99%

Effectiveness of ecological rescue for altered soil microbial communities and functions

et al. 2016

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Soil ecosystems worldwide are subjected to marked modifications caused by anthropogenic disturbances and global climate change, resulting in microbial diversity loss and alteration of ecosystem functions. Despite the paucity of studies, restoration ecology provides an appropriate framework for testing the potential of manipulating soil microbial communities for the recovery of ecosystem functioning. We used a reciprocal transplant design in experimentally altered microbial communities to investigate the effectiveness of introducing microbial communities in degraded soil ecosystems to restore N-cycle functioning. Microbial diversity loss resulted in alternative compositional states associated with impaired N-cycle functioning. Here, the addition of complex microbial communities to these altered communities revealed a pivotal role of deterministic community assembly processes. The diversity of some alternative compositional states was successfully increased but without significant restoration of soil N-cycle functioning. However, in the most degraded alternative state, the introduction of new microbial communities caused an overall decrease in phylogenetic diversity and richness. The successful soil colonization by newly introduced species for some compositional states indicates that priority effects could be overridden when attempting to manipulate microbial communities for soil restoration. Altogether, our result showed consistent patterns within restoration treatments with minor idiosyncratic effects. This suggests the predominance of deterministic processes and the predictability of restoration trajectories, which could be used to guide the effective management of microbial community assemblages for ecological restoration of soils

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Section: Nitrogen Cyclingmentioning

confidence: 99%

Effectiveness of ecological rescue for altered soil microbial communities and functions

et al. 2016

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“…Briefly, samples (10 g DNA extracts were then purified using PVPP columns (3,270 rpm, 4 min, 10 °C) (Petric et al, 2011).…”

Section: Enzyme Activity Analysesmentioning

confidence: 99%

Influence of the rhizosphere in a biopurification system on the dissipation of a pesticide mixture

Urrutia

Rubilar

Castillo

et al. 2015

J. Soil Sci. Plant Nutr.

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In a biopurification system such as a biobed, the rhizosphere of the grass layer may be a significant factor for promoting pesticide dissipation in the biomixture. The rhizosphere effect of a Lolium perenne, Festuca arundinacea and Trifolium repens mixture on the dissipation of a pesticide combination that was composed of atrazine, chlorpyrifos and isoproturon was studied. The assay was performed using glass pots divided into two separate compartments (root surface and root-free), each filled with an organic biomixture (oat husk, top soil and peat) and contaminated with the pesticide mixture at 5 mg kg -1 . Non-planted and noncontaminated pots were also used as controls. The results indicated that there were high atrazine, chlorpyrifos and isoproturon dissipation in the planted pots compared with the unplanted pots. An inverse correlation was found throughout the assay between phenoloxidase activity and residual pesticide (r=0.684 to 0.952). Indeed, fungal biomass was positively correlated with phenoloxidase activity on day 1 (r =0.825) and day 30 (r =0.855). Besides, exudation of oxalic and malic acid in contaminated pots was higher than in the control without pesticides, associated with oxidation of the pesticide mixture in the biomixture of a bioded system. Therefore, the grass layer enhances pesticide removal in biobeds.

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“…However, up to now, the number of known genes coding for pesticidedegrading enzymes, although increasing, is still limited, thereby restricting the application of this approach. Nonetheless, the recent publication of the ISO 11063 standard describing "a method to directly extract nucleic acid from soils" (Petrić et al, 2011) and the recent adoption by ISO TC190/SC4/WG4 of new work item 17601 "Estimation of abundance of selected microbial gene sequences by quantitative realtime PCR from DNA directly extracted from soil" is paving the way for applying molecular tools targeting pesticide-degrading genes to monitor the recovery of microbial communities in different compartments of the environment.…”

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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Inter-laboratory evaluation of the ISO standard 11063 “Soil quality — Method to directly extract DNA from soil samples”

Cited by 99 publications

References 32 publications

Effectiveness of ecological rescue for altered soil microbial communities and functions

Effectiveness of ecological rescue for altered soil microbial communities and functions

Influence of the rhizosphere in a biopurification system on the dissipation of a pesticide mixture

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

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