Venom-inspired somatostatin receptor 4 (SSTR4) agonists as new drug leads for peripheral pain conditions.

Persistent pain affects one in five people worldwide, often with severely debilitating consequences. Current treatment options, which can be effective for mild or acute pain, are ill-suited for moderate-to-severe persistent pain, resulting in an urgent need for new therapeutics. In recent years, the somatostatin receptor 4 (SSTR 4 ), which is expressed in sensory neurons of the peripheral nervous system, has emerged as a promising target for pain relief. However, the presence of several closely related receptors with similar ligand-binding surfaces complicates the design of receptor-specific agonists. In this study, we report the discovery of a potent and selective SSTR 4 peptide, consomatin Fj1, derived from extensive venom gene datasets from marine cone snails. Consomatin Fj1 is a mimetic of the endogenous hormone somatostatin and contains a minimized binding motif that provides stability and drives peptide selectivity. Peripheral administration of synthetic consomatin Fj1 provided analgesia in mouse models of postoperative and neuropathic pain. Using structure-activity studies, we designed and functionally evaluated several Fj1 analogs, resulting in compounds with improved potency and selectivity. Our findings present a novel avenue for addressing persistent pain through the design of venom-inspired SSTR 4 -selective pain therapeutics. One Sentence Summary: Venom peptides from predatory marine mollusks provide new leads for treating peripheral pain conditions through a non-opioid target.

Green Light Exposure Elicits Anti-inflammation, Endogenous Opioid Release and Dampens Synaptic Potentiation to Relieve Post-surgical Pain.

Light therapy improves multiple conditions such as seasonal affective disorders, circadian rhythm dysregulations, and neurodegenerative diseases. However, little is known about its potential benefits in pain management. While current pharmacologic methods are effective in many cases, the associated side effects can limit their use. Non-pharmacological methods would minimize drug dependence, facilitating a reduction of the opioid burden. Green light therapy has been shown to be effective in reducing chronic pain in humans and rodents. However, its underlying mechanisms remain incompletely defined. In this study, we demonstrate that green light exposure reduced postsurgical hypersensitivity in rats. Moreover, this therapy potentiated the antinociceptive effects of morphine and ibuprofen on mechanical allodynia in male rats. Importantly, in female rats, GLED potentiated the antinociceptive effects of morphine but did not affect that of ibuprofen. We showed that green light increases endogenous opioid levels while lessening synaptic plasticity and neuroinflammation. Importantly, this study reveals new insights into how light exposure can affect neuroinflammation and plasticity in both genders. Clinical translation of these results could provide patients with improved pain control and decrease opioid consumption. Given the noninvasive nature of green light, this innovative therapy would be readily implementable in hospitals. PERSPECTIVE: This study provides a potential additional therapy to decrease postsurgical pain. Given the safety, availability, and the efficacy of green light therapy, there is a significant potential for advancing the green light therapy to clinical trials and eventual translation to clinical settings.

Partial Sciatic Nerve Ligation: A Mouse Model of Chronic Neuropathic Pain to Study the Antinociceptive Effect of Novel Therapies.

Management of chronic pain remains challenging to this day, and current treatments are associated with adverse effects, including tolerance and addiction. Chronic neuropathic pain results from lesions or diseases in the somatosensory system. To investigate potential therapies with reduced side effects, animal pain models are the gold standard in preclinical studies. Therefore, well-characterized and well-described models are crucial for the development and validation of innovative therapies. Partial ligation of the sciatic nerve (pSNL) is a procedure that induces chronic neuropathic pain in mice, characterized by mechanical and thermal hypersensitivity, ongoing pain, and changes in limb temperature, making this model a great fit to study neuropathic pain preclinically. pSNL is an advantageous model to study neuropathic pain as it reproduces many symptoms observed in humans with neuropathic pain. Furthermore, the surgical procedure is relatively fast and straightforward to perform. Unilateral pSNL of one limb allows for comparison between the ipsilateral and contralateral paws, as well as evaluation of central sensitization. To induce chronic neuropathic hypersensitivity, a 9-0 non-absorbable nylon thread is used to ligate the dorsal third of the sciatic nerve. This article describes the surgical procedure and characterizes the development of chronic neuropathic pain through multiple commonly used behavioral tests. As a plethora of innovative therapies are now being investigated to treat chronic pain, this article provides crucial concepts for standardization and an accurate description of surgeries required to induce neuropathic pain.

Case Report: Green Light Exposure Relieves Chronic Headache Pain in a Colorblind Patient.

Patients with chronic headaches sometimes prefer non-pharmacological methods for pain management. We have shown previously that green light exposure (GLED, Green Light Emitting Diode) reversed thermal hyperalgesia and mechanical allodynia in a rat model of neuropathic pain. This effect is mediated through the visual system. Moreover, we recently showed that GLED was effective in decreasing the severity of headache pain and the number of headache-days per month in migraine patients. The visual system is comprised of image-forming and non-image-forming pathways; however, the contribution of different photosensitive cells to the effect of GLED is not yet known. Here, we report a 66-year-old man with headaches attributed to other disorders of homeostasis and color blindness who was recruited in the GLED study. The subject, diagnosed with protanomaly, cannot differentiate green, yellow, orange, and red colors. After completing the GLED exposure protocol, the subject noted significant decreases in headache pain intensity without reduction in the number of headache-days per month. The subject also reported improvement in the quality of his sleep. These findings suggest that green light therapy mediates the decrease of the headache pain intensity through non-image-forming intrinsically photosensitive retinal ganglion cells. However, the subject did not report a change in the frequency of his headaches, suggesting the involvement of cones in reduction of headache frequency by GLED. This is the first case reported of a colorblind man with chronic headache using GLED to manage his headache pain and may increase our understanding of the contribution of different photosensitive cells in mediating the pain-relieving effects of GLED.

Somatostatin venom analogs evolved by fish-hunting cone snails: From prey capture behavior to identifying drug leads.

Somatostatin (SS) is a peptide hormone with diverse physiological roles. By investigating a deep-water clade of fish-hunting cone snails, we show that predator-prey evolution has generated a diverse set of SS analogs, each optimized to elicit specific systemic physiological effects in prey. The increased metabolic stability, distinct SS receptor activation profiles, and chemical diversity of the venom analogs make them suitable leads for therapeutic application, including pain, cancer, and endocrine disorders. Our findings not only establish the existence of SS-like peptides in animal venoms but also serve as a model for the synergy gained from combining molecular phylogenetics and behavioral observations to optimize the discovery of natural products with biomedical potential.

Green Light Antinociceptive and Reversal of Thermal and Mechanical Hypersensitivity Effects Rely on Endogenous Opioid System Stimulation.

Benefits of phototherapy were characterized in multiple diseases including depression, circadian rhythm disruptions, and neurodegeneration. Studies on migraine and fibromyalgia patients revealed that green light-emitting diodes (GLED) exposure provides a pragmatic and safe therapy to manage chronic pain. In rodents, GLED reversed hypersensitivity related to neuropathic pain. However, little is known about the underlying mechanisms of GLED efficacy. Here, we sought to understand how green light modulates the endogenous opioid system. We first characterized how exposure to GLED stimulates release of ß-endorphin and proenkephalin in the central nervous system of male rats. Moreover, by individually editing each of the receptors, we found that µ- and δ-opioid receptors are required for green light's antinociceptive effect in naïve rats and a model of HIV-induced peripheral neuropathy. We investigated how GLED could increase pain thresholds, and explored its potential in reversing hypersensitivity in a model of HIV-related neuropathy. Through behavioral and gene editing approaches, we identified that green light provides antinociception via modulation of the endogenous opioid system in the spinal cord. This work identifies a previously unknown mechanism by which GLED can improve pain management. Clinical translation of these results will advance the development of an innovative therapy devoid of adverse effects. PERSPECTIVE: Development of new pain management therapies, especially for HIV patients, is crucial as long-term opioid prescription is not recommended due to adverse side effects. Green light addresses this necessity. Characterizing the underlying mechanisms of this potentially groundbreaking and safe antinociceptive therapy will advance its clinical translation.

Mechanisms and Pathways of Pain Photobiomodulation: A Narrative Review.

A growing body of evidence supports the modulation of pain by light exposure. As such, phototherapy is being increasingly utilized for the management of a variety of pain conditions. The modes of delivery, and hence applications of phototherapy, vary by wavelength, intensity, and route of exposure. As such, differing mechanisms of action exist depending upon those parameters. Cutaneous application of red light (660 nm) has been shown to reduce pain in neuropathies and complex regional pain syndrome-I, whereas visual application of the same wavelength of red light has been reported to exacerbate migraine headache in patients and lead to the development of functional pain in animal models. Interestingly visual exposure to green light can result in reduction in pain in variety of pain conditions such as migraine and fibromyalgia. Cutaneous application typically requires exposure on the order of minutes, whereas visual application requires exposure on the order of hours. Both routes of exposure elicit changes centrally in the brainstem and spinal cord, and peripherally in the dorsal root ganglia and nociceptors. The mechanisms of photobiomodulation of pain presented in this review provide a foundation in furtherance of exploration of the utility of phototherapy as a tool in the management of pain. PERSPECTIVE: This review synopsizes the pathways and mechanisms through which light modulates pain and the therapeutic utility of different colors and exposure modalities of light on pain. Recent advances in photobiomodulation provide a foundation for understanding this novel treatment for pain on which future translational and clinical studies can build upon.

Evaluation of green light exposure on headache frequency and quality of life in migraine patients: A preliminary one-way cross-over clinical trial.

BACKGROUND: Pharmacological management of migraine can be ineffective for some patients. We previously demonstrated that exposure to green light resulted in antinociception and reversal of thermal and mechanical hypersensitivity in rodent pain models. Given the safety of green light emitting diodes, we evaluated green light as a potential therapy in patients with episodic or chronic migraine. MATERIAL AND METHODS: We recruited (29 total) patients, of whom seven had episodic migraine and 22 had chronic migraine. We used a one-way cross-over design consisting of exposure for 1-2 hours daily to white light emitting diodes for 10 weeks, followed by a 2-week washout period followed by exposure for 1-2 hours daily to green light emitting diodes for 10 weeks. Patients were allowed to continue current therapies and to initiate new treatments as directed by their physicians. Outcomes consisted of patient-reported surveys. The primary outcome measure was the number of headache days per month. Secondary outcome measures included patient-reported changes in the intensity and frequency of the headaches over a two-week period and other quality of life measures including ability to fall and stay asleep, and ability to perform work. Changes in pain medications were obtained to assess potential reduction. RESULTS: When seven episodic migraine and 22 chronic migraine patients were analyzed as separate cohorts, white light emitting diodes produced no significant change in headache days in either episodic migraine or chronic migraine patients. Combining data from the episodic migraine and chronic migraine groups showed that white light emitting diodes produced a small, but statistically significant reduction in headache days from (days ± SEM) 18.2 ± 1.8 to 16.5 ± 2.01 days. Green light emitting diodes resulted in a significant decrease in headache days from 7.9 ± 1.6 to 2.4 ± 1.1 and from 22.3 ± 1.2 to 9.4 ± 1.6 in episodic migraine and chronic migraine patients, respectively. While some improvement in secondary outcomes was observed with white light emitting diodes, more secondary outcomes with significantly greater magnitude including assessments of quality of life, Short-Form McGill Pain Questionnaire, Headache Impact Test-6, and Five-level version of the EuroQol five-dimensional survey without reported side effects were observed with green light emitting diodes. Conclusions regarding pain medications reduction with green light emitting diode exposure were not possible. No side effects of light therapy were reported. None of the patients in the study reported initiation of new therapies. DISCUSSION: Green light emitting diodes significantly reduced the number of headache days in people with episodic migraine or chronic migraine. Additionally, green light emitting diodes significantly improved multiple secondary outcome measures including quality of life and intensity and duration of the headache attacks. As no adverse events were reported, green light emitting diodes may provide a treatment option for those patients who prefer non-pharmacological therapies or may be considered in complementing other treatment strategies. Limitations of this study are the small number of patients evaluated. The positive data obtained support implementation of larger clinical trials to determine possible effects of green light emitting diode therapy.This study is registered with clinicaltrials.gov under NCT03677206.

SARS-CoV-2 spike protein co-opts VEGF-A/neuropilin-1 receptor signaling to induce analgesia.

Global spread of severe acute respiratory syndrome coronavirus 2 continues unabated. Binding of severe acute respiratory syndrome coronavirus 2's spike protein to host angiotensin-converting enzyme 2 triggers viral entry, but other proteins may participate, including the neuropilin-1 receptor (NRP-1). Because both spike protein and vascular endothelial growth factor-A (VEGF-A)-a pronociceptive and angiogenic factor, bind NRP-1, we tested whether spike could block VEGF-A/NRP-1 signaling. VEGF-A-triggered sensory neuron firing was blocked by spike protein and NRP-1 inhibitor EG00229. Pronociceptive behaviors of VEGF-A were similarly blocked through suppression of spontaneous spinal synaptic activity and reduction of electrogenic currents in sensory neurons. Remarkably, preventing VEGF-A/NRP-1 signaling was antiallodynic in a neuropathic pain model. A "silencing" of pain through subversion of VEGF-A/NRP-1 signaling may underlie increased disease transmission in asymptomatic individuals.

SARS-CoV-2 Spike protein co-opts VEGF-A/Neuropilin-1 receptor signaling to induce analgesia.

Global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues unabated. Binding of SARS-CoV-2's Spike protein to host angiotensin converting enzyme 2 triggers viral entry, but other proteins may participate, including neuropilin-1 receptor (NRP-1). As both Spike protein and vascular endothelial growth factor-A (VEGF-A) - a pro-nociceptive and angiogenic factor, bind NRP-1, we tested if Spike could block VEGF-A/NRP-1 signaling. VEGF-A-triggered sensory neuronal firing was blocked by Spike protein and NRP-1 inhibitor EG00229. Pro-nociceptive behaviors of VEGF-A were similarly blocked via suppression of spontaneous spinal synaptic activity and reduction of electrogenic currents in sensory neurons. Remarkably, preventing VEGF-A/NRP-1 signaling was antiallodynic in a neuropathic pain model. A 'silencing' of pain via subversion of VEGF-A/NRP-1 signaling may underlie increased disease transmission in asymptomatic individuals.

Design of a degenerate primer pair to target a bacterial functional community: The hppd bacterial gene coding for the enzyme targeted by herbicides, a study case.

The present work aimed to design a degenerate primer pair to target a large part of the hppd soil bacterial community, possibly affected by herbicides. We validated these primers by qPCR and high-throughput sequencing analysis of soil samples.

Assessment of the impact of three pesticides on microbial dynamics and functions in a lab-to-field experimental approach.

The toxicity of pesticides on soil microorganisms is as an emerging area of concern. Novel and well-standardized tools could be now used to provide a robust assessment of the ecotoxicity of pesticides on soil microorganisms. We followed a tiered lab-to-field approach to assess the toxicity of three pesticides, widely used at EU level, (chlorpyrifos (CHL), isoproturon (IPU) and tebuconazole (TBZ)) on (i) the abundance of 11 microbial taxa and 8 functional microbial groups via q-PCR and (ii) the activity of enzymes involved in biogeochemical cycles via fluorometric analysis. Correlation of microbial measurements with the concentration of pesticides, and their transformation products (TPs) in soil enabled the identification of the compounds driving the effects observed. At lab tests (×1, ×2 and ×10 the recommended dose), CHL and TBZ significantly reduced the relative abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) which recovered by the end of the study, while all pesticides induced a persistent reduction in the relative abundance of sulfur-oxidizing bacteria (SOB). The two demethylated metabolites of IPU (MD-IPU and DD-IPU) adversely affected P-cycling enzymes and leucine aminopeptidase (Leu). At field tests (×1, ×2 and ×5 the recommended dose), a persistent reduction on the relative abundance of AOA was induced by all pesticides, but only CHL and its hydrolysis product 3,5,6 trichloro-2-pyridynol (TCP) soil levels were negatively correlated with AOA relative abundance. Our findings suggest that ammonia-oxidizing microorganisms constitute the most responsive microbial group to pesticides and could be potential candidates for inclusion in pesticide risk assessment.

Characterization of the biodegradation, bioremediation and detoxification capacity of a bacterial consortium able to degrade the fungicide thiabendazole.

Thiabendazole (TBZ) is a persistent fungicide used in the post-harvest treatment of fruits. Its application results in the production of contaminated effluents which should be treated before their environmental discharge. In the absence of efficient treatment methods in place, biological systems based on microbial inocula with specialized degrading capacities against TBZ could be a feasible treatment approach. Only recently the first bacterial consortium able to rapidly transform TBZ was isolated. This study aimed to characterize its biodegradation, bioremediation and detoxification potential. The capacity of the consortium to mineralize 14C-benzyl-ring labelled TBZ was initially assessed. Subsequent tests evaluated its degradation capacity under various conditions (range of pH, temperatures and TBZ concentration levels) and relevant practical scenarios (simultaneous presence of other postharvest compounds) and its bioaugmentation potential in soils contaminated with increasing TBZ levels. Finally cytotoxicity assays explored its detoxification potential. The consortium effectively mineralized the benzoyl ring of the benzimidazole moiety of TBZ and degraded spillage level concentrations of the fungicide in aqueous cultures (750 mg L-1) and in soil (500 mg kg-1). It maintained its high degradation capacity in a wide range of pH (4.5-7.5) and temperatures (15-37 °C) and in the presence of other pesticides (ortho-phenylphenol and diphenylamine). Toxicity assays using the human liver cancer cell line HepG2 showed a progressive decrease in cytotoxicity, concomitantly with the biodegradation of TBZ, pointing to a detoxification process. Overall, the bacterial consortium showed high potential for future implementation in bioremediation and biodepuration applications.

"LOVE TO HATE" pesticides: felicity or curse for the soil microbial community? An FP7 IAPP Marie Curie project aiming to establish tools for the assessment of the mechanisms controlling the interactions of pesticides with soil microorganisms.

Pesticides end up in soil where they interact with soil microorganisms in various ways. On the Yin Side of the interaction, pesticides could exert toxicity on soil microorganisms, while on the Yang side of interaction, pesticides could be used as energy source by a fraction of the soil microbial community. The LOVE TO HATE project is an IAPP Marie Curie project which aims to study these complex interactions of pesticides with soil microorganisms and provide novel tools which will be useful both for pesticide regulatory purposes and agricultural use. On the Yin side of the interactions, a new regulatory scheme for assessing the soil microbial toxicity of pesticides will be proposed based on the use of advanced standardized tools and a well-defined experimental tiered scheme. On the Yang side of the interactions, advanced molecular tools like amplicon sequencing and functional metagenomics will be applied to define microbes that are involved in the rapid transformation of pesticides in soils and isolate novel pesticide biocatalysts. In addition, a functional microarray has been designed to estimate the biodegradation genetic potential of the microbial community of agricultural soils for a range of pesticide groups.

Mapping field spatial distribution patterns of isoproturon-mineralizing activity over a three-year winter wheat/rape seed/barley rotation.

The temporal and spatial variability of the activity of soil microorganisms able to mineralize the herbicide isoproturon (IPU) pesticide was investigated over a three-year long crop rotation between 2008 and 2010. Isoproturon mineralization was higher in 2008, when winter wheat was treated with this herbicide, than in 2009 and 2010, when rape seed and barley were treated with different herbicides. Under laboratory conditions, we showed that isoproturon mineralization was not promoted by sulfonylurea herbicide applied on barley crop in 2010. IPU mineralization was shown to be highly variable at the field scale in years 2009 and 2010. Principal component analyses and analyses of similarities revealed that soil pH and equivalent humidity, and to a lesser extent soil organic matter content and cation exchange capacity (CEC) were the main drivers of isoproturon-mineralizing activity variance. Using a rather simple model that yields the rate of isoproturon mineralization as a function of soil pH and equivalent humidity, we explained up to 85% of the variance observed. Mapping field-scale distribution of isoproturon mineralization over the three-year survey indicated higher variability in 2009 and in 2010 as compared to 2008, suggesting that isoproturon treatment applied to winter wheat promoted isoproturon mineralization activity and reduced its spatial variability. Field-scale distribution of isoproturon mineralization showed important similarity to the distribution of soil pH, equivalent humidity and to a lesser extent to soil organic matter and cation exchange capacity (CEC) thereby confirming our model.

Long-term dynamics of the atrazine mineralization potential in surface and subsurface soil in an agricultural field as a response to atrazine applications.

The dynamics of the atrazine mineralization potential in agricultural soil was studied in two soil layers (topsoil and at 35-45 cm depth) in a 3 years field trial to examine the long term response of atrazine mineralizing soil populations to atrazine application and intermittent periods without atrazine and the effect of manure treatment on those processes. In topsoil samples, (14)C-atrazine mineralization lag times decreased after atrazine application and increased with increasing time after atrazine application, suggesting that atrazine application resulted into the proliferation of atrazine mineralizing microbial populations which decayed when atrazine application stopped. Decay rates appeared however much slower than growth rates. Atrazine application also resulted into the increase of the atrazine mineralization potential in deeper layers which was explained by the growth on leached atrazine as measured in soil leachates recovered from that depth. However, no decay was observed during intermittent periods without atrazine application in the deeper soil layer. atzA and trzN gene quantification confirmed partly the growth and decay of the atrazine degrading populations in the soil and suggested that especially trzN bearing populations are the dominant atrazine degrading populations in both topsoil and deeper soil. Manure treatment only improved the atrazine mineralization rate in deeper soil layers. Our results point to the importance of the atrazine application history on a field and suggests that the long term survival of atrazine degrading populations after atrazine application enables them to rapidly proliferate once atrazine is again applied.

In vitro evolution of an atrazine-degrading population under cyanuric acid selection pressure: evidence for the selective loss of a 47 kb region on the plasmid ADP1 containing the atzA, B and C genes.

The adaptation of microorganisms to pesticide biodegradation relies on the recruitment of catabolic genes by horizontal gene transfer and homologous recombination mediated by insertion sequences (IS). This environment-friendly function is maintained in the degrading population but it has a cost which could diminish its fitness. The loss of genes in the course of evolution being a major mechanism of ecological specialization, we mimicked evolution in vitro by sub-culturing the atrazine-degrading Pseudomonas sp. ADP in a liquid medium containing cyanuric acid as the sole source of nitrogen. After 120 generations, a new population evolved, which replaced the original one. This new population grew faster on cyanuric acid but showed a similar cyanuric acid degrading ability. Plasmid profiles and Southern blot analyses revealed the deletion of a 47 kb region from pADP1 containing the atzABC genes coding for the enzymes that turn atrazine into cyanuric acid. Long PCR and sequencing analyses revealed that this deletion resulted from a homologous recombination between two direct repeats of a 110-bp, identical to ISPps1 of Pseudomonas huttiensis, flanking the deleted 47 kb region. The loss of a region containing three functional genes constitutively expressed thereby constituting a genetic burden under cyanuric acid selection pressure was responsible for the gain in fitness of the new population. It highlights the IS-mediated plasticity of the pesticide-degrading potential and shows that IS not only favours the expansion of the degrading genetic potential thanks to dispersion and duplication events but also contribute to its reduction thanks to deletion events.

Evidence for shifts in the structure and abundance of the microbial community in a long-term PCB-contaminated soil under bioremediation.

Although the impact of bioremediation of PCB-contaminated sites on the indigenous microbial community is a key question for soil restoration, it remains poorly understood. Therefore, a small-scale bioremediation assay made of (a) a biostimulation treatment with carvone, soya lecithin and xylose and (b) two bioaugmentation treatments, one with a TSZ7 mixed culture and another with a Rhodococcus sp. Z6 pure strain was set up. Changes in the structure of the global soil microbial community and in the abundances of different taxonomic phyla were monitored using ribosomal intergenic spacer analysis (RISA) and real-time PCR. After an 18-month treatment, the structure of the bacterial community in the bioremediated soils was significantly different from that of the native soil. The shift observed in the bacterial community structure using RISA analysis was in accordance with the monitored changes in the abundances of 11 targeted phyla and classes. Actinobacteria, Bacteriodetes and α- and γ-Proteobacteria were more abundant under all three bioremediation treatments, with Actinobacteria representing the dominant phylum. Altogether, our results indicate that bioremediation of PCB-contaminated soil induces significant changes in the structure and abundance of the total microbial community, which must be addressed to implement bioremediation practices in order to restore soil functions.

Inter-laboratory evaluation of the ISO standard 11063 "Soil quality - Method to directly extract DNA from soil samples".

Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, as well as the abundance and genetic structure of the total bacterial community in the DNA extracted from 12 different soils by the 13 laboratories. High quality DNA was successfully extracted from all 12 soils, despite different physical and chemical characteristics and a range of origins from arable soils, through forests to industrial sites. Quantification of the 16S rRNA gene abundances by real time PCR and analysis of the total bacterial community structure by automated ribosomal intergenic spacer analysis (A-RISA) showed acceptable to good levels of reproducibility. Based on the results of both ring-tests, the method was unanimously approved by the ISO as an international standard method and the normative protocol will now be disseminated within the scientific community. Standardization of a soil DNA extraction method will improve data comparison, facilitating our understanding of soil microbial diversity and soil quality monitoring.

Taxonomic and functional diversity of atrazine-degrading bacterial communities enriched from agrochemical factory soil.

AIMS: To characterize atrazine-degrading potential of bacterial communities enriched from agrochemical factory soil by analysing diversity and organization of catabolic genes. METHODS AND RESULTS: The bacterial communities enriched from three different sites of varying atrazine contamination mineralized 65-80% of (14) C ring-labelled atrazine. The presence of trzN-atzBC-trzD, trzN-atzABC-trzD and trzN-atzABCDEF-trzD gene combinations was determined by PCR. In all enriched communities, trzN-atzBC genes were located on a 165-kb plasmid, while atzBC or atzC genes were located on separated plasmids. Quantitative PCR revealed that catabolic genes were present in up to 4% of the community. Restriction analysis of 16S rDNA clone libraries of the three enrichments revealed marked differences in microbial community structure and diversity. Sequencing of selected clones identified members belonging to Proteobacteria (α-, ß- and γ-subclasses), the Actinobacteria, Bacteroidetes and TM7 division. Several 16S rRNA gene sequences were closely related to atrazine-degrading community members previously isolated from the same contaminated site. CONCLUSIONS: The enriched communities represent a complex and diverse bacterial associations displaying heterogeneity of catabolic genes and their functional redundancies at the first steps of the upper and lower atrazine-catabolic pathway. The presence of catabolic genes in small proportion suggests that only a subset of the community has the capacity to catabolize atrazine. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides insights into the genetic specificity and the repertoire of catabolic genes within bacterial communities originating from soils exposed to long-term contamination by s-triazine compounds.