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See detailNo favorable effect of reduced tillage on microbial communities in a silty loam soil (Belgium)
Degrune, Florine ULg; Theodorakopoulos, Nicolas ULg; Dufrêne, Marc ULg et al

Poster (2015, December 01)

To date, only a few studies have applied metagenomics to investigate the influence of different tillage regimes and types of crop residue management on soil microbial communities. These studies were ... [more ▼]

To date, only a few studies have applied metagenomics to investigate the influence of different tillage regimes and types of crop residue management on soil microbial communities. These studies were conducted under specific climates on soils characterized by particular land-use histories. A very different ecological context is to be found in certain areas of Western Europe, such as central Belgium, whose loess-derived soils are among the most fertile in the world and have long been used for intensive agriculture. Specific objectives were to determine diversity levels and changes in microbial community composition under different combinations of tillage regime (conventional vs. reduced) and crop residue fate (residue removal R- vs. residues left R+ on the field). As reduced tillage results in two contrasting zones (the first centimeters of soil are mixed each year, while the soil below remains unperturbed), we chose to perform the analysis at two depths: 0 to 5 cm and 15 to 20 cm. [less ▲]

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See detailMetagenomic insights into the dynamics of microbial communities in food
Kergourlay, Gilles ULg; Taminiau, Bernard ULg; Daube, Georges ULg et al

in International Journal of Food Microbiology (2015), 213

Metagenomics has proven to be a powerful tool in exploring a large diversity of natural environments such as air, soil, water, and plants, as well as various human microbiota (e.g. digestive tract, lungs ... [more ▼]

Metagenomics has proven to be a powerful tool in exploring a large diversity of natural environments such as air, soil, water, and plants, as well as various human microbiota (e.g. digestive tract, lungs, skin). DNA sequencing techniques are becoming increasingly popular and less and less expensive. Given that high-throughput DNA sequencing approaches have only recently started to be used to decipher food microbial ecosystems, there is a significant growth potential for such technologies in the field of food microbiology. The aim of this review is to present a survey of recent food investigations via metagenomics and to illustrate how this approach can be a valuable tool in the better characterization of foods and their transformation, storage and safety. Traditional food in particular has been thoroughly explored by global approaches in order to provide information on multi-species and multi-organism communities. [less ▲]

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See detailEvaluation of the sensory quality of beef patties inoculated with Carnobacterium maltaromaticum strains with biopreservative potential
Didimo Imazaki, Pedro Henrique ULg; Jacques-Houssa, Charlotte ULg; Kergourlay, Gilles ULg et al

Conference (2015, October 16)

Biopreservation is the use of naturally occurring microorganisms and/or their inherent antimicrobial compounds to extend shelf life and to enhance the safety of foods. The aim of the present study was to ... [more ▼]

Biopreservation is the use of naturally occurring microorganisms and/or their inherent antimicrobial compounds to extend shelf life and to enhance the safety of foods. The aim of the present study was to perform a sensory evaluation of beef patties inoculated with potentially biopreservative strains of Carnobacterium maltaromaticum. Three different strains of C. maltaromaticum (lab. ref.: CM_824, CM_827 and CM_829) isolated from vacuum packaged beef with long shelf life were selected for this study. An untrained panel was requested to make a sensory evaluation of raw and cooked beef patties 8 and 10 days after inoculation with the selected strains at 104 and 106 UFC/g and storage in high-O2 atmosphere. After 8 days of storage, non inoculated samples (blank) were perceived as having the best studied sensory descriptors. The samples inoculated with strain CM_827 had a sensory quality very close to the blank. After 10 days of storage, samples inoculated with the strain CM_827 at 104 UFC/g received the highest scores for appearance and color. This study permitted to evaluate the effect of three C. maltaromaticum strains on the sensory quality of beef patties. Strain CM_827 did practically not change the sensory attributes of beef patties. Samples inoculated with strain CM_824 and CM_829 received the worst scores for several of the tested descriptors. Therefore, further research on the biopreservative capacity of C. maltaromaticum should be conducted with strain CM_827. [less ▲]

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See detailOptmization of culture media for Bifidobacterium bifidum and Bifidobacterium crudilactis and study of the antimicrobial effect of culture supernatants
Bondue, Pauline ULg; Delcenserie, Véronique ULg; Crevecoeur, Sébastien ULg et al

Poster (2015, October)

Complex oligosaccharides from human milk (HMO) contribute to infant health. Bifidobacteriumbifidum mainly found in breast-fed infant microbiota has all the enzymatic machinery for degradation of HMO. On ... [more ▼]

Complex oligosaccharides from human milk (HMO) contribute to infant health. Bifidobacteriumbifidum mainly found in breast-fed infant microbiota has all the enzymatic machinery for degradation of HMO. On the other hand, whey is rich in complex bovin milk oligosaccharides (BMO) very similar to HMO, including 3’-sialyllactose (3’SL). They are very likely to be metabolised by B. bifidum too, but also by B. crudilactis, a bovine origin strain. Fermentation of HMO or BMO by bifidobacteria can result in production of metabolites modulating virulence expression of several pathogenic bacteria. Two strains of bifidobacteria were used in this study: B. bifidum, isolated from breastfed infant feces and B. crudilactis, isolated from bovine raw milk. The ability of those strains to metabolise culture media enriched in glucose, whey and 3’SL has been assessed. Then, the obtained culture supernatant has been tested against virulence genes expression of E. coli O157:H7.  Both strains were able to grow in presence of BMO and 3’SL. B. crudilactis presented the best growth on all media. All culture supernatants obtained after supplementation with 3’SL resulted in significant under-expression of genes ler and qseA. The trend of genes stxB2 and luxS was also toward a down-regulation. BMO combined to some bovine or human origin bifidobacteria strains could be interesting synbiotics to maintain or restore the intestinal health of young children. These effects observed in vitro require further investigations to ensure repeatability in humans and to identify the exact nature of molecules obtained from fermentation media by B. bifidum and B. crudilactis. [less ▲]

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See detailFaecal microbiota characterisation of horses using 16 rdna barcoded pyrosequencing, and carriage rate of clostridium difficile at hospital admission
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Brévers, Bastien et al

in BMC Microbiology (2015), 15

Background The equine faecal microbiota is very complex and remains largely unknown, while interspecies interactions have an important contribution to animal health. Clostridium difficile has been ... [more ▼]

Background The equine faecal microbiota is very complex and remains largely unknown, while interspecies interactions have an important contribution to animal health. Clostridium difficile has been identified as an important cause of diarrhoea in horses. This study provides further information on the nature of the bacterial communities present in horses developing an episode of diarrhoea. The prevalence of C. difficile in hospitalised horses at the time of admission is also reported. Results Bacterial diversity of the gut microbiota in diarrhoea is lower than that in non-diarrhoeic horses in terms of species richness (p-value <0.002) and in population evenness (p-value: 0.02). Statistical differences for Actinobacillus, Porphyromonas, RC9 group, Roseburia and Ruminococcaceae were revealed. Fusobacteria was found in horses with diarrhoea but not in any of the horses with non-diarrheic faeces. In contrast, Akkermansia was among the three predominant taxa in all of the horses studied. The overall prevalence of C. difficile in the total samples of hospitalised horses at admission was 3.7 % (5/134), with five different PCR-ribotypes identified, including PCR-ribotype 014. Two colonised horses displayed a decreased bacterial species richness compared to the remaining subjects studied, which shared the same Bacteroides genus. However, none of the positive animals had diarrhoea at the moment of sampling. Conclusions The abundance of some taxa in the faecal microbiota of diarrhoeic horses can be a result of microbiome dysbiosis, and therefore a cause of intestinal disease, or some of these taxa may act as equine enteric pathogens. Clostridium difficile colonisation seems to be transient in all of the horses studied, without overgrowth to trigger infection. A large proportion of the sequences were unclassified, showing the complexity of horses’ faecal microbiota. [less ▲]

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See detailSensory quality of beef patties inoculated with strains of Carnobacterium maltaromaticum with potential as biopreservatives
Didimo Imazaki, Pedro Henrique ULg; Jacques-Houssa, Charlotte ULg; Kergourlay, Gilles ULg et al

Poster (2015, August)

Biopreservation is the use of naturally occurring microorganisms and/or their inherent antimicrobial compounds to extend shelf life and to enhance the safety of foods. The aim of the present study was to ... [more ▼]

Biopreservation is the use of naturally occurring microorganisms and/or their inherent antimicrobial compounds to extend shelf life and to enhance the safety of foods. The aim of the present study was to perform a sensory evaluation of beef patties inoculated with strains of C. maltaromaticum with potential as biopreservatives. Three different strains of C. maltaromaticum (CM_824, CM_827 and CM_829) isolated from vacuum packaged beef with long shelf life were selected for this study. An untrained panel was requested to make a sensory evaluation of raw and cooked beef patties 8 and 10 days after inoculation with the selected strains at 104 and 106 UFC/g and storage in high O2 atmosphere. This preliminary study permitted to evaluate the effect of three C. maltaromaticum strains on the sensory quality of beef patties. Strain CM_827 did practically not change the sensory attributes of beef patties. Samples inoculated with strain CM_824 and CM_829 received the worst scores for several of the tested descriptors. Therefore, further research on the biopreservative capacity of C. maltaromaticum should be conducted with strain CM_827. [less ▲]

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See detailMetagenomic analysis of samples
Daube, Georges ULg; Taminiau, Bernard ULg; Nezer, Carine et al

Patent (2015)

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See detailMethod of testing for animal-derived ingredients in foods
Daube, Georges ULg; Burteau, Sophie; Nezer, Carine et al

Patent (2015)

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See detailMorphological and functional characterization of Carnobacterium maltaromaticum isolated from vacuum-packed beef with long shelf life
Didimo Imazaki, Pedro Henrique ULg; Tahiri, Assia ULg; Ndedi Ekolo, François ULg et al

Poster (2015, June 17)

Temperatures near the freezing point of meat (−1.5 °C), associated with vacuum packaging, allows the preservation of this product up to several months, which makes possible the meat trade across the ... [more ▼]

Temperatures near the freezing point of meat (−1.5 °C), associated with vacuum packaging, allows the preservation of this product up to several months, which makes possible the meat trade across the planet without resorting to freezing. Other the type of packaging and the storage temperature, the shelf-life of meat is directly related to its initial microbiological ecosystem and its evolution. Carnobacterium maltaromaticum is a lactic acid bacterium, and many lactic acid bacteria associated with meat are known for their bactericidal or bacteriostatic activity against other strains, species or genera of bacteria. In this way, the presence of certain lactic acid bacteria adapted to a low temperature in fresh meat could extend the shelf life and improve the microbial stability and safety of this product. The aim of this study was to perform a morphological and functional characterization of a C. maltaromaticum strain (lab. ref. CFAUS2/DLC/4/E1) with potential bioprotective effect isolated from commercial vacuum packaged long shelf life beef. The morphological, biochemical and enzymatic profiles, the influence of different temperatures and atmospheres, and the microbial stability of fresh beef inoculated with the C. maltaromaticum strain were evaluated. Morphological, biochemical and enzymatic profiles of the isolated C. maltaromaticum strain were similar to those of two reference strains (LMG 11393 and LMG 22902). The evaluation of the influence of different atmospheres showed that the growth of C. maltaromaticum was the slowest in an atmosphere containing 70 % O2 and 30 % CO2. Vacuum packaging is therefore more suitable for the growth of this bacterium. An antimicrobial effect against Enterobacteriaceae was highlighted on inoculated fresh meat. The functional characterization of this strain will be further pursued by genotypic characterization and its potential bioprotective effect will also be studied. [less ▲]

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See detailUse of 16S rDNA Metagenetics and classical Microbiology to Assess the bacterial superficial Contamination Patterns in Bovines Classically Slaughtered or following the Halal Ritual
Korsak Koulagenko, Nicolas ULg; Taminiau, Bernard ULg; Hupperts, Caroline et al

Poster (2015, June 17)

In Belgium and in several European countries, two cattle slaughtering protocols exist: the classical method, that encompasses a stunning step before the sticking procedure, and the halal method, combining ... [more ▼]

In Belgium and in several European countries, two cattle slaughtering protocols exist: the classical method, that encompasses a stunning step before the sticking procedure, and the halal method, combining the stunning and the sticking in one single step. The main difference lies in the fact that, in the halal protocol, a single cut with a sharp knife is practiced directly on live cattle, instead of two cutting steps with two different knives for the sticking in the classical slaughtering technique. The unique section in the halal technique results generally in the cross section of trachea and esophagus of cattle. The aim of this study was to seek if the two slaughtering techniques were similar regarding the superficial contamination of carcasses, swabbed between 2 and 4 hours after the killing step. For this purpose, classical microbiological tests (TVC and Enterobacteriaceae) and 16S rDNA metagenetic analysis were carried out from 20 cattle carcasses (swabbing of “legal” zone – 1.600 cm2 – and in the neck area – 200 cm2). The classical microbiological results revealed no significant differences between the two slaughtering practices. Statistical analysis of pyrosequencing data showed that differences in bacterial population abundance between slaughtering methods were mainly found in the “legal” swabbing zone compared to the neck area. Bacterial genera belonging to Actinobacteria (Brevibacterium, Corynebacterium) were more aundant in “Halal” samples whereas populations from the Proteobacteria (Caulobacteraceae, Comamonadaceae, Bradyrhizobiaceae) and Firmicutes (Lactobacillus) were more abundand in the “classical” group. The analysis of OTU abundance of bacteria from the digestive or respiratory tract revealed no differences beteween groups. In conclusion, the slaughtering method does not influence the superficial microbiological pattern in terms of specific microbiological markers of the digestive or respiratory tract. However, precise analysis to the genus level underlines differences between methods, the legal swabbing zone being still the best sampling zone compared to the neckline. The next step will be the identification of precise contamination origin of the differences found between slaughtering methods. [less ▲]

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See detailOptimisation de milieux de culture pour Bifidobacterium bifidum et Bifidobacterium crudilactis et étude de l’effet antimicrobien des surnageants de culture
Bondue, Pauline ULg; Delcenserie, Véronique ULg; Crevecoeur, Sébastien ULg et al

Poster (2015, June)

Modulé entre autre par notre alimentation, le microbiote intestinal influence notre santé. Un enfant allaité sera en meilleure santé qu’un enfant nourri avec des formulations commerciales. Ceci est ... [more ▼]

Modulé entre autre par notre alimentation, le microbiote intestinal influence notre santé. Un enfant allaité sera en meilleure santé qu’un enfant nourri avec des formulations commerciales. Ceci est notamment dû à la présence d’oligosaccharides complexes dans le lait maternel (HMO). Les oligosaccharides ajoutés au lait maternisé sont d’origine végétale et leur structure est très éloignée de celle des HMO. Parce que les HMO ressemblent aux glycans de la paroi épithéliale, les pathogènes intestinaux infantiles s’y fixent et sont expulsés naturellement. Le lait de vache possède des oligosaccharides complexes (BMO), dont la structure est très similaire à celle des HMO. Les bifidobactéries rencontrées majoritairement dans les matières fécales d’un nourrisson devraient pouvoir métaboliser les BMO, tout comme celles isolées dans le lait de vache. Les objectifs de cette étude étaient d’étudier le potentiel de croissance de bifidobactéries d’origine bovine ou humaine sur des milieux de culture enrichis en lactosérum et BMO. Le deuxième objectif était de vérifier si le catabolisme de ces sucres complexes induisaient une synthèse de métabolites influençant l’expression de virulence de certains pathogènes tels qu’Escherichia coli O157 :H7. Une souche de Bifidobacterium bifidum, isolée à partir des matières fécales d’un nourrisson exclusivement allaité et une souche de Bifidobacterium crudilactis, isolée à partir de fromage au lait cru, ont été mises en culture dans des milieux contenant différentes sources d’hydrates de carbone (glucose, lactosérum naturellement riche en lactose et BMO, et 3’-syalillactose (3’SL)). Le 3’SL est un oligosaccharide complexe majoritaire parmi les BMO. Les surnageants des différents milieux de culture ont été prélevés et concentrés par lyophilisation puis mis en contact avec E. coli O157 :H7. L’expression relative de différents gènes de virulence d’E. coli O157:H7, fliC, ler, stx2b et luxS a été étudiée. Dans le futur, les BMO et certaines souches d’origine bovine ou humaine pourraient s’avérer être des compléments alimentaires intéressants pour maintenir ou rétablir la santé intestinale des jeunes enfants. [less ▲]

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See detailCARRIAGE OF CLOSTRIDIUM DIFFICILE IN HOSPITAL PATIENTS IN SPAIN, INCLUDING MOLECULAR CHARACTERIZATION AND ANTIMICROBIAL SUSCEPTIBILITY OF THE ISOLATES
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Van Broeck, Johan et al

Poster (2015, May 21)

Increasing age, several co-morbidities, environmental contamination, antibiotic exposure and other intestinal perturbations appear to be the greatest risk factors for C. difficile infection (CDI ... [more ▼]

Increasing age, several co-morbidities, environmental contamination, antibiotic exposure and other intestinal perturbations appear to be the greatest risk factors for C. difficile infection (CDI). Therefore, hospitalized patients are considered particularly vulnerable to CDI. The main objective of this study was to evaluate the prevalence of C. difficile in a Spanish hospital and to characterize the isolates with respect to the PCR-ribotype, antibiotic resistance and toxin activity. In addition, multilocus sequence typing (MLST) was performed in order to study clonal relationships between C. difficile isolates obtained from two different countries. Culture of samples was performed in a selective medium cycloserine cefoxitin fructose cholate. An identification of the isolated colonies was done by PCR detection of tpi, tcdA, tcdB and cdtA genes. Toxic activity was confirmed by a cytotoxic immunoassay. Further characterization was performed by PCR ribotyping. MLST was used in order to determine genetic relationships between Spanish and Belgian C. difficile isolates recovered from hospital patients in both countries. C. difficile was frequently detected in hospitalized patients. The isolates belonged to different PCR ribotypes, including type 027. Most of the strains obtained harboured tcdA and tcdB genes. The number of positive faecal samples considerably increased among elderly patients over 65 years old. The multi-locus sequence typing (MLST) analysis showed that some Spanish and Belgian isolates cluster in the same lineage. This study reveals the circulation of toxigenic C. difficile in a Spanish hospital. The relatedness between Belgian and Spanish isolates indicate a common source or a lack of diversity from some PCR-ribotypes. Moreover, data obtained suggest that the combination of ribotyping and MLST is a good tool for the inter-laboratory comparison of strains among different countries. Continuous inter-country surveillance is suitable to understand the spread of C. difficile isolates among hospitalized patients. [less ▲]

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See detailHeat survival of Clostridium difficile spores in ground meat during cooking process
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Avesani, Véronique et al

Poster (2015, April 21)

Introduction: Clostridium difficile is a spore-forming pathogen considered as a major cause of enteric disease in humans, with faecal-oral route as the primary mode of transmission. However, recent ... [more ▼]

Introduction: Clostridium difficile is a spore-forming pathogen considered as a major cause of enteric disease in humans, with faecal-oral route as the primary mode of transmission. However, recent studies have reported the occurrence of C. difficile in ground meats at retail stores, indicating that foods could be an additional source of infection in the community. Purpose: The objective of this study was to determine the resistance of C. difficile spores in contaminated ground meat during cooking process. Methods: Prior to testing, to obtain spores and to enhance heterogeneity, spores of two different strains were produced in two nutritious broths. C. difficile spores were experimentally inoculated in 45 g of ground meat (beef and pork) in order to obtain a final contamination of 4,500 ufc g-1. Six heating temperatures (70, 75, 80, 85, 90 and 95°C) were chosen. Samples were heating in a water bath with an integrated program for time-temperature. One sample without inoculum was used as control with a temperature probe placed inside. Once the desired temperature was research in the core of the sample, the heat treatment was prolonged for 10 min. Subsequently, all the samples were placed on the chilling room (4°C) before analyse. These experiments were conducted in duplicate with a spore enumeration in triplicate. Results: Heating contaminated ground meat at 70, 75 and 80°C for 10 min was not effective for C. difficile spores inhibition. However, 10 min of heat shock at 80°C was the only temperature that significantly reduced the number of countable colonies. Heat treatment at 85°C (or more) inhibits the germination of both of the strains tested. Significance: Ensure that ground meat, like burgers or sausages, is heated to more than 85°C would be an important measure to reduce the risk of C. difficile food transmission. [less ▲]

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See detailAssociation of classical microbiology and 16S rDNA metagenetic analysis to evaluate the presence of Clostridium difficile ina a belgian nursing home
Rodriguez Diaz, Cristina ULg; Taminiau, Bernard ULg; Avesani, Véronique et al

Poster (2015, April 01)

Increasing age, several co-morbidities, environmental contamination, antibiotic exposure and other intestinal perturbations appear to be the greatest risk factors for C. difficile infection (CDI ... [more ▼]

Increasing age, several co-morbidities, environmental contamination, antibiotic exposure and other intestinal perturbations appear to be the greatest risk factors for C. difficile infection (CDI). Therefore, elderly care home residents are considered particularly vulnerable to CDI. The main objective of this study was to evaluate and follow the prevalence of C. difficile in a Belgian nursing home. During a 4-month period, stool samples from a group of 23 elderly care home residents were collected weekly. A C. difficile microbiological detection scheme was performed along with an overall microbial biodiversity study of the faeces content by Targeted Metagenomic analysis. Culture of samples was performed in a selective medium cycloserine cefoxitin fructose cholate. An identification of the isolated colonies was done by PCR detection of tpi, tcdA, tcdB and cdtA genes. Toxic activity was confirmed by a cytotoxic immunoassay. Further characterization was performed by PCR ribotyping. The Metagenomic analysis was targeted on the v1-v3 hyper-variable region of 16S rDNA. The taxonomical assignment of the populations was performed with MOTHUR and Blast algorithms. Seven out of 23 (30.4%) residents were (at least one week) positive for C. difficile. The most common PCR-ribotype identified was 027. Targeted Metagenomic analyses reveals that each resident has his own bacterial imprint, which is stable during the entire study. Residents’ positives for C. difficile by classical microbiology showed an important proportion of C. difficile sequences. However, Metagenomics analysis can’t substitute targeted protocols. It was not used as a diagnostic tool to detect C. difficile but rather to determine the identification and correlations of the major bacterial populations that are present in the gut microbiota. In conclusion, this unique association of classical microbiology protocol with pyrosequencing allowed to follow C. difficile in patients and to identify several other bacterial populations whose abundance is correlated with C. difficile. [less ▲]

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See detailSoil microbial community composition changes according to the tillage practice and plant development stage
Degrune, Florine ULg; Dufrêne, Marc ULg; Taminiau, Bernard ULg et al

Poster (2015, April)

Agricultural practices have a strong impact on soil bacterial and fungal community composition. Furthermore, microbial community composition can change with the stage of plant development. We are ... [more ▼]

Agricultural practices have a strong impact on soil bacterial and fungal community composition. Furthermore, microbial community composition can change with the stage of plant development. We are interested in exploring these effects in relation to changes induced by agriculture (conventional and reduced tillage) and plant stage (germination and flowering) in soil conditions. Here, instead of examining this impact at a high taxonomic level such as phylum and/or class, thus missing potentially relevant information from lower levels, we propose an original method: exploiting the available sequence information at the lowest taxonomic level attainable for each operational taxonomic unit. Results show that some microbial communities were impacted only by the tillage practice , while others were impacted only by the stage of plant. Changes in microbial community composition could be due to the soil conditions induced by the soil practice and the stage of plant. [less ▲]

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See detailA novel sub-phylum method discriminates better the impact of crop management on soil microbial community
Degrune, Florine ULg; Dufrêne, Marc ULg; Colinet, Gilles ULg et al

in Agronomy for Sustainable Development (2015)

Soil microorganisms such as mycorrhizae and plant-growth-promoting rhizobacteria have beneficial effects on crop productivity. Agricultural practices are known to impact soil microbial communities, but ... [more ▼]

Soil microorganisms such as mycorrhizae and plant-growth-promoting rhizobacteria have beneficial effects on crop productivity. Agricultural practices are known to impact soil microbial communities, but past studies examining this impact have focused mostly on one or two taxonomic levels, such as phylum and class, thus missing potentially relevant information from lower levels. Therefore we propose here an original, sub-phylum method for studying how agricultural practices modify microbial communities. This method involves exploiting the available sequence information at the lowest taxonomic level attainable for each operational taxonomic unit. In order to validate this novel method we assessed microbial community composition using 454 pyrosequencing of 16S and 28S rRNA genes, then we compared the results with results of a phylum-level analysis. Agricultural practices included conventional tillage, reduced tillage, residue removal and residue retention. Results show that, at the lowest taxonomic level attainable, tillage is the main factor influencing both bacterial community composition, accounting for 13% of the variation, and fungal community composition, accounting for 18% of the variation. Whereas phylum-level analysis failed to reveal any effect of soil practice on bacterial community composition, and missed the fact that different members of the same phylum responded differently to tillage practice. For instance, the fungal phylum Chytridiomycota showed no impact of soil treatment, while sub-phylum-level analysis revealed an impact of tillage practice on the Chytridiomycota sub-groups Gibberella, which includes a notorious wheat pathogen, and Trichocomaceae. This clearly demonstrates the necessity of exploiting the information obtainable at sub-phylum level when assessing the effects of agricultural practice on microbial communities. [less ▲]

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