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See detailMicrobial diversity and activity in temperate forest and grassland ecosystems
Malchair, Sandrine ULg

Doctoral thesis (2009)

Ecosystems currently face widespread biodiversity losses and other environmental disturbances, such as climate warming, related to increased anthropogenic activities. Within this context, scientists ... [more ▼]

Ecosystems currently face widespread biodiversity losses and other environmental disturbances, such as climate warming, related to increased anthropogenic activities. Within this context, scientists consider the effects of such changes on the biodiversity, and hence on the activity, of soil microorganisms. Indeed, soil microorganisms mediate a wide range of soil processes. Currently, knowledge on soil microbial diversity is still limited, partially due to technical limitations. The advent of molecular-based analyses now allows studying the soil microbial diversity. These advances in the study of soil microbial communities have lead to a growing evidence of the critical role played by the microbial community in ecosystem functioning. This relationship is supposed to be relevant for narrow processes, regulated by a restricted group of microorganisms, such as the nitrification process. This PhD thesis aimed at studying ammonia oxidizing bacteria (AOB) community structure and richness as an integrated part of soil functioning. This research aimed at investigating the effect of aboveground plant diversity on ammonia oxidizing bacteria diversity and function in forest and grassland soils with focus on the influence of (a) functional group identity of grassland plants (legumes, grasses, forbs), (b) grassland plant species richness and (c) tree species, on AOB diversity and function. Another objective of this research was to study the effect of a 3°C increase in air temperature on AOB diversity and function. The link between AOB diversity and function (potential nitrification) is also investigated. For grassland ecosystems, a microcosm experiment was realized. An experimental platform containing 288 assembled grassland communities was established in Wilrijk (Belgium). Grassland species were grown in 12 sunlit, climate controlled chambers. Each chamber contained 24 communities of variable species richness (S) (9 S=1, 9 S=3 and 6 S=9).The grassland species belonged to three functional groups: three species of each grasses (Dactylis glomerata L., Festuca arundinacea SCHREB., Lolium perenne L.), forbs (non-N-fixing dicots; Bellis perennis L., Rumex acetosa L., Plantagolanceolata L.), and legumes (N-fixing dicots; Trifolium repens L., Medicago sativa L., Lotus corniculatus L.). Half of these chambers were exposed to ambient temperature and the other half were exposed to (ambient +3°C) temperature. One ambient and one (ambient+3°C) chambers were destructively harvested 4, 16 and 28 months after the start of the experiment. The influence of plant functional group identity on the nitrification process and on AOB community structure and richness (AOB diversity) was assessed in soils collected from the first two destructive amplings (chapter 2). The effect of plant species richness on AOB diversity and function was considered for soils sampled after 16 and 28 months (chapter 3). AOB function was determined by potential nitrification. AOB community structure and richness were assessed by polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) and sequencing of excised DGGE bands. I found that functional group identity can affect AOB community structure. In particular, the presence of legumes, both in monoculture or in mixture with forbs and grasses, lead to AOB community composition changes towards AOB clusters tolerating higher ammonium concentrations. This change in AOB community structure was only linked to increased potential nitrification under monocultures of legumes, when ammonium was supposed to be not limiting. This study revealed that physiological attributes of AOB and resource availability may be important factors in controlling the nitrification process. This research showed that the impact of plant species richness on the nitrification process could be mediated by the interactions between plants and AOB, through competition for substrate. A 3°C increase in air temperature did not affect AOB community structure, richness or function. In forest ecosystems, we studied the effect of tree species in forest sites located in Belgian and in the Grand-Duchy of Luxembourg covered each by several deciduous or coniferous tree species (Fagus sylvatica L., Quercus petraea (Mattuschka) Lieblein, Picea abies (L.) Karst, Pseudotsuga menziesii (Mirbel) Franco). We investigated the influence of these tree species on microbial processes (chapter 5) related to C and N cycling, particularly with emphasize on the nitrification process and on the diversity of AOB (chapter 6). The results showed that the effect of tree species on net N mineralization was likely to be mediated through their effect on soil microbial biomass, reflecting their influence on organic matter content and carbon availability. Influence of tree species on nitrification (potential and relative) might be related to the presence of ground vegetation through its influence on soil ammonium and labile C availability. AOB community structure was more site-specific than tree specific. However, within sites, AOB community structure under broadleaved trees differed from the one under coniferous trees. The effect on tree species on AOB was likely to be driven by the influence of tree species on net N mineralization, which regulates the substrate availability for AOB. The results also demonstrated that the relationship between AOB diversity and function might be related both to AOB abundance and AOB community structure and richness. This thesis showed no clear relationship between AOB community structure or richness and AOB function. However, we revealed that aboveground grassland plant richness, grassland plant functional groups and tree species influence AOB community structure and richness. [less ▲]

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See detailMicrobial Diversity and Processes in Lake Kivu (East Africa)
Llirós, M.; Darchambeau, François ULg; Garcia-Armisen, T. et al

Conference (2011)

Lake Kivu is a deep meromictic and oligotrophic tropical African lake with a permanent thermal- and haline stratification with huge accumulations of dissolved CO2 and CH4 (ca. 300 km3 and 60 km3 ... [more ▼]

Lake Kivu is a deep meromictic and oligotrophic tropical African lake with a permanent thermal- and haline stratification with huge accumulations of dissolved CO2 and CH4 (ca. 300 km3 and 60 km3, respectively) in the deep anoxic monimolimnion (from 60 o 480 m depth). Although there are a wealth of information on the ecology of small eukaryotes and their trophic role on Kivu, available information on prokaryotic planktonic assemblages is scarce. Molecular analysis of archaeal and bacterial communities showed a vertical segregation imposed by the permanent redoxcline. In relation to Bacteria, Actinobacteria, Betaproteobacteria, Green Sulfur Bacteria and Bacteroidetes were the most commonly retrieved groups. For Archaea, a marked dominance of Thaumarchaeota and Crenarchaeota (75% of all archaeal OTUs) over Euryarchaeota was observed. In the anoxic hypolimnion, Euryarchaoeta (Methanosarcinales and Methanocellales) lineages together with Miscellaneous Crenarchaeotic Group phylotypes were mainly recovered. In turn, Thaumarchaeota phylotypes were recovered in oxic and suboxic waters. CARDFISH analyses over the first 100 m revealed the dominance of Bacteria (51.4% – 95.7% of DAPI-stained cells), especially Actinobacteria (epilimnion), Betaproteobacteria (oxic-anoxic interface) and Bacteroidetes (upper hypolimnion), over Archaea (1.0% – 4.5%; maximum abundances at the oxic-anoxic interface). In turn, flow cytometry evidenced the dominance of HNA cells in the euphotic layer, whereas the proportion of LNA cells increased with depth. HNA and LNA populations were still observed in the anoxic hypolimnion suggesting facultative or strict anaerobic metabolisms. The detection of distinct depth maxima of nitrate, nitrite, archaeal amoA and Marine Thaumarchaeota 16S gene copy numbers together with regularly detection of deep maxima of 3H-Thymidine uptake, and the presence of low-light adapted GSB species point towards a strong link of N, C, and S cycles in the redoxcline of Lake Kivu. [less ▲]

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See detailMicrobial Ecology of Lake Kivu
Llirós, Marc; Descy, Jean-Pierre; Libert, Xavier et al

in Descy, Jean-Pierre; Darchambeau, François; Schmid, Martin (Eds.) Lake Kivu, Limnology and Biogeochemistry of a Tropical Great Lake (2012)

We review available data on archaea, bacteria and small eukaryotes in an attempt to provide a general picture of microbial diversity, abundances and microbe-driven processes in Lake Kivu surface and ... [more ▼]

We review available data on archaea, bacteria and small eukaryotes in an attempt to provide a general picture of microbial diversity, abundances and microbe-driven processes in Lake Kivu surface and intermediate waters (ca. 0–100 m). The various water layers present contrasting physical and chemical properties and harbour very different microbial communities supported by the vertical redox structure. For instance, we found a clear vertical segregation of archaeal and bacterial assemblages between the oxic and the anoxic zone of the surface waters. The presence of specific bacterial (e.g. Green Sulfur Bacteria) and archaeal (e.g. ammonia-oxidising archaea) communities and the prevailing physico-chemical conditions point towards the redoxcline as the most active and metabolically diverse water layer. The archaeal assemblage in the surface and intermediate water column layers was mainly composed by the phylum Crenarchaeota , by the recently defined phylum Thaumarchaeota and by the phylum Euryarchaeota . In turn, the bacterial assemblage comprised mainly ubiquitous members of planktonic assemblages of freshwater environments (Actinobacteria, Bacteroidetes and Betaproteobacteria among others) and other less commonly retrieved phyla (e.g. Chlorobi, Clostridium and Deltaproteobacteria). The community of small eukaryotes (<5 µm) mainly comprised Stramenopiles , Alveolata , Cryptophyta , Chytridiomycota , Kinetoplastea and Choanoflagellida, by decreasing order of richness. The total prokaryotic abundance ranged between 0.5 × 10^6 and 2.0 × 10^6 cells mL−1 , with maxima located in the 0–20 m layer, while phycoerythrin-rich Synechococcus-like picocyanobacteria populations were comprised between 0.5 × 10^5 and 2.0 × 10^5 cells mL−1 in the same surface layer. Brown-coloured species of Green Sulfur Bacteria permanently developed at 11m depth in Kabuno Bay and sporadically in the anoxic waters of the lower mixolimnion of the main basin. The mean bacterial production was estimated to 336 mg C m−2 day−1 . First estimates of the re-assimilation by bacterioplankton of dissolved organic matter excreted by phytoplankton showed high values of dissolved primary production (ca. 50% of total production). The bacterial carbon demand can totally be fuelled by phytoplankton production. Overall, recent studies have revealed a high microbial diversity in Lake Kivu, and point towards a central role of microbes in the biogeochemical and ecological functioning of the surface layers, comprising the mixolimnion and the upper chemocline. [less ▲]

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See detailMicrobial ecology of the closed artificial ecosystem MELiSSA (Micro-Ecological Life Support System Alternative): Reinventing and compartmentalizing the Earth's food and oxygen regeneration system for long-haul space exploration missions
Hendrickx, Larissa; De Wever, Heleen; Hermans, Veronik et al

in Research in Microbiology (2006), 157

MELiSSA is a bioregenerative life support system designed by the European Space Agency (ESA) for the complete recycling of gas, liquid and solid wastes during long distance space exploration. The system ... [more ▼]

MELiSSA is a bioregenerative life support system designed by the European Space Agency (ESA) for the complete recycling of gas, liquid and solid wastes during long distance space exploration. The system uses the combined activity of different living organisms: microbial cultures in bioreactors, a plant compartment and a human crew. In this minireview, the development of a short-cut ecological system for the biotransformation of organic waste is discussed from a microorganism's perspective. The artificial ecological model—still in full development—that is inspired by Earth's own geomicrobiological ecosystem serves as an ideal study object on microbial ecology and will become an indispensable travel companion in manned space exploration. [less ▲]

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See detailMicrobial heterogeneity affects bioprocess robustness: Dynamic single cell analysis contribute to understanding microbial populations
Delvigne, Frank ULg; Goffin, Philippe

in Biotechnology Journal (2014), 9(1), 61-72

Heterogeneity or segregation of microbial populations has been the subject of much research, but the real impact of this phenomenon on bioprocesses remains not well understood. The main reason behind this ... [more ▼]

Heterogeneity or segregation of microbial populations has been the subject of much research, but the real impact of this phenomenon on bioprocesses remains not well understood. The main reason behind this lack of knowledge is the difficulty for monitoring microbial population heterogeneity in dynamic process conditions. The main concepts leading to microbial population heterogeneity in the context of bioprocesses have been summarized by two distinct hypotheses. The first one involves the individual history of microbial cells or “path” followed during their residence time inside process equipment. The second one involves a coordinated response of the microbial population as a bet-hedging strategy in order to cope with process-related stresses. The respective contribution of each hypothesis to microbial heterogeneity in bioprocesses is still unclear. This statement illustrates the fact that, although microbial phenotypic heterogeneity has been thoroughly investigated at the fundamental level, the implications of this phenomenon in the context of microbial bioprocesses are still subjected to debate. At this time, automated flow cytometry is the best technique for the investigation of microbial heterogeneity in process conditions. However, dedicated software and relevant biomarkers are needed for its proper integration as a bioprocess control tool. [less ▲]

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See detailMicrobial inoculation for improving the growth and health of micropropagated strawberry
Vestberg, Mauritz; Kukkonen, Sanna; Saari, K. et al

in Applied Soil Ecology (2004), 27(3), 243-258

Multimicrobial inoculation has been proposed as a way of protecting plants against environmental stress and increasing the sustainability of plant production. To study these possibilities in a ... [more ▼]

Multimicrobial inoculation has been proposed as a way of protecting plants against environmental stress and increasing the sustainability of plant production. To study these possibilities in a micropropagation system, microplants of strawberry, Fragaria x ananssa, were inoculated or left uninoculated with five microorganisms (Glomus mosseae BEG29, Bacillus subtilis M3, Trichoderma harzianum DB11, Pseudomonas fluorescens C7rl2 and Gliocladium catenulatum Gliomix(R)), used either singly or in dual mixtures in the presence or absence of the strawberry diseases crown rot (Phytophthora cactorum) and red stele (P. fragariae). Finnish light Sphagnum peat was used as the growth substrate in the experiments. Seven experiments were performed as two to three months pot experiments in greenhouses of research laboratories in Finland and Belgium and in a nursery in Finland. In most experiments, the inoculated microorganims were detected at sufficient densities four weeks after inoculation. Exceptions were T harzianum and G. mosseae which were detected at insufficient densities in several experiments. This might have been due to the biological and/or nutritional properties of the peat. None of the microorganisms or their mixtures caused significant growth-promoting effects in more than two experiments. Dual inoculation did not increase growth more than inoculation with single organisms. B. subtilis was the most promising growth promoting microorganism. Most of the microbial treatments decreased crown rot shoot symptoms as well as the numbers of oospores in the roots when the experiment was performed in autumn. In the summer experiment with conditions more favourable for strawberry growth, no disease control was obtained, but some of the microorganisms increased the severity of crown rot. No microbial treatment decreased shoot symptoms of red stele, but the degree of root necrosis was slightly decreased by B. subtilis and G. mosseae + G. catenulatum. The numbers of oospores of P. fragariae in strawberry roots were not decreased by any treatment, but several treatments increased them. Both growth promotion and disease control considered, the single microorganisms T harzianum, G. catenulatum and B. subtilis as well as the mixture T harzianum + G. catenulatum were the most promising treatments in this study. However, the great variation between experiments indicates that more studies are needed for optimization of the whole plant-substrate-microorganism system. The importance of microbial inoculation for ensuring subsequent growth in the field also needs to be studied. (C) 2004 Elsevier B.V. All rights reserved. [less ▲]

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See detailMicrobial Processes for the Heavy Metal Recovery
Crine, Michel ULg; Hecq, W.

in Actes du Congrès organisé par l'Association Universitaire pour l'Environnement et le Groupe de contact FNRS "Génie chimique" (1990, April 12)

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See detailMicrobial volatile organic compounds as indicators of fungi. Can an electronic nose detect fungi in indoor environments?
Kuske, Martyna; Romain, Anne-Claude ULg; Nicolas, Jacques ULg

in Building and Environment (2005), 40(6), 824-831

The paper presents a review of several studies on the detection of microbial volatile organic compounds (MVOCs) considered as indicators of fungal contamination. As fungi produce specific profiles, or ... [more ▼]

The paper presents a review of several studies on the detection of microbial volatile organic compounds (MVOCs) considered as indicators of fungal contamination. As fungi produce specific profiles, or fingerprints of volatile compounds, the electronic nose technology is a very promising opportunity for rapid and non costly detection of fungi in buildings. E-noses are able to distinguish between mouldy and non-mouldy samples, and also to recognise certain species of fungi. However, two limiting factors may appear decisive for employment of electronic noses in indoor fungi detection: low concentrations of MVOCs and presence of interfering substances in indoor environments. [less ▲]

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See detailMicrobial, biochemical and sensorial quality assessment of Algerian farmed tilapia (Oreochromis niloticus) stored at 4 and 30°C
Dergal, Nadir; Abi-Ayad, S.M.E.-A.; Degand, Guy ULg et al

in African Journal of Food Science (2013), 7(12), 498-507

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See detailMicrobiological Analyses of Raw Milk Cheeses from Walloon Farms
Sanchez-Alcaraz, Maria-Thérésa ULg; Godrie, Thérèse ULg; Helleputte, Murielle ULg et al

Poster (2010, September 16)

For several years now, the Walloon Region has been supporting a project to help and follow farmers through their diversification activities: la Cellule Qualité Produits Fermiers (CQPF). Among their ... [more ▼]

For several years now, the Walloon Region has been supporting a project to help and follow farmers through their diversification activities: la Cellule Qualité Produits Fermiers (CQPF). Among their partners, the Process and Quality Engineering Laboratory in the Department of Food Technology of the Agricultural University of Gembloux is in charge of the hygienic supervision, ensuring the implementation of self-evaluation systems based on the HACCP principles and good hygiene practice guidelines. For four years, the CQPF has been following almost a hundred Walloon cheesemaking artisans using raw milk from cow, goat and ewe. According to the Commission Regulation (EC) No 2073/2005 on microbiological criteria for foodstuffs, analyses of microbiological pathogens have to be performed regularly to guarantee healthy and hazard free raw milk products. The results of microbiological analyses from raw milk cheeses of our artisans between January 2007 and June 2010 are presented below. We were interested on showing firstly, if the quality of the Walloon cheeses follow the standards of food safety criteria established by the European regulation, and secondly, if there is a trend for pathogen contamination throughout the year. [less ▲]

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See detailMicrobiological and chemical characterisation of St Anne cave, Belgium
Carnol, Monique ULg; Malchair, Sandrine ULg

Poster (2011, September)

In Belgium, most drinking water is provided by calcareous karst aquifers. Chemical and microbiological characterisation of these systems focalises mainly on the transfer of pollutants and microbial ... [more ▼]

In Belgium, most drinking water is provided by calcareous karst aquifers. Chemical and microbiological characterisation of these systems focalises mainly on the transfer of pollutants and microbial contaminants, major sources of sanitary risks. These studies are generally based on bacterial cultures, representing however only 1% of bacterial species present in the environment. Molecular techniques allow the study of the global microbial diversity of an environment, as they are based on direct ADN extractions, without previous culturing steps. The objective of this research was the study of the microbial diversity in the ‘St Anne’ cave, Belgium. Chemical composition of the water, cultivable bacteria and the diversity of ammonia-oxydizing bacteria (AOB) were studied in waters and sediments of the ‘Chawresse’ (underground river in St Anne), on the cave’s wall and in soils aboveground. Bacterial counts revealed that most cultivable bacteria were associated with suspended particles and that their numbers decreased underground. Molecular analyses revealed the presence of AOB in the karst system. AOB are responsible for the first, acidifying step of the nitrification process. Further studies will specify and quantify their activity in this karst system. [less ▲]

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See detailMicrobiological and chemical study of « Tiéré », senegalese millet fermented food.
Leite, N.; Diop, M.; Tine, E. et al

Poster (1999, July)

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See detailMicrobiological and ecological responses to global environmental changes in polar regions (MERGE): An IPY core coordinating project
Naganuma, Takeshi; Wilmotte, Annick ULg

in Polar Sciences (2009), 3

An integrated program, ‘‘Microbiological and ecological responses to global environmental changes in polar regions’’ (MERGE), was proposed in the International Polar Year (IPY) 2007e2008 and endorsed by ... [more ▼]

An integrated program, ‘‘Microbiological and ecological responses to global environmental changes in polar regions’’ (MERGE), was proposed in the International Polar Year (IPY) 2007e2008 and endorsed by the IPY committee as a coordinating proposal. MERGE hosts original proposals to the IPYand facilitates their funding. MERGE selected three key questions to produce scientific achievements. Prokaryotic and eukaryotic organisms in terrestrial, lacustrine, and supraglacial habitats were targeted according to diversity and biogeography; food webs and ecosystem evolution; and linkages between biological, chemical, and physical processes in the supraglacial biome. [less ▲]

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See detailMicrobiological and physico-chemical characteristic of Rwandese traditional beer «Ikigage»
Lyumugabe, F.; Kamaliza, C.; Bajyana, E. et al

in African Journal of Biotechnology (2010), 9(27), 4241-4246

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See detailMicrobiological and Physico-Chemical Quality of Smoked Shrimp, An Expanding Food Condiment in Beninese Local Markets
Kpoclou, Euloge Y.; Anihouvi, Victor B.; Azokpota, Paulin et al

in Food and Public Health (2013), 3(6), 277-283

Entire Smoked Shrimp (ESS) and Smoked Shrimp Powder (SSP) are two food condiments widely used in Beninese local cooking practices. Twelve samples of each product collected from local markets were ... [more ▼]

Entire Smoked Shrimp (ESS) and Smoked Shrimp Powder (SSP) are two food condiments widely used in Beninese local cooking practices. Twelve samples of each product collected from local markets were evaluated for safety assessment using standard methods. Regarding the microbiological status of the samples, the Enterobacteriaceae were detected in 83% and 75% of ESS and SSP respectively, whereas 25% of samples of each product were found to contain E. coli. Pathogenic bacteria such as S. aureus and Salmonella were absent. Except 8% and 17% of SSP sample exceeding the maximal limit of 106 UFC/g for Aerobic Mesophilic Bacteria and 104 UFC/g Enterobacteriaceae respectively, all the other samples were within the acceptable limits. Water activity values were low, ranging between 0.54±0.01 for SSP and 0.61±0.01 for ESS, showing a potential microbial stability. Considering the chemical hazards, 15 EU priority polycyclic aromatic hydrocarbon (PAHs) were detected in the samples examined with median Benzo(a) pyrene and PAH4 contents (91 μg kg-1 and 490 μg kg-1respectively) exceeding the European maximal limit (5.0 μg kg-1 and 30 μg kg-1). This study showed that smoked shrimps may be generally safe from a microbiological point of view, but they constitute a large source of exposure to possible carcinogenic PAHs. [less ▲]

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See detailMicrobiological and physicochemical characteristics of Rwandese traditional beer "ikigage"
Lyumugabe Loshima, François ULg

in African Journal of Biotechnology (2010), 9(27),

Samples of traditional sorghum beer Ikigage was collected in the southern province of Rwanda and analyzed for microbiological and physico-chemical contents. Ikigage contained total aerobic mesophilic ... [more ▼]

Samples of traditional sorghum beer Ikigage was collected in the southern province of Rwanda and analyzed for microbiological and physico-chemical contents. Ikigage contained total aerobic mesophilic bacteria (33.55 x 106 cfu/ml), yeast (10.15 x 106 cfu/ml), lactic acid bacteria (35.35 x 104 cfu/ml), moulds (4.12 x 104 cfu/ml), E. coli (21.90 x 103 cfu/ml), fecal streptococci (22.50 x 103 cfu/ml), Staphylococcus aureus (16.02 x 103 cfu/ml), total coliform (32.30 x 103 cfu/ml), ethanol, soluble protein, reducing sugars, total acidity, pH and Brix were 2.2% (v/v), 9.2 g/l, 2.3, 1.7%, 3.9 and 11.5 bx, respectively. The yeast was identified by API 20 C test and confirmed by PCR-Sequencing of ITS-5.8S region of rDNA. Seventy yeasts isolated in the samples were found to belong to either Saccharomyces cerevisae, Candida inconspicua, Issatchenkia orientalis, Candida magnolia and Candida humilis. Lactic acid bacteria were identified using the API 50 CHL system. Ten different isolates of lactic acid bacteria belonged exclusively to the genus Lactobacillus: Lactobacillus fermentum, Lactobacillus buchneri, and Lactobacillus sp. The micro-organisms of fecal origin are from the water and the operations postfermentation process. The presence of potential pathogens emphasizes the importance of developing starter cultures with GRAS status for commercialization of ikigage. [less ▲]

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See detailMicrobiological control of apple postharvest diseases: a case of study
Jijakli, Haissam ULg; Lepoivre, Philippe ULg; Grevesse, C.

in revista corpoica (1998), 2

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