Density of fecal coliforms (FC) such as Escherichia coli is the most commonly used indicator of fecal pathogen content of biosolids. When biosolids are disposed off or used for soil amendment, they pose public health risks. So far anaerobic digesters have been considered to be an effective treatment option for pathogen and FC reduction in biosolids. However, recent studies revealed that there is a significant re-growth and reactivation of indicator organisms in biosolids upon dewatering by centrifugation. Although the exact mechanism of FC reactivation is yet to be understood, a few extensive recent studies strongly suggest that FC go into a viable but non-culturable (VBNC) state during anaerobic digestion. Therefore, quantitative detection of live cells among the total in biosolids samples, without using culturing-based approaches, is highly critical from a public health risk assessment perspective. Since recent investigations proved the significant re-growth and reactivation of indicator organisms. Persistence of DNA in the environment after cell death in the range of days to weeks limits the application of DNA-based approaches for the detection of live bacteria. Using selective nucleic acid intercalating dyes such as ethidium monoazide (EMA) and propidium monoazide (PMA) is one of the alternative approaches to detect and quantify the viable cells by quantitative PCR. These compounds have the ability to penetrate only into dead cells with compromised membrane integrity. They intercalate in the DNA via photo-inducible azide groups and in turn inhibit DNA amplification during PCR reactions. PMA has been successfully used in different studies and microorganisms but it has not been evaluated sufficiently for the complex environmental samples such as biosolids. In this study Escherichia coli ATCC 25922 and uidA gene were used as model organism and as target sequence respectively in absolute quantification method with real-time PCR. Experiments with the known quantities of live and dead cell mixtures showed that PMA treatment inhibits PCR amplification from dead cells with over 99% efficiency. The results of this study conclusively demonstrated that PMA-modified PCR could be successfully applied to the biosolids when total suspended solid (TSS) concentration is 2000 mg/L or below.

Bacteriophages are viruses that specifically infect bacteria. The bactericidal nature of lytic bacteriophages has been exploited by scientists for decades with the hope to utilise them in the fight against bacterial infections and antibiotic resistant bacteria in medical settings. More recently, the potential applications of bacteriophages for biocontrol in the agrifood and environmental sectors have been investigated in an attempt to develop ‘natural’ antimicrobial products. Bacteriophages have a couple of decisive advantages over conventional methods of controlling pathogenic bacteria, such as high host specificity, the ability to self-replicate, and the ability to evolve with their hosts. However, more research is needed to optimise the parameters for phage applications, including the impact of environmental conditions on lysis efficiency, multiplicity of infection, and to significantly minimise the emergence of bacterial resistance to phages. Temperature plays a key role in every biological activity in nature. It is also assumed that temperature has an effect on phage lysis efficiency. A comprehensive study of it and how it affects both the host cells and their corresponding phages is crucial to ensure the efficient removal of bacterial pathogens. In this thesis, temperature (as selected parameter) was investigated to determine its influence on the lysis effectiveness of the three different phages belonging to the family of the Myoviridea that were isolated and purified from a single water sample taken from a brook receiving treated wastewater. We used the multiplicity of infection of 1 in all of our study in this project. Temperature was found to have a significant impact on phage-mediated lysis efficiency. Both the temperature of incubation of the phage-bacteria mixture (incubation temperature) and the temperature history of bacterial hosts were found to have profound effects on plaque sizes as well as plaque numbers. Plaque size and number decreased with increasing temperature. For the phages examined, bacterial lysis was more efficient at 20°C compared to 30 or 37°C. Phages were suggested to be well adapted to the environment where they were isolated from with general implications for use in biological disinfection. Furthermore, the temperature history of the bacteria (prior to phage encounter) was found to have a modulating effect on their susceptibility to lysis. A second part of this study compared the performance of the three phages in regard to bacterial resistance. The emergence of bacterial resistance is a major obstacle to the success of bacteriophages applications. The use of multiple phages is typically recommended and has proven better than the use of a single phage. However, the bestway to perform phage treatment is still very unclear. This study therefore compared simultaneous addition of multiple phages (in form of a cocktail) with the sequential addition of the individual phages at different time points in trying to delay the emergence of bacterial resistance. The data obtained from this work suggest that lysis effectiveness can be adjusted to optimize any treatment goal. For fast initial bacterial clearance the use of a single phage with short time maximal lysis efficiency proved most efficient, while the simultaneous addition of phages in the form of a cocktail was most successful strategy in our study. Addition of selected phages sequentially can be normalized in such a way that is just as effective as a cocktail. A third part of this thesis looked into the susceptibility of bacteria that had undergone sublethal disinfection. We addressed the question whether bacteria subjected to sublethal doses of chlorine and UV are still susceptible to phage-mediated lysis. The chlorine treatments indicated the development of a phage-insensitive phenotype for a critical chlorine dose in the transition zone between live and dead. The remaining live (and culturable) bacteria were shown insensitive to the selected phage. The lowest UV exposure at 2.8 mJ/cm2 eliminated bacteria susceptibility to the phages. This phage- resistant phenotype may have serious consequences for the application of phages on foods or water that have previously undergone a weak disinfection regime.

<p>  </p> <p>Plant-parasitic nematodes are amongst the most important pathogens impacting crops. Potatoes and soybean are vital crops for rural livelihoods and essential for food security, but their cyst nematode parasites remain a significant constraint globally. <em>Globodera</em> and <em>Heterodera </em>species are amongst the most damaging and internationally recognized quarantine pests of these crops, causing up to 80% yield loss. Their second stage juveniles (J2s) penetrate the host plant root tips and establish a residence close to the vascular bundle from where they extract nutrients as they complete their life cycle. Restrictions of control chemicals have led to an urgent need for alternative control strategies for cyst nematodes. Biological control is a promising alternative control measure, and fungi possess many characteristics that could make them great biological control agents of cyst nematodes. Most nematode populations are thought to be regulated by their natural enemy community. It is unclear which fungi are best adapted as natural enemies of these parasites and how they might do this. This project aimed to (a) characterize and compare the mycobiome diversity of cyst nematode species; (b) isolate and characterize fungi associated with potato and soybean cyst nematodes (c) screen isolated fungi for their efficacy as biocontrol agents against cyst nematodes; and (d) describe any isolated fungi identified as new and having potential for cyst nematode antagonism. Cyst populations were collected from different regions and screened for fungi using culture-based methods. For our next-generation sequence data analysis, we found differences in fungal community assemblages between center of origin of the potato cyst nematode (Peru; South America) and the regions where these nematodes were introduced such as Europe and North America.  There was no significant difference in fungal community assemblages of cysts collected between the years 2019 and 2020. We characterized fungi associated with the cyst nematodes and found that the most frequently isolated genera were <em>Fusarium, Penicillium, Cylindrocarpon, Phoma, Aspergillus </em>and<em> Verticillium</em>. Filtrates from <em>Trichoderma</em> sp. 2, <em>Alternaria alternata, </em>and <em>Fusarium acaciae-mearnsii </em>were toxic on SCN eggs while <em>Purpureucillium lilacinum, Fusarium proliferatum</em> and <em>Aureobasidium</em> <em>ellingtonae </em>sp. nov. were toxic on PCN eggs and juveniles. A new species of <em>Aureobasidium</em> isolated from the potato cyst nematode (<em>Globodera ellingtonae</em>) for the first time, and having biocontrol potentials against this nematode, was also identified, and described. </p>

Ce travail de thèse concerne l'étude de l'écologie microbienne d'un atelier de découpe de viande bovine, dans le but de mieux comprendre la persistance bactérienne, c'est-à-dire, la présence répétée d'un même clone bactérien pendant une longue période malgré l'application bien conduite et régulière du nettoyage et de la désinfection (N-D). Des prélèvements par « chiffonnages » multiples de surfaces d'équipements ont été réalisés lors de trois campagnes de prélèvement espacées les unes des autres d'au moins six mois. Les prélèvements ont été réalisés sur un tapis convoyeur en polychlorure de vinyle (PVC) et sur des machines éplucheuses en acier inoxydable avant et après N-D. Nous avons quantifié les cellules totales (les cellules vivantes et les cellules mortes) par PCR quantitative en temps réel (qPCR), les cellules viables par EMA-qPCR, et les UFC (provenant de cellules cultivables) par dénombrement après incubation à 25°C sur gélose tryptone soja. Les résultats montrent qu'avant N-D, les cellules totales (en moyenne 5,6 – exprimé en log10 cellules/cm2 – sur PVC et 4,7 sur acier inoxydable) sont plus nombreuses que les cellules viables (4,5 sur PVC et 4,4 sur acier inoxydable) lesquelles sont plus nombreuses que les UFC (3,8 sur PVC et 2,9 sur acier inoxydable). Le N-D entraîne moins d'une réduction décimale (RD) des populations à l'exception des UFC sur acier inoxydable qui subissent 1,5 RD en moyenne. Ce dernier chiffre s'explique par des forces d'adhésion faibles. L'étude de la diversité des bactéries cultivables montre que sur un total de 51 genres identifiés, 13 seulement sont retrouvés lors des trois campagnes de prélèvements. Les isolats de ces 13 genres représentent 75, 72 et 62% des isolats des campagnes1, 2 et 3 respectivement. Parmi ces isolats, les plus fréquents sont (par ordre décroissant du nombre d'isolats) : Pseudomonas, Staphylococcus, Microbacterium, Acinetobacter, Chryseobacterium, Psychrobacter et Kocuria. Le génotypage d'isolats de 3 genres majoritaires (Staphylococcus, Pseudomonas et Acinetobacter) montre qu'une seule souche, Staphylococcus equorum, est sans aucun doute persistante. L'ensemble de ces observations montrent que l'écosystème varie d'une campagne à une autre. Ces modifications de la diversité bactérienne reflèteraient les modifications de flores des viandes traitées dans l'atelier, qui ont des origines multiples. En outre, il apparaît que, contrairement à ce qui est généralement admis, les bactéries à coloration de Gram négative cultivables sont plus facilement inactivées par le N-D que les bactéries à coloration de Gram positive. L'étude de l'écosystème par PCR-DGGE a permis d'identifier sept genres bactériens et montre que les espèces dominantes sont toutes sous forme vivante, autrement dit, aucune des espèces dominantes n'a été détectée uniquement sous forme de cellules mortes. Sur les sept genres identifiés six sont des Gram – dont majoritairement les genres Acinetobacter, Pseudomonas et Psychrobacter. Cette dominance montre que le N-D permet une forte perte de cultivabilité des bactéries Gram – mais qu'une grande partie n'est pas détachée. La dominance des bactéries Gram – observée par PCR-DGGE masque les staphylocoques qui ne sont pas détectés alors qu'ils sont majoritaires parmi la flore cultivable. Seul un genre bactérien, Propionibacterium, est identifié par PCR-DGGE uniquement mais il n'est trouvé qu'à une seule campagne et uniquement sur l'acier inoxydable avant N-D. En conclusion, l'avancée majeure de ce travail est la mise en évidence qu'une proportion importante de bactéries survit après les opérations très poussées de N-D mais pour une période transitoire. / The aim of this work is to acquire a better knowledge of the microbial ecology of a beef processing plant to understand bacterial persistence, e.g. the presence of a clone isolated several times on several visits in the same processing plant despite regular Cleaning and disinfection (C&D) procedures. Successive swabbing were performed on a PVC conveyor belt and skinning machines made of stainless steel before and after C&D during three surveys in minimal 6 month-intervals. Total cells (live and dead cells) were quantified using real-time quantitative PCR (qPCR). Viable cells e.g. cells with intact membrane, were assessed using Ethidium Monoazide combined with qPCR. Culturable cells (CFU) were determined from plate counts on Tryptone Soy Agar. Before C&D, total cells (5.6 log cells/cm2 and 4.7 log10 cells/cm2 on PVC and stainless steel respectively) were greater than viable cells (4.5 and 4.4 log10 cells/cm2) and CFUs (3.8 and 2.9 log10 CFU/cm2). C&D lead to less than 1 log10 reduction in bacterial populations except for CFU counts on stainless steel where a 1.5 log reduction is observed. This result is highlighted by the weak attachment strengths observed on stainless steel for CFUs. Identification of the culturable microbiota revealed that out of 51 genera identified, 13 were found at all the visits. These genera represented 75, 72 and 62% of the total isolates. The most frequently identified bacteria were Pseudomonas, Staphylococcus, Microbacterium, Acinetobacter, Chryseobacterium, Psychrobacter and Kocuria. Molecular typing of three dominant genera (Staphylococcus, Pseudomonas and Acinetobacter) showed that only one strain, Staphylococcus equorum, was persistent in the premises. Our results show that the microbial ecosystem is different from one survey to another, which reflect the various geographical origins of meat products. Contrary to widespread belief, Gram negative strains were more easily eliminated by C&D than Gram positive strains. Furthermore, the microbial diversity assessed by PCR-DGGE allowed the identification of 7 genera. This molecular approach showed that dominant species are all in a viable state: none of these species was solely detected in a dead state. Of the 7 genera identified, 6 were Gram negative, Acinetobacter, Pseudomonas and Psychrobacter being predominant. This result highlights that C&D induced the lost of culturability of Gram negative bacteria although a high proportion was not detached from the surface. The predominance of Gram negative microflora, didn’t allow the detection of staphylococcal isolates which were numerous in the culturable microflora. One genus, Propionibacterium, isolated in one survey on stainless steel before C&D was only identified by PCR-DGGE. In conclusion, the present study has demonstrated that a large proportion of bacteria can survive drastic cleaning and disinfection for a transient period.

Xylanases have an important role as biocatalysts in different agroindustrial processes, such as saccharification of plant residues for the production of ethanol and bleaching of wood pulp for the production of pulp. On an industrial scale, these processes may require extreme pH or temperature, which require enzymes compatible with these conditions. Most enzymes available or showing commercial potential is synthesized by fungi or bacteria belonging to a few genera. Evaluation of rare isolation bacteria is an important strategy to expand the diversity of xylanases and their potential in terms of activity, stability and technological application. The aim of this study was to evaluate a collection of common and rare isolation soil bacteria regarding to xylanase activity and characterize the stability conditions of temperature and pH. The analyzed collection consists of 120 isolates with representatives from six phyla that were subjected to screening for xylanase activity in pure cultures and in the extracellular proteic extract (EPE). The ratio between the halos diameters of xylan hydrolysis and in the colonies on solid medium (ratio H:C), incubated at 30 ° C for up to 14 days, was used for the evaluation of cultures as a selection criteria. The effects of different sources of variation in the bacteria isolation stage (original soil, culture medium, solidifying agent, inoculum dilution and plating method and incubation time to colony appearance) and the group of bacterial isolation (rare or common) on the frequency of isolates with high xylanase activity were evaluated based on the ratio H:C. EPEs were obtained in liquid media containing xylan inoculated with the eleven isolates with highest ratios H:C. The extracts were evaluated for the specific xylanase activity at 50 °C for 1 h. Extracts of the three isolates with the highest potential for activity under this condition were evaluated for optimum activity, stability, activity at 60 oC and at pH 4.0, 5.5 and 8.0. Twenty-two isolates (25%), including eight from rare isolation, showed xylanase activity under the conditions evaluated, and found a high variability (> 230%) between these isolates. No isolation factor or rare or common isolation condition were associated with efficiency of xylanase activity in solid medium. High variability in specific xylanase activity in EPEs was also found among isolates (1500%), highlighting two rare isolates (TC119 and TC21), from Alfaproteobacteria class, and one common isolate (TC99), from Ralstoniaceae family. Extracellular xylanases from TC21 and TC119 showed high relative activity at temperatures up to 70 oC and were insensitive to pH in the range 4.0 to 8.0; however, TC99 isolate showed optimum temperature at 40 °C and low stability to temperature and pH. Extracellular xylanases from TC119 showed no cellulolytic activity. Rare isolation soil bacteria show high potential as a source of extracellular xylanases adapted to extreme pH and temperature conditions, which are required in agroindustrial processes. / As xilanases apresentam papel relevante como biocatalisadores de diferentes processos agroindustriais, como a sacarificação de resíduos vegetais para a produção de etanol e o clareamento de polpas de madeira para a produção de celulose. Em escala industrial, estes processos podem requerer pH e, ou, temperatura extremos, os quais demandam enzimas compatíveis com estas condições. A maioria das enzimas disponíveis ou com potencial comercial é sintetizada de fungos ou de bactérias pertencentes a poucos gêneros. A avaliação de bactérias de isolamento raro constitui-se em estratégia importante para ampliar a diversidade de xilanases e suas potencialidades em termos de atividade, estabilidade e aplicação tecnológica. O objetivo deste trabalho foi avaliar uma coleção de bactérias do solo de isolamento comum e raro quanto à atividade de xilanases e caracterizar estas enzimas quanto à estabilidade a condições contrastantes de temperatura e pH. A coleção analisada é composta de 120 isolados com representantes de seis filos e foi submetida à seleção quanto à atividade de xilanases em culturas puras e no extrato proteico extracelular (EPE). Para a avaliação das culturas, utilizou-se como critério de seleção a relação entre os diâmetros de halos de hidrólise de xilana e das colônias em meio sólido (relação H:C), incubado a 30 oC por até 14 dias. Os efeitos de diferentes fontes de variação da fase de isolamento destas bactérias (solo de origem, meio de cultura, agente solidificante, diluição do inóculo e método de plaqueamento e tempo de incubação até surgimento de colônias) e do grupo de isolamento bacteriano (raro ou comum) sobre a frequência de isolados com alta atividade de xilanase foram avaliados com base na relação H:C. EPEs foram obtidos em meios líquidos contendo xilana inoculados com os onze isolados com maiores relações H:C. Os extratos foram avaliados quanto à atividade específica de xilanases a 50 oC, por 1 h. Os extratos dos três isolados com maior potencial de atividade sob esta condição foram avaliados quanto à temperatura ótima de atividade, estabilidade de atividade a 60 oC e a valores de pH 4,0, 5,5 e 8,0. Vinte e dois isolados (25%), incluindo oito de isolamento raro, apresentaram atividade de xilanase nas condições avaliadas, sendo encontrada uma alta variabilidade (>230%) entre estes isolados. Nenhum fator de isolamento ou a condição de isolado raro ou comum foram associadas à eficiência de atividade de xilanases em meio sólido. Alta variabilidade de atividade específica de xilanases nos EPEs também foi encontrada entre os isolados (1500%), com destaque para dois de cultivo raro (TC119 e TC21), da classe Alfaproteobacteria, e um de cultivo comum (TC99), da família Ralstoniaceae. As xilanases extracelulares de TC119 e TC21 apresentaram elevada atividade relativa em temperaturas de até 70 oC e foram pouco sensíveis ao pH na faixa de 4,0 a 8,0; entretanto, as de TC99 apresentaram temperatura ótima de 40 oC, baixa estabilidade a temperatura e pH. Xilanases extracelulares de TC119 não apresentaram atividade celulolítica. Bactérias do solo de isolamento raro apresentam alto potencial como fonte de xilanases extracelulares adaptadas a condições extremas de pH e temperatura requeridas em processos agroindustriais.