Reconnu par leur effet toxique, inhibiteur et corrosif, les sulfures (S2-, SH-, SH2) sont un sous-produit indésirable de la digestion anaérobie des boues de station de traitement des eaux domestiques de la ville de Marrakech, Maroc (STEP). Ils proviennent essentiellement de la réduction "dissimilatrice" des composés soufrés (SO4 2-, SO3 2-, S2O4 2- ..) contenus dans ces boues. Ce processus est réalisé par un groupe bactérien anaérobie appelé bactéries sulfatoréductrices (BSR). Une fois dans le biogaz, les sulfures sous forme gazeuse réduisent en plus la durée de vie des installations et des équipements de la STEP. Elle est ainsi dotée d’installations biologiques et physico-chimiques lui permettant d’éliminer ces sulfures avant la transformation du biogaz en énergie électrique. Cependant, ces procédés sont onéreuses et grandes consommatrices d’énergies. D’où l’idée de minimiser la production des sulfures au sein même des digesteurs anaérobies. Pour cela, il était nécessaire d’abord de connaître les microorganismes à l'origine de la production des sulfures (BSR), ceux potentiellement impliqués dans leur élimination (bactéries sulfo-oxydantes), et d’un groupe de microorganismes fermentaires (Synergistetes) intervenant dans le bon fonctionnement de la digestion anaérobie. Ces études ont été menées à la fois sur des d'approches moléculaires et culturales. Les résultats obtenus, ont permis de comprendre comment ces groupes bactériens, d’intérêts écologique et économique importants, interviennent dans la digestion anaérobie des boues de la STEP permettant à la fois d’accélérer les processus d’oxydation de la matière organique combinée à la réduction des composés soufrés et de minimiser la concentration des en sulfure dans le biogaz. / Recognized by their toxic, inhibitory and corrosive effect, sulfides (S2-, SH-, H2S) are an undesirable by-product of the anaerobic digestion of from domestic wastewater treatment plants sludge in the city of Marrakech, Morocco (WWTP). They produced mainly by the dissimilatory reduction of sulfur compounds (SO42-, SO32-, S2O42-) contained in these sludges. This process is performed by an anaerobic bacterial group called sulfate reducing bacteria (SRB). Once in the biogas, the sulfides in gaseous form shorten in addition the lifetime of the installations and equipments of the WWTP. It is thus equipped with biological and physicochemical installations allowing it to eliminate these sulfides before the transformation of biogas into electrical energy. However, these processes are expensive and consume large amounts of energy. Hence the idea of minimizing the production of sulfides within anaerobic digesters. For this, it was first necessary to know the microorganisms originating of the production of sulfides (SRB), those potentially involved in their elimination (sulfur oxidizing bacteria), and a group of fermentative microorganisms (Synergistetes) involved in the good functioning of the anaerobic digestion. These studies were conducted on both molecular and cultural approaches. The results obtained allowed to understand how these bacterial groups, of great ecological and economic interest, are involved in the anaerobic digestion of sludge from the WWTP, which both accelerates the oxidation processes of the organic matter combined with the reduction of sulfur compounds and to minimize the concentration of sulfide in biogas.

A digestão anaeróbia tem se apresentado como um processo de grande interesse sob a ótica da potencial produção de energia renovável (H2 e CH4), considerando-se a ampla variedade de compostos orgânicos que podem ser utilizados. Neste estudo desejou-se avançar na compreensão do sistema de reatores anaeróbios de duas fases (acidogênico seguido de metanogênico) operados em condições termofílicas (55°C), alimentados com melaço da cana-de-açúcar, subproduto da indústria sucroalcooleira. Os experimentos foram conduzidos em reatores anaeróbios de leito fixo estruturado com fluxo ascendente e o melaço foi diluído com água de abastecimento, para adequação da concentração aos processos de tratamento de águas residuárias. Na 1ª Etapa dois reatores acidogênicos foram operados em paralelo para avaliar diferentes formas de inoculação e meios suportes, a fim de manter a produção continua e estável de hidrogênio. Para isso foram aplicadas diferentes cargas orgânicas (2,5, 5 e 10 gDQO.L-1) que resultam em COV de 30, 60 e 120 g.DQO.Lreator1.dia-1, com TDH fixo de 2 horas. A expressão do gene hidrogenase foi detectado em ambos os reatores, mas em maior proporção no reator inoculado com lodo de reator UASB e usando como material suporte a espuma de poliuretano. Sequencialmente a este reator, foi acoplado um reator metanogênico, alimentado com efluente do reator acidogênico, estabilizado nas condições apresentadas, e operado com COV crescentes de 1, 2, 5, 7, 14, 17 e 26,5 gDQO.Lreator-1.dia-1 e consequente diminuição do TDH de 240, 96, 48, 32, 24, 16 e 12 horas. O reator acidogênico na 2ª etapa foi operado por 417 dias consecutivos e COV de 120 g.DQO.Lreator1.dia-1, produzindo hidrogênio continuamente, alcançado valores de produção bruta de H2 de 7,60 LH2.dia-1. O reator metanogênico foi operado por 251 dias consecutivos, produzindo metano e alcançado valores de produção bruta de CH4 de 5,90 LCH4.dia-1. A eficiência de remoção de DQO do sistema de reatores foi de aproximadamente 90%, com contribuição aproximadamente de 10% para o reator acidogênico e contribuição aproximadamente de 80% para o reator metanogênico. O reator acidogênico alcançou rendimento de produção de hidrogênio por kg de melaço aplicado de 392 LH2.kgmelaço-1 e o reator metanogênico de 387 LCH4.kgmelaço-1. Para finalidade de comparações e aplicabilidade, o ganho energético global do sistema de reatores de duas fases foi de aproximadamente 5,7 kWh.kgmelaço-1 (1,4 kWh.kgmelaço-1 para o reator acidogênico e 4,3 kWh.kgmelaço-1 para o reator metanogênico). A produção continua de H2 obtida neste estudo está relacionada à associação das vias dos ácidos produtores de hidrogênio já consolidados pela literatura pertinente (acético e butírico) e pela produção de hidrogênio pela rota do ácido lático, devido a associação entre as comunidades de microrganismos estabelecidas no reator. O sequenciamento massivo MiSeq mostrou a seleção de diversos gêneros de microrganismos com redundância funcional e pertencentes principalmente aos Filos Firmicutes, Proteobacteria e Thermotogae, tais como Clostridium sensu stricto, Thermohydrogenium, Thermoanaerobacterium e Cellulosibacter (Firmicutes); Pseudomonas, Enterobacter, Shewanella e Petrobacter (Proteobacteria) e Fervidobacterium (Thermotogae). Microrganismos produtores de ácido lático também foram selecionados tais como: Lactobacillus, Leuconostoc, Sporolactobacillus e Trichococcus. Dos pontos de vista científico e tecnológico este estudo deu mais um passo para a compreensão dos bioprocessos envolvidos nos sistemas anaeróbios em dois estágios produzindo H2 e CH4 continuamente por longo período de tempo. / Anaerobic digestion has shown as an interesting process for renewable energy production (H2 and CH4), for a wide variety of organic compounds (carbon source). This study aimed to advance the understanding of a two-stage process anaerobic system (acidogenic bioreactor followed by methanogenic bioreactor) under thermophilic condition (55°C) fed with molasses, a sugarcane industry by-product. The experiments were conducted at up-flow structured bed reactors and sugarcane molasses was diluted with tap water, to adjust the concentration to the wastewater treatment. At first stage two acidogenic reactors were operated in parallel to evaluate different source of inocula and support bed, to obtain continuous and stable hydrogen production. It was applied 2.5, 5 and 10 gCOD.L-1 resulting in OLR of 30, 60 and 120 g.COD.Lreactor-1.day-1, with HRT fixed at 2 hours of hydrogenase gene was detected in both reactors but with higher number of copies of the gene in the reactor that showed higher hydrogen production: the reactor sed with sludge of UASB reactor and using polyurethane foam as support material. To this reactor was coupled a methanogenic reactor fed with effluent from acidogenic reactor and operated with increasing OLR (1, 2, 5, 7, 14, 17 e 26,5 gCOD.Lreactor-1.day-1) decreasing the HRT (240, 96, 48, 32, 24, 16 and 12 hours). The acidogenic reactor was operated during 471 days with OLR of 120 g.COD.Lreactor-1.day-1, with HRT fixed at 2 hours, with continuous hydrogen production with a gross production of 7.60 LH2.day-1. The methanogenic reactor was operated for 251 days, with continuous methane production of up to 5.90LCH4.day-1. The COD removal efficiency using the two-stage system was approximately 90% , with 10% contribution by the acidogenic reactor and 80% contribution by the methanogenic reactor. The acidogenic reactor achieved hydrogen yield per kg of applied molasses equal to 392 LH2.kgmolases-1. The methanogenic reactor achieved methane yield per kg of applied molasses equal to 387 LCH4.kgmolasses-1. For comparison and applicability purposes, the overall energy yield using the two stage reactor system was approximately 5.7 kWh.kgmolasses-1 (Acidogenic reactor 1.4 kWh.kgmolasses-1 and Methanogenic reactor 4.3 kWh.kgmolasses-1). The continuous production of H2 obtained in this study is related to the association of the hydrogen producer acids pathway established by the relevant literature (acetic and butyric) and the hydrogen production by the lactic acid pathway due to the microorganisms association established in the reactor. Metagenomic analysis by MiSeq Plataform revealed that hydrogen production was due the selection of microorganisms with functional redundancy mainly of Phyla Firmicutes, Proteobacteria and Thermotogae, such as Clostridium sensu stricto, Thermohydrogenium, Thermoanaerobacterium, Cellulosibacter (Firmicutes); Pseudomonas, Enterobacter, Shewanella and Petrobacter (Proteobacteria) and Fervidobacterium (Thermotogae). Genera of acid latic producers, such as Lactobacillus, Leuconostoc, Sporolactobacillus and Trichococcus, were also selected. From the scientific and technological point of view this study has taken another step towards the understanding of bioprocesses involving two stage anaerobic systems for a long term continuous production of H2 and CH4.

Le poisson est un produit très périssable dont l’altération résulte essentiellement de la croissance bactérienne. Comparé aux régions tempérées, peu d’études portent sur le microbiote d’altération des poissons tropicaux. En Martinique, le thon jaune (Thunnus albacares) et l’ombrine ocellée (Sciaenops ocellatus) représentent des poissons d’intérêt pour les filières pêche et aquaculture. Dans le but de mieux connaître le microbiote d’altération de ces poissons, des analyses culturales et aculturales (séquençage de nouvelle génération des amplicons d’ARNr 16S, Illumina MiSeq) ont été réalisées.Une grande diversité d’espèces bactériennes a été retrouvée dans le thon et l’ombrine fraîchement pêchés (104 et 887 OTUs, respectivement) et la plupart d’entre elles sont communément isolées des poissons (Chryseobacterium, Burkholderia, Flavobacterium, Psychrobacter, Arthrobacter, Staphylococcus). Certaines, comme Ralstonia sp. et Rhodanobacter terrae, en quantité importante dans le thon frais, sont plus atypiques. Au cours de l’entreposage du thon sous-glace, Pseudomonas et Brochothrix deviennent dominants. L’emballage sous atmosphère modifiée (MAP) ou sous vide (VP) entraine clairement la sélection de Brochothrix dans un cas et d’un mélange de Brochothrix, bactéries lactiques (Lactococcus piscium, Carnobacterium maltaromaticum) et d’entérobactéries (Hafnia paralvei) dans l’autre, et ne permet pas une augmentation significative de la durée de conservation. Pour les filets d’ombrine, peu de différences sont observées entre MAP et VP dont le microbiote se compose essentiellement de bactéries lactiques (Carnobacterium spp., Vagococcus spp., Lactococcus spp., Leuconostoc spp.). La durée de conservation est étendue de 15 jours par rapport au poisson entier sous air.L’inoculation de différentes espèces bactériennes dans de la chair pauci-microbienne de thon ou d’ombrine a montré que Hafnia paralvei et Serratia spp. sont les espèces les plus altérantes. Brochothrix thermosphacta et Carnobacterium spp. produisent aussi des odeurs indésirables mais de façon plus modérée. Chez Pseudomonas, les espèces ne sont pas toutes altérantes et présentent même parfois des capacités à empêcher le développement des mauvaises odeurs induites par d’autres bactéries (Pseudomonas psychrophila/fragi) et à dégrader l’histamine (Pseudomonas cedrina, Pseudomonas plecoglossicida/monteilii). En parallèle, des tests sensoriels et des dosages physico-chimiques ont également été réalisés pour comprendre les conséquences de la croissance bactérienne et identifier des indicateurs fiables pour l’évaluation du degré d’altération des produits. / Fish is a highly perishable product and spoilage is mainly due to the bacterial growth. Compared to temperate regions, few studies examined the spoilage microbiota of tropical fish. In Martinique, yellowfin tuna (Thunnus albacares) and red drum (Sciaenops ocellatus) are essential fish of fisheries and aquaculture sectors. For a better characterization of the microbial ecosystem, culture-dependent and culture-independent (next-generation sequencing of 16S rRNA amplicons, Illumina MiSeq) methods were carried out.A wide diversity of species was found in freshly caught tuna and red drum (104 and 887 OTUs, respectively) and most of them are commonly isolated from fish (Chryseobacterium, Burkholderia, Flavobacterium, Psychrobacter, Arthrobacter, Staphylococcus). Others, such as Ralstonia sp. and Rhodanobacter terrae, largely present in fresh tuna, are less familiar. During the ice-storage of tuna, Pseudomonas and Brochothrix became dominant. The modified atmosphere packaging (MAP) and vacuum packaging (VP) clearly leaded to the selection of Brochothrix in one case and to a mixture of Brochothrix, lactic acid bacteria (Lactococcus piscium, Carnobacterium maltaromaticum) and enterobacteria (Hafnia paralvei) in the other case, and not conduct to a significant increase of the shelf-life. For red drum fillets, few differences were observed between MAP and VP with a microbiota essentially composed by lactic acid bacteria (Carnobacterium spp., Vagococcus spp., Lactococcus spp., Leuconostoc spp.). The shelf-life was extended by 15 days compared to the whole fish ice-stored.The inoculation of different bacterial species into the pauci-microbial flesh of tuna or red drum showed that Hafnia paralvei and Serratia spp. were the most spoiling bacteria. Brochothrix thermosphacta and Carnobacterium spp. produced more moderate undesirable odors. Among the Pseudomonas genus, not all species induced spoiling effects and some of them are even able to prevent the development of unpleasant odors from other bacteria (Pseudomonas psychrophila/fragi) and to degrade histamine (Pseudomonas cedrina, Pseudomonas plecoglossicida/monteilii).At the same time, sensory tests and physico-chemical assays were performed to understand the consequences of the bacterial growth and to identify reliable indices for the evaluation of the spoilage degree of the products.

Cryptosporidium is a protozoan parasite infecting the intestines of its hosts, leading to acute diarrheal disease. Out of 26 recognized species, 14 are known to infect humans. Of most importance, from a human perspective are Cryptosporidium parvum and Cryptosporidium hominis, of which the former is known to have zoonotic potential. Globally, cryptosporidiosis affect people with lowered immune status particularly hard; among children under five it is the most important parasitic cause of gastroenteritis. In the region of KwaZulu-Natal, on the east coast of South Africa, Cryptosporidium is considered endemic. Drinking water is frequently collected from river systems and as Cryptosporidium spp. can be transmitted via contaminated water, this may be one source of infection. Research on the species distribution is important for outbreak investigations and prevention efforts. In water and wastewater such speciation is commonly performed using immunomagnetic separation, an antibody dependent method. There is however a suspicion that these antibodies have less affinity to some species and hence contorts the detected species distribution. An alternative approach is therefore of interest.   In the present study, Cryptosporidium diversity in wastewater collected from four different wastewater treatment plants in KwaZulu-Natal, is evaluated with an optimized antibody-free workflow and a single cell platform. It was shown that the workflow is suitable for complex samples, such as wastewater. Furthermore, diversity was assessed with amplicon sequencing, revealing four different species and genotypes. Further modifications of the methods used could benefit the field of Cryptosporidium research, along with improving global health and preventing disease outbreaks.

The decomposition of organic substrates represents an important part of the global carbon cycle and affects its global change through CO2 release. In temperate forests, deadwood represents a large carbon stock, its amount and decomposition is crucial for ecosystem biodiversity and functioning. The fungi are omnipresent powerful decayers in all terrestrial ecosystems. Their ability to decompose all deadwood compounds, mainly lignocellulose, is highly important. Without fungi, the wood decompositions and the release of withheld nutrients back to nutrient cycles couldn't be performed. While many studies were concerned with the estimation of decomposition rates of deadwood, still deeper knowledge about microbial decomposition processes and the diversity of saproxylic species and their interaction is needed. The fungi are still underrepresented in dead wood studies. This study had two main objectives. First was to describe the fungal community on downed deadwood of Fagus sylvatica and Abies alba in natural forest of Salajka in the Czech Republic, to reflect the substrate changes during the different decay stages, and to link the enzyme activities to fungal community composition and their described ecophysiologies. Second aim was to describe the fungal communities on standing and downed dead logs of...

The sea-surface microlayer (SML) is the boundary layer at the air-sea interface where many biogeochemical processes occur. Many organisms (e.g., bacteria) produce surface active agents (surfactants) for life processes, which accumulate in the SML and dampen short gravity-capillary waves, resulting in sea surface slicks. Synthetic aperture radar (SAR) is capable of remotely sensing these features on the sea surface by measuring reflected backscatter from the ocean surface in microwaves. This study coordinates SAR overpasses with in situ SML and subsurface (SSW) microbial sample collection to guide subsequent analysis after 16s rRNA sequencing on the Illumina MiSeq. In April 2017, 138 SML and SSW samples were collected near a targeted oil-seep where the Taylor Platform was knocked down in the Gulf of Mexico, both in and out of visually-observed oil slicks. In July and August 2018, 220 SML and SSW samples were collected near the Looe Key coral reef and a coastal seagrass area. Analysis of microbial abundance and diversity between the two experiments shows that within oil slicks, surfactant- and oil-associated bacteria prefer to reside within the SSW rather than in the SML. In natural slicks in the coastal seagrass area, these bacteria are more abundant in the SML. Outside of these slicks, surfactant-associated bacteria are more abundant within the SML than the SSW. This suggests that the presence of oil reduces the habitability of the SML, whereas natural slicks created by foam and other surfactants creates a more habitable environment in the SML. With lower wind speed, abundance of these bacteria are greater, as increased wind speed results in a harsher environment. The diurnal cycle had an effect on the relative abundance of surfactant-associated bacteria in the SML and SSW. Our results demonstrate the usefulness of synthetic aperture radar to remotely sense sea surface slicks in coordination with in situ surfactant-associated bacteria data collection of the sea surface slicks.

Soil microbial communities are affected extensively by addition of amendments to their environment. Of particular concern is the addition of poultry litter, which contains a substantial C, energy, and nutrient supply, but also antibiotic resistance genes (ARG), antimicrobials, and a multitude of microbial species. This project seeks to primarily assess if there is a change in bacterial community structure in response to poultry litter amendments to pasture land across geographically independent land across northern Georgia. It may be that changes in the relative abundance of bacterial communities also result in alteration in ARGs, and the community resistance to antibiotics (“resistome”) which in turn increases the potential threat of antibiotic resistance genes. While another part of this study will determine changes in integrons and specific ARGs, this project will focus on changes in bacterial communities and the potential functional changes in the community, which in turn have consequences for ARG levels and its horizontal transfer to various members of the soil community. Addition of waste from livestock is a historical method for increasing nutrients needed in the soil for the cultivation of crops, and in turn causes pronounced shifts in soil microbial communities due to the addition of large amounts of carbon, nutrients, foreign microbes, and other material. This study is unique because it utilizes a novel and relatively large landscape-scale to determine if there are discernable and repeatable patterns of bacterial community structure change in response to amendment regardless of exact soil type or source of chicken litter amendment. In the future, these data can also provide insight into the changes in the relative abundance antibiotic related genes associated with community change. / M.S. / Soil is complicated, both in terms of its physical makeup and the organisms that live inside of it. Predicting changes in soil based on the addition of foreign material such as chemicals or biological waste is not an easy process, and whether or not it is even possible to reliably predict those changes is a matter of some dispute. This study is designed to illustrate that such changes can in fact be reliably and consistently predicted even with regard to the addition of complicated materials to the soil. In this study, specifically, the material in question is chicken litter. A mix of the bedding and waste produced by chickens, litter is commonly handled by composting and is added to soil in farms as a fertilizer rich in organic matter. It is possible to point at specific elements of the soil such as the chemistry and bacteria and see how it is changed with the addition of chicken litter, which allows us to determine the nature and extent of the change that chicken litter has on soil. This study is conducted on a larger scale than similar experiments conducted in the past, making it apparent that these relationships exist on a repeated basis. It is the object of this study to pave the way and make it easier for scientists in the future to determine these relationships in other unique contexts.

Integrating crop and livestock is being considered to improve soil health by carbon sequestration. A two-year study (2019-2021) at CPBES in Newton, MS was aimed to evaluate soil microbial diversity in the warm, humid regions, specifically southeastern USA. Amplicons targeting bacterial 16S rRNA genes and fungal ITS2 regions were sequenced. Taxonomic assignment and microbial diversity characterization were performed using QIIME2®. Soil fungal diversity showed significant differences (alpha diversity, p = 0.031 in yr. 2020 and beta diversity, p = 0.037 in yr. 2021). Canonical Correspondence Analysis (CCA) and Mantel test showed significant influence on fungal diversity due to carbon (rm = 0.2581, p = 0.022), nitrogen (rm = 0.2921, p = 0.0165) in yr. 2021, and on bacterial diversity due to EE-GRSP (rm = 0.22, p = 0.02) in yr. 2020. Long term study of ICLS can help us better understand the shift in microbiome to improve crop production sustainably.

Dead wood plays an important role in forest ecosystems in the context of C dynamics, nutrient cycling, forest regeneration and biodiversity. Decaying wood sustains biodiversity by providing habitats and energy for fungi, bacteria, invertebrates, and many other organisms. Dead wood is resistant to decomposition and its decay is driven mainly by filamentous fungi. Community structure of wood- inhabiting fungi changes during decomposition, but the relationship between substrate quality and decomposer community is still poorly understood. This work studied fungal community composition with respect to tree species, stage of decay, volume and physico-chemical properties (such as pH, carbon and nitrogen content) of dead wood. Fungi were identified using next generation sequencing approaches - 454-pyrosequencing and Illumina MiSeq sequencing. Tree species, volume of dead wood (branches x logs) and stage of decay were the main variables affecting fungal community composition. Higher enzyme activities and content of fungal biomass indicate faster colonization of small branches than tree trunks by fungi. Fungal community composition, wood chemical properties and enzyme activities changed during decomposition. Both content of nitrogen and fungal biomass increased during decomposition. Enzyme activites peaked...

Le virus du syndrome reproducteur et respiratoire porcin (VSRRP) est un pathogène important, entrainant des pertes économiques de 130 millions de dollars annuellement au Canada. La surveillance est effectuée par séquençage Sanger du gène ORF5 mais nous croyons que le séquençage du génome entier (SGE) du VSRRP permettrait une meilleure surveillance épidémiologique comparé au séquençage du gène ORF5. Pour développer une méthode efficace de SGE du VSRRP, 149 échantillons (sérums, poumons, tissus, autres) d’animaux malades ou récoltés pour fin de surveillance ont été analysés. L'ARN viral a été concentré par enrichissement d'ARN à queue poly (A) et le séquençage effectué sur une plateforme Illumina. Le SGE a été efficace dans 67,11% des échantillons, réussissant dans certains échantillons de poumons et de sérums possédant une valeur de quantification (Cq) du virus par RTqPCR jusqu’à 26,50 et 34.13, respectivement. La méthodologie développée de SGE du VSRRP a été 4650 fois plus sensible que les méthodes décrites précédemment. Pour quantifier l’impact du SGE, 88 échantillons (dont le SGE a réussi) ont été utilisés pour comparer le SGE au séquençageORF5. Deux génomes de VSRRP différents ont été trouvés dans quatre échantillons différents (taux de coinfection de 4,55%). Six génomes de VSRRP (6,52% des souches) ont été classés différemment par rapport à la classification ORF5. Ainsi, le SGE du VSRRP a permis une meilleure caractérisation de 9,10% des échantillons VSRRP positifs comparé au séquençage ORF5. Donc, le SGE du VSRRP est à la fois sensible et plus précis que la classification par l’ORF5. / Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen, costing over 130 million dollars annually in Canada. Surveillance is done by Sanger sequencing of the ORF5 gene, but we hypothesized that whole genome sequencing (WGS) of PRRSV genome will allow a better epidemiological monitoring of PRRSV compared to ORF5 gene sequencing. To develop an efficient method of PRRSV WGS, 149 PRRSV samples (sera, lungs, pool of tissues and others) collected for surveillance or from sick animals were tested. Viral RNA was concentrated using a poly(A) tailed RNA enrichment method, and sequencing was done on an Illumina platform. WGS was successful in 67.11% of cases. WGS was successful in some tissues and lungs samples with RT-qPCR cycle quantification (Cq) values up to 26.50, and in some sera with Cq value up to 34.13. The developed WGS methodology was 4650 times more sensitive for PRRSV WGS than previously described methods. To quantify the impact of WGS, 88 successful samples for the WGS of PRRSV were used to compare efficiency of WGS and ORF5 sequencing. Two different full-length genomes of PRRSV were found in four of those samples (coinfection rate of 4.55%). Six full-length PRRSV genomes (6.52% of PRRSV strains) were found to cluster differently compared to ORF5 sequencing. WGS of PRRSV also enabled a better classification or characterisation of 9.10% of the PRRSV infected samples compared to ORF5 sequencing. Thus, WGS can be both sensitive and more accurate then ORF5 classification for the characterisation of PRRSV strains.