O 4-Nonilfenol (4-NF) é o principal produto formado a partir da degradação do Nonilfenol etoxilado, surfactante não iônico amplamente utilizado em formulações de uso doméstico e industrial. Objetivou-se neste estudo desenvolver método de quantificação de 4-NF em HPLC; avaliar a remoção de 4-NF em reatores em batelada com co-substratos (etanol, metanol e fumarato) e avaliar a remoção e degradação de 4-NF em Reator Anaeróbio de Leito Fluidificado (RALF) em escala aumentada (20L), bem como caracterizar a comunidade microbiana estabelecida no material suporte por meio das técnicas de PCR/DGGE do gene RNAr 16S e sequenciamento massivo via plataforma Illumina-Miseq®. O RALF foi preenchido com areia como material suporte, operado com Tempo de Detenção Hidráulico (TDH) de 18,2±1,1 horas e alimentado com meio de cultura acrescido de 4-NF PESTANAL® (Sigma-Aldrich®). Análises de monitoramento da concentração de 4-NF e matéria orgânica, bem como, dos parâmetros físico-químicos foram realizadas para avaliar a estabilidade do reator quanto a remoção e degradação do composto de interesse. A operação do reator foi dividida em distintas etapas, contando com inoculação do RALF em circuito fechado, adaptação ao meio de cultura e subsequentes fases com adição de 4-NF. Para reatores em batelada a adição de 4-NF (de 288,97±96,49 a 469,98±182,42 µg L-1) favoreceu a produção média de metano acumulada (de 2.292,3 para 2.744,7 mol, respectivamente) para todos os co-susbtratos testados, todavia, retardou o tempo médio de início da produção (de 15,9 h para 107,9 h), bem como reduziu a velocidade de produção (de 24,4 para 10,9 µmol d-1). Para ensaio com adição de 4-NF e Fumarato foram verificados os maiores valores de produção acumulada de metano (3.163,68±169,17 µmol) e de remoção de DQO (75,52±0,34% para DQO inicial de 1.242,00±27,48 mg L-1), em relação aos demais ensaios com adição de 4-NF. Para a remoção de 4-NF em reatores em batelada os valores não diferiram significativamente. Para o RALF, foram verificadas eficiências médias de remoção de DQO de 90,34±6,1% (Fase I), 94,0±1,2% (Fase II), 97,0±1,3% (Fase III) e 95±1,5% (Fase IV) e 4-NF de 73,2±11,1% (Fase II), 67,3±7,3% (Fase III) e 77,88±8,9% (Fase IV). As diferentes concentrações de 4-NF aplicadas ao RALF não afetaram a eficiência de remoção de DQO e promoveram a seleção dos microrganismos que compuseram a biomassa do leito. Os gêneros mais abundantes identificados no reator sem adição de 4-NF foram Prolixibacter, Geothrix, Klebsiella, Lactobacillus e Geobacter. Os gêneros com maior abundância relativa identificados após adição de 4-NF foram os seguintes: Geothrix, Holophaga, Elusimicrobium, Paludibacter, Lactobacillus, Aeromonas, Pelobacter, Aquaspirillum, Pseudomonas, Delftia, Acinetobacter, Arcobacter, Ignavibacterium, Treponema, Lysinibacillus e Enterococcus. / 4-Nonylphenol (4-NP) is the main product formed in the Nonylphenol ethoxylate degradation, nonionic surfactant used in formulations of domestic and industrial use. The objective of this study was to develop a method to determine 4-NP in HPLC; to evaluate the 4-NP removal in batch reactors with co-substrates (ethanol, methanol and fumarate) and removal and degradation of 4-NP in anaerobic Fluidized Bed Reactor (AFBR) on an enlarged scale (20L), as well as characterize the microbial community established in the support material by PCR / DGGE techniques of the 16S RNAr gene and massive sequencing by the Illumina-Miseq® platform. The AFBR was filled with sand as carrier material, operated with Hydraulic Retention Time (HRT) of 18.2±1.1 hours and fed with synthetic sewage plus 4-NP PESTANAL® (Sigma-Aldrich®). Monitoring of the 4-NP concentration and organic matter, as well as physical-chemical parameters were performed to evaluate the stability of the reactor for the removal and degradation of the compound of interest. Reactor operation was divided into different stages, with inoculation of the RALF in closed circuit, adaptation to the culture medium and subsequent phases with 4-NF addition. The addition of 4-NP (from 288.97±96.49 to 469.98±182.42 µg L-1) in batch reactors favored the average accumulated methane production (from 2,292.3 to 2,744.7 µmol, respectively) for all tested co-susbtrates, however, delayed the mean time to start production (from 15.9 h to 107.9 h), as well as reduced production rate (from 24.4 to 10.9 µmol d-1). The highest accumulated values of methane production (3,163.68 ± 169.17 µmol) and COD removal (75.52±0.34% for the initial COD of 1,242±27.48 mg L-1) were verified for the addition of 4-NP and Fumarate, compared to the other tests with addition of 4-NP. For the 4-NP removal in batch reactors the values did not differ significantly. Mean values of COD removal for the AFBR were 90.34±6.1% (Phase I), 94.0±1.2% (Phase II), 94.0±1.2% (Phase III) and 97.0±1.3% (Phase IV) and 4-NF of 73.2±11.1% (Phase II), 67.3±7.3% (Phase III) and 77.88±8.9% (Phase IV). Different concentrations of 4-NP applied to the AFBR did not affect the COD removal efficiency and promoted the selection of the microorganisms that composed the bed biomass. The most abundant genera identified in the reactor without addition of 4-NP were Prolixibacter, Geothrix, Klebsiella, Lactobacillus and Geobacter. The genotypes with the highest relative abundance identified after addition of 4-NP were as follows: Geothrix, Holophaga, Elusimicrobium, Paludibacter, Lactobacillus, Aeromonas, Pelobacter, Aquaspirillum, Pseudomonas, Delftia, Acinetobacter, Arcobacter, Ignavibacterium, Treponema, Lysinibacillus and Enterococcus.

Célèbres depuis l'accident de Seveso en 1976, les dioxines/furanes (PCCD/F) restent, malgré une forte baisse de leurs émissions, un sujet de préoccupation permanent en France et dans le monde. Le rémanence de ces composés organochlorés dans le sol et le risque toxique qu'ils représentent pour l'homme et l'environnement font que la gestion et la remédiation des sols contaminés par les PCDD/F sont devenues une priorité des industriels, législateurs et scientifiques. La phytoremédiation compte parmi les méthodes émergentes de dépollution des sols contaminés en raison de son adéquation avec le développement durable. Elle combine les capacités naturelles des plantes et de leur microbiote rhizosphérique à biodégrader les polluants organiques. Cependant, l'efficacité de cette phytotechnologie est encore souvent limitée, en particulier lorsqu'il s'agit de composés chlorés, à cause de leur récalcitrance, de leur phytotoxicité et leur faible biodisponibilité dans le sol. Ainsi, l'objectif de ce travail de thèse a consisté à étudier les performances de la phytoremédition assistée, en particulier par les champignons mycorhiziens arbusculaires, d'un sol agricole historiquement pollué par les PCDD/F prélevé sur une parcelle expérimentale située à proximité d'un ancien incinérateur. L'ensemble des résultats obtenus mettent en évidence, en particulier, le potentiel de deux espèces végétales, la luzerne et la fétuque, dans la rhizodégradation des PCCDD/F. La végétalisation du sol permet de moduler les communautés microbiennes du sol (bactéries, Archées et champignons) et notamment celles qui semblent impliquées dans la dissipation des PCCDD/F. En revanche, bien que la mycorhization agisse sur les communautés microbiennes du sol, celle-ci n'a pas eu d'impact, dans nos conditions expérimentales, sur la dissipation des PCCDD/F quelles que soit l'origine de l'inoculum utilisé et les espèces mycorhiziennes qui le compose. La dégradation de ces composés organochlorés est plus marquée dans un sol préalablement stérilisé, puis recolonisé par certaines communautés microbiennes spécifiques, impliquées dans la dissipation des PCCDD/F. L'utilisation combinée d'un mélange de rhamnolipides avec l'introduction dans le sol d'une bactérie Sphingomonas wittichii RWI, décrite pour ses capacités de dégradation des PCCDD/F, permet d'accroitre l'efficience de la rhizodégradation des PCDD/F qui se traduit par une baisse significative de la cytotoxicité du sol après phytoremédiation. / Famous since the Seveso accident in 1976, dioxins/furans (PCCD/F) remain, despite a sharp decline in emissions, a subject of permanent concern in France and in the world. The remanence of these organochlored compounds in soil and the toxic risk they represent for humans and the environment mean that the management and remediation of PCDD/F contaminated soil has become a priority for industrialists, legislators and scientists. Phytoremediation is one of the emerging depollution methods of contaminated soils due to Its suitability for sustainable development. It combines the natural capacities of plants and their rhizospheric microbiota to biodegrade organic pollutants. However, the effectiveness of this phytotechnology is still often limited, especially in the case of chlorinated compounds, due to their recalcitrance, phytotoxicity and low bioavailability in the soil. Thus, the thesis aims to study the performance of assisted phytoremission, in particular by mycorrhizal fungi, of an agricultural PCDD / F based-polluted soil from an experimental plot near an old incinerator. The results obtained show the potential of two plant species, alfalfa and tall fescue, in the rhizodegradation of PCCDD/F. Soil vegetation shows to modulate soil microbial communities (bacteria, archaea and fungi) includind those that appear to involved in the dissipation of the PCCDD/F. On the other hand, although mycorrhization affects soil microbial communities, it has not had any impact on the dissipation of PCCDD/F in our experimental conditions, whatever the inoculums origin and the mycorrhizal species which compose it. The degradation of these organochlorined compounds is more significant in a previously sterilized soil and then recolonized by specific microbial communities involved in the PCCDD/Fdissipation. The combined use of rhamnolipids mixture and Sphingomonas wittichii RWI bactrerium described for its degradation capabilities of PCCDD/F makes it possible to increase the efficiency of PCDD/F rhizodegradation which results in a significant decrease in soil cytotoxicity after phytoremediation.

Yes / We report the draft genome sequence of Pandoraea sp. strain E26 isolated from a former landfill site, sequenced by the Illumina MiSeq platform. This genome sequence will be useful to further understand the quorum-sensing system of this isolate. / University of Malaya High-Impact Research (HIR) grants (UM C/625/1/HIR/MOHE/CHAN/01, grant A-000001- 50001 and UM-MOHE HIR UM C/625/1/HIR/MOHE/CHAN/14/1, grant H-50001-A000027)

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.

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.

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.