In wetland soils, hydrology is considered to be one of the primary factors shaping wetland function and microbial community structure, but plant-soil interactions are also important mechanisms affecting microbial nutrient transformations. The research presented here considered the interactive effect to describe how hydrology and the presence of plants alter the soil profile, the development of the bacterial community, and their associated functions. To achieve this goal, plots were established in three hydrologically-distinct regimes (Wet, Intermediate, and Dry) within a non-tidal freshwater wetland along the James River (Charles City County, Virginia). Inside each main plot, ten subplots were cleared of all aboveground plant material; five plots were left to re-grow (“Vegetated” reference), while the remaining five were weeded each week to maintain bare soil (“Clipped” treatment subplots). Manipulations were started at the beginning of the growing season, and sampling continued until the following winter. Every eight weeks, soil cores (30 cm) were collected and analyzed for a variety of soil properties (e.g., pH, OM, C:N, redox, vegetation and root biomass), microbial community structure (16S-rDNA-based T-RFLP),bacterial abundance (Acridine Orange Direct Count), and soil function (Extracellular Enzyme Activity (EEA)). A mixed-effects repeated measures analysis of variance (ANOVA) was used to better understand how each variable responded within each hydrological regime and treatment. Principal component analysis (PCA) and Partial Mantel tests were used to elucidate how saturation and vegetation influence the microbial community structure and soil enzyme function. Bacterial community properties and soil functions followed differences in soil saturation and associated physicochemical parameters (i.e., pH and redox). Correlations with wetland vegetation were primarily related to seasonal changes in plant community composition and biomass, and differences between experimental treatments were small. Evidence suggests the present plant species and the amount of above- and belowground biomass plays a more selective role shaping bacterial communities and soil function. Due to the short-term of this study and tight soil correlations, it is difficult to determine if observed differences are a product of the plant community or soil saturation, but it is clear that each is important. Based on the literature, plant effects were smaller in this wetland than might be expected. This experiment took place in a recently exposed lake basin, so plant-soil-microbe interaction may not be well established. As the wetland matures, relative importance of vegetation is expected to increase and impact bacterial composition and function. Collectively, these results demonstrate that wetlands are not a product of one separate variable, but result from various factors interlinked to shape microbial communities and soil functions.

To gain a better understanding of contaminating bacteria in bioethanol industry, we profiled the bacterial community structure in corn-based bioethanol fermentations and evaluated its correlation to environmental variables. Twenty-three batches of corn-mash sample were collected from six bioethanol facilities. The V4 region of the collective bacterial 16S rRNA genes was analyzed by Illumina Miseq sequencing to investigate the bacterial community structure. Non-metric multidimensional scaling (NMDS) ordination plots were constructed to visualize bacterial community structure groupings among different samples, as well as the effects of multiple environmental variables on community structure variation. Our results suggest that bacterial community structure is facility-specific, although there are two core bacterial phyla, Firmicutes and Proteobacteria. Feedstock, facility, and fermentation technology may explain the difference in community structure between different facilities. Lactic acid, the most important environmental variable that influences bacterial community structure grouping, could be utilized as an indicator of bacterial contamination. We also identified genes responsible for the multiple antibiotic-resistance phenotype of an Enterobacter cloacae strain isolated from a bioethanol fermentation facility. We performed PCR assays and revealed the presence of canonical genes encoding resistance to penicillin and erythromycin. However, a gene encoding resistance to virginiamycin was not detected.

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Les hydrocarbures aromatiques polycycliques (HAP) sont des polluants organiques, ubiquistes, potentiellement toxiques et cancérigènes. Dans les sols, la dégradation des HAP est principalement due à l'activité microbienne. Certaines études ont montré que la biodégradation des HAP pouvait être augmentée dans la rhizosphère des plantes où le nombre et l'activité microbienne sont stimulés, grâce aux exsudats racinaires. Cependant les bénéfices des plantes ne sont pas toujours observés, et les exsudats pourraient aussi modifier la biodisponibilité des HAP. Les objectifs de ce travail ont été de mieux comprendre ces interactions sol-plante-microorganismes qui conditionnent le devenir des HAP dans la rhizosphère en suivant notamment (i) les bactéries possédant les gènes codant une HAP-dioxygènase, (ii) les espèces bactériennes impliquées dans la dégradation du phénanthrène, et (iii) la disponibilité et la biodégradation des HAP dans des terres industrielles historiquement contaminées.Les expériences ont été conduites dans des dispositifs à compartiments, lesquels permettent une diffusion des exsudats racinaires dans le sol tout en retenant physiquement les racines, puis en microcosmes avec un ajout d'exsudats racinaires naturels produits à partir d'une culture hydroponique de ray-grass (Lolium perenne, L). Les expériences ont été réalisées dans un premier temps avec du sable en ajoutant du phénanthrène (PHE) et un inoculum bactérien issu d'un sol d'une ancienne cokerie puis directement avec des sols historiquement contaminés en HAP. Les nombres de copies de gènes codant pour l'ADNr 16S et pour des HAP-dioxygènases ont été quantifiés par PCR en temps réel pour estimer la proportion de bactéries dégradantes. Les structures des communautés ont été comparées par électrophorèses (TTGE). En plus de l'analyse des 16 HAP totaux, une extraction non exhaustive des HAP a été réalisée à la cyclodextrine pour en estimer la disponibilité. L'utilisation de la méthode SIP (stable isotope probing) avec du 13C-phénanthrène a permis d'identifier les bactéries directement impliqués sa dégradation dans un sol historiquement contaminé. Les expériences en dispositifs à compartiments ont confirmé que la dissipation du phénanthrène est plus importante lorsque la distance aux racines est plus faible, et montrent que le nombre de copies de gène 16S et de gène de HAP-dioxygénase varie avec l'âge des plantes et du temps de contact des compartiments latéraux avec le tapis racinaire. Mais elles montrent aussi que la dissipation du phénanthrène n'est pas plus importante dans les pots plantés, tandis que dans les expériences en microcosmes une inhibition de la dissipation du PHE a même été observée en présence d'exsudats. La présence d'exsudats racinaires a profondément modifié la structure des communautés dégradant les HAP, et l'expérience SIP a permis d'identifier les bactéries directement impliquées dans la dégradation du 13C-phénanthrène et de montrer qu'elles étaient différentes en présence ou non d'exsudats. En présence d'exsudats, la proportion des bactéries dégradantes dans la population totale est passée de 1 % dans la terre d'origine et dans les traitements sans exsudats à plus de 10 %. Même si les exsudats racinaires ralentissent la dissipation du phénanthrène, en fournissant une source de carbone plus facilement métabolisable, ils ont augmenté la quantité de HAP extractibles à la cyclodextrine dans deux des trois sols historiquement contaminés, suggérant un effet de ceux-ci sur la biodisponibilité des HAP / Polycyclic Aromatic Hydrocarbons (PAH) are organics pollutants, ubiquitous, toxics and potentially carcinogenic. In soil, PAH degradation is mainly attributed to microbial organism. Several studies have thus reported enhanced PAH degradation in soil in the presence of plants. Rhizospheric soil increase the number et the activity of microorganisms in soil by the release of roots exudates. However, bene?cial effects of plants in the remediation are not always observed and roots exudates could be limited PAH biodegradation. The object of this study was to investigate the fate of PAHs in rhizosphere, following (i) the PAH-dioxygenase genes DNA to quantify the PAH-degrading bacteria, (ii) species implicated in phenanthrene biodegradation, and (iii) PAH availability and biodegradation from industrial soils.Different experimental devices have been designed to study detailed processes in the rhizosphere. First is a compartments devices were a nylon mesh permits diffusion of plant soluble substances towards the adjacent root free compartment as a rhizosphere. Secondly microcosms were enriched with natural roots exudates from hydroponic culture of ray-grass (Lolium perenne L.). In first time, experiments were conducted using sand and bacterial inoculum from an industrially PAH-contaminated soil and then directly with a soil historically contaminated by PAH. The Real-Time PCR quantification of 16S rRNA gene copy and of functional PAH-RHD? genes permitted to assess the proportion of a degrading bacteria. Bacterial community structure was approached from Temporal Thermal Gradient gel Electrophoresis (TTGE) fingerprinting, and bands sequencing. Nonexhaustive cyclodextrin-based extraction technique provided a estimate of the ?labile? or available pool of PAH in soil. Use of stable isotope probing (SIP) technique with [13C]phenanthrene allowed a bacterial identification of directly implicated in industrial soil.The presence of exudates modified microbial community of PAH-degrading bacteria. SIP experiment showed that 13C-labelled PHE-degrading bacteria was different depending on the exudates input. Many species having to degrade phenanthrene were able to use exudates. Presence of root exudates increased the proportion of PAH-RHD? genes compared to the bulk soil at the beginning and in microcosms without exudates (respectively 10% and 1 %). However, phenanthene dissipation in sand or soil were weaker with root exudates and aged PAH concentrations has not shifted during incubation time. Nevertheless, the root exudates increased the PAH labile fraction extract with cyclodextrin solution into two in three soils historically contaminated

Climate change is expected to increase the precipitation ~30% in higher latitudes during the next century, increasing the land runoff via rivers to aquatic ecosystems. The Baltic Sea will receive higher river discharges, accompanied by larger input of allochthonous dissolved organic matter (DOM) from terrestrial ecosystems. The salinity will decrease due to freshwater dilution. The allochthonous DOM constitute a potential growth substrate for microscopic bacterioplankton and phytoplankton, which together make up the basal trophic level in the sea. The aim of my thesis is to elucidate the bacterial processing of allochthonous DOM and to evaluate possible consequences of increased runoff on the basal level of the food web in the Baltic Sea. I performed field studies, microcosm experiments and a theoretical modeling study. Results from the field studies showed that allochthonous DOM input via river load promotes the heterotrophic bacterial production and influences the bacterial community composition in the northern Baltic Sea. In a northerly estuary ~60% of bacterial production was estimated to be sustained by terrestrial sources, and allochthonous DOM was a strong structuring factor for the bacterial community composition. Network analysis showed that during spring the diversity and the interactions between the bacteria were relatively low, while later during summer other environmental factors regulate the community, allowing a higher diversity and more interactions between different bacterial groups. The influence of the river inflow on the bacterial community allowed “generalists” bacteria to be more abundant than “specialists” bacteria.    Results from a transplantation experiment, where bacteria were transplanted from the northern Baltic Sea to the seawater from the southern Baltic Sea and vice versa, showed that salinity, as well as the DOM composition affect the bacterial community composition and their enzymatic activity. The results showed that α-proteobacteria in general were favoured by high salinity, β-proteobacteria by low salinity and terrestrial DOM compounds and γ-proteobacteria by the enclosure itself. However, effects on the community composition and enzymatic activity were not consistent when the bacterial community was retransplanted, indicating a functional redundancy of the bacterial communities.  Results of ecosystem modeling showed that climate change is likely to have quite different effect on the north and the south of the Baltic Sea. In the south, higher temperature and internal nutrient load will increase the cyanobacterial blooms and expand the anoxic or suboxic areas. In the north, climate induced increase in riverine inputs of allochthonous DOM is likely to promote bacterioplankton production, while phytoplankton primary production will be hampered due to increased light attenuation in the water. This, in turn, can decrease the production at higher trophic levels, since bacteria-based food webs in general are less efficient than food webs based on phytoplankton. However, complex environmental influences on the bacterial community structure and the large redundancy of metabolic functions limit the possibility of predicting how the bacterial community composition will change under climate change disturbances.