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Experimental nutrient additions are a fundamental approach to investigating plankton ecology. Possibilities range from whole-lake fertilization to flask assays encompassing a trade-off between closeness to the “real world” and feasibility and replication. Here we describe an enclosure type that minimizes the manipulation of planktonic communities during the enclosure filling. The enclosure (typically ~100 L volume) consists of a narrow translucent cylinder that can comprise the entire photic zone (or a large part of it in clear deep lakes, e.g. 20-m long) and holds a sediment trap at the bottom for recovering the sinking material. The enclosures are inexpensive and straightforward to build. Thus, many can be used in an experiment, favoring the diversity of treatments and the number of replicates. They also are lightweight with easy transport and use in lakes that cannot be reached by road. The enclosures are fundamentally aimed at investigating the short-term response of the planktonic community, integrated across the photic zone, to pulse perturbations using before and after comparisons and multiple replication and treatments. The pros and cons of the enclosure design are evaluated based on experience gained in Lake Redon, a high mountain ultraoligotrophic deep lake in the Pyrenees.

Antimicrobial resistance (AMR) has been considered one of the major challenges to global public health, and it is now seen as a One Health concept, under which people’s health is connected to the health of animals and their shared environment. Agriculture contributes to the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic residues in the environment as manure from (intensive) livestock production is widely used as fertilizer. Despite being a nutrient-rich and stable organic carbon source, the application of animal manure also results in the introduction of manure-derived bacteria and their ARGs into the soil, enriching the already occurring set of ARGs. The fate of ARGs in the environment, particularly in farmlands, is not yet clear, and this thesis set out to investigate ARG proliferation in microbial communities in the agricultural chain, from the animal gut to water (manure, soil, and water), and the extent of ARG transfer potential. Understanding the main factors driving ARG dissemination in farmlands will help define concrete points of action that aim to mitigate the spread of AMR at the farm level. Chapter 2 evaluated the soil texture’s role on ARG dynamics in manured soils and surrounding surface waters. It was demonstrated that rather than showing similar decay dynamics, factors such as the type of ARG and soil texture drive the ARG persistence in the environment. Chapter 3 explored the dynamics of bacteria and ARGs introduced by manuring to soils and adjacent water ditches, both at the community and individual scale, over three weeks. It showed that the bacteriome and resistome structures are shaped by different factors, where the bacterial community composition could not explain the changes in ARG diversity or abundances. Additionally, it also highlighted the potential of applying targeted metagenomic techniques, such as ResCap, to study the fate of AMR in the environment. Chapter 4 examined the ARG removal potential of a manure treatment process using a newly designed up-flow anaerobic sludge bed reactor operating at thermophilic conditions. It indicated that this treatment successfully removes some, but not all, bacterial groups. It also showed that the abundance of the selected ARGs was not reduced. Chapter 5 assessed how conjugation frequencies between E. coli strains in filter matings differ based on the temperature and nutrient availability. It showed that, despite less favorable conditions, plasmid transfer can occur in the environment. Therefore, fecal microorganisms in manure can be a source of AMR transmission. Chapter 6 investigated the fate of plasmids in manured soil microcosms introduced by fecal microorganisms over time. While being a laboratory simulation, it provided realistic quantifications of conjugation frequencies, and it identified the new hosts of the transferred plasmids. In the end, the findings reported throughout the thesis were discussed and the implications of research outcomes were contextualized. Action points to reduce the farm burden in environmental AMR spread were suggested.

To investigate the release and degradation of arsenolipids present in the marine brown macroalga Ecklonia radiata, tissues were collected in various stages of decomposition from intertidal environments, while tissues were also decomposed in laboratory-based microcosms prepared using combinations of autoclaved and natural (non-autoclaved) seawater and sand. Field collected macroalgae samples contained 20–120 μg g−1 total As of which 1–10% were arsenolipids comprising mainly an arsenic hydrocarbon (AsHC; 3–13% of total arsenolipids) and four di-acyl arsenic phospholipids (AsPLs; 86–95%). Additionally, a mono-acyl AsPL was found in all water-column decomposing samples. Arsenolipid concentrations in live tissues were similar to those in tissues decomposing in the water-column (1.3–2.9 μg g−1 dry mass), which were both up to four times higher than those in decomposing tissues collected from intertidal environments (0.7–1.3 μg g−1 dry mass). In the microcosm experiments, the arsenolipid content of E. radiata decreased substantially as decomposition proceeded. In the majority of microcosms, more than 75% of the arsenolipids present initially disappeared within 5 days with only the AsHC persisting until day 60 (the length of the experiment). This study demonstrates that the habitat in which decomposition occurs influences the release and degradation of arsenolipids with the greatest losses occurring when tissues decompose in intertidal environments. Microbial diversity, biomass, and overall activity are thus likely to play important roles in the persistence of arsenolipids in decomposing algae. Refereed/Peer-reviewed

El glifosato es el herbicida más utilizado a nivel mundial. Puede llegar a los cuerpos de agua y afectar a las comunidades microbianas. Comparamos los efectos del glifosato grado técnico y dos formulados comerciales sobre una comunidad periférica de agua dulce. Se llevó a cabo un experimento de laboratorio con cuatro tratamientos: glifosato ácido grado técnico, Glifosato II Atanor, Roundup Max, a una concentración de 3 mg de ingrediente activo/L, y un Control. A los 2, 5 y 9 días posteriores a la aplicación de los herbicidas se determinaron la concentración de pigmentos, peso seco, peso seco libre de cenizas y densidad algal del perifiton. Se registró un incremento de la abundancia de Cyanobacteria y una disminución de Chlorophyta y Bacillariophyta en todos los tratamientos con herbicida. Este efecto fue mayor con la adición de Roundup Max y Glifosato II Atanor, y fue menor con glifosato grado técnico, sugiriendo que los aditivos en los formulados comerciales pueden intensificar los efectos del glifosato Glyphosate is the most widely used herbicide worldwide. It may reach water bodies and affect microbial communities. We compared the effects of two commercial formulations and technical-grade glyphosate on a freshwater periphytic community. A laboratory bioassay was carried out with four treatments: technical-grade glyphosate acid, Glifosato II Atanor, Roundup Max, at a concentration of 3 mg active ingredient/L, and Control. At 2, 5 and 9 days after herbicide application, pigments concentration, dry weight, ash-free dry weight, and periphytic algal density were determined. An increase of Cyanobacteria and a decrease of Chlorophyta and Bacillariophyta abundances were registered in all treatments with the herbicide. This effect was greater when Roundup Max and Glifosato II Atanor® were added, and was lower with technical-grade glyphosate, suggesting that additives in the commercial formulations may enhance glyphosate effects. Fil: Gonzalez, Daniela. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina Fil: Juarez, Angela Beatriz. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Biodiversidad y Biología Experimental; Argentina Fil: Krug, Cecilia Pamela. Universidad Nacional de San Martín. Instituto de Investigación en Ingeniería Ambiental; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Santos, Marina. Instituto Nacional de Tecnología Industrial; Argentina Fil: Vera, Maria Solange. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina

The main objective of the current study was to assess the impact of the water taken from the ‘Tunisian Refining Industries Company’ on meiobenthic nematodes, before and after a series of treatments in decantation basins followed by its discharge in Bizerte bay, Tunisia. The comparison of environmental parameters of the two types of water was clearly indicative of an improvement in the quality of treated waters after a significant reduction in their loads in hydrocarbons. Overall, the water retained a good quality after being treated by ‘Tunisian Refining Industries Company’ before discharge in the sea. At the end of the experiment, differential responses were observed according to the richness of sediment in organic matter and hydrocarbons. Thus, it was apparent that the nematode assemblage exposed to the treated waters was closer to controls and associated to higher values of abundance, than that under untreated ones. It was also assumed that the species Microlaimus honestus De Man, 1922, Paramonohystera proteus Wieser, 1956 and Cyartonema germanicum Juario, 1972 are sensitive bioindicators of bad environmental statues and of hydrocarbon presence in the environment. On the other hand, Metoncholaimus pristiurus (Zur Strassen, 1894) Filipjev, 1918 would rather be classified as a positive bioindicative species of this type of pollutants. Resumo O principal objetivo do presente estudo foi avaliar o impacto da água retirada da “Tunisian Refining Industries Company” sobre os nematoides meiobentônicos, antes e depois de uma série de tratamentos em bacias de decantação seguidos de seu descarte na baía de Bizerte, Tunísia. A comparação dos parâmetros ambientais dos dois tipos de água foi claramente indicativa de uma melhoria na qualidade das águas tratadas após uma redução significativa das suas cargas em hidrocarbonetos. No geral, a água reteve uma boa qualidade após ser tratada pela “Tunisian Refining Industries Company” antes da descarga no mar. Ao final do experimento, foram observadas respostas diferenciais de acordo com a riqueza de sedimentos em matéria orgânica e hidrocarbonetos. Assim, ficou claro que a assembleia de nematoides exposta às águas tratadas estava mais próxima dos controles e associada a maiores valores de abundância do que nas não tratadas. Também foi assumido que as espécies Microlaimus honestus De Man, 1922, Paramonohystera proteus Wieser, 1956 e Cyartonema germanicum Juario, 1972 são bioindicadores sensíveis de más estátuas ambientais e da presença de hidrocarbonetos no meio ambiente. Por outro lado, Metoncholaimus pristiurus (Zur Strassen, 1894) Filipjev, 1918 preferiria ser classificado como uma espécie bioindicativa positiva deste tipo de poluentes.

Temperature and light play a crucial role in regulating phytoplankton blooms in the Ocean. To assess the importance of these two parameters experimentally, microcosms were conducted on seven picoplankton communities (

The dominance of MATα among cryptococcal strains has been ascribed to MATa strains being more sensitive to certain environmental factors; however no study has attempted to identify these factors. During the present study we determined whether the chemical composition of woody debris may influence the occurrence of Cryptococcus gattii MATa. We observed a positive correlation between the numbers of C. gattii MATa and the ammonium-nitrogen (NH4–N) concentration in woody debris samples. Subsequent growth studies conducted in woody debris microcosms indicated that this positive correlation is likely not due to additional NH4Cl improving the growth of selected MATa strains. Instead, it might be due to the MATa strains competing better with the MATα strains in the presence of a high NH4Cl concentration compared to a low NH4Cl concentration. This exploratory study paves the way for future studies focused on the interactions of MATa and MATα strains with environmental factors.

The freshwater lakes of southwestern France are subject to the development of invasive macrophytes which are associated with mercury (Hg) contamination of the food web. The aim of this study was to determine the bioavailability of methylmercury (MeHg) produced by plant roots in aquatic ecosystems. A microcosm experiment was performed using isotopically enriched inorganic Hg at environmental concentrations (1 &micro, g 199IHg&middot, L&minus, 1). For all conditions, total Hg in fish as well as Hg species associated with different compartments (water, sediments, plant roots, fish) were analyzed by gas chromatography-inductively coupled plasma-mass spectrometry (GC-ICP-MS). In addition, sediment, plants, and fish gut microbiota were studied by MiSEQ sequencing. Some strains were isolated and tested for their ability to methylate Hg. The results revealed 199MeHg production in plant roots and the presence of this form in fish (tissues and gut), highlighting a MeHg trophic transfer. Moreover, methylator bacteria were identified from the gut contents of the fish when they were in the presence of plants. Some of them were related to bacteria found in the plant roots. On the basis of these results, the transfer of MeHg and bacteria from plants to fish is highlighted, in addition, Hg methylation is strongly suspected in the fish gut, potentially increasing the Hg bioaccumulation.

Deep geological repository (DGR) is one of the internationally accepted options to dispose radioactive wastes. Bentonite formations from Almeria, Spain, were selected as reference material for artificial barriers for the future Spanish repository. However, the safety of this long-term disposal could be compromised not only by physicochemical factors but also by microbial processes. The highly radioactive waste must be safely stored at least for 100,000 years for the radioactivity to decrease to similar levels to those of natural uranium. To simulate a scenario where the mobilization of radionuclides from the repository to the host formations may occur, longterm microcosms were studied. After being exposed to uranyl nitrate for 5 months, the response of the bentonite microbial community to the addition of this radionuclide was evaluated. High throughput 16S rRNA gene sequencing revealed that the structure of the microbial community after the uranyl nitrate treatment differs to that of the control microcosms. The microbial diversity was dominated by Firmicutes and Proteobacteria. Moreover, after the uranyl nitrate treatment OTUs annotated as Paracoccus and Bacillus were highly enriched. The mineralogy of bentonites was not affected by the uranyl nitrate treatment as was demonstrated by X-ray diffraction analysis. In addition, the study of uranium-bacteria interaction revealed the ability of isolates to biomineralize uranium as uranium phosphate mineral phases. Thus, the changes induced by the release of uranium in the microbial population may also affect the mobility of this radionuclide, making it less mobile and therefore less harmful for this environment., This work was funded by the ERDF-financed Grants CGL-2012- 36505, CGL2014-59616-R (80% finding by FEDER), BES-2010-032098 and EEBB-I-14-08420 (Ministerio de Ciencia e Innovación, España).

In this study, a bioremediation approach was evaluated for the decontamination of an aquifer affected by the release of organohalides by an industrial landfill. After preliminary physicochemical and microbiological characterization of the landfill groundwater, the stimulation of natural organohalide respiration by the addition of a reducing substrate (i.e., molasse) was tested both at microcosm and at field scales, by the placement of an anaerobic permeable reactive bio-barrier. Illumina sequencing of cDNA 16S rRNA gene revealed that organohalide-respiring bacteria of genera Geobacter, Sulfurospirillum, Dehalococcoides, Clostridium and Shewanella were present within the aquifer microbial community, along with fermentative Firmicutes and Parvarchaeota. Microcosm experiments confirmed the presence of an active natural attenuation, which was boosted by the addition of the reducing substrate. Field tests showed that the bio-barrier decreased the concentration of chloroethenes at a rate of 23.74 kg d−1. Monitoring of organohalide respiration biomarkers by qPCR and Illumina sequencing revealed that native microbial populations were involved in the dechlorination process, although their specific role still needs to be clarified. The accumulation of lower-chloroethenes suggested the need of future improvement of the present approach by supporting bacterial vinyl-chloride oxidation, to achieve a complete degradation of chloroethenes.

A laboratory-scale study was carried out to evaluate the groundwater bioremediation potential of hexavalent chromium (Cr(VI)), taking into account the chromate pollution of an industrial site located in Southern Italy (Apulia Region). The reduction of Cr(VI) was studied on laboratory microcosms, set up in different experimental conditions, namely: ABIO (soil and water sterilized), BIO (soil and water not sterilized), LATT (with the addition of lactate), and YE (with the addition of yeast extract). Control test lines, set up by using sterilized matrices and amendments, were employed to assess the occurrence of the pollutant reduction via chemical processes. By combining molecular (microbial abundance, specific chromate reductase genes (ChR) and the Shewanella oinedensis bacterial strain) with chemical analyses of chromium (VI and III) in the matrices (water and soil) of each microcosm, it was possible to investigate the response of microbial populations to different experimental conditions, and therefore, to assess their bioremediation capability in promoting Cr(VI) reduction. The overall results achieved within this work evidenced the key role of amendments (lactate and yeast extract) in enhancing the biological reduction of hexavalent chromium in the contaminated aqueous phase of laboratory microcosms. The highest value of Cr(VI) removal (99.47%) was obtained in the YE amended microcosms at seven days.

The soil microbiota conducts important biological ecosystem functions, but the mechanism underlying community-environment interactions for soil microbiota remains unclear. By using two distinct soils for cross inoculation, we successfully simulated the assembly of the bacterial community in sterile soil. Thus, the reasons why inoculum and recipient have dominated community assembly in previous investigations are investigated in this study. We found that inoculated bacteria presided over environmental selection for community assembly due to the varied difference of ecological equivalent bacteria, either divergent or convergent. The significance of neutrality for the ecologically equivalent bacterial species that immigrated into the recipients should be emphasized in exploring the mechanisms of community assembly. Our finding is helpful for understanding the community-environment interaction, a basic question in ecology, and it would shed light on this issue that has perplexed scientists for many years., Exploring the assembly mechanism of microbiota is critical for understanding soil ecosystem functions. However, the relative importance of different biotic and abiotic factors in determining the bacterial community has not been properly clarified. In this study, the effects of inocula and recipients on the assembly of the soil community were investigated to evaluate their importance by inoculation experiments with sterile soil. Two distinct soils, conventional nitrogen-fertilized soil and aromatic-compound-contaminated soil, were sterilized, cross inoculated, and incubated for 2 months under different inoculation doses and oxygen conditions. The results showed that the greatest variation in community structure emerged in the samples inoculated with distinct inocula rather than in the samples of different soil recipients. The phylogenies in the two inocula were diverse and dissimilar, although there were many ecologically equivalent bacteria. When the inocula with dissimilar ecologically equivalent species were used, the assembled communities were primarily determined by the inocula as indicated by the beta diversity and variation partitioning analyses. In contrast, environmental selection dominated the process when ecologically equivalent species in the inocula were similar, as when only one type of inoculum was used, where the soil habitat selected the most adaptive bacteria from the defined inoculum pool. These results indicate that inoculated bacteria are dominant over environmental selection if they are sufficiently dissimilar, although the effect of environmental selection is more obvious when similar bacteria are inoculated in the soil for community assembly. Our findings suggest that the immigration of exotic bacteria could be a primary factor impacting community assembly. IMPORTANCE The soil microbiota conducts important biological ecosystem functions, but the mechanism underlying community-environment interactions for soil microbiota remains unclear. By using two distinct soils for cross inoculation, we successfully simulated the assembly of the bacterial community in sterile soil. Thus, the reasons why inoculum and recipient have dominated community assembly in previous investigations are investigated in this study. We found that inoculated bacteria presided over environmental selection for community assembly due to the varied difference of ecological equivalent bacteria, either divergent or convergent. The significance of neutrality for the ecologically equivalent bacterial species that immigrated into the recipients should be emphasized in exploring the mechanisms of community assembly. Our finding is helpful for understanding the community-environment interaction, a basic question in ecology, and it would shed light on this issue that has perplexed scientists for many years.

Himalayan mountains are subjected to the intensive and unjudicial application of chlorpyrifos (CP) in agricultural practices; hence it has spurred concerns over food safety and environmental consequences. These low-temperature mountainous regions are foremost ecosystems, representing the large-scale distribution of cold trapped CP residues. A bacterial consortium ECO-M was formed by isolating the CP degrading bacterial strains viz Agrobacterium tumefaciens strain ECO1, Cellulosimicrobium funkei strain ECO2, Shinella zoogloeoides strain ECO3 and Bacillus aryabhattai strain ECO4. At an initial concentration of 50 mg L−1, consortium ECO-M degraded 100% of CP within 6 days. Emergence and subsequent degradation of the two metabolites, 3, 5, 6-trichloro-2-pyridinol (TCP) and 2-hydroxypyridine were confirmed by GC-MS analysis. A degradation pathway of CP by isolated strains has been proposed. A general factorial experimental design was effectuated to prognosticate the optimum biodegradation by manifesting the optimal biological and physicochemical factors. Fitness of the experimental design was affirmed experimentally by employing optimized factors i.e., temperature 30 °C, CP concentration 50 mg L−1 and an inoculum size of 10% (v/v). The model appropriacy and the rationality of the optimization procedure were appraised by installing an in-situ microcosms experiment using the real contaminated soil collected from the Himalayan mountain ecosystem. The augmentation culture seems to be effectively conspicuous in stimulating maximum degradation up to 94.3% in the CP contaminated soil.

00000 ăWOS:000369212600010; International audience; The inflow of deep seawater in the surface layer by an Ocean Thermal Energy Conversion (OTEC) plant will generate artificial upwelling. In order to study the potential impact on biogeochemical processes that could result, in situ microcosms were designed to simulate seawater plant discharge and these were deployed off the Caribbean coast of Martinique. Seawater was collected in ultra-clean conditions at maximum chlorophyll a concentrations (45 m depth). The water was then mixed with either 2% or 10% deep seawater (1100 m depth) and put in 2.3 L polycarbonate bottles. These microcosms were immersed for 6 days at 45 m depth on a 220 m mooring. Samples from the surrounding environment and from the microcosms were analyzed by pigment quantification, counting of picophytoplankton groups and macronutrient analyses. Similar trends in the evolutions of the phytoplankton populations were observed over time between the control microcosms (without addition of deep seawater) and the surrounding environment, suggesting that these microcosms can be used as a realistic representation of the natural surrounding waters over a 6-day incubation period. Microcosm enrichment with 10% deep seawater induced a shift in the phytoplankton assemblage towards the development of diatoms, haptophytes, and Prochlorococcus, whereas 2% enrichment only led to an increase in the Prochlorococcus population.

Background: The bacterial community responses to oil spill events are key elements to predict the fate of hydrocarbon pollution in receiving aquatic environments. In polar systems, cold temperatures and low irradiance levels can limit the effectiveness of contamination removal processes. In this study, the effects of a simulated acute oil spillage on bacterial communities from polar sediments were investigated, by assessing the role of hydrocarbon mixture, incubation time and source bacterial community in selecting oil-degrading bacterial phylotypes. Methods: The bacterial hydrocarbon degradation was evaluated by gas chromatography. Flow cytometric and fingerprinting profiles were used to assess the bacterial community dynamics over the experimental incubation time. Results: Direct responses to the simulated oil spill event were found from both Arctic and Antarctic settings, with recurrent bacterial community traits and diversity profiles, especially in crude oil enrichment. Along with the dominance of Pseudomonas spp., members of the well-known hydrocarbon degraders Granulosicoccus spp. and Cycloclasticus spp. were retrieved from both sediments. Conclusions: Our findings indicated that polar bacterial populations are able to respond to the detrimental effects of simulated hydrocarbon pollution, by developing into a more specialized active oil degrading community.

The current knowledge about the role terrestrial ornamental plants play in constructed wetlands (CWs) has scarcely been evaluated. Likewise, little attention has been given towards the use of new support or fill media for subsurface flow CWs, which may result in the reduction of costs when implemented on a large scale. This study evaluated, during nine months, the effect of three terrestrial ornamental plants and two substrates on the elimination of pollutants in wastewaters by using fill-and-drain vertical subsurface flow CWs (FD-CWs). Sixteen microcosms were used, nine filled with polyethylene terephthalate (PET) and nine with porous river stone (PRS). For each type of substrate, duplicates of microcosms were used, utilizing Anthurium sp., Zantedeschia aethiopica, and Spathiphyllum wallisii as vegetation and two other CWs without vegetation as controls. The environmental conditions, number of flowers, and height of the plants were registered. The results revealed that both substrates in the FD-CWs were efficient in removing pollutants. The average removal of pollutants in systems with vegetation revealed a positive effect on the reduction of the biochemical oxygen demand (55–70%), nitrates (28–44%), phosphates (25–45%), and fecal coliforms (52–65%). Meanwhile, in units without vegetation, the reduction of pollutants was nearly 40–50% less than in those with vegetation. The use of PET as a filling substrate in CWs did not affect the growth and/or the flowering of the species; therefore, its use combined with the species studied in CWs may be replicated in villages with similar wastewater problems. This may represent a reduction in implementation costs when utilizing PET recycled wastes and PRS as substrates in these systems in comparison with the typical substrates used in CWs. More studies are needed to better understand the interactions among these novel support media and the commercial terrestrial ornamental plants.

International audience; We review methods and models that help to assess how root activity changes soil properties and affects the fluxes of matter in the soil. Subsections discuss (1) experimental systems including plant treatments in artificial media, studying the interaction of model root and microbial exudates with soil constituents, and microcosms to distinguish between soil compartments differing in root influence, (2) the sampling and characterization of rhizosphere soil and solution, focusing on the separation of soil at differentdistances from roots and the spatially resolved sampling of soil solution, (3) cutting-edge methodologies to study chemical effects in soil, including the estimation of bioavailable element or ion contents (biosensors, diffusive gradients in thin-films), studying the ultrastructure of soil components, localizing elements and determining their chemical form (microscopy, diffractometry, spectroscopy), tracing the compartmentalization of substances in soils (isotope probing, autoradiography), and imaging gradients insitu with micro electrodes or gels or filter papers containing dye indicators, (4) spectroscopic and geophysical methods to study the plants influence on the distribution of water in soils, and (5) the modeling of rhizosphere processes. Macroscopic models with a rudimentary depiction of rhizosphere processes are used to predict water or nutrient requirements by crops and forests, to estimate biogeochemical element cycles, to calculate soil water transport on a profile scale, or to simulate the development of root systems. Microscopic or explanatory models are based on mechanistic or empirical relations that describe processes on a single root or root system scale and/or chemical reactions in soil solution. We conclude that in general we have the tools at hand to assess individual processes on the microscale under rather artificial conditions. Microscopic, spectroscopic and tracer methods to look at processes in small “aliquots” of naturally structured soil seem to step out of their infancy and have become promising tools to better understand the complex interactions between plant roots, soil and microorganisms. On the field scale, while there are promising first results on using non-invasive geophysical methods to assess the plant's influence on soil moisture, there are no such tools in the pipeline to assess the spatial heterogeneity of chemical properties and processes in the field. Here, macroscopic models have to be used, or model results on the microscopic level have to be scaled up to the whole plant or plot scale. Upscaling is recognized as a major challenge.

International audience; Many scientific disciplines are currently experiencing a 'reproducibility crisis' because numerous scientific findings cannot be repeated consistently. A novel but controversial hypothesis postulates that stringent levels of environmental and biotic standardization in experimental studies reduce reproducibility by amplifying the impacts of laboratory-specific environmental factors not accounted for in study designs. A corollary to this hypothesis is that a deliberate introduction of controlled systematic variability (CSV) in experimental designs may lead to increased reproducibility. To test this hypothesis, we had 14 European laboratories run a simple microcosm experiment using grass (Brachypodium distachyon L.) monocultures and grass and legume (Medicago truncatula Gaertn.) mixtures. Each laboratory introduced environmental and genotypic CSV within and among replicated microcosms established in either growth chambers (with stringent control of environmental conditions) or glasshouses (with more variable environmental conditions). The introduction of genotypic CSV led to 18% lower among-laboratory variability in growth chambers, indicating increased reproducibility, but had no significant effect in glasshouses where reproducibility was generally lower. Environmental CSV had little effect on reproducibility. Although there are multiple causes for the 'reproducibility crisis', deliberately including genetic variability may be a simple solution for increasing the reproducibility of ecological studies performed under stringently controlled environmental conditions.

International audience; In order to assess the effect of mixed pollutants, the influence of different concentration levels of a mixture of metals (Cr, Co, Pb, Mn, Ni, Cu, Zn) on the biodegradation of some PAHs (phenanthrene, fluoranthene, pyrene, benzo[b]fluoranthene and benzo[a]pyrene) in soil samples was evaluated. To do so, groups of microcosms of a natural soil from the region of Sabadell (Barcelona, Spain) were prepared as a reproduction of the native environment at laboratory scale, under controlled conditions. Mixtures of PAHs and metals were carefully selected, according to soil characterization and microbiological growth preliminary assays, and were added to microcosms. These microcosms were analyzed at various times, along two months, to obtain PAHs dissipation time-courses. A first-order kinetic modelling allowed obtaining different rate constants and DT50 values as a function of the metal levels introduced in microcosms. As a general observation, the higher the concentration of metals, the lower the biodegradation of PAHs of 3–4 rings (phenanthrene, fluoranthene and pyrene). On the other hand, no important effect on the biodegradation of higher molecular weight PAHs (benzo[b]fluoranthene and benzo[a]pyrene) was observed at the different concentration levels of metals tested.

Microbes are considered to have a global distribution due to their high dispersal capabilities. However, our knowledge of the way geographically distant microbial communities assemble after dispersal in a new environment is limited. In this study, we examined whether communities would converge because similar taxa would be selected under the same environmental conditions, or would diverge because of initial community composition, after artificial dispersal. To this aim, a microcosm experiment was performed, in which the temporal changes in the composition and diversity of different prokaryoplankton assemblages from three distant geographic coastal areas (Banyuls-sur-Mer in northwest Mediterranean Sea, Pagasitikos Gulf in northeast Mediterranean and Woods Hole, MA, USA in the northwest Atlantic), were studied. Diversity was investigated using amplicon pyrosequencing of the V1–V3 hypervariable regions of the 16S rRNA. The three assemblages were grown separately in particle free and autoclaved Banyuls-sur-mer seawater at 18 °C in the dark. We found that the variability of prokaryoplankton community diversity (expressed as richness, evenness and dominance) as well as the composition were driven by patterns observed in Bacteria. Regarding community composition, similarities were found between treatments at family level. However, at the OTU level microbial communities from the three different original locations diverge rather than converge during incubation. It is suggested that slight differences in the composition of the initial prokaryoplankton communities, resulted in separate clusters the following days even when growth took place under identical abiotic conditions.

We studied the physiological response of phytoplankton to the interacting effects of 3 factors affected by global climate change: CO2, nutrient loading and irradiance. Treatments had a high and low level for each factor: CO2 was bubbled at 1000 ppm by volume versus present atmo spheric values; high nutrient treatments had a combination of inorganic and organic nutrients; and light treatments were obtained by covering the tanks with a single or double layer of screen. We measured esterase activity, oxidative stress (ROS), cell death, DNA damage, photosynthetic efficiency and 14C assimilation as particulate or dissolved organic material (POC and DOC respectively). Conditions simulating future global change scenarios showed similar chlorophyllnormalized primary productivity as present conditions. The main effect driving phytoplankton physiology was the downregulation of the photosynthetic apparatus by elevated CO2, which decreased esterase activity, ROS, cell death and DNA damage. Nutrient concentration and light acted as additional modulators, upregulating or contributing to downregulation. The percentage of DO14C extracellular release (PER) was low (0 to 27%), significantly lower under ultraviolet radiation (UVR) than under photosynthetically active radiation (PAR), and acted mainly to reequilibrate the internal balance when cells grown under UVR were exposed to PAR. PER was almost 3 times lower under high CO2, confirming a higher resource use efficiency of phytoplankton under future CO2 concentrations., SI

Three chromium resistant bacterial strains, Pseudomonas fluorescens PF28, Enterobacter amnigenus EA31 and Enterococcus gallinarum S34 isolated from tannery waste contaminated soil were used in this study. All strains could resist a high concentration of K2Cr2O7 that is up to 300 mg/L. The effect of these strains on clover plants (Trifolium campestre) in the presence of two chromium salts CrCl3 and K2Cr2O7 was studied in soil microcosm. Application of chromium salts adversely affected seed germination, root and shoot length. Bacterial inoculation improved the growth parameters under chromate stress when compared with non inoculated respective controls. There was observed more than 50% reduction of Cr(VI) in inoculated soil microcosms, as compared to the uninoculated soil under the same conditions. The results obtained in this study are significant for the bioremediation of chromate pollution.

We evaluated the effect of AsiMax 50®, a commercial formulation of 2,4-D (2,4-dichlorophenoxyacetic acid), on the structure of both micro + nano phytoplankton (>2 μm; species composition and abundance) and cytometric populations (photosynthetic picoplankton (PPP, 0.2–2 μm), which included prokaryotic phycocyanin-rich picocyanobacteria (PC-Pcy), phycoerythrin-rich picocyanobacteria (PE-Pcy) and eukaryotic phototrophs (PEuk); and bacterioplankton (HB), heterotrophic bacteria), using a microcosms-based approach and a single 7-day exposure. Assays were performed on two different microbial assemblages sampled from freshwater bodies of two contrasting turbidity status: clear (chlorophyll a = 7.6 μgL-1, turbidity = 1 NTU) and organic turbid systems (chlorophyll a = 25.0 μgL-1, turbidity = 9 NTU). For each system, the herbicide was applied to 500 mL-Erlenmeyer flasks, at seven concentration levels of the active ingredient (a.i.): 0 (control = no addition), 0.02, 0.2, 2, 20, 200 and 2,000 mg a.i.L−1. The impact of AsiMax 50® seemed to be greater in the turbid system. In this system, total abundance of living (live) micro + nano phytoplankton showed a significant increase at lower concentrations and data were fitted to a humped-shaped curve. For both clear and organic turbid systems, micro + nano phytoplankton decreased in species richness and abundance at higher herbicide concentrations. These results suggest that 2,4-D may mimic hormonal function. Some species, such as Ochromonas sp. and Chlamydomonas sp., showed different responses to herbicide exposure between water systems. In the turbid system, the increase in abundance of the PPP fraction observed at 7-d exposure was probably due to either an increase in PE-Pcy (thus suggesting the existence of auxin pathways) or a reduction in competitive pressure by micro + nano plankton. Our results provide some evidence of the importance of using community-scale approaches in ecotoxicological studies to predict changes in freshwater ecosystems exposed to a 2,4-D-based formulation. However, caution must be taken when extrapolating these effects to real scenarios, as assays were based on a laboratory microcosm experiment.

A focus of ecology is to determine drivers of community assembly. Here, we investigate effects of immigration and species sorting (environmental selection) on structuring aquatic bacterial communities in both colonised and previously uncolonised environments. We used nonsterilised and presterilised water from three chemically distinct ponds to establish microcosms, which were opened for 12, 24, 48, 96 or 167h and then closed again to allow airborne bacterial immigration and subsequent succession. Community similarity, richness, evenness and the parameters of a neutral model were investigated after 167h. Immigration appeared to govern the assembly of communities in the presterilised water as there were no significant differences in evenness among microcosm communities containing water from each pond. Statistical estimation of neutral model parameters confirmed these findings, because the estimated immigration rate changed significantly with time of exposure to immigration. Species sorting also occurred because significant differences in community similarity (for presterilised and nonsterilised communities) and evenness (only for nonsterilised communities) were detected among microcosms containing different pond water; the magnitude of these differences was greater for communities in nonsterilised microcosms. Our study provides evidence for both processes being important during the colonisation of aquatic environments and presents a novel way to apply the neutral model.

The attractiveness of a given leaf detritus to invertebrates depends on the chemical composition, physical structure, stage of microbial colonization and decomposition level. In addition to the leaf detritus quality, water temperature also affects organic matter cycling in aquatic environments. In this context, the objectives of this study were: i) to increase knowledge about the role of invertebrate shredders on fragmenting senescent, conditioned senescent and green leaves of Richeria grandis Vahl. (Phyllanthaceae) under gradual temperature rise and check leaf mass loss; ii) to verify the preference of Phylloicus sp. (Trichoptera) for leaves for larval case production. The experiment I consisted of three treatments with different water temperatures: 20°C, 24°C and 28°C. In the experiment II, we added 10 discs of green leaves of R. grandis and two shredder invertebrates (Phylloicus sp.) to each aquarium. Leaf mass loss in the presence or absence of fragmentation was not significantly influenced by differences in the intraspecific quality of the detritus or temperature. Intraspecific quality of resources mixed with green leaves can lead to increased contact of phenolic content on senescent leaves, leading to a similarity in food exploitation by invertebrates. However, the production of larval cases by Phylloicus sp. seems to be dependent on the resistance presented by the resource rather than the phenolic content, thus leading the shredders to use significantly more senescent detritus, regardless temperature. RESUMO A atratividade de um determinado detrito foliar pelos invertebrados depende da composição química, estrutura física, estágio de colonização microbiana e nível de degradação do detrito. Além da qualidade do detrito foliar, a temperatura da água tem sido outro fator que pode levar a variações na velocidade da ciclagem de matéria orgânica em ambientes aquáticos. Os objetivos deste estudo foram: i) ampliar os conhecimentos acerca do papel dos invertebrados fragmentadores sobre a atividade de fragmentação de folhas senescentes, senescentes condicionadas e verdes de Richeria grandis Vahl. (Phyllanthaceae) sob elevações graduais de temperatura e verificar as possíveis consequências sobre a perda de massa foliar; ii) verificar a preferência de recurso foliar para a construção de casulo pelo invertebrado fragmentador Phylloicus sp. (Trichoptera). O experimento I foi constituído de três tratamentos que se diferiram apenas na temperatura da água: Tratamento 1: 20°C, Tratamento 2: 24°C, Tratamento 3: 28°C. O experimento II se diferiu do I pelo acréscimo de dez discos de folhas verdes de R. grandis e dois invertebrados (Phylloicus sp.) em cada aquário. A perda de massa foliar na presença ou ausência de atividade de fragmentação não foi influenciada significativamente por diferenças na qualidade intraespecífica do detrito e ou por diferenças na temperatura. A qualidade intraespecífica de recursos misturados com folhas verdes pode levar ao aumento do contato de conteúdos fenólicos sobre folhas senescentes, levando a uma similaridade na exploração alimentar pelos invertebrados. No entanto, a construção de casulos pelos Phylloicus sp. parece ser dependente da resistência apresentada pelo recurso e não do conteúdo fenólico, levando assim os fragmentadores a utilizarem significativamente uma maior quantidade de detritos senescentes, independente da temperatura.

This work applied the radiotracer technique to evaluate the chromium (Cr) sorption by sediments of a mangrove degraded area under reforestation phase. The radiotracer 51 Cr(III) was used to assess the removal kinetics of this metal from tidal water by underlying sediments in two different environments from the mangrove area of the reserve Parque Natural Municipal Barao de Maua (Rio de Janeiro, SE Brazil).The results indicated a faster Cr(III) removal by sediments from the area with initial mangrove reforestation (t 1/2 = 12.1 ± 0.1 h) than estimated for the area with older mangrove reforestation (t 1/2 = 18.0 ± 0.2 h). However, this difference was explained by a stronger sediment bioturbation in the area that presented faster Cr removal (the initial mangrove reforestation zone). These results evidence the importance of the influence of biological activity, in the capacity of the mangrove sediment to remove Cr (III) from tidal waters.

Contamination of coastal environments is often due to a complex mixture of pollutants, sometimes in trace levels, that may have significant effects on diversity and function of organisms. The aim of this study was to evaluate the short-term dynamics of bacterioplankton exposed to natural and artificial mixtures of contaminants. Bacterial communities from a southwestern Mediterranean ecosystem, lagoon and the bay (offshore) of Bizerte were exposed to i) elutriate from resuspension of contaminated sediment, and ii) an artificial mixture of metals and herbicides mimicking the contamination observed during sediment resuspension. Elutriate incubation as well as artificial spiking induced strong enrichments in nutrients (up to 18 times), metals (up to six times) and herbicides (up to 20 times) relative to the in situ concentrations in the offshore station, whereas the increases in contaminants were less marked in the lagoon station. In the offshore waters, the artificial mixture of pollutants provoked a strong inhibition of bacterial abundance, production and respiration and significant modifications of the potential functional diversity of bacterioplankton with a strong decrease of the carbohydrate utilization. In contrast, incubation with elutriate resulted in a stimulation of bacterial activities and abundances, suggesting that the toxic effects of pollutants were modified by the increase in nutrient and DOM concentrations due to the sediment resuspension. The effects of elutriate and the artificial mixture of pollutants on bacterial dynamics and the functional diversity were less marked in the lagoon waters, than in offshore waters, suggesting a relative tolerance of lagoon bacteria against contaminants.

The use of glyphosate has increased dramatically during the past years around the world. Microbial communities are altered when glyphosate reaches water bodies. The freshwater golden mussel Limnoperna fortunei is an invasive species that has rapidly dispersed since it was introduced in Argentina two decades ago. Mussels alter aquatic conditions through their filtrating activity by increasing water clarity and nutrient recycling. We aim to evaluate the potential capacity of the golden mussel to reduce glyphosate concentration in water, in laboratory conditions. Firstly, the evasive response of mussels to glyphosate (10, 20, and 40mgl-1) was evaluated and a toxicity test was carried out for these concentrations. A three-week experiment was then performed to assess glyphosate variation under mussel presence for two mussel sizes. Finally, mussels' role on glyphosate concentration was evaluated considering different mussel parts (living organisms and empty shells) through another three-week experiment. Laboratory experiments were performed in triplicate using 2-l microcosms. An initial glyphosate concentration between 16 and 19mgl-1 was used, and when mussels or valvae were added, 20 organisms per aquaria were used. Samples were obtained at days 0, 1, 2, 4, 8, 14, and 21. Glyphosate decreased by 40% under large mussel presence in both experiments, and was reduced by 25% in empty shell treatments. We believe that part of the herbicide that disappears from the water column is adsorbed in valvae surface, while another proportion is being mineralized by microbial communities in shells' biofilm. The mechanisms by which living mussels increase glyphosate dissipation would be degradation, possibly mediated by bacteria associated to mussel's metabolism. Glyphosate half-life depended on mussel and valvae presence and varied with mussel size. L. fortunei presence (either alive or as empty valvae) alters glyphosate concentration in water. We provide preliminary observations from laboratory experiments, with strong potential ecological consequences, about two stressors that could be acting jointly on the environment. Fil: Di Fiori, Eugenia. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Pizarro, Haydee Norma. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Dos Santos Afonso, María. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Inorgánica, Analítica y Química Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Cataldo, Daniel Hugo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina

The spatial scale of disturbance is a factor potentially influencing the relationship between disturbance and diversity. There has been discussion on whether disturbances that affect local communities and create a mosaic of patches in different successional stages have the same effect on diversity as regional disturbances that affect the whole landscape. In a microcosm experiment with metacommunities of aquatic protists, we compared the effect of local and regional disturbances on the disturbance–diversity relationship. Local disturbances destroyed entire local communities of the metacommunity and required reimmigration from neighboring communities, while regional disturbances affected the whole metacommunity but left part of each local community intact. Both disturbance types led to a negative relationship between disturbance intensity and Shannon diversity. With strong local disturbance, this decrease in diversity was due to species loss, while strong regional disturbance had no effect on species richness but reduced the evenness of the community. Growth rate appeared to be the most important trait for survival after strong local disturbance and dominance after strong regional disturbance. The pattern of the disturbance–diversity relationship was similar for both local and regional diversity. Although local disturbances at least temporally increased beta diversity by creating a mosaic of differently disturbed patches, this high dissimilarity did not result in regional diversity being increased relative to local diversity. The disturbance–diversity relationship was negative for both scales of diversity. The flat competitive hierarchy and absence of a trade-off between competition and colonization ability are a likely explanation for this pattern. Electronic supplementary material The online version of this article (doi:10.1007/s00442-011-2140-8) contains supplementary material, which is available to authorized users.

The climatic-change related increase of temperatures, are expected to alter the distribution and survival of freshwater species, ecosystem functions, and also the effects of toxicants to aquatic biota. This study has thus assessed, as a first time, the modulating effect of climate-change drivers on the mercury (Hg) toxicity of freshwater algal photosynthesis. Natural benthic algal communities (periphyton) have been exposed to Hg under present and future temperature scenarios (rise of 5 °C). The modulating effect of other factors (also altered by global change), as the quality and amount of suspended and dissolved materials in the rivers, has been also assessed, exposing algae to Hg in natural river water or a synthetic medium. The EC50 values ranged from the 0.15–0.74 ppm for the most sensitive communities, to the 24–40 ppm for the most tolerant. The higher tolerance shown by communities exposed to higher Hg concentrations, as Jabarrella was in agreement with the Pollution Induced Community Tolerance concept. In other cases, the dominance of the invasive diatom Didymosphenia geminata explained the tolerance or sensitivity of the community to the Hg toxicity. Results shown that while increases in the suspended solids reduced Hg bioavailability, changes in the dissolved materials – such as organic carbon – may increase it and thus its toxic effects on biota. The impacts of the increase of temperatures on the toxicological behaviour of periphyton (combining both changes at species composition and physiological acclimation) would be certainly modulated by other effects at the land level (i.e., alterations in the amount and quality of dissolved and particulate substances arriving to the rivers)., This work was supported by the Spanish Ministry of Economy and Competitiveness (National Research Plan, ref. BFU2010-22053), by the regional Aragon Government (Consolidated Applied Research Group ref. E61) and by “Comunidad de Trabajo de los Pirineos” Ref. CTPP2/12.

The aim of this study was to investigate selective pressure of antibiotics on antibiotic resistance genes (ARGs) and bacterial communities in manure-polluted aquatic environment. Three treatment groups were set up in freshwater-sediment microcosms: tetracyclines group, sulfonamides group and fluoroquinolones group. Sediment and water samples were collected on day 14 after treatment. Antibiotic concentrations, ARGs abundances and bacterial community composition were analyzed. Antibiotic concentrations were determined by ultra-performance liquid chromatography-electrospray tandem mass spectrometry. ARGs abundances were quantified by real time quantitative PCR. Bacterial community composition was analyzed based on amplicon sequencing. Of the three classes of antibiotics analyzed in the treatment groups, accumulation amounts were tetracyclines> fluoroquinolone> sulfonamides in the sediment samples, while they were sulfonamides> fluoroquinolone> tetracyclines in the water samples. In the treatment groups, the relative abundances of some tet resistance genes (tet(W) and tet(X)) and plasmid-mediated quinolone resistance (PMQR) genes (oqx(B) and aac(6’)-Ib) in sediment samples were significantly higher than those in the paired water samples. Tetracyclines significantly selected the bacterial classes including Gammaproteobacteria, Clostridia, and the genera including Salmonella, Escherichia/Shigella, Clostridium, Stenotrophomonas in sediment samples. The significant selection on bacterial communities posed by sulfonamides and fluoroquinolones was also observed. The results indicated that sediment may supply an ideal setting for maintenance and persistence of tet resistance genes (tet(W) and tet(X)) and PMQR genes (oqx(B) and aac(6’)-Ib) under antibiotic pollution. The results also highlighted that antibiotics significantly selected specific bacterial communities including the taxa associated with opportunistic pathogens.

The vertical mixing between South Atlantic Central Water (SACW) and Coastal Water (CW) was simulated through microcosm experiments using the autochthonous phytoplankton community (fraction < 150 mm), without nutrient enrichments. SACW is cold (T< 18°C) and nutrient rich, while CW is warmer (T> 20°C) and oligotrophic. The phytoplankton growth potential of SACW, CW and an equivalent mixture of both (SACW+CW) was compared, under 100, 30 and 10% of sunlight, at surface seawater temperature, in winter and summer conditions. Results demonstrate the importance of SACW as a natural eutrophication agent for the mixing layer, allowing the occurrence of new production by nutrient input, and also as a biological seeder through the development of its autochthonous phytoplankton community when it reaches the euphotic zone. The time lag for phytoplankton development during winter was around 4-5 days, against 1-2 days in summer. The hypothesis of physiological differences between surface and bottom phytoplankton populations from a deep (80 m) and thermally homogeneous water column (common winter feature) was also tested through the microcosm experiments. Results obtained clearly demonstrate that bottom water presented higher phytoplankton growth potential than the surface one.A mistura vertical entre a Água Central do Atlântico Sul (ACAS) e a Água Costeira (AC) foi simulada através de experimentos tipo microcosmos, com o fitoplâncton autóctone (fração < 150 mm) e sem enriquecimentos nutricionais. A ACAS é fria (T< 18°C) e rica em nutrientes, enquanto a AC é mais quente (T> 20°C) e oligotrófica. O potencial trófico dessas águas e de uma mistura equivalente de ambas (ACAS+AC) foi comparado a 100, 30 e 10% da luz solar, sob temperatura da água do mar na superfície, em condições de inverno e verão. Os resultados demonstram a importância da ACAS como agente fertilizador da camada de mistura tanto por introduzir nutrientes, favorecendo a ocorrência de produção nova, como pelo incremento da biomassa fitoplanctônica autóctone ao atingir a zona eufótica. A fase de adaptação observada no inverno foi de 4-5 dias enquanto no verão foi de 1-2 dias. A hipótese da existência de diferenças fisiológicas entre as populações fitoplanctônicas de superfície e fundo em uma coluna de água profunda (80 m) e termicamente homogênea (padrão comum de inverno) foi também testada utilizando microcosmos. Os resultados mostraram que potencial de crescimento fitoplanctônico nas águas de fundo foi significativamente maior que nas de superfície.

Environmental science and pollution research 22(2), 1160-1174 (2015). doi:10.1007/s11356-014-3398-2, Published by Springer, Berlin

In the present study, the authors evaluated the vulnerability of aquatic invertebrates to insecticides based on their intrinsic sensitivity and their population-level recovery potential. The relative sensitivity of invertebrates to 5 different classes of insecticides was calculated at the genus, family, and order levels using the acute toxicity data available in the US Environmental Protection Agency ECOTOX database. Biological trait information was linked to the calculated relative sensitivity to evaluate correlations between traits and sensitivity and to calculate a vulnerability index, which combines intrinsic sensitivity and traits describing the recovery potential of populations partially exposed to insecticides (e.g., voltinism, flying strength, occurrence in drift). The analysis shows that the relative sensitivity of arthropods depends on the insecticide mode of action. Traits such as degree of sclerotization, size, and respiration type showed good correlation to sensitivity and can be used to make predictions for invertebrate taxa without a priori sensitivity knowledge. The vulnerability analysis revealed that some of the Ephemeroptera, Plecoptera, and Trichoptera taxa were vulnerable to all insecticide classes and indicated that particular gastropod and bivalve species were potentially vulnerable. Microcrustaceans (e.g., daphnids, copepods) showed low potential vulnerability, particularly in lentic ecosystems. The methods described in the present study can be used for the selection of focal species to be included as part of ecological scenarios and higher tier risk assessments.

In order to understand (re-)colonization of microhabitats and bacterial succession in soil, it is important to understand which members of soil bacterial communities are most motile in the porous soil matrix. To address this issue, we carried out a series of experiments in sterilized soil microcosms. Using two different model strains, Pseudomonas fluorescens strain Pf0–1 and Collimonas fungivorans strain Ter331, we first determined the influence of nutrient availability on bacterial expansion rates. Based on these results, we then conducted similar microcosm experiments to examine microbial mobility within natural soil bacterial communities under a single nutrient regime. The expansion of bacterial populations within the community was assayed by quantitative PCR and pyrosequencing of 16S rRNA gene fragments. We observed that only a relatively small subset of the total community was able to expand to an appreciable distance (more than 2 cm) within 48 hours, with the genera Undibacterium, Pseudomonas, and Massilia and especially the family Enterobacteriaceae dominating the communities more distant from the point of inoculation. These results suggest that (re-)colonization of open habitats in soil may be dominated by a few rapidly moving species, which may have important consequences for microbial succession.

cited By 4; International audience; Sediments from Bizerta lagoon were used in an experimental microcosm setup involving three scenarios for the bioremediation of anthracene-polluted sediments, namely bioaugmentation, biostimulation, and a combination of both bioaugmentation and biostimulation. In order to investigate the effect of the biotreatments on the benthic biosphere, 16S rRNA gene-based T-RFLP bacterial community structure and the abundance and diversity of the meiofauna were determined throughout the experiment period. Addition of fresh anthracene drastically reduced the benthic bacterial and meiofaunal abundances. The treatment combining biostimulation and bioaugmentation was most efficient in eliminating anthracene, resulting in a less toxic sedimentary environment, which restored meiofaunal abundance and diversity. Furthermore, canonical correspondence analysis showed that the biostimulation treatment promoted a bacterial community favorable to the development of nematodes while the treatment combining biostimulation and bioaugmentation resulted in a bacterial community that advantaged the development of the other meiofauna taxa (copepods, oligochaetes, polychaetes, and other) restoring thus the meiofaunal structure. The results highlight the importance to take into account the bacteria/meiofauna interactions during the implementation of bioremediation treatment.

The present work aims at evaluating the ability of the River Tiber natural microbial community to degrade naproxen in water samples collected downstream from a wastewater treatment plant. For this purpose, different water microcosms were set up (microbiologically active vs sterile ones) and treated with naproxen (100 μg/L) alone or in the co-presence of gemfibrozil in order to evaluate if the co-presence of the latter had an influence on naproxen degradation. The experiment was performed in the autumn and was compared with the same experimental set performed in spring of the same year to highlight if seasonal differences in the river water influenced the naproxen degradation. Pharmaceutical concentrations and microbial analysis (total cell number, viability, and microbial community composition) were performed at different times in the degradation experiments. The overall results show that the natural microbial community in the river water had a key role in the naproxen degradation. In fact, although there was a transient negative effect on the natural microbial community in all the experiments (3 h after adding the pharmaceutical), the latter was able to degrade naproxen within about 40 days. On the contrary, no decrease in the pharmaceutical concentration was observed in the sterile river water. Moreover, the co-presence of the two drugs lengthened the naproxen lag phase. As regards the natural microbial community composition detected by Fluorescence in situ Hybridization, Alpha and Gamma-Proteobacteria increased when the pharmaceutical halved, suggesting their role in the degradation. This study shows that with the concentration studied, naproxen was degraded by the natural microbial populations collected from a river chronically contaminated by this pharmaceutical.

Background We investigated the hatchability rates of freshly laid Anopheles gambiae s.s. eggs in presence of third instars larvae. These experiments were conducted using 30 eggs in larval densities of 20, 60 and 100 larvae in microcosms. These experiments were designed to evaluate the eggs hatchability in habitats with late larvae instars of the same species (experimental) or no larvae at all (control). Freshly laid eggs of An.gambiae s.s. were washed in microcosms containing larvae of third instars in different three densities (20, 60 and 100) and likewise in control microcosms (without larvae). Eggs hatchability was monitored twice daily until no more first instar larvae emerged. The numbers of first instars larvae were recorded daily and lost eggs were considered preyed upon by third instars. Findings The findings of this study showed that egg hatchability was significantly influenced by larval density. Conclusion The findings of this study suggest that presence of larvae in habitats may significantly reduce hatchability of eggs.

This is the author’s version of a work that was accepted for publication in Science of the Total Environment. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in [SCIENCE OF THE TOTAL ENVIRONMENT 470-471 (2014)] http://dx.doi.org/10.1016/j.scitotenv.2013.09.101, This research reports the risk assessment of an abandoned pyrite mine using direct toxicity assays of soil and groundwater samples taken at the site. The toxicity of As and heavy metals from mining soils to soil and aquatic organisms was studied using the Multispecies Soil System (MS-3) in soil columns. Ecotoxicological assessment was performed with soil samples diluted with a control soil at concentrations of 12.5, 25, 50 and 100% test soil/ soil (w/w). In this way, changes in the mobility and bioavailability of soil contaminants due to changes in geochemical soil properties via soil dilution were studied. The toxicity of water samples was tested on algae and Daphnia magna. The assessment of the mining area indicated that the current presence of As and heavy metals at the site may cause injuries to soil and aquatic organisms in the entire research area. Moreover, this investigation demonstrated that changes in geochemical conditions can increase the availability of arsenic and, consequently, the environmental risk of these soils. A good correlation was not found between toxicity parameters and the concentrations of soil contaminants based on total and extracted element concentrations. This finding reinforces the usefulness of direct toxicity assays for evaluating environmental risk, This work has been financed by the Community of Madrid through EIADES Project S-2009/AMB/1478 and by the Spanish Ministry of Education and Science, project CTM-2007-66401-CO2/ TECNO and CTM2010-21922-C02-02

“Bottle effects” are one of the most deeply rooted concerns of phytoplankton microcosm studies and are mainly related to incubation time and sample volume. Sample pre-filtration to remove larger grazers is also a common procedure in experimental phytoplankton ecology studies, particularly in nutrient enrichment experiments. However, the effects of bottle volume and sample pre-filtration on the outcomes of such experiments, particularly on the net growth rates of specific phytoplankton taxa, have never been addressed. Therefore, this study aims to evaluate the effects of different bottle volumes and sample pre-filtration on phytoplankton net growth rates in microcosm experiments. To accomplish this goal, unfiltered and filtered (

cited By 14; International audience; Biological interactions between metazoans and the microbial community play a major role in structuring food webs in aquatic sediments. Pollutants can also strongly affect the structure of meiofauna and microbial communities. This study aims investigating, in a non-contaminated sediment, the impact of meiofauna on bacteria facing contamination by a mixture of three PAHs (fluoranthene, phenanthrene and pyrene). Sediment microcosms were incubated in the presence or absence of meiofauna during 30. days. Bioremediation treatments, nutrient amendment and addition of a hydrocarbon-degrading bacterium, were also tested to enhance PAH biodegradation. Results clearly show the important role of meiofauna as structuring factor for bacterial communities with significant changes observed in the molecular fingerprints. However, these structural changes were not concomitant with changes in biomass or function. PAH contamination had a severe impact on total meiofaunal abundance with a strong decrease of nematodes and the complete disappearance of polychaetes and copepods. In contrast, correspondence analysis, based on T-RFLP fingerprints, showed that contamination by PAH resulted in small shifts in microbial composition, with or without meiofauna, suggesting a relative tolerance of bacteria to the PAH cocktail. The PAH bioremediation treatments were highly efficient with more than 95% biodegradation. No significant difference was observed in presence or absence of meiofauna. Nutrient addition strongly enhanced bacterial and meiofaunal abundances as compared to control and contaminated microcosms, as well as inducing important changes in the bacterial community structure. Nutrients thus were the main structural factor in shaping bacterial community composition, while the role of meiofauna was less evident.

This study is the first investigation of biodegradation of carbon disulphide (CS2) in soil that provides estimates of degradation rates and identifies intermediate degradation products and carbon isotope signatures of degradation. Microcosm studies were undertaken under anaerobic conditions using soil and groundwater recovered from CS2-contaminated sites. Proposed degradation mechanisms were validated using equilibrium speciation modelling of concentrations and carbon isotope ratios. A first-order degradation rate constant of 1.25 × 10-2 h-1 was obtained for biological degradation with soil. Carbonyl sulphide (COS) and hydrogen sulphide (H2S) were found to be intermediates of degradation, but did not accumulate in vials. A 13C/12C enrichment factor of -7.5 ± 0.8 ‰ was obtained for degradation within microcosms with both soil and groundwater whereas a 13C/12C enrichment factor of -23.0 ± 2.1 ‰ was obtained for degradation with site groundwater alone. It can be concluded that biological degradation of both CS2-contaminated soil and groundwater is likely to occur in the field suggesting that natural attenuation may be an appropriate remedial tool at some sites. The presence of biodegradation by-products including COS and H2S indicates that biodegradation of CS2 is occurring and stable carbon isotopes are a promising tool to quantify CS2 degradation.

International audience; Purpose: The main goals of this study were to investigate (1) the behavior of microbial communities in response to low-dose bioavailable anthracene addition in lightly contaminated sediment from Bizerte Lagoon and (2) the effects of bioremediation treatments on microbial biomass, activity, and community structure. Methods: Sediment microcosms amended with 1 ppm anthracene were incubated in triplicate during 30 days. Biostimulation (addition of nitrogen and phosphorus fertilizer) and bioaugmentation (inoculation of a hydrocarbonoclastic bacterium) were used as bioremediation treatments. Bacterial biomass was estimated using flow cytometry. Sediment oxygen consumption was measured with oxygen microelectrodes. Bacterial community structure was assessed by molecular fingerprints (terminal restriction fragment length polymorphism; T-RFLP) analysis. Results: Anthracene contamination resulted in a significant reduction of bacterial abundance with an impact on cell integrity. Concomitantly, sediment oxygen consumption was strongly inhibited. Correspondence analysis on T-RFLP data indicated that bacterial community structures from anthracene-contaminated microcosms were different from that of the control. Interestingly, the changes observed in microbial biomass, structure, and activities as a result of anthracene contamination were not alleviated even with the use of biostimulation and combination of biostimulation and bioaugmentation strategy for anthracene bioremediation. Nevertheless, both treatment methods resulted in different community structures relative to the contaminated and control microcosms with the appearance of distinct populations. Conclusion: Anthracene spiking severely affected microbial communities, suggesting dominance of nontolerant populations in this lightly-contaminated sediment. Although biostimulation and/or bioaugmentation treatments did not alleviate the anthracene toxic effects, the changes observed in microbial population and structure suggest that the proposed treatments might be promising to promote bacterial growth. Further works are still required to propose a more efficient strategy to stimulate biodegradation that takes into account the complex interactions between species for resource access. © 2012 Springer-Verlag.

13 pages, 4 figures, 2 tables, The effects of inorganic and/or organic (glucose+AAs) inputs on phytoplankton and heterotrophic bacteria were assessed, using a microcosm approach, in two contrasting marine environments: an open ocean oligotrophic site (North Atlantic Subtropical Gyre) and a highly productive coastal embayment (Ría de Vigo, NW Spain). Overall, changes in microbial plankton biomass were smaller than those of metabolic rates. The largest increases in primary production, bacterial production and community respiration were measured in response to mixed () nutrient additions in both sites. Primary production responded to additions only in oligotrophic waters. The distinct autotrophic responses to nutrient additions measured in these environments were related to the different initial composition of phytoplankton populations and, presumably, also to differences in grazing pressures in both marine ecosystems. Heterotrophic bacteria were limited by organic substrates in both ecosystems, although mixed additions further enhanced bacterial growth in the subtropical gyre. The differences detected in bacterial responses to nutrient additions may be related to differences in nutrient limitations and to the prevalence of different relationships between components of the microbial food web (e.g. coupling between heterotrophic bacteria and phytoplankton and predation pressure) in both environments. We found a more relevant role of inorganic nutrients in controlling the efficiency of bacterial growth in oligotrophic regions as compared with highly productive systems. Our results suggest that organic matter inputs into both ecosystems might result in a tendency towards heterotrophy and in increases in bacterial growth efficiency. © 2013 Copyright Taylor and Francis Group, LLC., This research was supported by the Xunta de Galicia AddEx contract (PGIDIT06PXIB312222PR). S.M-G. was funded by a F. P. U. MEC fellowship. E.T. was funded by a Juan de la Cierva and a Ramo´n y Cajal-MEC contract

Water availability is the main limiting factor in arid soils; however, few studies have examined the effects of drying and rewetting on nitrifiers from these environments. The effect of water availability on the diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) from a semiarid soil of the Chilean sclerophyllous matorral was determined by microcosm assays. The addition of water every 14 days to reach 60% of the WHC significantly increased nitrate content in rewetted soil microcosms (p < 0.001). This stimulation of net nitrification by water addition was inhibited by acetylene addition at 100 Pa. The composition of AOA and AOB assemblages from the soils microcosms was determined by clone sequencing of amoA genes (A-amoA and B-amoA, respectively), and the 16S rRNA genes specific for β-proteobacteria (beta-amo). Sequencing of beta-amo genes has revealed representatives of Nitrosomonas and Nitrosospira while B-amoA clones consisted only of Nitrosospira sequences. Furthermore, all clones from the archaeal amoA gene library (A-amoA) were related to “mesophilic Crenarchaeota” sequences (actually, reclassified as the phylum Thaumarchaeota). The effect of water availability on both microbial assemblages structure was determined by T-RFLP profiles using the genetic markers amoA for archaea, and beta-amo for bacteria. While AOA showed fluctuations in some T-RFs, AOB structure remained unchanged by water pulses. The relative abundance of AOA and AOB was estimated by the Most Probable Number coupled to Polymerase Chain Reaction (MPN-PCR) assay. AOB was the predominant guild in this soil and higher soil water content did not affect their abundance, in contrast to AOA, which slightly increased under these conditions. Therefore, these results suggest that water addition to these semiarid soil microcosms could favor archaeal contribution to ammonium oxidation.

The distribution of neutrophilic microbial iron oxidation is mainly determined by local gradients of oxygen, light, nitrate and ferrous iron. In the anoxic top part of littoral freshwater lake sediment, nitrate-reducing and phototrophic Fe(II)-oxidizers compete for the same e(-) donor; reduced iron. It is not yet understood how these microbes co-exist in the sediment and what role they play in the Fe cycle. We show that both metabolic types of anaerobic Fe(II)-oxidizing microorganisms are present in the same sediment layer directly beneath the oxic-anoxic sediment interface. The photoferrotrophic most probable number counted 3.4·10(5) cells·g(-1) and the autotrophic and mixotrophic nitrate-reducing Fe(II)-oxidizers totaled 1.8·10(4) and 4.5·10(4) cells·g(-1) dry weight sediment, respectively. To distinguish between the two microbial Fe(II) oxidation processes and assess their individual contribution to the sedimentary Fe cycle, littoral lake sediment was incubated in microcosm experiments. Nitrate-reducing Fe(II)-oxidizing bacteria exhibited a higher maximum Fe(II) oxidation rate per cell, in both pure cultures and microcosms, than photoferrotrophs. In microcosms, photoferrotrophs instantly started oxidizing Fe(II), whilst nitrate-reducing Fe(II)-oxidizers showed a significant lag-phase during which they probably use organics as e(-) donor before initiating Fe(II) oxidation. This suggests that they will be outcompeted by phototrophic Fe(II)-oxidizers during optimal light conditions; as phototrophs deplete Fe(II) before nitrate-reducing Fe(II)-oxidizers start Fe(II) oxidation. Thus, the co-existence of the two anaerobic Fe(II)-oxidizers may be possible due to a niche space separation in time by the day-night cycle, where nitrate-reducing Fe(II)-oxidizers oxidize Fe(II) during darkness and phototrophs play a dominant role in Fe(II) oxidation during daylight. Furthermore, metabolic flexibility of Fe(II)-oxidizing microbes may play a paramount role in the conservation of the sedimentary Fe cycle.

An environmentally friendly procedure suitable to restore a protected area was evaluated at laboratory scale. Soil contaminated by high molecular weight (C > 10) aliphatic hydrocarbons and by chromium was withdrawn from the study site and a qualitative study of soil hydrocarbon components was first performed in order to assess the potential source of contamination. To this aim, a number of characteristic diagnostic ratios of hydrocarbon components were derived by processing chromatographic data, and were used as indicators for distinguishing anthropogenic from natural hydrocarbons. Then, the efficiency of landfarming for soil remediation was tested by comparing the effect of a few selected amendments and by monitoring the fate of chromium. Soil microbial abundance and activity were also evaluated. Results showed that soil hydrocarbons were mainly of anthropogenic origin and land treatment allowed effective degradation by native microbial populations even in the absence of amendments. The investigated procedures had no effect on the mobilisation of chromium that remained in its stable form of Cr(III). Conventional land treatment may therefore be an effective and safe procedure for the removal of hydrocarbons even in the presence of chromium, and may be applied to areas where low-impact procedures are strictly required.