Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats

Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs) contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel). Our approach provided a robust ecological framework for the partition of the taxa abundance distribution into 859 core Operational taxonomic units (OTUs) and 6629 satellite OTUs. OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC) and PAH concentrations as main drivers of community assembly. The core communities were dominated by Gammaproteobacteria and Deltaproteobacteria for Bacteria, by Thaumarchaeota, Bathyarchaeota and Thermoplasmata for Archaea and Metazoa and Dinoflagellata for Eukarya. In order to find associations among microorganisms, we generated a co-occurrence network in which PAHs were found to impact significantly the potential predator – prey relationship in one microbial consortium composed of ciliates and Actinobacteria. Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the network structure and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.

INTERACTIVE EFFECTS OF CLIMATE CHANGE AND FUNGAL COMMUNITIES ON THE DECOMPOSITION OF WOOD-DERIVED CARBON IN FOREST SOILS

Soils are the largest sinks of carbon in terrestrial ecosystems. Soil organic carbon is important for ecosystem balance as it supplies plants with nutrients, maintains soil structure, and helps control the exchange of CO2 with the atmosphere. The processes in which wood carbon is stabilized and destabilized in forest soils is still not understood completely. This study attempts to measure early wood decomposition by different fungal communities (inoculation with pure colonies of brown or white rot, or the original microbial community) under various interacting treatments: wood quality (wood from +CO2, +CO2+O3, or ambient atmosphere Aspen-FACE treatments from Rhinelander, WI), temperature (ambient or warmed), soil texture (loamy or sandy textured soil), and wood location (plot surface or buried 15cm below surface). Control plots with no wood chips added were also monitored throughout the study. By using isotopically-labelled wood chips from the Aspen-FACE experiment, we are able to track wood-derived carbon losses as soil CO2 efflux and as leached dissolved organic carbon (DOC). We analyzed soil water for chemical characteristics such as, total phenolics, SUVA254, humification, and molecular size. Wood chip samples were also analyzed for their proportion of lignin:carbohydrates using FTIR analysis at three time intervals throughout 12 months of decomposition. After two years of measurements, the average total soil CO2 efflux rates were significantly different depending on wood location, temperature, and wood quality. The wood-derived portion soil CO2 efflux also varied significantly by wood location, temperature, and wood quality. The average total DOC and the wood-derived portion of DOC differed between inoculation treatments, wood location, and temperature. Soil water chemical characteristics varied significantly by inoculation treatments, temperature, and wood quality. After 12 months of decomposition the proportion of lignin:carbohydrates varied significantly by inoculation treatment, with white rot having the only average proportional decrease in lignin:carbohydrates. Both soil CO2 efflux and DOC losses indicate that wood location is important. Carbon losses were greater from surface wood chips compared with buried wood chips, implying the importance of buried wood for total ecosystem carbon stabilization. Treatments associated with climate change also had an effect on the level of decomposition. DOC losses, soil water characteristics, and FTIR data demonstrate the importance of fungal community on the degree of decomposition and the resulting byproducts found throughout the soil.

Irrigation with Treated Wastewater: Potential Impacts on Microbial Function and Diversity in Agricultural Soils

The reuse of treated wastewater could be a promising measure to attenuate the water scarcity burden. In agriculture, irrigation with wastewater may contribute to improve production yields, reduce the ecological footprint and promote socioeconomic benefits. However, it cannot be considered exempt of adverse consequences in environmental and human health. Apart from the introduction of some biological and chemical hazardous agents, the disturbance of the indigenous soil microbial communities and, thus, of vital soil functions impacting soil fertility may occur. The consequences of these disturbances are still poorly understood. This chapter summarises the physicochemical and microbiological alterations in soil resultant from irrigation with treated wastewater that are described in scientific literature. These alterations, which involve a high complexity of variables (soil, wastewater, climate, vegetal cover), may have impacts on soil quality and productivity. In addition, possible health risks may arise, in particular through the direct or indirect contamination of the food chain with micropollutants, pathogens or antibiotic resistance determinants. The current state of the art suggests that irrigation with treated wastewater may have a multitude of long-term implications on soil productivity and public health. Although further research is needed, it seems evident that the analysis of risks associated with irrigation with treated wastewater must take into account not only the quality of water, but other aspects as diverse as soil microbiota, soil type or the cultivated plant species.

Mineralisation of the fungicide 14C-labelled metalaxyl fungicide in Brazilian soils.

Laboratory incubation experiments were carried out to estimate the mineralisation of metalaxyl 14C {N-(2-6 dimethyphenyl)-N-(methoxyacetyl) alanine methyl ester} in four Brazilian soils with different physico-chemical properties, at 3 and 30 ?g a.i. g-1. In the Petrolina sandy soil the mineralisation presented higher 14CO2 production rates, at two essayed concentrations, after 70 days. Microbiological studies were done to determine the numbers of bacteria, actinobacteria and fungi (CFU g-1 soil). In relation with other microbial community, bacterial population demonstrated to be a major component of the cultivable heterotrophic community after the application.of the compound. No detectable metabolites were found in this study. The results suggest that soil properties and application history may have a strong influence on the fungicide behavior in these soil samples.

Impact of anthropogenic stressors on the microbial communities in marine holobionts and ecosystems

Free-living or host-associated marine microbiomes play a determinant role in supporting the functioning and biodiversity of marine ecosystems, providing essential ecological services, and promoting the health of the entire biosphere. Currently, the fast and restless increase of World’s human population strongly impacts life on Earth in the forms of ocean pollution, coastal zone destruction, overexploitation of marine resources, and climate change. Thanks to their phylogenetic, metabolic, and functional diversity, marine microbiomes represent the Earth’s biggest reservoir of solutions against the major threats that are now impacting marine ecosystems, possibly providing valuable insights for biotechnological applications to preserve the health of the ocean ecosystems. Microbial-based mitigation strategies heavily rely on the available knowledge on the specific role and composition of holobionts associated microbial communities, thus highlighting the importance of pioneer studies on microbial-mediated adaptive mechanisms in the marine habitats. In this context, we propose different models representing ecologically important, widely distributed, and habitat-forming organisms, to further investigate the ability of marine holobionts to dynamically adapt to natural environmental variations, as well as to anthropogenic stress factors. In this PhD thesis, we were able to supply the characterization of the microbial community associated with the model anthozoan cnidaria Corynactis viridis throughout a seasonal gradient, to provide critical insights into microbiome-host interactions in a biomonitoring perspective. We also dissected in details the microbial-derived mitigation strategies implemented by the benthonic anthozoan Anemonia viridis and the gastropod Patella caerulea as models of adaptation to anthropogenic stressors, in the context of bioremediation of human-impacted habitats and for the monitoring and preservation of coastal marine ecosystems, respectively. Finally, we provided a functional model of adaptation to future ocean acidification conditions by characterizing the microbial community associated with the temperate coral Balanophyllia europaea naturally living at low pH conditions, to implement microbial based actions to mitigate climate change.

Bioremediation of polychlorinated biphenyls (PCBs) polluted marine sediments: a study of the effectiveness of bioaugmentation and biostimulation via microbial electrochemical technologies and polyhydroxyalkanoates

Polychlorinated biphenyls (PCBs) are chemicals largely employed in the industry, banned at the end of the last century yet still persistent in the environment. Bioremediation, namely exploiting bacteria to reduce PCBs’ toxicity, is receiving attention as a promising approach to remediate polluted site in situ. Natural bioremediation is constrained by several factors as the low amount of the required growth substrates (e.g. electron donors, oxygen) and the scarcity of bacteria able to metabolize PCBs. In this regard, use of biodegradable polymers or applied potentials have been demonstrated effective in priming bioremediation of freshwater environments (e.g. river sediments) polluted by chlorinated solvents or PCBs. Yet, little is known regarding the application in marine sediments, where the abundance of anaerobic competitors (i.e. sulfate reducing bacteria) and the different sediment’s features might affect the bioremediation. In this study, polyhydroxyalkanoates (PHAs) and Microbial Electrochemical Technologies (METs) were applied for the first time to prime bioremediation of PCBs polluted marine sediments. The influence of PHAs was studied on the main anaerobic metabolisms and on the microbial community of the heavily polluted sediments coming from the Pialassa della Baiona, a micro-tidal coastal lagoon in Ravenna, and from Mar Piccolo, the marine basin aside Taranto. The impact of METs was deepened by monitoring the physical-chemical parameters and the main anaerobic metabolisms of the sediments coming from Ravenna. The effectiveness of biostimulating with PHAs depended on the features of the treated site, possibly due to the availability of the amendments and to the competition of the indigenous microbial communities. The bioelectrochemical stimulation inhibited the bioremediation process. In both cases, the presence of an inoculated bacterial community was required to perform bioremediation. The collected results led to a comprehensive analysis of the available literature, questioning what could be the further approaches for an effective in situ bioremediation.

New Fefe-hydrogenase Genes Identified In A Metagenomic Fosmid Library From A Municipal Wastewater Treatment Plant As Revealed By High-throughput Sequencing.

A fosmid metagenomic library was constructed with total community DNA obtained from a municipal wastewater treatment plant (MWWTP), with the aim of identifying new FeFe-hydrogenase genes encoding the enzymes most important for hydrogen metabolism. The dataset generated by pyrosequencing of a fosmid library was mined to identify environmental gene tags (EGTs) assigned to FeFe-hydrogenase. The majority of EGTs representing FeFe-hydrogenase genes were affiliated with the class Clostridia, suggesting that this group is the main hydrogen producer in the MWWTP analyzed. Based on assembled sequences, three FeFe-hydrogenase genes were predicted based on detection of the L2 motif (MPCxxKxxE) in the encoded gene product, confirming true FeFe-hydrogenase sequences. These sequences were used to design specific primers to detect fosmids encoding FeFe-hydrogenase genes predicted from the dataset. Three identified fosmids were completely sequenced. The cloned genomic fragments within these fosmids are closely related to members of the Spirochaetaceae, Bacteroidales and Firmicutes, and their FeFe-hydrogenase sequences are characterized by the structure type M3, which is common to clostridial enzymes. FeFe-hydrogenase sequences found in this study represent hitherto undetected sequences, indicating the high genetic diversity regarding these enzymes in MWWTP. Results suggest that MWWTP have to be considered as reservoirs for new FeFe-hydrogenase genes.

Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove

Mangrove sediments are anaerobic ecosystems rich in organic matter. This environment is optimal for anaerobic microorganisms, such as sulphate-reducing bacteria and methanogenic archaea, which are responsible for nutrient cycling. In this study, the diversity of these two functional guilds was evaluated in a pristine mangrove forest using denaturing gradient gel electrophoresis (DGGE) and clone library sequencing in a 50 cm vertical profile sampled every 5.0 cm. DGGE profiles indicated that both groups presented higher richness in shallow samples (0-30 cm) with a steep decrease in richness beyond that depth. According to redundancy analysis, this alteration significantly correlated with a decrease in the amount of organic matter. Clone library sequencing indicated that depth had a strong effect on the selection of dissimilatory sulphate reductase (dsrB) operational taxonomic units (OTUs), as indicated by the small number of shared OTUs found in shallow (0.0 cm) and deep (40.0 cm) libraries. On the other hand, methyl coenzyme-M reductase (mcrA) libraries indicated that most of the OTUs found in the shallow library were present in the deep library. These results show that these two guilds co-exist in these mangrove sediments and indicate important roles for these organisms in nutrient cycling within this ecosystem.

Performance evaluation and phylogenetic characterization of anaerobic fluidized bed reactors using ground tire and pet as support materials for biohydrogen production

This study evaluated two different support materials (ground tire and polyethylene terephthalate [PET]) for biohydrogen production in an anaerobic fluidized bed reactor (AFBR) treating synthetic wastewater containing glucose (4000 mg L(-1)). The AFBR, which contained either ground tire (R1) or PET (R2) as support materials, were inoculated with thermally pretreated anaerobic sludge and operated at a temperature of 30 degrees C. The AFBR were operated with a range of hydraulic retention times (HRT) between 1 and 8 h. The reactor R1 operating with a HRT of 2 h showed better performance than reactor R2, reaching a maximum hydrogen yield of 2.25 mol H(2) mol(-1) glucose with 1.3 mg of biomass (as the total volatile solids) attached to each gram of ground tire. Subsequent 16S rRNA gene sequencing and phylogenetic analysis of particle samples revealed that reactor R1 favored the presence of hydrogen-producing bacteria such as Clostridium, Bacillus, and Enterobacter. (C) 2010 Elsevier Ltd. All rights reserved.

Hydrogen production from soft-drink wastewater in an upflow anaerobic packed-bed reactor

The production of hydrogen from soft-drink wastewater in two upflow anaerobic packed-bed reactors was evaluated. The results show that soft-drink wastewater is a good source for hydrogen generation. Data from both reactors indicate that the reactor without medium containing macro- and micronutrients (R2) provided a higher hydrogen yield (3.5 mol H(2) mol(-1) of sucrose) as compared to the reactor (R1) with a nutrient-containing medium (3.3 mol H(2) mol(-1) of sucrose). Reactor R2 continuously produced hydrogen, whereas reactor R1 exhibited a short period of production and produced lower amounts of hydrogen. Better hydrogen production rates and percentages of biogas were also observed for reactor R2, which produced 0.4 L h(-1) L(-1) and 15.8% of H(2), compared to reactor R1, which produced 0.2 L h(-1) L(-1) and 2.6% of H(2). The difference in performance between the reactors was likely due to changes in the metabolic pathway for hydrogen production and decreases in bed porosity as a result of excessive biomass growth in reactor R1. Molecular biological analyses of samples from reactors R1 and R2 indicated the presence of several microorganisms, including Clostridium (91% similarity), Enterobacter (93% similarity) and Klebsiella (97% similarity). Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Evaluation of the anaerobic degradation of black liquor from a Kraft pulp plant with addition of organic co-substrates

The purpose of this study was to assess the anaerobic degradation of black liquor with and without additional carbon sources. Batch experiments were conducted using black liquor, from an integrated pulp and paper mill adding ethanol, methanol and nutrients. The PCR/DGGE technique was used to characterize the structure of the microbial community. The addition of extra sources of carbon did not significantly influence the degradation of black liquor under the conditions evaluated and the microbial community was similar in all experiments. It was observed an increase in some members of the archaeal in reactors that had the best efficiencies for removal of black liquor (around 7.5%). Either ethanol or methanol can be used as co-substrates because the produce the same quantitative and qualitative effect.

Effects of bed materials on the performance of an anaerobic sequencing batch biofilm reactor treating domestic sewage

The objective of this study was to determine the best performance of an anaerobic sequencing batch biofilm reactor (AnSBBR) based on the use of four different bed materials as support for biomass immobilization. The bed materials utilized were Polyurethane foam (PU), vegetal carbon (VC), synthetic pumice (SP), and recycled low-density polyethylene (PE). The AnSBBR. with I total volume Of 7.2 L, was operated in 8-h batch cycles over 10 months, and fed with domestic sewage with an average influent chemical oxygen demand (COD) of 358 +/- 110 mg/L. The average effluent COD values were 121 +/- 31, 208 +/- 54, 233 +/- 52, and 227 +/- 51 mg/L. for PU, VC, SP, and PE, respectively. A modified first-order kinetic model was adjusted to temporal profiles of COD during a batch cycle, and the apparent kinetic constants were 0.52 +/- 0.05, 0.37 +/- 0.05, 0.80 +/- 0.04, and 0.30 +/- 0.021h(-1) for PU, VC, SP, and PE, respectively. Specific substrate utilization rates of 1.08, 0.11, and 0.86 mg COD/mg VS day were obtained for PU, VC, and PE, respectively. Although SP yielded the highest kinetic coefficient, PU was considered the best support, since SP presented loss of chemical constituents during the reactor`s operational phase. In addition, findings oil the microbial community were associated with the reactor`s performance data. Although PE did not show a satisfactory performance, an interesting microbial diversity was found oil its surface. Based oil the morphology and denaturing gradient gel electrophoresis (DGGE) results, PE showed the best capacity for promoting the attachment of methanogenic organisms, and is therefore a material that merits further analysis. PU was considered the Most suitable material showing the best performance in terms of efficiency of solids and COD removal. (C) 2007 Elsevier Ltd. All rights reserved.

Long-term stability of hydrogen and organic acids production in an anaerobic fluidized-bed reactor using heat treated anaerobic sludge inoculum

This study evaluates the stability of hydrogen and organic acids production in an anaerobic fluidized-bed reactor (AFBR) that contains expanded clay (2.8-3.35 mm in diameter) as a support medium and is operated on a long-term basis. The reactor was inoculated with thermally pre-treated anaerobic sludge and operated with decreasing hydraulic retention time (HRT), from 8 h to 1 h, at a controlled temperature of 30 degrees C and a pH of about 3.8. Glucose (2000 mg L(-1)) was used as the substrate, generating conversion rates of 92-98%. Decreasing the HRT from 8 h to 1 h led to an increase in average hydrogen-production rates, with a maximum value of 1.28 L h(-1) L(-1) for an HRT of 1 h. In general, hydrogen yield production increased as HRT decreased, reaching 2.29 mol of H(2)/mol glucose at an HRT of 2 h and yielding a maximum hydrogen content of 37% in the biogas. No methane was detected in the biogas throughout the period of operation. The main soluble metabolites (SMP) were acetic acid (46.94-53.84% of SMP) and butyric acid (34.51-42.16% of SMP), with less than 15.49% ethanol. The steady performance of the AFBR may be attributed to adequate thermal treatment of the inoculum, the selection of a suitable support medium for microbial adhesion, and the choice of satisfactory environmental conditions imposed on the system. The results show that stable hydrogen production and organic acids production were maintained in the AFBR over a period of 178 days. (C) 2009 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.

Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere

The role of dominant bacterial groups in the plant rhizosphere, e.g., those belonging to the phyla Acidobacteria and Verrucomicrobia, has, so far, not been elucidated, and this is mainly due to the lack of culturable representatives. This study aimed to isolate hitherto-uncultured bacteria from the potato rhizosphere by a combination of cultivation approaches. An agar medium low in carbon availability (oligotrophic agar medium) and either amended with potato root exudates or catalase or left unamended was used with the aim to improve the culturability of bacteria from the potato rhizosphere. The colony forming unit numbers based on colonies and microcolonies were compared with microscopically determined fluorescence-stained cell numbers. Taxonomical diversity of the colonies was compared with that of library clones made from rhizosphere DNA, on the basis of 16S rRNA gene comparisons. The oligotrophic media amended or not with catalase or rhizosphere extract recovered up to 33.6% of the total bacterial numbers, at least seven times more than the recovery observed on R2A. Four hitherto-uncultured Verrucomicrobia subdivision 1 representatives were recovered on agar, but representatives of this group were not found in the clone library. The use of oligotrophic medium and its modifications enabled the growth of colony numbers, exceeding those on classical agar media. Also, it led to the isolation of hitherto-uncultured bacteria from the potato rhizosphere. Further improvement in cultivation will certainly result in the recovery of other as-yet-unexplored bacteria from the rhizosphere, making these groups accessible for further investigation, e.g., with respect to their possible interactions with plants.

Particle size and concentration of poly(epsilon-caprolactone) and adipate modified starch blend on mineralization in soils with differing textures

The objective of this study was to evaluate the effect of particle size and concentration of poly(F.-caprolactone) and adipate modified starch blend on mineralization in soils with differing textures, comparing it with polyethylene under the same experimental conditions. Two soil types were used: a Kandiudalfic Eutrudox with a clayey texture and an Arenic Hapludult with a sandy texture. The two different plastic specimens were incorporated in the form of plastic films with three increasing particle sizes and six doses, from 0 to 2.5 mg C g(-1) soil. Each plastic dose was incorporated into 200 g of soil placed in a hermetically closed jar at 28 degrees C, and incubated for a 120-day period to determine CO(2) evolution. Once again it was confirmed that polyethylene is almost non-biodegradable, in contrast to PCL/S, which can be defined as a biodegradable material. Soil texture affected the mineralization kinetics of the plastic specimens, with higher values for the clayey soil. No changes in soil microbial biomass-C or -N were observed by adding polyethylene and PCL/S to the soil. Also, no significant differences were observed on seed emergence and development of rice seedlings (Oryza sativa L.) in plastic modified soil. (C) 2009 Elsevier Ltd. All rights reserved.