Changes in the microbial community based on seawater pH variations

Ocean acidification is an effect of the rise in atmospheric CO2, which causes a reduction in the pH of the ocean and generates a number of changes in seawater chemistry and consequently potentially impacts seawater life. The effect of ocean acidification on metabolic processes (such as net community production and community respiration and on particulate organic carbon (POC) concentrations was investigated in summer 2012 at Cap de la Revellata in Corsica (Calvi, France). Coastal surface water was enclosed in 9 mesocosms and subjected to 6 pCO2 levels (3 replicated controls and 6 perturbations) for approximately one month. No trend was found in response to increasing pCO2 in any of the biological and particulate analyses. Community respiration was relatively stable throughout the experiment in all mesocosms, and net community production was most of the time close to zero. Similarly, POC concentrations were not affected by acidification during the whole experimental period. Such as the global ocean, the Mediterranean Sea has an oligotrophic nature. Based on present results, it seems likely that seawater acidification will not have significant effects on photosynthetic rates, microbial metabolism and carbon transport.

Preliminary identification of dehalogenation specificities exhibited by dehalorespiring bacteria from a marine microbial community

The ability of a previously PCB-enriched microbial culture from Venice Lagoon marine sediments to dechlorinate pentachlorophenol (PCP) and 2,3,5-trichlorophenol (2,3,5-TCP) was confirmed under anaerobic conditions in microcosms consisting of site water and sediment. Dechlorination activities against Aroclor 1254 PCB mixture were also confirmed as control. Pentachlorophenol was degraded to 2,4,6-TCP (75.92±0.85 mol%), 3,5-DCP (6.40±0.75 mol%), and phenol (15.40±0.87 mol%). From the distribution of the different dechlorination products accumulated in the PCP-spiked cultures over time, two dechlorination pathways for PCP were proposed: (i) PCP to 2,3,4,6-TeCP, then to 2,4,6-TCP through the removal of both meta double-flanked chlorine substituents (main pathway); (ii) alternately, PCP to 2,3,5,6-TeCP, 2,3,5-TCP, 3,5-DCP, then phenol, through the removal of the para double-flanked chlorine, followed by ortho single-flanked chlorines, and finally meta unflanked chlorines (minor pathway). Removal of meta double-flanked chlorines is thus preferred over all other substituents. 2,3,5-TCP, that completely lacks double-flanked chlorines, was degraded to 3,5-DCP through removal of the ortho single-flanked chlorine, with a 99.6% reduction in initial concentration of 2,3,5-TCP by week 14. 16S rRNA PCR-DGGE using Chloroflexi-specific primers revealed a different role of the two microorganisms VLD-1 and VLD-2, previously identified as dechlorinators in the Aroclor 1254 PCB-enriched community, in the dehalogenation of chlorophenols. VLD-1 was observed both in PCP- and TCP-dechlorinating communities, whereas VLD-2 only in TCP-dechlorinating communities. This indicates that VLD-1 and VLD-2 may both dechlorinate ortho single-flanked chlorines, but only VLD-1 is able to remove double-flanked meta or para chlorines.

Diversity of microbial communities at shallow-hydrothermal vents off Dominica, Lesser Antilles

Hydrothermal vents are often compared to desert oases, because of the presence of highly diverse and abundant biotic communities inhabiting these extreme environments. Nevertheless, the microbial communities associated with shallow-hydrothermal systems have been poorly studied. Hydrothermal activity at Dominica Island is quite well known under the geological and geochemical aspects, but no previous information existed about the microbial communities associated to this area. This thesis is therefore targeting the microbiology of hydrothermal sediments combining geochemical and molecular biological investigations, focusing on differences between hydrothermal vents and background (i.e. control) areas, and between hydrothermal sites. It was also intended to assess relationship between geochemical parameters and microbial diversity at the two hydrothermally impacted sites. Two shallow-sea hydrothermal vents located south-west off Dominica Island (Lesser Antilles) have been investigated in this study: Champagne Hot Springs and Soufriere Bay offshore vent. During this study, sediments for geochemical and molecular analyses were collected every 2 cm from the two impacted areas and from two control sites not associated with hydrothermal activity; in situ temperatures measurements were also taken every 5 cm deep in the sediment for all the sites. A geochemical characterization of the sediment porewater was performed through the analysis of several elements’ concentrations (i.e. H2S, Cl-, Br-, SO42-, Fe2+, Na+, K+, B+, Si+). Microbial communities at the different sites were studied by Automated Intergenic Spacer Analysis (ARISA). Inspection of the operational taxonomic units (OTUs) distribution was performed, as well as statistical analyses for communities’ structure and composition differences, and for changes of β-diversity along with sediment geochemistry. Data suggested that mixing between hydrothermal fluids and seawater results in distinct different environmental gradients and potential ecological niches between the two investigated hydrothermal vents, reflecting a difference in microbial community structures between them.

Prokaryotic community structure in ultra-slow spreading Southwest Indian Ridge.

The Southwest Indian Ridge segment that extends between 10° and 16° E has the slowest spreading rate of any other oceanic ridge (about 8.4 mm/year). In 2013 during the expedition ANTXXIX/8 seismology, geology, microbiology, heat flow analyses were carried out. Here, no hydrothermal plumes or black smoker systems were found but the results of the survey allowed to identify areas with peculiar characteristics: Area 1 with higher heat flux bsf; Area 2 where in 2002 the presence of hydrothermal emissions was hypothesized (Bach et al., 2002); Area 3 with anomalies of methane, ammonium, sulphide and dissolved inorganic carbon in pore water sediment profiles, and recovery of fauna vents. All these aspects suggest the presence of a hydrothermal circulation. Using Illumina 16S gene tag, statistical tools and phylogenetic trees, I provided a biological proof of the presence of hydrothermal circulation in this ridge segment. At Area 3, alpha and beta diversity indexes showed similarities with those described for venting microbial communities and about 40-70% of the dominant microbial community was found phylogenetically related to clones isolated hydrothermal-driven environments. Although the majority of chemosynthetic environment related taxa were not classified like autotrophic prokaryotes, some of them are key taxa in support of the presence of hydrothermal circulation, since they are partners of consortia or mediate specific reaction typically described for hydrothermal and seep environments, or are specialized organisms in exploiting labile organic substrates. Concluding, these results are remarkable because support the importance of ultra slow spreading ridge systems in contributing to global geochemical cycles and larval dispersion of vent fauna.

Bioremediation of PAHs - Limitations and soultions

Introduction 1.1 Occurrence of polycyclic aromatic hydrocarbons (PAH) in the environment Worldwide industrial and agricultural developments have released a large number of natural and synthetic hazardous compounds into the environment due to careless waste disposal, illegal waste dumping and accidental spills. As a result, there are numerous sites in the world that require cleanup of soils and groundwater. Polycyclic aromatic hydrocarbons (PAHs) are one of the major groups of these contaminants (Da Silva et al., 2003). PAHs constitute a diverse class of organic compounds consisting of two or more aromatic rings with various structural configurations (Prabhu and Phale, 2003). Being a derivative of benzene, PAHs are thermodynamically stable. In addition, these chemicals tend to adhere to particle surfaces, such as soils, because of their low water solubility and strong hydrophobicity, and this results in greater persistence under natural conditions. This persistence coupled with their potential carcinogenicity makes PAHs problematic environmental contaminants (Cerniglia, 1992; Sutherland, 1992). PAHs are widely found in high concentrations at many industrial sites, particularly those associated with petroleum, gas production and wood preserving industries (Wilson and Jones, 1993). 1.2 Remediation technologies Conventional techniques used for the remediation of soil polluted with organic contaminants include excavation of the contaminated soil and disposal to a landfill or capping - containment - of the contaminated areas of a site. These methods have some drawbacks. The first method simply moves the contamination elsewhere and may create significant risks in the excavation, handling and transport of hazardous material. Additionally, it is very difficult and increasingly expensive to find new landfill sites for the final disposal of the material. The cap and containment method is only an interim solution since the contamination remains on site, requiring monitoring and maintenance of the isolation barriers long into the future, with all the associated costs and potential liability. A better approach than these traditional methods is to completely destroy the pollutants, if possible, or transform them into harmless substances. Some technologies that have been used are high-temperature incineration and various types of chemical decomposition (for example, base-catalyzed dechlorination, UV oxidation). However, these methods have significant disadvantages, principally their technological complexity, high cost , and the lack of public acceptance. Bioremediation, on the contrast, is a promising option for the complete removal and destruction of contaminants. 1.3 Bioremediation of PAH contaminated soil & groundwater Bioremediation is the use of living organisms, primarily microorganisms, to degrade or detoxify hazardous wastes into harmless substances such as carbon dioxide, water and cell biomass Most PAHs are biodegradable unter natural conditions (Da Silva et al., 2003; Meysami and Baheri, 2003) and bioremediation for cleanup of PAH wastes has been extensively studied at both laboratory and commercial levels- It has been implemented at a number of contaminated sites, including the cleanup of the Exxon Valdez oil spill in Prince William Sound, Alaska in 1989, the Mega Borg spill off the Texas coast in 1990 and the Burgan Oil Field, Kuwait in 1994 (Purwaningsih, 2002). Different strategies for PAH bioremediation, such as in situ , ex situ or on site bioremediation were developed in recent years. In situ bioremediation is a technique that is applied to soil and groundwater at the site without removing the contaminated soil or groundwater, based on the provision of optimum conditions for microbiological contaminant breakdown.. Ex situ bioremediation of PAHs, on the other hand, is a technique applied to soil and groundwater which has been removed from the site via excavation (soil) or pumping (water). Hazardous contaminants are converted in controlled bioreactors into harmless compounds in an efficient manner. 1.4 Bioavailability of PAH in the subsurface Frequently, PAH contamination in the environment is occurs as contaminants that are sorbed onto soilparticles rather than in phase (NAPL, non aqueous phase liquids). It is known that the biodegradation rate of most PAHs sorbed onto soil is far lower than rates measured in solution cultures of microorganisms with pure solid pollutants (Alexander and Scow, 1989; Hamaker, 1972). It is generally believed that only that fraction of PAHs dissolved in the solution can be metabolized by microorganisms in soil. The amount of contaminant that can be readily taken up and degraded by microorganisms is defined as bioavailability (Bosma et al., 1997; Maier, 2000). Two phenomena have been suggested to cause the low bioavailability of PAHs in soil (Danielsson, 2000). The first one is strong adsorption of the contaminants to the soil constituents which then leads to very slow release rates of contaminants to the aqueous phase. Sorption is often well correlated with soil organic matter content (Means, 1980) and significantly reduces biodegradation (Manilal and Alexander, 1991). The second phenomenon is slow mass transfer of pollutants, such as pore diffusion in the soil aggregates or diffusion in the organic matter in the soil. The complex set of these physical, chemical and biological processes is schematically illustrated in Figure 1. As shown in Figure 1, biodegradation processes are taking place in the soil solution while diffusion processes occur in the narrow pores in and between soil aggregates (Danielsson, 2000). Seemingly contradictory studies can be found in the literature that indicate the rate and final extent of metabolism may be either lower or higher for sorbed PAHs by soil than those for pure PAHs (Van Loosdrecht et al., 1990). These contrasting results demonstrate that the bioavailability of organic contaminants sorbed onto soil is far from being well understood. Besides bioavailability, there are several other factors influencing the rate and extent of biodegradation of PAHs in soil including microbial population characteristics, physical and chemical properties of PAHs and environmental factors (temperature, moisture, pH, degree of contamination). Figure 1: Schematic diagram showing possible rate-limiting processes during bioremediation of hydrophobic organic contaminants in a contaminated soil-water system (not to scale) (Danielsson, 2000). 1.5 Increasing the bioavailability of PAH in soil Attempts to improve the biodegradation of PAHs in soil by increasing their bioavailability include the use of surfactants , solvents or solubility enhancers.. However, introduction of synthetic surfactant may result in the addition of one more pollutant. (Wang and Brusseau, 1993).A study conducted by Mulder et al. showed that the introduction of hydropropyl-ß-cyclodextrin (HPCD), a well-known PAH solubility enhancer, significantly increased the solubilization of PAHs although it did not improve the biodegradation rate of PAHs (Mulder et al., 1998), indicating that further research is required in order to develop a feasible and efficient remediation method. Enhancing the extent of PAHs mass transfer from the soil phase to the liquid might prove an efficient and environmentally low-risk alternative way of addressing the problem of slow PAH biodegradation in soil.