Effect of Acidic Industrial Effluent Release on Microbial Diversity and Trace Metal Dynamics During Resuspension of Coastal Sediment

Both industrial effluent discharge and the resuspension of contaminated marine sediments are important sources of trace metals in seawater which potentially affect marine ecosystems. The aim of this study was to evaluate the impact of the industrial wastewaters having acidic pH (2–3) and containing trace metals on microbial diversity in the coastal ecosystem of the Gulf of Gabès (Tunisia, southern Mediterranean Sea) subjected to resuspension events of marine sediments. Four trace elements (As, Cd, U, and V) were monitored during 10-day sediment resuspension experiments. The highest enrichment in the seawater dissolved phase was observed for Cd followed by U, V, and As. Cd remobilization was improved by indigenous microbial community, while U release was mainly abiotic. Acidic effluent addition impacted both trace metal distribution and microbial diversity, particularly that of the abundant phylum Bacteroidetes. Members of the order Saprospirales were enriched from sediment in natural seawater (initial pH > 8), while the family Flavobacteriaceae was favored by acidified seawater (initial pH < 8). Some Flavobacteriaceae members were identified as dominant species in both initial sediment and experiments with acidic wastewater, in which their relative abundance increased with increasing dissolved Cd levels. It could be therefore possible to consider them as bioindicators of metal pollution and/or acidification in marine ecosystems

Metabolic challenges and key players in serpentinite-hosted microbial ecosystems

Serpentinite-hosted systems are amongst the most challenging environments for life on Earth. Serpentinization, a geochemical alteration of exposed ultramafic rock, produces hydrothermal fluids enriched in abiotically derived hydrogen (H2), methane (CH4), and small organic molecules. The hyperalkaline pH of these fluids poses a great challenge for metabolic energy and nutrient acquisition, curbing the cellular membrane potential and limiting electron acceptor, carbon, and phosphorous availability. Nevertheless, serpentinization supports the growth of diverse microbial communities whose metabolic make-up might shed light on the beginning of life on Earth and potentially elsewhere. Here, we outline current hypotheses on metabolic energy production, carbon fixation, and nutrient acquisition in serpentinizing environments. A taxonomic survey is performed for each important metabolic function, highlighting potential key players such as H2 and CH4 cycling Serpentinimonas, Hydrogenophaga, Methanobacteriales, Methanosarcinales, and novel candidate phyla. Methodological biases of the available data and future approaches are discussed

Magmatism, serpentinization and life: Insights through drilling the Atlantis Massif (IODP Expedition 357)

IODP Expedition 357 used two seabed drills to core 17 shallow holes at 9 sites across Atlantis Massif ocean core complex (Mid-Atlantic Ridge 30°N). The goals of this expedition were to investigate serpentinization processes and microbial activity in the shallow subsurface of highly altered ultramafic and mafic sequences that have been uplifted to the seafloor along a major detachment fault zone. More than 57 m of core were recovered, with borehole penetration ranging from 1.3 to 16.4 meters below seafloor, and core recovery as high as 75% of total penetration in one borehole. The cores show highly heterogeneous rock types and alteration associated with changes in bulk rock chemistry that reflect multiple phases of magmatism, fluid-rock interaction and mass transfer within the detachment fault zone. Recovered ultramafic rocks are dominated by pervasively serpentinized harzburgite with intervals of serpentinized dunite and minor pyroxenite veins; gabbroic rocks occur as melt impregnations and veins. Dolerite intrusions and basaltic rocks represent the latest magmatic activity. The proportion of mafic rocks is volumetrically less than the amount of mafic rocks recovered previously by drilling the central dome of Atlantis Massif at IODP Site U1309. This suggests a different mode of melt accumulation in the mantle peridotites at the ridge-transform intersection and/or a tectonic transposition of rock types within a complex detachment fault zone. The cores revealed a high degree of serpentinization and metasomatic alteration dominated by talc-amphibole-chlorite overprinting. Metasomatism is most prevalent at contacts between ultramafic and mafic domains (gabbroic and/or doleritic intrusions) and points to channeled fluid flow and silica mobility during exhumation along the detachment fault. The presence of the mafic lenses within the serpentinites and their alteration to mechanically weak talc, serpentine and chlorite may also be critical in the development of the detachment fault zone and may aid in continued unroofing of the upper mantle peridotite/gabbro sequences. New technologies were also developed for the seabed drills to enable biogeochemical and microbiological characterization of the environment. An in situ sensor package and water sampling system recorded real-time variations in dissolved methane, oxygen, pH, oxidation reduction potential (Eh), and temperature and during drilling and sampled bottom water after drilling. Systematic excursions in these parameters together with elevated hydrogen and methane concentrations in post-drilling fluids provide evidence for active serpentinization at all sites. In addition, chemical tracers were delivered into the drilling fluids for contamination testing, and a borehole plug system was successfully deployed at some sites for future fluid sampling. A major achievement of IODP Expedition 357 was to obtain microbiological samples along a west–east profile, which will provide a better understanding of how microbial communities evolve as ultramafic and mafic rocks are altered and emplaced on the seafloor. Strict sampling handling protocols allowed for very low limits of microbial cell detection, and our results show that the Atlantis Massif subsurface contains a relatively low density of microbial life

Functional versus phylogenetic fingerprint analyses for monitoring hydrogen-producing bacterial populations in dark fermentation cultures

International audienceThe fermentative hydrogen production occurs during the anaerobic digestion of organic matter. It is a promising technology to produce renewable energy. However, the mixed culture fermentation performances vary considerably depending on the operating conditions such as pH. We investigated the potential of a molecular CE-SSCP (capillary electrophoresis-single strand conformation polymorphism) fingerprinting method based on the hydA functional genes to better describe the bacterial community dynamics, with regards to the standard 16S rDNA-based method. A series of batch experiments was performed from sucrose at different initial pH from 4 to 6. As expected, the highest H2 production potentials (Hmax) and rates (Rmax) were obtained at the highest pH. Changes in batch performances were clearly associated with shifts in the hydA diversity and structure. In contrast, 16S rDNA-based fingerprints were less sensitive to changes in H2 production performances. The Hmax was related to lower hydA diversity, with Clostridium sporogenes as the major H2 producer. Communities harboring larger hydA diversities were found in experiments with the higher Rmax, suggesting that species coexistence may have positive effects on H2 production

Development and application of a functional CE-SSCP fingerprinting method based on [Fe–Fe]-hydrogenase genes for monitoring hydrogen-producing Clostridium in mixed cultures

International audienceA Capillary Electrophoresis Single Strand Conformation Polymorphism (CE-SSCP) method based on functional [Fe Fe]-hydrogenase genes was developed for monitoring the hydrogen (H-2)-producing clostridial population in mixed-culture bioprocesses. New non-degenerated primers were designed and then validated on their specific PCR detection of a broad range of clostridial hydA genes. The hydA-based CE-SSCP method gave a specific and discriminating profile for each of the Clostridium strains tested. This method was validated using H-2-producing mixed cultures incubated at temperatures ranging from 25 C to 45 degrees C. The hydA CE-SSCP profiles clearly differed between temperatures tested. Hence, they varied according to variations of the H-2 production performances. The HydA sequences amplified with the new primer set indicated that diverse Clostridium strains impacted the H-2 production yields. The highest performances were related to the dominance of Clostridium sporogenes-like hydA sequences. This CE-SSCP tool offers highly reliable and throughput analysis of the functional diversity and structure of the hydA genes for better understanding of the H-2-producing clostridial population dynamics in H-2 dark fermentation bioreactors

Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia)

International audienceAnaerobic biotechnology using sulfate-reducing bacteria (SRB) is a promising alternative for reducing long-term stockpiling of phosphogypsum (PG), an acidic (pH ∼3) by-product of the phosphate fertilizer industries containing high amounts of sulfate. The main objective of this study was to evaluate, for the first time, the diversity and ability of anaerobic marine microorganisms to convert sulfate from PG into sulfide, in order to look for marine SRB of biotechnological interest. A series of sulfate-reducing enrichment cultures were performed using different electron donors (i.e., acetate, formate, or lactate) and sulfate sources (i.e., sodium sulfate or PG) as electron acceptors. Significant sulfide production was observed from enrichment cultures inoculated with marine sediments, collected near the effluent discharge point of a Tunisian fertilizer industry (Sfax, Tunisia). Sulfate sources impacted sulfide production rates from marine sediments as well as the diversity of SRB species belonging to Deltaproteobacteria. When PG was used as sulfate source, Desulfovibrio species dominated microbial communities of marine sediments, while Desulfobacter species were mainly detected using sodium sulfate. Sulfide production was also affected depending on the electron donor used, with the highest production obtained using formate. In contrast, low sulfide production (acetate-containing cultures) was associated with an increase in the population of Firmicutes. These results suggested that marine Desulfovibrio species, to be further isolated, are potential candidates for bioremediation of PG by immobilizing metals and metalloids thanks to sulfide production by these SRB

Do by-products of thermochemical treatment of lignocellulosic materials inhibit anaerobic mixed cultures? Overview of recent findings

International audienceThis paper reviews and discusses the impact of byproducts released during pretreatment of lignocellulosic materials on anaerobic mixed cultures producing hydrogen and methane. 5-HMF, furfural, phenolic compounds and aldehydes, are strong inhibitors of biohydrogen production but can be further converted into methane. This finding can be explained by differences in both process parameters: anaerobic digestion is performed with more complex mixed cultures, lower substrate/inoculum or byproducts/inoculum ratios and longer batch incubation times than dark fermentation. Indeed, the presence of byproducts may require an adaptation phase of the microbial community leading to longer lag phase in dark fermentation. Finally, the presence of pretreatment by-products may lead to a metabolic shift from hydrogen production to no H2-producing ethanol and lactate pathways and whatever the route of dark fermentation, metabolites can be all further converted into methane, at different rates

Inhibition of fermentative hydrogen production by lignocellulose-derived compounds in mixed cultures

International audienceDark fermentation using mixed cultures is an attractive biological process for producing hydrogen (H-2) from lignocellulosic biomass at a low cost. Physicochemical pretreatment is generally used to convert lignocellulosic materials into monosaccharides. However, the processes also involved release degradation byproducts which can, in turn, inhibit microbial growth and metabolism and, hence, impact substrate conversion. In this study, the impact on H-2 production of lignocellulose-derived compounds (i.e. furan derivatives, phenolic compounds and lignins) was assessed along with their effect on bacterial communities and metabolisms. Batch tests were carried out using xylose as model substrate (1.67 mol(H2) mol(xylose)(-1) in the control test). All the putative inhibitory compounds showed a significant negative impact on H-2 production performance (ranging from 0.34 to 1.39 mol(H2) mol(xylose)(-1)). The H-2 yields were impacted more strongly by furan derivatives (0.40-0.51 mol(H2) mol(xylose)(-1)) than by phenolic compounds (1.28-1.39 mol(H2) mol(xylose)(-1)). Except for the batch tests supplemented with lignins, the lag phase was shorter for inhibitors having the highest molecular weight (8 days versus 22 days for the lowest MW). Variability of the lag phase was clearly related to a shift in bacterial community structure, as shown by multivariate ordination statistics. The decrease in H-2 yield was associated with a decrease in the relative abundance of several H-2-producing clostridial species. Interestingly, Clostridium beijerinkii was found to be more resistant to the inhibitors, making this bacterium an ideal candidate for H-2 production from hydrolyzates of lignocellulosic biomass

Bacterial community structure and functional arrAgene diversity associated with arsenic reductionand release in an industrially contaminated soil

International audienceThis study aimed at evaluating potential arsenic (As) mobility in an industrially contaminatedsoil (64 mg As kg-1) of the Meuse River basin, and at identifying key bacterial groups that drive soil As dynamics. Both speciation and release of As from this soil was followed under anaerobicconditions using a laboratory batch experiment. In the presence of exogenous carbon sources,AsV initially present in the soil matrix and/or adsorbed on synthetic hydrous ferric oxides wassolubilized and mainly reduced into AsIII by indigenous soil microfora. After a one-monthincubation period in these biotic conditions, AsIII accounted for 80-85% of the total dissolved Asand more than 60% of the solid-phase As. Bacterial community structure (i.e. 16S rDNA-basedCE-SSCP profiles) changed with incubation time and As amendment. The detection of distantlyrelated arsenate respiratory reductase genes (arrA), as functional markers of AsV-respirers,indicates that novel dissimilatory AsV-reducing bacteria may be involved in Asbiotransformation and mobility in anoxic soils. Since As and iron were concomitantly released, acrucial role of indirect As-mobilizing bacteria on As behavior was also revealed. Our results show that the majority of As within the soil matrix was bioavailable and bioaccessible forheterotrophic AsV reduction to AsIII, which may increase As toxicity and mobility in thecontaminated soils

Endolithic microbial communities in carbonate precipitates from serpentinite-hosted hyperalkaline springs of the Voltri Massif (Ligurian Alps, Northern Italy)

The Voltri Massif is an ophiolitic complex located in the Ligurian Alps close to the city of Genova (Northern Italy) where several springs discharge high pH (up to 11.7), low salinity waters produced by the active serpentinization of the ultramafic basement. Mixing of these hyperalkaline waters with the river waters along with the uptake of atmospheric carbon dioxide forms brownish carbonate precipitates covering the bedrock at the springs. Diverse archaeal and bacterial communities were detected in these carbonate precipitates using 454 pyrosequencing analyses of 16S ribosomal RNA (rRNA) genes. Archaeal communities were dominated by members of potential methane-producing and/or methane-oxidizing Methanobacteriales and Methanosarcinales (Euryarchaeota) together with ammonia-oxidizing Nitrososphaerales (Thaumarchaeota) similar to those found in other serpentinization-driven submarine and terrestrial ecosystems. Bacterial communities consisted of members of the Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, and Verrucomicrobia phyla, altogether accounting for 92.2 % of total retrieved bacterial 16S rRNA gene sequences. Amongst Bacteria, potential chemolithotrophy was mainly associated with Alpha- and Betaproteobacteria classes, including nitrogen-fixing, methane-oxidizing or hydrogen-oxidizing representatives of the genera Azospirillum, Methylosinus, and Hydrogenophaga/'Serpentinomonas', respectively. Besides, potential chemoorganotrophy was attributed mainly to representatives of Actinobacteria and Planctomycetales phyla. The reported 16S rRNA gene data strongly suggested that hydrogen, methane, and nitrogen-based chemolithotrophy can sustain growth of the microbial communities inhabiting the carbonate precipitates in the hyperalkaline springs of the Voltri Massif, similarly to what was previously observed in other serpentinite-hosted ecosystems