Consortia cultivation of the Desulfobacterota from macrophyte periphyton: tool for increasing the cultivation of microorganisms involved in mercury methylation

Invasive macrophytes are a persistent environmental problem in aquatic ecosystems. They also cause potential health issues, since periphyton colonizing their aquatic roots are hot spot of mercury methylation. Because periphytons are at the base of the trophic chain, the produced methylmercury is bioamplified through the food webs. In this work, a consortia cultivation approach was applied in order to investigate methylators in the periphyton of Ludwigia sp., an invasive macrophyte. Five growth conditions were used in order to favor the growth of different sulfate reducers, the major mercury methylators in this periphyton. A total of 33 consortia containing putative Hg methylators were obtained. Based on the amino acid sequences of HgcA (essential enzyme for Hg methylation), the obtained consortia could be subdivided into five main clusters, affiliated with Desulfovibrionaceae, Desulfobulbaceae and Syntrophobacteraceae. The main cluster, related to Desulfovibrionaceae, showed the highest sequence diversity; notwithstanding most of the sequences of this cluster showed no close representatives. Through the consortia approach, species thus far uncultivated were cultivated. The successful cultivation of these species was probably possible through the metabolites produced by other members of the consortium. The analysis of the microbial composition of the consortia uncover certain microbial interactions that may exist within this complex environment.

In Vivo Mercury (De)Methylation Metabolism in Cephalopods under Different pCO2 Scenarios

This work quantified the accumulation efficiencies of Hg in cuttlefish, depending on both organic (MeHg) and inorganic (Hg(II)) forms, under increased pCO₂ (1600 μatm). Cuttlefish were fed with live shrimps injected with two Hg stable isotopic tracers (Me²⁰²Hg and ¹⁹⁹Hg(II)), which allowed for the simultaneous quantification of internal Hg accumulation, Hg(II) methylation, and MeHg demethylation rates in different organs. Results showed that pCO₂ had no impact on Hg bioaccumulation and organotropism, and both Hg and pCO₂ did not influence the microbiota diversity of gut and digestive gland. However, the results also demonstrated that the digestive gland is a key organ for in vivo MeHg demethylation. Consequently, cuttlefish exposed to environmental levels of MeHg could exhibit in vivo MeHg demethylation. We hypothesize that in vivo MeHg demethylation could be due to biologically induced reactions or to abiotic reactions. This has important implications as to how some marine organisms may respond to future ocean change and global mercury contamination.

Active microbial communities during biodegradation of biodegradable plastics by mesophilic and thermophilic anaerobic digestion

Biodegradable plastics, if they are not properly managed at their end-of-life, can have the same hazardous environmental consequences as conventional plastics. This study investigates the treatment of the main biodegradable plastics under mesophilic and thermophilic anaerobic digestion using biochemical methane potential test and the microorganisms involved in the process using amplicon sequencing of the 16 S rRNA. Here we showed that, only PHB and TPS undergone important and rapid biodegradation under mesophilic condition (38 °C). By contrast, PCL and PLA exhibited very low biodegradation rate as 500 days were required to reach the ultimate methane yield. Little or no degradation occurred for PBAT and PBS at 38 °C. Under thermophilic conditions (58 °C), TPS, PHB, and PLA reached high levels of biodegradation in a relatively short period (< 100 d). While PBS, PBAT, and PCL could not be converted into methane at 58 °C. PHB degraders (Enterobacter and Cupriavidus) and lactate-utilizing bacteria (Moorella and Tepidimicrobium) appeared to play an important role in the PHB and PLA degradation, respectively. This work not only provides crucial data on the anaerobic digestion of the main biodegradable plastics but also enriches the understanding of the microorganisms involved in this process, which are of great importance for future development of the treatment of biodegradable plastics in anaerobic digestion systems.

Simulation of biowastes and biodegradable plastics co-digestion in semi-continuous reactors: Performances and agronomic evaluation

The development of selective biowaste collection in most European countries provides new opportunities for the anaerobic digestion sector. In parallel, extensive development of biodegradable plastics like polylactic-acid (PLA) and polyhydroxybutyrate (PHB), which facilitates the replacement of conventional plastics, has taken place in the past decade. This study investigated anaerobic co-digestion in semi-continuous reactors of biowastes (75 % Volatil Solids) and biodegradable plastics (25 % Volatil Solids, PLA and PHB). PHB was estimated to be fully biodegraded in the reactors. By contrast, PLA accumulated in the reactor, and an average biodegradation of 47.6 ± 17.9 % was estimated during the third hydraulic retention time. Pretreatment of PLA, by thermo-alkaline hydrolysis at 70 °C, with 2.5 w/v of Ca(OH)₂ for 48 h, improved the biodegradation yield of PLA to 77.5 ± 9.3 %. Finally, it was highlighted that PLA or PHB addition to the feed did not further affect the agronomic properties of the digestate.

Biochemical methane potential and active microbial communities during anaerobic digestion of biodegradable plastics at different inoculum-substrate ratios

The influence of the inoculum-substrate ratio (ISR) on the mesophilic and thermophilic biochemical methane potential test of two biodegradable plastics was evaluated. Poly(lactic acid) (PLA) and polyhydroxybutyrate (PHB) were selected for this study, the first for being recalcitrant to mesophilic anaerobic digestion (AD) and the second, by contrast, for being readily biodegradable. Several ISRs, calculated on the basis of volatile solids (VS), were tested: 1, 2, 2.85, 4, and 10 g(VS of inoculum).g(VS of substrate)^-1. A high ISR was associated with an enhanced methane production rate (i.e., biodegradation kinetics). However, the ultimate methane production did not change, except when inhibition was observed. Indeed, applying the lowest ISR to readily biodegradable plastics such as PHB resulted in inhibition of methane production. Based on these experiments, in order to have reproducible degradation kinetics and optimal methane production, an ISR between 2.85 and 4 is recommended for biodegradable plastics. The active microbial communities were analyzed, and the active bacteria differed depending on the plastic digested (PLA versus PHB) and the temperature of the process (mesophilic versus thermophilic). Previously identified PHB degraders (Ilyobacter delafieldii and Enterobacter) were detected in PHB-fed reactors. Thermogutta and Tepidanaerobacter were detected during the thermophilic AD of PLA, and they are probably involved in PLA hydrolysis and lactate conversion, respectively.

Methane production and active microbial communities during anaerobic digestion of three commercial biodegradable coffee capsules under mesophilic and thermophilic conditions

Biodegradable plastics market is increasing these last decades, including for coffee capsules. Anaerobic digestion, as a potential end-of-life scenario for plastic waste, has to be investigated. For this purpose, mesophilic (38 °C) and thermophilic (58 °C) anaerobic digestion tests on three coffee capsules made up with biodegradable plastic (Beanarella®, Launay® or Tintoretto®) and spent coffee (control) were compared by their methane production and the microbial communities active during the process. Mesophilic biodegradation of the capsules was slow and did not reach completion after 100 days, methane production ranged between 67 and 127 NL (CH₄) kg^-1 (VS). Thermophilic anaerobic digestion resulted in a better biodegradation and reached completion around 100 days, methane productions were between 257 and 294 NL (CH₄) kg^-1 (VS). The microbial populations from the reactors fed with plastics versus spent coffee grounds were significantly different, under both the mesophilic and the thermophilic conditions. However, the different biodegradable plastics only had a small impact on the main microbial community composition at a similar operational temperature and sampling time. Interestingly, the genus Tepidimicrobium was identified as a potential key microorganisms involved in the thermophilic conversion of biodegradable plastic in methane.

Microbial degradation of hydrophobic emerging contaminants from marine sediment slurries (Capbreton Canyon) to pure bacterial strain

Despite emerging contaminants (ECs) are more and more monitored in environmental matrices, there is still a lack of data in marine ecosystems, especially on their fate and degradation potentials. In this work, for the first time, the degradation potential of synthetic musks (galaxolide and tonalide), UV filters (padimate O and octocrylene) and a pharmaceutical compound (carbamazepine) was studied in marine sediment samples, under laboratory conditions using sediment slurry incubations under biotic and abiotic conditions. Minimum half life times under biotic conditions were found at 21 days, 129 days and 199 days for padimate O, galaxolide and carbamazepine, respectively. Enrichments conducted under anoxic and oxic conditions demonstrated that degradations after one month of incubation either under both biotic and abiotic conditions were limited under anoxic conditions compared to oxic conditions for all the contaminants. Novel aerobic bacteria, able to degrade synthetic musks and UV filters have been isolated. These novel strains were mainly related to the Genus Bacillus. Based on these results, the isolated strains able to degrade such ECs, can have a strong implication in the natural resilience in marine environment, and could be used in remediation processes.

Marine mercury-methylating microbial communities from coastal to Capbreton Canyon sediments (North Atlantic Ocean)

Microbial mercury (Hg) methylation transforms inorganic mercury to neurotoxic methylmercury (MeHg) mainly in aquatic anoxic environments. Sampling challenges in marine ecosystems, particularly in submarine canyons, leads to a lack of knowledge about the Hg methylating microbia in marine sediments. A previous study showed an enrichment of mercury species in sediments from the Capbreton Canyon where both geochemical parameters and microbial activities constrained the net MeHg production. In order to characterize Hg-methylating microbial communities from coastal to deeper sediments, we analysed the diversity of microorganisms' (16S rDNA-based sequencing) and Hg methylators (hgcA based cloning and sequencing). Both, 16S rDNA and hgcA gene analysis demonstrated that the putative Hg-methylating prokaryotes were likely within the Deltaproteobacteria, dominated by sulfur-compounds based reducing bacteria (mainly sulfate reducers). Additionally, others clades were also identified as carrying HgcA gene, such as, Chloroflexi, Spirochaetes, Elusimicrobia, PVC superphylum (Plantomycetes, Verrucomicrobia and Chlamydiae) and Euryarchaea. Nevertheless, 61% of the hgcA sequences were not assigned to specific clade, indicating that further studies are needed to understand the implication of new microorganisms carrying hgcA in the Hg methylation in marine environments. These first results suggest that sulfur cycle drives the Hg-methylation in marine ecosystem.

Extreme Arsenic Bioaccumulation Factor Variability in Lake Titicaca, Bolivia

Latin America, like other areas in the world, is faced with the problem of high arsenic (As) background in surface and groundwater, with impacts on human health. We studied As biogeochemical cycling by periphyton in Lake Titicaca and the mine-impacted Lake Uru Uru. As concentration was measured in water, sediment, totora plants (Schoenoplectus californicus) and periphyton growing on stems, and As speciation was determined by X-ray absorption spectroscopy in bulk and EDTA-extracted periphyton. Dissolved arsenic was between 5.0 and 15 μg L⁻¹ in Lake Titicaca and reached 78.5 μg L⁻¹ in Lake Uru Uru. As accumulation in periphyton was highly variable. We report the highest As bioaccumulation factors ever measured (BAFs_periphyton up to 245,000) in one zone of Lake Titicaca, with As present as As(V) and monomethyl-As (MMA(V)). Non-accumulating periphyton found in the other sites presented BAFs_periphyton between 1281 and 11,962, with As present as As(III), As(V) and arsenosugars. DNA analysis evidenced several taxa possibly related to this phenomenon. Further screening of bacterial and algal isolates would be necessary to identify the organism(s) responsible for As hyperaccumulation. Impacts on the ecosystem and human health appear limited, but such organisms or consortia would be of great interest for the treatment of As contaminated water.

Linking Microbial Activities and Low-Molecular-Weight Thiols to Hg Methylation in Biofilms and Periphyton from High-Altitude Tropical Lakes in the Bolivian Altiplano

The sources and factors controlling concentrations of monomethylmercury (MMHg) in aquatic ecosystems need to be better understood. Here, we investigated Hg transformations in sediments, periphyton associated with green algae's or aquatic plants, and benthic biofilms from the Lake Titicaca hydrosystem and compared them to the occurrence of active methylating microorganisms and extracellular Hg ligands. Intense Hg methylation was found in benthic biofilms and green algae's periphyton, while it remained low in sediments and aquatic plants' periphyton. Demethylation varied between compartments but remained overall in the same range. Hg methylation was mainly carried out by sulfate reducers, although methanogens also played a role. Its variability between compartments was first explained by the presence or absence of the hgcAB genes. Next, both benthic biofilm and green algae's periphyton exhibited a great diversity of extracellular low-molecular-weight (LMW) thiols (13 or 14 compounds) present at a range of a few nmol L^-1 or μmol L^-1 but clearly dominated by cysteine and 3-mercaptopropionic acid. Hg methylation was overall positively correlated to the total thiol concentrations, albeit to different extents according to the compartment and conditions. This work is the first examining the interplay between active methylating bacterial communities and extracellular ligands in heterotrophic biofilms and supports the involvement of LMW thiols in Hg methylation in real aquatic systems.

Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters

Estuaries are highly dynamic ecosystems in which freshwater and seawater mix together. Depending on tide and river inflows, particles originating from rivers or from the remobilization of sediments accumulate in the water column. Due to the salinity gradient and the high heterotrophic activity in the estuarine plume, hypoxic and anoxic microniches may form in oxygenated waters, sustaining favorable conditions for resuspended anaerobic microorganisms. In this context, we tested the hypothesis that anaerobic sulfate-reducing prokaryotes may occur in the water column of the Adour River. Using 16S ribosomal RNA (rRNA) and dsrAB-based terminal restriction fragment length polymorphism (T-RFLP) techniques, we characterized total prokaryotic and sulfate-reducing communities along a gradient from estuarine to marine bay waters. Sulfate-reducing prokaryotes were further characterized by the description of dsrB genes and the cultivation of sulfidogenic anaerobic microorganisms. As a result, physical-chemical parameters had a significant effect on water bacterial diversity and community structure along the studied gradient. The concentration of cultured sulfidogenic microorganisms ranged from 1 to 60 × 10³ cells l^-1 in the water column. Sulfate-reducing prokaryotes occurring in estuarine waters were closely related to microorganisms previously detected in freshwater sediments, suggesting an estuarine origin, mainly by the remobilization of the sediments. In the marine bay station, sediment-derived sulfate-reducing prokaryotes were not cultured anymore, probably due to freshwater dilution, increasing salinity and extended oxic stress. Nevertheless, isolates related to the type strain Desulfovibrio oceani were cultured from the diluted plume and deep marine waters, indicating the occurrence of autochthonous sulfate-reducing bacteria offshore.

Diurnal variability and biogeochemical reactivity of mercury species in an extreme high-altitude lake ecosystem of the Bolivian Altiplano

Methylation and demethylation represent major transformation pathways regulating the net production of methylmercury (MMHg). Very few studies have documented Hg reactivity and transformation in extreme high-altitude lake ecosystems. Mercury (Hg) species concentrations (IHg, MMHg, Hg°, and DMHg) and in situ Hg methylation (M) and MMHg demethylation (D) potentials were determined in water, sediment, floating organic aggregates, and periphyton compartments of a shallow productive Lake of the Bolivian Altiplano (Uru Uru Lake, 3686 m). Samples were collected during late dry season (October 2010) and late wet season (May 2011) at a north (NS) and a south (SS) site of the lake, respectively. Mercury species concentrations exhibited significant diurnal variability as influenced by the strong diurnal biogeochemical gradients. Particularly high methylated mercury concentrations (0.2 to 4.5 ng L(-1) for MMHgT) were determined in the water column evidencing important Hg methylation in this ecosystem. Methylation and D potentials range were, respectively, <0.1-16.5 and <0.2-68.3 % day(-1) and were highly variable among compartments of the lake, but always higher during the dry season. Net Hg M indicates that the influence of urban and mining effluent (NS) promotes MMHg production in both water (up to 0.45 ng MMHg L(-1) day(-1)) and sediment compartments (2.0 to 19.7 ng MMHg g(-1) day(-1)). While the sediment compartment appears to represent a major source of MMHg in this shallow ecosystem, floating organic aggregates (dry season, SS) and Totora's periphyton (wet season, NS) were found to act as a significant source (5.8 ng MMHg g(-1) day(-1)) and a sink (-2.1 ng MMHg g(-1) day(-1)) of MMHg, respectively. This work demonstrates that high-altitude productive lake ecosystems can promote MMHg formation in various compartments supporting recent observations of high Hg contents in fish and water birds.

Effect of physical sediments reworking on hydrocarbon degradation and bacterial community structure in marine coastal sediments

The present study aimed to examine whether the physical reworking of sediments by harrowing would be suitable for favouring the hydrocarbon degradation in coastal marine sediments. Mudflat sediments were maintained in mesocosms under conditions as closer as possible to those prevailing in natural environments with tidal cycles. Sediments were contaminated with Ural blend crude oil, and in half of them, harrowing treatment was applied in order to mimic physical reworking of surface sediments. Hydrocarbon distribution within the sediment and its removal was followed during 286 days. The harrowing treatment allowed hydrocarbon compounds to penetrate the first 6 cm of the sediments, and biodegradation indexes (such as n-C18/phytane) indicated that biodegradation started 90 days before that observed in untreated control mesocosms. However, the harrowing treatment had a severe impact on benthic organisms reducing drastically the macrofaunal abundance and diversity. In the harrowing-treated mesocosms, the bacterial abundance, determined by 16S rRNA gene Q-PCR, was slightly increased; and terminal restriction fragment length polymorphism (T-RFLP) analyses of 16S rRNA genes showed distinct and specific bacterial community structure. Co-occurrence network and canonical correspondence analyses (CCA) based on T-RFLP data indicated the main correlations between bacterial operational taxonomic units (OTUs) as well as the associations between OTUs and hydrocarbon compound contents further supported by clustered correlation (ClusCor) analysis. The analyses highlighted the OTUs constituting the network structural bases involved in hydrocarbon degradation. Negative correlations indicated the possible shifts in bacterial communities that occurred during the ecological succession.

Exploring Actinobacteria assemblages in coastal marine sediments under contrasted Human influences in the West Istria Sea, Croatia

The exploration of marine Actinobacteria has as major challenge to answer basic questions of microbial ecology that, in turn, will provide useful information to exploit Actinobacteria metabolisms in biotechnological processes. The ecological functions performed by Actinobacteria in marine sediments are still unclear and belongs to the most burning basic questions. The comparison of Actinobacteria communities inhabiting marine sediments that are under the influence of different contamination types will provide valuable information in the adaptation capacities of Actinobacteria to colonize specific ecological niche. In the present study, the characterization of different Actinobacteria assemblages according to contamination type revealed the ecological importance of Actinobacteria for maintaining both general biogeochemical functions through a "core" Actinobacteria community and specific roles associated with the presence of contaminants. Indeed, the results allowed to distinguish Actinobacteria genera and species operational taxonomic units (OTUs) able to cope with the presence of either (i) As, (ii) metals Ni, Fe, V, Cr, and Mn, or (iii) polycyclic aromatic hydrocarbons (PAHs) and toxic metals (Hg, Cd, Cu, Pb, and Zn). Such observations highlighted the metabolic capacities of Actinobacteria and their potential that should be taken into consideration and advantage during the implementation of bioremediation processes in marine ecosystems.

Response of archaeal communities to oil spill in bioturbated mudflat sediments

The response of archaeal community to oil spill with the combined effect of the bioturbation activity of the polychaetes Hediste diversicolor was determined in mudflat sediments from the Aber-Benoît basin (Brittany, French Atlantic coast), maintained in microcosms. The dynamics of the archaeal community was monitored by combining comparative terminal restriction fragment length polymorphism (T-RFLP) fingerprints and sequence library analyses based on 16S rRNA genes and 16S cDNA. Methanogens were also followed by targeting the mcrA gene. Crenarchaeota were always detected in all communities irrespective of the addition of H. diversicolor and/or oil. In the presence of oil, modifications of archaeal community structures were observed. These modifications were more pronounced when H. diversicolor was added resulting in a more diverse community especially for the Euryarchaeota and Thaumarchaeota. The analysis of mcrA transcripts showed a specific structure for each condition since the beginning of the experiment. Overall, oiled microcosms showed different communities irrespective of H. diversicolor addition, while similar hydrocarbon removal capacities were observed.