A consensus protocol for the recovery of mercury methylation genes from metagenomes

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes

Three-year survey of sulfate-reducing bacteria community structure in Carnoules acid mine drainage (France), highly contaminated by arsenic

A 3-year survey on sulfate-reducing bacteria (SRB) was conducted in the waters of the arsenic-rich acid mine drainage (AMD) located at Carnoules (France) to determine the influence of environmental parameters on their community structure. The source (S5 station) exhibited most extreme conditions with pH lowering to similar to 1.2; iron, sulfate, and arsenic concentrations reaching 6843, 29593, and 638mgL1, respectively. The conditions were less extreme at the downstream stations S1 (pH similar to 3.7; iron, sulfate, and arsenic concentrations of 1114, 4207, and 167mgL1, respectively) and COWG (pH similar to 3.4; iron, sulfate, and arsenic concentrations of 854, 3134, and 110mgL1, respectively). SRB community structures were characterized by terminal restriction fragment length polymorphism and library analyses based on dsrAB genes. The predominant dsrAB sequences detected were most similar to the family Desulfobulbaceae. Additionally, certain phylotypes could be related to spatio-temporal fluctuations of pH, iron, and arsenic species. For example, Desulfohalobiaceae-related sequences were detected at the most acidic sample (pH 1.4) with high iron and arsenic concentrations (6379 and 524mgL1, respectively). New dsrAB sequences, with no isolated representatives, were found exclusively in COWG. This study gives new insights on SRB community dynamics in AMD systems

Consequences of contamination on the interactions between phytoplankton and bacterioplankton

Sediment resuspension can provoke strong water enrichment in nutrients, contaminants, and microorganisms. Microcosm incubations were performed in triplicate for 96 h, with lagoon and offshore waters incubated either with sediment elutriate or with an artificial mixture of contaminants issued from sediment resuspension. Sediment elutriate provoked a strong increase in microbial biomass, with little effects on the phytoplankton and bacterioplankton community structures. Among the pool of contaminants released, few were clearly identified as structuring factors of phytoplanktdn and bacterioplankton communities, namely simazine, Cu, Sn, Ni, and Cr. Effects were more pronounced in the offshore waters, suggesting a relative tolerance of the lagoon microbial communities to contamination. The impacts of contamination on the microbial community structure were direct or indirect, depending on the nature and the strength of the interactions between phytoplankton and bacterioplankton

Bacterial community structure along the Adour estuary (French Atlantic coast): influence of salinity gradient versus metal contamination

Salinity, other physico-chemical parameters and anthropogenic pollution are the main factors affecting bacterial communities in estuaries. We estimated the impact of these parameters on the distribution of bacterial communities in the Adour estuary (France), a moderately Polluted water body characterized by short residence times of particles and water and absence of a maximum turbidity zone. Eight stations were established along the salinity gradient from freshwater to marine conditions. For the 3 typical estuarine stations (water mixing zone), samples were collected at both low and high tide and at different depths according to the position of the halocline. This sampling strategy generated 35 samples with different degrees of mixing between fresh water and seawater. All the samples were characterized by their physico-chemical parameters and trace metal contents (as a contamination tracer). The structure of bacterial communities was determined by T-RFLP fingerprinting. The metal-salinity profiles suggested dilution processes and/or usual geochemical reactivity for the elements sensitive to sorption/desorption mechanisms (Cd, Mn). Metal concentrations were low, with no evidence of contaminated plumes, suggesting that metal concentrations were not influencing bacterial diversity. A well-established estuarine bacterial community was observed, comprising mostly Cyanobacteria, Planctomyces and Alphaproteobacteria. This community was different from fresh and seawater communities, and a shift in community composition was observed between 10 and 34 PSU. Although residence time in the Adour estuary is very short, the salinity and halocline in this water body are likely to be the main parameters influencing bacterial community composition

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 mu mol 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

Benthic foraminifera from the deep-water Niger delta (gulf of Guinea): Assessing present-day and past activity of hydrate pockmarks

We present ecological and isotopic (δ18O and δ13C) data on benthic foraminifera sampled from 4 deep-sea stations in a pockmark field from the deep-water Niger delta (Gulf of Guinea, Equatorial Atlantic Ocean). In addition, a series of sedimentological and (bio)geochemical data are shown to back up foraminiferal observations. All stations are located within 1.2 km of each other, so prevailing oceanographic conditions can be assumed to be similar at each site. Two of the sites (GMMC-01 and GMMC-02) are located in a pockmark (named “pockmark A”) where current methane seepages were recorded by ROV observations. A third station (GMMC-03) is located in the topographic depression interpreted as a collapsed pockmark (named “pockmark B”). The fourth site (GMMC-04) is a reference station, without evidence of past or present seepages. Our observations show that degraded organic matter with low bio-availability is present at all stations with a preferential burial of organic compounds in topographic depressions (GMMC-03 station). Authigenic aragonite is abundant in surface sediments at stations GMMC-01 and -02. Its precipitation is likely related to high rates of methane oxidation during past seep events in episodically active pockmark A. In contrast, the absence of anaerobic methanotrophic Archaea (ANME) during the sampling period (November 2011) suggests that only moderate sulphide and methane oxidation take place close to the sediment-water interface. Compared to the reference site GMMC-04, living foraminifera at the collapsed and episodically active pockmarks show minor changes in terms of diversity, standing stocks and faunal composition. However, the δ13C signal of living and dead (but well-preserved) foraminiferal species (Ceratobulimina contraria, Melonis barleeanus, Uvigerina peregrina) is depleted in the episodically active pockmark A compared to the other stations. Overgrowth of authigenic carbonate on altered foraminifera generates an important shift to lower δ13C values. Dead faunas carry a complex time-averaged message, integrating taphonomic gains and losses related to the temporal variability of gas emission. They reveal major faunal differences that may be useful to detect gas hydrate seepages in different pockmark stages