Substrate-specific clades of active marine methylotrophs associated with a phytoplankton bloom in a temperate coastal environment

Marine microorganisms that consume one-carbon (C1) compounds are poorly described, despite their impact on global climate via an influence on aquatic and atmospheric chemistry. This study investigated marine bacterial communities involved in the metabolism of C1 compounds. These communities were of relevance to surface seawater and atmospheric chemistry in the context of a bloom that was dominated by phytoplankton known to produce dimethylsulfoniopropionate. In addition to using 16S rRNA gene fingerprinting and clone libraries to characterize samples taken from a bloom transect in July 2006, seawater samples from the phytoplankton bloom were incubated with 13C-labeled methanol, monomethylamine, dimethylamine, methyl bromide, and dimethyl sulfide to identify microbial populations involved in the turnover of C1 compounds, using DNA stable isotope probing. The [13C]DNA samples from a single time point were characterized and compared using denaturing gradient gel electrophoresis (DGGE), fingerprint cluster analysis, and 16S rRNA gene clone library analysis. Bacterial community DGGE fingerprints from 13C-labeled DNA were distinct from those obtained with the DNA of the nonlabeled community DNA and suggested some overlap in substrate utilization between active methylotroph populations growing on different C1 substrates. Active methylotrophs were affiliated with Methylophaga spp. and several clades of undescribed Gammaproteobacteria that utilized methanol, methylamines (both monomethylamine and dimethylamine), and dimethyl sulfide. rRNA gene sequences corresponding to populations assimilating 13C-labeled methyl bromide and other substrates were associated with members of the Alphaproteobacteria (e.g., the family Rhodobacteraceae), the Cytophaga-Flexibacter-Bacteroides group, and unknown taxa. This study expands the known diversity of marine methylotrophs in surface seawater and provides a comprehensive data set for focused cultivation and metagenomic analyses in the future

Methane-carbon flow into the benthic food web at cold seeps – a case study from the Costa Rica subduction zone

Cold seep ecosystems can support enormous biomasses of free-living and symbiotic chemoautotrophic organisms that get their energy from the oxidation of methane or sulfide. Most of this biomass derives from animals that are associated with bacterial symbionts, which are able to metabolize the chemical resources provided by the seeping fluids. Often these systems also harbor dense accumulations of non-symbiotic megafauna, which can be relevant in exporting chemosynthetically fixed carbon from seeps to the surrounding deep sea. Here we investigated the carbon sources of lithodid crabs (Paralomis sp.) feeding on thiotrophic bacterial mats at an active mud volcano at the Costa Rica subduction zone. To evaluate the dietary carbon source of the crabs, we compared the microbial community in stomach contents with surface sediments covered by microbial mats. The stomach content analyses revealed a dominance of epsilonproteobacterial 16S rRNA gene sequences related to the free-living and epibiotic sulfur oxidiser Sulfurovum sp. We also found Sulfurovum sp. as well as members of the genera Arcobacter and Sulfurimonas in mat-covered surface sediments where Epsilonproteobacteria were highly abundant constituting 10% of total cells. Furthermore, we detected substantial amounts of bacterial fatty acids such as i-C15:0 and C17:1ω6c with stable carbon isotope compositions as low as −53‰ in the stomach and muscle tissue. These results indicate that the white microbial mats at Mound 12 are comprised of Epsilonproteobacteria and that microbial mat-derived carbon provides an important contribution to the crab's nutrition. In addition, our lipid analyses also suggest that the crabs feed on other 13C-depleted organic matter sources, possibly symbiotic megafauna as well as on photosynthetic carbon sources such as sedimentary detritus

Physiological impacts of soil pollution and arsenic uptake in three plant species: Agrostis capillaris, Solanum nigrum and Vicia faba

In order to revegetate an industrial soil polluted by trace metals and metalloids (As, Pb, Cu, Cd, Sb), the impact of pollution on three plant species, Solanum nigrum and Agrostis capillaris, both native species in an industrial site, and Vicia faba, a plant model species, is studied. Following the study of soil pollution from the industrial wasteland of Auzon, it appears that the As is the principal pollutant. Particular attention is given to this metalloid, both in its content and its speciation in the soil that the level of its accumulation in plants. In V. faba and A. capillaris, the trace metals and metalloids inhibit the biomass production and involve a lipid peroxidation in the leaves. Furthermore, these pollutants cause a photosynthesis perturbation by stomatal limitations and a dysfunction of photosystem II. Whatever the plant, the As content is less than 0.1 percent of dry matter, the majority of As absorbed is stored in the roots which play the role of trap organ. In parallel, the culture of S. nigrum decreases significantly the exchangeable and weakly adsorbed fraction of As in rhizospheric soil. This study has highlighted the ability of tolerance to trace metals of S. nigrum and to a lesser extent A. capillaris. Our data indicate that V. faba is not tolerant to soil pollution and is not a metallophyte species. (C) 2012 Elsevier Inc. All rights reserved

Identification of active methylotrophic bacteria inhabiting surface sediment of a marine estuary

Methylotrophs play an essential role in the global carbon cycle due to their participation in methane oxidation and C-1 metabolism. Despite this important biogeochemical role, marine and estuarine microorganisms that consume C-1 compounds are poorly characterized. In this study, we investigated the diversity of active methylotrophs and methanotrophs in sediment from the Colne Estuary (Brightlingsea, UK). Aerobic surface sediment samples were examined for the presence of C-1-utilizing communities using DNA stable-isotope probing (DNA-SIP) with 13C-labelled methane, methanol and monomethylamine. Active methylotrophic bacteria were confirmed after DNA-SIP and denaturing gradient gel electrophoresis analyses. Clone libraries of 16S rRNA gene amplicons revealed the presence of methylotrophic bacteria affiliated with Methylophaga spp. in methanol and monomethylamine incubations. The addition of marine ammonium mineral salts medium to the microcosms increased the rate of substrate metabolism in DNA-SIP incubations, although nutrient addition did not affect the active populations contributing 13C-labelled DNA. The 13CH(4) SIP incubations indicated the predominant activity of type I methanotrophs and microarray hybridization of amplified particulate methane monooxygenase (pmoA) genes confirmed the role of type Ia methanotrophs in SIP incubations. Type II methanotrophs (i.e. Methylocystis and Methylosinus) were only detected in the original sediment and in the unlabelled DNA fractions, which indicated that type II methanotrophs were not actively involved in C-1 compound assimilation in DNA-SIP incubations with estuarine surface sediment samples

Thermodesulfatator indicus gen. nov., sp nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge

A thermophilic, marine, anaerobic, chemolithoautotrophic, sulfate-reducing bacterium, strain CIR29812(T), was isolated from a deep-sea hydrothermal vent site at the Kairei vent field on the Central Indian Ridge. Cells were Gram-negative motile rods that did not form spores. The temperature range for growth was 55-80 degreesC, with an optimum at 70 degreesC. The NaCl concentration range for growth was 10-35 g l(-1), with an optimum at 25 g l(-1). The pH range for growth was 6-6(.)7, with an optimum at approximately pH 6(.)25. H-2 and CO2 were the only electron donor and carbon source found to support growth of the strain. However, several organic compounds were stimulatory for growth. Sulfate was used as electron acceptor, whereas elemental sulfur, thiosulfate, sulfite, cystine, nitrate and fumarate were not. No fermentative growth was observed with malate, pyruvate or lactate. The phenotypic characteristics of strain CIR29812(T) were similar to those of Therm odesulfobacterium hydrogeniphilum, a recently described thermophilic, chemolithoautotrophic sulfate-reducer. However, phylogenetic; analyses of the 16S rRNA gene sequences showed that the new isolate was distantly related to members of the family Thermodesuffobacteriaceae (similarity values of less than 90%). The chemotaxonomic data (fatty acids and polar lipids composition) also indicated that strain CIR29812(T) Could be distinguished from Thermodesulfobacterium commune, the type species of the type genus of the family Thermodesulfobacteriaceae. Finally, the G + C content of the genomic DNA of strain CIR29812(T) (46(.)0 mol%) was not in the range of values obtained for members of this family. On the basis of phenotypic, chemotaxonomic and genomic features, it is proposed that strain CIR29812(T) represents a novel species of a new genus, Thermodesulfatator, of which Thermodesulfatator indicus is the type species. The type strain is CIR29812(T) (= DSM 15286(T) = JCM 11887(T))

Synthèse du projet BEEST

Projet BEEST : vers une approche multicritère du Bon Etat écologique des grands ESTuaires