Enrichment of a microbial community performing anaerobic oxidation of methane in a continuous high-pressure bioreactor

<p>Abstract</p> <p>Background</p> <p>Anaerobic oxidation of methane coupled to sulphate reduction (SR-AOM) prevents more than 90% of the oceanic methane emission to the atmosphere. In a previous study, we demonstrated that the high methane pressure (1, 4.5, and 8 MPa) stimulated <it>in vitro </it>SR-AOM activity. However, the information on the effect of high-pressure on the microbial community structure and architecture was still lacking.</p> <p>Results</p> <p>In this study we analysed the long-term enrichment (286 days) of this microbial community, which was mediating SR-AOM in a continuous high-pressure bioreactor. 99.7% of the total biovolume represented cells in the form of small aggregates (diameter less then 15 μm). An increase of the total biovolume was observed (2.5 times). After 286 days, the ANME-2 (anaerobic methanotrophic archaea subgroup 2) and SRB (sulphate reducing bacteria) increased with a factor 12.5 and 8.4, respectively.</p> <p>Conclusion</p> <p>This paper reports a net biomass growth of communities involved in SR-AOM, incubated at high-pressure.</p

Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater

Microorganisms can increase the open-circuit potential of stainless steel immersed in seawater of several hundred millivolts in a phenomenon called ennoblement. It raises the chance of corrosion as the open-circuit potential may go over the pitting corrosion potential. Despite the large impact of the ennoblement, no unifying mechanisms have been described as responsible for the phenomenon. Here we show that the strict electrotroph bacterium “Candidatus Tenderia electrophaga” is detected as an ennoblement biomarker and is only present at temperatures at which we observe ennoblement. This bacterium was previously enriched in biocathode systems. Our results suggest that “Candidatus Tenderia electrophaga,” and its previously described extracellular electron transfer metabolism coupled to oxygen reduction activity, could play a central role in modulating stainless steel open-circuit potential and consequently mediating ennoblement

Anaerobic oxidation of methane in hypersaline cold seep sediments

Life in hypersaline environments is typically limited by bioenergetic constraints. Microbial activity at the thermodynamic edge, such as the anaerobic oxidation of methane (AOM) coupled to sulphate reduction (SR), is thus unlikely to thrive in these environments. In this study, carbon and sulphur cycling was investigated in the extremely hypersaline cold seep sediments of Mercator mud volcano. AOM activity was partially inhibited but still present at salinity levels of 292 g L−1 (c. eightfold sea water concentration) with rates of 2.3 nmol cm−3 day−1 and was even detectable under saturated conditions. Methane and evaporite-derived sulphate comigrated in the ascending geofluids, which, in combination with a partial activity inhibition, resulted in AOM activity being spread over unusually wide depth intervals. Up to 79% of total cells in the AOM zone were identified by fluorescence in situ hybridization (FISH) as anaerobic methanotrophs of the ANME-1. Most ANME-1 cells formed monospecific chains without any attached partner. At all sites, AOM activity co-occurred with SR activity and sometimes significantly exceeded it. Possible causes of these unexpected results are discussed. This study demonstrates that in spite of a very low energy yield of AOM, microorganisms carrying this reaction can thrive in salinity up to halite saturatio

Oligotyping : differentiating between closely related microbial taxa using 16S rRNA gene data

© The Authors. Methods in Ecology and Evolution © 2013 British Ecological Society.. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Methods in Ecology and Evolution 4 (2013): 1111–1119, doi:10.1111/2041-210X.12114.Bacteria comprise the most diverse domain of life on Earth, where they occupy nearly every possible ecological niche and play key roles in biological and chemical processes. Studying the composition and ecology of bacterial ecosystems and understanding their function are of prime importance. High-throughput sequencing technologies enable nearly comprehensive descriptions of bacterial diversity through 16S ribosomal RNA gene amplicons. Analyses of these communities generally rely upon taxonomic assignments through reference data bases or clustering approaches using de facto sequence similarity thresholds to identify operational taxonomic units. However, these methods often fail to resolve ecologically meaningful differences between closely related organisms in complex microbial data sets. In this paper, we describe oligotyping, a novel supervised computational method that allows researchers to investigate the diversity of closely related but distinct bacterial organisms in final operational taxonomic units identified in environmental data sets through 16S ribosomal RNA gene data by the canonical approaches. Our analysis of two data sets from two different environments demonstrates the capacity of oligotyping at discriminating distinct microbial populations of ecological importance. Oligotyping can resolve the distribution of closely related organisms across environments and unveil previously overlooked ecological patterns for microbial communities. The URL http://oligotyping.org offers an open-source software pipeline for oligotyping.This work was supported by the National Institutes of Health [1UH2DK083993 to M.L.S.] and the Alfred P. Sloan Foundation

Draft Genome of Halomonas lionensis RHS90 T , a Stress-Tolerant Gammaproteobacterium Isolated from Mediterranean Sea Sediments

Members of the genus Halomonas are physiologically versatile and harbor ecological adaptations enabling the colonization of contrasted environments. We present here the draft genome of Halomonas lionensis RHS90T, isolated from Mediterranean Sea sediments. Numerous genes related to stress tolerance, DNA repair, or external signal-sensing systems were predicted, which could represent selective advantages of this marine bacterium

Draft Genome Sequence of Phaeobacter leonis Type Strain 306, an Alphaproteobacterium Isolated from Mediterranean Sea Sediments

International audiencePhaeobacter leonis strain 306T is an alphaproteobacterium isolated from Mediterranean Sea sediments. It belongs to the genus Phaeobacter, which was recently proposed and is still poorly characterized. In an effort to better understand the fundamental aspects of the microbiology of this genus, we present here the 4.82-Mb draft genome sequence of Phaeobacter leonis strain 306T

Données génétiques et indicateurs de biodiversité microbienne pélagique

Suivi par Isabelle Gailhard-RocherLe projet INDIGENE (2020-2022) a pour objectif d'évaluer la pertinence des données génétiques (métabarcodes) pour le développement d'indicateurs de changements de composition utilisables dans le cadre de la DCE et de la DCSMM pour le compartiment pélagique en milieu marin. Ce projet s'est appuyé sur les données de biodiversité génétique acquises régulièrement au cours de plusieurs années consécutives sur les sites d'observation à long terme des services nationaux d'observation (SNO) SOMLIT et PHYTOBS, complétés par des échantillonnages récents dans le port de la marina du château à Brest (2019-2020). Les sites sélectionnés, répartis le long de gradients côte-large et dans des milieux plus ou moins fermés comme la rade de Brest ainsi que sur des gradients d'anthropisation., offraient ainsi un panel varié de conditions environnementales. Le projet INDIGENE a permis de démontrer la faisabilité de s'appuyer sur des données génétiques pour alimenter certains indicateurs d'évaluation de l'état écologique des communautés planctoniques aujourd'hui développés pour répondre aux besoins des directives, et de dégager des hypothèses quant à la sensibilité de ces indicateurs aux pressions anthropiques, en fonction des données utilisées (métabarcodes ou dénombrements microscopiques)

Données génétiques et indicateurs de biodiversité microbienne pélagique

Suivi par Isabelle Gailhard-RocherLe projet INDIGENE (2020-2022) a pour objectif d'évaluer la pertinence des données génétiques (métabarcodes) pour le développement d'indicateurs de changements de composition utilisables dans le cadre de la DCE et de la DCSMM pour le compartiment pélagique en milieu marin. Ce projet s'est appuyé sur les données de biodiversité génétique acquises régulièrement au cours de plusieurs années consécutives sur les sites d'observation à long terme des services nationaux d'observation (SNO) SOMLIT et PHYTOBS, complétés par des échantillonnages récents dans le port de la marina du château à Brest (2019-2020). Les sites sélectionnés, répartis le long de gradients côte-large et dans des milieux plus ou moins fermés comme la rade de Brest ainsi que sur des gradients d'anthropisation., offraient ainsi un panel varié de conditions environnementales. Le projet INDIGENE a permis de démontrer la faisabilité de s'appuyer sur des données génétiques pour alimenter certains indicateurs d'évaluation de l'état écologique des communautés planctoniques aujourd'hui développés pour répondre aux besoins des directives, et de dégager des hypothèses quant à la sensibilité de ces indicateurs aux pressions anthropiques, en fonction des données utilisées (métabarcodes ou dénombrements microscopiques)