The hydrological context determines the beta-diversity of aerobic anoxygenic phototrophic bacteria in European Arctic seas but does not favor endemism

International audienceDespite an increasing number of studies over the last 15 years, aerobic anoxygenic photoheterotrophic (AAP) bacteria remain a puzzling functional group in terms of physiology, metabolism, and ecology. To contribute to a better knowledge of their environmental distribution, the present study aims at analyzing their diversity and structure at the boundary between the Norwegian, Greenland, and Barents Seas. The polymorphism of a marker gene encoding a sub-unit of the photosynthetic apparatus (pufM gene) was analyzed and attempted to be related to environmental parameters. The Atlantic or Arctic origin of water masses had a strong impact on the AAP bacterial community structure whose populations mostly belonged to the Alpha- and Gammaproteobacteria. A majority (>60%) of pufM sequences were affiliated to the Gammaproteobacteria reasserting that this class often represents the major component of the AAP bacterial community in oceanic regions. Two alphaproteobacterial groups dominate locally suggesting that they can constitute key players in this marine system transiently. We found that temperature is a major determinant of alpha diversity of AAP bacteria in this marine biome with specific clades emerging locally according to the partitioning of water masses. Whereas we expected specific AAP bacterial populations in this peculiar and newly explored ecosystem, most pufM sequences were highly related to sequences retrieved elsewhere. This observation highlights that the studied area does not favor AAP bacteria endemism but also opens new questions about the truthfulness of biogeographical patterns and on the extent of AAP bacterial diversity

Des plantes tropicales qui forment des mares : les broméliacées-citerne : un écosystème aquatique miniature capital pour la biodiversité

Les plantes qui présentent des structures anatomiques permettant de retenir de l'eau en permanence sont assez répandues en milieu tropical. Si beaucoup sont maintenant cultivées pour être vendues en jardineries, faisant le bonheur des amateurs, elles forment en milieu naturel des écosystèmes aquatiques encore très peu étudiés et renferment une biodiversité que l'on est loin d'avoir recensée. En Amérique centrale et du Sud, les broméliacées-citerne, qui représentent les plus nombreuses et les plus diversifiées de ces "plantes-mares", permettent à des organismes très variés d'accomplir leur cycle de vie

Clades of huge phages from across Earth's ecosystems.

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems

La communauté procaryotique dans les zones anoxiques de deux écosystèmes lacustres : structure et diversité. Etude plus particulière de son rôle fonctionnel dans le monimolimnion

The studies presented in this manuscript address the diversity and ecology of prokaryotic communities in anoxic zones of two pelagic lake ecosystems: the Lake Aydat typically eutrophic, which presents a period of thermal stratification anoxic hypolimnion, and Lake Pavin, unique meromictic lake in France, showing an area permanently anoxic. The analyzes of the structure, diversity, and spatial dynamics-and / or temporal bacterioplankton anoxic strata of these two lakes by molecular approaches have revealed high microbial diversity enhanced by spatial stratification of bacterioplankton. Further investigations on phylogenetic relationships and the study of microbial metabolism have focused on communities in the anoxic zone of Lake Pavin because of its original character. The clone libraries constructed from samples anoxic water taken at different strata in the monimolimnion revealed that bacterial communities are dominated by species affiliated to δ-Proteobacteria, to Verrucomicrobia, Bacteroidetes and the candidate division OP11. The sequences of 16S rRNA Archaea are mainly affiliated to the group of Methanosarcinales, an observation confirmed by in situ hybridization. In vitro studies of dissimilatory reduction of Fe (III), in cultures of enrichment, confirmed that high concentrations of ferrous iron observed in the sub-chemocline of Lake Pavin resulted partly from the activity of microorganisms. In these enrichments, microorganisms couple the reduction of Fe (III) with the preferential oxidation of fumarate, H2, CH4, and lactate. No accumulation of Fe (II) was observed in the enrichments supplemented with acetate as the electron donor. This observation suggests that this metabolite could be mainly used in the process of methanogenesis, and could be produced in part by the activity of gram-positive bacteria homoacétogènes. The heterogeneity of TTGE profiles made from the different conditions of enhancements WCR suggests that they may occupy very different ecological niches in the monimolimnion of Lac Pavin. No sequence was affiliated with the WCR * Required identified in other ecosystems. The affiliation of sequences in species of the genus Suggests that some SRB Desulfovibrio † use this electron acceptor. Activities Significant reduction of Fe (III) were also identified in strains fermentative isolated from the anoxic zone of the lake. The more specific study of the strain BS2 has revealed that this pathway could confer an advantage and therefore environmentally friendly energy. All the work that lies in the field of microbial ecology and environment opens a wide field of investigation as applied to the cognitive level. The provide opportunities to refine the understanding of the role of anaerobic microorganisms lake systems in biogeochemical cycles and more generally in understanding the role of microbial biodiversity in order to respond in a reasoned way to a societal demand strong in these areas.Les études présentées dans ce manuscrit traitent de la diversité et de l'écologie des communautés procaryotiques des zones anoxiques pélagiques de deux écosystèmes lacustres : le lac d'Aydat, typiquement eutrophe, qui présente en période de stratification thermique un hypolimnion anoxique ; et le lac Pavin, unique lac méromictique de France, exhibant une zone anoxique permanente. Les analyses de la structure, de la diversité, et de la dynamique spatiale et- /ou temporelle du bacterioplancton des strates anoxiques de ces deux lacs par des approches moléculaires ont révélé une forte diversité microbienne accentuée par une stratification spatiale du bacterioplancton. Les investigations complémentaires sur les relations phylogénétiques et sur l'étude de métabolismes microbiens ont été focalisées sur les communautés de la zone anoxique du Lac Pavin en raison de son caractère original. Les banques de clones construites à partir d'échantillons d'eau anoxique prélevés à différentes strates dans le monimolimnion ont révélé que les communautés bactériennes sont dominées par des espèces affiliées aux δ-Proteobacteria, aux Verrucomicrobia, aux Bacteroidetes et à la division candidate OP11. Les séquences ARNr16S des Archaea sont principalement affiliées au groupe des Méthanosarcinales, observation confirmée par hybridation in situ. Les études in vitro de la réduction dissimilatrice du Fe (III), dans des cultures d'enrichissements, ont confirmé que les concentrations élevées en fer ferreux observées dans la sub-chémocline du Lac Pavin résultaient pour partie de l'activité de microorganismes. Dans ces enrichissements, les microorganismes couplent la réduction du Fe (III) avec l'oxydation préférentielle du fumarate, de l'H2, du CH4 et du lactate. Aucune accumulation de Fe (II) n'a été notée dans les enrichissements supplémentés en acétate comme donneur d'électrons. Cette observation suggère que ce métabolite pourrait être principalement utilisé dans le processus de méthanogénèse, et pourrait être produit pour partie par l'activité de bactéries Gram-positives homoacétogènes. L'hétérogénéité des profils TTGE réalisés à partir des différentes conditions d'enrichissements de BFR suggère que ces dernières peuvent occuper des niches écologiques très diverses dans le monimolimnion du Lac Pavin. Aucune séquence n'a été affiliée à des BFR* obligatoires identifiées dans d'autres écosystèmes. L'affiliation de séquences à des espèces appartenant au genre Desulfovibrio suggère que certaines BSR† utilisent cet accepteur d'électron. Des activités significatives de réduction du Fe (III) ont également été mises en évidence chez des souches fermentatives isolées de la zone anoxique de ce lac. L'étude plus particulière de la souche BS2 a révélé que cette voie métabolique pouvait lui conférer un avantage énergétique et donc écologique. L'ensemble du travail qui se situe dans les domaine de l'écologie microbienne et de l'environnement ouvre un large champ d'investigations tant au niveau cognitif qu'appliqué. Les perspectives prévoient d'affiner la compréhension du rôle des microorganismes anaérobies des systèmes lacustres dans les cycles biogéochimiques et plus généralement dans la compréhension du rôle de la biodiversité microbienne afin de répondre de façon raisonnée à une demande sociétale forte dans ces domaines

La communauté procaryotique dans les zones anoxiques de deux écosystèmes lacustres (structure et diversité)

Les études présentées dans ce manuscrit traitent de la diversité et de l'écologie des communautés procaryotiques des zones anoxiques pélagiques de deux écosystèmes lacustres : le lac d'Aydat, typiquement eutrophe, qui présente en période de stratification thermique un hypolimnion anoxique ; et le lac Pavin, unique lac méromictique de France, exhibant une zone anoxique permanente. Ces travaux associent des approches d'écologie moléculaire (basées sur l'ARNr16S) et des approches culturales anaérobies visant à caractériser respectivement la diversté phylogénétique et métabolique des microorganismes de ces strates anoxiques. Les perspectives prévoient d'affiner la compréhension du rôle des microorganismes anaérobies des systèmes lacustres dans les cycles biogéochimiques et plus généralement du rôle de la biodiversité microbienne dans le fonctionnement global de ces écosystèmesCLERMONT FD-BCIU Sci.et Tech. (630142101) / SudocSudocFranceF

Biogeographic patterns of aerobic anoxygenic phototrophic bacteria reveal an ecological consistency of phylogenetic clades in different oceanic biomes

Abstract In marine environments, aerobic anoxygenic phototrophic (AAP) bacterial assemblages vary in space and along environmental gradients but the factors shaping their diversity and distribution at different taxonomic levels remain poorly identified. Using sets of sequences encoding the M sub-unit of the photosynthetic apparatus from different oceanic regions, we prioritized the processes underlying AAP bacterial biogeographical patterns. The present analysis offers novel insights into the ecological distribution of marine AAP bacteria and highlights that physiological constraints play a key role in structuring AAP bacterial assemblages at a global scale. Salinity especially seems to favor lineage-specific adaptations. Moreover, by inferring the evolutionary history of habitat transitions, a substantial congruence between habitat and evolutionary relatedness was highlighted. The identification of ecological cohesive clades for AAP bacteria suggests that prediction of AAP bacterial assemblages is possible from marine habitat properties

Members of candidate divisions OP11, OD1 and SR1 are widespread along the water column of the meromictic Lake Pavin (France).

International audienceThe vertical distribution of OP11, OD1 and SR1 divisions in the oxycline and in the anoxic water column of Lake Pavin, a freshwater permanently stratified mountain lake in France, was determined by temporal temperature gel gradient electrophoresis and 16S rRNA clone libraries. Gradual changes in the community structure were noted in relation to environmental variables along the oxidized/reduced environment. In addition, a separate effort to identify members of these lineages in the oxic mixolimnion identified sequences affiliated to SR1 and OP11 divisions, indicating that they are more widespread than previously expected

The atmosphere as an inoculator of a functional phyllosphere microbiota

International audienceThe aerial parts of plants constituting the phyllosphere are in constant interaction with the atmosphere and the microorganisms it transports. Some plants have specialized structures that allow them to collect rainwater, the phytotelms. Dipsacus fullonum is a pioneer plant found in the Auvergne region of France that forms water reservoirs around its stem, called phytotelms. Rainfall feeds these reservoirs with water and inoculate them with a particular microbiota, including a high population of anoxygenic phototrophic bacteria (APB), i.e. bacteria capable of utilizing light to generate energy, without fixing carbon dioxide and releasing oxygen. These bacteria often have an impressive capacity to fix atmospheric nitrogen, which is likely beneficial to the plant, which stimulates their development through specialized molecules and structures found inside the phytotelms: glandular hairs. A high concentration of bacteriochlorophyll, a photosynthetic pigment typical of APBs, has been identified by HPLC in reservoir’s water. The pufM gene coding for the small subunit of the photosynthetic reaction centre of APBs was detected by PCR in DNA extracted from phytotelm water, and it was also found prevalent in cloud and rain water samples. Living APB strains were also cultured and isolated from cloud water samples. The prevalence of these bacteria in the atmosphere suggests that anoxygenic photosynthesis could represent a strong selective advantage for survival, and so for long distance microbial dispersion. These bacteria could participate to the fixation of nitrogen in clouds and wet aerosols, and contribute to the biogeochemical cycle of nitrogen by reducing atmospheric N2 into NH3/NH4+ to an unsuspected extent globally

Phylogenetic Diversity of Archaea and Bacteria in the Anoxic Zone of a Meromictic Lake (Lake Pavin, France)

The compositions of archaeal and bacterial populations at different depths (60 m [mixolimnion-chemocline interface], 70 m [chemocline-subchemocline interface], 90 m, and 92 m [the water-sediment interface]) in the anoxic zone of the water column in Lake Pavin, a freshwater permanently stratified mountain lake in France, were determined. Phylogenetic trees were constructed from sequences to assess archaeal and bacterial diversity at the four sites

Diversity of culturable bacteria, from the anaerobic zone of the meromictic lake pavin, able to perform dissimilatory-iron reduction in different in vitro conditions

International audienceA culture-dependent study was performed with the aim of assessing the carbon, electron and Fe(III) sources used for the dissimilatory Fe(III) reduction pathway and the diversity of culturable Fe(III)-reducers in the anoxic zone of the meromictic Lake Pavin. This metabolic pathway was investigated in enrichment cultures inoculated with water samples collected at 70 m depth in the anoxic zone of Lake Pavin. Combinations of different media, organic acids, and incubation gas phases were performed. The potential for Fe(III) reduction in the different growth conditions was assessed by measuring the accumulation of Fe(II) overtime. Bacterial community structure was determined in each growth conditions by Temporal Temperature gradient Gel Electrophoresis (TTGE) profiles of 16S rDNA genes and bands of interest in positive enrichments were sequenced. Comparisons of bacterial community structure between growth conditions revealed that the electron donor, the basal media as well as the Fe(III) source yielded to the selection of different bacterial populations, suggesting that Fe(III) reducers occupy different ecological niches in the anoxic zone of Lake Pavin. Facultative Fe(III) reducers, such as fermentative (e.g., Pseudomonas, Clostridium) and sulphate-reducing (e.g., Desulfovibrio sp.) bacteria, were retrieved in enrichments but well-known obligatory Fe(III) reducers (e.g., Geobacter) were not detected. A greater Fe(III) reduction was noted under H2:CO2 gas phase, suggesting that H2 is used as an electron donor for Fe(III) reduction. Acetate was not used as a precursor for this terminal electron-accepting process, and a high Fe(III) reduction was observed with fumarate provided as the electron donor and carbon sources suggesting that this metabolite may be energetically more beneficial for Fe(III)-reducers