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Aragno, Michel
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Aragno, Michel
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Michel.Aragno@unine.ch
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- PublicationAccès libreAnaerobic iron cycling in a neoarchean ocean analogue(2011)
In the second chapter, we show direct evidences of a photoferrotrophic activity in the ferruginous meromictic lake La Cruz (Spain) that sustains dense populations of purple and green anoxygenic phototrophic bacteria despite low sulfate and sulfide concentrations. We observed in situ photoferrotrophic activity through stimulation of phototrophic carbon uptake in the presence of Fe(II), and quantified light-dependent Fe(II)-oxidation by the natural chemocline microbiota to assess their potential quantitative contribution to ancient BIF formation. In addition, a green photoferrotrophic bacterial consortium was enriched for the first time from a ferruginous water column. This new model ecosystem will allow testing current concepts on ancient primary productivity and its interactions with the iron- and sulphur cycles and may help to refine paleoenvironmental proxies.
In the third chapter, our results indicate, for the first time, that nitrate-dependent chemoautotrophic iron-oxidation occurred within Lake La Cruz chemocline. The organisms responsible for this Fe(II)-oxidation demonstrated, in optimized conditions, that their Fe(II)-oxidation rate was sufficiant to oxidize the totality of the dissolved Fe(II) arriving in the chemocline compartment (21.6 - 38.4 μmol Fe(II) I-1 d-1 and 0.174 - 1.393 μmol Fe(II) -1 d-1 respectively). MPN counts for anaerobic nitrate-dependent iron-oxidizers in other stratified water columns suggest that this metabolism is more widespread than previously thought. In addition, those results support a possible participation of such metabolism to BIFs formation during the Neoarchean, once nitrates were made available after the apparition of oxygenic photosynthesis.
In the forth chapter, the results from this study combined with those of previous studies allowed us to establish a biogeochemical model, including all the metabolisms thought to have existed in the Late Archean Ocean. Thus, Lake La Cruz illustrates how those microorganisms could have driven and shaped biogeochemical cycles during this period. Accordingly, the water column of Lake La Cruz may represent an ecotone between the two main Neoarchean Ocean compartments and, consequently, be a good model system, or samples source, for studying metabolic activity interactions in experimental conditions that reflect theoretical models of the Archean Ocean. - PublicationAccès libreDiscovery of anammox bacteria in terrestrial ecosystems(2011)
; Avant cette étude, le processus anammox (oxydation anaérobie de l’ammonium) était uniquement étudié dans les usines de traitement des eaux usées et dans les milieux aquatiques, sédiments inclus. Cependant, rien n'était connu encore sur la distribution, la diversité, l'abondance et l'activité des bactéries anammox dans les écosystèmes terrestres. Dans cette étude, nous apportons l’évidence, par approche moléculaire, de la présence de bactéries anammox dans les sols de zones humides, les sédiments des marais, le profil de sol d’un Reductisol, des sols de rives de lacs, un sol sur Permafrost et un aquifère poreux. L'analyse phylogénétique des séquences du gène ARNr 16S a démontrée que les bactéries anammox présentes dans les écosystèmes terrestres sont affiliées à Candidatus ‘Brocadia’, ‘Kuenenia’, ‘Scalindua’, ‘Jettenia’ and ‘Anammoxoglobus’ ainsi qu’à deux groupes non identifiés. Ces candidats anammox étaient largement distribués dans les différents environnements terrestres indiquant une plus grande diversité que dans les colonnes d’eau des milieux marins. Les bactéries anammox n'étaient pas présentes dans tous les milieux et fractions de sol échantillonnés, l’analyse démontrant leur distribution hétérogène et leurs besoins écologiques spécifiques comme la présence d’interfaces oxique / anoxique à long terme et de composés azotés inorganiques. Nous avons quantifié les bactéries anammox dans ces différents environnements en développant une nouvelle approche qPCR spécifique anammox, et leur abondance variait de 104 à 106 copies / g de sol. Finalement, le Réductisol a été sélectionné pour réaliser une analyse détaillée de l’activité anammox le long du profil de sol par des expériences d'incubation à l’isotope 15N. Pour chaque date d'échantillonnage, une production de 29N2 était observée à toutes les profondeurs du Réductisol, démontrant la présence de bactéries anammox actives. La contribution d‘anammox à la production totale de N2 était inférieure à 14%. Cette étude fournit la première preuve que les bactéries anammox sont présentes, diverses et actives dans les écosystèmes terrestres., Until this study, the anammox (anaerobic ammonium oxidation) process has been only studied in waste water treatment plants and aquatic environments, including sediments. However, nothing is known so far about the distribution, diversity, abundance and activity of anammox bacteria in terrestrial ecosystems. In this study, we provided molecular evidence for the presence of anammox bacteria in wetlands, sediments of marshes, a Reductisol profile, lake shores, a permafrost soil and a porous aquifer. Phylogenetic analysis of the 16S rRNA gene sequences showed that anammox bacteria from terrestrial ecosystems are affiliated to Candidatus ‘Brocadia’, ‘Kuenenia’, ‘Scalindua’, ‘Jettenia’ and ‘Anammoxoglobus’, as well as two unidentified clusters. They were widely distributed in the different terrestrial environments indicating a higher diversity than in marine water column environments. Anammox bacteria were not present in every sampled environments and soil fractions demonstrating their heterogeneous distribution and their specific ecological requirements as the presence of long term oxic/anoxic interfaces and inorganic nitrogen compounds. We quantified Anammox bacteria using a new developed qPCR approach applied to the different soil environments and their abundance ranged from 104 to 106 copies/g of soil. Finally, the Reductisol has been selected for a detailed analysis of their activity along the soil profile by 15N-isotope incubation experiments. For each sampling date, production of 29N2 was observed at all depths in the soil profile demonstrating the presence of active anammox bacteria. The amount of N2 produced by anammox is less than 14% of the total N2 production. This study provides the first evidence that anammox bacteria are present, diverse and active in terrestrial ecosystems. - PublicationMétadonnées seulementUse of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil(2009)
; ; Oxalate catabolism, which can have both medical and environmental implications, is performed by phylogenetically diverse bacteria. The formyl-CoA-transferase gene was chosen as a molecular marker of the oxalotrophic function. Degenerated primers were deduced from an alignment of frc gene sequences available in databases. The specificity of primers was tested on a variety of frc-containing and frc-lacking bacteria. The frc-primers were then used to develop PCR-DGGE and real-time SybrGreen PCR assays in soils containing various amounts of oxalate. Some PCR products from pure cultures and from soil samples were cloned and sequenced. Data were used to generate a phylogenetic tree showing that environmental PCR products belonged to the target physiological group. The extent of diversity visualised on DGGE pattern was higher for soil samples containing carbonate resulting from oxalate catabolism. Moreover, the amount of frc gene copies in the investigated soils was detected in the range of 1.64x10(7) to 1.75x10(8)/g of dry soil under oxalogenic tree (representing 0.5 to 1.2% of total 16S rRNA gene copies), whereas the number of frc gene copies in the reference soil was 6.4x10(6) (or 0.2% of 16S rRNA gene copies). This indicates that oxalotrophic bacteria are numerous and widespread in soils and that a relationship exists between the presence of the oxalogenic trees Milicia excelsa and Afzelia africana and the relative abundance of oxalotrophic guilds in the total bacterial communities. This is obviously related to the accomplishment of the oxalate-carbonate pathway, which explains the alkalinization and calcium carbonate accumulation occurring below these trees in an otherwise acidic soil. The molecular tools developed in this study will allow in-depth understanding of the functional implication of these bacteria on carbonate accumulation as a way of atmospheric CO2 sequestration. (c) 2008 Elsevier B.V. All rights reserved. - PublicationAccès libreUse of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil(2009)
; ; Oxalate catabolism, which can have both medical and environmental implications, is performed by phylogenetically diverse bacteria. The formyl-CoA-transferase gene was chosen as a molecular marker of the oxalotrophic function. Degenerated primers were deduced from an alignment of frc gene sequences available in databases. The specificity of primers was tested on a variety of frc-containing and frc-lacking bacteria. The frc-primers were then used to develop PCR-DGGE and real-time SybrGreen PCR assays in soils containing various amounts of oxalate. Some PCR products from pure cultures and from soil samples were cloned and sequenced. Data were used to generate a phylogenetic tree showing that environmental PCR products belonged to the target physiological group. The extent of diversity visualised on DGGE pattern was higher for soil samples containing carbonate resulting from oxalate catabolism. Moreover, the amount of frc gene copies in the investigated soils was detected in the range of 1.64 × 107 to 1.75 × 108/g of dry soil under oxalogenic tree (representing 0.5 to 1.2% of total 16S rRNA gene copies), whereas the number of frc gene copies in the reference soil was 6.4 × 106 (or 0.2% of 16S rRNA gene copies). This indicates that oxalotrophic bacteria are numerous and widespread in soils and that a relationship exists between the presence of the oxalogenic trees Milicia excelsa and Afzelia africana and the relative abundance of oxalotrophic guilds in the total bacterial communities. This is obviously related to the accomplishment of the oxalate–carbonate pathway, which explains the alkalinization and calcium carbonate accumulation occurring below these trees in an otherwise acidic soil. The molecular tools developed in this study will allow in-depth understanding of the functional implication of these bacteria on carbonate accumulation as a way of atmospheric CO2 sequestration. - PublicationMétadonnées seulementEcological determinants of fungal diversity on deadwood in European forests(2008)
; ; The fine-scale ecological determinants for wood-inhabiting aphyllophoroid basidiomycetes were investigated with statistical analyses of the occurrence of fruit bodies on woody debris collected in Switzerland and Ukraine. Three substrate descriptors were considered: diameter, degree of decomposition to those local environmental descriptors were detected. Three classes for diameter, as well as for degree of decomposition were thus delimited. They revealed the importance of very small sizes, which were not reported in the literature so far: the relevant diameter class limits were about 0.72 cm and 1.35 cm. Within the host tree species, a clear distinction between coniferous and broadleaf species was found. The next splits followed rather climatic determinants of tree distribution than taxonomical entities such as families or genera. The fidelity of the 59 fungal species to diameter classes, decomposition classes and host tree species was measured by the Dufrene-Legendre index and only significant responses after permutation tests were retained. This brought new insights on the ecology of many wood-inhabiting aphyllophoroid basidiomycetes. Redundancy Analysis was applied to investigate the response of fungal species to diameter and degree of decompostion of woody debris from the most common host tree species, Fagus sylvatica. This direct gradient analysis made it possible to reconstruct the succession of fungal species along the wood decomposition process. - PublicationAccès librePlant and soil microbe interactions in controlled conditions: rhizosphere protozoa and bacterial community structure(2008)
; Plants influence the soil system by the large proportion of photosynthesized matters translocated to the roots and secreted into the soil. This root exudation provides an abundant energy source for rhizosphere living microorganisms. Plants are also strongly affected, positively and negatively, by the presence of soil microbiota, particularly bacteria, protozoa and fungi. Throughout the experiments conducted in this work, we aimed to better understand the influence of protozoa on plant growth. The first part of this work focused on the development of a microcosm method. Firstly, physical soil sterilization methods (autoclaving (A) gamma-ray irradiation (i) and both successively (AI)) were tested to eliminate the soil microbiota and their resistance form (spores and cysts). Although all sterilization methods tested were efficient to eliminate protozoa, AI was the only efficient method to eliminate aerobic heterotrophic cultivable bacteria without changing the soil pH. However the release of NH4+ in the soil after AI sterilization was higher than for other methods. Secondly, a procedure to re-inoculate the sterilized soil with a complex microbial community without protozoa was developed. The protozoa-free bacterial suspension was obtained from rhizosphere soil by subsequent filtering steps to exclude protozoa. The structure of bacterial communities characterised by 16SrDNA PCR-DGGE in the protozoa-free bacterial suspension was similar to that of the native soil. Diversity (Shannon) and evenness indexes increased with time in the sterile soil inoculated with the protozoa-free bacterial suspension. However the final bacterial community composition after 2 months of incubation in the re-inoculated soil presented a lower diversity as compared to the native soil. The second part of this work focused on the plant-microbiota interactions and on protozoa effects on plant growth. The microcosms developed in the first part of the work were re-inoculated with either sterile water or bacterial protozoa-free suspension or bacterial protozoa-free suspension and Acanthamoeba castellanii or with native soil suspension. The growth of Arabidopsis thaliana was clearly influenced by the inoculum and was particularly increased in presence of protozoa. Plants cultivated in presence of protozoa presented higher nitrogen content in leaves. The effect of leaf clipping (simulating herbivore damage) and nitrogen fertilization on soil microorganisms (bacteria, protozoa and nematodes) associated to the rhizosphere of barley was investigated in a pot experiment. The roots-shoots ratio decreased during the plant growth and was lower in the leaf clipping treatment. The abundance of bacteria was not significantly affected by leaf clipping and was higher in the high nitrogen-treatment. The abundance of bacterial-feeders (i.e. protozoa and nematodes) in the rhizosphere of 2, 4 and 6 weeks old plants was marginally affected by the nitrogen treatment as well as by leaf clipping. The role of protozoa in controlling the structure of bacterial community was investigated in the different experiment. The presence of protozoa did not change significantly the richness (numbers of bands) and the diversity (Shannon index) of the DNA-based DGGE fingerprints. The structure of the “total” bacterial communities was significantly changed in response to the functional group of protozoa (amoeba, ciliates and flagellates) inoculated as compared to the control (bacteria inoculum). The presence of protozoa did not change significantly the richness and the diversity of the RNA-based DGGE fingerprints. The structure of the active bacterial communities was significantly influenced by amoebas. - PublicationAccès libreSpatio-temporal dynamics of bacterial communities associated with two plant species differing in organic acid secretion: A one-year microcosm study on lupin and wheat(2008)
; ; - PublicationAccès libreRhizosphere bacterial communities associated with Lolium perenne: structuration and plant-mediated influences(2008)
- PublicationAccès librePlant growth stage, fertiliser management and bio-inoculation of arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria affect the rhizobacterial community structure in rain-fed wheat fields(2006)
- PublicationAccès librePhenotypic structure of Pseudomonas populations is altered under elevated pCO2 in the rhizosphere of perennial grasses(2006)
; Fromin, NathalieThe increasing atmospheric CO2 content (pCO2) is likely to modify the ecosystem functioning including rhizosphere bacteria that are directly dependent on rhizodeposition. This may include alteration of Pseudomonas populations that display phenotypic traits in relation with plant fitness. In the present study, 1228 Pseudomonas strains were isolated from the non-rhizosphere soil, rhizosphere soil and root fractions of perennial grassland systems: Lolium perenne and Molinia coerulea. Both plants were grown under ambient (36 Pa) and elevated (60 Pa) pCO2 in the Swiss Free Air CO2 Enrichment (FACE) system. Pseudomonas spp. were tested for their ability to produce auxin, siderophores and hydrogen cyanide, and to dissimilate nitrate. No effect of root proximity and elevated pCO2 was observed on the proportions of auxin producers. For L. perenne and M. coerulea, siderophore and hydrogen cyanide Pseudomonas producers were stimulated in the root fraction. In contrast lower frequencies of nitrate reducers were observed in the root fraction compared to non-rhizosphere soil. The frequencies of siderophore producers and nitrate dissimilating strains were higher, and those of hydrogen cyanide producers lower, under elevated pCO2 for L. perenne. This alteration of the phenotypic structure of Pseudomonas guild in the root fraction is discussed in relation with the physico-biochemical modifications of the rhizosphere condition via rhizodeposition and environmental changes occurring under elevated pCO2.