Résultat de la recherche
Anaerobic iron cycling in a neoarchean ocean analogue
The deposition of Banded Iron Formation (BIF) during the Archean and Paleoproterozoic is conventionally attributed to the precipitation of iron-oxides resulting from the abiotic reaction of ferrous iron (Fe(II)) with oxygen (Cloud, 1968). Oxygenic photosynthesis, however, appeared only around 2.7 Ga (Des Marais, 2000; Kump, 2008; Godfrey & Falkowski, 2009 ), thus raising questions as to what may have caused BIF precipitation before that time. The discovery of anoxygenic phototrophs thriving through the oxidation of Fe(II) (Widdel et al., 1993; Heisinget al., 1999) has provided support for a bacterial origin for early BIFs (Konhauseret al., 2002; Kappler et al., 20051). Despite reports of anoxygenic phototrophs that may oxidise Fe(II) in the environment (Crowe et al., 2008), a model ecosystem where photoferrotrophs are demonstrably active is still lacking (Svermann & Anbar, 2009; Johnston et al., 2009). Therefore, the ferruginous meromictic lake La Cruz (Spain) that sustains dense populations of purple and green anoxygenic phototrophic bacteria despite low sulfate and sulfide concentrations was investigated. First, the system was characterized by a physico-chemical analysis of its water column and sediments. Then we focuses on the chemocline compartment where iron oxides were found to be produced. On the one hand, We performed in situ 14C-bicarbonate incubations to detect any stimulation of autotrophy by Fe(II) addition, while on the other hand ex situ incubations were carried out with the same natural sample to detect any Fe(II) oxidation by Lake La Cruz microbiota. In parallel, we have done enrichment cultures targeting anaerobic iron oxidizing metabolisms.
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.
Use of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil
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.
Rhizosphere bacterial communities associated with Lolium perenne: structuration and plant-mediated influences
Du fait de leur présence, leur activité et leur physiologie, les racines des plantes influencent physiquement, chimiquement et biologiquement leur sol environnant. Certains microorganismes du sol vont être favorisés, ou au contraire inhibés par les racines. La rhizosphère, à la jonction entre le sol et la plante, favorise de plus une activité intense en raison de la stimulation de la microflore par la rhizodéposition et de la variété des micro-habitats. Un lien étroit existe entre les microorganismes du sol et la plante, en particulier lorsque l’on considère les plantes pérennes qui, se maintenant d’année en année au même endroit, présentent des communautés particulièrement adaptées à leur environnement. Parmi ces plantes, la graminée nitrophile Lolium perenne a été choisie dans cette étude comme plante modèle pour son abondance et son importance dans le domaine agricole en tant que plante fourragère. Les activités des microorganismes sont extrêmement diversifiées et ont un impact important au niveau de la fertilité des sols (ex : cycles des éléments nutritifs, formation et décomposition de la matière organique) et de la santé des plantes. Ces organismes constituent de ce fait le principal champ d’investigation pour le développement de bio-fertilisants et de bio-pesticides. L’impact des microorganismes et en particulier des bactéries, sur la croissance et la résistance de la plante est couramment reconnu. Les connaissances concernant l’importance des différents groupes fonctionnels bactériens de la rhizosphère, leur écologie et leur structuration, doivent cependant être enrichies afin d’améliorer la compréhension des interactions entre plantes et microorganismes dans la rhizosphère, et d’augmenter le potentiel des bio-fertilisants. Les objectifs principaux des expériences menées dans cette étude consistent à élargir les connaissances du fonctionnement de la rhizosphère, et de la structuration des communautés bactériennes. Les communautés bactériennes totales, actives et cultivables de la rhizosphère sont caractérisées en relation avec différentes perturbations (variations au niveau du génotype de la plante, modifications dues au développement de la plante, changements liés au climat global). Ceci afin de cibler les modifications spécifiques aux différentes conditions et d’identifier les populations susceptibles de tenir une place importante dans le fonctionnement de la rhizosphère et la promotion de la croissance des plantes. Toutes les approches de communautés sont réalisées dans le même sol agricole afin de conserver la contribution du sol dans le fonctionnement rhizosphérique. Les approches génotypiques des communautés bactériennes totales et actives, au champ et en serre, montrent que les influences liées à la racine affectent peu la diversité globale, et que les communautés métaboliquement actives se révèlent être plus sensibles aux perturbations liées à la plante que les communautés totales. Ce qui indique que l’influence des racines se manifeste par la prolifération, ou au contraire la mise en dormance, de populations spécifiques au sein du réservoir bactérien représenté par les communautés du sol. L’établissement, in vitro, du profil fonctionnel des populations bactériennes associées à différents cultivars (diploïdes: Cavia, Lipresso ; tétraploïdes: Anaconda, Bastion) et stades de développement de L. perenne, permet de mettre en évidence les fonctions bactériennes dont la fréquence est affectée par ces deux facteurs liés à la plante. Le cultivar Anaconda semble héberger des communautés particulièrement spécifiques. De plus, quel que soit le cultivar, le passage de la floraison de la plante semble être un stade critique, à partir duquel l’influence de la plante s’estompe et les caractéristiques des communautés rhizosphériques tendent à rejoindre celles du sol nu. Cette approche fonctionnelle est également employée pour comparer, dans l’environnement racinaire et dans le sol nu, les fréquences de certaines capacités bactériennes connues comme étant impliquées dans les interactions entre plantes et bactéries, ainsi que pour mettre en évidence les corrélations entre ces différentes capacités. La caractérisation du sol rhizosphérique des différents cultivars, ainsi que l’analyse de leurs exudats racinaires (acides organiques, composés phénoliques), mettent en évidence des différences cohérentes avec les celles observées au niveau du profil fonctionnel de leurs communautés bactériennes rhizosphériques. Une approche génotypique (au champ) des communautés bactériennes associées à L. perenne, effectuée précédemment au LAMUN, a révélé l’importance du groupe des Pseudomonas. Dans l’étude présentée ici, l’approche génotypique (au champ) ainsi que l’approche fonctionnelle (in vitro) de ces communautés mettent toutes les deux en évidence le groupe des Actinobacteria. Connu pour être particulièrement résistant aux perturbations et adapté au statut nutritionnel limité du sol. Ce groupe s’avère tenir une place importante au sein des populations actives de la rhizosphère. Il est également le principal groupe de minéralisateurs potentiel de phytate dans des conditions limitantes en P inorganique et en présence de C soluble; deux conditions fréquemment rencontrées dans la rhizosphère. Les capacités des Actinobacteria semblent être essentielles pour le maintien à long terme des environnements changeants et devraient être étudiés dans la rhizosphère avec beaucoup plus d’attention., Due to their presence, activity and physiology, plant roots influence physically, chemically and biologically their surrounding soil. Some microorganisms will be favoured, or on the contrary inhibited by roots. As the junction between soil and plant, the rhizosphere presents an intense activity because of the stimulation of microflora by rhizodeposition and of the existence of various micro-habitats. A close link exists between soil microorganisms and plants, in particular when considering perennial plants which, growing at the same place from year to year, present particularly adapted associated microbial communities. Among these plants, the nitrophilic perennial grass Lolium perenne, was choosen in this study as model plant because of its abundance, and its agricultural importance as forage plant. Microorganisms’ activities are extremely diversified and strongly implicated in soil fertility (nutrient cycling, organic matter formation and decomposition) and plant health. These organisms are therefore the main investigation field for development of bio-fertilisers and biopesticides. The impact of microorganisms, in particular of bacteria, on plant growth and resistance is currently well recognised. Knowledge about the importance of the different functional groups of bacteria in the rhizosphere, their ecology, and their structuration, have nevertheless to be enriched to improve the understanding of plant-bacteria interactions in the rhizosphere, and to increase the potential of biofertilisers. Throughout the experiments conducted in this work, the main aims are to gain additionnal knowledge about rhizosphere functionning and structuration of bacterial communities. Total, active and culturable rhizosphere bacterial communities are characterised in relation with different perturbations (plant genotype variations, modifications due to plant development, and to global climate changes), in order to target the modifications, which are specific of the different conditions, and to identify bacterial groups likely to take an important place in rhizosphere functionning and plant growth promotion. All the community approaches were conducted in the same agricultural soil in order to conserve the soil contributions in the rhizosphere functionning. Genomic approaches of total and active bacterial communities, performed in field and in greenhouse conditions in the same agricultural soil, revealed that root-mediated perturbations affect only slightly the global divesity, and that the metabolically active part of the communities was more sensitive to plant-mediated influences than the total communities. Indicating that root influence lead to the proliferation or, on the contrary, to the dormance, of specific populations among the bacterial reservoir represented by soil bacterial communities. The establishment, in vitro, of the functional profiles of bacterial populations associated with different cultivars (diploïdes: Cavia, Lipresso ; tetraploïdes: Anaconda, Bastion) and development stages of L. perenne, allows to highlight the bacterial functions presenting frequencies which are affected by these two plant-related factors. Anaconda cultivar seems to harbour particularly specific bacterial communities. Furthermore, whatever the cultivar, plant flowering appears to be a critical stage beyond which plant influence is attenuated, and characteristics of rhizosphere communities tend to gather with those of bulk soil communities. This functional approach is also used to compare, in the root environment and in the bulk soil, the frequencies of some bacterial abilities known to be implicated in plant-bacteria interactions, and to highlight the existence of correlations between these different abilities. Furthermore, the characterisation of the rhizosphere soil of the different cultivars, and the analysis of their root exudates (organic acids, phenolics), allows to highlight differences coherent with those observed on the functional profiles of their bacterial communities. A genomic approach (field conditions) of bacterial communities associated to L. perenne, performed in previous experiments, revealed the importance of the Pseudomonas group. In the present study, the genomic approach (field conditions), as well as the functional approach (in vitro) of these communities, both highlighted the Actinobacteria group. Known to be particularly resitant to perturbations and to be adapted to the poor nutrient status of the soil, this group take an important place in the key active rhizosphere populations. It is also the main group of potential phytate mineralisers under limiting inorganic P conditions and in presence of soluble C sources; two frequent characteristics of the rhizosphere environment. The abilities of Actinobacteria are thought to be essential for long term maintaning of changing environments and have to be investigated in the rhizosphere whith more attention.
How elevated pCO2 modifies total and metabolically active bacterial communities in the rhizosphere of two perennial grasses grown under field conditions
The response of total (DNA-based analysis) and active (RNA-based analysis) bacterial communities to a pCO2 increase under field conditions was assessed using two perennial grasses: the nitrophilic Lolium perenne and the oligonitrophilic Molinia coerulea. PCR- and reverse transcriptase-PCR denaturing gradient gel electrophoresis analysis of 16S rRNA genes generated contrasting profiles. The pCO2 increase influenced mainly the active and root-associated component of the bacterial community. Bacterial groups responsive to the pCO2 increase were identified by sequencing of corresponding denaturing gradient gel electrophoresis bands. About 50% of retrieved sequences were affiliated to Proteobacteria. Our data suggest that Actinobacteria in soil and Myxococcales (Deltaproteobacteria) in root are stimulated under elevated pCO2.
Discovery of anammox bacteria in terrestrial ecosystems
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.
Ecological determinants of fungal diversity on deadwood in European forests
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.
Plant and soil microbe interactions in controlled conditions: rhizosphere protozoa and bacterial community structure
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.
Use of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil
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.
Spatio-temporal dynamics of bacterial communities associated with two plant species differing in organic acid secretion: A one-year microcosm study on lupin and wheat
Plants are generally assumed to influence the surrounding soil microflora through rhizodeposition. However, the role of rhizodeposits, and especially organic acids, in structuring the bacterial communities is still poorly understood. In this study, we asked the question whether plants differing in organic acid secretion have a different impact on the soil bacterial communities, and if this is the case, to which extent this impact is due to different organic acid concentrations in the rhizosphere. To investigate this question, we compared white lupin and wheat. The former is a high organic acid-secreting species, while the latter secretes only low amounts of carboxylates. We grew the plants in large microcosms including root-free control compartments for one year (replanted every second month) and analyzed the spatio-temporal changes in soil ATP concentrations, as well as in diversity and structure of bacterial communities (using DNA- and RNA-based DGGE) along a root-soil gradient after two, six and twelve month's cultivation. Our results showed: i) that white lupin and wheat differed in their impact on soil ATP concentrations and on the structure of root bacterial communities; ii) that cultivation time was a key factor in explaining the observed differences in all the parameters studied; and iii) that the amounts of organic acids accounted for a significant proportion (15%) of the variability within root active communities. These results indicate that plants influence their associated bacterial communities in a species-specific way and that for communities living in the direct vicinity of roots (rhizoplane-endorhizosphere), a significant part of this influence can be attributed to root-secreted organic acids.
Plant 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
The goal of this study was first to assess the dynamics of the bacterial community during a growing season in three Indian rain-fed wheat fields which differ mainly through their fertilizer management and yield and then to study the effects of PGPR/AMF bio-inoculations on the bacterial community structure and wheat growth. The bacterial community structure of the rhizosphere soil (RS) and the rhizoplane/endorhizosphere (RE) was determined by PCR-denaturing gradient gel electrophoresis. Seed treatments consisted of consortia of two PGPR strains alone or combined with AMF or AMF alone. The PGPR strains were Pseudomonas spp. which included some or all of the following plant growth promoting properties: phosphate solubilisation and production of indole-3-acetic acid, siderophores, 1-aminocyclopropane-1-carboxylate deaminase and diacetyl-phloroglucinol. The mycorrhizal inoculum was an indigenous AMF consortium isolated from the field with the lowest level of fertilization and yield. Variation partitioning analysis of the DGGE data indicated a predominant effect of the wheat growth stage (30.4% of the variance, P=0.001) over the type of field (9.0%, P=0.027) on the bacterial community structure in the RE. The impact of plant age in the RS was less than in the RE and the bacterial community structure of the field with the highest input of fertilization was very different from the low input fields. The bio-inoculants induced a significant modification in the bacterial community structure. In the RS, the bacterial consortia explained 28.3% (P=0.001) and the presence of AMF 10.6% (P=0.02) of the variance and the same trend was observed in the RE. Plant yield or grain quality was either increased or remained unaffected. For example, protein content was significantly higher in the treated plants' grain compared to the control plants; maximum values were obtained when the PGPR were co-inoculated with the AMF. The percentage of root colonization by AMF was significantly higher in the treatments containing a mycorrhizal inoculum than in the untreated control and remained unaffected by the PGPR treatments. In conclusion, the wheat rhizobacterial community structure is highly dynamic and influenced by different factors such as the plant's age, the fertilizer input and the type of bio-inoculant. In addition, there is a distance-related effect of the root on the bacterial community. Finally, a combined bio-inoculation of diacetyl-phloroglucinol producing PGPR strains and AMF can synergistically improve the nutritional quality of the grain without negatively affecting mycorrhizal growth.