Michel Aragno

Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots

Abstract The rhizosphere of Trifolium repens and Lolium perenne was divided into three fractions: the bulk soil; the soil adhering to the roots; and the washed roots (rhizoplane and endorhizosphere). After isolation and purification of DNA from these fractions, 16S rDNA was amplified by PCR and cloned to obtain a collection of 16S rRNA genes representative of the bacterial communities of these three fractions. The cloned 16S rRNA genes were then partially sequenced and analysed by a molecular phylogenetic approach. Our data show a high diversity in the bulk soil, which is dominated by clones related to Gram-positive, Cytophaga–Flexibacter–Bacteroides, Proteobacteria , and Holophaga–Acidobacterium groups. The ubiquity of members of the Holophaga–Acidobacterium group, which is composed of sequences of yet-uncultivated microorganisms, is confirmed. The plant roots have a selective effect towards the gamma Proteobacteria , to the detriment of the Gram-positive and the Holophaga–Acidobacterium bacteria, leading to a dominance of Pseudomonas . This work shows by a culture independent approach that the phylogenetic diversity decreases in the proximity of plant roots.

Molecular detection of anammox bacteria in terrestrial ecosystems: distribution and diversity

Anaerobic oxidation of ammonium (anammox) is recognized as an important process in the marine nitrogen cycle yet nothing is known about the distribution, diversity and activity of anammox bacteria in the terrestrial realm. In this study, we report on the detection of anammox sequences of Candidatus ‘Brocadia’, ‘Kuenenia’, ‘Scalindua’ and ‘Jettenia’ in marshes, lakeshores, a contaminated porous aquifer, permafrost soil, agricultural soil and in samples associated with nitrophilic or nitrogen-fixing plants. This suggests a higher diversity of anammox bacteria in terrestrial than in marine ecosystems and could be a consequence of the larger variety of suitable niches in soils. Anammox bacteria were not ubiquitously present but were only detected in certain soil types and at particular depths, thus reflecting specific ecological requirements. As opposed to marine water column habitats where Candidatus ‘Scalindua’ dominates anammox guilds, ‘Kuenenia’ and ‘Brocadia’ appear to be the most common representatives in terrestrial environments.

Influence of an Elevated Atmospheric CO2 Content on Soil and Rhizosphere Bacterial Communities Beneath Lolium perenne and Trifolium repens under Field Conditions

A bstractThe increase in atmospheric CO2 content alters C3 plant photosynthetic rate, leading to changes in rhizodeposition and other root activities. This may influence the activity, the biomass, and the structure of soil and rhizosphere microbial communities and therefore the nutrient cycling rates and the plant growth. The present paper focuses on bacterial numbers and on community structure. The rhizospheres of two grassland plants, Lolium perenne (ryegrass) and Trifolium repens (white clover), were divided into three fractions: the bulk soil, the rhizospheric soil, and the rhizoplane–endorhizosphere. The elevated atmospheric CO2 content increased the most probable numbers of heterotrophic bacteria in the rhizosphere of L. perenne. However, this effect lasted only at the beginning of the vegetation period for T. repens. Community structure was assessed after isolation of DNA, PCR amplification, and construction of cloned 16S rDNA libraries. Amplified ribosomal DNA restriction analysis (ARDRA) and colony hybridization with an oligonucleotide probe designed to detect Pseudomonas spp. showed under elevated atmospheric CO2 content an increased dominance of pseudomonads in the rhizosphere of L. perenne and a decreased dominance in the rhizosphere of T. repens. This work provides evidence for a CO2-induced alteration in the structure of the rhizosphere bacterial populations, suggesting a possible alteration of the plant-growth-promoting-rhizobacterial (PGPR) effect.

Bacterial diversity in the bulk soil and rhizosphere fractions of Lolium perenne and Trifolium repens as revealed by PCR restriction analysis of 16S rDNA

The rhizosphere of Trifolium repens and Lolium perenne was divided into three fractions: the bulk soil, the soil adhering to the roots and the washed roots (rhizoplane and endorhizosphere). After isolation and purification of DNA from these fractions, 16S rDNA was amplified by PCR and cloned to obtain a collection of 16S rRNA genes representative of the bacterial communities of these three fractions. The genes were then characterized by PCR restriction analysis. Each different profile was used to define an operational taxonomic unit (OTU). The numbers of OTUs and the numbers of clones among these OTUs allowed to calculate a diversity index. The number of OTUs decreased as root proximity increased and a few OTUs became dominant, resulting in a lower diversity index. In the root fraction of T. repens, the restriction profile of the dominant OTU matched the theoretical profile of the 16S rRNA gene of Rhizobium leguminosarum. This study showed that plant roots create a selective environment for microbial populations.

Is the contribution of bacteria to terrestrial carbon budget greatly underestimated

Abstract. Some commonly found species of soil bacteria use low molecular weight organic acids as their sole source of carbon and energy. This study shows that acids such as citrate and oxalate (produced in large amounts by fungi and plants) can rapidly be consumed by these bacteria. Two strains, Ralstonia eutropha and Xanthobacter autotrophicus, were cultured on acetate- and citrate-rich media. The resulting CO2 and/or HCO3– reacted with calcium ions to precipitate two polymorphs of calcium carbonate (CaCO3), calcite and vaterite, depending on the quantity of slime produced by the strains. This production of primary calcium carbonate crystals by oxalate- and citrate-degrading bacteria from soil organic carbon sources highlights the existence of an important and underestimated potential carbon sink.

Taxonomic and Metabolic Microbial Diversity During Composting

A great variety and high numbers of aerobic thermophilic heterotrophic and/or autotrophic bacteria growing at temperatures between 60–80°C have been isolated from thermogenic (temperature 60–80°C) composts in several composting facilities in Switzerland. They include strains related to the genus Thermus (T. thermophilus. T. aquaticlls. and several other new strains). Bacillus schlegelii, Hydrogenohacter spp., and of course heterotrophic sporeforming Bacilli. This contrasts with the generally held belief that thermogenic composts (> 60°C) support only a very low diversity of heterotrophic thermophiles. This biodiversity suggests efficient decomposition of organic matter at temperatures above 60°C, and a good thermo-hygienization.

Bacteria associated with spores of the arbuscular mycorrhizal fungi Glomus geosporum and Glomus constrictum.

ABSTRACT Spores of the arbuscular mycorrhizal fungi (AMF) Glomus geosporum and Glomus constrictum were harvested from single-spore-derived pot cultures with either Plantago lanceolata or Hieracium pilosella as host plants. PCR-denaturing gradient gel electrophoresis analysis revealed that the bacterial communities associated with the spores depended more on AMF than host plant identity. The composition of the bacterial populations linked to the spores could be predominantly influenced by a specific spore wall composition or AMF exudate rather than by specific root exudates. The majority of the bacterial sequences that were common to both G. geosporum and G. constrictum spores were affiliated with taxonomic groups known to degrade biopolymers (Cellvibrio, Chondromyces, Flexibacter, Lysobacter, and Pseudomonas). Scanning electron microscopy of G. geosporum spores revealed that these bacteria are possibly feeding on the outer hyaline spore layer. The process of maturation and eventual germination of AMF spores might then benefit from the activity of the surface microorganisms degrading the outer hyaline wall layer.

The Hydrogen-Oxidizing Bacteria

The group of aerobic hydrogen-oxidizing bacteria is physiologically defined and comprises bacteria from different taxonomic units. This group is defined by the ability to utilize gaseous hydrogen as electron donor with oxygen as electron acceptor and to fix carbon dioxide; i.e., to grow chemolithoautotro-phically. These hydrogen-oxidizing bacteria sensu stricto are different from those other bacteria (Acetobacter, Azotobacter, Enterobacteriaceae, and others) that also oxidize hydrogen under aerobic conditions, but without autotrophic CO2 fixation. Furthermore, they are different from the bacteria that utilize hydrogen under anaerobic conditions, with sulfate or carbon dioxide as hydrogen acceptors (e.g., Desulfovibrio, Clostridium aceticum, Aceto-bacterium woodii, and Methanobacterium thermo-autotrophicum).

Obligately and facultatively autotrophic, sulfur- and hydrogen-oxidizing thermophilic bacteria isolated from hot composts

Abstract A variety of autotrophic, sulfur- and hydrogen-oxidizing thermophilic bacteria were isolated from thermogenic composts at temperatures of 60–80° C. All were penicillin G sensitive, which proves that they belong to the Bacteria domain. The obligately autotrophic, non-spore-forming strains were gram-negative rods growing at 60–80°C, with an optimum at 70–75°C, but only under microaerophilic conditions (5 kPa oxygen). These strains had similar DNA G+C content (34.7–37.6 mol%) and showed a high DNA:DNA homology (70–87%) with Hydrogenobacter strains isolated from geothermal areas. The facultatively autotrophic strains isolated from hot composts were gram-variable rods that formed spherical and terminal endospores, except for one strain. The strains grew at 55–75° C, with an optimum at 65–70° C. These bacteria were able to grow heterotrophically, or autotrophically with hydrogen; however, they oxidized thiosulfate under mixotrophic growth conditions (e.g. pyruvate or hydrogen plus thiosulfate). These strains had similar DNA G+C content (60–64 mol%) to and high DNA:DNA homology (> 75%) with the reference strain of Bacillus schlegelii. This is the first report of thermogenic composts as habitats of thermophilic sulfur- and hydrogen-oxidizing bacteria, which to date have been known only from geothermal manifestations. This contrasts with the generally held belief that thermogenic composts at temperatures above 60° C support only a very low diversity of obligatory heterotrophic thermophiles related to Bacillus stearothermophilus.

Differences between Bacterial Communities in the Gut of a Soil-Feeding Termite (Cubitermes niokoloensis) and Its Mounds

ABSTRACT In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by the Actinobacteria phylum, whereas the Firmicutes and Proteobacteria phyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering of Actinobacteria phylotypes between the mound and the surrounding soil. The Actinobacteria clones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by the Nocardioidaceae family. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.