Academic literature on the topic 'Collimonas'

ABSTRACT The bacterial genus Collimonas has the remarkable characteristic that it grows at the expense of living fungal hyphae under laboratory conditions. Here, we report the first field inventory of the occurrence and abundance of Collimonas in soils (n = 45) with naturally different fungal densities, which was performed in order to test the null hypothesis that there is a relationship between the presence of Collimonas and fungal biomass. Estimates of fungal densities were based on ergosterol measurements. Each soil was also characterized in terms of its physical and chemical properties and vegetation and management types. Culturable Collimonas was identified in plate-spread soil samples by its ability to clear colloidal chitin, in combination with a Collimonas-specific restriction fragment length polymorphism analysis of 16S rRNA PCR amplified from individual colonies. Using this approach, we found culturable collimonads only in (semi)natural grasslands. A real-time PCR assay for the specific quantification of Collimonas 16S rRNA in total soil DNA was developed. Collimonas was detectable in 80% of the soil samples, with densities up to 105 cells g−1 (dry weight) soil. The numbers of Collimonas cells per gram of soil were consistently lowest in fungus-poor arable soils and, surprisingly, also in fungus-rich organic layers of forest soils. When all soils were included, no significant correlation was observed between the number of Collimonas cells and ergosterol-based soil fungal biomass. Based on this result, we rejected our null hypothesis, and possible explanations for this were addressed.

Strains Cr9-30T and Cr9-12 were isolated from alpine glacier cryoconite. Both strains were Gram-negative-staining, non-motile, rod-shaped and psychrophilic, showing good growth over the temperature range 1–20 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that the two strains formed a distinct branch within the family Oxalobacteraceae and were most closely related to members of the genus Collimonas. The 16S rRNA gene sequence similarity between strains Cr9-30T and Cr9-12 was 99.0 %. The two strains showed highest 16S rRNA gene sequence pairwise similarity with Collimonas pratensis LMG 23965T (96.6 and 96.1 % for strains Cr9-30T and Cr9-12, respectively), Collimonas arenae LMG 23964T (96.5 and 96.3 %, respectively) and Collimonas fungivorans LMG 21973T (96.4 and 96.2 %, respectively). The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. The DNA G+C content of strain Cr9-30T was 51.0 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strains Cr9-30T and Cr9-12 represent a novel species in a new genus of the family Oxalobacteraceae, for which the name Glaciimonas immobilis gen. nov., sp. nov. is proposed. The type strain of Glaciimonas immobilis is Cr9-30T ( = DSM 23240T = LMG 25547T).

A polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. These isolates, which were found in slightly acidic dune soils in the Netherlands, were strictly aerobic, Gram-negative rods. Cells grown in liquid cultures were flagellated and possessed pili. A wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and trisaccharides could not be used as substrates. The major cellular fatty acids were C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. DNA G+C contents were 57–62 mol%. Analysis of nearly full-length 16S rDNA sequences showed that the isolates were related closely to each other (>98·6 % sequence similarity) and could be assigned to the β-Proteobacteria, family ‘Oxalobacteraceae’, order ‘Burkholderiales’. The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, exhibiting 95·9–96·7 % (Herbaspirillum species) and 94·3–95·6 % (Janthinobacterium species) 16S rDNA sequence similarity to the isolates. Several physiological and biochemical properties indicated that the isolates could be distinguished clearly from both of these genera. Therefore, it is proposed that the isolates described in this study are representatives of a novel genus, Collimonas gen. nov. Genomic fingerprinting (BOX-PCR), detailed analysis of 16S rDNA patterns and physiological characterization (Biolog) of the isolates revealed the existence of four subclusters. The name Collimonas fungivorans gen. nov., sp. nov. has been given to one subcluster (four isolates) that appears to be in the centre of the novel genus; isolates in the other subclusters have been tentatively named Collimonas sp. The type strain of Collimonas fungivorans gen. nov., sp. nov. is Ter6T (=NCCB 100033T=LMG 21973T).

In a continued effort to discover microorganisms with plant-protective properties, we characterized a collection of bacterial isolates from multiple geographic origins and belonging to the genus Collimonas, for their ability to inhibit in vitro the growth of a wide range of plant-pathogenic fungi and oomycetes. Isolate Collimonas arenae Cal35 showed the greatest all-round performance and was the single-best inhibitor of several of the tested pathogens, including Fusarium oxysporum f. sp. lycopersici, the causal agent of Fusarium wilt of tomato. In greenhouse trials, neither C. arenae Cal35 nor the control treatment, i.e., the commercially available Bacillus-based biofungicide Serenade Soil, was able to prevent symptom formation on tomato plants challenged with F. oxysporum f. sp. lycopersici. However, a mixture of Cal35 and Serenade Soil (referred to as Collinade) significantly reduced vascular discoloration and F. oxysporum f. sp. lycopersici-induced loss of shoot dry weight. In replicated field experiments, a Collinade application reduced vascular symptoms as well as the relative abundance of F. oxysporum in the root endosphere of F. oxysporum f. sp. lycopersici-challenged plants. We discuss the emerging property of “biocombicontrol” by Collimonas and Bacillus in the context of synergy-based formulations for the protection of crops against pathogens.

ABSTRACT To date, several bacterial species have been described as mineral-weathering agents which improve plant nutrition and growth. However, the possible relationships between mineral-weathering potential, taxonomic identity, and metabolic ability have not been investigated thus far. In this study, we characterized a collection of 61 bacterial strains isolated from Scleroderma citrinum mycorrhizae, the mycorrhizosphere, and the adjacent bulk soil in an oak forest. The ability of bacteria to weather biotite was assessed with a new microplate bioassay that measures the pH and the quantity of iron released from this mineral. We showed that weathering bacteria occurred more frequently in the vicinity of S. citrinum than in the bulk soil. Moreover, the weathering efficacy of the mycorrhizosphere bacterial isolates was significantly greater than that of the bulk soil isolates. All the bacterial isolates were identified by partial 16S rRNA gene sequence analysis as members of the genera Burkholderia, Collimonas, Pseudomonas, and Sphingomonas, and their carbon metabolism was characterized by the BIOLOG method. The most efficient isolates belonged to the genera Burkholderia and Collimonas. Multivariate analysis resulted in identification of three metabolic groups, one of which contained mainly bacterial isolates associated with S. citrinum and exhibiting high mineral-weathering potential. Therefore, our results support the hypothesis that by its carbon metabolism this fungus selects in the bulk soil reservoir a bacterial community with high weathering potential, and they also address the question of functional complementation between mycorrhizal fungi and bacteria in the ectomycorrhizal complex for the promotion of tree nutrition.

Dans les régions tempérées, les minéraux et les roches représentent la source principale de cations nutritifs des sols des écosystèmes à faible intrants telles que les forêts. Dans de tels environnements pauvres en nutriments, l’accès et le recyclage des cations nutritifs sont des processus clés pour la croissance et la productivité des arbres. Cependant, ces cations nutritifs ne sont pas directement accessibles aux racines des arbres car piégés dans les minéraux et roches des sols. En conséquence, le processus d’altération des minéraux joue un rôle essentiel car il contribue à restaurer la fertilité des sols et à fournir des nutriments inorganiques nécessaires à la croissance des arbres. L’altération des minéraux peut être dûe à des processus abiotiques (pH, érosion…) ou des processus biotiques (plantes, champignons, bactéries…). Parmi les acteurs biotiques, les bactéries sont capables d’altérer les minéraux par différents mécanismes comme la production de protons (acidolyse) ou la production de molécules chélatrices (complexolyse). Néanmoins, les gènes et protéines impliqués dans l’altération des minéraux par les bactéries sont mal connus. Dans le cadre de cette thèse, la souche bactérienne Collimonas pratensis PMB3(1) a été utilisée comme modèle pour identifier les gènes de l’altération. Cette souche a été isolée de la mycorhizosphère du chêne et est particulièrement efficace pour altérer les minéraux. Dans cette thèse l’analyse du génome de la souche PMB3(1) a mis en évidence l’absence certains gènes décrits dans l’altération (comme les glucose déshydrogénases PQQ dépendantes) et a souligné la nécessité de développer deux approches complémentaires : avec et sans a priori. (i) La démarche sans a priori a été développée via la création d’une banque de mutants aléatoires. Le criblage de cette banque de mutants sur des biotests mimant l’altération des minéraux a permis de sélectionner 3 mutants impactés dans leur capacité à altérer les minéraux. La caractérisation de ces mutants a révélé des mutations dans différents gènes impliqués dans la synthèse d’une glucose/méthanol/choline oxidoréductase (GMC). La comparaison de composés chimiques présents dans le surnageant de la souche sauvage et des mutants a révélé que cette GMC était responsable de la métabolisation du glucose en gluconate et de la production de protons, conduisant à une acidification du milieu et à une acidolyse des minéraux. (ii) La démarche avec a priori a été réalisée par la création d’un mutant ciblé au niveau du gène mbaA codant pour un NRPS (Non-Ribosomal Peptide Synthetase) responsable de la synthèse de sidérophore. L’utilisation conjointe de méthodes de chromatographie et de spectrométrie de masse a permis de caractériser chimiquement ce sidérophore, qui a été identifié comme étant une malléobactine. La comparaison de la souche sauvage et du mutant a révélé que la production de la malléobactine est impliquée dans l’altération de l’hématite par complexolyse et ce dans un milieu avec un fort pouvoir tampon. Les tests d’altération réalisés avec différents types de minéraux en présence de deux sources de carbones (glucose ou mannitol) et deux milieux ayant un pouvoir tampon différent ont révélé que la souche PMB3(1) était efficace pour altérer tous les minéraux testés. De plus, la source de carbone et le tampon du milieu avaient une forte influence sur l’efficacité des agents altérants. Enfin, des résultats préliminaires ont été obtenus sur la régulation des gènes et protéines en fonction de la disponibilité en nutriments inorganiques et de la présence du minéral par des techniques de transcriptomique et protéomique. Pour conclure, cette thèse a permis de (i) découvrir de nouveaux gènes liés à l’altération des minéraux par les bactéries, (ii) mettre en évidence l’influence des facteurs environnementaux dans l’efficacité des mécanismes d’altération utilisés par les bactéries
In temperate regions, minerals and rocks represent one of the main sources of nutritive cations in the soil of low-input ecosystems such as forests. In such nutrient-poor and non-amended environments, the access and the recycling of nutritive cations are key processes for tree growth and productivity. However, these nutritive cations are almost inaccessible to the tree roots as they are entrapped into organic matter or into soil minerals and rocks. Consequently, the mineral weathering process is essential, as it allows the restauration of soil fertility and provides the inorganic nutrients for tree growth. Mineral weathering can be attributed to abiotic (temperature, pH, erosion…) or biotic (plants, fungi, bacteria…) processes. Among the biotic processes, bacteria are able to weather minerals by different mechanisms such as the production of protons (acidolysis) or the production of chelating molecules (complexolysis). However, genes and proteins involved in mineral weathering by bacteria are not yet elucidated. As part of this thesis, a bacterial Collimonas pratensis strain PMB3(1) was used as a model to identify genes involved in mineral weathering. This strain was isolated from oak mycorrhizosphere and is efficient in weathering minerals. In this thesis, the analysis of the genome of the strain PMB3(1) evidenced the absence of certain genes described in mineral weathering (such as PQQ-dependent glucose dehydrogenases) and highlighted the need to develop two complementary approaches: with and without a priori. (i) The without a priori approach, has been developed with the building of a mutant library with the insertion of a plasposon pOT-182. The screening of this mutant library on biotests miming mineral weathering allowed the selection of three mutants impacted in their mineral weathering ability. The characterisation of these mutants revealed mutations in different genes involved in a glucose/methanol/choline oxidoreductase (GMC) synthesis. Comparisons between wild type and mutants chemical compounds in the culture supernatants showed that this GMC was able to converts glucose to gluconate and produce protons, leading to the acidification of the medium and minerals acidolysis. (ii) The with a priori approach was the building of a mbaA mutant coding for a NRPS (non-ribosomal peptide synthetase) responsible of siderophore biosynthesis. The combined use of chromatography (HPLC) and mass spectrometry (LC-ESI-MS and MS/MS) methods allowed to chemically characterize the siderophore as malleobactin X. Comparisons between wild ype and mbaA mutant strains revealed that the production of malleobactin was involved in mineral weathering by complexolysis in a strong buffered medium. Weathering tests performed with different mineral types in presence of two carbon sources (glucose or mannitol) and two media with different buffering capacities showed that the strain PMB3(1) was efficient to weather all tested minerals and that weathering molecules (GMC and malleobactin) had a similar effect whatever the mineral type. Furthermore, the carbon source and the buffering capacity had a strong influence on weathering molecules efficiency. Finally, preliminary results have been obtained on the regulation of genes and proteins according to inorganic nutrients availability and the presence of minerals by transcriptomic and proteomic technics. To conclude, this thesis (i) allowed the discovery of new genes involved in mineral weathering by bacteria, (ii) evidenced the influence of environmental factors in efficiency of molecular mechanisms involved in mineral weathering and used by bacteria