Mineral types and tree species determine the functional and taxonomic structures of forest soil bacterial communities

Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands ( beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and - independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems

Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect

To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed

Dégradation des N-acyl homosérine lactones, médiateurs de la régulation quorum sensing (les organismes, les mécanismes, les applications potentielles)

Les souches bactériennes d'une rhizosphere de tabac appartenant aux genres Comamonas, Pseudomonas, Rhodococcus et Variovorax présentent des cinétiques et des spectres de dégradation de N-AHSL variables. Parmi celles-ci, les souches de Comamonas sp. (D1) et de Rhodococcus (W2) sont capables d'inactiver toutes les N-AHSL quelques soient leurs substitutions sur le carbone 3. Ces deux souches sont capables d'interférer efficacement avec des fonctions régulées par QS chez d'autres bactéries. La dégradation des N-AHSL par la souche W2 est due à au moins deux activités enzymatiques : une activité oxydoréductase qui et une activité amidohydrolase, qui clive la liaison amide des N-AHSL, libérant de l'homosérine lactone et un acide gras. La première activité est non spécifique des N-AHSL puisque des analogues modifiés au niveau de leur chaîne latérale ou dépourvus du noyau lactone sont aussi réduits. La dégradation des N-AHSL par la souche D1 est aussi due à une activité amidohydrolase. Le criblage d'une banque d'ADN génomique de la souche W2 de Rhodococcus erythropolis a permis d'isoler un gène (qsdA) déterminant une activité " N-AHSLase ". Ce gène confère l'aptitude à dégrader les N-AHSL endogènes et exogènes à ses hôtes hétérologues. Il détermine une protéine présentant de fortes homologies avec les protéines de la famille des métallohydrolases : les phosphotriestérases (PTE). Cette protéine ne possède pas d'activité phosphotriestérase. La souche W2 possède au moins une seconde activité N-AHSLase, puisqu'un mutant possède toujours la capacité de dégrader les N-AHSL. Le gène qsdA, et l'activité qu'il code, semblent limités au genre Rhodococcus.Various bacterial strains from a tobacco rhizosphere belonging to the Comamonas, Pseudomonas, Rhodococcus and Variovorax genera harbour variable N-AHSL degradation kinetics and spectra. Among them, the strains Comamonas sp. (D1) and Rhodococcus erythropolis (W2) were capable to interfere with various functions regulated by quorum sensing. Strains D1 and W2 are able to inactivate a large range of N-AHSL as observed by HPLC analysis. The Rhodococcus strain harbours two N-AHSLase activities: the first one is an oxidoreductase and an amidohydrolase. This activity appeared to be also able to reduce N-AHSL analogues lacking in lactone ring or with a modified acyl chain. Another amidohydrolase activity was detected in the strain Comamonas sp. D1. It appeared that sequence or activity homologies were not so efficient tools to find functional homologues of N-AHSLases. Screening of the genomic library of the Rhodococcus erythropolis strain W2 permitted us to isolate and characterize one gene encoding an N-AHSLase activity that termed qsdA. This gene presents a strong homology with members of the metalohydrolase super family: the phosphotriesterases (PTE). However, QsdA did not exhibit any phosphotriesterases activity and a strain with a PTE activity had no ability to degrade N-AHSL. In addition, strain W2 harbors a second N-AHSLase activity as a mutant harbouring a disrupted qsdA gene retains the ability to degrade N-AHSL. The qsdA gene and the relevant encoded activity are characteristic, so far, for the Rhodococcus genera. It may have evolved from PTE genes after the emergence of this genus in the bacterial evolution.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Degradation of N-acyl homoserine lactone quorum sensing signal molecules by forest root-associated fungi

International audienceA collection of mycorrhizal and nonmycorrhizal root-associated fungi coming from forest environments was screened for their ability to degrade N-acyl homoserine lactones (AHL) or to prevent AHL recognition by producing quorum sensing inhibitors (QSI). No production of QS-inhibitors or -activators was detected using the two biosensors Chromobacterium violaceum CV026 and Agrobacterium tumefaciens in the culture supernatant of these fungi. However, the ability to degrade C6- and 3O,C6-HSL was detected for three fungal isolates. Acidification assay revealed that the AHL were degraded by a lactonase activity for two of these isolates. These results demonstrated for the first time that the forestroot-associated fungi are capable of degrading the AHL signal molecules

Caballeronia mineralivorans sp. nov., isolated from oak-Scleroderma citrinum mycorrhizosphere.

Six bacterial strains were isolated from the oak-Scleroderma citrinum ectomycorrhizosphere in acidic and nutrient-poor forest soil for their high efficacy to weather minerals. Four of the six isolates, PML1(12)(T) and PML1(4), PML1(14) and PML1(16), were further characterized extensively. They were Gram negative, obligate aerobic, motile, non spore forming and rod-shaped. The major fatty acids of strain PML1(12)(T) were cyclo-C17:0, cyclo-C19:0-ω8c, C16:0 and C18:1-ω7c. The GC content of the DNA was 60.8%. The 16S rRNA and GyrB analyses showed that the four PML strains formed a distinct phylogenetic lineage within the genus Caballeronia, most closely related to Caballeronia udeis. This result was confirmed by whole-genome phylogeny analyses done on strain PML1(12)(T). The results of digital DNA-DNA relatedness further supported the separation of the new isolates from closely related species. Morphological, chemotaxonomic properties were also consistent with the description of the genus Caballeronia. It is therefore proposed that strains PML1(12)(T) and PML1(4), PML1(14) and PML1(16) be recognized as a novel species, for which the name Caballeronia mineralivorans sp. nov. is proposed. The type strain is PML1(12)(T) (=DSM 104028 and LMG 2991)

Preface

International audienc

Screening for N-AHSL-Based-Signaling Interfering Enzymes

International audienc

Screening for N-AHSL-Based-Signaling Interfering Enzymes

International audienc

Linking diversity to function: highlight on the mineral weathering bacteria

International audienceWhat is the best way to identify new functions for which we currently know nothing? Here, we discuss the importance of combining cultivation-dependent and -independent approaches to identify new functions and new genes. We argue that although the cultivationdependent approach is presently viewed as an "old fashioned", focusing only on a limited proportion of the total bacterial communities, it remains essential to the characterization as well as the discovery of new potential functions in bacteria. This will allow us to highlight potential model bacterial strains for further genomic and genetic studies and to identify genes of interest. By illustrating an example of a function for which our current knowledge is so far limited, mineral weathering, we highlight different steps necessary to study of the mineral weathering bacterial communities, decipher their respective role as well as their distribution in various ecological niches of the soil

Screening for N-AHSL-Based-Signaling Interfering Enzymes

Quorum sensing (QS)-based signaling is a widespread pathway used by bacteria for the regulation of functions involved in their relation to the environment or their host. QS relies upon the production, accumulation and perception of small diffusable molecules by the bacterial population, hence linking high gene expression with high cell population densities.Among the different QS signal molecules, an important class of signal molecules is the N-acyl homoserine lactone (N-AHSL). In pathogens such as Erwinia or Pseudomonas, N-AHSL based QS is crucial to overcome the host defenses and ensure a successful infection. Interfering with QS-regulation allows the algae Delisea pulcra to avoid surface colonization by bacteria.Thus, interfering the QS-regulation of pathogenic bacteria is a promising antibiotic-free antibacterial therapeutic strategy. To date, two N-AHSL lactonases and one amidohydrolase families of N-ASHL degradation enzymes have been characterized and have proven to be efficient in vitro to control N-AHSL-based QS-regulated functions in pathogens.In this chapter, we provide methods to screen individual clones or bacterial strains as well as pool of clones for genomic and metagenomic libraries, that can be used to identify strains or clones carrying N-ASHL degradation enzymes