Bacterial conjugation between pseudomonads in the rhizosphere of wheat

VANELSAS, J; Trevors, J. T.; Starodub, M.E.

doi:10.1016/0378-1097(88)90487-9

Cited by 91 publications

(75 citation statements)

References 6 publications

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“…Loose soil was manually removed from the roots by kneading and shaking with sterile gloves (sprayed with 70% EtOH) and by patting roots with a sterile (flamed) metal spatula—this ‘neighbouring soil’ fell to the sterile (flamed) work surface. We followed the established convention of defining rhizosphere soil as extending up to 1 mm from the root surface 25 and we removed loose soil on all root surfaces until remaining aggregates were within this range. Roots were placed in a clean and sterile 50-ml tube containing 25 ml phosphate buffer (per litre: 6.33 g of NaH 2 PO 4 ·H 2 O, 16.5g of Na 2 HPO 4 ·7H 2 O, 200 μl Silwet L-77).…”

Section: Methodsmentioning

confidence: 99%

Defining the core Arabidopsis thaliana root microbiome

Lundberg

Lebeis

Paredes

et al. 2012

Nature

2,428

196

1,982

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Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing therhizosphere(immediately surroundingthe root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation1-3. Colonization of the root occurs despite a sophisticated plant immune system4,5, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plantmicrobe interactions derived from complex soil communities.

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Section: Methodsmentioning

confidence: 99%

Defining the core Arabidopsis thaliana root microbiome

Lundberg

Lebeis

Paredes

et al. 2012

Nature

2,428

196

1,982

View full text Add to dashboard Cite

show abstract

“…The R2f strain was isolated from the rhizosphere of wheat [59] and was provided by S. Binnerup. The P. putida KT2440 strain, used as a control of known copy number, was isolated from soil [32] and was provided by J. L. Ramos.…”

Section: Methodsmentioning

confidence: 99%

Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas

et al. 2012

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Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas strains, we determined the 16S rRNA copy number in four other Pseudomonas strains by Southern hybridization and Pulsed-Field Gel Electrophoresis, and studied the intra-genomic heterogeneities by Denaturing Gradient Gel Electrophoresis and sequencing. Although the variable copy number (from four to seven) seems to be correlated with the evolutionary distance, some close strains in the P. fluorescens lineage showed a different number of 16S rRNA genes, whereas all the strains in the P. aeruginosa lineage displayed the same number of genes (four copies). Further study of the intra-genomic heterogeneities revealed that most of the Pseudomonas strains (15 out of 19 strains) had at least two different 16S rRNA alleles. A great difference (5 or 19 nucleotides, essentially grouped near the V1 hypervariable region) was observed only in two sequenced strains. In one of our strains studied (MFY30 strain), we found a difference of 12 nucleotides (grouped in the V3 hypervariable region) between copies of the 16S rRNA gene. Finally, occurrence of partial lateral transfers of the 16S rRNA gene was further investigated in 1803 full-length sequences of Pseudomonas available in the databases. Remarkably, we found that the two most variable regions (the V1 and V3 hypervariable regions) had probably been laterally transferred from another evolutionary distant Pseudomonas strain for at least 48.3 and 41.6% of the 16S rRNA sequences, respectively. In conclusion, we strongly recommend removing these regions of the 16S rRNA gene during the intra-genus diversity studies.

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“…In other habitats, such events have been shown to occur at highest rates when cells are in a nutrient rich environment, with nutrient limitation observed to reduce transfer rates 160 , 179 - 182 . In general the GIT should provide indigenous microbes with an ample and steady supply of nutrients, and this may also be true for some transiently colonizing organisms.…”

Section: Plasmid Transfer In the Gitmentioning

confidence: 99%

Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome

2012

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Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed.

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Bacterial conjugation between pseudomonads in the rhizosphere of wheat

Cited by 91 publications

References 6 publications

Defining the core Arabidopsis thaliana root microbiome

Defining the core Arabidopsis thaliana root microbiome

Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas

Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome

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