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Interspecific coexistence selects for variants enhancing mutualism and productivity. Xanthomonas retroflexus strain variants.

ABSTRACT: Interspecific coexistence selects for variants enhancing mutualism and productivity. Xanthomonas retroflexus strain variants.

PROVIDER: PRJEB18990 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1795430_1.fastq.gz	Fastqsanger.gz
	ERR1795430_2.fastq.gz	Fastqsanger.gz
	ERR1795431_1.fastq.gz	Fastqsanger.gz
	ERR1795431_2.fastq.gz	Fastqsanger.gz
	ERR1795432_1.fastq.gz	Fastqsanger.gz

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Interspecific coexistence selects for variants enhancing mutualism and productivity. Paenibacillus amylolyticus strain variants

Project description:Interspecific coexistence selects for variants enhancing mutualism and productivity. Paenibacillus amylolyticus strain variants.

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Distinct gene expression profile of Xanthomonas retroflexus engaged in synergistic multispecies biofilm formation

Project description:It is well known that bacteria often exist in naturally formed multispecies biofilms. Within these biofilms, interspecies interactions seem to play an important role in ecological processes. Little is known about the effects of interspecies interactions on gene expression in these multispecies biofilms. This study presents a comparative gene expression analysis of the Xanthomonas retroflexus transcriptome when grown in a single-species biofilm and in dual- and four-species consortia with Stenotrophomonas rhizophila, Microbacterium oxydans and Paenibacillus amylolyticus. The results revealed complex interdependent interaction patterns in the multispecies biofilms. Many of the regulated functions are related to interactions with the external environment and suggest a high phenotypic plasticity in response to coexistence with other species. Furthermore, the changed expression of genes involved in aromatic and branched chain amino acid biosynthesis suggests nutrient cross feeding as an contribution factor for the observed synergistic biofilm production when these four species coexists in a biofilm. X. retroflexus was cultivated in three replicates of single-species biofilm and combined with S. rhizophila, M. oxydans and P. amylolyticus in dual-species biofilms with three respective replicates. At last, we combined all four species in a multispecies biofilm with five replicates and conducted a RNA seq based comparative gene expression study utilizing the Illumina sequencing technology. Please note that the 'prodigal_all_new.txt' contains gene names (which are listed in the matrix_sum.txt) and their position in the genomes, which are included in the file 'all_contigs_500.fasta'.

2016-07-22 | E-GEOD-80267 | biostudies-arrayexpress

Distinct gene expression profile of Xanthomonas retroflexus engaged in synergistic multispecies biofilm formation

2016-07-22 | GSE80267 | GEO

Proteomics profiling of xanthomonas retroflexus colony variants

Project description:Plasmid conjugation is a key facilitator of horizontal gene transfer. Since plasmids often carry antibiotic resistance genes, they are crucial drivers of the world-wide rise of antibiotic resistance among pathogens. In natural, engineered and clinical environments, bacteria often grow in protective biofilms. Therefore, a better understanding of plasmid transfer in biofilms is needed. Our aim was to investigate plasmid transfer in a biofilm adapted wrinkly colony mutant of Xanthomonas retroflexus (XRw) with enhanced matrix production and reduced motility. We found that XRw biofilms had an increased uptake of the broad host-range IncP-1ϵ plasmid pKJK5 compared to the wild type. Proteomics revealed fewer flagellum associated proteins in XRw, suggesting that flagella were responsible for reducing plasmid uptake. This was confirmed by the higher plasmid uptake of non-flagellated ∆fliM mutants of X. retroflexus wild type and wrinkly mutant. Moreover, testing several flagella mutants of Pseudomonas putida suggested that the flagella effect was more general. We identified seven mechanisms with the potential to explain the flagella effect and simulated them in an individual-based model. Two mechanisms could thus be eliminated (increased distances between cells and increased lag times due to flagella). Another mechanism identified as viable in the modelling was eliminated by further experiments. Four additional proposed mechanisms have a reduced probability of plasmid transfer in common. Our findings highlight the important yet complex effects of flagella during bacterial conjugation in biofilms.

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Draft Genome of Xanthomonas retroflexus strain Sp953

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Metabolic profiling of interspecies interactions during sessile bacterial cultivation reveals growth and sporulation induction in Paenibacillus amylolyticus in response to Xanthomonas retroflexus - Samples from Xanthomonas retroflexus

Project description:An in-depth characterization of an observed interspecies interaction between two co-isolated bacteria, Xanthomonas retroflexus and Paenibacillus amylolyticus. Using microsensor measurements for mapping the chemical environment, we show how X. retroflexus promoted an alkalization of its local environment through degradation of amino acids and release of ammonia. When the two species were grown in proximity, the modified local environment induced a morphological change and increased growth of P. amylolyticus followed by sporulation. 2D spatial metabolomics enabled visualization and mapping of the degradation of oligopeptide structures by X. retroflexus and morphological changes of P. amylolyticus through e.g. the release of membrane-associated metabolites. Proteome analysis and microscopy were used to validate the shift from vegetative growth towards sporulation. In summary, we demonstrate how environmental profiling by combined application of microsensor, microscopy, metabolomics and proteomics approaches can reveal growth and sporulation promoting effects resulting from interspecies interactions.

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Project description:According to apparent competition theory, sharing a predator should cause indirect interactions among prey that can affect the structure and the dynamics of natural communities. Though shifts in prey dominance and predator resource use along environmental gradients are rather common, empirical evidence on the role of indirect prey-prey interactions through shared predation particularly with increasing productivity, is still scarce. In an 8-week lake mesocosm experiment, we manipulated both the addition of inorganic nutrients and the presence of generalist fish predators (crucian carp, Carassius carassius L.), to test for the effects of indirect interactions through shared predation along a productivity gradient. We found that apparent mutualism (indirect positive interaction) between benthic and pelagic prey strongly affected short-term responses of aquatic food webs to increasing productivity in the presence of a generalist fish. Increasing productivity favoured the relative abundance of benthic prey, following trends in natural productive lake systems. This led to a shift in fish selectivity from pelagic to benthic prey driven by changes in fish behaviour, which resulted in apparent mutualism due to the lower and delayed top-down control of pelagic prey at increasing productivity. Our results show empirical evidence that the coupling of multiple production pathways can lead to strong indirect interactions through shared predation, whereby prey dynamics on short time-scales are highly dependent on the foraging behaviour of generalist predators. This mechanism may play an important role in short-term responses of food webs across environmental gradients.

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