Virulence, cellular masking, and grazing resistance in the struggle to survive under long term protozoan predation the genetics of survival
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ABSTRACT:
PROVIDER: PRJNA853259 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19860350_1.fastq.gz | Fastqsanger.gz | |||
| SRR19860350_2.fastq.gz | Fastqsanger.gz | |||
| SRR19860351_1.fastq.gz | Fastqsanger.gz | |||
| SRR19860351_2.fastq.gz | Fastqsanger.gz | |||
| SRR19860352_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Generalist protozoan predators change the pace of evolution in microbial communities, but investigations into the molecular consequences of predation for the genomic evolution of defence or coadaptation are scarce. We have previously performed a 90-day co-evolution experiment to address these effects using the bacterium Pseudomonas fluorescens SBW25 on solid media in the presence and absence of a wild Acanthamoeba sp. predator. Coevolution led to genomic divergence, altered phenotypes and resistance to predation in coevolved bacterial lineages. Strong parallel phenotypic evolution was observed among the coevolved replicates leading to Wrinkly Spreader, Volcano and Mountain colony phenotypes. Here, we describe the genomic mutations underlying this parallelism with a focus on these morphotypes. Methods: Pseudomonas fluorescens SBW25 and a wild Acanthamoeba sp. isolate as a predator prey pair co-evolved for 90 days yielded novel colony morphotype (Mountain; MNT, and Volcano; VOL) isolates with conferred grazing resistance. These isolates were subjected to RNAseq profiling with and without predation to determine transcriptional changes contributing to grazing resistance. Results: We made a profile of differentially expressed genes (DEG) for the coevolved Vol-L1 (Volcano L1; ∆fadD2-fadD1 & luxR T2675G) while predated by ancestral Acanthamoebae. WT P. fluorescens SBW25 was used as the baseline and significant differential expression was considered for genes with log2 FC ≥ 2, P-value ≤ 0.05 between conditions. We identified a total of 953 DEGs, of which 293 were upregulated and 660 were downregulated. Differentially expressed gene (DEG) profiles were made for the coevolved strains Mnt-L2 (Mountain L2; ∆4974-4975 & PFLU_0924 C790T) while under predation by ancestral Acanthamoebae. In this case we also used WT P. fluorescens SBW25 without predation as a baseline as described previously. In this condition and compared to the WT SBW25, we identified a total of 209 DEGs, of which 118 were upregulated and 91 were downregulated. Conclusions: In this study, from the DEG profile of Mnt-L2 and Vol-L1 while predated by the ancestral Acanthamoebae we found 12 and 21 upregulated genes in O-antigen biosynthesis, respectively. The polysaccharide capsule (LPS) is considered as one of the main virulence factors produced by pathogenic bacteria to protect bacteria against phagocytosis by the host’s immune system as well. We found enrichments in lipopolysaccharide-A production and three viscosin genes in Vol-L1 (a finding unique to the Vol-L1 strain). Vol-L1 had significant downregulation of seven efflux genes, most significantly PFLU_3263 (an efflux transporter), as well as a fatty acid transporter (PFLU4903). These results, taken with the finding of altered survivability only when evolved strains are grown with Acanthamoebae and the abundance of mutations found in FadD genes, led to our hypothesis that the evolved bacteria might be altering transporters to counter increased exposure to LC fatty acids from the Acanthamoeba by increased oxidative stress from LC fatty acid degradation, masking, etc. Furthermore, we found upregulation of an efflux RND transporter downstream of the deletion (PFLU_4976) and a unique enrichment (5 genes) in the cyclophilin-like domain (immunophilin) in Mnt-L2. Among all DEGs, 72 upregulated and 66 downregulated genes were shared between the Vol-L1 and Mnt-L2 conditions.
2022-06-30 | GSE206989 | GEO
Project description:Purpose: Protozoan predators affect the structure of bacterial communities, but investigations into how predation influences bacterial evolution and antagonistic behaviours are scarce. We performed a 20-day predator-prey evolution experiment on solid media to investigate the adaptive traits that arise in bacterial prey under continuous protozoan predation. Methods: Pseudomonas fluorescens SBW25 and a wild Acanthamoeba sp. isolate as a predator prey pair co-evolved for 20 days yielded both previously described (Wrinkly Spreader; WS) and novel colony morphotype (Wrinkly Fried Egg; WFE) isolates with conferred grazing resistance. These isolates were subjected to RNAseq profiling with and without predation to determine transcriptional changes contributing to grazing resistance. Results: For differential gene expression the WT SBW25 without predation was used as a baseline. For the WS condition, a total of 881 differentially expressed genes (DEGs) were identified, of which 424 were upregulated and 457 were downregulated. In the WFE condition, a total of 908 DEGs were identified, of which 475 were upregulated and 434 were downregulated. Among all DEGs, 335 upregulated and 313 downregulated genes were shared between the WS1 and WFE conditions Conclusions: Our findings suggest that protozoan predation can profoundly influence the course of genetic and phenotypic evolution in a short period of time. Together, the differential expression results suggest expression of features that would be expected to increase biofilm formation in WFE according to previous studies. However, increased expression of these traits may not lead to a stronger biofilm, but may still provide predation resistance. For example, fibrils may increase the effective profile size of a bacterial cell. Increased Fap-mediated biofilm formation also induces increased alginate synthesis in P. aeruginosa PA01, an exopolysaccharide that protects mucoid P. aeruginosa against macrophage killing. Interestingly, we found increased expression of alginate biosynthesis genes in both WFE and WS1 (algA, algF), suggesting alternate mechanisms leading to increased alginate production in these two strains.
2022-04-20 | GSE200723 | GEO
Project description:Soil fungi are key players in biomass recycling. Predation influences fungal communities and modulates ecosystem services provided by fungi. Fungal chemical defense against predation comprises toxic proteins and secondary metabolites. The intent of this experiment was to generate transcriptomic information when a fungus, in this case Fusarium graminearum, was in the presence of a predator (Folsomia candida). We assumed that defense metabolites are synthesized on demand and transcriptome analysis can be used to pinpoint genes of defense pathways. To carry out the experiment, cultures of F. graminearum were subjected to grazing by springtail F. candida. After 48 hours at 15°C in dark, springtails were removed, and RNA was extracted from mycelium. Controls were incubated under the same conditions without animals. Each group consisted of four replicates. Strand-specific cDNA libraries were prepared using Illumina’s TruSeq stranded mRNA kit (75 bp paired-end) and sequenced on Illumina NextSeq 500V2.
2018-07-01 | E-MTAB-6939 | biostudies-arrayexpress
Project description:Horizontal gene transfer by conjugative plasmids plays a critical role in the evolution of antibiotic resistance. Interactions between bacteria and other organisms can affect the persistence and spread of conjugative plasmids. Here we show that protozoan predation increased the persistence and spread of the antibiotic resistance plasmid RP4 in populations of the opportunist bacterial pathogen Serratia marcescens. A conjugation-defective mutant plasmid was unable to survive under predation, suggesting that conjugative transfer is required for plasmid persistence under the realistic condition of predation. These results indicate that multi-trophic interactions can affect the maintenance of conjugative plasmids with implications for bacterial evolution and the spread of antibiotic resistance genes.
| S-EPMC4780553 | biostudies-literature
Project description:By comparing transcriptomes of tolerant and intolerant plants of sickle alfalfa subject to intensive animal grazing, we identified pathways involved in nutrient-responsive signaling, light and wound response, cell wall formation, and energy metabolism. In these pathways, grazing suppressed 39 genes, but less severe in the tolerant plant, and activated 5 genes all carrying polymorphisms in their homologous transcripts between the tolerant and intolerant plants. These genes and pathways - responsive to grazing and differentially expressed between the tolerant and intolerant plants – underline a defense mechanism in alfalfa against grazing stresses.
2016-08-24 | GSE50430 | GEO
Project description:By comparing transcriptomes of tolerant and intolerant plants of sickle alfalfa subject to intensive animal grazing, we identified pathways involved in nutrient-responsive signaling, light and wound response, cell wall formation, and energy metabolism. In these pathways, grazing suppressed 39 genes, but less severe in the tolerant plant, and activated 5 genes all carrying polymorphisms in their homologous transcripts between the tolerant and intolerant plants. These genes and pathways - responsive to grazing and differentially expressed between the tolerant and intolerant plants â?? underline a defense mechanism in alfalfa against grazing stresses. We examined transcriptomes of 3 alfalfa plants: grazing tolerant and grazed, grazing tolerant and not grazed, grazing intolerant and grazed, all at single replicate each.
2016-08-24 | E-GEOD-50430 | biostudies-arrayexpress
Project description:To investigate the potential effect of grazing movement on miRNA circulation in cattle, here we profiled miRNA expression in centrifugally prepared exosomes from the plasma of both grazing and housed Japanese Shorthorn cattle. Microarray analysis of the c-miRNAs resulted in detection of a total of 231 bovine exosomal miRNAs in the plasma, with a constant expression level of let-7g across the duration and cattle groups. Expression of muscle-specific miRNAs such as miR-1, miR-133a, miR-206, miR-208a/b, and miR-499 were undetectable, suggesting the mildness of grazing movement as exercise.
2016-01-01 | GSE69717 | GEO
Project description:Protozoan predation drives rapid adaptive divergence by selecting for tuned cellulose production and amyloid fibrils in Pseudomonas fluorescens SBW25
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Project description:To investigate the potential effect of grazing movement on miRNA circulation in cattle, here we profiled miRNA expression in centrifugally prepared exosomes from the plasma of both grazing and housed Japanese Shorthorn cattle. Microarray analysis of the c-miRNAs resulted in detection of a total of 231 bovine exosomal miRNAs in the plasma, with a constant expression level of let-7g across the duration and cattle groups. Expression of muscle-specific miRNAs such as miR-1, miR-133a, miR-206, miR-208a/b, and miR-499 were undetectable, suggesting the mildness of grazing movement as exercise. Changes in miRNA expression in plasma exosome of cattle was measured at during 0, 1, 2 and 4 months of grazing or housing. Plasma exosome samples prepared from three cattle for each treatment were collected and mixed within the treatment at each time for microarray analysis .
2016-07-03 | E-GEOD-69717 | biostudies-arrayexpress
Project description:RNA-sequencing was used to evaluate the transcriptomic response to grazing stress for P. tricornutum strain CCAP 1055/1.
2017-01-10 | GSE93297 | GEO