Conjugation is necessary for a bacterial plasmid to survive under protozoan predation.
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ABSTRACT:
SUBMITTER: Cairns J
PROVIDER: S-EPMC4780553 | biostudies-literature | 2016 Feb
REPOSITORIES: biostudies-literature
Publications
Conjugation is necessary for a bacterial plasmid to survive under protozoan predation.
Cairns Johannes J Jalasvuori Matti M Ojala Ville V Brockhurst Michael M Hiltunen Teppo T
Biology letters 20160201 2
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, sugge ...[more]
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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.
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Project description:Phage predation is generally assumed to reduce microbial proliferation while not contributing to the spread of antibiotic resistance. However, this assumption does not consider the effect of phage predation on the spatial organization of different microbial populations. Here, we show that phage predation can increase the spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth by reshaping spatial organization. Using two strains of the bacterium Escherichia coli, we demonstrate that phage predation slows the spatial segregation of the strains during growth. This increases the number of cell-cell contacts and the extent of conjugation-mediated plasmid transfer between them. The underlying mechanism is that phage predation shifts the location of fastest growth from the biomass periphery to the interior where cells are densely packed and aligned closer to parallel with each other. This creates straighter interfaces between the strains that are less likely to merge together during growth, consequently slowing the spatial segregation of the strains and enhancing plasmid transfer between them. Our results have implications for the design and application of phage therapy and reveal a mechanism for how microbial functions that are deleterious to human and environmental health can proliferate in the absence of positive selection.
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Project description:BackgroundThe therapeutic potential of faecal microbiota transplantation (FMT) is under investigation for a range of inflammatory conditions. While mechanisms of benefit are poorly understood, most models rely on the viability of transplanted microbes. We hypothesised that protocols commonly used in the preparation of faecal transplants will substantially reduce the number, diversity and functional potential of viable microbes.MethodsStools from eight screened donors were processed under strict anaerobic conditions, in ambient air, and freeze-thawed. Propidium monoazide (PMA) sample treatment was combined with quantitative PCR, 16S rRNA gene amplicon sequencing and short-chain fatty acid (SCFA) analysis to define the viable microbiota composition and functional potential.FindingsApproximately 50% of bacterial content of stool processed immediately under strict anaerobic conditions was non-viable. Homogenisation in ambient air or freeze-thaw reduced viability to 19% and 23% respectively. Processing of samples in ambient air resulted in up to 12-fold reductions in the abundance of important commensal taxa, including the highly butyrogenic species Faecalibacterium prausnitzii, Subdoligranulum variable, and Eubacterium hallii. The adverse impact of atmospheric oxygen exposure on the capacity of the transplanted microbiota to support SCFA biosynthesis was demonstrated by significantly reduced butyrate and acetate production by faecal slurries processed in ambient air. In contrast, while reducing overall levels of viable bacteria, freeze-thaw did not significantly alter viable microbiota composition.InterpretationThe practice of preparing material for faecal transplantation in ambient air profoundly affects viable microbial content, disproportionately reducing the abundance of anaerobic commensals and the capacity for biosynthesis of important anti-inflammatory metabolites. FUND: This work was supported by the South Australian Health and Medical Research Institute. LP is supported by a scholarship from the Flinders Foundation. GR is supported by a Matthew Flinders Research Fellowship.
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