Additional file 6 of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

The concatenated tree based on six housekeeping MLSA genes (including trpB; right) and five MLSA gene sequences (rpoD, dnaK, tuf, gyrB, atpA; left). The arrow shows disagreement concerning the position of strain G2 (B399) between the two trees. (PDF 77 kb)

Bacteriophage Adherence to Mucus Mediates Preventive Protection against Pathogenic Bacteria

The mucosal surfaces of animals are habitat for microbes, including viruses. Bacteriophages—viruses that infect bacteria—were shown to be able to bind to mucus. This may result in a symbiotic relationship in which phages find bacterial hosts to infect, protecting the mucus-producing animal from bacterial infections in the process. Here, we studied phage binding on mucus and the effect of mucin on phage-bacterium interactions. The significance of our research is in showing that phage adhesion to mucus results in preventive protection against bacterial infections, which will serve as basis for the development of prophylactic phage therapy approaches. Besides, we also reveal that exposure to m…

Environmentally triggered evolutionary cascade across trophic levels in an experimental phage-bacteria-insect system

Abstract Environmental changes can cause strong cascading effects in species communities due to altered biological interactions between species (Zarnetske et al., 2012). Highly specialized interactions arising from the co-evolution of hosts and parasites, such as bacteria and phages, and short generation times of these species could rapidly lead to considerable evolutionary changes in their biotic interactions (Kerr, 2012; Buck and Ripple, 2017), with potential large-scale ramifications to other trophic levels. Here we report experimental evidence of cascading environmental effects across trophic levels in an experimental system where phage-bacteria coevolution in an abiotically altered env…

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Multispecies coinfections and presence of antibiotics shape resistance and fitness costs in a pathogenic bacterium

Increasing antimicrobial resistance (AMR) poses a challenge for treatment of bacterial diseases. In real life, bacterial infections are typically embedded within complex multispecies communities and influenced by the environment, which can shape costs and benefits of AMR. However, knowledge of such interactions and their implications for AMR in vivo is limited. To address this knowledge gap, we investigated fitness-related traits of a pathogenic bacterium (Flavobacterium columnare) in its fish host, capturing the effects of bacterial antibiotic resistance, coinfections between bacterial strains and metazoan parasites (fluke Diplostomum pseudospathaceum) and antibiotic exposure. We quantifie…

Opposing health effects of hybridization for conservation

The continuing decline of many natural plant and animal populations emphasizes the importance of conservation strategies. Hybridization as a management tool has proven successful in introducing gene flow to small, inbred populations, but can be also associated with health risks. For example, hybridization can change susceptibility to infection in either direction due to heterosis (hybrid vigor) and outbreeding depression, but such health effects have rarely been considered in the genetic management of populations. Here, we investigated the effects of experimental outcrossing between the critically endangered Saimaa landlocked salmon (Salmo salar m. sebago) and the genetically more diverse A…

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Thermal Tolerance is linked with Virulence in a Fish Pathogen

ABSTRACTAlthough increase in temperatures may boost the number of pathogens, a complex process involving the interaction of a susceptible host, a virulent strain, and environmental factors would influence disease virulence in unpredictable ways. Here we explored if the virulence of an environmentally growing opportunistic fish pathogen,Flavobacterium columnare, would be malleable to evolutionary changes via correlated selection on thermal tolerance. Virulence among the strains increased over years, but tolerance to higher temperatures was associated with reduced virulence. Our results suggest that observed increase in frequency of columnaris epidemics over the last decade is most likely ass…

Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and Type IX Secretion System

AbstractIncreasing problems with antibiotic resistance has directed interest towards phages as tools to treat bacterial infections in the aquaculture industry. However, phage resistance evolves rapidly in bacteria posing a challenge for successful phage therapy. To investigate phage resistance in the fish pathogenic bacterium Flavobacterium columnare, two phage-sensitive, virulent wild-type isolates, FCO-F2 and FCO-F9, were exposed to phages and subsequently analyzed for bacterial viability and colony morphology. Twenty-four phage-exposed isolates were further characterized for phage resistance, antibiotic susceptibility, motility, adhesion and biofilm formation on polystyrene surface, prot…

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Exploring evolutionary responses to increasing temperature in an environmental opportunistic pathogen

Quantity and Quality of Aquaculture Enrichments Influence Disease Epidemics and Provide Ecological Alternatives to Antibiotics

Environmental heterogeneity is a central component influencing the virulence and epidemiology of infectious diseases. The number and distribution of susceptible hosts determines disease transmission opportunities, shifting the epidemiological threshold between the spread and fadeout of a disease. Similarly, the presence and diversity of other hosts, pathogens and environmental microbes, may inhibit or accelerate an epidemic. This has important applied implications in farming environments, where high numbers of susceptible hosts are maintained in conditions of minimal environmental heterogeneity. We investigated how the quantity and quality of aquaculture enrichments (few vs. many stones

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Additional file 1 of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Site, year of isolation, source of isolation (fish or water), location of isolation, host species, sequence type (ST), and allelic profile data for the 83Â F. columnare strains from Finland analyzed by MLST. (DOCX 46 kb)

The effect of a temperature-sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen.

https://doi.org/10.1111/mec.16638 Abstract Viruses are key actors of ecosystems and have major impacts on global biogeochemical cycles. Prophages deserve particular attention as they are ubiquitous in bacterial genomes and can enter a lytic cycle when triggered by environmental conditions. We explored how temperature affects the interactions between prophages and other biological levels by using an opportunistic pathogen, the bacterium Serratia marcescens, that harbours several prophages and that had undergone an evolution experiment under several temperature regimes. We found that the release of one of the prophages was temperature-sensitive and malleable to evolutionary changes. We furthe…

Roles of adenosine and cytosine methylation changes and genetic mutations in adaptation to different temperatures

Abstract Epigenetic modifications have been found to be involved in evolution, but the relative contributions of genetic and epigenetic variation in adaptation are unknown. Furthermore, previous studies on the role of epigenetic changes in adaptation have nearly exclusively focused on cytosine methylation in eukaryotes. We collected phenotypic, genetic, and epigenetic data from populations of the bacterium Serratia marcescens that had undergone experimental evolution in contrasting temperatures to investigate the relationship between environment, genetics, epigenetic, and phenotypic traits. The genomic distribution of methylated adenosines (m6A) pointed to their role in regulation of gene e…

Additional file 4 of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

The fluorescence peak profiles for the ARISA genotypes analysed with ABI Prism 3130xl Genetic Analyser and the GeneMapper v.5.0 software (Applied Biosystems, Carlsbad, California, USA). For the 83 strains isolated from Finland, we also determined the ARISA (automated ribosomal intergenic spacer analysis) genotypes following the procedure described by Suomalainen et al. [8]. However, the previously published method was modified so that ABI Prism 3130xl Genetic Analyser is used instead of LI-COR 4200 automatic sequencer The analysis revealed that ARISA genotypes associate uniformly with the clusters from the MLSA scheme. Briefly, the PCR reaction mixture (total volume 10 ul) contained 1X Drea…

Additional file 3 of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Neighbor Joining phylogenetic trees based on the individual sequences of six MLST loci (trpB, rpoD, gyrB, dnaK, atpA,and tuf). MEGA v5.2 was used to evaluate the models for nucleotide substitution for each protein-coding locus and to construct the phylogenetic trees for Finnish F. columnare strains. The F. columnare type strain NCIMB 2248T isolated in the USA and two reference strains JIP39/87 and ATCC49512, both isolated in France, were also included in the phylogenetic analysis. The best model indicated by the lowest Bayesian Information Criterion (BIC) value was used to generate the Neighbor-Joining tree based on 1000 replicates. The T92 model was selected for dnaK, tuf, and gyrB, while …

Population genetic structure of aposematic alpine wood tiger moths (Parasemia plantaginis)

Alpine landscape with natural fragmentation restricts gene flow among populations and causes spatio-genetic structuring (high genetic differentiation) in species living there. Consequently, alpine habitat fragmentation and dispersal barriers should make isolated populations such as wood tiger moth (Parasemia plantaginis) populations prone to lose genetic diversity by local adaptation and fixation of fittest phenotype in each local population. This species is also known to be aposematic. Yellow colour on the males’ hind wings in wood tiger moth is presumed to work more efficiently against visual hunting predators due to increased conspicuousness. In addition, in field experiments with wood t…

Additional file 2 of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Target genes and primers for the housekeeping genes of F. columnare. The loci used for the MLST/MLSA scheme are shown in bold font. Length refers to the length of the target sequence. * Reference for 16S rDNA primers [52]. (DOCX 20 kb)

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Additional file 2 of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Target genes and primers for the housekeeping genes of F. columnare. The loci used for the MLST/MLSA scheme are shown in bold font. Length refers to the length of the target sequence. * Reference for 16S rDNA primers [52]. (DOCX 20 kb)

Additional file 5 of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Phylogenetic tree based on the 16Â s rDNA sequence data obtained from the representatives of Finnish F .columnare genotypes (A-H) studied in this study and other F .columnare sequences obtained from the GenBank. The tree was constructed by a UPGMA clustering method with a resampling of 1,000 bootstrap replicates and the Jukes Cantor model. Two strains representative of each ARISA genotype/MLSA cluster studied in this study were used for tree construction (identical sequences removed for clarity of representation). (PDF 191 kb)

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

of A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Data from: Rearing background and exposure environment together explain higher survival of aquaculture fish during a bacterial outbreak

1. Parasitic diseases represent one of the greatest challenges for aquaculture worldwide and there is an increasing emphasis on ecological solutions to prevent infections. One proposed solution is enriched rearing, where traditional stimulus-poor rearing tanks are equipped with different types of structures to increase habitat complexity. Such spatial enrichment is known to increase survival of fish during parasite epidemics, but the underlying mechanisms are still unclear. 2. We studied whether enriched rearing affected infection of an important fish pathogen Flavobacterium columnare in young Atlantic salmon (Salmo salar) and sea-migrating brown trout (Salmo trutta). First, we used natural…

Data from: Broad thermal tolerance is negatively correlated with virulence in an opportunistic bacterial pathogen

Predicting the effects of global increase in temperatures on disease virulence is challenging, especially for environmental opportunistic bacteria, because pathogen fitness may be differentially affected by temperature within and outside host environment. So far, there is very little empirical evidence on the connections between optimal temperature range and virulence in environmentally growing pathogens. Here we explored if the virulence of an environmentally growing opportunistic fish pathogen, Flavobacterium columnare, is malleable to evolutionary changes via correlated selection on thermal tolerance. To this end, we experimentally quantified the thermal performance curves (TPCs) for max…

Original data for manuscript: Quantity and Quality of Aquaculture Enrichments Influence Disease Epidemics and Provide Ecological Alternatives to Antibiotics

The data processed and analyzed in this study are given in a single file: Karvonen et al. exposure data.xlsx. For detailed description of the material, methods and results of the study, see the article.

Research data of an article: "Application of high resolution melting assay (HMR) to study temperature dependent infraspecific competition in an pathogenic bacterium."

Studies on species’ responses to climate change have focused largely on the direct effect of abiotic factors and in particular temperature, neglecting the effects of biotic interactions in determining the outcome of climate change projections. Many microbes rely on strong interference competition; hence the fitness of many pathogenic bacteria could be a function of both their growth properties and intraspecific competition. However, due to technical challenges in distinguishing and tracking individual strains, experimental evidence on intraspecific competition has been limited so far. Here, we developed a robust application of the high-resolution melting (HRM) assay to study head-to-head co…