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Povzetek: Background: Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains. Results: We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen. Conclusions: Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.
Ključne besede: whole-genome assembly, non-axenic culture, plasmid, marine bacteria, marine biology
Objavljeno v DiRROS: 28.03.2024; Ogledov: 118; Prenosov: 43
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Povzetek: Timber harvesting constitutes extensive anthropogenic disturbance in temperate forests, producing a broad range of ecological impacts that most often enhance the demographic processes of vegetation. This study monitored post-harvest herb layer demography over a 6-year period in mesic Dinaric fir-beech forests (Slovenia), a vascular plant diversity hotspot among European forests. Three experimental harvesting intensities, i.e. full harvest (FH), partial harvest (PH) and a control treatment (NH), were each applied over a circular area of 4000 m2 and replicated three times at each of three study sites. Vegetation sampling was conducted before harvesting (in 2012), and two (2014) and six (2018) years following it, in a 400 m2 circular plot positioned in the centre of each treatment area. We focused on identifying general demographic patterns and evaluating the effects of various pre-disturbance abiotic and biotic predictors on compositional responses to disturbance. Two years after harvest (2012-2014), compositional shifts were larger than those in the next 4-year period (2014-2018), confirming the general theoretical prediction that species turnover rate decreases along a successional gradient. The degree of compositional shifts in gaps (FH) and thinned stands (PH) was affected by local abiotic factors (geomorphology of karst sinkholes) and community attributes, such as pre-harvest species richness. Our results indicate that compositional stability is positively associated with pre-disturbance species richness. Over the whole study period, increases in plot-level species richness (alpha diversity) and overall enrichment of the species pool (gamma diversity) were accompanied by compositional convergence, i.e. a decline in floristic dissimilarity (beta diversity) between and within study sites. However, the observed tendency towards homogenization was rather weak and would have been even more pronounced if the demographic type of persistent resident species had not shown a high degree of resistance, thus leaving a strong imprint on post-harvest vegetation development by preserving the forest characteristics of the herb layer community.
Ključne besede: forest succession, demographic types, community assembly, pre-disturbance factors, floristic convergence, fir-beech forests
Objavljeno v DiRROS: 22.07.2022; Ogledov: 481; Prenosov: 299
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