| 1. |
- Ahlinder, J., et al.
(författare)
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Use of metagenomic microbial source tracking to investigate the source of a foodborne outbreak of cryptosporidiosis
- 2022
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Ingår i: FOOD AND WATERBORNE PARASITOLOGY. - : Elsevier. - 2405-6766. ; 26
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Tidskriftsartikel (refereegranskat)abstract
- Cryptosporidium is a protozoan parasite of global public health importance that causes gastroenteritis in a variety of vertebrate hosts, with many human outbreaks reported yearly, often from ingestion of contaminated water or food. Despite the major public health implications, little is typically known about sources of contamination of disease outbreaks caused by Cryptosporidium. Here, we study a national foodborne outbreak resulted from infection with Cryptosporidium parvum via romaine lettuce, with the main goal to trace the source of the parasite. To do so, we combined traditional outbreak investigation methods with molecular detection and characterization methods (i.e. PCR based typing, amplicon and shotgun sequencing) of romaine lettuce samples collected at the same farm from which the contaminated food was produced. Using 18S rRNA typing, we detected C. parvum in two out of three lettuce samples, which was supported by detections in the metagenome analysis. Microbial source tracking analysis of the lettuce samples suggested sewage water as a likely source of the contamination, albeit with some uncertainty. In addition, the high degree of overlap in bacterial species content with a public human gut microbial database corroborated the source tracking results. The combination of traditional and molecular based methods applied here is a promising tool for future source tracking investigations of food- and waterborne outbreaks of Cryptosporidium spp. and can help to control and mitigate contamination risks.
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| 2. |
- Andersson, Agneta, et al.
(författare)
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Predators and nutrient availability favor protozoa-resisting bacteria in aquatic systems
- 2018
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Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The long co-existence of bacteria and protozoa has led to the development of bacterial protozoa resistance strategies, which are suggested to serve as drivers for the evolution of pathogenic bacteria. However, the ecological mechanisms underpinning selection for protozoa-resistance in aquatic bacteria are poorly known. To assess the role of nutrient availability and predation-pressure on selection for protozoa-resisting bacteria (PRB), an enrichment-dilution experiment was designed using laboratory microcosms containing natural lake water. PRB was monitored by screening 16S rRNA amplicon sequence data for reads assigned to bacteria that previously has been shown to resist degradation by amoebae. To estimate the effects of the microbial food web dynamics (microscopy of; heterotrophic bacteria, phytoplankton, protozoa and rotifers) and physicochemical variables on the PRB abundance in the study system, a joint species distribution modelling approach was used. The predation-pressure (ratio between predator and bacterial biomass) had a positive effect on the abundance of the PRB genus Mycobacterium, while perturbation (enrichment and dilution) favored the PRB genus Pseudomonas that dominated the bacterial community in the disturbed systems. Our results show that PRB with different ecological strategies can be expected in water of high and intermediate nutrient levels and after major disturbances of an aquatic system.
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| 3. |
- Brindefalk, B., et al.
(författare)
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Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities
- 2022
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Ingår i: Microbiologyopen. - : Wiley. - 2045-8827. ; 11:5
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Tidskriftsartikel (refereegranskat)abstract
- Background Surface raw water used as a source for drinking water production is a critical resource, sensitive to contamination. We conducted a study on Swedish raw water sources, aiming to identify mutually co-occurring metacommunities of bacteria, and environmental factors driving such patterns. Methods The water sources were different regarding nutrient composition, water quality, and climate characteristics, and displayed various degrees of anthropogenic impact. Water inlet samples were collected at six drinking water treatment plants over 3 years, totaling 230 samples. The bacterial communities of DNA sequenced samples (n = 175), obtained by 16S metabarcoding, were analyzed using a joint model for taxa abundance. Results Two major groups of well-defined metacommunities of microorganisms were identified, in addition to a third, less distinct, and taxonomically more diverse group. These three metacommunities showed various associations to the measured environmental data. Predictions for the well-defined metacommunities revealed differing sets of favored metabolic pathways and life strategies. In one community, taxa with methanogenic metabolism were common, while a second community was dominated by taxa with carbohydrate and lipid-focused metabolism. Conclusion The identification of ubiquitous persistent co-occurring bacterial metacommunities in freshwater habitats could potentially facilitate microbial source tracking analysis of contamination issues in freshwater sources.
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| 4. |
- Navarro, J. R. G., et al.
(författare)
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Surface-Initiated Controlled Radical Polymerization Approach to in Situ Cross-Link Cellulose Nanofibrils with Inorganic Nanoparticles
- 2020
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Ingår i: Biomacromolecules. - : American Chemical Society (ACS). - 1525-7797 .- 1526-4602. ; 21:5, s. 1952-1961
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Tidskriftsartikel (refereegranskat)abstract
- This paper investigates a strategy to convert hydrophilic cellulose nanofibrils (CNF) into a hydrophobic highly cross-linked network made of cellulose nanofibrils and inorganic nanoparticles. First, the cellulose nanofibrils were chemically modified through an esterification reaction to produce a nanocellulose-based macroinitiator. Barium titanate (BaTiO3, BTO) nanoparticles were surface-modified by introducing a specific monomer on their outer-shell surface. Finally, we studied the ability of the nanocellulose-based macroinitiator to initiate a single electron transfer living radical polymerization of stearyl acrylate (SA) in the presence of the surface-modified nanoparticles. The BTO nanoparticles will transfer new properties to the nanocellulose network and act as a cross-linking agent between the nanocellulose fibrils, while the monomer (SA) directly influences the hydrophilic-lipophilic balance. The pristine CNF and the nanoparticle cross-linked CNF are characterized by FTIR, SEM, and solid-state 13C NMR. Rheological and dynamic mechanical analyses revealed a high dregee of cross-linking.
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| 5. |
- Abrahamsson, Sara, et al.
(författare)
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Maternal heterozygosity and progeny fitness association in an inbred Scots pine population
- 2013
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Ingår i: Genetica. - : Springer Netherlands. - 0016-6707 .- 1573-6857. ; 141:1-3, s. 41-50
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Tidskriftsartikel (refereegranskat)abstract
- Associations between heterozygosity and fitness traits have typically been investigated in populations characterized by low levels of inbreeding. We investigated the associations between standardized multilocus heterozygosity (stMLH) in mother trees (obtained from12 nuclear microsatellite markers) and five fitness traits measured in progenies from an inbred Scots pine population. The traits studied were proportion of sound seed, mean seed weight, germination rate, mean family height of one-year old seedlings under greenhouse conditions (GH) and mean family height of three-year old seedlings under field conditions (FH). The relatively high average inbreeding coefficient (F) in the population under study corresponds to a mixture of trees with different levels of co-ancestry, potentially resulting from a recent bottleneck. We used both frequentist and Bayesian methods of polynomial regression to investigate the presence of linear and non-linear relations between stMLH and each of the fitness traits. No significant associations were found for any of the traits except for GH, which displayed negative linear effect with stMLH. Negative HFC for GH could potentially be explained by the effect of heterosis caused by mating of two inbred mother trees (Lippman and Zamir 2006), or outbreeding depression at the most heterozygote trees and its negative impact on the fitness of the progeny, while their simultaneous action is also possible (Lynch. 1991). However,since this effect wasn’t detected for FH, we cannot either rule out that the greenhouse conditions introduce artificial effects that disappear under more realistic field conditions.
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| 6. |
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| 7. |
- Frank, Ellinor M., et al.
(författare)
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Marine sediments are identified as an environmental reservoir for Escherichia coli : Comparing signature-based and novel amplicon sequencing approaches for microbial source tracking
- 2024
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Ingår i: Science of the Total Environment. - 0048-9697. ; 907
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Tidskriftsartikel (refereegranskat)abstract
- Viable Escherichia coli were detected in sediments near a point of wastewater discharge in a marine coastal environment in Sweden. Since high concentrations were found in the sediments nearest the pipe, this suggested that treated wastewater effluent was the source of the microbes. In order to examine this hypothesis, different bioinformatics approaches were applied using 16S rRNA gene V3-V4 amplicon sequences from the sediments. Both signature-based source tracking using sequence libraries describing known sources of fecal water pollution (SourceTracker); and, a curated source tracking method, indicated that sediments were contaminated with wastewater. The results from the curated approach were independently confirmed using differential abundance analysis (DESeq2). A number of taxa originating from wastewater were identified which can be used to describe contamination of the sediments, and examine the spread of these specific taxa, even at low relative abundance, along the urban coast. Sequences of phylum Bacteroidetes (such as Bacteroides and Prevotella) and Firmicutes (such as Romboutsia) increased in sediments with higher concentrations of E. coli. In addition, sequences from Trichococcus are proposed as an indicator for treated wastewater. All three source tracking approaches, and the detection of viable E. coli, suggest that urban sediments can be a reservoir for indicator bacteria.
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| 8. |
- Karlsson, Edvin, et al.
(författare)
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Airborne microbial biodiversity and seasonality in Northern and Southern Sweden
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Microorganisms are essential constituents of ecosystems. To improve our understanding of how various factors shape microbial diversity and composition in nature it is important to study how microorganisms vary in space and time. Factors shaping microbial communities in ground level air have been surveyed in a limited number of studies, indicating that geographic location, season and local climate influence the microbial communities. However, few have surveyed more than one location, at high latitude or continuously over more than a year. We surveyed the airborne microbial communities over two full consecutive years in Kiruna, in the Arctic boreal zone, and Ljungbyhed, in the Southern nemoral zone of Sweden, by using a unique collection of archived air filters. We mapped both geographic and seasonal differences in bacterial and fungal communities and evaluated environmental factors that may contribute to these differences and found that location, season and weather influence the airborne communities. Location had stronger influence on the bacterial community composition compared to season, while location and season had equal influence on the fungal community composition. However, the airborne bacterial and fungal diversity showed overall the same trend over the seasons, regardless of location, with a peak during the warmer parts of the year, except for the fungal seasonal trend in Ljungbyhed, which fluctuated more within season. Interestingly, the diversity and evenness of the airborne communities were generally lower in Ljungbyhed. In addition, both bacterial and fungal communities varied significantly within and between locations, where orders like Rhizobiales, Rhodospirillales and Agaricales dominated in Kiruna, whereas Bacillales, Clostridiales and Sordariales dominated in Ljungbyhed. These differences are a likely reflection of the landscape surrounding the sampling sites where the landscape in Ljungbyhed is more homogenous and predominantly characterized by artificial and agricultural surroundings. Our results further indicate that local landscape, as well as seasonal variation, shapes microbial communities in air.
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| 9. |
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| 10. |
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| 11. |
- Pullerits, Kristjan, et al.
(författare)
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Impact of coagulation–ultrafiltration on long-term pipe biofilm dynamics in a full-scale chloraminated drinking water distribution system
- 2020
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Ingår i: Environmental Science: Water Research & Technology. - 2053-1419. ; 6:11, s. 3044-3056
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Tidskriftsartikel (refereegranskat)abstract
- While pipe biofilms in DWDSs (drinking water distribution systems) are thought to affect the quality of distributed water, studies regarding the microbial processes are impeded by the difficulties in accessing biofilm undisturbed by DWDS maintenance. In this study, pipe sections were removed from a fully operational DWDS for biofilm sampling over two years and three months, and before and after start of ultrafiltration (UF) with coagulation treatment in the drinking water treatment plant (DWTP). Water (n = 31), surface biofilm (obtained by swabbing, n = 34) and deep pipe biofilm (obtained by scraping, n = 34) were analyzed with 16S rRNA gene amplicon sequencing; with flow cytometry, and chemical and natural organic matter (NOM) analysis as additional parameters for water quality. UF with coagulation decreased the total cell concentration in the DWDS bulk water from 6.0 × 105 ± 2.3 × 105 cells per ml to 6.0 × 103 ± 8.3 × 103 cells per ml, including fluctuations due to seasonal change, as well as decreasing most analyzed fractions of NOM. UF treatment of the water revealed that 75% ± 18% of the cells in the water originated from DWDS biofilm, confirmed by SourceTracker analysis, with the rest of the cells likely released from biofilm on DWTP storage tanks. Following UF start, the ASVs (amplicon sequence variants) in the deep pipe biofilm decreased, and Evenness and Shannon diversity indices decreased, reflecting the community's response to the new environment created by the altered water quality. The pipe biofilm community was dominated by ASVs classified as Nitrosomonadaceae, Nitrospira, Hyphomicrobium and Sphingomonas, with relative abundances ranging from 5–78%, and also included ASVs of genus Mycobacterium, genus Legionella and order Legionellales. This community composition, together with the observation that turnover of nitrogen compounds was unchanged by UF start, indicate that nitrification in the DWDS was localized to the pipe biofilm.
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| 12. |
- Pullerits, Kristjan, et al.
(författare)
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Impact of UV irradiation at full scale on bacterial communities in drinking water
- 2020
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Ingår i: npj Clean Water. - : Springer Science and Business Media LLC. - 2059-7037. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Water in a full-scale drinking water treatment plant was irradiated with ultraviolet (UV) doses of 250, 400, and 600 J/m2, and the effect on bacterial communities investigated using 16s rRNA gene amplicon sequencing, heterotrophic plate counts (HPCs), coliform, and Escherichia coli counts. The bacteria in the irradiated water were also analyzed following storage for 6 days at 7 °C, to approximate the conditions in the distribution system. The log10 reduction of HPCs at 400 J/m2 was 0.43 ± 0.12. Phylogenetic examination, including DESeq2 analysis, showed that Actinobacteria was more resistant to UV irradiation, whereas Bacteroidetes was sensitive to UV. Phylum Proteobacteria contained monophyletic groups that were either sensitive or resistant to UV exposure. The amplicon sequence variants (ASVs) resistant to UV irradiation had a greater average GC content than the ASVs sensitive to UV, at 55% ± 1.7 (n = 19) and 49% ± 2.5 (n = 16), respectively. Families Chitinophagaceae, Pelagibacteraceae, Holophagaceae, Methylophilaceae, and Cytophagaceae decreased linearly in relative abundance, with increasing UV dose (P < 0.05, Pearson’s correlation). When irradiated water was stored, Chitinophagaceae, Comamonadaceae, and Flavobacteriaceae families decreased in relative abundance, whereas ACK-M1, Mycobacteriaceae, and Nitrosomonadaceae were increasing in relative abundance. This suggests that the impact of UV irradiation cannot only be considered directly after application but that this treatment step likely continues to influence microbial dynamics throughout the distribution system.
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| 13. |
- Rosenqvist, Tage, et al.
(författare)
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Inoculation with adapted bacterial communities promotes development of full scale slow sand filters for drinking water production
- 2024
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Ingår i: Water Research. - 1879-2448. ; 253
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Tidskriftsartikel (refereegranskat)abstract
- Gravity-driven filtration through slow sand filters (SSFs) is one of the oldest methods for producing drinking water. As water passes through a sand bed, undesired microorganisms and chemicals are removed by interactions with SSF biofilm and its resident microbes. Despite their importance, the processes through which these microbial communities form are largely unknown, as are the factors affecting these processes. In this study, two SSFs constructed using different sand sources were compared to an established filter and observed throughout their maturation process. One SSF was inoculated through addition of sand scraped from established filters, while the other was not inoculated. The operational and developing microbial communities of SSFs, as well as their influents and effluents, were studied by sequencing of 16S ribosomal rRNA genes. A functional microbial community resembling that of the established SSF was achieved in the inoculated SSF, but not in the non-inoculated SSF. Notably, the non-inoculated SSF had significantly (p < 0.01) higher abundances of classes Armatimonadia, Elusimicrobia, Fimbriimonadia, OM190 (phylum Planctomycetota), Parcubacteria, Vampirivibrionia and Verrucomicrobiae. Conversely, it had lower abundances of classes Anaerolineae, Bacilli, bacteriap25 (phylum Myxococcota), Blastocatellia, Entotheonellia, Gemmatimonadetes, lineage 11b (phylum Elusimicrobiota), Nitrospiria, Phycisphaerae, subgroup 22 (phylum Acidobacteriota) and subgroup 11 (phylum Acidobacteriota). Poor performance of neutral models showed that the assembly and dispersal of SSF microbial communities was mainly driven by selection. The temporal turnover of microbial species, as estimated through the scaling exponent of the species-time relationship, was twice as high in the non-inoculated filter (0.946 ± 0.164) compared to the inoculated filter (0.422 ± 0.0431). This study shows that the addition of an inoculum changed the assembly processes within SSFs. Specifically, the rate at which new microorganisms were observed in the biofilm was reduced. The reduced temporal turnover may be driven by inoculating taxa inhibiting growth, potentially via secondary metabolite production. This in turn would allow the inoculation community to persist and contribute to SSF function.
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| 14. |
- Rosenqvist, Tage, et al.
(författare)
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Succession of bacterial biofilm communities following removal of chloramine from a full-scale drinking water distribution system
- 2023
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Ingår i: npj Clean Water. - 2059-7037. ; 2023:6
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Tidskriftsartikel (refereegranskat)abstract
- Monochloramine is used to regulate microbial regrowth in drinking water distribution systems (DWDS) but produces carcinogenic disinfection byproducts and constitutes a source of energy for nitrifying bacteria. This study followed biofilm-dispersed microbial communities of a full-scale DWDS distributing ultrafiltered water over three years, before and after removal of monochloramine. Communities were described using flow cytometry and amplicon sequencing, including full-length 16S rRNA gene sequencing. Removal of monochloramine increased total cell counts by up to 440%. Increased abundance of heterotrophic bacteria was followed by emergence of the predatory bacteria Bdellovibrio, and a community potentially metabolizing small organic compounds replaced the nitrifying core community. No increased abundance of Mycobacterium or Legionella was observed. Co-occurrence analysis identified a network of Nitrosomonas, Nitrospira, Sphingomonas and Hyphomicrobium, suggesting that monochloramine supported this biofilm community. While some species expanded into the changed niche, no immediate biological risk to consumers was indicated within the DWDS.
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| 15. |
- Sjödin, Andreas, et al.
(författare)
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Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish
- 2012
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 13, s. 268-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Prior to this study, relatively few strains of Francisella had been genome-sequenced. Previously published Francisella genome sequences were largely restricted to the zoonotic agent F. tularensis. Only limited data were available for other members of the Francisella genus, including F. philomiragia, an opportunistic pathogen of humans, F. noatunensis, a serious pathogen of farmed fish, and other less well described endosymbiotic species. Results: We determined the phylogenetic relationships of all known Francisella species, including some for which the phylogenetic positions were previously uncertain. The genus Francisella could be divided into two main genetic clades: one included F. tularensis, F. novicida, F. hispaniensis and Wolbachia persica, and another included F. philomiragia and F. noatunensis. Some Francisella species were found to have significant recombination frequencies. However, the fish pathogen F. noatunensis subsp. noatunensis was an exception due to it exhibiting a highly clonal population structure similar to the human pathogen F. tularensis. Conclusions: The genus Francisella can be divided into two main genetic clades occupying both terrestrial and marine habitats. However, our analyses suggest that the ancestral Francisella species originated in a marine habitat. The observed genome to genome variation in gene content and IS elements of different species supports the view that similar evolutionary paths of host adaptation developed independently in F. tularensis (infecting mammals) and F. noatunensis subsp. noatunensis (infecting fish).
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