| 1. |
- Ahmed Osman, Omneya, et al.
(författare)
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Interactions of Freshwater Cyanobacteria with Bacterial Antagonists
- 2017
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 83:7
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Tidskriftsartikel (refereegranskat)abstract
- Cyanobacterial and algal mass development, or blooms, have severe effects on freshwater and marine systems around the world. Many of these phototrophs produce a variety of potent toxins, contribute to oxygen depletion, and affect water quality in several ways. Coexisting antagonists, such as cyanolytic bacteria, hold the potential to suppress, or even terminate, such blooms, yet the nature of this interaction is not well studied. We isolated 31 cyanolytic bacteria affiliated with the genera Pseudomonas, Stenotrophomonas, Acinetobacter, and Delftia from three eutrophic freshwater lakes in Sweden and selected four phylogenetically diverse bacterial strains with strong-to-moderate lytic activity. To characterize their functional responses to the presence of cyanobacteria, we performed RNA sequencing (RNA-Seq) experiments on coculture incubations, with an initial predator-prey ratio of 1: 1. Genes involved in central cellular pathways, stress-related heat or cold shock proteins, and antitoxin genes were highly expressed in both heterotrophs and cyanobacteria. Heterotrophs in coculture expressed genes involved in cell motility, signal transduction, and putative lytic activity. L, D-Transpeptidase was the only significantly upregulated lytic gene in Stenotrophomonas rhizophila EK20. Heterotrophs also shifted their central metabolism from the tricarboxylic acid cycle to the glyoxylate shunt. Concurrently, cyanobacteria clearly show contrasting antagonistic interactions with the four tested heterotrophic strains, which is also reflected in the physical attachment to their cells. In conclusion, antagonistic interactions with cyanobacteria were initiated within 24 h, and expression profiles suggest varied responses for the different cyanobacteria and studied cyanolytes. IMPORTANCE Here, we present how gene expression profiles can be used to reveal interactions between bloom-forming freshwater cyanobacteria and antagonistic heterotrophic bacteria. Species-specific responses in both heterotrophs and cyanobacteria were identified. The study contributes to a better understanding of the interspecies cellular interactions underpinning the persistence and collapse of cyanobacterial blooms.
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| 2. |
- Bravo, Andrea Garcia, et al.
(författare)
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Methanogens and Iron-Reducing Bacteria : the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes
- 2018
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 84:23
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Tidskriftsartikel (refereegranskat)abstract
- Methylmercury is a potent human neurotoxin which biomagnifies in aquatic food webs. Although anaerobic microorganisms containing the hgcA gene potentially mediate the formation of methylmercury in natural environments, the di- versity of these mercury-methylating microbial communities remains largely unex- plored. Previous studies have implicated sulfate-reducing bacteria as the main mer- cury methylators in aquatic ecosystems. In the present study, we characterized the diversity of mercury-methylating microbial communities of boreal lake sediments us- ing high-throughput sequencing of 16S rRNA and hgcA genes. Our results show that in the lake sediments, Methanomicrobiales and Geobacteraceae also represent abun- dant members of the mercury-methylating communities. In fact, incubation experi- ments with a mercury isotopic tracer and molybdate revealed that only between 38% and 45% of mercury methylation was attributed to sulfate reduction. These re- sults suggest that methanogens and iron-reducing bacteria may contribute to more than half of the mercury methylation in boreal lakes.
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| 3. |
- Eklöf, Karin, et al.
(författare)
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Formation of mercury methylation hotspots as a consequence of forestry operations
- 2018
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 613-614, s. 1069-1078
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Tidskriftsartikel (refereegranskat)abstract
- Earlier studies have shown that boreal forest logging can increase the concentration and export of methylmercury (MeHg) in stream runoff. Here we test whether forestry operations create soil environments of high MeHg net formation associated with distinct microbial communities. Furthermore, we test the hypothesis that Hg methylation hotspots are more prone to form after stump harvest than stem-only harvest, because of more severe soil compaction and soil disturbance. Concentrations of MeHg, percent MeHg of total Hg (THg), and bacterial community composition were determined at 200 soil sampling positions distributed across eight catchments. Each catchment was either stem-only harvested (n = 3), stem-and stump-harvested (n = 2) or left undisturbed (n = 3). In support of our hypothesis, higher MeHg to THg ratios was observed in one of the stump-harvested catchments. While the effects of natural variation could not be ruled out, we noted that most of the highest % MeHg was observed in water-filled cavities created by stump removal or driving damage. This catchment also featured the highest bacterial diversity and highest relative abundance of bacterial families known to include Hg methylators. We propose that water-logged and disturbed soil environments associated with stump harvest can favor methylating microorganisms, which also enhance MeHg formation.
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| 4. |
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| 5. |
- Jingying, Xu, 1984-, et al.
(författare)
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Mercury methylating microbial communities of boreal forest soils
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- The formation of the potent neurotoxic methylmercury (MeHg) is a microbially mediated process that has raised much concern because MeHg poses threats to wildlife and human health. Since boreal forest soils can be a source of MeHg in aquatic networks, it is crucial to understand the biogeochemical processes involved in the formation of this pollutant. High-throughput sequencing of 16S rRNA and the mercury methyltransferase, hgcA, combined with geochemical characterisation of soils, were used to determine the microbial populations contributing to MeHg formation in forest soils across Sweden. The hgcA sequences obtained were distributed among diverse clades, including Proteobacteria, Firmicutes, and Methanomicrobia, with Deltaproteobacteria, particularly Geobacteraceae, dominating the libraries across all soils examined. Our results also suggest that MeHg formation is linked to the composition of also non-mercury methylating bacterial communities, likely providing growth substrate (e.g. acetate) for the hgcA-carrying microorganisms responsible for the actual methylation process. While previous research focused on mercury methylating microbial communities of wetlands, this study provides some first insights into the diversity of mercury methylating microorganisms in boreal forest soils.
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| 6. |
- Osman, Omneya Ahmed, et al.
(författare)
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Isolation And Characterization Of Surface Active Compounds Produced By Halophilic Bacteria
- 2012
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Ingår i: Book of Proceedings. - Prague : ICT Press. - 9788070808252 ; , s. 164-168
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Biosurfactants or bioemulsifiers produced by microorganisms is considered an essential step in hydrocarbon biodegradation in the marine environment. Four bacterial strains isolated from Maruit lake, Egypt displayed hemolytic activity when grown on blood agar. 16S rRNA sequencing revealed that these strains were affiliated to Halomonas, Chromohalobacter and Halobacillus. Bacterial adhesion to benzene, xylene and lubricant motor oil ranged between 60-80 % indicating the presence of surface active compounds. The 4 strains had the capacity to produce surface active compounds when grown with 1% of motor oil, rapeseed oil and olive oil as sole carbon source and in the presence of different NaCl concentrations (0.0, 0.5 and 1.0 M). Most of the strains showed enhanced growth in the presence of 0.5 and 1.0 M NaCl, emphasizing the importance of NaCl in controlling the growth of halophilic bacteria. Drop collapse test was positive in all strains. Surface tension measurements ranged between 72-58 mN/m for motor oil, olive oil and rapeseed oil. All the isolates exhibit emusification stability of 69-100% with the tested oils. Resultant emulsion found stable without any phase separation. We concluded that these strains have a potential application as a bioemulsifiers which can grow in different types of oils.
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| 7. |
- Osman, Omneya, et al.
(författare)
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Diversity and abundance of aromatic catabolic genes in lake sediments in response to temperature change
- 2014
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 88:3, s. 468-481
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Tidskriftsartikel (refereegranskat)abstract
- The abundance and composition of genes involved in the catabolism of aromatic compounds provide important information on the biodegradation potential of organic pollutants and naturally occurring compounds in the environment. We studied catechol 2, 3 dioxygenase (C23O) and benzylsuccinate synthase (bssA) genes coding for key enzymes of aerobic and anaerobic degradation of aromatic compounds in experimental incubations with sediments from two contrasting lakes; humic lake Svarttjärn and eutrophic Vallentunasjön, respectively. Sediment cores from both lakes were incubated continuously for 5 months at constant temperatures ranging from 1.0 to 21.0 °C. The difference in C23O gene composition of the sediment analyzed at the end of the experiment was larger between lakes, than among temperature treatments within each lake. The abundance of C23O gene copies and measured respiration was positively correlated with temperature in Vallentunasjön, whereas putative C23O genes were present in lower concentrations in Svarttjärn sediments. Putative bssA genes were only detected in Svarttjärn. For both lakes, the two catabolic genes were most abundant in the surface sediment. The results emphasize the important role of temperature and nutrient availability in controlling the functional potential of sediment microorganisms and reveal differences between systems with contrasting trophic status. A better understanding of catabolic pathways and enzymes will enable more accurate forecasting of the functional properties of ecosystems under various scenarios of environmental change.
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| 8. |
- Petursdottir, Dagbjort H., et al.
(författare)
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Early-Life Human Microbiota Associated With Childhood Allergy Promotes the T Helper 17 Axis in Mice
- 2017
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Ingår i: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The intestinal microbiota influences immune maturation during childhood, and is implicated in early-life allergy development. However, to directly study intestinal microbes and gut immune responses in infants is difficult. To investigate how different types of early-life gut microbiota affect immune development, we collected fecal samples from children with different allergic heredity (AH) and inoculated germ-free mice. Immune responses and microbiota composition were evaluated in the offspring of these mice. Microbial composition in the small intestine, the cecum and the colon were determined by 16S rRNA sequencing. The intestinal microbiota differed markedly between the groups of mice, but only exposure to microbiota associated with AH and known future allergy in children resulted in a T helper 17 (Th17)-signature, both systemically and in the gut mucosa in the mouse offspring. These Th17 responses could be signs of a particular microbiota and a shift in immune development, ultimately resulting in an increased risk of allergy.
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| 9. |
- Roger, Fabian, et al.
(författare)
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Effects of multiple dimensions of bacterial diversity on functioning, stability and multifunctionality
- 2016
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Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 97:10, s. 2716-2728
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Tidskriftsartikel (refereegranskat)abstract
- Bacteria are essential for many ecosystem services but our understanding of factors controlling their functioning is incomplete. While biodiversity has been identified as an important driver of ecosystem processes in macrobiotic communities, we know much less about bacterial communities. Due to the high diversity of bacterial communities, high functional redundancy is commonly proposed as explanation for a lack of clear effects of diversity. The generality of this claim has, however, been questioned. We present the results of an outdoor dilution-to-extinction experiment with four lake bacterial communities. The consequences of changes in bacterial diversity in terms of effective number of species, phylogenetic diversity, and functional diversity were studied for (1) bacterial abundance, (2) temporal stability of abundance, (3) nitrogen concentration, and (4) multifunctionality. We observed a richness gradient ranging from 15 to 280 operational taxonomic units (OTUs). Individual relationships between diversity and functioning ranged from negative to positive depending on lake, diversity dimension, and aspect of functioning. Only between phylogenetic diversity and abundance did we find a statistically consistent positive relationship across lakes. A literature review of 24 peer-reviewed studies that used dilution-to-extinction to manipulate bacterial diversity corroborated our findings: about 25% found positive relationships. Combined, these results suggest that bacteria-driven community functioning is relatively resistant to reductions in diversity.
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| 10. |
- Sinclair, Lucas, et al.
(författare)
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Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons : Evaluating the Illumina Platform
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:2
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Tidskriftsartikel (refereegranskat)abstract
- As new sequencing technologies become cheaper and older ones disappear, laboratories switch vendors and platforms. Validating the new setups is a crucial part of conducting rigorous scientific research. Here we report on the reliability and biases of performing bacterial 16S rRNA gene amplicon paired-end sequencing on the MiSeq Illumina platform. We designed a protocol using 50 barcode pairs to run samples in parallel and coded a pipeline to process the data. Sequencing the same sediment sample in 248 replicates as well as 70 samples from alkaline soda lakes, we evaluated the performance of the method with regards to estimates of alpha and beta diversity. Using different purification and DNA quantification procedures we always found up to 5-fold differences in the yield of sequences between individually barcodes samples. Using either a one-step or a two-step PCR preparation resulted in significantly different estimates in both alpha and beta diversity. Comparing with a previous method based on 454 pyrosequencing, we found that our Illumina protocol performed in a similar manner – with the exception for evenness estimates where correspondence between the methods was low. We further quantified the data loss at every processing step eventually accumulating to 50% of the raw reads. When evaluating different OTU clustering methods, we observed a stark contrast between the results of QIIME with default settings and the more recent UPARSE algorithm when it comes to the number of OTUs generated. Still, overall trends in alpha and beta diversity corresponded highly using both clustering methods. Our procedure performed well considering the precisions of alpha and beta diversity estimates, with insignificant effects of individual barcodes. Comparative analyses suggest that 454 and Illumina sequence data can be combined if the same PCR protocol and bioinformatic workflows are used for describing patterns in richness, beta-diversity and taxonomic composition.
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| 11. |
- Svoboda, Pavel, et al.
(författare)
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Dispersal timing determines the importance of priority effects in bacterial communities
- 2018
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 12:2, s. 644-646
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Tidskriftsartikel (refereegranskat)abstract
- The order and timing of species arrival during community assembly can have long term effects on community structure due to priority effects. The importance of such processes in complex bacterial communities where dispersal involves mixing of entire communities is currently not known. Here we used a transplant experiment with two bacterioplankton communities of different origin (freshwater and brackish). Sterile medium of each origin was initially inoculated with a bacterial community of different ('alien') origin, followed by dispersal of the respective 'home' community at different time points after initial inoculation. We found that the later the dispersal with the 'home' community occurred the smaller the effect on the final community composition. This suggests that priority effects by the initially inoculated community reduce the establishment success of taxa from the later arriving community and that this effect depends on dispersal timing.
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| 12. |
- Söderqvist, Karin, et al.
(författare)
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Emerging microbiota during cold storage and temperature abuse of ready-to-eat salad
- 2017
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Ingår i: Infection Ecology & Epidemiology. - : Informa UK Limited. - 2000-8686. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Ready-to-eat (RTE) leafy vegetables have a natural leaf microbiota that changes during different processing and handling steps from farm to fork. The objectives of this study were (i) to compare the microbiota of RTE baby spinach and mixed-ingredient salad before and after seven days of storage at 8°C or 15°C; (ii) to explore associations between bacterial communities and the foodborne pathogens Listeria monocytogenes, pathogenic Yersinia enterocolitica, and pathogen model organism Escherichia coli O157:H7 gfp+ when experimentally inoculated into the salads before storage; and (iii) to investigate if bacterial pathogens may be detected in the 16S rRNA amplicon dataset. Material and methods: The microbiota was studied by means of Illumina 16S rRNA amplicon sequencing. Subsets of samples were inoculated with low numbers (50-100 CFU g(-1)) of E. coli O157:H7 gfp+, pathogenic Y. enterocolitica or L. monocytogenes before storage. Results and discussion: The composition of bacterial communities changed during storage of RTE baby spinach and mixed-ingredient salad, with Pseudomonadales as the most abundant order across all samples. Although pathogens were present at high viable counts in some samples, they were only detected in the community-wide dataset in samples where they represented approximately 10% of total viable counts. Positive correlations were identified between viable counts of inoculated strains and the abundance of Lactobacillales, Enterobacteriales, and Bacillales, pointing to positive interactions or similar environmental driver variables that may make it feasible to use such bacterial lineages as indicators of microbial health hazards in leafy vegetables. The data from this study contribute to a better understanding of the bacteria present in RTE salads and may help when developing new types of biocontrol agents.
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| 13. |
- Töpel, Mats, et al.
(författare)
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Verifiering av sterilisering i processen för materialåtervinning av plast
- 2024
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Den nationella plastkartläggningen visade att år 2017 användes över 813 miljoner engångsprodukter av plast inom hälso- och sjukvården i Sverige. Den största delen av detta avfall hanteras genom förbränning, och för att minska den miljöpåverkan detta leder till har ett antal initiativ tagits för att inkludera materialet i slutna kretslopp, där plasten används i samma applikation på nytt och där materialets höga kvalité kan behållas.För att kunna göra det på ett säkert sätt krävs dock att materialet kan steriliseras för att vara säkert att hantera. Detta projekt har haft som mål att ta fram en metod för att mäta den eventuella steriliseringsprocess som sker när plast återvinns i den så kallade regranuleringsprocessen. Denna process innebär att plasten mals ner och smälts vid omkring 200°C. Om denna process är effektiv för att sterilisera materialet behövs inget separat steriliseringssteg innan regranuleringen. Vi har i projektet tillsatt bakterien Bacillus atrophaeus, en organism som ofta används för verifiering av sterilisering, till regranuleringen av LDPE-plast.Vi har sedan utvärderat olika metoder för att extrahera DNA från det regranulerade materialet samt utvecklat en qPCR-metod för att kvantifiera antalet överlevande bakterier. På så sätt har vi försökt mäta den eventuella steriliseringen av det regranulerade plastmaterialet.Resultatet visar att det fortfarande finns svårigheter att frigöra DNA-molekylerna från plasten, och att detta steg även kan ha en negativ påverkan på DNA-kvalitén. qPCR-metoden kan detektera B. atrophaeus och visar i ett separat värmeexperiment på en förväntad steriliseringseffekt över tid.Denna effekt kunde dock inte reproduceras i de labbförsök som utfördes med extruder (en utrustning som används för att pressa smält plastgranulat till den profil som önskas). Ett antal möjliga förklaringar till detta, samt förslag till vidare forskning presenteras avslutningsvis i rapporten. Exempel på fortsatta forskningsfrågor som presenteras är; fördelning av bakterier i plastmassan, inneslutande av celler i plastmaterialet, steriliseringseffekt i extrudern samt metod för bestrykning av bioindikator.
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| 14. |
- Urrutia-Cordero, Pablo, et al.
(författare)
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Functionally reversible impacts of disturbances on lake food webs linked to spatial and seasonal dependencies
- 2021
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Ingår i: Ecology. - : John Wiley & Sons. - 0012-9658 .- 1939-9170. ; 102:4
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Tidskriftsartikel (refereegranskat)abstract
- Increasing human impact on the environment is causing drastic changes in disturbance regimes and how they prevail over time. Of increasing relevance is to further our understanding on biological responses to pulse disturbances (short duration) and how they interact with other ongoing press disturbances (constantly present). Because the temporal and spatial contexts of single experiments often limit our ability to generalize results across space and time, we conducted a modularized mesocosm experiment replicated in space (five lakes along a latitudinal gradient in Scandinavia) and time (two seasons, spring and summer) to generate general predictions on how the functioning and composition of multitrophic plankton communities (zoo-, phyto- and bacterioplankton) respond to pulse disturbances acting either in isolation or combined with press disturbances. As pulse disturbance, we used short-term changes in fish presence, and as press disturbance, we addressed the ongoing reduction in light availability caused by increased cloudiness and lake browning in many boreal and subarctic lakes. First, our results show that the top-down pulse disturbance had the strongest effects on both functioning and composition of the three trophic levels across sites and seasons, with signs for interactive impacts with the bottom-up press disturbance on phytoplankton communities. Second, community composition responses to disturbances were highly divergent between lakes and seasons: temporal accumulated community turnover of the same trophic level either increased (destabilization) or decreased (stabilization) in response to the disturbances compared to control conditions. Third, we found functional recovery from the pulse disturbances to be frequent at the end of most experiments. In a broader context, these results demonstrate that top-down, pulse disturbances, either alone or with additional constant stress upon primary producers caused by bottom-up disturbances, can induce profound but often functionally reversible changes across multiple trophic levels, which are strongly linked to spatial and temporal context dependencies. Furthermore, the identified dichotomy of disturbance effects on the turnover in community composition demonstrates the potential of disturbances to either stabilize or destabilize biodiversity patterns over time across a wide range of environmental conditions.
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| 15. |
- Vass, Mate, et al.
(författare)
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Warming mediates the resistance of aquatic bacteria to invasion during community coalescence
- 2021
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 30:5, s. 1345-1356
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Tidskriftsartikel (refereegranskat)abstract
- The immigration history of communities can profoundly affect community composition. For instance, early‐arriving species can have a lasting effect on community structure by reducing the invasion success of late‐arriving ones through priority effects. This can be particularly important when early‐arriving communities coalesce with another community during dispersal (mixing) events. However, the outcome of such community coalescence is unknown as we lack knowledge on how different factors influence the persistence of early‐arriving communities and the invasion success of late‐arriving taxa. Therefore, we implemented a full‐factorial experiment with aquatic bacteria where temperature and dispersal rate of a better adapted community were manipulated to test their joint effects on the resistance of early‐arriving communities to invasion, both at community and population level. Our 16S rRNA gene sequencing‐based results showed that invasion success of better adapted late‐arriving bacteria equaled or even exceeded what we expected based on the dispersal ratios of the recipient and invading communities suggesting limited priority effects on the community level. Patterns detected at the population level, however, showed that resistance of aquatic bacteria to invasion might be strengthened by warming as higher temperatures (a) increased the sum of relative abundances of persistent bacteria in the recipient communities, and (b) restricted the total relative abundance of successfully established late‐arriving bacteria. Warming‐enhanced resistance, however, was not always found and its strengths differed between recipient communities and dispersal rates. Nevertheless, our findings highlight the potential role of warming in mitigating the effects of invasion at the population level.
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