Papers by Barbara Kraigher
Soil Biology and Biochemistry, 2006
Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is... more Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled from the Ljubljana Marsh under different seasonal conditions. Substrate-induced respiration and dehydrogenase activity were used as indicators of total microbial activity. Both methods indicated higher microbial activities in the fen soil with the higher SOC content on all dates of sampling. To determine whether the differences in microbial activity were associated with differences in the microbial community structures, terminal restriction fragment length polymorphism (T-RFLP) of bacterial 16S rRNA genes was performed. Comparison of the T-RFLP profiles revealed very similar community structures in both fens and in the two seasonal extremes investigated. This suggested a stable community structure in the two fens, which is not affected by the SOC content or seasonal variation. In addition, a bacterial 16S ribosomal RNA gene based clone library was prepared from the fen soil with the higher SOC content. Out of 114 clones analysed, approximately 53% belonged to the Proteobacteria, 23% to the Acidobacteria, 21% to a variety of other taxa, and less than 3% were affiliated with the Firmicutes.
Food Technology and Biotechnology, 2003
Summary Bacteria communicate with one another by (emitting and/or reacting) to chemical signals. ... more Summary Bacteria communicate with one another by (emitting and/or reacting) to chemical signals. These communications, also known as quorum sensing, enable cells to control gene expression in response to cell density at the intra- and inter-species level. While bacteria use common signaling themes, variations in the design of the extracellular signals, the signal detection apparatus, and the biochemical mechanisms of signal relay have allowed quorum sensing systems to be adapted to diverse uses. The quorum sensing systems that govern natural genetic competence in Bacillus subtilis involve the ComX pheromones and the ComP-ComA, two-component regulator. ComX is synthesized as an inactive precursor and is then cleaved and modified by ComQ before export to the extra-cellular environment. The comQXP' loci of a set of natural Bacillus isolates have been sequenced and a striking polymorphism that correlates with specific patterns of activation of the quorum sensing response was shown. ...
Summary Many peatlands in Europe have been subjected to land reclamation and systematic drainage,... more Summary Many peatlands in Europe have been subjected to land reclamation and systematic drainage, which have substantially affected nutrient cycles in the soil. This work reviews published studies on microbial processes linked to carbon and nitrogen transformations in the soils of the Ljubljana marsh, a drained peatland positioned close to Ljubljana, the capital of Slovenia. This region is known for its dramatic diversity of animal and plant life, but below ground it hides diverse bacterial and archaeal communities that are highly responsive to environmental changes and make the Ljubljana marsh soils a good source of N2O and CO2, and a sink for CH4. Methanogenesis is highly restricted in these soils due to competition for electron donors with iron reducers. In addition, methane is efficiently removed by methanotrophs, which are highly active, especially in the soil layers exposed to the changing water table. Denitrification is limited by electron acceptors and in deeper soil layers ...
Food Technology and Biotechnology, 2020
SUMMARY Research background The occurrence and environmental toxicity of pharmaceuticals have rec... more SUMMARY Research background The occurrence and environmental toxicity of pharmaceuticals have recently attracted increasing attention. Diclofenac is a highly consumed non-steroidal anti-inflammatory drug, which is often detected in wastewaters, but investigations of its influence on bacteria are scarce. Experimental approach We investigated the influence of this pharmaceutical on bacterial community in activated sludge exposed to increasing concentrations of diclofenac in fed-batch reactors over 41 days. Nitrification activity of the activated sludge was measured and changes in bacterial community structure were followed using culture-independent molecular method (terminal restriction fragment length polymorphism, T-RFLP) and by the cultivation approach. Results and conclusions Nitrification activity was not detectably influenced by the addition of diclofenac, while the main change of the bacterial community structure was detected only at the end of incubation (after 41 days) when d...
Nature Communications
Bacillus subtilis is a soil bacterium that is competent for natural transformation. Genetically d... more Bacillus subtilis is a soil bacterium that is competent for natural transformation. Genetically distinct B. subtilis swarms form a boundary upon encounter, resulting in killing of one of the strains. This process is mediated by a fast-evolving kin discrimination (KD) system consisting of cellular attack and defence mechanisms. Here, we show that these swarm antagonisms promote transformation-mediated horizontal gene transfer between strains of low relatedness. Gene transfer between interacting non-kin strains is largely unidirectional, from killed cells of the donor strain to surviving cells of the recipient strain. It is associated with activation of a stress response mediated by sigma factor SigW in the donor cells, and induction of competence in the recipient strain. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, do not upregulate transformation upon encounter. This result indicates that social inter...
The ISME Journal
Swarming is the collective movement of bacteria across a surface. It requires the production of s... more Swarming is the collective movement of bacteria across a surface. It requires the production of surfactants (public goods) to overcome surface tension and provides an excellent model to investigate bacterial cooperation. Previously, we correlated swarm interaction phenotypes with kin discrimination between B. subtilis soil isolates, by showing that less related strains form boundaries between swarms and highly related strains merge. However, how kin discrimination affects cooperation and territoriality in swarming bacteria remains little explored. Here we show that the pattern of surface colonization by swarming mixtures is influenced by kin types. Closely related strain mixtures colonize the surface in a mixed swarm, while mixtures of less related strains show competitive exclusion as only one strain colonizes the surface. The outcome of nonkin swarm expansion depends on the initial ratio of the competing strains, indicating positive frequency-dependent competition. We find that ad...
Microorganisms in nature form multicellular groups called biofilms. In biofilms bacteria embedded... more Microorganisms in nature form multicellular groups called biofilms. In biofilms bacteria embedded in a matrix of extracellular polymeric substances (EPS) interact intensely, due to their proximity to each other. Most studies have investigated genetically homogeneous biofilms, leaving a gap in knowledge on genetically heterogeneous biofilms. Recent insights show that a Gram-positive model bacterium, Bacillus subtilis, discriminates between strains of high (kin) and low (non-kin) phylogenetic relatedness, reflected in merging (kin) and boundaries (non-kin) between swarms. However, it is not clear how kinship between interacting strains affects their fitness, the genotype distribution, and the EPS sharing in floating biofilms (pellicles). To address this gap in knowledge we cultivate B. subtilis strains as mixtures of kin and non-kin strains in static cultures, allowing them to form pellicles. We show here that in non-kin pellicles only one strain’s fitness was reduced; at the same tim...
B. subtilis is a soil dwelling bacterium with a diverse social life that includes quorum sensing-... more B. subtilis is a soil dwelling bacterium with a diverse social life that includes quorum sensing-regulated interactions 1. These interactions result in bacterial equivalent of sex, and subsequently have a profound influence on bacterial evolution2. Sexual isolation in B. subtilis predicts for more frequent uptake of DNA isolated from closely related strains3–5, but DNA exchange between two interacting B. subtilis strains has never been addressed previously. Recently we discovered kin discrimination among highly related strains of B. subtilis, where less related strains showed antagonistic behaviour towards each other in the form of killing6. Here we show that antagonistic interactions between two less closely related B. subtilis strains result in increased recombination, which is in contrast to current dogma. We demonstrate that the induction of competence between non-kin strains is responsible for the observed elevated DNA uptake, which, through increased genetic variation, can inc...
Journal of Hazardous Materials, Apr 1, 2011
Pharmaceuticals represent a group of the new emerging contaminants, which might influence microbi... more Pharmaceuticals represent a group of the new emerging contaminants, which might influence microbial communities in the activated sludge. Nitrification activity and Nitrospira community structure in the small-scale reactors supplied with different concentrations (0, 50, 200, 500 g L −1) of the selected pharmaceuticals (ibuprofen, naproxen, ketoprofen, diclofenac and clofibric acid) were evaluated. Ammonia removal was not influenced by selected pharmaceuticals. However, in the two reactors operated with 50 g L −1 of pharmaceuticals (R50 and R50P), the effluent concentration of N-(NO 2 − + NO 3 −) was significantly higher than in the other reactors. Nitrospira community structure was assessed by terminal restriction fragment length polymorphism (T-RFLP) and by cloning and sequencing of the partial genes for 16S rRNA. Nitrospira spp. were detected in all reactors. The two dominant T-RFs represented the sublineages I and II of the genus Nitrospira. Main shifts were observed in the reactors R50 and R50P, where the T-RF representing sublineage II was much higher as compared to the other reactors. Consistent with this, the Nitrospira sublineage II was detected only in the clone libraries from the reactors R50 and R50P. Our results suggest that the relative abundance of Nitrospira sublineage II could be related to the effluent N-(NO 2 − + NO 3 −) concentration.
Soil Biology and Biochemistry, 2009
... Luka Ausec a , Barbara Kraigher a and Ines Mandic-Mulec Corresponding Author Contact Informat... more ... Luka Ausec a , Barbara Kraigher a and Ines Mandic-Mulec Corresponding Author Contact Information , a , E-mail The Corresponding Author. ... North and South America (Fierer and Jackson, 2006) and in temperate freshwater wetlands from two North American sites (Hartman et al ...
Journal of Hazardous Materials, 2011
Pharmaceuticals represent a group of the new emerging contaminants, which might influence microbi... more Pharmaceuticals represent a group of the new emerging contaminants, which might influence microbial communities in the activated sludge. Nitrification activity and Nitrospira community structure in the small-scale reactors supplied with different concentrations (0, 50, 200, 500 g L −1) of the selected pharmaceuticals (ibuprofen, naproxen, ketoprofen, diclofenac and clofibric acid) were evaluated. Ammonia removal was not influenced by selected pharmaceuticals. However, in the two reactors operated with 50 g L −1 of pharmaceuticals (R50 and R50P), the effluent concentration of N-(NO 2 − + NO 3 −) was significantly higher than in the other reactors. Nitrospira community structure was assessed by terminal restriction fragment length polymorphism (T-RFLP) and by cloning and sequencing of the partial genes for 16S rRNA. Nitrospira spp. were detected in all reactors. The two dominant T-RFs represented the sublineages I and II of the genus Nitrospira. Main shifts were observed in the reactors R50 and R50P, where the T-RF representing sublineage II was much higher as compared to the other reactors. Consistent with this, the Nitrospira sublineage II was detected only in the clone libraries from the reactors R50 and R50P. Our results suggest that the relative abundance of Nitrospira sublineage II could be related to the effluent N-(NO 2 − + NO 3 −) concentration.
Bioresource Technology, 2012
h i g h l i g h t s " SMF (B = 17 mT) negatively influenced the growth of Escherichia coli and Ps... more h i g h l i g h t s " SMF (B = 17 mT) negatively influenced the growth of Escherichia coli and Pseudomonas putida. " The SMF driven growth inhibition was less pronounced at B = 5 mT and B = 50 mT. " The SMF effect was most pronounced at optimal growth temperatures. " SMF (B = 17 mT) increased dehydrogenase activity and intracellular ATP concentrations. " SMF increased expression of the rpoS gene in E. coli.
Water Research, 2008
Concern is growing over contamination of the environment with pharmaceuticals because of their wi... more Concern is growing over contamination of the environment with pharmaceuticals because of their widespread use and incomplete removal during wastewater treatment, where microorganisms drive the key processes. The influence of pharmaceuticals on bacterial community structure in activated sludge was assessed in small-scale wastewater treatment bioreactors containing different concentrations (5, 50, 200 and 500 mg L À1) of several commonly used pharmaceuticals (ibuprofen, naproxen, ketoprofen, diclofenac and clofibric acid). T-RFLP analyses of the bacterial 16S rRNA genes indicated a minor but consistent shift in the bacterial community structure in the bioreactor R50 supplied with pharmaceuticals at a concentration of 50 mg L À1 , compared to the control reactor R0, which was operated without addition of pharmaceuticals. In the reactors operated with higher concentrations of pharmaceuticals, a greater structural divergence was observed. Bacterial community composition was further investigated by preparation of two clone libraries of bacterial 16S rRNA genes from reactors R0 and R50. Most clones in both libraries belonged to the Betaproteobacteria, among which Thauera, Sphaerotilus, Ideonella and Acidovorax-related spp. dominated. Nitrite-oxidizing bacteria of the genus Nitrospira sp., which are key organisms for the second stage of nitrification in wastewater treatment plants, were found only in the clone library of the reactor without pharmaceuticals. In addition, diversity indices were calculated for the two clone libraries, indicating a reduced diversity of activated sludge bacterial community in the reactor supplied with 50 mg L À1 of each of selected pharmaceuticals.
Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is... more Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled from the Ljubljana Marsh under different seasonal conditions. Substrate-induced respiration and dehydrogenase activity were used as indicators of total microbial activity. Both methods indicated higher microbial activities in the fen soil with the higher SOC content on all dates of sampling. To determine whether the differences in microbial activity were associated with differences in the microbial community structures, terminal restriction fragment length polymorphism (T-RFLP) of bacterial 16S rRNA genes was performed. Comparison of the T-RFLP profiles revealed very similar community structures in both fens and in the two seasonal extremes investigated. This suggested a stable community structure in the two fens, which is not affected by the SOC content or seasonal variation. In addition, a bacterial 16S ribosomal RNA gene based clone library was prepared from the fen soil with the higher SOC content. Out of 114 clones analysed, approximately 53% belonged to the Proteobacteria, 23% to the Acidobacteria, 21% to a variety of other taxa, and less than 3% were affiliated with the Firmicutes. r
Journal of Bacteriology, 2001
A quorum-sensing mechanism involving the pheromone ComX and the ComP-ComA two-component system co... more A quorum-sensing mechanism involving the pheromone ComX and the ComP-ComA two-component system controls natural competence in Bacillus subtilis. ComX is expressed as a cytoplasmic inactive precursor that is released into the extracellular medium as a cleaved, modified decapeptide. This process requires the product of comQ. In the presence of ComX, the membrane-localized ComP histidine kinase activates the response regulator ComA. We compared the sequences of the quorum-sensing genes from four closely related bacilli, and we report extensive genetic polymorphism extending through comQ, comX, and the 5 two-thirds of comP. This part of ComP encodes the membrane-localized and linker domains of the sensor protein. We also determined the sequences of the comX genes of four additional wild-type bacilli and tested the in vivo activities of all eight pheromones on isogenic strains containing four different ComP receptor proteins. A striking pattern of specificity was discovered, providing strong evidence that the pheromone contacts ComP directly. Furthermore, we show that coexpression of comQ and comX in Escherichia coli leads to the production of active pheromone in the medium, demonstrating that comQ is the only dedicated protein required for the processing, modification, and release of active competence pheromone. Some of the implications of these findings for the evolution and the mechanism of the quorum-sensing system are discussed. 451 on February 7, 2016 by guest http://jb.asm.org/ Downloaded from produced in Escherichia coli in the presence of ComQ. Our results show that ComQ and ComX are the only dedicated proteins required for production of the competence pheromone, and that comQ, comX, and comP are the sole determinants of the QS pherotype.
Current Biology, 2016
Multicellularity inherently involves a number of cooperative behaviors that are potentially susce... more Multicellularity inherently involves a number of cooperative behaviors that are potentially susceptible to exploitation but can be protected by mechanisms such as kin discrimination. Discrimination of kin from non-kin has been observed in swarms of the bacterium Bacillus subtilis, but the underlying molecular mechanism has been unknown. We used genetic, transcriptomic, and bioinformatic analyses to uncover kin recognition factors in this organism. Our results identified many molecules involved in cell-surface modification and antimicrobial production and response. These genes varied significantly in expression level and mutation phenotype among B. subtilis strains, suggesting interstrain variation in the exact kin discrimination mechanism used. Genome analyses revealed a substantial diversity of antimicrobial genes present in unique combinations in different strains, with many likely acquired by horizontal gene transfer. The dynamic combinatorial effect derived from this plethora of kin discrimination genes creates a tight relatedness cutoff for cooperation that has likely led to rapid diversification within the species. Our data suggest that genes likely originally selected for competitive purposes also generate preferential interactions among kin, thus stabilizing multicellular lifestyles.
Proceedings of the National Academy of Sciences, 2015
Kin discrimination, broadly defined as differential treatment of conspecifics according to their ... more Kin discrimination, broadly defined as differential treatment of conspecifics according to their relatedness, could help biological systems direct cooperative behavior toward their relatives. Here we investigated the ability of the soil bacterium Bacillus subtilis to discriminate kin from nonkin in the context of swarming, a cooperative multicellular behavior. We tested a collection of sympatric conspecifics from soil in pairwise combinations and found that despite their history of coexistence, the vast majority formed distinct boundaries when the swarms met. Some swarms did merge, and most interestingly, this behavior was only seen in the most highly related strain pairs. Overall the swarm interaction phenotype strongly correlated with phylogenetic relatedness, indicative of kin discrimination. Using a subset of strains, we examined cocolonization patterns on plant roots. Pairs of kin strains were able to cocolonize roots and formed a mixed-strain biofilm. In contrast, inoculating roots with pairs of nonkin strains resulted in biofilms consisting primarily of one strain, suggestive of an antagonistic interaction among nonkin strains. This study firmly establishes kin discrimination in a bacterial multicellular setting and suggests its potential effect on ecological interactions.
Food Technology and Biotechnology, 2015
Water Research, 2008
Pharmaceuticals Bacterial community structure T-RFLP 16S rRNA Diversity a b s t r a c t Concern i... more Pharmaceuticals Bacterial community structure T-RFLP 16S rRNA Diversity a b s t r a c t Concern is growing over contamination of the environment with pharmaceuticals because of their widespread use and incomplete removal during wastewater treatment, where microorganisms drive the key processes. The influence of pharmaceuticals on bacterial community structure in activated sludge was assessed in small-scale wastewater treatment bioreactors containing different concentrations (5, 50, 200 and 500 mg L À1 ) of several commonly used pharmaceuticals (ibuprofen, naproxen, ketoprofen, diclofenac and clofibric acid). T-RFLP analyses of the bacterial 16S rRNA genes indicated a minor but consistent shift in the bacterial community structure in the bioreactor R50 supplied with pharmaceuticals at a concentration of 50 mg L À1 , compared to the control reactor R0, which was operated without addition of pharmaceuticals. In the reactors operated with higher concentrations of pharmaceuticals, a greater structural divergence was observed. Bacterial community composition was further investigated by preparation of two clone libraries of bacterial 16S rRNA genes from reactors R0 and R50. Most clones in both libraries belonged to the Betaproteobacteria, among which Thauera, Sphaerotilus, Ideonella and Acidovorax-related spp. dominated. Nitrite-oxidizing bacteria of the genus Nitrospira sp., which are key organisms for the second stage of nitrification in wastewater treatment plants, were found only in the clone library of the reactor without pharmaceuticals. In addition, diversity indices were calculated for the two clone libraries, indicating a reduced diversity of activated sludge bacterial community in the reactor supplied with 50 mg L À1 of each of selected pharmaceuticals. (I. Mandic-Mulec).
Soil Biology and Biochemistry, 2006
Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is... more Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled from the Ljubljana Marsh under different seasonal conditions. Substrate-induced respiration and dehydrogenase activity were used as indicators of total microbial activity. Both methods indicated higher microbial activities in the fen soil with the higher SOC content on all dates of sampling. To determine whether the differences in microbial activity were associated with differences in the microbial community structures, terminal restriction fragment length polymorphism (T-RFLP) of bacterial 16S rRNA genes was performed. Comparison of the T-RFLP profiles revealed very similar community structures in both fens and in the two seasonal extremes investigated. This suggested a stable community structure in the two fens, which is not affected by the SOC content or seasonal variation. In addition, a bacterial 16S ribosomal RNA gene based clone library was prepared from the fen soil with the higher SOC content. Out of 114 clones analysed, approximately 53% belonged to the Proteobacteria, 23% to the Acidobacteria, 21% to a variety of other taxa, and less than 3% were affiliated with the Firmicutes. r
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Papers by Barbara Kraigher