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  • 1.
    Attermeyer, Katrin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Andersson, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Catalán, Núria
    Catalan Institute for Water Research (ICRA), Girona, Spain.
    Einarsdóttir, Karólina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Groeneveld, Marloes M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Szekely, Anna J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Potential terrestrial influence on transparent exopolymer particle (TEP) concentrations in boreal freshwaters2019In: Journal of limnology, ISSN 1129-5767, E-ISSN 1723-8633Article in journal (Refereed)
    Abstract [en]

    Transparent exopolymer particles (TEP) are ubiquitous in aquatic ecosystems and contribute, for example, to sedimentation of organic matter in oceans and freshwaters. Earlier studies indicate that the formation of TEP is related to the in situ activity of phytoplankton or bacteria. However, terrestrial sources of TEP and TEP precursors are usually not considered. We investigated TEP concentration and its driving factors in boreal freshwaters, hypoth- esizing that TEP and TEP precursors can enter freshwaters via terrestrial inputs. In a field survey, we measured TEP concentrations and other environmental factors across 30 aquatic ecosystems in Sweden. In a mesocosm experi- ment, we further investigated TEP dynamics over time after manipulating terrestrial organic matter input and light conditions. The TEP concentrations in boreal freshwaters ranged from 83 to 4940 μg Gum Xanthan equivalent L−1, which is comparable to other studies in freshwaters. The carbon fraction in TEP in the sampled boreal freshwaters is much higher than the phytoplanktonic carbon, in contrast to previous studies in northern temperate and Medi- terranean regions. Boreal TEP concentrations were mostly related to particulate organic carbon, dissolved organic carbon, and optical indices of terrestrial influence but less influenced by bacterial abundance, bacterial production, and chlorophyll a. Hence, our results do not support a major role of the phytoplankton community or aquatic bac- teria on TEP concentrations and dynamics. This suggests a strong external control of TEP concentrations in boreal freshwaters, which can in turn affect particle dynamics and sedimentation in the recipient aquatic ecosystem.

  • 2.
    Berga, Mercè
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Yinghua, Zha
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Székely, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Testing responses of bacterial communities to environmental change using whole ecosystem manipulation experimentsManuscript (preprint) (Other academic)
  • 3.
    Berga, Mercè
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Germany.
    Zha, Yinghua
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Székely, Anna J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Functional and Compositional Stability of Bacterial Metacommunities in Response to Salinity Changes2017In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, article id 948Article in journal (Refereed)
    Abstract [en]

    Disturbances and environmental change are important factors determining the diversity,composition, and functioning of communities. However, knowledge about how naturalbacterial communities are affected by such perturbations is still sparse. We performeda whole ecosystem manipulation experiment with freshwater rock pools where weapplied salinity disturbances of different intensities. The aim was to test how thecompositional and functional resistance and resilience of bacterial communities,alpha- and beta-diversity and the relative importance of stochastic and deterministiccommunity assembly processes changed along a disturbance intensity gradient.We found that bacterial communities were functionally resistant to all salinity levels (3, 6, and 12 psu) and compositionally resistant to a salinity increase to 3 psu andresilient to increases of 6 and 12 psu. Increasing salinities had no effect on local richnessand evenness, beta-diversity and the proportion of deterministically vs. stochasticallyassembled communities. Our results show a high functional and compositional stabilityof bacterial communities to salinity changes of different intensities both at localand regional scales, which possibly reflects long-term adaptation to environmentalconditions in the study system.

  • 4.
    Berga, Mercé
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Székely, Anna J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Effects of Disturbance Intensity and Frequency on Bacterial Community Composition and Function2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 5, p. e36959-Article in journal (Refereed)
    Abstract [en]

    Disturbances influence community structure and ecosystem functioning. Bacteria are key players in ecosystems and it is therefore crucial to understand the effect of disturbances on bacterial communities and how they respond to them, both compositionally and functionally. The main aim of this study was to test the effect of differences in disturbance strength on bacterial communities. For this, we implemented two independent short-term experiments with dialysis bags containing natural bacterial communities, which were transplanted between ambient and 'disturbed' incubation tanks, manipulating either the intensity or the frequency of a salinity disturbance. We followed changes in community composition by terminal restriction fragment analysis (T-RFLP) and measured various community functions (bacterial production, carbon substrate utilization profiles and rates) directly after and after a short period of recovery under ambient conditions. Increases in disturbance strength resulted in gradually stronger changes in bacterial community composition and functions. In the disturbance intensity experiment, the sensitivity to the disturbance and the ability of recovery differed between different functions. In the disturbance frequency experiment, effects on the different functions were more consistent and recovery was not observed. Moreover, in case of the intensity experiment, there was also a time lag in the responses of community composition and functions, with functional responses being faster than compositional ones. To summarize, our study shows that disturbance strength has the potential to change the functional performance and composition of bacterial communities. It further highlights that the overall effects, rates of recovery and the degree of congruence in the response patterns of community composition and functioning along disturbance gradients depend on the type of function and the character of the disturbance.

  • 5. Bohus, Veronika
    et al.
    Tóth, Erika M.
    Székely, Anna J.
    Makk, Judit
    Baranyi, Krisztián
    Patek, Gábor
    Schunk, János
    Márialigeti, Károly
    Microbiological investigation of an industrial ultra pure supply water plant using cultivation-based and cultivation-independent methods2010In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 44, no 20, p. 6124-6132Article in journal (Refereed)
    Abstract [en]

    Ultra pure waters (UPW), characterized by extremely low salt and nutrient concentrations, can suffer from microbial contamination which causes biofouling and biocorrosion, possibly leading to reduced lifetime and increased operational costs. Samples were taken from an ultra pure supply water producing plant of a power plant. Scanning electron microscopic examination was carried out on the biofilms formed in the system. Biofilm, ion exchange resin, and water samples were characterized by culture-based methods and molecular fingerprinting (terminal restriction fragment length polymorphism [T-RFLP] analysis and molecular cloning). Identification of bacteria was based on 16S rDNA sequence comparison. A complex microbial community structure was revealed. Nearly 46% of the clones were related to as yet uncultured bacteria. The community profiles of the water samples were the most diverse and most of bacteria were recruited from bacterial communities of tube surface and ion exchange resin biofilms. Microbiota of different layers of the mixed bed ion exchange resin showed the highest similarity. Most of the identified taxa (dominated by β-Proteobacteria) could take part in microbially influenced corrosion. © 2010 Elsevier Ltd.

  • 6.
    Csitári, Bianka
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Macrophyte cover and groundwater as the key drivers of the extremelyhigh organic carbon concentration of soda pans2019Data set
  • 7. Felföldi, Tamás
    et al.
    Székely, Anna J
    Gorál, Róbert
    Barkács, Katalin
    Scheirich, Gergely
    András, Judit
    Rácz, Anikó
    Márialigeti, Károly
    Polyphasic bacterial community analysis of an aerobic activated sludge removing phenols and thiocyanate from coke plant effluent2010In: Bioresource Technology, ISSN 0960-8524, E-ISSN 1873-2976, Vol. 101, no 10, p. 3406-3414Article in journal (Refereed)
    Abstract [en]

    Biological purification processes are effective tools in the treatment of hazardous wastes such as toxic compounds produced in coal coking. In this study, the microbial community of a lab-scale activated sludge system treating coking effluent was assessed by cultivation-based (strain isolation and identification, biodegradation tests) and culture-independent techniques (sequence-aided T-RFLP, taxon-specific PCR). The results of the applied polyphasic approach showed a simple microbial community dominated by easily culturable heterotrophic bacteria. Comamonas badia was identified as the key microbe of the system, since it was the predominant member of the bacterial community, and its phenol degradation capacity was also proved. Metabolism of phenol, even at elevated concentrations (up to 1500 mg/L), was also presented for many other dominant (Pseudomonas, Rhodanobacter, Oligella) and minor (Alcaligenes, Castellaniella, Microbacterium) groups, while some activated sludge bacteria (Sphingomonas, Rhodopseudomonas) did not tolerate it even in lower concentrations (250 mg/L). In some cases, closely related strains showed different tolerance and degradation properties. Members of the genus Thiobacillus were detected in the activated sludge, and were supposedly responsible for the intensive thiocyanate biodegradation observed in the system. Additionally, some identified bacteria (e.g. C. badia and the Ottowia-related strains) might also have had a significant impact on the structure of the activated sludge due to their floc-forming abilities. © 2009 Elsevier Ltd. All rights reserved.

  • 8.
    Garcia, Sarahi L
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Szekely, Anna J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bergvall, Christoffer
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Schattenhofer, Martha
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Peura, S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Swedish Univ Agr Sci, Sci Life Lab, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden;Uppsala Univ, Dept Cell & Mol Biol, Uppsala, Sweden.
    Decreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic Capacity2019In: MSPHERE, ISSN 2379-5042, Vol. 4, no 1, article id e00626-18Article in journal (Refereed)
    Abstract [en]

    Climate change scenarios anticipate decreased spring snow cover in boreal and subarctic regions. Forest lakes are abundant in these regions and substantial contributors of methane emissions. To investigate the effect of reduced snow cover, we experimentally removed snow from an anoxic frozen lake. We observed that the removal of snow increased light penetration through the ice, increasing water temperature and modifying microbial composition in the different depths. Chlorophyll a and b concentrations increased in the upper water column, suggesting activation of algal primary producers. At the same time, Chlorobiaceae, one of the key photosynthetic bacterial families in anoxic lakes, shifted to lower depths. Moreover, a decrease in the relative abundance of methanotrophs within the bacterial family Methylococcaceae was detected, concurrent with an increase in methane concentration in the water column. These results indicate that decreased snow cover impacts both primary production and methane production and/or consumption, which may ultimately lead to increased methane emissions after spring ice off. IMPORTANCE Small lakes are an important source of greenhouse gases in the boreal zone. These lakes are severely impacted by the winter season, when ice and snow cover obstruct gas exchange between the lake and the atmosphere and diminish light availability in the water column. Currently, climate change is resulting in reduced spring snow cover. A short-term removal of the snow from the ice stimulated algal primary producers and subsequently heterotrophic bacteria. Concurrently, the relative abundance of methanotrophic bacteria decreased and methane concentrations increased. Our results increase the general knowledge of microbial life under ice and, specifically, the understanding of the potential impact of climate change on boreal lakes.

  • 9.
    Langenheder, Silke
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Berga, Mercé
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Östman, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Székely, Anna J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Temporal variation of beta-diversity and assembly mechanisms in a bacterial metacommunity2012In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 6, no 6, p. 1107-1114Article in journal (Refereed)
    Abstract [en]

    The turnover of community composition across space, beta-diversity, is influenced by different assembly mechanisms, which place varying weight on local habitat factors, such as environmental conditions and species interactions, and regional factors such as dispersal and history. Several assembly mechanisms may function simultaneously; however, little is known about how their importance changes over time and why. Here, we implemented a field survey where we sampled a bacterial metacommunity consisting of 17 rock pools located at the Swedish Baltic Sea coast at 11 occasions during 1 year. We determined to which extent communities were structured by different assembly mechanisms using variation partitioning and studied changes in beta-diversity across environmental gradients over time. beta-Diversity was highest at times of high overall productivity and environmental heterogeneity in the metacommunity, at least partly due to species sorting, that is, selection of taxa by the prevailing environmental conditions. In contrast, dispersal-driven assembly mechanisms were primarily detected at times when beta-diversity was relatively low. There were no indications for strong and persistent differences in community composition or beta-diversity between permanent and temporary pools, indicating that the physical disturbance regime is of relatively minor importance. In summary, our study clearly suggests that there are temporal differences in the relative importance of different assembly mechanisms related to abiotic factors and shows that the temporal variability of those factors is important for a more complete understanding of bacterial metacommunity dynamics.

  • 10.
    Langenheder, Silke
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Szekely, Anna J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Species sorting and neutral processes are both important during the initial assembly of bacterial communities2011In: The ISME Journal, ISSN 1751-7362, Vol. 5, no 7, p. 1086-1094Article in journal (Refereed)
    Abstract [en]

    Many studies have shown that species sorting, that is, the selection by local environmental conditions is important for the composition and assembly of bacterial communities. On the other hand, there are other studies that could show that bacterial communities are neutrally assembled. In this study, we implemented a microcosm experiment with the aim to determine, at the same time, the importance of species sorting and neutral processes for bacterial community assembly during the colonisation of new, that is, sterile, habitats, by atmospheric bacteria. For this we used outdoor microcosms, which contained sterile medium from three different rock pools representing different environmental conditions, which were seeded by rainwater bacteria. We found some evidence for neutral assembly processes, as almost every 4th taxon growing in the microcosms was also detectable in the rainwater sample irrespective of the medium. Most of these taxa belonged to widespread families with opportunistic growth strategies, such as the Pseudomonadaceae and Comamonadaceae, indicating that neutrally assembled taxa may primarily be generalists. On the other hand, we also found evidence for species sorting, as one out of three media selected a differently composed bacterial community. Species sorting effects were relatively weak and established themselves via differences in relative abundance of generalists among the different media, as well as media-specific occurrences of a few specific taxa. In summary, our results suggest that neutral and species sorting processes interact during the assembly of bacterial communities and that their importance may differ depending on how many generalists and specialists are present in a community.

  • 11. Máthé, I.
    et al.
    Táncsics, A.
    György, Éva
    Pohner, Zsuzsanna
    Vladár, P.
    Székely, Anna J.
    Márialigeti, K.
    Investigation of mineral water springs of Miercurea Ciuc (Csíkszereda) region (Romania) with cultivation-dependent microbiological methods2010In: Acta Microbiologica et Immunologica Hungarica, ISSN ISSN 1217-8950, EISSN 1588-2640 (Online), Vol. 57, no 2, p. 109-122Article in journal (Refereed)
    Abstract [en]

    Water samples of ten mineral water springs at Miercurea Ciuc (Csíkszereda) region (Romania) were examined during 2005-2006 using cultivation-dependent microbiological methods. The results of standard hygienic bacteriological tests showed that the Hargita Spring had perfect and five other springs had microbiologically acceptable water quality (Zsögöd-, Nagy-borvíz-, Taploca-, Szentegyháza- and Lobogó springs). The water of Borsáros Spring was exceptionable (high germ count, presence of Enterococcus spp.).Both standard bacteriological and molecular microbiological methods indicated that the microbiological water quality of the Szeltersz-, Nádasszék- and Délo springs was not acceptable. Bad water quality resulted from inadequate spring catchment and hygiene (low yield, lack of runoff, negligent usage of the springs, horse manure around the spring).The 16S rRNA gene-based identification of strains isolated on standard meat-peptone medium resulted in the detection of typical aquatic organisms such as Shewanella baltica, Aeromonas spp., Pseudomonas veronii, Psychrobacter sp,. Acinetobacter spp. and allochthonous microbes, like Nocardia, Streptomyces, Bacillus, Microbacterium , and Arthrobacter strains indicating the impact of soil. Other allochthonous microbes, such as Staphylococcus spp., Micrococcus sp., Lactococcus sp., Clostridium butyricum, Yersinia spp., Aerococcus sp., may have originated from animal/human sources. © 2010 Akadémiai Kiadó, Budapest.

  • 12.
    Nikolausz, Marcell
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Kappelmeyer, Uwe
    Székely, Anna
    Rusznyák, Anna
    Márialigeti, Károly
    Kästner, Matthias
    Diurnal redox fluctuation and microbial activity in the rhizosphere of wetland plants2008In: European journal of soil biology, ISSN 1164-5563, E-ISSN 1778-3615, Vol. 44, no 3, p. 324-333Article in journal (Refereed)
    Abstract [en]

    Wetland plants release oxygen through the aerenchyma system to the roots, providing oxic habitats in the rhizosphere. The consumption of the oxygen during the night establishes a diurnal fluctuation of the redox conditions (-320 mV to +300 mV) that explains the coexistence of aerobic and anaerobic microorganisms in the rhizosphere. The redox fluctuation and its effect on the activity of rhizosphere microorganisms were investigated by RNA-based fingerprinting techniques in a laboratory scale reactor planted with Juncus effusus. The denaturing gradient gel electrophoresis (DGGE) patterns of 16S rRNA obtained with "universal" primers were very similar regardless of the time of sampling, indicating that the overall ribosome level of the predominantly active members did not change significantly. The amoA transcript DGGE patterns showed moderate diurnal dynamics with specific bands observed either in day or night samples. However, the majority of amoA genes were continuously expressed, indicating that the activity of functional genes may only partly be a measure sensitive enough for tracing the physiological activity on a short time scale. The results indicate that loose regulation of functional genes can be the main strategy for accommodation to fluctuating environmental conditions. The spatial separation of microbial activities as a result of diurnal fluctuating oxygen availability probably contributes to niche differentiation in the rhizosphere but this is difficult to track it at transcriptome level. © 2008 Elsevier Masson SAS. All rights reserved.

  • 13. Nikolausz, Marcell
    et al.
    Sipos, Rita
    Révész, Sára
    Szekely, Anna
    Department of Microbiology, Eötvös Loránd University of Science, Budapest, Hungary.
    Márialigeti, Károly
    Observation of bias associated with re-amplification of DNA isolated from denaturing gradient gels2005In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 244, p. 385-390Article in journal (Refereed)
    Abstract [en]

    DNA from environmental PCR products separated by denaturing gradient gel electrophoresis (DGGE) was isolated from the background smear rather than from discrete bands of the DGGE gel. The ‘‘interband’’ region was considered as a potential source of less dominant members of natural microbial communities. Surprisingly, instead of detecting new bands from the re-amplified PCR products, patterns very similar to the original ones were obtained regardless of the position of the ‘‘interband’’ region. The results suggest that the separation of amplicons by DGGE may not be perfect and band re-amplification based sequence analyses need careful interpretation.

  • 14.
    Segura, Javier
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umea, Sweden.
    Nilsson, Mats B.
    Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umea, Sweden.
    Schleucher, Jürgen
    Umea Univ, Dept Med Biochem & Biophys, SE-90187 Umea, Sweden.
    Haei, Mahsa
    Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umea, Sweden.
    Sparrman, Tobias
    Umea Univ, Dept Chem, SE-90187 Umea, Sweden.
    Szekely, Anna J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Öquist, Mats G.
    Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umea, Sweden.
    Microbial utilization of simple carbon substrates in boreal peat soils at low temperatures2019In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 135, p. 438-448Article in journal (Refereed)
    Abstract [en]

    Boreal peatlands are key high-latitude ecosystem types and act as a carbon (C) sink storing an estimated 25% of the world's soil C. These environments are currently seeing the most substantial changing climate, especially during the winter. CO2 emissions during the winter can correspond to 80% of the growing season's net CO2 assimilation. Yet, our conceptual understanding of the controls on microbial metabolic activity in peat soils at temperatures <= 0 degrees C is poor. We used stable isotope probing of peat samples and tracked the fate of C-13-glucose using C-13-NMR. We show that microorganisms in frozen boreal peat soils utilize monomeric C-substrates to sustain both catabolic and anabolic metabolism at temperatures down to -5 degrees C. The C-13-substrate was transformed into C-13-CO2, different metabolites, and incorporated into membrane phospholipid fatty acids. The 16S rRNA-based community analyses revealed the activity at -3 degrees C changes the composition of the bacterial cornmunity over relevant timescales. Below 0 degrees C, small temperature changes have strong effects on process rates and small differences in winter soil temperature may affect C dynamics of northern peatlands. Understanding biological processes at low and below zero temperatures are central for the overall functioning of these systems representing one of the world's major soil C pools.

  • 15. Sipos, Rita
    et al.
    Székely, Anna J.
    Palatinszky, Márton
    Révész, Sára
    Márialigeti, Károly
    Nikolausz, Marcell
    Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis2007In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 60, no 2, p. 341-350Article in journal (Refereed)
    Abstract [en]

    In the attempt to explore complex bacterial communities of environmental samples, primers hybridizing to phylogenetically highly conserved regions of 16S rRNA genes are widely used, but differential amplification is a recognized problem. The biases associated with preferential amplification of multitemplate PCR were investigated using ’universal’ bacteria-specific primers, focusing on the effect of primer mismatch, annealing temperature and PCR cycle number. The distortion of the template-to-product ratio was measured using predefined template mixtures and environmental samples by terminal restriction fragment length polymorphism analysis. When a 1 : 1 genomic DNA template mixture of two strains was used, primer mismatches inherent in the 63F primer presented a serious bias, showing preferential amplification of the template containing the perfectly matching sequence. The extent of the preferential amplification showed an almost exponential relation with increasing annealing temperature from 47 to 61°C. No negative effect of the various annealing temperatures was observed with the 27F primer, with no mismatches with the target sequences. The number of PCR cycles had little influence on the template-to-product ratios. As a result of additional tests on environmental samples, the use of a low annealing temperature is recommended in order to significantly reduce preferential amplification while maintaining the specificity of PCR. © 2007 Federation of European Microbiological Societies.

  • 16.
    Székely, Anna J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Berga, Mercé
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Mechanisms determining the fate of dispersed bacterial communities in new environments2013In: ISME Journal, ISSN 1751-7362, Vol. 7, no 1, p. 61-71Article in journal (Refereed)
    Abstract [en]

    Recent work has shown that dispersal has an important role in shaping microbial communities. However, little is known about how dispersed bacteria cope with new environmental conditions and how they compete with local resident communities. To test this, we implemented two full-factorial transplant experiments with bacterial communities originating from two sources (freshwater or saline water), which were incubated, separately or in mixes, under both environmental conditions. Thus, we were able to separately test for the effects of the new environment with and without interactions with local communities. We determined community composition using 454-pyrosequencing of bacterial 16S rRNA to specifically target the active fraction of the communities, and measured several functional parameters. In absence of a local resident community, the net functional response was mainly affected by the environmental conditions, suggesting successful functional adaptation to the new environmental conditions. Community composition was influenced both by the source and the incubation environment, suggesting simultaneous effects of species sorting and functional plasticity. In presence of a local resident community, functional parameters were higher compared with those expected from proportional mixes of the unmixed communities in three out of four cases. This was accompanied by an increase in the relative abundance of generalists, suggesting that competitive interactions among local and immigrant taxa could explain the observed functional overachievement. In summary, our results suggest that environmental filtering, functional plasticity and competition are all important mechanisms influencing the fate of dispersed communities.

  • 17.
    Székely, Anna J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Univ S Florida, Coll Marine Sci, St Petersburg, FL 33701 USA..
    Breitbart, Mya
    Univ S Florida, Coll Marine Sci, St Petersburg, FL 33701 USA..
    Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology2016In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 363, no 6, article id fnw027Article, review/survey (Refereed)
    Abstract [en]

    Single-stranded DNA (ssDNA) phages are profoundly different from tailed phages in many aspects including the nature and size of their genome, virion size and morphology, mutation rate, involvement in horizontal gene transfer, infection dynamics and cell lysis mechanisms. Despite the importance of ssDNA phages as molecular biology tools and model systems, the environmental distribution and ecological roles of these phages have been largely unexplored. Viral metagenomics and other culture-independent viral diversity studies have recently challenged the perspective of tailed, double-stranded DNA (dsDNA) phages, dominance by demonstrating the prevalence of ssDNA phages in diverse habitats. However, the differences between ssDNA and dsDNA phages also substantially limit the efficacy of simultaneously assessing the abundance and diversity of these two phage groups. Here we provide an overview of the major differences between ssDNA and tailed dsDNA phages that may influence their effects on bacterial communities. Furthermore, through the analysis of 181 published metaviromes we demonstrate the environmental distribution of ssDNA phages and present an analysis of the methodological biases that distort their study through metagenomics.

  • 18.
    Székely, Anna J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Dispersal timing and drought history influence the response of bacterioplankton to drying–rewetting stress2017In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 11, no 8, p. 1764-1776Article in journal (Refereed)
    Abstract [en]

    The extent and frequency of drought episodes is expected to increase in the following decades making it a crucial stress factor for smaller water bodies. However, very little is known about how bacterioplankton is affected by increased evaporation and how these communities reassemble after rewetting. Here, we present results from a microcosm experiment that assessed the effect of drying–rewetting stress on bacterioplankton in the light of the stress history and the rate and timing of dispersal after the rewetting. We found that the drying phase resulted mainly in a change of function, whereas the complete desiccation and rewetting processes strongly affected both composition and function, which were, however, influenced by the initial conditions and stress history of the communities. Effects of dispersal were generally stronger when it occurred at an early stage after the rewetting. At this stage, selective establishment of dispersed bacteria coupled with enhanced compositional and functional recovery was found, whereas effects of dispersal were neutral, that is, predictable by dispersal rates, at later stages. Our studies therefore show that both the stress history and the timing of dispersal are important factors that influence the response of bacterial communities to environmental change and stress events.

  • 19.
    Székely, Anna J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    The importance of species sorting in bacterial communities differs between habitat generalists and specialists2014In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 87, no 1, p. 102-112Article in journal (Refereed)
    Abstract [en]

    Recent studies have shown that the spatial turnover of bacterial communities, that is, beta-diversity, is determined by a combination of different assembly mechanisms, such as species sorting, that is, environmental filtering, and dispersal-related mechanisms. However, it is currently unclear to what extent the importance of the different mechanisms depends on community traits. Here, we implemented a study using a rock pool metacommunity to test whether habitat specialization of bacterial taxa and groups or their phylogenetic identity influenced by which mechanisms communities were assembled. Ingeneral, our results show that species sorting was the most important assembly mechanism. However, we found that a larger fraction of the variation in bacterial community composition between pools could be explained by environmental factors in case of habitat generalists, that is, taxa that were widespread and abundant in the metacommunity, compared with habitat specialists, that is, taxa that had a more restricted distribution range and tended to be rare. Differences in assembly mechanisms were observedbetween different major phyla and classes. However, also here, a larger fraction of the variation incommunity composition among pools could be explained for taxonomic groups that contained on average more habitat generalists. In summary, our results show that species sorting is stronger for themost common taxa, indicating that beta-diversity along environmental gradients can be adequately described without considering rare taxa.

  • 20. Székely, Anna J.
    et al.
    Sipos, Rita
    Berta, Birgitta
    Vajna, Balázs
    Hajdú, Csaba
    Márialigeti, Károly
    DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence-aided T-RFLP profile of mature compost2009In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 57, no 3, p. 522-533Article in journal (Refereed)
    Abstract [en]

    The amount of button mushroom (Agaricus bisporus) harvested from compost is largely affected by the microbial processes taking place during composting and the microbes inhabiting the mature compost. In this study, the microbial changes during the stages of this specific composting process were monitored, and the dominant bacteria of the mature compost were identified to reveal the microbiological background of the favorable properties of the heat-treated phase II mushroom compost. 16S ribosomal deoxyribonucleic acid (rDNA)-based denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) molecular fingerprinting methods were used to track the succession of microbial communities in summer and winter composting cycles. DNA from individual DGGE bands were reamplified and subjected to sequence analysis. Principal component analysis of fingerprints of the composting processes showed intensive changes in bacterial community during the 22-day procedure. Peak temperature samples grouped together and were dominated by Thermus thermophilus. Mature compost patterns were almost identical by both methods (DGGE, T-RFLP). To get an in-depth analysis of the mature compost bacterial community, the sequence data from cultivation of the bacteria and cloning of environmental 16S rDNA were uniquely coupled with the output of the environmental T-RFLP fingerprints (sequence-aided T-RFLP). This method revealed the dominance of a supposedly cellulose-degrading consortium composed of phylotypes related to Pseudoxanthomonas, Thermobifida, and Thermomonospora. © 2008 Springer Science+Business Media, LLC.

  • 21. Tauber, T.
    et al.
    Berta, B.
    Székely, Anna
    Gyarmati, I.
    Kékesi, K.
    Márialigeti, K.
    Tóth, E.
    Characterisation of community structure of bacteria in parallel mesophilic and thermophilic pilot scale anaerobe sludge digesters2007In: Acta Microbiologica et Immunologica Hungarica, ISSN 1588-2640, Vol. 54, no 1, p. 47-55Article in journal (Other academic)
1 - 21 of 21
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