Caroline Souffreau

University of Leuven, Louvain, Flanders, Belgium

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Publications (14)44.03 Total impact

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    ABSTRACT: While metacommunities of bacterioplankton are generally considered to be structured primarily by local environmental conditions (through species sorting), additional ecological processes such as dispersal limitation, neutral dynamics or mass effects can influence community structure. Under the mass effects paradigm, continuous or large influxes of organisms, not self-maintaining in the target environment, affect community structure.We used communities of freshwater bacterioplankton to quantify the outcome of mass effects and species sorting in a laboratory experiment in which we exchanged cells between two communities from contrasting ponds (eutrophic and mesotrophic) at a rate of 0.025, 0.25, 2.5 and 12.5% of the cells present per day.When cells were exchanged only once on day 1 of the experiment, the reciprocally exchanged communities in all dispersal treatments remained as divergent, after 20 days, as the unexchanged control communities, reflecting strong species sorting and no strong influences of dispersal limitation and neutral dynamics on the observed bacterioplankton.Under daily cell exchange, however, community similarity between the reciprocally exchanged communities increased significantly with increasing dispersal rate, indicating an increasing influence of mass effects relative to species sorting. The responses differed at the level of community composition and ecosystem processes, and depended on pond identity. At the community level, a daily exchange of 2.5% was necessary to increase community similarity compared with the unexchanged controls, while at the ecosystem process level (Biolog GN2 metabolic profiles), a daily exchange rate of 0.25% was sufficient.Mass effects can evidently overcome species sorting in freshwater bacterioplankton, but only under relatively high dispersal rates that are unlikely to occur in nature among habitats without a direct hydrological connection. Mass effects in the freshwater bacterioplankton acted differently at the community composition and ecosystem process level.
    Freshwater Biology 07/2014; · 3.93 Impact Factor
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    ABSTRACT: To select and characterize potential probiotic bacteria from the gut microbiota of Siberian sturgeon (Acipenser baerii), 129 strains isolated from the hindgut were screened for antagonistic activity against five fish pathogens. Ten isolates showed antagonism towards three or more pathogens. Nine of these isolates were Gram‐positive, belonging to Lactococcus (seven) and Bacillus (two), and a single strain belonging to the Gram‐negative Citrobacter. These inhibitory isolates were identified using genetic, phentotypic and biochemical traits, and further characterized by in vitro tests assessing the adhesion and growth in mucus and resistance to gastric and intestinal fluids. The candidate probiotics were determined to be non‐pathogenic through an in vivo study. Based on these assays, Lactococcus lactis ssp. lactis STG45 and STG81 showed the broadest inhibitory potential, a high viability in simulated gastrointestinal juice and the highest adhesion capacity to mucus. They were therefore selected as the most promising candidate probiotics. This is the first study screening probiotics among the gut microflora of Siberian sturgeon.
    Aquaculture Research 01/2014; 45(2). · 1.42 Impact Factor
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    ABSTRACT: We investigated the effects of administration of putative endogenous probiotics Lactococcus lactis spp. lactis or Bacillus circulans, alone and in combination with arabinoxylan-oligosaccharides (AXOS), a new class of candidate prebiotics, in juvenile Siberian sturgeon (Acipenser baerii). Eight experimental diets were tested: basal diet (Diet 1), basal diet supplemented with 2% AXOS (Diet 2), or L. lactis ST G81 (Diet 3), L. lactis ST G45 (Diet 4), B. circulans ST M53 (Diet 5), L. lactis ST G81+2% AXOS (Diet 6), L. lactis ST G45+2% AXOS (Diet 7), B. circulans ST M53+2% AXOS (Diet 8). After four weeks, growth performance and feed conversion rate significantly improved in fish fed diet 7. Innate immune responses of fish were boosted with both AXOS and probiotic diets, however synergistic effects of AXOS and probiotic diets were only observed for phagocytic and alternative complement activity. Phagocytic and respiratory burst activity of fish macrophage increased in fish fed diet 2 and 7, while humoral immune responses only increased in fish fed diet 7. Pyrosequencing analysis (16S rDNA) of the hindgut microbiota demonstrated that AXOS improved the colonization or/and growth capacity of L. lactis, as a higher relative abundance of L. lactis was observed in fish receiving diet 7. However, no observable colonization of B. circulans was found in the hindgut of fish fed diet 5 or 8, containing this bacterium. The dietary L. lactis ST G45+2% AXOS caused significant alterations in the intestinal microbiota by significantly decreasing in bacterial diversity, demonstrated by the fall in richness and Shannon diversity, and improved growth performance and boosted immune responses of Siberian sturgeon.
    Fish &amp Shellfish Immunology 06/2013; · 2.96 Impact Factor
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    ABSTRACT: The potential of a novel class of prebiotics, arabinoxylan-oligosaccharides (AXOS), was investigated on growth performance and gut microbiota of juvenile Acipenser baerii. Two independent feeding trials of 10 or 12 weeks were performed with basal diets supplemented with 2% or 4% AXOS-32-0.30 (trial 1) and 2% AXOS-32-0.30 or AXOS-3-0.25 (trial 2), respectively. Growth performance improved by feeding 2% AXOS-32-0.30 in both trials, although not significantly. Microbial community profiles were determined using 454-pyrosequencing with barcoded primers targeting the V3 region of the 16S rDNA. AXOS significantly affected the relative abundance of bacteria at the phylum, family, genus, and species level. The consumption of 2% AXOS-32-0.30 increased the relative abundance of Eubacteriaceae, Clostridiaceae, Streptococcaceae and Lactobacillaceae while the abundance of Bacillaceae was greater in response to 4% AXOS-32-0.30 and 2% AXOS-3-0.25. The abundance of Lactobacillus spp. and Lactococcus lactis was greater after 2% AXOS-32-0.30 intake. Redundancy analysis showed a distinct and significant clustering of the gut microbiota of individuals consuming an AXOS diet. In both trials, concentration of acetate, butyrate and total short chain fatty acids increased in fish fed 2% AXOS-32-0.30. Our data demonstrate a beneficial shift in the hindgut microbiome of fish consuming different preparation of AXOS, with potential application as prebiotics. This article is protected by copyright. All rights reserved.
    FEMS Microbiology Ecology 06/2013; · 3.56 Impact Factor
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    ABSTRACT: The potential of a novel class of prebiotics, arabinoxylan oligosaccharides (AXOS), was investigated on growth performance and gut microbiota of juvenile Acipenser baerii. Two independent feeding trials of 10 or 12 weeks were performed with basal diets supplemented with 2% or 4% AXOS‐32‐0.30 (trial 1) and 2% AXOS‐32‐0.30 or AXOS‐3‐0.25 (trial 2), respectively. Growth performance was improved by feeding 2% AXOS‐32‐0.30 in both trials, although not significantly. Microbial community profiles were determined using 454‐pyrosequencing with barcoded primers targeting the V3 region of the 16S rRNA gene. AXOS significantly affected the relative abundance of bacteria at the phylum, family, genus and species level. The consumption of 2% AXOS‐32‐0.30 increased the relative abundance of Eubacteriaceae, Clostridiaceae, Streptococcaceae and Lactobacillaceae, while the abundance of Bacillaceae was greater in response to 4% AXOS‐32‐0.30 and 2% AXOS‐3‐0.25. The abundance of Lactobacillus spp. and Lactococcus lactis was greater after 2% AXOS‐32‐0.30 intake. Redundancy analysis showed a distinct and significant clustering of the gut microbiota of individuals consuming an AXOS diet. In both trials, concentration of acetate, butyrate and total short‐chain fatty acids (SCFAs) increased in fish fed 2% AXOS‐32‐0.30. Our data demonstrate a shift in the hindgut microbiome of fish consuming different preparation of AXOS, with potential application as prebiotics.
    FEMS Microbiology Ecology 01/2013; 86(2). · 3.56 Impact Factor
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    ABSTRACT: Arabinoxylan-oligosaccharides (AXOS) are a newly discovered class of candidate prebiotics that exert different properties depending on their structure. In this study the effects of two different structures of AXOS, namely AXOS-32-0.30 (average degree of polymerization: 32, average degree of substitution: 0.30) and AXOS-3-0.25, were investigated on growth performance, immune responses, gut microbial fermentation and gut bacterial composition of juvenile Siberian sturgeon (Acipenser baerii). After a two weeks acclimation, fish (25.9 ± 0.9 g) were distributed over 24 aquariums (8 replicates per treatment) and fed a control diet or a diet containing 2% AXOS-32-0.30 or AXOS-3-0.25 for 12 weeks. Growth performance and feed utilization tend to improve in sturgeon fed on diets supplemented with AXOS-32-0.30, however not significant. Survival was high in all groups. Both AXOS preparations significantly enhanced the phagocytic activity of fish macrophages compared to the control group, while the alternative haemolytic complement activity and total serum peroxidase content improved only in the group fed AXOS-32-0.30 (P < 0.05). The lysozyme activity was not affected by AXOS addition. Simultaneously, the amount of short-chain fatty acids (SCFAs) was highest in the hind gut of sturgeon fed AXOS-32-0.30. The concentrations of acetate, butyrate and total SCFAs in fish fed AXOS-32-0.30 was significantly higher than in the groups fed the control diet or AXOS-3-0.25. Study of the bacterial community in the sturgeon hindgut using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) revealed that both preparations of AXOS induced changes in the bacterial composition. According to redundancy analysis (RDA), hindgut microbiota of each treatment group clustered apart from one another (P = 0.001). DNA sequencing of the dominant DGGE bands recovered from the different treatments showed that AXOS mainly stimulated the growth of lactic acid bacteria and Clostridium sp., with more pronounced effects of AXOS-32-0.30. It is concluded that AXOS improves sturgeon health through prebiotic action, but the induced effects depend on the specific structure of AXOS. A higher degree of polymerization of AXOS had a stronger beneficial impact in this sturgeon species.
    Fish &amp Shellfish Immunology 07/2012; 33(4):718-24. · 2.96 Impact Factor
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    ABSTRACT: Recent morphology-based studies indicate that freshwater diatom floras in the Antarctic comprise a significant share of endemics among a majority of apparently cosmopolitan species. Given the widespread (pseudo)cryptic species diversity in diatoms, we assessed the molecular divergence and temperature-dependent growth characteristics between Antarctic and non-Antarctic strains for two presumed species with a cosmopolitan distribution, namely Pinnularia borealis and Hantzschia amphioxys. Molecular phylogenies based on the plastid gene rbcL and the nuclear 28S rDNA (D1-D3 region) revealed that both taxa consist of multiple lineages, each including a distinct Antarctic lineage. A molecular clock estimates the origin of P. borealis at 35.8 (30-47) million years (Ma) ago, making this the oldest known diatom species complex. The Antarctic P. borealis lineage is estimated to have diverged 7.8 (2-15) Ma ago, after the geographical and thermal isolation of the Antarctic continent. Despite not being psychrophilic, the Antarctic lineages of P. borealis and H. amphioxys have a lower optimal growth temperature and upper lethal temperature than most lineages from more temperate regions, indicating niche differentiation. Together, this suggests that many presumed cosmopolitan Antarctic diatom species are in fact species complexes, possibly containing Antarctic endemics with low temperature preferences.
    Protist 05/2012; · 4.14 Impact Factor
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    ABSTRACT: Membrane biofouling was investigated during the early stages of filtration in a laboratory-scale membrane bioreactor operated on molasses wastewater. The bacterial diversity and composition of the membrane biofilm and activated sludge were analyzed using terminal restriction fragment length polymorphism coupled with 16S rRNA clone library construction and sequencing. The amount of extracellular polymeric substances produced by bacteria was investigated using spectroscopic methods. The results reveal that the bacterial community of activated sludge differs significantly from that of the membrane biofilm, especially at the initial phase. Phylogenetic analysis based on 16S rRNA gene sequences identified 25 pioneer OTUs responsible for membrane surface colonization. Also, the relationship between the identified bacterial strains and the system specifications was explored.
    Biofouling 02/2012; 28(2):225-38. · 3.40 Impact Factor
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    ABSTRACT: Polar lakes respond quickly to climate-induced environmental changes. We studied the chemical limnological variability in 127 lakes and ponds from eight ice-free regions along the East Antarctic coastline, and compared repeat specific conductance measurements from lakes in the Larsemann Hills and Skarvsnes covering the periods 1987–2009 and 1997–2008, respectively. Specific conductance, the concentration of the major ions, pH and the concentration of the major nutrients underlie the variation in limnology between and within the regions. This limnological variability is probably related to differences in the time of deglaciation, lake origin and evolution, geology and geomorphology of the lake basins and their catchment areas, sub-regional climate patterns, the distance of the lakes and the lake districts to the ice sheet and the Southern Ocean, and the presence of particular biota in the lakes and their catchment areas. In regions where repeat surveys were available, inter-annual and inter-decadal variability in specific conductance was relatively large and most pronounced in the non-dilute lakes with a low lake depth to surface area ratio. We conclude that long-term specific conductance measurements in these lakes are complementary to snow accumulation data from ice cores, inexpensive, easy to obtain, and should thus be part of long-term limnological and biological monitoring programmes.
    Antarctic Science 01/2012; 24(01):23 - 33. · 1.63 Impact Factor
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    ABSTRACT: Pinnularia is an ecologically important and species-rich genus of freshwater diatoms (Bacillariophyceae) showing considerable variation in frustule morphology. Interspecific evolutionary relationships were inferred for 36 Pinnularia taxa using a five-locus dataset. A range of fossil taxa, including newly discovered Middle Eocene forms of Pinnularia, was used to calibrate a relaxed molecular clock analysis and investigate temporal aspects of the genus' diversification. The multi-gene approach resulted in a well-resolved phylogeny of three major clades and several subclades that were frequently, but not universally, delimited by valve morphology. The genus Caloneis was not recovered as monophyletic, confirming that, as currently delimited, this genus is not evolutionarily meaningful and should be merged with Pinnularia. The Pinnularia-Caloneis complex is estimated to have diverged between the Upper Cretaceous and the early Eocene, implying a ghost range of at least 10 million year (Ma) in the fossil record.
    Molecular Phylogenetics and Evolution 09/2011; 61(3):866-79. · 4.07 Impact Factor
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    Phycologia 01/2010; 49(4):309-324. · 1.65 Impact Factor
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    ABSTRACT: Diatoms are the largest group of microalgae, play an enormous role in the biosphere, and have major significance as bioindicators. Traditional identification requires inter alia long training, considerable microscopical skill, and use of a vast and scattered literature. During the life cycle, diatom cells change in size and pattern, often also shape, but the full cycle is known in <1% of described species. Recent evidence shows that there are many pseudocryptic and cryptic species of diatoms, requiring molecular methods for discovery and recognition. These and other factors argue that DNA barcoding would be highly beneficial. It could be ‘strong’, resolving nearly all species, or ‘weak’, resolving mostly species already recognized from light microscopy. Attempts have already been made to identify suitable genes and we evaluate these on the basis of universality and practicality, and ability to discriminate between species in the very few ‘model’ systems offering likely examples of sister-species-pairs. No candidate marker is ideal but LSU rDNA and rbcL may be acceptable, though their discriminatory power is lower than that of some other markers. We discuss the next steps in developing a full barcode system.
    Cryptogamie Algologie 01/2010; 31(4):557-577. · 1.17 Impact Factor
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    ABSTRACT: To date, little is known about the relative importance of dispersal related versus local factors in shaping microbial metacommunities. A common criticism regarding existing datasets is that the level of taxonomic resolution might be too coarse to reliably assess microbial community structure and study biogeographical patterns. Moreover, few studies have assessed the importance of geographic distance between habitats, which may influence metacommunity dynamics through its effect on dispersal rates. We applied variation partitioning analyses to 15 separate regional datasets on diatoms found in lakes in Eurasia, Africa and Antarctica. These analyses quantified the relative contributions of dispersal related and local factors in determining patterns of taxonomic turnover at the species and at the genus level. In general, results were similar at both taxonomic levels. Local environmental factors accounted for most of the explained variation (median=21%), whereas dispersal related factors were much less important (median of significant fractions=5.5% variation explained) and failed to significantly explain any variation, independent of the environmental variables, in the majority of the datasets. However, the amount of variation explained by dispersal related factors increased with increasing geographic distance and increasing taxonomic resolution. We extrapolated our regional scale observations to the global scale by combining the regional datasets into a global dataset comprising 1039 freshwater lakes from both hemispheres and spanning a geographic distance of over 19 000 km. At this global scale, taxonomic turnover was lowest in highly connected habitats, once environmental factors were partialled out. In common with many other studies of macro-organisms, these analyses showed that both dispersal related and local variables significantly contribute to the structure of global lacustrine diatom communities.
    Oikos 07/2009; 118(8):1239 - 1249. · 3.33 Impact Factor
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    ABSTRACT: The arrival order of colonists in developing populations can have a lasting influence on community and population structure, a phenomenon referred to as priority effects. To explore whether such priority effects are important in determining strain composition of populations of the cyanobacterium Microcystis, four Microcystis strains, isolated from a single lake and differing in functional traits, were grown during 4 weeks in the laboratory in all possible pairwise combinations, with the two strains either inoculated at the same time or with a time lag of 1 week, in the presence or absence of grazing Daphnia magna. The relative abundance of strains in the mixtures was assessed using denaturing gradient gel electrophoresis, and the growth rate of each strain in the mixtures was determined for the last 2 weeks of the experiment. We observed strong effects of inoculation order on the final population structure, and these effects were influenced by grazing Daphnia. The priority effects were strain-specific and occurred in two directions: some of the strains grew slower while others grew faster when inoculated second compared with when inoculated first. Our results indicate that priority effects may have a profound impact on strain composition of Microcystis populations.
    Environmental Microbiology 07/2009; 11(10):2564-73. · 6.24 Impact Factor