12165 research outputs found
Sort by
Discovery of new regulatory genes of lipopeptide biosynthesis in Pseudomonas fluorescens
No full textPseudomonas fluorescens SS101 produces the cyclic lipopeptide massetolide with diverse functions in antimicrobial activity, motility, and biofilm formation. To understand how massetolide biosynthesis is genetically regulated in SS101, c. 8000 random plasposon mutants were screened for reduced or loss of massetolide production. Of a total of 58 putative mutants, 45 had a mutation in one of the three massetolide biosynthesis genes massA, massB, or massC. For five mutants, the insertions were located in the known regulatory genes gacS, gacA, and clpP. For the remaining eight mutants, insertions were located in clpA, encoding the ClpP chaperone, in phgdh, encoding D-3-phosphoglycerate dehydrogenase, in the heat shock protein-encoding dnaK, or in the transmembrane regulatory gene prtR. Genetic, chemical, and phenotypic analyses showed that phgdh, dnaK, and prtR are indeed involved in the regulation of massetolide biosynthesis, most likely by transcriptional repression of the LuxR-type regulator genes massAR and massBCR. In addition to their role in massetolide biosynthesis, dnaK and prtR were found to affect siderophore and extracellular protease(s) production, respectively. The identification of new regulatory genes substantially extended insights into the signal transduction pathways of lipopeptide biosynthesis in P. fluorescens and into regulation of other traits that may contribute to its life-style in the rhizosphere.
Nieuwe tinten grijs?
No full textNu de omvangrijke naoorlogse geboortegeneraties de pensioenleeftijd bereiken, zijn we ons in rap tempo op een grijzere bevolking aan het voorbereiden. Dit geldt vooral als het gaat om de betaalbaarheid van de pensioenen, de kosten van de zorg en de krimp van de beroepsbevolking. Maar is Nederland wel zo grijs als we vaak denken?
Long-term allelopathic control of phytoplankton by the submerged macrophyte Elodea nuttallii
No full textKeywords:
allelochemicals;
chemical ecology;
competition;
nutrient limitation;
shallow lakes
Summary
1.It is well known that submerged macrophytes can suppress phytoplankton blooms in lakes and thus promote water quality and biodiversity. One of the possible mechanisms through which submerged macrophytes control phytoplankton is by producing allelochemicals that suppress phytoplankton growth rates. The in situ importance of allelopathy, however, is often questioned because it is assumed that phytoplankton communities can rapidly evolve resistance to allelochemicals.
2.Here, we present the results of two mesocosm experiments in which we evaluated whether the submerged macrophyte Elodea nuttallii is capable of controlling phytoplankton biomass over periods of 4 to 8 weeks. Such a timescale is long relative to the generation time of phytoplankton and is therefore expected to allow the development of resistance through compositional shifts at both population and community levels.
3.Although the mesocosms were inoculated with a diverse phytoplankton inoculum including species that had previously been exposed to Elodea, phytoplankton biomass remained consistently low during the course of the experiments in the treatments with Elodea. As zooplankton grazing and competition for nutrients and light by macrophytes were excluded in our experiments, this suggests that phytoplankton was controlled by allelopathy.
4.Dialysis bag assays, performed at the end of each mesocosm experiment, showed that phytoplankton communities from mesocosms with Elodea were equally sensitive to exudates from Elodea than phytoplankton communities from mesocosms without Elodea.
5.These results suggest that phytoplankton communities do not evolve resistance to allelochemicals from Elodea. This may allow Elodea to control phytoplankton in natural ecosystems over prolonged time periods through allelopathy.
Weak phylogenetic signal in physiological traits of methane-oxidizing bacteria.
No full textThe presence of phylogenetic signal is assumed to be ubiquitous. However, for microorganisms, this may not be true given that they display high physiological flexibility and have fast regeneration. This may result in fundamentally different patterns of resemblance, that is, in variable strength of phylogenetic signal. However, in microbiological inferences, trait similarities and therewith microbial interactions with its environment are mostly assumed to follow evolutionary relatedness. Here, we tested whether indeed a straightforward relationship between relatedness and physiological traits exists for aerobic methane-oxidizing bacteria (MOB). We generated a comprehensive data set that included 30 MOB strains with quantitative physiological trait information. Phylogenetic trees were built from the 16S rRNA gene, a common phylogenetic marker, and the pmoA gene which encodes a subunit of the key enzyme involved in the first step of methane oxidation. We used a Blomberg's K from comparative biology to quantify the strength of phylogenetic signal of physiological traits. Phylogenetic signal was strongest for physiological traits associated with optimal growth pH and temperature indicating that adaptations to habitat are very strongly conserved in MOB. However, those physiological traits that are associated with kinetics of methane oxidation had only weak phylogenetic signals and were more pronounced with the pmoA than with the 16S rRNA gene phylogeny. In conclusion, our results give evidence that approaches based solely on taxonomical information will not yield further advancement on microbial eco-evolutionary interactions with its environment. This is a novel insight on the connection between function and phylogeny within microbes and adds new understanding on the evolution of physiological traits across microbes, plants and animals.
Prevalence, thresholds, and the performance of presence-absence models
No full text1.The use of species distribution models to understand and predict species’ distributions necessitates tests of fit to empirical data. Numerous performance metrics have been proposed, many of which require continuous occurrence probabilities to be converted to binary “present or absent” predictions using threshold transformations. It is widely accepted that both continuous and binary performance metrics should be independent of prevalence (the proportion of locations that are occupied). However, because these metrics have been mostly assessed on a case-specific basis, there are few general guidelines for measuring performance.
2.Here, we develop a conceptual framework for classifying performance metrics, based on whether they are sensitive to prevalence, and whether they require binary predictions. We use this framework to investigate how these performance metric properties influence the predictions made by the models they select.
3.A literature survey reveals that binary metrics are widely employed and that prevalence-independent metrics are used more frequently than prevalence-dependent metrics. However, we show that prevalence-dependent metrics are essential to assess the numerical accuracy of model predictions, and are more useful in applications that require occupancy estimates. Furthermore, we demonstrate that in comparison with continuous metrics, binary metrics often select models that have reduced ability to separate presences from absences, make predictions which over- or under-estimate occupancy, and give misleading estimates of uncertainty. Importantly, models selected using binary metrics will often be of reduced practical use even when applied to ecological problems that require binary decision-making.
4.We suggest that SDM performance should be assessed using prevalence-dependent performance metrics whenever the absolute values of occurrence predictions are important, and that continuous metrics should be used instead of binary metrics whenever possible. We thus recommend the wider application of prevalence-dependent continuous metrics, particularly likelihood-based metrics such as Akaike's information criterion (AIC), to assess the performance of presence-absence models.
Large-scale geographical variation in eggshell heavy metal and calcium content in a passerine bird (Ficedula hypoleuca)
No full textBirds have been used as bioindicators of pollution, such as toxic metals. Levels of pollutants in eggs are especially interesting, as developing birds are more sensitive to detrimental effects of pollutants than adults. Only very few studies have monitored intraspecific, large-scale variation in metal pollution across a species' breeding range. We studied large-scale geographic variation in metal levels in the eggs of a small passerine, the pied flycatcher (Ficedula hypoleuca), sampled from 15 populations across Europe. We measured 10 eggshell elements (As, Cd, Cr, Cu, Ni, Pb, Zn, Se, Sr, and Ca) and several shell characteristics (mass, thickness, porosity, and color). We found significant variation among populations in eggshell metal levels for all metals except copper. Eggshell lead, zinc, and chromium levels decreased from central Europe to the north, in line with the gradient in pollution levels over Europe, thus suggesting that eggshell can be used as an indicator of pollution levels. Eggshell lead levels were also correlated with soil lead levels and pH. Most of the metals were not correlated with eggshell characteristics, with the exception of shell mass, or with breeding success, which may suggest that birds can cope well with the current background exposure levels across Europe.
Lower foraging efficiency of offspring constrains use of optimal habitat in birds with extended parental care
No full textKeywords:
food intake rate;
giving-up density;
habitat switch;
parental costs;
social dominance
After reproducing successfully, birds with extended parental care form family groups. Despite being the dominant social unit, such family groups have been reported to switch to alternative habitat earlier than adults without offspring, with potential negative carry-over effects for the next breeding season. Here we test a proposed mechanism for this earlier habitat switch, namely a low foraging efficiency in juveniles. Such a test is best performed under controlled conditions because in the field families may occupy food patches of a different quality than singles or pairs without young. We studied this mechanism in Bewick's Swans Cygnus columbianus bewickii, which trample (or ‘treadle’) for food buried in the sediment. The gross intake rate of juveniles was as low as 60% of that of adults, depending on the burial depth of the food. Trampling effort did not differ between age classes, but differences in intake rate were related to body size, suggesting that larger or heavier birds were trampling more efficiently. Corresponding giving-up densities in the field were calculated to be c. 60% higher for juveniles than for adults. Our findings are consistent with the hypothesis that the lower foraging efficiency of juveniles may be responsible for the segregation of family groups from adults without offspring.
Seasonal phenology of interactions involving short-lived annual plants, a multivoltine herbivore and its endoparasitoid wasp
No full textSpatial-temporal realism is often missing in many studies of multitrophic interactions, which are conducted at a single time frame and/or involving interactions between insects with a single species of plant. In this scenario, an underlying assumption is that the host-plant species is ubiquitous throughout the season and that the insects always interact with it.
We studied interactions involving three naturally occurring wild species of cruciferous plants, Brassica rapa, Sinapis arvensis and Brassica nigra, that exhibit different seasonal phenologies, and a multivoltine herbivore, the large cabbage white butterfly, Pieris brassicae, and its gregarious endoparasitoid wasp, Cotesia glomerata. The three plants have very short life cycles.
In central Europe, B. rapa grows in early spring, S. arvensis in late spring and early summer, and B. nigra in mid to late summer. P. brassicae generally has three generations per year, and C. glomerata at least two. This means that different generations of the insects must find and exploit different plant species that may differ in quality and which may be found some distance from one another.
Insects were either reared on each of the three plant species for three successive generations or shifted between generations from B. rapa to S. arvensis to B. nigra. Development time from neonate to pupation and pupal fresh mass were determined in P. brassicae and egg-to-adult development time and body mass in C. glomerata.
Overall, herbivores performed marginally better on S. arvensis and B. nigra plants than on B. rapa plants. Parasitoids performance was closely tailored with that of the host. Irrespective as to whether the insects were shifted to a new plant in successive generations or not, development time of P. brassicae and C. glomerata decreased dramatically over time.
Our results show that there were some differences in insect development on different plant species and when transferred from one species to another. However, all three plants were of generally high quality in terms of insect performance. We discuss ecological and evolutionary constraints on insects that must search in new habitats for different plant species over successive generations
