Potential for synergy in soil inoculation for nature restoration by mixing inocula from different successional stages

Background and aims

Due to the well-known importance of biocrusts for several ecosystem properties linked to soil functionality, we aim to go deeper into the physiological performance of biocrusts components. Possible functional convergences in the physiology of biocrust constituents would facilitate the understanding of both species and genus distributional patterns and improve the possibility of modelling their response to climate change.

Methods

We measured gas exchange in the laboratory under controlled conditions of lichen- and moss-dominated biocrusts from four environmentally different locations in Europe. Field data were used to determine the natural hydration sources that drive metabolic activity of biocrusts.

Results

Our results show different activity drivers at the four sites. Within site analyses showed similar C fixation for the different crust types in the three sites without hydric stress whilst light use related parameters and respiration at 15 °C were similar in the between sites analyses. There were significant differences in water relations between the biocrusts types, with moss-dominated crusts showing higher maximum and optimum water contents.

Conclusions

The functional type approach for biocrusts can be justified from a physiological perspective when similar values are found in the within and between site analyses, the latter indicating habitat independent adaptation patterns. Our multi-site analyses for biocrusts functional performance provide comparisons of C fluxes and water relations in the plant-soil interface that will help to understand the adaptation ability of these communities to possible environmental changes.

     

DNA barcoding of South Africa’s ornamental freshwater fish – are the names reliable?

Trade in freshwater ornamental fish in South Africa is currently regulated by a ‘blacklist’ to prevent potentially invasive taxa from establishing in the country. Because its effective implementation requires accurate identification, the aim of the present study was to test whether DNA barcoding is a useful tool to identify freshwater fishes in the South African pet trade. A total of 351 aquarium fish specimens, representing 185 traded taxa, were sequenced for the mitochondrial COI barcoding marker in 2011 and 2012. Lake Malawi cichlids were treated as a single group due to a lack of resolution in their COI marker, resulting in a data set of 137 successfully sequenced taxa. The Barcode Of Life Database (BOLD) and GenBank were used for taxonomic assignment comparisons. The genetic identification matched the scientific name inferred from the trade name for 60 taxa (43.8%) using BOLD, and for 67 taxa (48.9%) using GenBank. A genetic ID could not be assigned in 47 (34.3%) cases using BOLD and in 37 cases (27%) using GenBank. Whereas DNA barcoding can be a useful tool to help identify imported freshwater fishes, it requires further development of publicly available databases to become a reliable means of identification.     

Genetic differences in fruit-set patterns are determined by differences in fruit sink strength and a source : sink threshold for fruit set

Background and Aims

Fruit set in indeterminate plant species largely depends on the balance between source and sink strength. Plants of these species show fluctuations in fruit set during the growing season. It was tested whether differences in fruit sink strength among the cultivars explained the differences in fruit-set patterns.

Methods

Capsicum was chosen as a model plant. Six cultivars with differences in fruit set, fruit size and plant growth were evaluated in a greenhouse experiment. Fruit-set patterns, generative and vegetative sink strength, source strength and the source : sink ratio at fruit set were determined. Sink strength was quantified as potential growth rate. Fruit set was related to total fruit sink strength and the source : sink ratio. The effect of differences observed in above-mentioned parameters on fruit-set patterns was examined using a simple simulation model.

Key Results

Sink strengths of individual fruits differed greatly among cultivars. Week-to-week fruit set in large-fruited cultivars fluctuated due to large fluctuations in total fruit sink strength, but in small-fruited cultivars, total fruit sink strength and fruit set were relatively constant. Large variations in week-to-week fruit set were correlated with a low fruit-set percentage. The source : sink threshold for fruit set was higher in large-fruited cultivars. Simulations showed that within the range of parameter values found in the experiment, fruit sink strength and source : sink threshold for fruit set had the largest impact on fruit set: an increase in these parameters decreased the average percentage fruit set and increased variation in weekly fruit set. Both were needed to explain the fruit-set patterns observed. The differences observed in the other parameters (e.g. source strength) had a lower effect on fruit set.

Conclusions

Both individual fruit sink strength and the source : sink threshold for fruit set were needed to explain the differences observed between fruit-set patterns of the six cultivars.     

Going against the flow: a case for upstream dispersal and detection of uncommon dispersal events

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Divergence across diet,time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

Diverse microbial consortia profoundly influence animal biology, necessitating an understanding of microbiome variation in studies of animal adaptation. Yet, little is known about such variability among fish, in spite of their importance in aquatic ecosystems. The Trinidadian guppy, Poecilia reticulata, is an intriguing candidate to test microbiome-related hypotheses on the drivers and consequences of animal adaptation, given the recent parallel origins of a similar ecotype across streams. To assess the relationships between the microbiome and host adaptation, we used 16S rRNA amplicon sequencing to characterize gut bacteria of two guppy ecotypes with known divergence in diet, life history, physiology and morphology collected from low-predation (LP) and high-predation (HP) habitats in four Trinidadian streams. Guts were populated by several recurring, core bacteria that are related to other fish associates and rarely detected in the environment. Although gut communities of lab-reared guppies differed from those in the wild, microbiome divergence between ecotypes from the same stream was evident under identical rearing conditions, suggesting host genetic divergence can affect associations with gut bacteria. In the field, gut communities varied over time, across streams and between ecotypes in a stream-specific manner. This latter finding, along with PICRUSt predictions of metagenome function, argues against strong parallelism of the gut microbiome in association with LP ecotype evolution. Thus, bacteria cannot be invoked in facilitating the heightened reliance of LP guppies on lower-quality diets. We argue that the macroevolutionary microbiome convergence seen across animals with similar diets may be a signature of secondary microbial shifts arising some time after host-driven adaptation.     

Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum

Background

The identification of genetic changes that confer drug resistance or other phenotypic changes in pathogens can help optimize treatment strategies, support the development of new therapeutic agents, and provide information about the likely function of genes. Elucidating mechanisms of phenotypic drug resistance can also assist in identifying the mode of action of uncharacterized but potent antimalarial compounds identified in high-throughput chemical screening campaigns against Plasmodium falciparum.

Results

Here we show that tiling microarrays can detect de novo a large proportion of the genetic changes that differentiate one genome from another. We show that we detect most single nucleotide polymorphisms or small insertion deletion events and all known copy number variations that distinguish three laboratory isolates using readily accessible methods. We used the approach to discover mutations that occur during the selection process after transfection. We also elucidated a mechanism by which parasites acquire resistance to the antimalarial fosmidomycin, which targets the parasite isoprenoid synthesis pathway. Our microarray-based approach allowed us to attribute in vitro derived fosmidomycin resistance to a copy number variation event in the pfdxr gene, which enables the parasite to overcome fosmidomycin-mediated inhibition of isoprenoid biosynthesis.

Conclusions

We show that newly emerged single nucleotide polymorphisms can readily be detected and that malaria parasites can rapidly acquire gene amplifications in response to in vitro drug pressure. The ability to define comprehensively genetic variability in P. falciparum with a single overnight hybridization creates new opportunities to study parasite evolution and improve the treatment and control of malaria.