Christian Laforsch

The ecoresponsive genome of Daphnia pulex

The Daphnia genome reveals a multitude of genes and shows adaptation through gene family expansions. We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia’s genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.

Contamination of beach sediments of a subalpine lake with microplastic particles

Summary Plastic waste is of increasing concern in marine ecosystems [1–3]. Buoyant plastic particles accumulate in pelagic habitats whereas non-floating debris accumulates on the seafloor and in beach sediments, posing risk to the respective communities [1–4]. Microplastic particles (

Coral surface area quantification–evaluation of established techniques by comparison with computer tomography

The surface area of scleractinian corals represents an important reference parameter required for various aspects of coral reef science. However, with advancements in detection accuracy and novel approaches for coral surface area quantification, evaluation of established techniques in comparison with state-of-the-art technology gains importance to coral researchers. This study presents an evaluation of methodological accuracy for established techniques in comparison to a novel approach composed of computer tomography (CT) and 3-dimensional surface reconstruction. The skeleton surface area of reef corals from six genera representing the most common morphological growth forms was acquired by CT and subsequently measured by computer-aided 3-dimensional surface reconstruction. Surface area estimates for the same corals were also obtained by application of four established techniques: Simple and Advanced Geometry, Wax Coating and Planar Projection Photography. Comparison of the resulting area values revealed significant differences between the majority (82%) of established techniques and the CT reference. Genus-specific analysis assigned the highest accuracy to geometric approximations (Simple or Advanced Geometry) for the majority of assessed coral genera (maximum accuracy: 104%; Simple Geometry with Montipora sp.). The commonly used and invasive Wax Coating technique reached intermediate accuracy (47–74%) for the majority of genera, but performed outstanding in the measurement of branching Acropora spp. corals (maximum accuracy: 101%), while the Planar Projection Photography delivered genera-wide low accuracy (12–36%). Comparison of area values derived from established techniques and CT additionally yielded approximation factors (AFs) applicable as factors in the mathematical improvement of surface area estimates by established techniques in relation to CT reference accuracy.

Beyond the ocean: contamination of freshwater ecosystems with (micro-)plastic particles

Massive accumulation of plastic particles has been reported for marine ecosystems around the world, posing a risk to the biota. Freshwater ecosystems have received less attention despite the majority of plastic litter being produced onshore and introduced into marine environments by rivers. Some studies report not only the presence of microplastics in freshwater ecosystems, but show that contamination is as severe as in the oceans. In continental waters microplastics have been observed in both sediments (predominantly lakeshores but also riverbanks) and water samples (predominantly surface water of lakes and rivers). This review highlights recent findings and discusses open questions, focusing on the methodology of assessing this contaminant in freshwater ecosystems. In this context, method harmonization is needed in order to obtain comparable data from different environmental compartments and sites. This includes sampling strategies (at spatial and temporal 18 scales), sample treatment (taking into consideration high levels of organic matter and suspended 19 solids) and reliable analytical methods to identify microplastics.

Single and combined toxicity of pharmaceuticals at environmentally relevant concentrations in Daphnia magna : A multigenerational study

Pharmaceuticals are continuously discharged into the environment, resulting in the chronic exposure of aquatic organisms to these compounds. In this multigenerational study, we examined the influence of four pharmaceuticals (carbamazepine (CBZ), diclofenac (DIC), 17alpha-ethinylestradiol (EE2) and metoprolol (MET)) as single substances and as a drug mixture at environmentally relevant concentrations on life-history and morphological parameters over six generations of the cladoceran Daphnia magna. Detectable effects of the used pharmaceuticals occured in the first observed generation, followed by an acclimation period and a recurrence of drug effects in later generations: daphnids exposed to MET were affected by the pharmaceutical, resulting in a decreased body length at first reproduction in the generations F0, F3 and F4 and in a reduced number of offspring in the generations F0 and F4. Similar effects were observed in daphnids exposed to EE2. DIC delayed age at first reproduction in the F0 and F2 generations and increased the body length of neonates in the generations F1 and F5. Daphnids exposed to CBZ showed a delay in the age at first reproduction for the F0 generation only. The drug mixture reduced the age at first reproduction of daphnids in the F0 and F2 generation and increased the body length at first reproduction in the generations F0 and F3. Neither the single drugs nor the pharmaceutical mixture influenced the successive generations of D. magna in a steady way. Thus, multigenerational studies are necessary to prevent insufficient assessments on the impact of pharmaceuticals in aquatic ecosystems.

A “crown of thorns” is an inducible defense that protects Daphnia against an ancient predator

Genetic data has become an essential part of ecological studies, because the analyses of diversity within and among natural populations may grant access to previously overlooked ecological and evolutionary causalities, especially among cryptic species. Here, we present an example of how phylogenetic analysis of molecular data obtained within a DNA barcoding study, in combination with morphological and ecological data from the field and laboratory experiments, unraveled a striking predator-prey interaction between aquatic organisms. The “crown of thorns,” a conspicuous morphological feature among water fleas of the Daphnia atkinsoni species complex (Crustacea: Cladocera), is considered to represent a species-specific trait. However, our study, initiated by the analysis of sequence variation in 2 mitochondrial genes, shows that this feature is phenotypically plastic and is induced by chemical cues released by Triops cancriformis, the tadpole shrimp (Notostraca). The trait acts as an effective antipredator defense, and is found in several Daphnia lineages coexisting with notostracans. These facts suggest that the “crown of thorns” evolved in coexistence with this ancient predator group.

Resolving the infection process reveals striking differences in the contribution of environment, genetics and phylogeny to host-parasite interactions

BackgroundInfection processes consist of a sequence of steps, each critical for the interaction between host and parasite. Studies of host-parasite interactions rarely take into account the fact that different steps might be influenced by different factors and might, therefore, make different contributions to shaping coevolution. We designed a new method using the Daphnia magna - Pasteuria ramosa system, one of the rare examples where coevolution has been documented, in order to resolve the steps of the infection and analyse the factors that influence each of them.ResultsUsing the transparent Daphnia hosts and fluorescently-labelled spores of the bacterium P. ramosa, we identified a sequence of infection steps: encounter between parasite and host; activation of parasite dormant spores; attachment of spores to the host; and parasite proliferation inside the host. The chances of encounter had been shown to depend on host genotype and environment. We tested the role of genetic and environmental factors in the newly described activation and attachment steps. Hosts of different genotypes, gender and species were all able to activate endospores of all parasite clones tested in different environments; suggesting that the activation cue is phylogenetically conserved. We next established that parasite attachment occurs onto the host oesophagus independently of host species, gender and environmental conditions. In contrast to spore activation, attachment depended strongly on the combination of host and parasite genotypes.ConclusionsOur results show that different steps are influenced by different factors. Host-type-independent spore activation suggests that this step can be ruled out as a major factor in Daphnia-Pasteuria coevolution. On the other hand, we show that the attachment step is crucial for the pronounced genetic specificities of this system. We suggest that this one step can explain host population structure and could be a key force behind coevolutionary cycles. We discuss how different steps can explain different aspects of the coevolutionary dynamics of the system: the properties of the attachment step, explaining the rapid evolution of infectivity and the properties of later parasite proliferation explaining the evolution of virulence. Our study underlines the importance of resolving the infection process in order to better understand host-parasite interactions.

Predator-induced defense makes Daphnia more vulnerable to parasites.

Inducible defensive traits against herbivores or predators are widespread in plants and animals. Theory predicts that defended morphs have greater fitness in the presence of predators, but lower fitness than undefended morphs in the absence of predators. If such costs did not exist, then a constitutively defended morph would be favored by natural selection; yet, evidence for such costs has been elusive. Our current work reveals a significant cost to inducible defenses. Using the waterflea (Daphnia) model system, we show that induced defended morphs are significantly more vulnerable to infection by a virulent yeast parasite than undefended morphs. In two independent experiments, the proportion of successful infections and the number of parasite spores were higher among defended versus undefended Daphnia. Thus, by demonstrating a previously unknown and environmentally relevant cost to inducible defenses, this study enhances our understanding of adaptive phenotypic plasticity and its evolution.

Detection and enumeration of microbial cells within highly porous calcareous reef sands

In order to assess and to compare the abundances of prokaryotes in coral sands from three different areas in the Indo-Pacific, a technique was developed and evaluated for enumeration of prokaryotes living on and within calcareous grains. Propidium iodide labelling of prokaryotes and consecutive confocal laser scanning microscopy showed microbial colonisation within pores and small fissures of the coral sands. This embedded microbial colonisation required at least four extractions with weak acetic acid to dissolve the grain surface layer in order to detach 97% of the prokaryotic cells. Microbial enumeration based on this technique revealed that the abundance of prokaryotes in the carbonate sands were not significantly different among the three sites, but were about one order of magnitude higher than reported for silicate sands of a similar grain size spectrum. A possible reason for this high abundance of prokaryotes is the complex surface structure of the biogenic calcareous grains, their correspondingly highly porous matrix and the associated ability of prokaryotes to penetrate into carbonate grains. Our results highlight the role of calcareous reef sands as a substratum with a large specific surface area for prokaryotic colonisation and emphasise the contribution of calcium carbonate reef sands for element cycles in subtropical and tropical ecosystems.

LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia

BackgroundDaphniids, commonly known as waterfleas, serve as important model systems for ecology, evolution and the environmental sciences. The sequencing and annotation of the Daphnia pulex genome both open future avenues of research on this model organism. As proteomics is not only essential to our understanding of cell function, and is also a powerful validation tool for predicted genes in genome annotation projects, a first proteomic dataset is presented in this article.ResultsA comprehensive set of 701,274 peptide tandem-mass-spectra, derived from Daphnia pulex, was generated, which lead to the identification of 531 proteins. To measure the impact of the Daphnia pulex filtered models database for mass spectrometry based Daphnia protein identification, this result was compared with results obtained with the Swiss-Prot and the Drosophila melanogaster database. To further validate the utility of the Daphnia pulex database for research on other Daphnia species, additional 407,778 peptide tandem-mass-spectra, obtained from Daphnia longicephala, were generated and evaluated, leading to the identification of 317 proteins.ConclusionPeptides identified in our approach provide the first experimental evidence for the translation of a broad variety of predicted coding regions within the Daphnia genome. Furthermore it could be demonstrated that identification of Daphnia longicephala proteins using the Daphnia pulex protein database is feasible but shows a slightly reduced identification rate. Data provided in this article clearly demonstrates that the Daphnia genome database is the key for mass spectrometry based high throughput proteomics in Daphnia.