Effect of a glyphosate formulation on freshwater plankton: A community combined metric approach

Aim: The aim of this study was to experimentally assess the effects of glyphosate formulation on plankton composition by using different community parameters through a mesocosm experiment. Methodology: A 600 l mesocosm experiment was performed for 7 days, including a control (without glyphosate) and two concentrations of glyphosate. Results: Glyphosate caused a significant decrease in cladoceran density and a significant increase in rotifer, Chlorophyceae, and Euglenophyceae densities. In addition, zooplankton size diversity as well as microalgal evenness diminished. Interpretation: The decrease in cladoceran density may have benefited rotifers since they are less competitive for food resources. Moreover, the decrease in cladoceran foraging pressure over Chlorophyceae and Euglenophyceae may have benefited them. The different tolerances and competitiveness within the plankton components make the structure of this community a good indicator of environmental disturbance.

A synthesis tree of the Copepoda: integrating phylogenetic and taxonomic data reveals multiple origins of parasitism

The Copepoda is a clade of pancrustaceans containing 14,485 species that are extremely varied in their morphology and lifestyle. Not only do copepods dominate marine plankton and sediment communities and make up a sizeable component of the freshwater plankton, but over 6,000 species are symbiotically associated with every major phylum of marine metazoans, mostly as parasites. Unfortunately, our understanding of copepod evolutionary relationships is relatively limited in part because of their extremely divergent morphology, sparse taxon sampling in molecular phylogenetic analyses, a reliance on only a handful of molecular markers, and little taxonomic overlap between phylogenetic studies. Here, a synthesis tree method is used to integrate published phylogenies into a more comprehensive tree of copepods by leveraging phylogenetic and taxonomic data. A literature review in this study finds fewer than 500 species of copepods have been sampled in molecular phylogenetic studies. Using the Open Tree of Life platform, those taxa that have been sampled in previous phylogenetic studies are grafted together and combined with the underlying copepod taxonomic hierarchy from the Open Tree of Life Taxonomy to make a synthesis phylogeny of all copepod species. Taxon sampling with respect to molecular phylogenetic analyses is reviewed for all orders of copepods and shows only 3% of copepod species have been sampled in phylogenetic studies. The resulting synthesis phylogeny reveals copepods have transitioned to a parasitic lifestyle on at least 14 occasions. We examine the underlying phylogenetic, taxonomic, and natural history data supporting these transitions to parasitism; review the species diversity of each parasitic clade; and identify key areas for further phylogenetic investigation.

A unified framework for herbivore-to-producer biomass ratio reveals the relative influence of four ecological factors

The biomass ratio of herbivores to primary producers reflects the structure of a community. Four primary factors have been proposed to affect this ratio, including production rate, defense traits and nutrient contents of producers, and predation by carnivores. However, identifying the joint effects of these factors across natural communities has been elusive, in part because of the lack of a framework for examining their effects simultaneously. Here, we develop a framework based on Lotka–Volterra equations for examining the effects of these factors on the biomass ratio. We then utilize it to test if these factors simultaneously affect the biomass ratio of freshwater plankton communities. We found that all four factors contributed significantly to the biomass ratio, with carnivore abundance having the greatest effect, followed by producer stoichiometric nutrient content. Thus, the present framework should be useful for examining the multiple factors shaping various types of communities, both aquatic and terrestrial.

The Suspected Contradictory Role of Parental Care in the Adaption of Planktonic Calanoida to Temporary Freshwater

Calanoida have the highest number of species among Copepoda in marine plankton, but not in fresh water, where the greatest number are Cyclopoida. Freshwater Cyclopoida also live in more freshwater sites than Calanoida. This could be a consequence of an invasion of freshwater by marine Cyclopoida before Calanoida. Similar to Cyclopoida, but different from marine Calanoida, freshwater Calanoida females produce egg sacs and care for eggs. This strategy is common among all freshwater plankton, suggesting that the evolution of parental care is an obliged adaption to conquer fresh water. Calanoida, different from Cyclopoida, survive adverse conditions as resting eggs. This life-cycle constraint obliges eggs to survive their mother’s death and wait in the benthos for a certain period. The necessity of completing embryonic development and the hatching of eggs far from the mother’s protection may be responsible for the relatively lower evolutionary success of Calanoida in fresh water compared to Cyclopoida (which rest as juveniles, thus protecting eggs in any moment of their development). Therefore, the brooding of eggs appears to be the obliged solution for Calanoida’s final establishment in fresh water, but the dispersion of eggs on the bottom after the mother’s death and during the rest period is probably the weak point in Calanoida’s competition with Cyclopoida.

PriSeT: Efficient De Novo Primer Discovery

MotivationDNA metabarcoding is a commonly applied technique used to infer the species composition of environmental samples. These samples can comprise hundreds of organisms that can be closely or very distantly related in the taxonomic tree of life. DNA metabarcoding combines polymerase chain reaction (PCR) and next-generation sequencing (NGS), whereby a short, homologous sequence of DNA is amplified and sequenced from all members of the community. Sequences are then taxonomically identified based on their match to a reference database. Ideally, each species of interest would have a unique DNA barcode. This short, variable sequence needs to be flanked by relatively conserved regions that can be used as primer binding sites. Appropriate PCR primer pairs would match to a broad evolutionary range of taxa, such that we only need a few to achieve high taxonomic coverage. At the same time however, the DNA barcodes between primer pairs should be different to allow us to distinguish between species to improve resolution. This poses an interesting optimization problem. More specifically: Given a set of references ℛ = {R1, R2, …, Rm}, the problem is to find a primer set P balancing both: high taxonomic coverage and high resolution. This goal can be captured by filtering for frequent primers and ranking by coverage or variation, i.e. the number of unique barcodes. Here we present the software PriSeT, an offline primer discovery tool that is capable of processing large libraries and is robust against mislabeled or low quality references. It tackles the computationally expensive steps with linear runtime filters and efficient encodings.ResultsWe first evaluated PriSeT on references (mostly 18S rRNA genes) from 19 clades covering eukaryotic organisms that are typical for freshwater plankton samples. PriSeT recovered several published primer sets as well as additional, more chemically suitable primer sets. For these new sets, we compared frequency, taxon coverage, and amplicon variation with published primer sets. For 11 clades we found de novo primer pairs that cover more taxa than the published ones, and for six clades de novo primers resulted in greater sequence (i.e., DNA barcode) variation. We also applied PriSeT to 19 SARS-CoV-2 genomes and computed 114 new primer pairs with the additional constraint that the sequences have no co-occurrences in other taxa. These primer sets would be suitable for empirical testing.Availabilityhttps://github.com/mariehoffmann/[email protected]

Quantitative proteomics reveals remodeling of protein repertoire across life phases ofDaphnia pulex

The microcrustaceanDaphniais becoming an organism of choice for genomic and proteomic studies of the effects of environmental stressors. However, the changes in protein expression across the life cycle have not been fully characterized. We analyzed the proteomes of adult females, juveniles, asexually produced embryos, and the ephippia - resting stages containing two sexually produced diapausing freezing- and desiccation-resistant embryos. Overall, we were significantly more likely to detect proteins with known molecular functions than proteins with no detectable orthology. Similarly we could detect those with stronger gene model support, as judged by mutual best BLAST hits between two independent genome assemblies than those without such support. This suggests that we could apply our proteomics pipeline to verify hypothesized proteins, even given less-than-perfect reference gene models. In particular, we observed up-regulation of vitellogenins and down-regulation of actins and myosins in embryos of both types, as compared to juveniles and adults and overrepresentation of cell-cycle related proteins in the developing embryos, as compared to both diapausing embryos and adults. We found upregulation of small heat-shock proteins and redox peroxidases, as well as overrepresentation of stress-response proteins in the ephippium relative to the asexually produced non-diapausing embryos. The ephippium also showed up-regulation of three trehalose-synthesis proteins and down-regulation of a trehalose hydrolase, consistent with the role of trehalose in protection against freezing and desiccation.Statement of significance of the studyFreshwater plankton crustaceanDaphniais rapidly becoming a model organism of choice for ecological and developmental genomics. While there have been several advances towards establishing the protocols and reference datasets for proteomics, a detailed dataset covering several main steps of asexual and sexual phases ofDaphnialife cycle is not yet available. Moreover, different versions ofD. pulexgenome differ in the number of protein-coding genes identified; it is unclear whether these differences are caused by differences between sequenced genotypes or between gene model methodology used. In this study we report LC-MS2/MS3 proteomes of whole body adult females, juvenile females, asexually produces embryos and diapausing eggs capable of surviving freezing and desiccation.