Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive

Mycoplasmas are notorious contaminants of cell culture and can have profound effects on host cell biology by depriving cells of nutrients and inducing global changes in gene expression. Over the last two decades, sentinel testing has revealed wide-ranging contamination rates in mammalian culture. To obtain an unbiased assessment from hundreds of labs, we analyzed sequence data from 9395 rodent and primate samples from 884 series in the NCBI Sequence Read Archive. We found 11% of these series were contaminated (defined as ≥100 reads/million mapping to mycoplasma in one or more samples). Ninety percent of mycoplasma-mapped reads aligned to ribosomal RNA. This was unexpected given 37% of contaminated series used poly(A)-selection for mRNA enrichment. Lastly, we examined the relationship between mycoplasma contamination and host gene expression in a single cell RNA-seq dataset and found 61 host genes (P < 0.001) were significantly associated with mycoplasma-mapped read counts. In all, this study suggests mycoplasma contamination is still prevalent today and poses substantial risk to research quality.     

Annual nitrogen budget of a temperate coastal barrier salt-marsh system along a productivity gradient at low and high marsh elevation

An annual nitrogen budget was established for a temperate back barrier salt-marsh system along a productivity gradient at low and high marsh elevation. We measured plant biomass and nitrogen content in three plant compartments to deduce plant N-allocation patterns. Measurements were done along a successional sequence in a salt-marsh system. In addition, N-mineralization, wet and dry atmospheric N-deposition and sediment N-deposition were measured.

Plant-species dominance changed along the successional sequence. In early stages, Elymus farctus and Spergularia media formed a large part of total plant biomass. Festuca rubra and Puccinellia maritima were dominant at intermediate stages, whereas Elymus pycnanthus and Limonium vulgare were dominant at late stages of succession. Shoot biomass was highest in June, whereas litter biomass was highest in September and December. Root biomass formed by far the largest fraction of total plant biomass, especially at a low-marsh elevation.

Wet deposition of nitrate and ammonium was 1.7 g N m⁻² yr⁻¹, whereas throughfall deposition (dry and wet deposition) amounted to 2.1–3.6 g N m⁻² yr⁻¹, and was positively related to the height of an artificial plant canopy. Sediment organic nitrogen deposition rate was 0.3–5.4 g N m⁻² yr⁻¹, and negatively related to marsh elevation. Nitrogen mineralization rate increased from 2.5–2.8 g N m⁻² yr⁻¹ in young marshes towards 8.0–12.7 g N m⁻² yr⁻¹ at older marshes, depending on marsh elevation.

At a low-marsh elevation, plant N-availability depended equally on tidal N, atmospheric N and mineralized N, especially in young marshes, whereas the decomposition pathway became more important in older marshes. Tidal N contributed most to ecoystem N-accumulation rate at early successional stages, whereas atmospheric N was more important at later stages. Tidal influence was low at high-marsh elevation sites. Here, atmospheric deposition was the dominant exogenous nitrogen source both in young and old marshes.     

Differential effects of jasmonic acid treatment of Brassica nigra on the attraction of pollinators, parasitoids, and butterflies

Herbivore-induced plant defences influence the behaviour of herbivores as well as that of their natural enemies. Jasmonic acid is one of the key hormones involved in both these direct and indirect induced defences. Jasmonic acid treatment of plants changes the composition of defence chemicals in the plants, induces volatile emission, and increases the production of extrafloral nectar. However, few studies have addressed the potential influence of induced defences on flower nectar chemistry and pollinator behaviour. These have shown that herbivore damage can affect pollination rates and plant fitness. Here, we have investigated the effect of jasmonic acid treatment on floral nectar production and the attraction of pollinators, as well as the effect on the behaviour of an herbivore and its natural enemy. The study system consisted of black mustard plants, Brassica nigra L. (Brassicaceae), pollinators of Brassica nigra (i.e., honeybees and syrphid flies), a specialist herbivore, Pieris rapae L. (Lepidoptera: Pieridae), and a parasitoid wasp that uses Pieris larvae as hosts, Cotesia glomerata L. (Hymenoptera: Braconidae). We show that different trophic levels are differentially affected by jasmonic acid-induced changes. While the herbivore prefers control leaves over jasmonic acid-treated leaves for oviposition, the parasitoid C. glomerata is more attracted to jasmonic acid-treated plants than to control plants. We did not observe differences in pollinator preference, the rates of flower visitation by honeybees and syrphid flies were similar for control and jasmonic acid-treated plants. Plants treated with jasmonic acid secreted less nectar than control plants and the concentrations of glucose and fructose tended to be lower than in nectar from control plants. Jasmonic acid treatment resulted in a lower nectar production than actual feeding damage by P. rapae caterpillars.