cDNA library preparation from total RNA extracts of Single-cell marine protists (e.g. Acantharia, Strombidium basimorphum, and Prymnesium parvum) for transcriptome sequencing v2

Many marine protists are not culturable and therefore challenging to study, nonetheless, they are essential in all marine ecosystems. The development of single-cell techniques is allowing for more marine protists to be studied. Such genomic approaches aim to help to disentangle heterotrophic processes such as phagotrophy from osmotrophy and phototrophic-induced anabolic activities. This information will then support cellular and metabolic modeling by better elucidating the physiological mechanisms and quantifying their importance in different scenarios. However, single-cell protocols and low input RNA kits for transcriptomics are usually made for and tested with mammalian cells, as such the feasibility and efficiency of single-cell transcriptomics on highly diverse mixotrophic protists is not always known. Often single-cell transcriptomics of microbial eukaryotes shows low transcript recovery rates and large variability. We report on transcriptomic methods that we have successfully performed on single cells of Acantharia, Strombidium basimorphum, and Prymnesium parvum. This protocol follows up after total RNA extraction (from the protocol at dx.doi.org/10.17504/protocols.io.bp6xmrfn) to prepare cDNA libraries for Illumina sequencing. The described protocol uses the SMART-Seq4 kit (Takara #634891) for cDNA synthesis and amplification, but this can also be successfully performed with the NEBNext kit (NEB #E6421). The NEBNext kit protocol is very similar to the protocol described here and generally the manufacture's protocol can be followed but see the notes at step 4 and step 18 of this protocol, and do the final elution after cDNA purification in 10 mM Tris (pH 8.0). The subsequent cDNA library is prepared following the .

Gill Transcriptomic Responses to Toxin-producing Alga Prymnesium parvum in Rainbow Trout

The gill of teleost fish is a multifunctional organ involved in many physiological processes, including protection of the mucosal gill surface against pathogens and other environmental antigens by the gill-associated lymphoid tissue (GIALT). Climate change associated phenomena, such as increasing frequency and magnitude of harmful algal blooms (HABs) put extra strain on gill function, contributing to enhanced fish mortality and fish kills. However, the molecular basis of the HAB-induced gill injury remains largely unknown due to the lack of high-throughput transcriptomic studies performed on teleost fish in laboratory conditions. We used juvenile rainbow trout (Oncorhynchus mykiss) to investigate the transcriptomic responses of the gill tissue to two (high and low) sublethal densities of the toxin-producing alga Prymnesium parvum, in relation to non-exposed control fish. The exposure time to P. parvum (4–5 h) was sufficient to identify three different phenotypic responses among the exposed fish, enabling us to focus on the common gill transcriptomic responses to P. parvum that were independent of dose and phenotype. The inspection of common differentially expressed genes (DEGs), canonical pathways, upstream regulators and downstream effects pointed towards P. parvum-induced inflammatory response and gill inflammation driven by alterations of Acute Phase Response Signalling, IL-6 Signalling, IL-10 Signalling, Role of PKR in Interferon Induction and Antiviral Response, IL-8 Signalling and IL-17 Signalling pathways. While we could not determine if the inferred gill inflammation was progressing or resolving, our study clearly suggests that P. parvum blooms may contribute to the serious gill disorders in fish. By providing insights into the gill transcriptomic responses to toxin-producing P. parvum in teleost fish, our research opens new avenues for investigating how to monitor and mitigate toxicity of HABs before they become lethal.

Yeast Cell as a Bio-Model for Measuring the Toxicity of Fish-Killing Flagellates

Harmful algal blooms are a significant environmental problem. Cells that bloom are often associated with intercellular or dissolved toxins that are a grave concern to humans. However, cells may also excrete compounds that are beneficial to their competition, allowing the cells to establish or maintain cells in bloom conditions. Here, we develop a yeast cell assay to assess whether the bloom-forming species can change the toxicity of the water environment. The current methods of assessing toxicity involve whole organisms. Here, yeast cells are used as a bioassay model to evaluate eukaryotic cell toxicity. Yeast is a commonly used, easy to maintain bioassay species that is free from ethical concerns, yet is sensitive to a wide array of metabolic and membrane-modulating agents. Compared to methods in which the whole organism is used, this method offers rapid and convenient cytotoxicity measurements using a lower volume of samples. The flow cytometer was employed in this toxicology assessment to measure the number of dead cells using alive/dead stain analysis. The results show that yeast cells were metabolically damaged after 1 h of exposure to our model toxin-producing euryhaline flagellates (Heterosigma akashiwo and Prymnesium parvum) cells or extracts. This amount was increased by extending the incubation time.

A Case Study of a Prymnesium parvum Harmful Algae Bloom in the Ohio River Drainage: Impact, Recovery and Potential for Future Invasions/Range Expansion

Inland waters provide valuable ecosystem goods and services and are intrinsically linked to downstream coastal areas. Water quality impairments that lead to harmful algal blooms damage valuable commercial and recreational fishing economies, threaten food security, and damage already declining native species. Prymnesium parvum is a brackish water golden alga that can survive in salinities less than 1 ppm and when it blooms it can create toxins that kill aquatic life. Blooms have been documented globally including 23 U.S. states. We report a case study of an aquatic life kill associated with P. parvum in Dunkard Creek (WV-PA, USA), in the Ohio River Drainage. We document the immediate impact to aquatic life and responses of the aquatic community ten years post-kill. Most fish species returned within a year. Excellent connectivity to unimpacted tributaries and a river downstream likely aided the reestablishment of most species, although some had not reached pre-kill abundances after ten years. Mussel taxa did not recover despite significant efforts to relocate adult mussels and stocking of host fish inoculated with glochidia; probably due to other water quality impairments. Given the potential for lateral transport of P. parvum via industry and natural vectors we conducted an ecological risk assessment mapping the spatial extent of U.S. waters that could be threatened by golden algae colonization and blooms using a national water quality database and a state database. Overall, about 4.5% of lotic systems appeared to have some level of risk of harboring P. parvum, making them at risk for potential golden algae blooms in the face of increasing salinization and eutrophication of freshwaters.

Application of uniform design to evaluate the different conditions on the growth of algae Prymnesium parvum

Prymnesium parvum is an environmentally harmful algae and well known for its toxic effects to the fish culture. However, there is a dearth of studies on the growth behavior of P. parvum and information on how the availability of nutrients and environmental factors affect their growth rate. To address this knowledge gap, we used a uniform design approach to quantify the effects of major nutrients (N, P, Si and Fe) and environmental factors (water temperature, pH and salinity) on the biomass density of P. parvum. We also generated the growth model for P. parvum as affected by each of these nutrients and environmental factors to estimate optimum conditions of growth. Results showed that P. parvum can reach its maximum growth rate of 0.789, when the water temperature, pH and salinity is 18.11 °C, 8.39, and 1.23‰, respectively. Moreover, maximum growth rate (0.895–0.896) of P. parvum reached when the concentration of nitrogen, phosphorous, silicon and iron reach 3.41, 1.05, 0.69 and 0.53 mg/l, respectively. The order of the effects of the environmental factors impacting the biomass density of P. parvum was pH > salinity > water temperature, while the order of the effects of nutrients impacting the biomass density of P. parvum was nitrogen > phosphorous > iron > silicon. These findings may assist to implement control measures of the population of P. parvum where this harmful alga threatens aquaculture industry in the waterbodies such as Ningxia region in China.