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Ordination plots (A) Principal component analysis (PCA) and (B) redundancy analysis (RDA) of normalized intensity matrix. Samples are depicted as numbers, different days are indicated by colours and symbols show samples kept under dark (circle) and light (triangle) conditions. The coloured background indicates the separation between samples in light (light grey) and dark (dark grey) conditions in the PCA. Arrows in (B) show significant factors of the reduced model. Samples were numbered for readability according to S1 Table.
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Aquatic environments are heavily impacted by human activities including climate warming and the introduction of xenobiotics. Due to the application of silver nanoparticles as bactericidal agent the introduction of silver into the environment strongly has increased during the past years. Silver ions affect the primary metabolism of algae, in particu...
Citations
... The potential of microalgae in the production of proteins with biotechnological application has been widely validated [12][13][14][15][16]. Nevertheless, there are only a few proteomics approaches to microalgae, most of them related to biofuels production [11,[17][18][19][20] without any reference to the potential biotechnological use of this information [21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36]. Only 17 species have been studied from the several million different species of algae and microalgae [37]. ...
Proteomics is a crucial tool for unravelling the molecular dynamics of essential biological processes, becoming a pivotal technique for basic and applied research. Diverse bioinformatic tools are required to manage and explore the huge amount of information obtained from a single proteomics experiment. Thus, functional annotation and protein–protein interactions are evaluated in depth leading to the biological conclusions that best fit the proteomic response in the system under study. To gain insight into potential applications of the identified proteins, a novel approach named “Applied Proteomics” has been developed by comparing the obtained protein information with the existing patents database. The development of massive sequencing technology and mass spectrometry (MS/MS) improvements has allowed the application of proteomics nonmodel microorganisms, which have been deeply described as a novel source of metabolites. Between them, Nannochloropsis gaditana has been pointed out as an alternative source of biomolecules. Recently, our research group has reported the first complete proteome analysis of this microalga, which was analysed using the applied proteomics concept with the identification of 488 proteins with potential industrial applications. To validate our approach, we selected the UCA01 protein from the prohibitin family. The recombinant version of this protein showed antiproliferative activity against two tumor cell lines, Caco2 (colon adenocarcinoma) and HepG-2 (hepatocellular carcinoma), proving that proteome data have been transformed into relevant biotechnological information. From Nannochloropsis gaditana has been developed a new tool against cancer—the protein named UCA01. This protein has selective effects inhibiting the growth of tumor cells, but does not show any effect on control cells. This approach describes the first practical approach to transform proteome information in a potential industrial application, named “applied proteomics”. It is based on a novel bioalgorithm, which is able to identify proteins with potential industrial applications. From hundreds of proteins described in the proteome of N. gaditana, the bioalgorithm identified over 400 proteins with potential uses; one of them was selected as UCA01, “in vitro” and its potential was demonstrated against cancer. This approach has great potential, but the applications are potentially numerous and undefined.
... amount of information itself, from where we can find proteins with biotechnological applications (applied proteomics) [26], such as anti-cancer proteins (Patent number: 201930775) [98]. Several [26,27,49,[99][100][101][102][103][104][105][106][107][108][109][110][111][112][113][114]. ...
Microalgae are eukaryotic organisms with photoautotrophic metabolism. There are several million-different species of algae and microalgae, compared to about 250,000 species of terrestrial plants. Marine microalgae encompass 40% of global primary production, making a great ecological contribution to biogeochemical carbon cycling. Microalgae are good candidates as biomolecules producers, since they are more efficient in energy conversion of the sunlight than higher plants. They have tremendous biotechnological applications due to the production of many bioactive molecules with commercial potential. This is reflected in the amount of current research about the potential use of microalgae, which addresses alternative energy production, cancer treatment, agri-food sector, the removal of diverse contaminants from the environment and developments in the aquaculture sector. Microalgae products cover different types of metabolites such as proteins, lipids or carbohydrates, that are employed in animal feed additives, human nutritional supplements, cosmetics and energy.
... Mixotrophy has been found to be a widespread phenomenon among protozoa and has attracted considerable attention in the research community during the last few decades (Esteban et al. 2010;Gawryluk et al. 2019). Poterioochromonas malhamensis is a well-known and widespread mixotrophic flagellate, capable of both photosynthesis and phagotrophy that is now recognized as playing an important role in grazing bacteria and in regenerating nutrients within marine and freshwater planktonic ecosystems (Sanders et al. 1990;Zhang and Watanabe 2001), and is also used as a model organism to study the mechanism of trophic transformation (Beisser et al. 2017). Recently, it was reported that the grazing of P. malhamensis might pose the greatest contamination threat for mass algal cultures of Chlorella (Ma et al. 2018;Wang et al. 2017Wang et al. , 2018, which is recognized as one of the most successful commercial microalgae because of its high growth rate and high lipid content (Milano et al. 2016;Ndimba et al. 2013). ...
Grazing behaviour between protozoa and phytoplankton exists widely in planktonic ecosystems. Poterioochromonas malhamensis is a well‐known and widespread mixotrophic flagellate, which is recognized to play an important role within marine and freshwater planktonic ecosystems and regarded as the greatest contamination threat for mass algal cultures of Chlorella. In this study, a comprehensive range of factors, including morphological characters, biochemical compositions, and specific growth rate of ten species or strains of Chlorella, were evaluated for their effect on the feeding ability of P. malhamensis, which was assessed by two parameters: the clearance rate of P. malhamensis on Chlorella spp. and the specific growth rate of P. malhamensis. The results showed that the clearance rate of P. malhamensis was negatively correlated with cell wall thickness and specific growth rate of Chlorella spp., while the specific growth rate of P. malhamensis was positively correlated with carbohydrate percentage and C/N ratio, and negatively correlated with protein, lipid percentage and nitrogen mass. In conclusion, the factors influencing feeding selectivity include not only the morphological character and chemical composition of Chlorella, but also its population dynamics. Our study provides useful insights into the key factors that affect the feeding selectivity of P. malhamensis and provides basic and constructive data to help in screening for grazing‐resistant microalgae.
... Three different softwares were employed to assemble P. lunula transcriptome through a de novo approach, considering there is no reference genome available to date, which were further assessed to contrast the obtained assemblies by a proteomic analysis. The four preprocessed sequence datasets described above were assembled into contigs using 5 different parametrizations of kmer (21,31,41,51,71) with RAY 2.3.1. assembler [63], yielding a total of 20 assemblies. ...
Pyrocystis lunula (Schutt) is a photoautotrophic dinoflagellate without armored form, frequently found in marine environments. Today, there are several biotechnological applications derived from the bioluminescent system of this species. From a post-genomic perspective, in order to have a starting point for studying the proteome of P. lunula, an “omics” approach (transcriptomics-proteomics) was assessed using fresh microalgae samples. A total of 80,874,825 raw reads were generated (11,292,087,505 bp; 55.82% GC) by mRNA sequencing. Very high-quality sequences were assembled into 414,295 contigs (219,203,407 bp; 55.38% GC) using Trinity software, generating a comprehensive reference transcriptome for this species. Then, a P. lunula proteome was inferred and further employed for its analysis on this species. A total of 17,461 peptides were identified, yielding 3182 protein identification hits, including 175 novel proteins. The identified proteins were further categorized according to functional description and gene ontology classification.
https://authors.elsevier.com/a/1ZiZB_gdcMSxMY
... Three different softwares were employed to assemble P. lunula transcriptome through a de novo approach, considering there is no reference genome available to date, which were further assessed to contrast the obtained assemblies by a proteomic analysis. The four pre-processed sequence datasets described above were assembled into contigs using 5 different parametrizations of kmer (21,31,41,51,71) with RAY 2.3.1. assembler [63], yielding a total of 20 assemblies. ...
Background: Pyrocystis lunula (Schutt) is a photoautotrophic dinoflagellate without armored, frequently found in marine environments. Today, there are several biotechnological applications derived from the bioluminescent system of this species. From a post-genomic perspective, in order to study the whole proteome of P. lunula, an ”omic“ approach (transcriptomic-proteomic analysis) was assessed using fresh microalgae samples. Results: A total of 80,874,825 raw reads were generated (11,292,087,505 pb; 55.82 % GC) by mRNA sequencing. Very high quality sequences were assembled into 414,295 contigs (219,203,407 pb; 55.38 % GC) by the Trinity software, generating a comprehensive reference transcriptome for this species. Then, a P. lunula proteome was predicted and further employed through the first proteomic analysis on this species. A total of 17,461 peptides were identified, yielding 3,182 protein identification hits. The identified proteins were further categorized according to functional description and gene ontology classification. Conclusions: The first comprehensive molecular analysis of the microalgae P. lunula using both, transcriptomic and proteomic approaches, has been reported. Proteomic results represent a valuable piece in the understanding of this microalgae regulation at molecular level, and shed light on the identification of important factors involved in gene expression regulation. Indeed, the presence of the luciferin-binding protein (LBP), which had not been described so far in the genus Pyrocystis has been highlighted.
... belongs to the family Dinobryonaceae, order Chromulinales, class Chrysophyeeae, and phylum Chrysophyta. This algae is widespread in freshwater (31,32), sharing the similar environment with P. canaliculata snail. No previous report indicated algae could infect P. canaliculata, and this research is the first likely report of Poterioochromonas infection in P. canaliculata snails. ...
Background
Pomacea canaliculata (P.canaliculata) lung nodules, were commonly caused by Angiostrongylus cantonensis infection. Here, we found a new nodule type without any parasites.
Methods
Overall, 447 P. canaliculata snails were collected in Ning Bo, Zhe Jiang, China in 2018. In order to exhibit the similarities and differences between two nodules types (2018, Huzhou Zhejiang, China), both types were collected in formalin for tissue pathological sectioning. Besides, to obtain the microbial community of the new nodule, the 18S ribosomal RNA (rRNA) gene of it was amplified and analyzed using the Illumina second-generation sequencing platform.
Results
Although two nodules were found in the lungs of P. canaliculata, they were different in shape and pathology. Illumina sequencing indicated Poterioochromonas sp., a species of golden algae, might be the causing agent of the new nodule.
Conclusion
We firstly found a new pathological nodule type in the lungs of P. canaliculata, and this nodule might be induced by golden algae infection, however, the direct link between the golden algae and the new nodules, as well as the nodules’ impact on the snails’ physiology and A. cantonensis infection require further study.
... The mixotrophic spectrum covers nutritional modes from primarily phototrophic to primarily heterotrophic with all the different gradations being realized. Furthermore, the relative contribution of phototrophy and heterotrophy in distinct taxa may change depending on environmental conditions such as light intensity and the availability of bacteria (Sanders 1991;Jones 2000;Liu et al. 2015;Beisser et al. 2017b). As shifts in the prevailing mode of nutrition usually require more than 24 h, a switch of nutritional mode within mixotrophs is no subject of a diurnal variation . ...
Shifts in the nutritional mode between phototrophy, mixotrophy and heterotrophy are a widespread phenomenon in the evolution of eukaryotic diversity. The transition between nutritional modes is particularly pronounced in chrysophytes and occurred independently several times through parallel evolution. Thus, chrysophytes provide a unique opportunity for studying the molecular basis of nutritional diversification and of the accompanying pathway reduction and degradation of plastid structures. In order to analyze the succession in switching the nutritional mode from mixotrophy to heterotrophy, we compared the transcriptome of the mixotrophic Poterioochromonas malhamensis with the transcriptomes of three obligate heterotrophic species of Ochromonadales. We used the transcriptome of P. malhamensis as a reference for plastid reduction in the heterotrophic taxa. The analyzed heterotrophic taxa were in different stages of plastid reduction. We investigated the reduction of several photosynthesis related pathways e.g. the xanthophyll cycle, the mevalonate pathway, the shikimate pathway and the tryptophan biosynthesis as well as the reduction of plastid structures and postulate a presumable succession of pathway reduction and degradation of accompanying structures.
... On the functional level a test for differential expression reveals 34 KEGG orthologous genes that differ significantly (FDR <0.1) between the two groups and show an enrichment of photosynthesis pathways. It is known that silver ions affect the primary metabolism in particular photosynthesis by direct interference [53,56]. On the other hand, it has been shown that for low concentrations of silver green algae grows is increased as observed in Fig. 8 A [57]. ...
Background
High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach is at the moment largely limited to prokaryotic communities and communities of few eukaryotic species with sequenced genomes. For eukaryotes the analysis is hindered mainly by a low and fragmented coverage of the reference databases to infer the community composition, but also by lack of automated workflows for the task. ResultsFrom the databases of the National Center for Biotechnology Information and Marine Microbial Eukaryote Transcriptome Sequencing Project, 142 references were selected in such a way that the taxa represent the main lineages within each of the seven supergroups of eukaryotes and possess predominantly complete transcriptomes or genomes. From these references, we created an annotated microeukaryotic reference database. We developed a tool called TaxMapper for a reliably mapping of sequencing reads against this database and filtering of unreliable assignments. For filtering, a classifier was trained and tested on each of the following: sequences of taxa in the database, sequences of taxa related to those in the database, and random sequences. Additionally, TaxMapper is part of a metatranscriptomic Snakemake workflow developed to perform quality assessment, functional and taxonomic annotation and (multivariate) statistical analysis including environmental data. The workflow is provided and described in detail to empower researchers to apply it for metatranscriptome analysis of any environmental sample. Conclusions
TaxMapper shows superior performance compared to standard approaches, resulting in a higher number of true positive taxonomic assignments. Both the TaxMapper tool and the workflow are available as open-source code at Bitbucket under the MIT license: https://bitbucket.org/dbeisser/taxmapperand as a Bioconda package: https://bioconda.github.io/recipes/taxmapper/README.html.
... On the functional level a test for differential expression reveals 34 KEGG orthologous genes that differ significantly (FDR < 0.1) between the two groups and show an enrichment of photosynthesis pathways. It is known that silver ions affect the primary metabolism in particular photosynthesis by direct interference [52,53]. On the other hand, it has been shown that for low concentrations of silver green algae grows is increased as observed in Figure 7 A [54]. ...
Background
High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach is at the moment largely limited to prokaryotic communities and communities of few eukaryotic species with sequenced genomes. For eukaryotes the analysis is hindered mainly by a low and fragmented coverage of the reference databases to infer the community composition, but also by lack of automated workflows for the task.
Results
From the databases of the National Center for Biotechnology Information and Marine Microbial Eukaryote Transcriptome Sequencing Project, 142 references were selected in such a way that the taxa represent the main lineages within each of the seven supergroups of eukaryotes and possess predominantly complete transcriptomes or genomes. From these references, we created an annotated microeukaryotic reference database. We developed a tool called TaxMapper for a reliably mapping of sequencing reads against this database and filtering of unreliable assignments. For filtering, a classifier was trained and tested on sequences in the database, sequences of related taxa to those in the database and randomly generated sequences. Additionally, TaxMapper is part of a metatranscriptomic Snakemake workflow developed to perform quality assessment, functional and taxonomic annotation and (multivariate) statistical analysis including environmental data. The workflow is provided and described in detail to empower researchers to easily apply it for metatranscriptome analysis of any environmental sample.
Conclusions
TaxMapper shows superior performance compared to standard approaches, resulting in a higher number of true positive taxonomic assignments. Both the TaxMapper tool and the workflow are available as open-source code at Bitbucket under the MIT license: https://bitbucket.org/dbeisser/taxmapper and as a Bioconda package: https://bioconda.github.io/recipes/taxmapper/README.html .
... Three different softwares were employed to assemble P. lunula transcriptome through a de novo approach, considering there is no reference genome available to date, which were further assessed to contrast the obtained assemblies by a proteomic analysis. The four pre-processed sequence datasets described above were assembled into contigs using 5 different parametrizations of kmer (21,31,41,51,71) with RAY 2.3.1. assembler [63], yielding a total of 20 assemblies. ...
