Intra-population genetic diversity and its effects on outlining genetic diversity of ciliate populations: Using Paramecium multimicronucleatum as an example

Assessing genetic diversity and population structure of Iranian melons (Cucumis melo) collection using primer pair markers in association with resistance to Fusarium wilt

We evaluated genetic diversity and population structure of Iranian melons (Cucumis melo L.) using combinations of 35 primer pairs: 15 Simple-Sequence-Repeats (SSR); 10 Inter-Simple-Sequence-Repeats (ISSR); and 10 Sequence-related amplified polymorphism (SRAP) markers in association with resistance to melon Fusarium wilt, caused by Fusarium oxysporum f. sp. melonis (FOM ). Genetic similarity was determined by simple matching coefficient (SSM) and dendrogram by clustering-analysis with unweighted pair groups using arithmetic averages (UPGMA). By combining ISSR-SSR-SRAP markers, a high degree of variation among the melons was detected. The mean polymorphism information content (PIC), marker index (MI), effective-number of alleles (I), expected heterozygosity (H), and Nei's gene diversity parameters were 0.392, 0.979, 1.350, 0.551 and 0.225, respectively. According to MI, PIC, I, H, and Nei indices evaluation, ISSR6, ISSR9, SRAP3, SRAP5, SSR3 and SSR6 had the best performance in genetic diversity of the related melons population. The 35 primers yielded a total of 264 bands, of which 142 showed polymorphism. Clustering of genotypes based on resistance to Fusarium wilt, and comparison with grouping on SSR, SRAP and ISSR marker revealed a significant compliance between disease severity and molecular marker dendrograms. Thus, increasing the number of molecular markers for genetic diversity provides a powerful tool for future agricultural and conservation tasks.

Cryptic Diversity in Paramecium multimicronucleatum Revealed with a Polyphasic Approach

Paramecium (Ciliophora) systematics is well studied, and about twenty morphological species have been described. The morphological species may include several genetic species. However, molecular phylogenetic analyses revealed that the species diversity within Paramecium could be even higher and has raised a problem of cryptic species whose statuses remain uncertain. In the present study, we provide the morphological and molecular characterization of two novel Paramecium species. While Paramecium lynni n. sp., although morphologically similar to P. multimicronucleatum, is phylogenetically well separated from all other Paramecium species, Paramecium fokini n. sp. appears to be a cryptic sister species to P. multimicronucleatum. The latter two species can be distinguished only by molecular methods. The number and structure of micronuclei, traditionally utilized to discriminate species in Paramecium, vary not only between but also within each of the three studied species and, thus, cannot be considered a reliable feature for species identification. The geographic distribution of the P. multimicronucleatum and P. fokini n. sp. strains do not show defined patterns, still leaving space for a role of the geographic factor in initial speciation in Paramecium. Future findings of new Paramecium species can be predicted from the molecular data, while morphological characteristics appear to be unstable and overlapping at least in some species.

The Codon Usage Bias Analysis of Free-Living Ciliates' Macronuclear Genomes and Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Vector Construction of Stylonychia lemnae

Ciliates represent higher unicellular animals, and several species are also important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome in ciliates can not only promote a better understanding of the genetic mode and evolution history of these organisms but also help optimize codons to improve the gene editing efficiency of model ciliates. In this study, macronuclear genome sequences of nine free-living ciliates were analyzed with CodonW software to calculate the following indices: the guanine-cytosine content (GC); the frequency of the nucleotides U, C, A, and G at the third position of codons (U3s, C3s, A3s, G3s); the effective number of codons (ENC); the correlation between GC at the first and second positions (GC12); the frequency of the nucleotides G + C at the third position of synonymous codons (GC3s); the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, neutrality plot analysis, and correlation analysis were performed to explore the factors that influence codon preference. The results showed that the GC contents in nine ciliates' MAC genomes were lower than 50% and appeared AT-rich. The base compositions of GC12 and GC3s are markedly distinct and the codon usage pattern and evolution of ciliates are affected by genetic mutation and natural selection. According to the synonymous codon analysis, the codons of most ciliates ended with A or U and eight codons were the general optimal codons of nine ciliates. A clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) expression vector of Stylonychia lemnae was constructed by optimizing the macronuclear genome codon and was successfully used to knock out the Adss gene. This is the first such extensive investigation of the MAC genome CUB of ciliates and the initial successful application of the CRISPR/Cas9 technique in free-living ciliates.

Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters

Microeukaryotes are key components of aquatic ecosystems and play crucial roles in aquatic food webs. However, influencing factors and potential assembly mechanisms for microeukaryotic community on biofilms are rarely studied. Here, those of microeukaryotic biofilms in subtropical eutrophic freshwaters were investigated for the first time based on 2,585 operational taxonomic units (OTUs) from 41 samples, across different environmental conditions and substrate types. Following conclusions were drawn: (1) Environmental parameters were more important than substrate types in structuring microeukaryotic community of biofilms in subtropical eutrophic freshwaters. (2) In the fluctuating river, there was a higher diversity of OTUs and less predictability of community composition than in the stable lake. Sessile species were more likely to be enriched on smooth surfaces of glass slides, while both free-swimming and attached organisms occurred within holes inside PFUs (polyurethane foam units). (3) Both species sorting and neutral process were mechanisms for assembly of microeukaryotic biofilms, but their importance varied depending on different habitats and substrates. (4) The effect of species sorting was slightly higher than the neutral process in river biofilms due to stronger environmental filtering. Species sorting was a stronger force structuring communities on glass slides than PFUs with more niche availability. Our study sheds light on assembly mechanisms for microeukaryotic community on different habitat and substrate types, showing that the resulting communities are determined by both sets of variables, in this case primarily habitat type. The balance of neutral process and species sorting differed between habitats, but the high alpha diversity of microeukaryotes in both led to similar sets of lifecycle traits being selected for in each case.

Ciliates as model organisms for the ecotoxicological risk assessment of heavy metals: A meta-analysis

Ciliates are key components of aquatic ecosystems, significantly contributing to the decomposition of organic matter and energy transfer to higher trophic levels. They are considered good biological indicators of chemical pollution and relatively sensitive to heavy metal contamination. In this study, we performed a meta-analysis of the available toxicity data of heavy metals and ciliates to assess: (1) the sensitivity of freshwater ciliates to different heavy metals, (2) the relative sensitivity of ciliates in comparison to the standard test species used in ecotoxicological risk assessment, and (3) the difference in sensitivity across ciliate taxa. Our study shows that the tolerance of ciliates to heavy metals varies notably, which is partly influenced by differences in methodological conditions across studies. Ciliates are, in general, sensitive to Mercury > Cadmium > Copper > Zinc > Lead > Chromium. Also, this study shows that most ciliates are more tolerant to heavy metal pollution than the standard test species used in ecotoxicological risk assessments, i.e., Raphidocelis subcapitata, Daphnia magna, and Onchornyncus mykiss. Threshold concentrations derived from toxicity data for these species is expected to confer sufficient protection for the vast majority of ciliate species. Our data analysis also shows that the most commonly tested ciliate species, Paramecium caudatum and Tetrahymena thermophila, are not necessarily the most sensitive ones to heavy metal pollution. Finally, this study stresses the importance of developing standard toxicity test protocols for ciliates, which could lead to a better comprehension of the toxicological impact of heavy metals and other contaminants to ciliate species.

Paramecium Diversity and a New Member of the Paramecium aurelia Species Complex Described from Mexico

Paramecium (Ciliophora) is an ideal model organism to study the biogeography of protists. However, many regions of the world, such as Central America, are still neglected in understanding Paramecium diversity. We combined morphological and molecular approaches to identify paramecia isolated from more than 130 samples collected from different waterbodies in several states of Mexico. We found representatives of six Paramecium morphospecies, including the rare species Paramecium jenningsi, and Paramecium putrinum, which is the first report of this species in tropical regions. We also retrieved five species of the Paramecium aurelia complex, and describe one new member of the complex, Paramecium quindecaurelia n. sp., which appears to be a sister species of Paramecium biaurelia. We discuss criteria currently applied for differentiating between sibling species in Paramecium. Additionally, we detected diverse bacterial symbionts in some of the collected ciliates.