Decryption of the survival "black box": gene family expansion promotes the encystment in ciliated protists.

BACKGROUND: Encystment is an important survival strategy extensively employed by microbial organisms to survive unfavorable conditions. Single-celled ciliated protists (ciliates) are popular model eukaryotes for studying encystment, whereby these cells degenerate their ciliary structures and develop cyst walls, then reverse the process under more favorable conditions. However, to date, the evolutionary basis and mechanism for encystment in ciliates is largely unknown. With the rapid development of high-throughput sequencing technologies, genome sequencing and comparative genomics of ciliates have become effective methods to provide insights into above questions. RESULTS: Here, we profiled the MAC genome of Pseudourostyla cristata, a model hypotrich ciliate for encystment studies. Like other hypotrich MAC genomes, the P. cristata MAC genome is extremely fragmented with a single gene on most chromosomes, and encodes introns that are generally small and lack a conserved branch point for pre-mRNA splicing. Gene family expansion analyses indicate that multiple gene families involved in the encystment are expanded during the evolution of P. cristata. Furthermore, genomic comparisons with other five representative hypotrichs indicate that gene families of phosphorelay sensor kinase, which play a role in the two-component signal transduction system that is related to encystment, show significant expansion among all six hypotrichs. Additionally, cyst wall-related chitin synthase genes have experienced structural changes that increase them from single-exon to multi-exon genes during evolution. These genomic features potentially promote the encystment in hypotrichs and enhance their ability to survive in adverse environments during evolution. CONCLUSIONS: We systematically investigated the genomic structure of hypotrichs and key evolutionary phenomenon, gene family expansion, for encystment promotion in ciliates. In summary, our results provided insights into the evolutionary mechanism of encystment in ciliates.

Comparative genome analysis of three euplotid protists provides insights into the evolution of nanochromosomes in unicellular eukaryotic organisms.

One of the most diverse clades of ciliated protozoa, the class Spirotrichea, displays a series of unique characters in terms of eukaryotic macronuclear (MAC) genome, including high fragmentation that produces nanochromosomes. However, the genomic diversity and evolution of nanochromosomes and gene families for spirotrich MAC genomes are poorly understood. In this study, we assemble the MAC genome of a representative euplotid (a new model organism in Spirotrichea) species, Euplotes aediculatus. Our results indicate that: (a) the MAC genome includes 35,465 contigs with a total length of 97.3 Mb and a contig N50 of 3.4 kb, and contains 13,145 complete nanochromosomes and 43,194 predicted genes, with the majority of these nanochromosomes containing tiny introns and harboring only one gene; (b) genomic comparisons between E. aediculatus and other reported spirotrichs indicate that average GC content and genome fragmentation levels exhibit interspecific variation, and chromosome breaking sites (CBSs) might be lost during evolution, resulting in the increase of multi-gene nanochromosome; (c) gene families associated with chitin metabolism and FoxO signaling pathway are expanded in E. aediculatus, suggesting their potential roles in environment adaptation and survival strategies of E. aediculatus; and (d) a programmed ribosomal frameshift (PRF) with a conservative motif 5'-AAATAR-3' tends to occur in longer genes with more exons, and PRF genes play an important role in many cellular regulation processes. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-023-00175-0.

Morphology, cell division, and phylogeny of Notohymena antarctica Foissner, 1996 and Engelmanniella mobilis (Engelmann, 1862) Foissner, 1982 (Ciliophora, Hypotrichia).

The morphogenesis of two hypotrich ciliates, Notohymena antarctica Foissner, 1996 and Engelmanniella mobilis (Engelmann, 1862) Foissner, 1982, were investigated using protargol staining. The main events of the oxytrichid Notohymena antarctica during binary fission are as follows: (1) the oral primordium of the opisthe is formed apokinetally left of transverse cirrus II/1; (2) six streaks of frontal-ventral-transverse cirral anlagen are segmented in the ordinary pattern 1: 3: 3: 3: 4: 4 from left to right, which form three frontal, four frontoventral, one buccal, three ventral, two pretransverse ventral and five transverse cirri; (3) marginal anlagen are formed intrakinetally and the right marginal anlagen develop much earlier than those on the left. Phylogenetic analyses based on SSU rDNA sequence data indicate that Notohymena is monophyletic. A remarkable morphogenetic feature in E. mobilis is the mode of formation of the right marginal rows. In this paper, we clarified that the right marginal anlagen of E. mobilis are formed and develop to the right of the parental outer right marginal row, and that the grandparental (inner) right marginal row and great-grand parental (the outermost) left marginal row are resorbed. It is the first time to report a population of E. mobilis with comprehensive information, i.e. the morphology, ontogeny and molecular sequence.

Morphogenesis and molecular phylogeny of a freshwater ciliate, Oxytricha multilineata n. sp. (Ciliophora, Hypotrichia).

The morphology, morphogenesis, and molecular phylogeny of a new oxytrichid ciliate, Oxytricha multilineata n. sp. isolated from a tributary of the YuYao River, Ningbo, China, were investigated. Oxytricha multilineata n. sp. is characterized as follows: body size about 85-110 × 30-40 µm in vivo; 18 frontoventral-transverse cirri; paroral distinctly bipartite; seven dorsal kineties with cilia about 18 µm long; two macronuclear nodules and two micronuclei. The main events during morphogenesis follow a typical Oxytricha pattern with two exceptions: (1) only one anlage is formed initially within parental dorsal kineties 1-3, each of which then divides and is distributed into the two filial products, that is, the dorsal kineties anlagen are formed in primary mode; (2) dorsal kineties 3 and 4 are formed by incomplete fragmentation. Phylogenetic analyses based on SSU rDNA sequence data reveal that O. multilineata n. sp. clusters with Oxytricha lithofera, Heterourosomoida lanceolata and Quadristicha setigera, and species of the genus Oxytricha did not form a monophyletic group, however nodal support is not sufficiently high to recover a robust phylogeny of the Oxytrichidae.

Taxonomy and SSU rDNA-Based Phylogeny of Two Heterotrich Ciliates (Ciliophora, Heterotrichea) Collected From Subtropical Wetlands of China, Including the Description of a New Species, Linostomella pseudovorticella n. sp.

The Heterotrichea Stein, 1859 are a group of ciliated protists (single-celled eukaryotes) that occur in a wide variety of aquatic habitat where they play important roles in the flow of nutrients and energy within the microbial food web. Many species are model organisms for research in cytology and regenerative biology. In the present study, the morphology and phylogeny of two heterotrich ciliates, namely, Linostomella pseudovorticella n. sp. and Peritromus kahli Villeneuve-Brachon, 1940, collected from subtropical wetlands of China, were investigated using morphological and molecular methods. L. pseudovorticella n. sp. differs from its only known congener, Linostomella vorticella Ehrenberg, 1833 Aescht in Foissner et al., 1999, by having more ciliary rows (48-67, mean about 56 vs. 26-51, mean about 42) and its small-subunit (SSU) rDNA sequence, which shows a 15-bp divergence. Although P. kahli has been reported several times in recent decades, its infraciliature has yet to be described. A redescription and improved diagnosis of this species based on a combination of previous and present data are here supplied. Phylogenetic analyses based on SSU rDNA sequences revealed that the genus Linostomella is positioned within Condylostomatidae, and Peritromidae is sister to Climacostomidae with relatively low support, and the family Spirostomidae is the root branch of the class Heterotrichea.

[Distribution Characteristics of Microplastics in Surface Water and Sediments of Haizhou Bay, Lianyungang].

In recent years, microplastics have emerged as a new marine pollutant and have attracted wide research attention. As the main activity areas of human beings in the coastal environment, gulfs have always been the hotspots of marine pollution. However, the distribution of microplastics in most small and medium-sized coastal environments has been rarely reported in China. To understand the characteristics of microplastic pollution in small and medium-sized inshore bays in China, the main types, abundance, and spatial distribution characteristics of microplastics in the surface water and sediments in Haizhou Bay of Jiangsu province were studied by qualitative and quantitative methods. The results showed that the abundances of microplastics in the surface water and sediments of Haizhou Bay were (2.60±1.40) n·m-3 and (0.33±0.26) n·g-1, respectively. In the domestic offshore environment, the abundance of microplastics was at a low level in the surface water, but at a high level in the sediments in Haizhou Bay (0.33-545.00 n·m-3 and 0.07-2.58 n·g-1, respectively). The range of size distribution of microplastics in water and sediments was 0.08-13.48 mm and 0.04-14.74 mm, respectively. More than 60% of the microplastics in water and sediments were small particles of sizes less than 2.00 mm. The shape of microplastics in Haizhou Bay was mainly fibrous, accounting for 92%. The main colors were blue and black, accounting for 70%. The materials were mainly man-made fibers and PET, accounting for 79.4%. There was a significant correlation between the distribution of microplastics in surface water and suspended matter concentration (P<0.05). The distribution of microplastics in sediments was affected by many factors, and its distribution pattern between the distribution of microplastics in surface water and the distribution of particle size in sediments was quite different. Through analysis of the morphological characteristics and composition of microplastics, the results showed that the microplastics in Haizhou Bay mainly come from mariculture and coastal land sources.