Functional Ecology of Two Contrasting Freshwater Ciliated Protists in Relation to Temperature.
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ABSTRACT:
SUBMITTER: Lu X
PROVIDER: S-EPMC8044924 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Many marine microbial eukaryotes combine photosynthetic with phagotrophic nutrition, but incomplete understanding of such mixotrophic protists, their functional diversity, and underlying physiological mechanisms limits the assessment and modeling of their roles in present and future ocean ecosystems. We developed an experimental system to study responses of mixotrophic protists to availability of living prey and light, and used it to characterize contrasting physiological strategies in two stramenopiles in the genus Ochromonas. We show that oceanic isolate CCMP1393 is an obligate mixotroph, requiring both light and prey as complementary resources. Interdependence of photosynthesis and heterotrophy in CCMP1393 comprises a significant role of mitochondrial respiration in photosynthetic electron transport. In contrast, coastal isolate CCMP2951 is a facultative mixotroph that can substitute photosynthesis by phagotrophy and hence grow purely heterotrophically in darkness. In contrast to CCMP1393, CCMP2951 also exhibits a marked photoprotection response that integrates non-photochemical quenching and mitochondrial respiration as electron sink for photosynthetically produced reducing equivalents. Facultative mixotrophs similar to CCMP2951 might be well adapted to variable environments, while obligate mixotrophs similar to CCMP1393 appear capable of resource efficient growth in oligotrophic ocean environments. Thus, the responses of these phylogenetically close protists to the availability of different resources reveals niche differentiation that influences impacts in food webs and leads to opposing carbon cycle roles.
| S-EPMC7065223 | biostudies-literature
Project description:Simple sequence repeats (SSRs) are prevalent in the genomes of all organisms. They are widely used as genetic markers, and are insertion/deletion mutation hotspots, which directly influence genome evolution. However, little is known about such important genomic components in ciliated protists, a large group of unicellular eukaryotes with extremely long evolutionary history and genome diversity. With recent publications of multiple ciliate genomes, we start to get a chance to explore perfect SSRs with motif size 1-100 bp and at least three motif repeats in nine species of two ciliate classes, Oligohymenophorea and Spirotrichea. We found that homopolymers are the most prevalent SSRs in these A/T-rich species, with AAA (lysine, charged amino acid; also seen as an SSR with one-adenine motif repeated three times) being the codons repeated at the highest frequencies in coding SSR regions, consistent with the widespread alveolin proteins rich in lysine repeats as found in Tetrahymena. Micronuclear SSRs are universally more abundant than the macronuclear ones of the same motif-size, except for the 8-bp-motif SSRs in extensively fragmented chromosomes. Both the abundance and A/T content of SSRs decrease as motif-size increases, while the abundance is positively correlated with the A/T content of the genome. Also, smaller genomes have lower proportions of coding SSRs out of all SSRs in Paramecium species. This genome-wide and cross-species analysis reveals the high diversity of SSRs and reflects the rapid evolution of these simple repetitive elements in ciliate genomes.
| S-EPMC7285179 | biostudies-literature
Project description:Forming cysts is a common and important bionomic strategy for microorganisms to persist in harsh environments. In ciliated protists, many species have been reported to form cysts when facing unfavorable conditions. Despite traditional studies on the morphological features of cysts and the chemical composition of cyst wall, recent research has focused more on the molecular mechanisms of encystment. The present work reviews studies on developmental features and molecular information of resting cysts in ciliates, and pays more attention to the following questions: what are the inducing factors of encystment and excystment? How does the cell change morphologically during these dynamic processes? And what molecular mechanisms underlie those changes? We also present and summarize the characteristics of cysts from diverse ciliate lineages in a phylogenetic framework, aiming to provide new perspectives for studies on adaptive evolution of unicellular eukaryotes.
| S-EPMC8891572 | biostudies-literature
Project description:BackgroundCiliated protists are a widely distributed, morphologically diverse, and genetically heterogeneous group of unicellular organisms, usually known for containing two types of nuclei: a transcribed polyploid macronucleus involved in gene expression and a silent diploid micronucleus responsible for transmission of genetic material during sexual reproduction and generation of the macronucleus. Although studies in a few species of culturable ciliated protists have revealed the highly dynamic nature of replicative and recombination events relating the micronucleus to the macronucleus, the broader understanding of the genomic diversity of ciliated protists, as well as their phylogenetic relationships and metabolic potential, has been hampered by the inability to culture numerous other species under laboratory conditions, as well as the presence of symbiotic bacteria and microalgae which provide a challenge for current sequencing technologies. Here, we optimized single-cell sequencing methods and associated data analyses, to effectively remove contamination by commensal bacteria, and generated high-quality genomes for a number of Euplotia species.ResultsWe obtained eight high-quality Euplotia genomes by using single-cell genome sequencing techniques. The genomes have high genomic completeness, with sizes between 68 and 125 M and gene numbers between 14K and 25K. Through comparative genomic analysis, we found that there are a large number of gene expansion events in Euplotia genomes, and these expansions are closely related to the phenotypic evolution and specific environmental adaptations of individual species. We further found four distinct subgroups in the genus Euplotes, which exhibited considerable genetic distance and relative lack of conserved genomic syntenies. Comparative genomic analyses of Uronychia and its relatives revealed significant gene expansion associated with the ciliary movement machinery, which may be related to the unique and strong swimming ability.ConclusionsWe employed single-cell genomics to obtain eight ciliate genomes, characterized the underestimated genomic diversity of Euplotia, and determined the divergence time of representative species in this subclass for the first time. We also further investigated the extensive duplication events associated with speciation and environmental adaptation. This study provides a unique and valuable resource for understanding the evolutionary history and genetic diversity of ciliates.
| S-EPMC8670190 | biostudies-literature
Project description:Seasonal community dynamics of microbial eukaryotes in freshwater deep lakes
| PRJEB37597 | ENA
Project description:BackgroundEncystment 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.ResultsHere, 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.ConclusionsWe 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.
| S-EPMC10946202 | biostudies-literature
Project description:Gene-sized chromosomes are a distinct feature of the macronuclear genome in ciliated protists known as spirotrichs. These nanochromosomes are often only several kilobase pairs long and contain a coding region for a single gene. However, the ways in which transcription is regulated on nanochromosomes is still largely unknown. Here, we generated macronuclear genome assemblies for two species of Pseudokeronopsis ciliates to better understand transcription regulation on gene-sized chromosomes. We searched within the short subtelomeric regions for potential cis-regulatory elements and identified distinct AT-rich sequences conserved in both species, at both the 5' and 3' end of each gene. We further acquired transcriptomic data for these species, which showed the 5' cis-regulatory element is associated with active gene expression. Gene family evolution analysis suggests nanochromosomes in spirotrichs may originated approximately 900 million years ago. Together our comparative genomic analyses reveal novel insights into the biological roles of cis-regulatory elements on gene-sized chromosomes.
| S-EPMC8899921 | biostudies-literature
Project description:Habitat fragmentation impacts the distribution of genetic diversity and population genetic structure. Therefore, protecting the evolutionary potential of species, especially in the context of the current rate of human-induced environmental change, is an important goal. In riverine ecosystems, migration barriers affect the genetic structure of native species, while also influencing the spread of invasive species. In this study, we compare genetic patterns of two native and one highly invasive riverine fish species in a Belgian river basin, namely the native three-spined stickleback (Gasterosteus aculeatus) and stone loach (Barbatula barbatula), and the non-native and invasive topmouth gudgeon (Pseudorasbora parva). We aimed to characterize both natural and anthropogenic determinants of genetic diversity and population genetic connectivity. Genetic diversity was highest in topmouth gudgeon, followed by stone loach and three-spined stickleback. The correlation between downstream distance and genetic diversity, a pattern often observed in riverine systems, was only marginally significant in stone loach and three-spined stickleback, while genetic diversity strongly declined with increasing number of barriers in topmouth gudgeon. An Isolation-By-Distance pattern characterizes the population genetic structure of each species. Population differentiation was only associated with migration barriers in the invasive topmouth gudgeon, while genetic composition of all species seemed at least partially determined by the presence of migration barriers. Among the six barrier types considered (watermills, sluices, tunnels, weirs, riverbed obstructions, and others), the presence of watermills was the strongest driver of genetic structure and composition. Our results indicate that conservation and restoration actions, focusing on conserving genetic patterns, cannot be generalized across species. Moreover, measures might target either on restoring connectivity, while risking a rapid spread of the invasive topmouth gudgeon, or not restoring connectivity, while risking native species extinction in upstream populations.
| S-EPMC9753842 | biostudies-literature
Project description:BackgroundLow temperature (LT) stress is one of the major environmental stress factors affecting the growth and yield of maize (Zea mays L.). Hence, it is important to unravel the molecular mechanisms behind LT stress tolerance to improve molecular breeding in LT tolerant genotypes. In the present study, two maize genotypes viz. Gurez local from Kashmir Himalaya and tropical grown GM6, were dissected for their LT stress response in terms of accumulation of differentially regulated proteins (DRPs). Leaf proteome analysis at three-leaf stage of maize seedlings subjected to LT stress of 6 °C for a total of 12 h duration was performed using two dimensional gel electrophoresis (2D-PAGE) followed by subsequent identification of the proteins involved.ResultsAfter MALDI-TOF (Matrix-assisted laser desorption/ionization-time of flight) and bioinformatics analysis, 19 proteins were successfully identified in Gurez local, while as 10 proteins were found to get successful identification in GM6. The interesting observations from the present investigation is the identification of three novel proteins viz. threonine dehydratase biosynthetic chloroplastic, thylakoidal processing peptidase 1 chloroplastic, and nodulin-like protein, whose role in abiotic stress tolerance, in general, and LT stress, in particular, has not been reported so far. It is important to highlight here that most of LT responsive proteins including the three novel proteins were identified from Gurez local only, owing to its exceptional LT tolerance. From the protein profiles, obtained in both genotypes immediately after LT stress perception, it was inferred that stress responsive protein accumulation and their expression fashion help the Gurez local in seedling establishment and withstand unfavorable conditions as compared to GM6. This was inferred from the findings of pathway enrichment analysis like regulation of seed growth, timing of floral transition, lipid glycosylation, and aspartate family amino acid catabolic processes, besides other key stress defense mechanisms. However, in GM6, metabolic pathways enriched were found to be involved in more general processes including cell cycle DNA replication and regulation of phenylpropanoid metabolism. Furthermore, majority of the qRT-PCR results of the selected proteins demonstrated positive correlation between protein levels and transcript abundance, thereby strengthening our findings.ConclusionsIn conclusion, our findings reported majority of the identified proteins in Gurez local exhibiting up-regulated pattern under LT stress as compared to GM6. Furthermore, three novel proteins induced by LT stress were found in Gurez local, requiring further functional validation. Therefore, our results offer more insights for elucidating the molecular networks mediating LT stress tolerance in maize.
| S-EPMC10074880 | biostudies-literature
Project description:This first comprehensive analysis of the global biogeography of marine protistan plankton with acquired phototrophy shows these mixotrophic organisms to be ubiquitous and abundant; however, their biogeography differs markedly between different functional groups. These mixotrophs, lacking a constitutive capacity for photosynthesis (i.e. non-constitutive mixotrophs, NCMs), acquire their phototrophic potential through either integration of prey-plastids or through endosymbiotic associations with photosynthetic microbes. Analysis of field data reveals that 40-60% of plankton traditionally labelled as (non-phototrophic) microzooplankton are actually NCMs, employing acquired phototrophy in addition to phagotrophy. Specialist NCMs acquire chloroplasts or endosymbionts from specific prey, while generalist NCMs obtain chloroplasts from a variety of prey. These contrasting functional types of NCMs exhibit distinct seasonal and spatial global distribution patterns. Mixotrophs reliant on 'stolen' chloroplasts, controlled by prey diversity and abundance, dominate in high-biomass areas. Mixotrophs harbouring intact symbionts are present in all waters and dominate particularly in oligotrophic open ocean systems. The contrasting temporal and spatial patterns of distribution of different mixotroph functional types across the oceanic provinces, as revealed in this study, challenges traditional interpretations of marine food web structures. Mixotrophs with acquired phototrophy (NCMs) warrant greater recognition in marine research.
| S-EPMC5563798 | biostudies-literature