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One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid–liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.Ribosome biogenesis, including ribosomal RNA (rRNA) production, occurs in the nucleolus. Recent studies have revealed how the integrity and copy number of rRNA genes is maintained through a unique recombination system, how rRNA transcription is regulated and how phase separation orchestrates nucleolus function.

Tetrahymenosis, caused by about 10 Tetrahymena species, is an emerging problem inflicting a significant economic loss on the aquaculture industry worldwide. However, in the order Tetrahymenida, there are many unresolved evolutionary relationships among taxa. Here we report 21 new sequences, including SSU‐rRNA, ITS1‐5.8S‐ITS2 rRNA and LSU‐rRNA, genes of 10 facultative parasitic Tetrahymena associated with tetrahymenosis, and conduct phylogenetic analyses based on each individual gene and a three‐gene concatenated dataset. The main findings are: (1) All the parasitic and facultative parasitic species cluster in borealis group. (2) With the addition of new sequences, Tetrahymena is still divided into three groups, namely the “borealis group”, the “australis group,” and the “paravorax group.” (3) the cluster pattern of all the newly sequenced facultative parasitic Tetrahymena species shows that members of the “borealis” group may be more susceptible to parasitism. (4) phylogeny based on concatenated genes show that T. pyriformis, T. setosa, and T. leucophrys have close relationship. (1) All the parasitic and facultative parasitic species cluster in borealis group. (2) With the addition of new sequences, Tetrahymena is still divided into three groups, namely the “borealis group,” the “australis group,” and the “paravorax group.” (3) the cluster pattern of all the newly sequenced facultative parasitic Tetrahymena species shows that members of the “borealis” group may be more susceptible to parasitism. (4) phylogeny based on concatenated genes show that T. pyriformis, T. setosa, and T. leucophrys have close relationship.

In the class Colpodea, there are many unresolved evolutionary relationships among taxa. Here, we report 30 new sequences including SSU‐rRNA, ITS1‐5.8S‐ ITS2 rRNA, and the mitochondrial small subunit ribosomal RNA (mtSSU‐rRNA) genes of five colpodeans, and conduct phylogenetic analyses based on each individual gene and a two‐gene concatenated dataset. For the first time, multi‐genes were used to analyze phylogenetic relationships in the class Colpodea. The main findings are: (1) SSU‐rRNA, ITS1‐5.8S‐ ITS2 rRNA, and mtSSU‐rRNA gene sequences of C. reniformis and C. grandis are provided for the first time, and these two species group into the clade including C. inflata, C. lucida, C. cucullus, and C. henneguyi; (2) clustering pattern and morphological similarity indicate that Bresslauides discoideus has a close relation with Colpodidae spp.; (3) Emarginatophrya genus diagnosis is improved to be ‘Hausmanniellidae with sharply shortened and isometric leftmost 1‐4 ciliary rows’ and Colpoda elliotti is transferred to Emarginatophrya; (4) the genus Colpoda is still non‐monophyletic with the addition of 10 populations from five Colpoda species sequences, but there are only two Colpoda groups left based on the present work: Group I comprises C. inflata, C. lucida, C. cucullus, C. henneguyi, C. reniformis, and C. grandis, Group II comprises C. maupasi and C. ecaudata, and the presence of diagonal grooves and the way the vestibular opens might be the two key features that differentiates Colpoda species groups; (5) a close molecular relationship, and highly similar merotelokinetal mode, somatic ciliary pattern, and basic organization of the oral apparatus with P. steinii suggests Bromeliothrix metopoides should be temporarily assigned to Colpodidae. In the class Colpodea, there are many unresolved evolutionary relationships among taxa. Here, we report 30 new sequences, including SSU‐rRNA, ITS1‐5.8S‐ ITS2 rRNA, and the mitochondrial small subunit ribosomal RNA (mtSSU‐rRNA) genes of five colpodeans, and conduct phylogenetic analyses based on each individual gene and a two‐gene concatenated dataset. For the first time, multi‐genes were used to analyze phylogenetic relationships in the class Colpodea.

Background Accurate identification of bacterial communities is crucial for research applications, diagnostics, and clinical interventions. Although 16S ribosomal RNA (rRNA) gene sequencing is a widely employed technique for bacterial taxonomic classification, it often results in misclassified or unclassified bacterial taxa. This study sought to refine the full-length 16S rRNA gene sequencing protocol using the MinION sequencer, focusing on the V1–V9 regions. Our methodological enquiry examined several factors, including the number of PCR amplification cycles, choice of primers and Taq polymerase, and specific sequence databases and workflows employed. We used a microbial standard comprising eight bacterial strains (five gram-positive and three gram-negative) in known proportions as a validation control. Results Based on the MinION protocol, we employed the microbial standard as the DNA template for the 16S rRNA gene amplicon sequencing procedure. Our analysis showed that an elevated number of PCR amplification cycles introduced PCR bias, and the selection of Taq polymerase and primer sets significantly affected the subsequent analysis. Bacterial identification at genus level demonstrated Pearson correlation coefficients ranging from 0.73 to 0.79 when assessed using BugSeq, Kraken-Silva and EPI2ME-16S workflows. Notably, the EPI2ME-16S workflow exhibited the highest Pearson correlation with the microbial standard, minimised misclassification, and increased alignment accuracy. At the species taxonomic level, the BugSeq workflow was superior, with a Pearson correlation coefficient of 0.92. Conclusions These findings emphasise the importance of careful selection of PCR settings and a well-structured analytical framework for 16S rRNA full-length gene sequencing. The results showed a robust correlation between the predicted and observed bacterial abundances at both the genus and species taxonomic levels, making these findings applicable across diverse research contexts and with clinical utility for reliable pathogen identification.

Although experiments show a positive association between vascular plant and arbuscular mycorrhizal fungal (AMF) species richness, evidence from natural ecosystems is scarce. Furthermore, there is little knowledge about how AMF richness varies with belowground plant richness and biomass. We examined relationships among AMF richness, above‐ and belowground plant richness, and plant root and shoot biomass in a native North American grassland. Root‐colonizing AMF richness and belowground plant richness were detected from the same bulk root samples by 454‐sequencing of the AMF SSU rRNA and plant trnL genes. In total we detected 63 AMF taxa. Plant richness was 1.5 times greater belowground than aboveground. AMF richness was significantly positively correlated with plant species richness, and more strongly with below‐ than aboveground plant richness. Belowground plant richness was positively correlated with belowground plant biomass and total plant biomass, whereas aboveground plant richness was positively correlated only with belowground plant biomass. By contrast, AMF richness was negatively correlated with belowground and total plant biomass. Our results indicate that AMF richness and plant belowground richness are more strongly related with each other and with plant community biomass than with the plant aboveground richness measures that have been almost exclusively considered to date.

Symbioses between nitrogen (N) 2 —fixing prokaryotes and photosynthetic eukaryotes are important for nitrogen acquisition in N-limited environments. Recently, a widely distributed planktonic uncultured nitrogen-fixing cyanobacterium (UCYN-A) was found to have unprecedented genome reduction, including the lack of oxygen-evolving photosystem II and the tricarboxylic acid cycle, which suggested partnership in a symbiosis. We showed that UCYN-A has a symbiotic association with a unicellular prymnesiophyte, closely related to calcifying taxa present in the fossil record. The partnership is mutualistic, because the prymnesiophyte receives fixed N in exchange for transferring fixed carbon to UCYN-A. This unusual partnership between a cyanobacterium and a unicellular alga is a model for symbiosis and is analogous to plastid and organismal evolution, and if calcifying, may have important implications for past and present oceanic N 2 fixation.

Background Microbiome studies often involve sequencing a marker gene to identify the microorganisms in samples of interest. Sequence classification is a critical component of this process, whereby sequences are assigned to a reference taxonomy containing known sequence representatives of many microbial groups. Previous studies have shown that existing classification programs often assign sequences to reference groups even if they belong to novel taxonomic groups that are absent from the reference taxonomy. This high rate of “over classification” is particularly detrimental in microbiome studies because reference taxonomies are far from comprehensive. Results Here, we introduce IDTAXA, a novel approach to taxonomic classification that employs principles from machine learning to reduce over classification errors. Using multiple reference taxonomies, we demonstrate that IDTAXA has higher accuracy than popular classifiers such as BLAST, MAPSeq, QIIME, SINTAX, SPINGO, and the RDP Classifier. Similarly, IDTAXA yields far fewer over classifications on Illumina mock microbial community data when the expected taxa are absent from the training set. Furthermore, IDTAXA offers many practical advantages over other classifiers, such as maintaining low error rates across varying input sequence lengths and withholding classifications from input sequences composed of random nucleotides or repeats. Conclusions IDTAXA’s classifications may lead to different conclusions in microbiome studies because of the substantially reduced number of taxa that are incorrectly identified through over classification. Although misclassification error is relatively minor, we believe that many remaining misclassifications are likely caused by errors in the reference taxonomy. We describe how IDTAXA is able to identify many putative mislabeling errors in reference taxonomies, enabling training sets to be automatically corrected by eliminating spurious sequences. IDTAXA is part of the DECIPHER package for the R programming language, available through the Bioconductor repository or accessible online ( http://DECIPHER.codes ).

Soil biota play key roles in the functioning of terrestrial ecosystems, however, compared to our knowledge of above-ground plant and animal diversity, the biodiversity found in soils remains largely uncharacterized. Here, we present an assessment of soil biodiversity and biogeographic patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system harbours large amounts of undescribed soil biodiversity. Despite high variability across the Park, below-ground diversity patterns were predictable based on soil characteristics, with prokaryotic and eukaryotic communities exhibiting overlapping biogeographic patterns. Further, Central Park soils harboured nearly as many distinct soil microbial phylotypes and types of soil communities as we found in biomes across the globe (including arctic, tropical and desert soils). This integrated cross-domain investigation highlights that the amount and patterning of novel and uncharacterized diversity at a single urban location matches that observed across natural ecosystems spanning multiple biomes and continents.

Oxygen minimum zones, also known as oceanic \"dead zones,\" are widespread oceanographic features currently expanding because of global warming. Although inhospitable to metazoan life, they support a cryptic microbiota whose metabolic activities affect nutrient and trace gas cycling within the global ocean. Here, we report metagenomic analyses of a ubiquitous and abundant but uncultivated oxygen minimum zone microbe (SUP05) related to chemoautotrophic gill symbionts of deep-sea clams and mussels. The SUP05 metagenome harbors a versatile repertoire of genes mediating autotrophic carbon assimilation, sulfur oxidation, and nitrate respiration responsive to a wide range of water-column redox states. Our analysis provides a genomic foundation for understanding the ecological and biogeochemical role of pelagic SUP05 in oxygen-deficient oceanic waters and its potential sensitivity to environmental changes.

Although the molecular phylogeny, evolution and biodiversity of arbuscular mycorrhizal fungi (AMF) are becoming clearer, phylotaxonomically reliable sequence data are still limited. To fill this gap, a data set allowing resolution and environmental tracing across all taxonomic levels is provided. Two overlapping nuclear DNA regions, totalling c. 3 kb, were analysed: the small subunit (SSU) rRNA gene (up to 1800 bp) and a fragment spanning c. 250 bp of the SSU rDNA, the internal transcribed spacer (ITS) region (c. 475–520 bp) and c. 800 bp of the large subunit (LSU) rRNA gene. Both DNA regions together could be analysed for 35 described species, the SSU rDNA for c. 76 named and 18 as yet undefined species, and the ITS region or LSU rDNA, or a combination of both, for c. 91 named and 16 as yet undefined species. Present phylogenetic analyses, based on the three rDNA markers, provide reliable and robust resolution from phylum to species level. Altogether, 109 named species and 27 cultures representing as yet undefined species were analysed. This study provides a reference data set for molecular systematics and environmental community analyses of AMF, including analyses based on deep sequencing.