Reduced compounds fuel the productivity of deep-sea chemosynthetic ecosystems, yet how animals locate these patchy, aphotic resources and aggregate to form ecological hotspots remains poorly understood. Here, we focus on the squat lobster Shinkaia crosnieri, a dominant species in chemosynthetic ecosystems of the northwestern Pacific, known for forming dense aggregations around reduced-compound emissions. By integrating controlled behavioral experiments with transcriptomic analyses, we explore how chemosensory mechanisms facilitate the formation of S. crosnieri aggregations, contributing to the development of deep-sea faunal hotspots. Behavioral experiments revealed a significant attraction of S. crosnieri for hydrogen sulfide (H₂S), a response abolished by antennule ablation, implicating antennules as key chemosensory organs. Transcriptomic profiling revealed antennule-specific enrichment in pathways related to membrane protein biosynthesis and environmental sensing. We identified 11 ionotropic receptors and 5 transient receptor potential channels expressed in S. crosnieri, with ScroIR8a and ScroTRPA pyrexia-like gene significantly upregulated upon H₂S exposure. These findings suggest that S. crosnieri utilizes an antennule-based chemosensory system to detect H2S cues, facilitating habitat localization and aggregation around active seepage zones. This study provides new insights into the molecular basis of chemosensory adaptation in deep-sea species and advances our understanding of faunal hotspot formation in chemosynthetic ecosystems.
Dissolved oxygen (DO) is a fundamental determinant in assessing the integrity and resilience of marine ecosystems. However, the influence of DO fluctuations on microbial community assembly, metabolic potentials, and interactions remain unresolved from the open ocean surface to the seafloor, especially in the Ninety East Ridge (NER) region of the southern Indian Ocean. Here, DO profiles from 30 to 1000 m water depths at six stations proximate to the NER were characterized. Three stations exhibited significantly lower DO concentrations at mesopelagic-to-bathypelagic depths, which was potentially modulated by the local topography. Comparative analyses of microbial taxonomic diversity and metabolic potential between lower DO and normal DO stations were conducted by integrating 16S rRNA gene sequencing and metagenomic profiling. Our results show distinct DO-driven shifts, with reduced metabolic diversity and enhanced heterotrophic pathways under lower DO. Co-occurrence network topology found prevalent positive interactions in normal DO communities versus more negative relationships under lower DO. Notably, sulfur oxidation and denitrification were tightly coupled, especially at depths with lower DO, with sulfur-oxidizing denitrifiers identified as key players mediating nitrogen and sulfur transformations. This study found that the NER’s topography shapes oxygen availability, which in turn structures microbial ecological strategies and biogeochemical transformations in the deep ocean.
Tetrahymena thermophila is one of the best-characterized unicellular eukaryotic models for investigating genome organization, chromatin biology, and epigenetic regulation. Over the past two decades, advances in genome sequencing and multi-omics have fundamentally reshaped the field, yielding increasingly comprehensive genomic resources that enable integrative analyses spanning linear genome sequences, chromatin states, and three-dimensional nuclear architecture. These studies have revealed distinct genome conformations between the transcriptionally active macronucleus (MAC) and transcriptionally silent micronucleus (MIC), including telomere-associated and promoter-centered folding in the MAC versus topologically associating domain (TAD)-like organization in the MIC. Concurrently, functional studies have elucidated epigenetic and chromatin-based mechanisms that coordinate transcription, genome stability, and nuclear differentiation, including DNA N6-methyladenine (6mA), chromatin remodeling, DNA repair, and small-RNA-guided programmed genome rearrangement during sexual development. In parallel, the ongoing expansion of genomic resources and experimental technologies has significantly broadened the molecular toolkit for functional and mechanistic dissection in Tetrahymena. Collectively, these advances establish Tetrahymena as a powerful and versatile model for probing genome plasticity, chromatin dynamics, epigenetic inheritance, and the evolutionary principles underlying eukaryotic genome regulation.
Shallow-water ascidians are invasive, fouling marine organisms that rapidly metamorphose from planktonic larvae to sessile forms. To gain insights into their environmental adaptability and develop methods for biofouling control, it is crucial to explore the molecular and cellular orchestration of metamorphosis. Here, we employed 4D label-free quantitative proteomics combined with transcriptomics to monitor protein and gene expression during ascidian Ciona metamorphosis across five post-embryonic stages. We identified a total of 6043 proteins. The temporal dynamics of protein and gene expression, along with differentially expressed proteins and genes, revealed biological processes associated with metamorphosis. We focused on phosphocreatine biosynthesis and protein secretion potentially involved in early metamorphosis, as well as cilium assembly/movement implicated in the regulation of juvenile physiology. We showed that several creatine kinases specifically expressed in larval tail muscles were up-regulated prior to metamorphosis, and phosphocreatine treatment significantly increased ATP levels and accelerated tail regression, suggesting that phosphocreatine shuttle system contributes to the initiation of metamorphosis. The secretory and extracellular matrix proteins up-regulated at pre-metamorphosis were revealed to be expressed by multiple tissues, including the nervous system, notochord, and epidermis; inhibition of the protein secretory pathway effectively reduced the proportion of larval adhesion and tail regression, highlighting the significance of extracellular proteins in larval settlement and metamorphosis. Moreover, the presence of systemic ciliary structures in various tissues/organs of juveniles supported the crucial role of cilium assembly/movement in the regulation of juvenile physiology. Overall, our study provides a valuable resource for investigating ascidian metamorphosis and contributes to a better understanding of its molecular basis.
Millions of individuals experience prolonged symptoms following the acute phase of SARS‐CoV‐2 infection, known as post-acute sequelae of COVID-19 (PASC), but the mechanistic basis remains poorly understood. In this study, we used single-cell RNA sequencing (scRNA-seq) to determine the immunological landscape of peripheral blood samples from patients with COVID-19 with viral persistence (VP) and pulmonary fibrosis (PF). In conjunction with B-cell receptor profiling and mass cytometry (CyTOF) analyses, we found that patients with VP had systemic inflammation and dysregulation of the innate immune cells, including global deficiency and dysfunction relating to antiviral activity, inflammatory responses, and antigen presentation. In contrast, molecular features were substantially different in patients with PF. Specifically, we observed evidence for an immune-megakaryocyte subpopulation expansion in patients with PF. The immune-megakaryocyte facilitated PF by expanding and reinforcing antigen-presenting activity, which emphasized the important role of antigen-presenting cells in PASC. Further, analyses demonstrated reduced T and B-cell immune activation in patients with VP and hyperactive CD4+ T and B-cell status in patients with PF. These findings illustrate the dynamic nature of both innate and adaptive immune responses during PASC development, explaining the underlying pathogenesis and illuminating potential therapeutic targets in PASC.
