Marine Life Science & Technology最新文献

Marine heterotrophic prokaryotes initially release extracellular enzymes to cleave large organic molecules and then take up ambient substrates via transporters. Given the direct influence of extracellular enzymes on nutrient availability, understanding their diversity and dynamics is crucial in comprehending microbial interactions and organic matter cycling in aquatic ecosystems. In this study, metagenomics was employed to investigate the functional diversity and dynamics of extracellular enzymes and transporters in coastal waters over a 22-day period. The metagenome-derived gene pool of organic matter-degrading secretory enzymes and transporters was primarily contributed by three major bacterial classes. Bacteroidota were the primary contributors to the gene pool of secretory carbohydrate-active enzymes (CAZymes), whereas Gammaproteobacteria contribute more to secretory peptidases and TonB-dependent transporters (TBDTs), and Alphaproteobacteria to ATP-binding cassette (ABC) transporters. The distinct substrate targets of the enzymes and transporters combined with the unique dynamics of these taxa across depth layers suggest that organic matter degradation and uptake machinery played a role in ecological niche partitioning. At the community level, the abundance of TBDT genes was more positively correlated with extracellular enzymes than ABC transporters. To further explore taxon-specific differences, we reconstructed 163 bacterial and archaeal metagenome-assembled genomes (MAGs). Correlation patterns at the MAG level varied across taxa: Bacteroidota MAGs exhibited significant positive correlations between TBDTs and extracellular enzymes, whereas Gammaproteobacteria and Alphaproteobacteria MAGs showed weak or no significant correlations. These results suggest the diversity of ecological strategies among marine heterotrophic bacteria and highlight a potential coregulation or functional linkage between extracellular enzymes and TBDTs in the metabolism of marine heterotrophic prokaryotes. Our study advances the understanding of the microbial adaptations driving carbon and nutrient cycling.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-025-00314-9.

Anaerobic ammonium oxidation (anammox) plays a critical role in nitrogen loss in estuarine and marine environments. However, the mechanisms underlying the formation and maintenance of the anammox bacterial community remain unclear. This study analyzed the anammox bacterial diversity, community structure, and interspecific relationships in three estuaries along the Chinese coastline -the Changjiang Estuary (CJE), the Oujiang Estuary (OJE), and the Jiulong River Estuary (JLE) - as well as the South China Sea (SCS) to elucidate their community assembly mechanisms. The results indicated that the anammox bacterial community exhibited the highest ammonium concentration as well as the Shannon's diversity index reflecting both species richness and evenness in the JLE. The lowest Shannon index was observed in the SCS. However, the anammox bacterial species richness was greatest in the CJE. Candidatus Scalindua was the predominant anammox bacteria identified in the coastal sediments, especially in the SCS sediments. Candidatus Brocadia and Candidatus Kuenenia were more abundant in the estuarine sediments, particularly in JLE, than in the SCS. Phylogenetic analysis revealed distinct differentiation among Candidatus Scalindua, Candidatus Brocadia, and Candidatus Kuenenia, with the former exhibiting a greater level of diversity. There was significant spatial heterogeneity in the anammox bacteria across the four regions, characterized by distinct distribution patterns for rare species. Low-abundance (rare) bacteria thrived in their native habitats, whereas abundant taxa displayed greater dispersal capabilities. An analysis of the community assembly mechanism suggested that ecological drift predominantly shaped the overall anammox bacterial community in the coastal sediments. Rare species were more susceptible to dispersal limitations and environmental selection. Co-occurrence network analysis identified Candidatus Scalindua as a keystone genus and highlighted that rare species may play a crucial role in maintaining the ecological stability of the anammox bacterial community in coastal sediments.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-025-00315-8.

Microhabitat heterogeneity results in significant variations in the thermal environment on a small spatial scale, leading to different intensities of cold stress during extreme low-temperature events. Investigating variations in body temperature and metabolomic responses of organisms inhabiting different microhabitats emerges as an important task for understanding how organisms respond to more frequent extreme low-temperature events in the face of climate change. In the present study, we measured substrate temperature, air temperature, wind speed, light intensity, and body temperature to evaluate the relative importance of drivers that affect body temperature in different microhabitats, and determined the metabolomic responses of intertidal snails Littorina brevicula and limpets Cellana toreuma from different microhabitats (snail: exposed vs. shaded rock; limpet, rock vs. tidal pool) during extreme low-temperature event in winter. Results showed that microhabitat type, substrate temperature, air temperature, wind speed, and light intensity contribute notably to the body temperatures. During extreme low-temperature events, mollusks collected from different microhabitats exhibited microhabitat-specific metabolomic responses that are associated with cellular stress response, energy metabolism, immune response, nucleotide metabolism, and osmoregulation. These metabolic pathways were highly induced in the more exposed areas (exposed rock for snails and rocky environment for limpets). Notably, in different microhabitats, the metabolites enriched from these pathways showed significant correlations with microclimate environmental variables (i.e., substrate temperature, wind speed, and body temperature). Overall, these findings highlight the importance of microhabitat heterogeneity for intertidal species surviving extreme cold events and are essential for understanding cold adaptation of intertidal species in the context of climate change.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-025-00302-z.

Natural products are effective in the treatment and the prevention of human, animal and plant diseases. Therefore, natural products may also be considered to treat fish diseases. Acori Tatarinowii Rhizoma (ATR) is a herbal medicine with anti-inflammatory and antioxidant effects. However, little is known about how its active ingredients exert the beneficial effects. Here, Four effective active ingredients of ATR and their 81 targets were investigated, which affected the anti-inflammatory response. Among them, kaempferol-JUN was identified as a key regulatory module in anti-inflammatory immune responses, and kaempferol interacted with the CiJUN protein and inhibited CiJUN levels. Silencing CiJUN gene in Ctenopharyngodon idella kidney (CIK) cells enhanced anti-inflammatory activity and resistance to Aeromonas hydrophila, whereas anti-inflammatory activity and resistance were impaired after CiJUN overexpression. The mortality rate of diseased grass carp was reduced after treatment with kaempferol, as were the inflammatory and oxidant effects. Also, grass carp showed enhanced anti-inflammatory and antioxidant effects after feeding with kaempferol. The results provide further insights into the use of kaempferol to prevent and treat fish diseases.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-025-00304-x.

Glucocorticoids, crucial regulatory hormones involved in the stress response, significantly influence growth, development, and metabolism through activation of the glucocorticoid receptor (GR). Hypoxia-inducible factor 3 alpha (HIF-3α), the least characterized paralog among three HIF-α proteins, plays a role in adaptation to oxygen level changes and metabolic reprogramming. Despite the potential functional overlaps between GR and HIF-3α pathways in regulating metabolism, their crosstalk remains poorly understood. Here, we demonstrate a regulatory mechanism governing the crosstalk between these two transcription factor pathways. We found that upon ligand activation, GR binds to the intronic region of the HIF3A gene and upregulates its mRNA transcription. Additionally, HIF-3α and GR engage in protein-protein interactions through the oxygen-dependent degradation domain of HIF-3α and all major domains of GR (i.e. the N-terminal, DNA-binding, and ligand-binding domains). Furthermore, we discovered that this interaction results in reciprocal attenuation of the transcriptional activities of both GR and HIF-3α, causing a negative feedback loop upon HIF3A gene expression. The GR-HIF-3α interaction may offer a targetable pivot to modulate these two TF pathways, potentially providing a novel therapeutic avenue for related diseases.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-025-00306-9.

Urochordate Ciona spp. are ideal marine model organisms for studying embryogenesis and developmental and evolutionary biology. However, the effective implementation of genetic labeling and CRISPR/Cas9-based editing tools at cellular resolution remains challenging. This study successfully developed and validated a collection of Gateway-based vectors for cell labeling in Ciona spp. The destination vector sets contained two Gateway cassettes flanked by Minos sites, allowing the N- or C-terminal tagging of a protein of interest with various fluorescent markers. In addition, we optimized the CRISPR/Cas9 and CRISPR/dCas9 systems by incorporating P2A-mCherry, a fluorescent indicator for Cas9 expression at cellular resolution. We demonstrated the effective destruction or inhibition of target genes when CRISPR constructs were introduced into fertilized eggs. Furthermore, we engineered a dual fluorescence sensor system that helps visualize successful gene knockouts at the cellular level in specific tissues. The genetic tools developed in this study offer a robust method for gene expression, cell tracking, and subcellular protein localization while also facilitating tissue-specific functional analysis in Ciona embryos and other model systems.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-025-00300-1.

Although anisotropic NMR spectroscopy has emerged as a powerful method for determining the relative configuration of complex natural products, major challenges persist with structurally flexible molecules. In this study, we conducted a systematic comparative analysis of stereochemical elucidation, combining anisotropic NMR spectroscopy and density functional theory (DFT) calculations on spiroepicoccin B (1) and epicoccin V (2), which were characterized as thiodiketopiperazine marine natural products isolated from the deep-sea-derived fungus Epicoccum nigrum SD-388. For the flexible compound 2, we compared various conformational sampling approaches, including an assessment of the quality of relative energies within the obtained ensembles. We demonstrated the critical role of dispersion correction within DFT computations to precisely account for weak non-bonded intramolecular interactions. By integrating anisotropic NMR analysis, chemical shifts, electronic circular dichroism, and DFT computations, we determined the absolute configurations and conformational ensembles for 1 and 2, respectively, highlighting the significance of the intramolecular methyl-π interaction in stabilizing one of the conformers. Our study introduces new strategies to address conformational flexibility in the stereochemical elucidation of challenging organic molecules.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-025-00294-w.

The sea-land transition is one of the most dramatic evolutionary changes and requires an adaptive genetic response to salinity changes and osmotic stress. Here, we used multi-species genomes and multi-tissue transcriptomes of the talitrid crustaceans, a living sea-land transition model, to investigate the adaptive genetic changes and osmoregulatory organs that facilitated their salinity adaptation. Genomic analyses detected numerous osmoregulatory genes in terrestrial talitrids undergoing gene family expansions and positive selection. Gene expression comparisons among species and tissues confirmed the gill being the primary organ responsible for ion transport and identified the genetic expression variation that enable talitrids to adapt to marine and land habitats. V-type H⁺-ATPases related to H⁺ transport play a crucial role in land adaptations, while genes related to the transport of inorganic ions (Na⁺, K⁺, Cl^-) are upregulated in marine habitats. Our results demonstrate that talitrids have divergent genetic responses to salinity change that led to the uptake or excretion of ions in the gills and promoted habitat adaptation. These findings suggest that detecting gene expression changes in talitrids presents promising potential as a biomarker for salinity monitoring.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-025-00298-6.

Methanogenic endosymbionts are the only known intracellular archaeans and are especially common in anaerobic ciliated protists. Studies on the evolution of associations between anaerobic ciliates and their methanogenic endosymbionts offer an excellent opportunity to broaden our knowledge about symbiosis theory and adaptation of eukaryotes to anoxic environments. Here, the diversity of methanogenic endosymbionts was analyzed with the addition of nine anaerobic ciliate populations that were newly studied by various methods. Results showed that diverse anaerobic ciliates host methanogenic endosymbionts that are limited to a few genera in orders Methanomicrobiales, Methanobacteriales, and Methanosarcinales. For the first time, anaerobic ciliates of the classes Muranotrichea and Prostomatea were found to host methanogenic endosymbionts. Distinct origins of endosymbiosis were revealed for classes Armophorea and Plagiopylea. We posit that armophoreans and plagiopyleans might have harbored Methanoregula (order Methanomicrobiales) and Methanocorpusculum (order Methanomicrobiales), respectively, as methanogenic endosymbionts at the beginning of their evolution. Subsequently, independent endosymbiont replacement events occurred in methanogen-ciliate associations, probably due to ecological transitions, species radiation of ciliate hosts, and vertical transmission bottlenecks of endosymbionts. Our results shed light on the evolution of associations between anaerobic ciliates and methanogens, and identifies the necessary preconditions for illustrating mechanisms by which endosymbioses between these partners were established.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-025-00295-9.

The queen snapper (Etelis oculatus Valenciennes in Cuvier & Valenciennes, 1828) is a deep-sea snapper whose commercial importance continues to increase in the US Caribbean. However, little is known about the biology and ecology of this species. In this study, the presence of a fine-scale population structure and genetic diversity of queen snapper from Puerto Rico was assessed through 16,188 SNPs derived from the Restriction site Associated DNA Sequencing (RAD-Seq) technique. Summary statistics estimated low genetic diversity (HO = 0.333-0.264) and did not reveal population differentiation within our samples (F _ST = - 0.001-0.025). Principal component analysis and a model-based clustering method did not detect a fine-scale subpopulation structure among sampling sites, however, there was genetic variability within regions and sites. Our results have revealed comparable genetic and dispersal patterns to those observed in other shallow-water snapper species in Puerto Rico waters. It is crucial to further enhance our understanding of the ecological and biological aspect of the queen snapper to effectively manage and conserve this species as fishing pressure has been extended to deep water species in the US Caribbean.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-025-00289-7.