We described Leitoscoloplos fangchengensis sp. nov., a new species of orbiniid polychaete from Fangchenggang City, Guangxi Province, Beibu Gulf. The species differs from all congeners by the distinctive membranous pouches located below and posterior to neuropodial lobes on the last thoracic and abdominal chaetigers. We also re-examined material previously identified as Scoloplos marsupialis Southern, 1921 and found that these correspond to Leodamas weizhouensis Sun et al., 2022 and S. tumidus Mackie, 1991. A detailed redescription of S. tumidus Mackie, 1991 was here provided based on Chinese material, together with a table summarizing all known orbinid species bearing membranous pouches. With this study, we are contributing to clarify long-standing taxonomic confusion within Orbiniidae.

This study presents the complete mitogenome sequence of Atheraster arandae, providing valuable information for its genetic and taxonomic research. Through next-generation sequencing, we successfully obtained the complete mitogenome of A. arandae, with a length of 16,292 bp. The mitogenome consisted of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. Both Maximum Likelihood and Bayesian inference phylogenetic trees demonstrated that A. arandae clustered closely with Iconaster longimanus. By revealing its mitogenome and positioning its phylogenetic placement within the Goniasteridae lineage, this study provides insights into the phylogenetic context of A. arandae.

Coastal marine ecosystems in the Yellow and Bohai Seas face severe anthropogenic and environmental pressures, but macrobenthic biomonitoring is constrained by traditional survey methods. Here, we used eDNA metabarcoding targeting 18S rRNA and COI genes to systematically investigate macrobenthic diversity, spatial distribution, and environmental drivers at 18 sites during spring 2024. This study identified a total of 278 species, revealing a pronounced asymmetry between taxonomic richness and sequence richness. Annelida, particularly polychaetes, dominated species richness (40.65%), whereas crustacean arthropods accounted for the vast majority of sequence abundance (64.93%), highlighting the efficacy of eDNA in capturing active dynamics such as spring ecdysis. Alpha diversity showed no significant difference between the two seas due to strong hydrodynamic connectivity, yet beta diversity revealed substantial spatial heterogeneity, with regional clustering shaped by geographic barriers and water mass characteristics. Redundancy analysis identified bottom-water dissolved oxygen (DO) and nitrogen cycling dynamics (ammonia and nitrite) as primary environmental determinants driving community succession and niche partitioning of dominant taxa (e.g., Kamaka biwae and Hemigrapsus penicillatus ). Ultimately, these findings demonstrate the exceptional sensitivity and taxonomic resolution of eDNA metabarcoding for coastal biomonitoring, providing robust molecular evidence to support marine biodiversity conservation, habitat assessment, and ecosystem-based management.

The deep-sea supergiant isopod is renowned for surviving over 5 years without food, which is a crucial adaptive trait for megafauna inhabiting extreme environments. Here, morphological, physiological, and genomic comparisons of deep-sea isopods reveal a dual adaptive strategy underlying this trait: a distended, food-retentive stomach that enables episodic hyperphagia and a markedly reduced basal metabolic rate (BMR). Notably, central to this adaptation is the ancient horizontal acquisition of the microbial energy metabolism-related gene ND1, which thereafter achieved significant dosage enhancement via post-transfer duplication and ultra-high expression that is specifically regulated by histone acetylation at its promoter. Functional assays in transgenic zebrafish, nematodes, and cell lines demonstrate that ND1 reduces BMR by downregulating endogenous energy-production genes and thus extends starvation survival under cold-induced metabolic suppression. These findings uncover an exceptional evolutionary strategy whereby deep-sea megafauna co-opts and epigenetically optimizes exogenous microbial genes to reconcile the metabolic conflict between energy-demanding gigantism and extreme energy limitation.

The continental shelves of Yellow Sea and East China Sea harbor complex macrozoobenthic communities, and they are shaped by unique hydrographic features such as the Yellow Sea Cold Water Mass and the Kuroshio. To address the lack of full-coverage spatial baselines for these ecologically critical assemblages, we constructed a continental shelf-scale community distribution model (CDM). By integrating community point data from benthic trawl surveys conducted between 2000 and 2015 with benthic environmental data from Bio-ORACLE, we developed CDMs based on binomial generalized linear model (GLM) and multi-algorithm ensemble species distribution models (SDMs). Spatial probability distribution maps of communities were generated at a resolution of 0.5° and subsequently integrated into a comprehensive map of the most probable macrozoobenthic community distribution across the study area. The results indicate: (1) model predictions exhibit high consistency with observed distributions (GLM: 90.4

A poorly known callianassid ghost shrimp species, Praedatrypaea modesta (De Man, 1905), is redescribed and illustrated based on new material recently collected off the south coast of Hainan Island, northern continental shelf of the South China Sea. Genetic data were obtained and compared with other six congeners. With the inclusion of this species, the monophyly of Praedatrypaea Poore, Dworschak, Robles, Mantelatto & Felder, 2019 is reevaluated. The inferred phylogenetic trees, based on two matrices (4-gene and 21-gene), both support the monophyly of this genus and its placement as sister taxon to all other genera of Callianassidae Dana, 1852.

Abstract Animal mitochondrial rRNAs are commonly viewed as structurally reduced, yet sponge mt SSU rRNAs range from compact to highly expanded structures. Using nine conserved structural anchors, we compared 216 taxonomically resolved records from four classes and 22 orders, including 16 freshwater Spongillida and 200 marine sponges. Twelve homologous hypervariable substructures were coded as structural types, and their ordered combinations as composite types. We identified 38 structural types and 62 composite types across molecules ranging from 853 to 2,019 nt. Hexactinellida and freshwater Spongillida were each uniform for a distinct composite type but differed markedly in overall structure: hexactinellid mt SSU rRNAs were compact, whereas those of Spongillida were long and contained four to five candidate insertion regions. These results show that a conserved scaffold can accommodate extensive lineage-associated structural variation and provide a practical framework for comparing highly divergent mitochondrial rRNAs.

The deep-sea penaeoid shrimp Cerataspis monstrosa performs a vertical ontogenetic migration, with its early larval stages are typically found in surface waters, while adults inhabit the deep-sea. In this study, we present the complete mitogenome of C. monstrosa, which is 15,911 bp in length and comprises 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. Phylogenetic analysis indicates that C. monstrosa has closest genetic relationship with Aristeus virilis and is clustered within the Aristeidae family. The mitogenome of C. monstrosa provides valuable molecular data for further research into the evolution of penaeoid shrimps.

Climate warming and mariculture activities are reshaping marine ecosystems, yet how these drivers differentially influence coastal benthic ecosystems, especially within temperate bays, remains insufficiently resolved. This study examined 30 years (1991-2020) of benthic data from a large northern temperate bay - Jiaozhou Bay - China to disentangle the links between climate warming, mariculture activities, and coastal benthic ecosystem change. The results showed that benthic α diversity trajectories varied among the ten fixed inshore/offshore sites, displaying non-monotonic relationships with mariculture activities and winter warming (peaking under moderate pressure) while declining with summer warming; β diversity displayed a non-monotonic temporal trend while declined with mariculture activities and winter warming; γ diversity displayed a significant downward temporal trend. Assemblage structure shifted significantly over space and time, with most sites following similar directional trajectories and significantly related to both stressors. Climate warming explained more than twice the variation in α diversity than mariculture activities, whereas the opposite occurred in β diversity and assemblage structure. Furthermore, among 19 taxa showing significant temporal trends, none of the species sensitive to disturbance increased in abundance. These findings offer valuable insights for understanding and predicting the distinct ecological links of climate change and anthropogenic activities to coastal ecosystems.

Microbial communities at Site F cold seep, ubiquitous in both the environment and the associated fauna, demonstrate clear habitat-specific partitioning. Metagenomic sequencing and binning demonstrated a striking partitioning of microbial taxa at the cold seep: whereas the sponge-associated microbiome was distinctly enriched with specialized sulfur- and methane-oxidizing bacteria that were rare in the environment, it simultaneously exhibited a significantly reduced archaeal content, lower α-diversity, and a simpler overall community structure compared to the sediment and seawater communities. Distinct evolutionary lineages and varying abundances were observed among the microbiomes from seawater, sediment, and sponges. Furthermore, their Metagenome-Assembled Genomes (MAGs) exhibited significant differences in genomic features, including genome size and GC content. The sponge-associated microbiome exhibits lower diversity but maintains a high abundance of key functional genes, particularly those involved in sulfur cycling (e.g., apr, dsr, metZ), indicating enhanced metabolic efficiency in energy conservation and nutrient acquisition. This study reveals that the seawater, sediment, and sponge-associated microbiomes exhibit genome simplification and functional specialization in the cold seep environment, with varying lifestyles driving structural optimization and functional remodeling of the symbiotic microbiomes.

Microhabitat environmental factors (e.g., temperature, oxygen concentration, nutrients, osmotic stress, and topography) are critical to the survival of intertidal organisms. Understanding how transcription responses are regulated in relation to intertidal microhabitat variation has important implications for studying adaptive evolution in these organisms. The barnacle Chthamalus challengeri, which survives in the intertidal zone and is subjected to periodic tidal changes, serves as an ideal species for detecting adaptive evolution in intertidal organisms. In this study, we designed a series of in situ tidal conditions for C. challengeri and sequenced their transcriptome collected from various microhabitats. We aimed to detect the genetic adaptation mechanisms of barnacles responding to the microhabitat changes in the intertidal zone based on comparative transcriptomics. Our results indicated that different intertidal microhabitats significantly affected the gene expression models of C. challengeri, particularly for genes related to physiological and biochemical functions. Specifically, the expression of genes such as CYP450, HSP70, CYTB, and COX1 was significantly increased under low tide (air-exposed conditions), while genes like CNGA3, AK, and CP52 showed significantly increased expression under high tide (seawater-immersed conditions). The results suggest that C. challengeri relies on cytochrome p450 enzymes to enhance oxidative capacity, counts on heat shock proteins and cell phagocytosis to resist microhabitat changes in response to different tidal conditions, and produces a hypoxic stress response to regulate energy metabolism and body temperature changes upon entering into seawater. This study provides genetic resources and clues for investigating the adaptation mechanisms of intertidal barnacles and identifies different gene expression models for C. challengeri responding to various microhabitats.

Brachyura represents the focus of species diversity within Decapoda. However, this diversity increases the difficulty of species identification and obscures the natural phylogenetic relationships. Mitogenomes, with their rich phylogenetic signal and evolutionary informatics, provide critical insights into brachyuran systematics. Here, we present 12 newly sequenced mitogenomes spanning 10 families, which exhibit diverse lengths, ranging from 15,320 to 16,135 bp. All circular genomes except Conchoecetes artificiosus (lacking tRNA-S2) encode the typical 37 mitochondrial genes. Meanwhile, we identified unique gene order of Pleistacantha cervicornis and provided preliminary speculation on its hypothetical evolutionary history, which involved four gene inversion and translocation events. Phylogenomic reconstruction revealed: (1) Goneplacidae was closely related to Xanthoidea; meanwhile, Tetraliidae and Trapeziidae show divergence, resulting in the polyphyly of Goneplacoidea and Trapezioidea; (2) freshwater crabs were intimately related to thoracotrematan, and we recommended Potamoidea and Gecarcinucoidea should be classified under Thoracotremata; (3) Extensive mitochondrial gene order (MGO) diversity across Brachyura, with lineage-specific rearrangement patterns serving as phylogenetic markers. Our research offers new insights into the phylogenetic relationships within Brachyura from mitogenome perspective, unraveling the diversity and rearrangement trajectories of MGO in Brachyura.

A recently collected specimen of the rare deep-sea nematocarcinid genus Segonzackomaius Burukovsky, 2011 from the Philippine Basin is new to science and we revealed that the material previously reported as S. altus (Spence Bate, 1888) from Taiwan also belongs to this new species, based on a DNA sequence comparison. The new species S. sursus sp. nov. differs from S. altus by having a relatively shorter but ascending rostrum, and a longer telson, which distinctly exceeds the uropodal endopod. An identification key to the three known species of Segonzackomaius is provided. The multi-gene analyses do not support the monophyly of Nematocarcinus A. Milne-Edwards, 1881 because S. sursus sp. nov. forms a robust clade with N. lanceopes Spence Bate, 1888 and this clade is very separated from other species of Nematocarcinus. Nevertheless, a more extensive molecular study on the phylogenetic relationships amongst the taxa within the family Nematocarcinidae Smith, 1884 is necessary for a better comprehension of its evolution.

BACKGROUND:Cold seep sponges typically reside in the carbonate rock areas surrounding the vents, often comprising only a few individuals of a limited number of species. Previous limited studies have indicated that sponges living in seeps or vents host chemolithotrophic microorganisms, including sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB), regardless of their feeding habits. This suggests that they may utilize compounds from their environment. However, when multiple sponge species are found co-occurring in a single sponge ground sharing identical environmental and material conditions, it remains unclear how their symbiotic community structure will behave. Specifically, it is uncertain whether the community will exhibit greater similarity or, as seen in most studies, demonstrate host specificity. RESULTS:We utilize metagenomics and binning analysis to characterize six new sponge species belonging to two classes and two distinct dietary habits, all discovered in the same cold seep. Our findings reveal that their associated microbial communities, primarily composed of SOB and MOB from the phylum Proteobacteria, exhibit a high abundance of groups with the same chemosynthetic functions. Binning recovered diverse, novel MAGs (metagenome-assembled genomes) primarily dominated by order PS1 (SOB) and order Methylococcales (MOB). This similarity extends beyond the dietary habits and higher taxonomic levels of the sponge hosts. Phylogenetic and abundance difference analyses of MAGs indicate significant host specificity in the selection of symbiotic microbial species among different sponge species. Notably, these MOB and SOB exhibit potential novelty within their clade compared to known taxa. Furthermore, the genomes of these SOB and MOB contain abundant functions related to their adaptation to the chemoautotrophic environment and symbiotic lifestyle within the cold seep. CONCLUSIONS:The chemosynthetic environment shapes the high relative abundance of key functional groups that dominate the symbiotic community, while the species differences among host sponges determine the strain selection within these groups. The metabolic functions expressed by this "convergence with divergence" community structure collectively endow the holobionts with the ability to adapt to the cold seep environment.

The intertidal zone, occupying the critical interface between marine and terrestrial ecosystems, exhibits heightened sensitivity to climatic variations with accelerated ecological dynamics under dual environmental forcing. Species Distribution Models (SDMs), which establish statistical correlations between species occurrence records and environmental parameters, have become predominant tools for projecting biogeographic patterns under climate change scenarios. However, traditional SDMs frequently receive criticism for disregarding species-specific physiological constraints in environmental response mechanisms. Incorporating empirical physiological thresholds is therefore imperative for enhancing model biological realism and predictive accuracy. To date, this integrative approach remains unexplored for the Asian shore crab Hemigrapsus sanguineus (Crustacea: Varunidae), a keystone intertidal crustacean widely distributed along China's rocky coastlines. In this study, we developed novel Functional SDMs (F-SDMs) through the integration of thermal performance curves derived from laboratory experiments with ensemble SDM frameworks. Comparative analyses were conducted on both model predictive capacity (AUC/TSS metrics) and projected habitat shifts under Shared Socioeconomic Pathway scenarios. Our results demonstrate that physiological integration improved the predictive performance of the models, and F-SDMs predicted habitat changes were more moderate than traditional SDMs. These findings underscore the critical role of experimental physiology in marine biogeographic modeling, providing valuable information for predicting the distribution changes of marine species.

Crabs encompass the infra-orders Brachyura and Anomura, collectively constitute the clade Meiura within order Decapoda. Despite their considerable diversity, genomic resources for crabs remain scarce, hindering our understanding of their phylogeny and genetic mechanisms underlying such unique traits as carcinization. To address these questions, here we sequenced genomes of 10 crab species covering all currently controversial taxonomies at section level. Our whole-genome phylogenetic results support Raninoida is closer to Eubrachyura rather than Dromiacea, challenging the traditional classifications. Notably, the freshwater crab subsection Potamoida, represented by S. planum, is found to be more closely related to subsection Thoracotremata than to Heterotremata as previously suggested, indicating that crab classification based solely on morphology may be misleading. Our results also clarify that the family Gecarcinidae should be classified into Thoracotremata, contrary to previous placements in Heterotremata. Comparative genomic analyses identified lineage-specific families related to crab traits, including ionotropic glutamate receptors, neurotransmitters, and energy metabolism. Additionally, transcriptomic studies of Chinese mitten crab larval stages suggest that some lineage-specific genes such as ghrA, and TCB2, may account for the prominent carcinization in brachyurans. This study not only significantly expands the genomic repository for crabs, but also provides insights into the phylogeny and trait evolution of crabs.

The phylum Hemichordata includes colonial pterobranchs and solitary enteropneusts displaying morphological traits that consistent with those of both Chordata and Echinodermata. While molecular genetic data largely support hemichordates as sister to echinoderms, morphological anatomy, particularly the structural composition of nerve cords, indicates a closer similarity to chordates. To further explore the evolutionary relationship between hemichordates and chordates, we sequenced four hemichordate mitochondrial genomes and conducted comprehensive analyses, including phylogenetic, mitochondrial gene arrangement, and codon usage bias assessments, in conjunction with publicly available data. Our analysis revealed noteworthy similarities in mitochondrial gene arrangement and codon usage bias between hemichordates and vertebrates. Moreover, the constructed phylogenetic tree, based on mitochondrial gene rearrangement data or codon usage information, highlights deep mitochondrial homology between hemichordates and vertebrates. In summary, our study presents four novel hemichordate mitochondrial genomes and explores the evolutionary relationship between hemichordates and chordates from multiple perspectives, enriching our understanding of the early evolutionary history of deuterostomes.

Understanding when and how habitat transitions occurred is essential for a comprehensive insight into the succession of marine ecosystem and biodiversity. Here we investigated the evolutionary process of an ancient, widespread and ecologically diversified lineage of marine benthic fauna, the ghost and mud shrimps (Decapoda: Axiidea). To reconstruct a robust, time-calibrated phylogeny of this intractable group, we sampled more comprehensively than in previous studies and utilized three types of sequencing data: Sanger, genome-skimming and ultra-conserved elements (UCEs). The UCEs tree supports a monophyletic Axiidea sister to the 'Gebiidea + (Brachyura + Anomura)' clade. Our findings reveal the monophyletic status of Callianideidae and Micheleidae, whereas Axiidae and Strahlaxiidae as presently understood are shown to be non-monophyletic. Axiidae s.s. is now restricted to four genera, Strahlaxiidae to one genus, with most former "axiid" genera reclassified under Calocarididae. We determine that crown axiidean shrimps diverged in the Middle Triassic, with a significant habitat transition from epibenthic to endobenthic during the Middle to Late Jurassic, possibly in response to environmental changes and available ecological niche. We hypothesize that the extreme morphological and behavioural adaptations to the obligate/subsurface burrowing life facilitated the radiation and diversification of ghost shrimps, despite some instances of adaptive convergence.

To evaluate the potential impact of climate change on the distributions of eight epifaunal species in the southern Yellow Sea and the East China Sea, species distribution models were established using species data collected from bottom trawling surveys and marine environment data connected with the Sixth Phase of the Coupled Model Intercomparison Project. The modeling results revealed that temperature and depth were the most important environmental factors in shaping the distribution patterns of epifauna. The coastal waters of China between 32°N and 34°N are projected to become a key region where climate change will significantly influence the distribution of epifaunal species under future scenarios. Under future climate scenarios, the distributions of Alpheus digitalis, Alpheus japonicus, Amblychaeturichthys hexanema and Solenocera crassicornis are projected to expand northward, crossing the 32°N ecological barrier zone. Even if the targets of the Paris Agreement are achieved, the potential distributions of epifauna will undergo substantial changes. These findings indicated that the ecological barrier is a multi-dimensional environmental space defined by various marine environmental factors, and future climate change may further diminish its effect.

Munidopsis species represent some of the dominant macrobenthos in cold seep habitats of the northern South China Sea. Earlier studies documented high abundances of M. verrilli Benedict, 1902 at Site F cold seep and M. lauensis Baba & de Saint Laurent, 1992 at Haima cold seep. However, comparative morphological and genetic analysis of additional materials from the deep waters of California, Manus Basin, and southern Okinawa Trough now indicate that those specimens in the South China Sea require taxonomic revision: the specimens at Site F should be M. longispinosa Cubelio, Tsuchida & Watanabe, 2007 and the specimens at Haima cold seep belong to M. ryukyuensis Cubelio, Tsuchida & Watanabe, 2007. Complementary descriptions of M. ryukyuensis, M. longispinosa and M. verrilli, as well as their geographic distributions, are provided to facilitate future identification.