Frontiers in Marine Science最新文献

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Elemental analysis in the scales of commercially important coastal fishes and their connections with fish feeding habits and habitats
IF 3.7 2区 生物学
Frontiers in Marine Science Pub Date : 2025-04-01 DOI: 10.3389/fmars.2025.1546313
Md. Sohel Parvez, Md. Imdadul Hoque, Md. Nurul Momen Siddique, Mohammad Mizanur Rahman, Edina Baranyai, Zsófi Sajtos, Boglárka Döncző, Haithem Aib, Md. Abdul Kader, Edina Simon, Herta Czédli
{"title":"Elemental analysis in the scales of commercially important coastal fishes and their connections with fish feeding habits and habitats","authors":"Md. Sohel Parvez, Md. Imdadul Hoque, Md. Nurul Momen Siddique, Mohammad Mizanur Rahman, Edina Baranyai, Zsófi Sajtos, Boglárka Döncző, Haithem Aib, Md. Abdul Kader, Edina Simon, Herta Czédli","doi":"10.3389/fmars.2025.1546313","DOIUrl":"https://doi.org/10.3389/fmars.2025.1546313","url":null,"abstract":"Fish scales absorb different elements into the calcified matrix from surrounding waters as well as from the foods consumed. Scales microchemistry is drawing rising attention for its applicability in a wide range of fields, including environmental and ecological studies. The article represents an elemental analysis of the scales of five commercially important coastal fishes: <jats:italic>Tenualosa ilisha, Sillaginopsis panijus, Lates calcarifer, Otolithoides pama, and Rhinomugil corsula</jats:italic>. The concentrations of different essential and trace elements were measured using inductively coupled plasma optical emission spectrometry (ICP-OES), and their distribution on scales was mapped using micro-X-ray fluorescence (μ-XRF). The detected elements were categorized into five groups based on their overall mean concentrations: the most, considerable, moderate, low, and least available. The concentration (mg kg<jats:sup>−1</jats:sup>) of Ca was the highest (107472.32-181002.76) followed by P (41572.43-79042.02) among the elements in the studied fish scales, independent of species. The hierarchy of the overall mean concentration of elements was Ca&amp;gt;P&amp;gt;S&amp;gt;Mg&amp;gt;Na&amp;gt;K&amp;gt;Sr&amp;gt;Zn&amp;gt;Fe&amp;gt;Al&amp;gt;Ba&amp;gt;Mn&amp;gt;Cu&amp;gt;Cr. Element concentrations varied across fish feeding habits and habitats. Carnivore fish were found to have higher concentrations of K, Sr, and lower Fe than that in planktivore fish. The concentrations of Cr, Fe, S, Sr, and Zn were higher in demersal fish’s scales, whereas pelagic fish were found to have higher levels of Al, Ba, Ca, Cu, K, Mg, Mn, Na, and P. Element: Ca ratios, especially Sr: Ca, Mn: Ca, and Ba: Ca ratios, have potential implications as habitat signatures. Typically, fish otoliths are used for environmental and ecological purposes that involve cutting and sacrificing the sample. Employing scales instead could be a non-lethal alternative, crucial for sustainable fisheries management, especially for rare, vulnerable, or migratory fish.","PeriodicalId":12479,"journal":{"name":"Frontiers in Marine Science","volume":"23 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143745088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effects of upwelling and submarine groundwater discharges on phytoplankton communities off the north coast of the Yucatan peninsula
IF 3.7 2区 生物学
Frontiers in Marine Science Pub Date : 2025-04-01 DOI: 10.3389/fmars.2025.1516784
Román Becerra-Reynoso, Ismael Mariño-Tapia, Jorge Herrera-Silveira, Cecilia Enriquez
{"title":"Effects of upwelling and submarine groundwater discharges on phytoplankton communities off the north coast of the Yucatan peninsula","authors":"Román Becerra-Reynoso, Ismael Mariño-Tapia, Jorge Herrera-Silveira, Cecilia Enriquez","doi":"10.3389/fmars.2025.1516784","DOIUrl":"https://doi.org/10.3389/fmars.2025.1516784","url":null,"abstract":"IntroductionCoastal regions around the world are influenced by numerous dynamical processes that supply nutrients for primary producers and trigger the food web. Rivers, submarine groundwater discharges (SGD), sediment suspension events, and upwelling, are amongst the more important. However, it is not just the concentration, but also the composition of nutrient supply that determines the type of phytoplankton community that develops, subsequently influencing the entire food web. It is therefore necessary to better understand the link between physical processes, nutrient composition and phytoplankton response in coastal oceans. This study investigates the effects of upwelling and submarine groundwater discharges on the phytoplankton community of a wide and shallow continental shelf.MethodsResults are achieved by using numerical modeling of dispersion events, as well as field data obtained from three oceanographic cruises, each representing a different hydrographic scenario (“No upwelling”, “Minor upwelling and SGD” and “Major upwelling and minor SGD”).ResultsThe upwelled water mass (SUW – Subtropical Underwater) was primarily found at the eastern end of the shelf (Cabo Catoche), where it rises and is transported westward by advection. The oceanographic stations influenced by the upwelled water showed an increase in diatom species population, known to thrive in environments with abundant inorganic nutrients. In contrast, submarine groundwater discharges were recorded nearshore on the western half of the shelf, mainly related to karst features of hydrogeological importance (a sinkhole ring associated with the Chicxulub crater). The stations with SGD influence had higher presence of nutrients such as NH4, suggesting recycling processes. This can modify either the phytoplankton community advected from Cabo Catoche, or promote local growth, leading to a dominance of dinoflagellates and unknown flagellates.DiscussionThis result implies a food web, similar to that of the mixoplankton-dominated microbial loop, which would be fed by organic matter of continental origin.","PeriodicalId":12479,"journal":{"name":"Frontiers in Marine Science","volume":"90 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143757763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Underwater instance segmentation: a method based on channel spatial cross-cooperative attention mechanism and feature prior fusion
IF 3.7 2区 生物学
Frontiers in Marine Science Pub Date : 2025-04-01 DOI: 10.3389/fmars.2025.1557965
Zhiqian He, Lijie Cao, Xiaoqing Xu, Jianhao Xu
{"title":"Underwater instance segmentation: a method based on channel spatial cross-cooperative attention mechanism and feature prior fusion","authors":"Zhiqian He, Lijie Cao, Xiaoqing Xu, Jianhao Xu","doi":"10.3389/fmars.2025.1557965","DOIUrl":"https://doi.org/10.3389/fmars.2025.1557965","url":null,"abstract":"In aquaculture, underwater instance segmentation methods offer precise individual identification and counting capabilities. However, due to the inherent unique optical characteristics and high noise in underwater imagery, existing underwater instance segmentation models struggle to accurately capture the global and local feature information of objects, leading to generally lower detection accuracy in underwater instance segmentation models. To address this issue, this study proposes a novel Channel Space Coordinates Attention (CSCA) attention module and a Channel A Prior Attention Fusion (CAPAF) feature fusion module, aiming to improve the accuracy of underwater instance segmentation. The CSCA module effectively captures local and global information by combining channel and spatial attention weight, while the CAPAF module optimizes feature fusion by removing redundant information through learnable parameters. Experimental results demonstrate significant improvements when these two modules are applied to the YOLOv8 model, with the mAP@0.5 metric increasing by 3.2% and 2% on the UIIS underwater instance segmentation dataset. Furthermore, the instance segmentation accuracy is significantly improved on the UIIS and USIS10K datasets after these two modules are applied to other networks.","PeriodicalId":12479,"journal":{"name":"Frontiers in Marine Science","volume":"103 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143757760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rapid sample purification approach for 3H determination in seawater using ion exchange resin
IF 3.7 2区 生物学
Frontiers in Marine Science Pub Date : 2025-04-01 DOI: 10.3389/fmars.2025.1518506
Hong Ren, Xiaoxiang Ma, Peng Wang, Shunfei Yu, Hua Zou, Yiyao Cao
{"title":"Rapid sample purification approach for 3H determination in seawater using ion exchange resin","authors":"Hong Ren, Xiaoxiang Ma, Peng Wang, Shunfei Yu, Hua Zou, Yiyao Cao","doi":"10.3389/fmars.2025.1518506","DOIUrl":"https://doi.org/10.3389/fmars.2025.1518506","url":null,"abstract":"IntroductionTritium exists in the environment primarily in the form of tritiated water (HTO). There is a significant correlation between the radioactive levels of tritium in seawater and the safety of seafood. By accurately and rapidly detecting the tritium activity concentration in seawater, it is possible to effectively assess its potential impact on the seafood supply chain. At present, the detection of tritium in environmental water samples is often by liquid scintillation counting (LSC). To enable the measure of tritium by LSC, sample purification is necessary, which is commonly performed by distillation. The sample purification by distillation method is somewhat time consuming, especially when processing many samples or large volumes.MethodsTo improve the analytical efficiency in tritium determination, a method for the purification of tritium in seawater using ion exchange resin was developed in this work, which is highly suitable for large-scale environmental monitoring in emergency situations as it significantly shortens the sample processing time (A sample can be purified in 10 min, and multiple samples can be processed simultaneously, which is at least 50 min shorter than the distillation method). The influence of the <jats:sup>90</jats:sup>Sr-<jats:sup>90</jats:sup>Y on the detection of tritium in seawater treated with ion-exchange resin was also discussed. The removal of metal ions from the seawater was achieved using magnetic agitation and filtration by mixing the sample with ion exchange resins.ResultsThe results show that the ion exchange resin can effectively remove metal ions from seawater, and reduce the conductivity of seawater to&amp;lt; 1 μS/cm, and effectively reduce the influence of the <jats:sup>90</jats:sup>Sr-<jats:sup>90</jats:sup>Y on tritium detection. The method was validated using spiked samples and compared with other methods.DiscussionThe recovery of tritium for standard solutions treated by ion exchange method ranged from 85.1% to 98.45%, indicating satisfactory efficiency in sample purification for tritium determination in seawater. 10 seawater samples were collected and used to verify the applicability of the method.","PeriodicalId":12479,"journal":{"name":"Frontiers in Marine Science","volume":"183 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143757791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Morphology and evolution of submarine sand ridges and sand waves off the southwestern coast of Hainan Island, China
IF 3.7 2区 生物学
Frontiers in Marine Science Pub Date : 2025-04-01 DOI: 10.3389/fmars.2025.1561392
Yonghang Li, Huiqiang Yao, Zongheng Chen, Weidong Luo, Shi Zhang
{"title":"Morphology and evolution of submarine sand ridges and sand waves off the southwestern coast of Hainan Island, China","authors":"Yonghang Li, Huiqiang Yao, Zongheng Chen, Weidong Luo, Shi Zhang","doi":"10.3389/fmars.2025.1561392","DOIUrl":"https://doi.org/10.3389/fmars.2025.1561392","url":null,"abstract":"A substantial quantity of sedimentary sand bodies, including sand ridges, sand waves, and sand ripples, have been developed off the southwest coast of Hainan Island, China, with submarine sand ridges exhibiting the most considerable development scale. Determining the distribution, morphology, and evolutionary characteristics of the submarine sand ridges is crucial for exploiting marine sand resources and investigating engineering geological hazards. A comprehensive assessment of the study area was conducted utilizing marine survey techniques, including single-beam echo sounding, multi-beam echo sounding, side-scan sonar, single-channel seismic, and sediment sampling. The findings indicate the presence of eight substantial submarine sand ridges in the study area, delineated by tidal scour gullies and predominantly oriented in a NW-SE direction, with an average length of 21.3 km, an average width of 2.9 km, and an average height of 13.3 m. The sand ridges have a high-angle oblique bedding configuration. The grain size distribution of sediments in the study area is generally characterized by coarser near the shore and relatively finer away from the shore. The sediment type of the sand ridges is mainly sand-grade sediments (i.e., mean grain size Mz &amp;lt; 4Φ). A significant quantity of linear and barchan sand waves has developed within the sand ridge field, exhibiting variations in morphology, distribution, and scale. The coexistence and transformation of micro-geomorphic units, including sand waves, sand patches, and sand sheets, alongside sand ridges, reflect the complexity of the bedform-sediment-hydrodynamic system in the study area. The formation of the sand ridges may result from the late alteration of the ancient nearshore residual sand body. The study area revealed the presence of erosion-dominated, erosional-depositional, and deposition-dominated sand ridges, leading to the proposal of a development and evolution model for these sand ridges.","PeriodicalId":12479,"journal":{"name":"Frontiers in Marine Science","volume":"60 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143745087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Hybrid machine learning algorithms accurately predict marine ecological communities
IF 3.7 2区 生物学
Frontiers in Marine Science Pub Date : 2025-03-31 DOI: 10.3389/fmars.2025.1458014
Luciana Erika Yaginuma, Fabiane Gallucci, Danilo Cândido Vieira, Paula Foltran Gheller, Simone Brito de Jesus, Thais Navajas Corbisier, Gustavo Fonseca
{"title":"Hybrid machine learning algorithms accurately predict marine ecological communities","authors":"Luciana Erika Yaginuma, Fabiane Gallucci, Danilo Cândido Vieira, Paula Foltran Gheller, Simone Brito de Jesus, Thais Navajas Corbisier, Gustavo Fonseca","doi":"10.3389/fmars.2025.1458014","DOIUrl":"https://doi.org/10.3389/fmars.2025.1458014","url":null,"abstract":"Predicting ecological communities is highly challenging but necessary to establish effective conservation and monitoring programs. This study aims to predict the spatial distribution of nematode associations from 25 m to 2500 m water depth over an area of 350,000 km² and understand the major oceanographic processes influencing them. The study considered data from 245 nematode genera and 44 environmental parameters from 100 stations. Data was analyzed by means of a hybrid machine learning (ML) approach, which combines unsupervised and supervised methods. The unsupervised phase detected that the nematodes were geographically structured in six associations, each with representative genera. In the supervised stage, these associations were modeled as a function of the environmental features by five supervised algorithms (Support Vector Machine, Random Forest, k-Nearest Neighbors, Naive Bayes, and Stochastic Gradient Boosting), using 80% of the samples for training, leaving the remaining for testing. Among them, the random forest was the best model with an accuracy of 86.4% in the test portion. The Random Forest (RF) model recognized 8 environmental features as significant in predicting the associations. Depth, the concentration of dissolved oxygen in the water near the bottom, the quality and quantity of phytodetritus, the proportion of coarse sand and carbonate, the sediment skewness, pH, and redox potential were the most important features structuring them. The inference of each association across the whole study area was based on the modeling results of the 8 significant environmental features. This model still correctly classified 90% of test data. Such findings demonstrated that it is possible to infer the spatial distribution of the nematode associations using only a small set of environmental features. The recommendation is thus to permanently monitor these environmental variables and run the ML models. Implementing ML approaches in monitoring programs of benthic systems will increase our prediction capacity, reduce monitoring costs, and, ultimately, support the conservation of marine systems.","PeriodicalId":12479,"journal":{"name":"Frontiers in Marine Science","volume":"31 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143736620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Observed seasonal evolution and origins of the western Yellow Sea Cold Water Mass
IF 3.7 2区 生物学
Frontiers in Marine Science Pub Date : 2025-03-31 DOI: 10.3389/fmars.2025.1556069
Chuanjie Wei, Xiaohui Tang, Kai Ge, Anqi Xu, Yuanlong Li, Yong Jiang, Zengrui Rong, Fei Yu
{"title":"Observed seasonal evolution and origins of the western Yellow Sea Cold Water Mass","authors":"Chuanjie Wei, Xiaohui Tang, Kai Ge, Anqi Xu, Yuanlong Li, Yong Jiang, Zengrui Rong, Fei Yu","doi":"10.3389/fmars.2025.1556069","DOIUrl":"https://doi.org/10.3389/fmars.2025.1556069","url":null,"abstract":"The Yellow Sea Cold Water Mass (YSCWM) is one of the most prominent hydrological features of the Yellow Sea. As a low-temperature, nutrient-rich subsurface water mass, the YSCWM fundamentally regulates biogeochemical cycles, functions of marine ecosystems, and fishery resources of the YS. In boreal summer, the YSCWM shows a robust triple-core structure, in which the western component, dubbed the “western YSCWM”, is revisited in this study. Through analyzing <jats:italic>in-situ</jats:italic> observational data collected by research cruises of the Institute of Oceanology, Chinese Academy of Sciences (IOCAS) and Lagrangian tracing experiments based on a high-resolution ocean model, we provide a thorough investigation for seasonal evolution and origins of the western YSCWM. <jats:italic>In-situ</jats:italic> observations during 2006-2007 and 2014-2015 suggest that the western YSCWM bears a tight connection to the colder coastal waters near the Shandong Peninsula and achieves the coldest temperature in summer. Analysis of model simulations confirms that the cooling of the western YSCWM in spring and summer is caused mainly by southward cold-water transport of the Shandong Coastal Current (SDCC) from the Shandong coasts and the northern Yellow Sea. We also reveal a contribution of the Subei Shoal water via the Subei Coastal Current (SCC) in summer, which plays a critical role in the quick vanishing of the western YSCMW in early autumn. These findings contribute to our understanding of the formation, seasonal evolution, and heat budgets of the YSCWM.","PeriodicalId":12479,"journal":{"name":"Frontiers in Marine Science","volume":"38 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143736619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring the drivers of otolith Sr/Ca during the early life stages of Larimichthys polyactis: insights from cultured and wild populations
IF 3.7 2区 生物学
Frontiers in Marine Science Pub Date : 2025-03-28 DOI: 10.3389/fmars.2025.1513070
Zhongjie Kang, Dade Song, Hushun Zhang, Long Liang, Chengbin Zhang, Tao Jiang, Fei Zhu, Ying Xiong
{"title":"Exploring the drivers of otolith Sr/Ca during the early life stages of Larimichthys polyactis: insights from cultured and wild populations","authors":"Zhongjie Kang, Dade Song, Hushun Zhang, Long Liang, Chengbin Zhang, Tao Jiang, Fei Zhu, Ying Xiong","doi":"10.3389/fmars.2025.1513070","DOIUrl":"https://doi.org/10.3389/fmars.2025.1513070","url":null,"abstract":"Otolith Sr/Ca profiles are widely used to investigate early life migration and habitat use in both diadromous and oceanodromous fishes. This study focuses on <jats:italic>Larimichthys polyactis</jats:italic>, an oceanodromous species of significant ecological and commercial importance in East Asian waters. This study investigates the influence of environmental factors on the otolith Sr/Ca ratios during its early life stages (ELS). In Experiment A, we analyzed both laboratory-reared specimens—maintained under stable temperature (19–21°C) and salinity (27–28 PSU) conditions—and wild-captured specimens. The results revealed a consistent decline in Sr/Ca ratios throughout the ELS in both groups, suggesting that temperature and salinity may not be the primary drivers of otolith Sr/Ca ratios during early development. In Experiment B, Sr/Ca ratios in the core (incubation stage) and edge (recently spawned stage) zones of otoliths from both wild and laboratory-reared adult fish were compared. Sr/Ca ratios were significantly higher in the core zone than in the edge zone, indicating that maternal influences are may not be the main cause of elevated Sr/Ca ratios in the otolith core. Collectively, these findings suggest that otolith Sr/Ca ratios during ELS in <jats:italic>L. polyactis</jats:italic> are more affected by the ontogenetic developmental stage than by environmental factors such as temperature, salinity, or maternal effects. This challenges previous assumptions about the dominance of environmental factors in shaping otolith chemistry and highlights the need for more nuanced interpretations of Sr/Ca data, especially in studies of oceanodromous fishes. When utilizing otolith microchemistry to reconstruct life history, it is essential to minimize physiological effects through controlled culture experiments to ensure the accuracy and reliability of the results.","PeriodicalId":12479,"journal":{"name":"Frontiers in Marine Science","volume":"132 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143734114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Occurrence frequency, molecular evolution and phylogenetic utility of Ulva-specific chloroplast group II intron infA-62 family
IF 3.7 2区 生物学
Frontiers in Marine Science Pub Date : 2025-03-28 DOI: 10.3389/fmars.2025.1557121
Feng Liu, Shuangle Jin, Jang Kyun Kim, Xiaochan Wu, Jing Wang
{"title":"Occurrence frequency, molecular evolution and phylogenetic utility of Ulva-specific chloroplast group II intron infA-62 family","authors":"Feng Liu, Shuangle Jin, Jang Kyun Kim, Xiaochan Wu, Jing Wang","doi":"10.3389/fmars.2025.1557121","DOIUrl":"https://doi.org/10.3389/fmars.2025.1557121","url":null,"abstract":"Chloroplast intron <jats:italic>infA</jats:italic>-62 as a degenerated group II intron family was previously observed to exist specifically in <jats:italic>infA</jats:italic> genes of chloroplast/plastid genomes (plastomes) in the genus <jats:italic>Ulva</jats:italic> (Ulvophyceae, Chlorophyta). To understand occurrence frequency, molecular evolution and phylogenetic utility of this intron family in <jats:italic>Ulva</jats:italic> species, in this study, we conducted more sampling tests based on newly designed specific primers, analyzed evolutionary features of its secondary structures, and employed intron <jats:italic>infA</jats:italic>-62 for phylogenetic analysis of <jats:italic>Ulva</jats:italic> species. The 100% occurrence frequency of this intron has been observed in <jats:italic>Ulva</jats:italic> plastomes, supporting its acquisition by the earliest progenitor of <jats:italic>Ulva</jats:italic> species. The GC content of this intron family is unprecedentedly low (21.0-25.2%) for group II introns. The intron <jats:italic>infA</jats:italic>-62 family is classified as an atypical form of ORF-less group IIB-like secondary structures. Some new evolutionary features have been revealed in this intron family, including the extremely low GC content in some domains (e.g. domains IB, ICa, ID2, IDa, II and IV), a very short stem in domain I, a drastically changing domain IC2, and a completely degenerated domain IV. Secondary structures of this intron family showed progressive RNA structural deviations and species-specific variations during the <jats:italic>Ulva</jats:italic> evolution. Nine mutation hotspots have been detected in loop regions of domains IA, IB, IC1, IC2, ICa, IDa, II, IV and VI. The ML phylogenetic tree constructed based on the nucleotide sequences of intron <jats:italic>infA</jats:italic>-62 showed that <jats:italic>Ulva</jats:italic> species were classified into two clades representing two <jats:italic>Ulva</jats:italic> lineages, <jats:italic>Ulva</jats:italic> I and II, which was consistent with those based on organelle multigene datasets. Our evidences show that intron <jats:italic>infA</jats:italic>-62 coevolved with the plastomes during the evolution and speciation of <jats:italic>Ulva</jats:italic> species. The intron <jats:italic>infA</jats:italic>-62 that combines primary sequence and secondary structure can be used as an efficient phylogenetic marker for identification and classification of <jats:italic>Ulva</jats:italic> species.","PeriodicalId":12479,"journal":{"name":"Frontiers in Marine Science","volume":"31 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143734110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Impact chains for the deep seafloor: assessing pressures footprint under limited knowledge and uncertainty
IF 3.7 2区 生物学
Frontiers in Marine Science Pub Date : 2025-03-28 DOI: 10.3389/fmars.2025.1532964
Fábio L. Matos, Ana Hilário, Heliana Teixeira
{"title":"Impact chains for the deep seafloor: assessing pressures footprint under limited knowledge and uncertainty","authors":"Fábio L. Matos, Ana Hilário, Heliana Teixeira","doi":"10.3389/fmars.2025.1532964","DOIUrl":"https://doi.org/10.3389/fmars.2025.1532964","url":null,"abstract":"Pressures on the marine environment threaten biodiversity, ecosystem functions and services. Current marine environmental policies, such as the European Marine Strategy Framework Directive, require the assessment of combined effects and the application of ecosystem-based management approaches to maintain or achieve Good Environmental Status (GES) of marine ecosystems. We mapped the major activities and pressures affecting deep-sea benthic habitats in the mainland component of the Portuguese EEZ to assess their combined effects and support decision-making on management and conservation. Activities related to marine traffic, fisheries, and climate change processes are among the most prevalent in the study area. As a data-poor case study, most of the pressure layers were only partially mapped due to a lack of information or the inadequacy of the available data on activities to derive suitable proxies of pressure intensity. Pressures related to chemical changes, chemicals and other pollutants were the most widespread, while abrasion and damage were the most geographically limited. Endogenic pressures dominate in bathyal benthic habitats and decrease their prevalence with depth, while exogenic pressures are more widespread in the abyss than in the bathyal area. Benthic habitats in the bathyal zone, closer to the 200-meter bathymetric contour, consistently exhibited higher combined effect scores, suggesting higher risk of potential impacts on these ecosystem components. Research directed towards these areas is required to assess the state of these habitats and develop conservation and restoration measures, if necessary, to achieve GES. A continuous support for open-access databases containing high-quality, standardized, and harmonized marine data is crucial for future assessments of the combined effects of human pressures on deep-sea ecosystems.","PeriodicalId":12479,"journal":{"name":"Frontiers in Marine Science","volume":"13 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143734113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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